From 663eecd3c4782c85cbbd42732a3cc0738b6fd08c Mon Sep 17 00:00:00 2001 From: Henrik Bengtsson Date: Fri, 22 Mar 2024 17:01:01 -0700 Subject: [PATCH 01/25] REVDEP: Checked 359 revdep packages [ci skip] --- revdep/README.md | 743 +++++----- revdep/cran.md | 16 +- revdep/failures.md | 591 +++++++- revdep/problems.md | 3339 +++++++++++++++++++++++++++++++++----------- 4 files changed, 3549 insertions(+), 1140 deletions(-) diff --git a/revdep/README.md b/revdep/README.md index bd0e585b..e0a69f60 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,361 +1,412 @@ # Platform -|field |value | -|:--------|:----------------------------------------------------------------------| -|version |R version 4.3.2 (2023-10-31) | -|os |Rocky Linux 8.8 (Green Obsidian) | -|system |x86_64, linux-gnu | -|ui |X11 | -|language |(EN) | -|collate |en_US.UTF-8 | -|ctype |en_US.UTF-8 | -|tz |America/Los_Angeles | -|date |2023-12-21 | -|pandoc |3.1.10 @ /wynton/home/cbi/shared/software/CBI/pandoc-3.1.10/bin/pandoc | +|field |value | +|:--------|:---------------------------------------------------------------| +|version |R version 4.3.3 (2024-02-29) | +|os |CentOS Linux 7 (Core) | +|system |x86_64, linux-gnu | +|ui |X11 | +|language |en | +|collate |en_US.UTF-8 | +|ctype |en_US.UTF-8 | +|tz |America/Los_Angeles | +|date |2024-03-22 | +|pandoc |3.1.11.1 @ /software/c4/cbi/software/pandoc-3.1.11.1/bin/pandoc | # Dependencies -|package |old |new |Δ | -|:----------|:------|:------|:--| -|future |1.33.0 |1.33.1 |* | -|codetools |0.2-19 |0.2-19 | | -|digest |0.6.33 |0.6.33 | | -|globals |0.16.2 |0.16.2 | | -|listenv |0.9.0 |0.9.0 | | -|parallelly |1.36.0 |1.36.0 | | +|package |old |new |Δ | +|:----------|:------|:-----------|:--| +|future |1.33.1 |1.33.1-9009 |* | +|codetools |0.2-19 |0.2-19 | | +|digest |0.6.35 |0.6.35 | | +|globals |0.16.3 |0.16.3 | | +|listenv |0.9.1 |0.9.1 | | +|parallelly |1.37.1 |1.37.1 | | # Revdeps -## Failed to check (2) +## Failed to check (9) |package |version |error |warning |note | |:----------------|:-------|:-----|:-------|:----| -|[QDNAseq](failures.md#qdnaseq)|1.38.0 |1 | | | +|arkdb |? | | | | +|[cft](failures.md#cft)|1.0.0 |1 | | | +|[erah](failures.md#erah)|2.0.1 |1 | |1 | +|flowml |? | | | | +|marginaleffects |? | | | | +|[Prostar](failures.md#prostar)|1.34.6 |1 | | | +|[startR](failures.md#startr)|2.3.1 |1 | | | +|[TKCat](failures.md#tkcat)|1.0.7 |1 | | | |[TriDimRegression](failures.md#tridimregression)|1.0.2 |1 | | | -## All (321) +## New problems (1) -|package |version |error |warning |note | -|:--------------------------|:----------|:-----|:-------|:----| -|adestr |0.5.0 | | | | -|AICcPermanova |0.0.2 | | | | -|[AIPW](problems.md#aipw) |0.6.3.2 | | |1 | -|alphaci |1.0.0 | | | | -|[AlpsNMR](problems.md#alpsnmr)|4.4.0 |1 | | | -|antaresEditObject |0.6.1 | | | | -|arkdb |0.0.16 | | | | -|aroma.affymetrix |3.2.1 | | | | -|aroma.cn |1.7.0 | | | | -|[aroma.core](problems.md#aromacore)|3.3.0 | | |1 | -|ARPALData |1.5.0 | | | | -|BAMBI |2.3.5 | | | | -|[bamm](problems.md#bamm) |0.4.3 | | |1 | -|BatchGetSymbols |2.6.4 | | | | -|[batchtools](problems.md#batchtools)|0.9.17 | | |2 | -|bayesian |0.0.9 | | | | -|bayesmove |0.2.1 | | | | -|bbknnR |1.1.0 | | | | -|bcmaps |2.1.0 | | | | -|[BEKKs](problems.md#bekks) |1.4.3 | | |2 | -|bhmbasket |0.9.5 | | | | -|[bigDM](problems.md#bigdm) |0.5.3 | | |2 | -|[bistablehistory](problems.md#bistablehistory)|1.1.2 | | |2 | -|bkmrhat |1.1.3 | | | | -|[blavaan](problems.md#blavaan)|0.5-2 | | |3 | -|bolasso |0.2.0 | | | | -|[brms](problems.md#brms) |2.20.4 | | |1 | -|[brpop](problems.md#brpop) |0.3.0 |1 | | | -|bsitar |0.1.0 | | | | -|[campsis](problems.md#campsis)|1.5.0 |2 | | | -|canaper |1.0.1 | | | | -|[ceRNAnetsim](problems.md#cernanetsim)|1.14.1 | | |1 | -|cft |1.0.0 | | | | -|chatAI4R |0.2.10 | | | | -|[ChromSCape](problems.md#chromscape)|1.12.0 |1 | | | -|civis |3.1.2 | | | | -|[clickR](problems.md#clickr)|0.9.39 | | |1 | -|Clustering |1.7.7 | | | | -|ClustIRR |1.0.0 | | | | -|codalm |0.1.2 | | | | -|[codebook](problems.md#codebook)|0.9.2 | | |3 | -|[collinear](problems.md#collinear)|1.1.1 | | |1 | -|conformalInference.fd |1.1.1 | | | | -|conformalInference.multi |1.1.1 | | | | -|crossmap |0.4.0 | | | | -|CSCNet |0.1.2 | | | | -|[cSEM](problems.md#csem) |0.5.0 | | |1 | -|[CSGo](problems.md#csgo) |0.6.7 | | |1 | -|cvCovEst |1.2.1 | | | | -|dataquieR |2.0.1 | | | | -|DeclareDesign |1.0.4 | | | | -|delayed |0.4.0 | | | | -|deseats |1.0.0 | | | | -|dipsaus |0.2.8 | | | | -|disk.frame |0.8.3 | | | | -|[dispositionEffect](problems.md#dispositioneffect)|1.0.1 |1 | | | -|doFuture |1.0.1 | | | | -|DQAstats |0.3.3 | | | | -|[dragon](problems.md#dragon)|1.2.1 | | |2 | -|[drake](problems.md#drake) |7.13.8 | | |1 | -|drimmR |1.0.1 | | | | -|drtmle |1.1.2 | | | | -|dsos |0.1.2 | | | | -|DT |0.31 | | | | -|easyalluvial |0.3.2 | | | | -|ecic |0.0.3 | | | | -|[EFAtools](problems.md#efatools)|0.4.4 | | |2 | -|[EGAnet](problems.md#eganet)|2.0.3 |1 | | | -|elevatr |0.99.0 | | | | -|[envi](problems.md#envi) |0.1.17 | |1 |1 | -|epe4md |0.1.4 | | | | -|[EpiNow2](problems.md#epinow2)|1.4.0 | | |2 | -|[epitweetr](problems.md#epitweetr)|2.2.16 | | |2 | -|epwshiftr |0.1.3 | | | | -|erah |2.0.1 | | | | -|ezcox |1.0.4 | | | | -|fabletools |0.3.4 | | | | -|FAMoS |0.3.0 | | | | -|[fastRhockey](problems.md#fastrhockey)|0.4.0 | | |1 | -|[fdacluster](problems.md#fdacluster)|0.3.0 | | |1 | -|[fect](problems.md#fect) |1.0.0 | | |3 | -|fiery |1.2.0 | | | | -|finbif |0.9.3 | | | | -|fitlandr |0.1.0 | | | | -|[FLAMES](problems.md#flames)|1.8.0 |1 | |4 | -|[flowGraph](problems.md#flowgraph)|1.10.0 | | |3 | -|flowml |0.1.2 | | | | -|[forecastML](problems.md#forecastml)|0.9.0 | | |1 | -|fst4pg |1.0.0 | | | | -|fundiversity |1.1.1 | | | | -|funGp |0.3.2 | | | | -|furrr |0.3.1 | | | | -|future.apply |1.11.0 | | | | -|[future.batchtools](problems.md#futurebatchtools)|0.12.1 | | |1 | -|future.callr |0.8.2 | | | | -|future.tests |0.7.0 | | | | -|fxTWAPLS |0.1.2 | | | | -|genBaRcode |1.2.7 | | | | -|geocmeans |0.3.4 | | | | -|GetBCBData |0.7.0 | | | | -|[googleComputeEngineR](problems.md#googlecomputeenginer)|0.3.0 | | |1 | -|googlePubsubR |0.0.4 | | | | -|[googleTagManageR](problems.md#googletagmanager)|0.2.0 | | |1 | -|[greed](problems.md#greed) |0.6.1 | | |3 | -|greta |0.4.3 | | | | -|gsdensity |0.1.2 | | | | -|gstat |2.1-1 | | | | -|GSVA |1.50.0 | | | | -|[gsynth](problems.md#gsynth)|1.2.1 | | |1 | -|gtfs2emis |0.1.0 | | | | -|[gtfs2gps](problems.md#gtfs2gps)|2.1-1 |1 | | | -|gWQS |3.0.5 | | | | -|[hackeRnews](problems.md#hackernews)|0.1.0 | | |1 | -|hacksig |0.1.2 | | | | -|hal9001 |0.4.6 | | | | -|haldensify |0.2.3 | | | | -|[hero](problems.md#hero) |0.6 | | |2 | -|heterogen |1.2.33 | | | | -|[hoopR](problems.md#hoopr) |2.1.0 | | |1 | -|[hwep](problems.md#hwep) |2.0.2 | | |2 | -|hydroloom |1.0.0 | | | | -|idmodelr |0.4.0 | | | | -|imagefluency |0.2.4 | | | | -|iml |0.11.1 | | | | -|incubate |1.2.1 | | | | -|[infercnv](problems.md#infercnv)|1.18.1 | | |1 | -|inlinedocs |2023.9.4 | | | | -|[InPAS](problems.md#inpas) |2.10.0 | | |1 | -|[interflex](problems.md#interflex)|1.2.6 | | |1 | -|ipc |0.1.4 | | | | -|ISAnalytics |1.12.0 | | | | -|isopam |1.3.0 | | | | -|ivDiag |1.0.6 | | | | -|[ivmte](problems.md#ivmte) |1.4.0 | | |1 | -|jlmerclusterperm |1.1.0 | | | | -|JointAI |1.0.5 | | | | -|jstor |0.3.11 | | | | -|JuliaConnectoR |1.1.3 | | | | -|kernelboot |0.1.10 | | | | -|[keyATM](problems.md#keyatm)|0.5.0 | | |1 | -|latentcor |2.0.1 | | | | -|lava |1.7.3 | | | | -|ldaPrototype |0.3.1 | | | | -|[ldsr](problems.md#ldsr) |0.0.2 | | |1 | -|lemna |1.0.1 | | | | -|LexFindR |1.0.2 | | | | -|lgr |0.4.4 | | | | -|[lidR](problems.md#lidr) |4.0.4 | | |1 | -|[lightr](problems.md#lightr)|1.7.0 | | |2 | -|lmtp |1.3.2 | | | | -|LWFBrook90R |0.5.3 | | | | -|[MAI](problems.md#mai) |1.8.0 | | |1 | -|malariaAtlas |1.5.1 | | | | -|MAMS |2.0.1 | | | | -|mapme.biodiversity |0.4.0 | | | | -|marginaleffects |0.17.0 | | | | -|matric |0.2.0 | | | | -|mcmcensemble |3.0.0 | | | | -|mcp |0.3.3 | | | | -|merTools |0.6.1 | | | | -|metaGE |1.0.3 | | | | -|mice |3.16.0 | | | | -|[migraph](problems.md#migraph)|1.2.1 |1 | | | -|mikropml |1.6.1 | | | | -|[MineICA](problems.md#mineica)|1.42.0 | |3 |5 | -|missSBM |1.0.4 | | | | -|[mistyR](problems.md#mistyr)|1.10.0 | | |2 | -|mlr3 |0.17.1 | | | | -|mlr3db |0.5.2 | | | | -|mlr3pipelines |0.5.0-2 | | | | -|[mlr3resampling](problems.md#mlr3resampling)|2023.12.20 |1 | | | -|mlr3spatial |0.4.1 | | | | -|modelsummary |1.4.3 | | | | -|momentuHMM |1.5.5 | | | | -|MOSS |0.2.2 | | | | -|mplusParallel.automation |0.0.1.1 | | | | -|[mrgsim.parallel](problems.md#mrgsimparallel)|0.2.1 | | |1 | -|mslp |1.4.0 | | | | -|multitool |0.1.3 | | | | -|multiverse |0.6.1 | | | | -|[nebula](problems.md#nebula)|1.4.2 | | |1 | -|netShiny |1.0 | | | | -|NetSimR |0.1.5 | | | | -|[nfl4th](problems.md#nfl4th)|1.0.4 | |1 |1 | -|[nflfastR](problems.md#nflfastr)|4.6.0 | | |1 | -|nflseedR |1.2.0 | | | | -|nhdplusTools |1.0.0 | | | | -|nncc |1.0.1 | | | | -|[oncomsm](problems.md#oncomsm)|0.1.4 | | |2 | -|[onemapsgapi](problems.md#onemapsgapi)|1.1.0 | | |1 | -|[OOS](problems.md#oos) |1.0.0 | | |1 | -|optic |1.0.1 | | | | -|OptimalGoldstandardDesigns |1.0.1 | | | | -|optimLanduse |1.2.0 | | | | -|origami |1.0.7 | | | | -|paramsim |0.1.0 | | | | -|[pareg](problems.md#pareg) |1.6.0 |3 | |2 | -|[partR2](problems.md#partr2)|0.9.1 | | |1 | -|[pavo](problems.md#pavo) |2.9.0 | |1 | | -|pbapply |1.7-2 | | | | -|[PCRedux](problems.md#pcredux)|1.1-2 |2 | | | -|PeakSegDisk |2023.11.27 | | | | -|penaltyLearning |2023.8.31 | | | | -|pGRN |0.3.5 | | | | -|[photosynthesis](problems.md#photosynthesis)|2.1.4 | | |1 | -|[phylolm](problems.md#phylolm)|2.6.2 | | |2 | -|phylopath |1.2.0 | | | | -|PINstimation |0.1.2 | | | | -|[PLNmodels](problems.md#plnmodels)|1.0.4 | | |1 | -|plumber |1.2.1 | | | | -|polle |1.3 | | | | -|POMADE |0.1.0 | | | | -|[portvine](problems.md#portvine)|1.0.2 | | |2 | -|powRICLPM |0.1.1 | | | | -|progressr |0.14.0 | | | | -|[projpred](problems.md#projpred)|2.8.0 | | |1 | -|promises |1.2.1 | | | | -|[Prostar](problems.md#prostar)|1.34.3 |1 |1 | | -|proteus |1.1.4 | | | | -|protti |0.6.0 | | | | -|PSCBS |0.66.0 | | | | -|[pseudohouseholds](problems.md#pseudohouseholds)|0.1.1 | | |1 | -|PUMP |1.0.2 | | | | -|qape |2.1 | | | | -|[QDNAseq](failures.md#qdnaseq)|1.38.0 |1 | | | -|qgcomp |2.15.2 | | | | -|qgcompint |0.7.0 | | | | -|[RAINBOWR](problems.md#rainbowr)|0.1.33 | | |1 | -|rangeMapper |2.0.3 | | | | -|rBiasCorrection |0.3.4 | | | | -|receptiviti |0.1.6 | | | | -|refineR |1.6.1 | | | | -|[regmedint](problems.md#regmedint)|1.0.0 | | |1 | -|remiod |1.0.2 | | | | -|[reproducible](problems.md#reproducible)|2.0.10 |1 | |1 | -|reval |3.1-0 | | | | -|[rgee](problems.md#rgee) |1.1.7 | | |1 | -|[robotstxt](problems.md#robotstxt)|0.7.13 | | |2 | -|robust2sls |0.2.2 | | | | -|[rpm](problems.md#rpm) |0.7-1 | | |1 | -|RTransferEntropy |0.2.21 | | | | -|s3fs |0.1.4 | | | | -|[sapfluxnetr](problems.md#sapfluxnetr)|0.1.4 | | |1 | -|scBubbletree |1.4.0 | | | | -|scDiffCom |1.0.0 | | | | -|[sctransform](problems.md#sctransform)|0.4.1 | | |1 | -|[sdmApp](problems.md#sdmapp)|0.0.2 | | |2 | -|[sdmTMB](problems.md#sdmtmb)|0.4.1 | | |1 | -|seer |1.1.8 | | | | -|semPower |2.1.0 | | | | -|semtree |0.9.19 | | | | -|[sentopics](problems.md#sentopics)|0.7.2 | | |2 | -|[Seurat](problems.md#seurat)|5.0.1 | | |3 | -|[SeuratObject](problems.md#seuratobject)|5.0.1 | | |2 | -|shiny |1.8.0 | | | | -|[shiny.worker](problems.md#shinyworker)|0.0.1 | | |2 | -|sigminer |2.3.0 | | | | -|[Signac](problems.md#signac)|1.12.0 | | |2 | -|[signeR](problems.md#signer)|2.4.0 | | |4 | -|SimDesign |2.13 | | | | -|simfinapi |0.2.4 | | | | -|simglm |0.8.9 | | | | -|simhelpers |0.1.2 | | | | -|simIDM |0.1.0 | | | | -|sims |0.0.3 | | | | -|simtrial |0.3.2 | | | | -|[sits](problems.md#sits) |1.4.2-1 | | |1 | -|skewlmm |1.1.0 | | | | -|[skpr](problems.md#skpr) |1.6.1 | | |1 | -|[SmCCNet](problems.md#smccnet)|2.0.1 | |1 | | -|smoots |1.1.4 | | | | -|sNPLS |1.0.27 | | | | -|[solitude](problems.md#solitude)|1.1.3 | | |1 | -|sovereign |1.2.1 | | | | -|[SpaDES.core](problems.md#spadescore)|2.0.3 |1 | | | -|[spaMM](problems.md#spamm) |4.4.16 | | |2 | -|[sparrpowR](problems.md#sparrpowr)|0.2.7 | |1 | | -|[SPARSEMODr](problems.md#sparsemodr)|1.2.0 | | |1 | -|spatialTIME |1.3.4-2 | | | | -|[spatialwarnings](problems.md#spatialwarnings)|3.0.3 | |1 | | -|spdesign |0.0.2 | | | | -|specr |1.0.0 | | | | -|sperrorest |3.0.5 | | | | -|spFSR |2.0.4 | | | | -|[sphunif](problems.md#sphunif)|1.3.0 | | |2 | -|[spNetwork](problems.md#spnetwork)|0.4.3.8 | | |1 | -|[squat](problems.md#squat) |0.2.1 | | |1 | -|[ssdtools](problems.md#ssdtools)|1.0.6 | | |1 | -|[stars](problems.md#stars) |0.6-4 | | |1 | -|startR |2.3.1 | | | | -|steps |1.3.0 | | | | -|[stppSim](problems.md#stppsim)|1.3.2 | |1 | | -|supercells |0.9.5 | | | | -|[synergyfinder](problems.md#synergyfinder)|3.10.0 | |1 |2 | -|[tableschema.r](problems.md#tableschemar)|1.1.2 | | |1 | -|[targeted](problems.md#targeted)|0.4 | | |1 | -|[targets](problems.md#targets)|1.4.0 | | |1 | -|TaxaNorm |2.4 | | | | -|tealeaves |1.0.6 | | | | -|templr |0.2-0 | | | | -|[text](problems.md#text) |1.0 | | |1 | -|tglkmeans |0.3.11 | | | | -|tidyqwi |0.1.2 | | | | -|tidySEM |0.2.6 | | | | -|tipmap |0.5.2 | | | | -|TKCat |1.0.7 | | | | -|TreeSearch |1.4.0 | | | | -|[TriDimRegression](failures.md#tridimregression)|1.0.2 |1 | | | -|tsfeatures |1.1.1 | | | | -|[txshift](problems.md#txshift)|0.3.8 | | |1 | -|uci |0.3.0 | | | | -|UCSCXenaShiny |1.1.10 | | | | -|updog |2.1.5 | | | | -|[vmeasur](problems.md#vmeasur)|0.1.4 | |1 | | -|webdeveloper |1.0.5 | | | | -|[WeightedCluster](problems.md#weightedcluster)|1.6-4 | |1 | | -|whitewater |0.1.3 | | | | -|wildmeta |0.3.2 | | | | -|[wru](problems.md#wru) |1.0.1 | | |2 | -|[XNAString](problems.md#xnastring)|1.10.0 | |1 |2 | -|yfR |1.1.0 | | | | +|package |version |error |warning |note | +|:-------|:-------|:-----------|:-------|:----| +|[stars](problems.md#stars)|0.6-4 |1 -1 __+1__ | |2 | + +## All (359) + +|package |version |error |warning |note | +|:--------------------------|:----------|:-----------|:-------|:----| +|adestr |0.5.0 | | | | +|AICcPermanova |0.0.2 | | | | +|[AIPW](problems.md#aipw) |0.6.3.2 | | |1 | +|ale |0.3.0 | | | | +|alookr |0.3.9 | | | | +|alphaci |1.0.1 | | | | +|[AlpsNMR](problems.md#alpsnmr)|4.4.0 |1 | | | +|[altdoc](problems.md#altdoc)|0.3.0 |1 | | | +|antaresEditObject |0.6.1 | | | | +|arkdb |? | | | | +|aroma.affymetrix |3.2.2 | | | | +|aroma.cn |1.7.1 | | | | +|[aroma.core](problems.md#aromacore)|3.3.1 | | |1 | +|ARPALData |1.5.2 | | | | +|[BAMBI](problems.md#bambi) |2.3.5 | |1 |1 | +|[bamm](problems.md#bamm) |0.4.3 | |1 |1 | +|baseballr |1.6.0 | | | | +|BatchGetSymbols |2.6.4 | | | | +|[batchtools](problems.md#batchtools)|0.9.17 | | |2 | +|bayesian |0.0.9 | | | | +|[bayesmove](problems.md#bayesmove)|0.2.1 | |1 | | +|bbknnR |1.1.1 | | | | +|bcmaps |2.2.0 | | | | +|[BEKKs](problems.md#bekks) |1.4.4 | |1 |1 | +|bhmbasket |0.9.5 | | | | +|[bigDM](problems.md#bigdm) |0.5.3 | | |2 | +|[bistablehistory](problems.md#bistablehistory)|1.1.2 | | |2 | +|bkmrhat |1.1.3 | | | | +|[blavaan](problems.md#blavaan)|0.5-3 | | |3 | +|bolasso |0.2.0 | | | | +|[brms](problems.md#brms) |2.21.0 | | |2 | +|brpop |0.3.0 | | | | +|bsitar |0.2.1 | | | | +|bspcov |1.0.0 | | | | +|calmr |0.6.1 | | | | +|campsis |1.5.1 | | | | +|canaper |1.0.1 | | | | +|[ceRNAnetsim](problems.md#cernanetsim)|1.14.1 |3 | |1 | +|[cft](failures.md#cft) |1.0.0 |1 | | | +|chatAI4R |0.2.10 | | | | +|[ChromSCape](problems.md#chromscape)|1.12.0 | |4 |4 | +|civis |3.1.2 | | | | +|[clickR](problems.md#clickr)|0.9.39 | | |1 | +|Clustering |1.7.7 | | | | +|ClustIRR |1.0.0 | | | | +|codalm |0.1.2 | | | | +|[codebook](problems.md#codebook)|0.9.2 | | |3 | +|[collinear](problems.md#collinear)|1.1.1 | | |1 | +|conformalInference.fd |1.1.1 | | | | +|conformalInference.multi |1.1.1 | | | | +|[Coxmos](problems.md#coxmos)|1.0.1 | | |1 | +|crossmap |0.4.0 | | | | +|CSCNet |0.1.2 | | | | +|[cSEM](problems.md#csem) |0.5.0 | | |1 | +|[CSGo](problems.md#csgo) |0.6.7 | | |1 | +|cvCovEst |1.2.2 | | | | +|dagHMM |0.1.0 | | | | +|dataquieR |2.0.1 | | | | +|DeclareDesign |1.0.8 | | | | +|delayed |0.4.0 | | | | +|[deseats](problems.md#deseats)|1.0.0 | |1 |1 | +|[dipsaus](problems.md#dipsaus)|0.2.8 | | |1 | +|[disk.frame](problems.md#diskframe)|0.8.3 |1 | | | +|[dispositionEffect](problems.md#dispositioneffect)|1.0.1 |1 | | | +|doFuture |1.0.1 | | | | +|DQAstats |0.3.3 | | | | +|[dragon](problems.md#dragon)|1.2.1 |1 | |2 | +|[drake](problems.md#drake) |7.13.9 | | |1 | +|drimmR |1.0.1 | | | | +|drtmle |1.1.2 | | | | +|dsos |0.1.2 | | | | +|[DT](problems.md#dt) |0.32 | | |1 | +|easyalluvial |0.3.2 | | | | +|ecic |0.0.3 | | | | +|eCV |0.0.2 | | | | +|[EFAtools](problems.md#efatools)|0.4.4 | |1 |3 | +|EGAnet |2.0.5 | | | | +|elevatr |0.99.0 | | | | +|[envi](problems.md#envi) |0.1.19 | |1 | | +|epe4md |0.1.4 | | | | +|EpiForsk |0.1.1 | | | | +|[EpiNow2](problems.md#epinow2)|1.4.0 | | |2 | +|[epitweetr](problems.md#epitweetr)|2.2.16 | | |2 | +|epwshiftr |0.1.4 | | | | +|[erah](failures.md#erah) |2.0.1 |1 | |1 | +|ezcox |1.0.4 | | | | +|fabletools |0.4.1 | | | | +|FAMoS |0.3.0 | | | | +|fastRhockey |0.4.0 | | | | +|[fdacluster](problems.md#fdacluster)|0.3.0 | |1 |1 | +|fdWasserstein |1.0 | | | | +|[fect](problems.md#fect) |1.0.0 | |1 |3 | +|fiery |1.2.1 | | | | +|finbif |0.9.5 | | | | +|fitlandr |0.1.0 | | | | +|[FLAMES](problems.md#flames)|1.8.0 | | |5 | +|[flowGraph](problems.md#flowgraph)|1.10.0 | | |2 | +|flowml |? | | | | +|[forecastML](problems.md#forecastml)|0.9.0 | | |1 | +|fst4pg |1.0.0 | | | | +|fundiversity |1.1.1 | | | | +|funGp |0.3.2 | | | | +|furrr |0.3.1 | | | | +|future.apply |1.11.1 | | | | +|future.batchtools |0.12.1 | | | | +|future.callr |0.8.2 | | | | +|future.tests |0.7.0 | | | | +|fxTWAPLS |0.1.2 | | | | +|[genBaRcode](problems.md#genbarcode)|1.2.7 | |1 | | +|[geocmeans](problems.md#geocmeans)|0.3.4 | |1 |1 | +|[geohabnet](problems.md#geohabnet)|2.0.0 |1 | | | +|GetBCBData |0.7.0 | | | | +|[googleComputeEngineR](problems.md#googlecomputeenginer)|0.3.0 | | |1 | +|googlePubsubR |0.0.4 | | | | +|[googleTagManageR](problems.md#googletagmanager)|0.2.0 | | |1 | +|greatR |1.1.0 | | | | +|[greed](problems.md#greed) |0.6.1 | |1 |3 | +|greta |0.4.5 | | | | +|gsdensity |0.1.2 | | | | +|gstat |2.1-1 | | | | +|GSVA |1.50.1 | | | | +|[gsynth](problems.md#gsynth)|1.2.1 | |1 |2 | +|gtfs2emis |0.1.0 | | | | +|gtfs2gps |2.1-1 | | | | +|gWQS |3.0.5 | | | | +|[hackeRnews](problems.md#hackernews)|0.1.0 | | |1 | +|hacksig |0.1.2 | | | | +|[hal9001](problems.md#hal9001)|0.4.6 | | |1 | +|haldensify |0.2.3 | | | | +|[hbamr](problems.md#hbamr) |2.2.1 | | |2 | +|[hero](problems.md#hero) |0.6 | | |2 | +|[heterogen](problems.md#heterogen)|1.2.33 | |1 |1 | +|hoopR |2.1.0 | | | | +|[httpgd](problems.md#httpgd)|2.0.1 |1 | |2 | +|[hwep](problems.md#hwep) |2.0.2 | | |2 | +|[hydroloom](problems.md#hydroloom)|1.0.2 |2 | | | +|idmodelr |0.4.0 | | | | +|imagefluency |0.2.5 | | | | +|iml |0.11.1 | | | | +|incubate |1.2.1 | | | | +|iNEXT.beta3D |1.0.0 | | | | +|[infercnv](problems.md#infercnv)|1.18.1 | | |2 | +|inlinedocs |2023.9.4 | | | | +|[InPAS](problems.md#inpas) |2.10.0 | | |1 | +|[interflex](problems.md#interflex)|1.2.6 | |1 |2 | +|ipc |0.1.4 | | | | +|[ISAnalytics](problems.md#isanalytics)|1.12.0 | | |1 | +|isopam |2.0 | | | | +|ivDiag |1.0.6 | | | | +|[ivmte](problems.md#ivmte) |1.4.0 | | |1 | +|jlmerclusterperm |1.1.3 | | | | +|JointAI |1.0.5 | | | | +|jstor |0.3.11 | | | | +|JuliaConnectoR |1.1.3 | | | | +|kernelboot |0.1.10 | | | | +|[keyATM](problems.md#keyatm)|0.5.1 | | |1 | +|LandComp |0.0.5 | | | | +|latentcor |2.0.1 | | | | +|lava |1.8.0 | | | | +|ldaPrototype |0.3.1 | | | | +|[ldsr](problems.md#ldsr) |0.0.2 | |1 |1 | +|lemna |1.0.1 | | | | +|LexFindR |1.0.2 | | | | +|lgr |0.4.4 | | | | +|[lidR](problems.md#lidr) |4.1.1 |1 |1 |1 | +|lightr |1.7.1 | | | | +|lmtp |1.3.2 | | | | +|LTFHPlus |2.1.1 | | | | +|LWFBrook90R |0.5.3 | | | | +|[MAI](problems.md#mai) |1.8.0 | | |1 | +|malariaAtlas |1.5.1 | | | | +|MAMS |2.0.1 | | | | +|[manynet](problems.md#manynet)|0.4.4 | | |2 | +|mapme.biodiversity |0.5.0 | | | | +|marginaleffects |? | | | | +|[matric](problems.md#matric)|0.2.0 |1 | | | +|mbbe |0.1.0 | | | | +|mcmcensemble |3.1.0 | | | | +|mcp |0.3.4 | | | | +|merTools |0.6.2 | | | | +|[metabolomicsR](problems.md#metabolomicsr)|1.0.0 | |1 |1 | +|[metaGE](problems.md#metage)|1.0.3 | | |1 | +|mice |3.16.0 | | | | +|[microservices](problems.md#microservices)|0.2.0 |1 | | | +|migraph |1.3.4 | | | | +|mikropml |1.6.1 | | | | +|[MineICA](problems.md#mineica)|1.42.0 | |3 |4 | +|[missSBM](problems.md#misssbm)|1.0.4 | |1 |1 | +|[mistyR](problems.md#mistyr)|1.10.0 |1 | |1 | +|mlr3 |0.18.0 | | | | +|mlr3db |0.5.2 | | | | +|mlr3pipelines |0.5.0-2 | | | | +|mlr3resampling |2024.1.23 | | | | +|mlr3spatial |0.5.0 | | | | +|modelsummary |1.4.5 | | | | +|[momentuHMM](problems.md#momentuhmm)|1.5.5 | |1 |1 | +|[MOSS](problems.md#moss) |0.2.2 | |1 | | +|mplusParallel.automation |0.0.1.1 | | | | +|[mrgsim.parallel](problems.md#mrgsimparallel)|0.2.1 | | |2 | +|mslp |1.4.0 | | | | +|multilevelmediation |0.3.1 | | | | +|multitool |0.1.4 | | | | +|multiverse |0.6.1 | | | | +|[nebula](problems.md#nebula)|1.5.3 | | |1 | +|netShiny |1.0 | | | | +|NetSimR |0.1.5 | | | | +|[nfl4th](problems.md#nfl4th)|1.0.4 | |1 |1 | +|nflfastR |4.6.1 | | | | +|nflseedR |1.2.0 | | | | +|[nhdplusTools](problems.md#nhdplustools)|1.0.0 |1 | | | +|nncc |2.0.0 | | | | +|[oncomsm](problems.md#oncomsm)|0.1.4 | | |2 | +|[onemapsgapi](problems.md#onemapsgapi)|1.1.0 |1 | | | +|[OOS](problems.md#oos) |1.0.0 | | |1 | +|optic |1.0.1 | | | | +|OptimalGoldstandardDesigns |1.0.1 | | | | +|optimLanduse |1.2.1 | | | | +|origami |1.0.7 | | | | +|paramsim |0.1.0 | | | | +|[pareg](problems.md#pareg) |1.6.0 |3 | |2 | +|[parseRPDR](problems.md#parserpdr)|1.1.0 | | |1 | +|[partR2](problems.md#partr2)|0.9.2 | | |1 | +|[pavo](problems.md#pavo) |2.9.0 | |1 |1 | +|pbapply |1.7-2 | | | | +|[PCRedux](problems.md#pcredux)|1.1-2 | |1 | | +|PeakSegDisk |2023.11.27 | | | | +|penaltyLearning |2024.1.25 | | | | +|pGRN |0.3.5 | | | | +|[photosynthesis](problems.md#photosynthesis)|2.1.4 | | |2 | +|[phylolm](problems.md#phylolm)|2.6.2 | | |2 | +|phylopath |1.2.1 | | | | +|PINstimation |0.1.2 | | | | +|[PLNmodels](problems.md#plnmodels)|1.2.0 | |1 |1 | +|[plumber](problems.md#plumber)|1.2.1 | | |2 | +|polle |1.3 | | | | +|POMADE |0.2.0 | | | | +|[portvine](problems.md#portvine)|1.0.3 | | |1 | +|powRICLPM |0.1.1 | | | | +|[ProFAST](problems.md#profast)|1.4 | |1 |2 | +|progressr |0.14.0 | | | | +|[projpred](problems.md#projpred)|2.8.0 | |1 |2 | +|promises |1.2.1 | | | | +|[Prostar](failures.md#prostar)|1.34.6 |1 | | | +|proteus |1.1.4 | | | | +|protti |0.7.0 | | | | +|PSCBS |0.67.0 | | | | +|[pseudohouseholds](problems.md#pseudohouseholds)|0.1.1 | | |1 | +|PUMP |1.0.3 | | | | +|qape |2.1 | | | | +|[QDNAseq](problems.md#qdnaseq)|1.38.0 | | |1 | +|qgcomp |2.15.2 | | | | +|qgcompint |0.7.0 | | | | +|[RAINBOWR](problems.md#rainbowr)|0.1.35 | | |1 | +|rangeMapper |2.0.3 | | | | +|rBiasCorrection |0.3.4 | | | | +|Rcurvep |1.3.1 | | | | +|[receptiviti](problems.md#receptiviti)|0.1.7 |1 | |2 | +|refineR |1.6.1 | | | | +|[regmedint](problems.md#regmedint)|1.0.1 | | |1 | +|remiod |1.0.2 | | | | +|reproducible |2.0.10 | | | | +|reval |3.1-0 | | | | +|[rgee](problems.md#rgee) |1.1.7 | | |1 | +|rkeops |2.2.2 | | | | +|[robotstxt](problems.md#robotstxt)|0.7.13 | | |2 | +|robust2sls |0.2.2 | | | | +|[rpm](problems.md#rpm) |0.7-1 | |1 |1 | +|rsi |0.1.2 | | | | +|RTransferEntropy |0.2.21 | | | | +|s3fs |0.1.5 | | | | +|saeczi |0.1.1 | | | | +|[sapfluxnetr](problems.md#sapfluxnetr)|0.1.4 | | |1 | +|[SCArray.sat](problems.md#scarraysat)|1.2.1 | |1 |1 | +|scBubbletree |1.4.0 | | | | +|scDiffCom |1.0.0 | | | | +|[sctransform](problems.md#sctransform)|0.4.1 | |1 |1 | +|[sdmApp](problems.md#sdmapp)|0.0.2 | | |1 | +|[sdmTMB](problems.md#sdmtmb)|0.4.3 |1 | |1 | +|seer |1.1.8 | | | | +|semPower |2.1.0 | | | | +|semTests |0.5.0 | | | | +|semtree |0.9.19 | | | | +|[sentopics](problems.md#sentopics)|0.7.2 | |1 |3 | +|[Seurat](problems.md#seurat)|5.0.3 | | |3 | +|[SeuratObject](problems.md#seuratobject)|5.0.1 | | |3 | +|[sharp](problems.md#sharp) |1.4.6 | | |2 | +|[shiny](problems.md#shiny) |1.8.0 | | |1 | +|[shiny.worker](problems.md#shinyworker)|0.0.1 | | |2 | +|[sigminer](problems.md#sigminer)|2.3.0 | | |1 | +|[Signac](problems.md#signac)|1.12.0 | | |1 | +|[signeR](problems.md#signer)|2.4.0 | |1 |4 | +|[SimDesign](problems.md#simdesign)|2.14 | | |2 | +|simglm |0.8.9 | | | | +|simhelpers |0.2.1 | | | | +|simIDM |0.1.0 | | | | +|sims |0.0.3 | | | | +|simtrial |0.3.2 | | | | +|[sits](problems.md#sits) |1.4.2-1 | |1 |1 | +|skewlmm |1.1.0 | | | | +|[skpr](problems.md#skpr) |1.6.2 | | |1 | +|[SmCCNet](problems.md#smccnet)|2.0.2 |1 | | | +|[smoots](problems.md#smoots)|1.1.4 | |1 | | +|sNPLS |1.0.27 | | | | +|[solitude](problems.md#solitude)|1.1.3 | | |1 | +|sovereign |1.2.1 | | | | +|[SpaDES.core](problems.md#spadescore)|2.0.3 | | |2 | +|[spaMM](problems.md#spamm) |4.4.16 | | |2 | +|[sparrpowR](problems.md#sparrpowr)|0.2.8 | |1 | | +|[SPARSEMODr](problems.md#sparsemodr)|1.2.0 | | |1 | +|spatialTIME |1.3.4-3 | | | | +|[spatialwarnings](problems.md#spatialwarnings)|3.0.3 | |2 |1 | +|spdesign |0.0.3 | | | | +|specr |1.0.0 | | | | +|sperrorest |3.0.5 | | | | +|spFSR |2.0.4 | | | | +|[sphunif](problems.md#sphunif)|1.3.0 | |1 |2 | +|[spNetwork](problems.md#spnetwork)|0.4.3.8 | |1 |1 | +|[squat](problems.md#squat) |0.3.0 | |1 |1 | +|[ssdtools](problems.md#ssdtools)|1.0.6 | | |1 | +|stacks |1.0.4 | | | | +|[stars](problems.md#stars) |0.6-4 |1 -1 __+1__ | |2 | +|[startR](failures.md#startr)|2.3.1 |1 | | | +|steps |1.3.0 | | | | +|[stppSim](problems.md#stppsim)|1.3.2 | |1 | | +|supercells |1.0.0 | | | | +|[survstan](problems.md#survstan)|0.0.7 | | |3 | +|[synergyfinder](problems.md#synergyfinder)|3.10.3 | |1 |3 | +|[tableschema.r](problems.md#tableschemar)|1.1.2 | | |1 | +|[targeted](problems.md#targeted)|0.5 | |1 |1 | +|[targets](problems.md#targets)|1.6.0 | | |1 | +|TaxaNorm |2.4 | | | | +|tealeaves |1.0.6 | | | | +|templr |0.2-0 | | | | +|[text](problems.md#text) |1.2.0 | | |1 | +|[tglkmeans](problems.md#tglkmeans)|0.5.4 | | |2 | +|tidyMC |1.0.0 | | | | +|tidyqwi |0.1.2 | | | | +|tidySEM |0.2.6 | | | | +|tipmap |0.5.2 | | | | +|[TKCat](failures.md#tkcat) |1.0.7 |1 | | | +|[TreeSearch](problems.md#treesearch)|1.4.0 | | |1 | +|[TriDimRegression](failures.md#tridimregression)|1.0.2 |1 | | | +|[tsdistributions](problems.md#tsdistributions)|1.0.0 | |1 |1 | +|tsfeatures |1.1.1 | | | | +|tune |1.2.0 | | | | +|[txshift](problems.md#txshift)|0.3.8 | | |1 | +|uci |0.3.0 | | | | +|[UCSCXenaShiny](problems.md#ucscxenashiny)|2.0.0 | | |1 | +|[updog](problems.md#updog) |2.1.5 | |1 |1 | +|[vmeasur](problems.md#vmeasur)|0.1.4 |1 | | | +|webdeveloper |1.0.5 | | | | +|[WeightedCluster](problems.md#weightedcluster)|1.6-4 | |1 | | +|whitewater |0.1.3 | | | | +|wildmeta |0.3.2 | | | | +|wingen |2.1.1 | | | | +|[wru](problems.md#wru) |3.0.1 | |1 |2 | +|xegaPopulation |1.0.0.0 | | | | +|[XNAString](problems.md#xnastring)|1.10.0 | |1 |3 | +|yfR |1.1.0 | | | | diff --git a/revdep/cran.md b/revdep/cran.md index 83f08fe3..08bdce77 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,12 +1,22 @@ ## revdepcheck results -We checked 321 reverse dependencies (300 from CRAN + 21 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. +We checked 359 reverse dependencies (334 from CRAN + 25 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. - * We saw 0 new problems - * We failed to check 1 packages + * We saw 1 new problems + * We failed to check 5 packages Issues with CRAN packages are summarised below. +### New problems +(This reports the first line of each new failure) + +* stars + checking examples ...sh: line 1: 76201 Aborted (core dumped) LANGUAGE=en _R_CHECK_INTERNALS2_=1 '/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/bin/R' --vanilla --encoding=UTF-8 > 'stars-Ex.Rout' 2>&1 < 'stars-Ex.R' + ### Failed to check +* cft (NA) +* erah (NA) +* startR (NA) +* TKCat (NA) * TriDimRegression (NA) diff --git a/revdep/failures.md b/revdep/failures.md index 602c540f..366c1a40 100644 --- a/revdep/failures.md +++ b/revdep/failures.md @@ -1,22 +1,589 @@ -# QDNAseq +# arkdb
-* Version: 1.38.0 -* GitHub: https://github.com/ccagc/QDNAseq -* Source code: https://github.com/cran/QDNAseq -* Date/Publication: 2023-10-24 -* Number of recursive dependencies: 93 +* Version: +* GitHub: https://github.com/HenrikBengtsson/future +* Source code: NA +* Number of recursive dependencies: 0 -Run `revdep_details(, "QDNAseq")` for more info +
+ +## Error before installation + +### Devel + +``` +g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_catalog.cpp -o duckdb/ub_src_catalog.o +g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_catalog_catalog_entry.cpp -o duckdb/ub_src_catalog_catalog_entry.o +g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_catalog_catalog_entry_dependency.cpp -o duckdb/ub_src_catalog_catalog_entry_dependency.o +g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_catalog_default.cpp -o duckdb/ub_src_catalog_default.o +g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_common_adbc.cpp -o duckdb/ub_src_common_adbc.o +g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_common_adbc_nanoarrow.cpp -o duckdb/ub_src_common_adbc_nanoarrow.o +g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_common.cpp -o duckdb/ub_src_common.o +g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_common_arrow_appender.cpp -o duckdb/ub_src_common_arrow_appender.o +g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_common_arrow.cpp -o duckdb/ub_src_common_arrow.o +g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_common_crypto.cpp -o duckdb/ub_src_common_crypto.o +... +g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c statement.cpp -o statement.o +g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c register.cpp -o register.o +g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c relational.cpp -o relational.o +g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c scan.cpp -o scan.o +g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c transform.cpp -o transform.o +g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c utils.cpp -o utils.o +g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c reltoaltrep.cpp -o reltoaltrep.o +g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c types.cpp -o types.o +g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c cpp11.cpp -o cpp11.o +g++ -std=gnu++17 -shared -L/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/lib -L/usr/local/lib64 -o duckdb.so database.o connection.o statement.o register.o relational.o scan.o transform.o utils.o reltoaltrep.o types.o cpp11.o duckdb/ub_src_catalog.o duckdb/ub_src_catalog_catalog_entry.o duckdb/ub_src_catalog_catalog_entry_dependency.o duckdb/ub_src_catalog_default.o duckdb/ub_src_common_adbc.o duckdb/ub_src_common_adbc_nanoarrow.o duckdb/ub_src_common.o duckdb/ub_src_common_arrow_appender.o duckdb/ub_src_common_arrow.o duckdb/ub_src_common_crypto.o duckdb/ub_src_common_enums.o duckdb/ub_src_common_exception.o duckdb/ub_src_common_operator.o duckdb/ub_src_common_progress_bar.o duckdb/ub_src_common_row_operations.o duckdb/ub_src_common_serializer.o duckdb/ub_src_common_sort.o duckdb/ub_src_common_types.o duckdb/ub_src_common_types_column.o duckdb/ub_src_common_types_row.o duckdb/ub_src_common_value_operations.o duckdb/src/common/vector_operations/boolean_operators.o duckdb/src/common/vector_operations/comparison_operators.o duckdb/src/common/vector_operations/generators.o duckdb/src/common/vector_operations/is_distinct_from.o duckdb/src/common/vector_operations/null_operations.o duckdb/src/common/vector_operations/numeric_inplace_operators.o duckdb/src/common/vector_operations/vector_cast.o duckdb/src/common/vector_operations/vector_copy.o duckdb/src/common/vector_operations/vector_hash.o duckdb/src/common/vector_operations/vector_storage.o duckdb/ub_src_core_functions_aggregate_algebraic.o duckdb/ub_src_core_functions_aggregate_distributive.o duckdb/ub_src_core_functions_aggregate_holistic.o duckdb/ub_src_core_functions_aggregate_nested.o duckdb/ub_src_core_functions_aggregate_regression.o duckdb/ub_src_core_functions.o duckdb/ub_src_core_functions_scalar_array.o duckdb/ub_src_core_functions_scalar_bit.o duckdb/ub_src_core_functions_scalar_blob.o duckdb/ub_src_core_functions_scalar_date.o duckdb/ub_src_core_functions_scalar_debug.o duckdb/ub_src_core_functions_scalar_enum.o duckdb/ub_src_core_functions_scalar_generic.o duckdb/ub_src_core_functions_scalar_list.o duckdb/ub_src_core_functions_scalar_map.o duckdb/ub_src_core_functions_scalar_math.o duckdb/ub_src_core_functions_scalar_operators.o duckdb/ub_src_core_functions_scalar_random.o duckdb/ub_src_core_functions_scalar_secret.o duckdb/ub_src_core_functions_scalar_string.o duckdb/ub_src_core_functions_scalar_struct.o duckdb/ub_src_core_functions_scalar_union.o duckdb/ub_src_execution.o duckdb/ub_src_execution_expression_executor.o duckdb/ub_src_execution_index_art.o duckdb/ub_src_execution_index.o duckdb/ub_src_execution_nested_loop_join.o duckdb/ub_src_execution_operator_aggregate.o duckdb/ub_src_execution_operator_csv_scanner_buffer_manager.o duckdb/ub_src_execution_operator_csv_scanner_scanner.o duckdb/ub_src_execution_operator_csv_scanner_sniffer.o duckdb/ub_src_execution_operator_csv_scanner_state_machine.o duckdb/ub_src_execution_operator_csv_scanner_table_function.o duckdb/ub_src_execution_operator_csv_scanner_util.o duckdb/ub_src_execution_operator_filter.o duckdb/ub_src_execution_operator_helper.o duckdb/ub_src_execution_operator_join.o duckdb/ub_src_execution_operator_order.o duckdb/ub_src_execution_operator_persistent.o duckdb/ub_src_execution_operator_projection.o duckdb/ub_src_execution_operator_scan.o duckdb/ub_src_execution_operator_schema.o duckdb/ub_src_execution_operator_set.o duckdb/ub_src_execution_physical_plan.o duckdb/ub_src_function_aggregate_distributive.o duckdb/ub_src_function_aggregate.o duckdb/ub_src_function.o duckdb/ub_src_function_cast.o duckdb/ub_src_function_cast_union.o duckdb/ub_src_function_pragma.o duckdb/ub_src_function_scalar_compressed_materialization.o duckdb/ub_src_function_scalar.o duckdb/ub_src_function_scalar_generic.o duckdb/ub_src_function_scalar_list.o duckdb/ub_src_function_scalar_operators.o duckdb/ub_src_function_scalar_sequence.o duckdb/ub_src_function_scalar_string.o duckdb/ub_src_function_scalar_string_regexp.o duckdb/ub_src_function_scalar_struct.o duckdb/ub_src_function_scalar_system.o duckdb/ub_src_function_table_arrow.o duckdb/ub_src_function_table.o duckdb/ub_src_function_table_system.o duckdb/ub_src_function_table_version.o duckdb/ub_src_main.o duckdb/ub_src_main_buffered_data.o duckdb/ub_src_main_capi.o duckdb/ub_src_main_capi_cast.o duckdb/ub_src_main_chunk_scan_state.o duckdb/ub_src_main_extension.o duckdb/ub_src_main_relation.o duckdb/ub_src_main_secret.o duckdb/ub_src_main_settings.o duckdb/ub_src_optimizer.o duckdb/ub_src_optimizer_compressed_materialization.o duckdb/ub_src_optimizer_join_order.o duckdb/ub_src_optimizer_matcher.o duckdb/ub_src_optimizer_pullup.o duckdb/ub_src_optimizer_pushdown.o duckdb/ub_src_optimizer_rule.o duckdb/ub_src_optimizer_statistics_expression.o duckdb/ub_src_optimizer_statistics_operator.o duckdb/ub_src_parallel.o duckdb/ub_src_parser.o duckdb/ub_src_parser_constraints.o duckdb/ub_src_parser_expression.o duckdb/ub_src_parser_parsed_data.o duckdb/ub_src_parser_query_node.o duckdb/ub_src_parser_statement.o duckdb/ub_src_parser_tableref.o duckdb/ub_src_parser_transform_constraint.o duckdb/ub_src_parser_transform_expression.o duckdb/ub_src_parser_transform_helpers.o duckdb/ub_src_parser_transform_statement.o duckdb/ub_src_parser_transform_tableref.o duckdb/ub_src_planner.o duckdb/ub_src_planner_binder_expression.o duckdb/ub_src_planner_binder_query_node.o duckdb/ub_src_planner_binder_statement.o duckdb/ub_src_planner_binder_tableref.o duckdb/ub_src_planner_expression.o duckdb/ub_src_planner_expression_binder.o duckdb/ub_src_planner_filter.o duckdb/ub_src_planner_operator.o duckdb/ub_src_planner_subquery.o duckdb/ub_src_storage.o duckdb/ub_src_storage_buffer.o duckdb/ub_src_storage_checkpoint.o duckdb/ub_src_storage_compression_alp.o duckdb/ub_src_storage_compression.o duckdb/ub_src_storage_compression_chimp.o duckdb/ub_src_storage_metadata.o duckdb/ub_src_storage_serialization.o duckdb/ub_src_storage_statistics.o duckdb/ub_src_storage_table.o duckdb/ub_src_transaction.o duckdb/src/verification/copied_statement_verifier.o duckdb/src/verification/deserialized_statement_verifier.o duckdb/src/verification/external_statement_verifier.o duckdb/src/verification/fetch_row_verifier.o duckdb/src/verification/no_operator_caching_verifier.o duckdb/src/verification/parsed_statement_verifier.o duckdb/src/verification/prepared_statement_verifier.o duckdb/src/verification/statement_verifier.o duckdb/src/verification/unoptimized_statement_verifier.o duckdb/third_party/fmt/format.o duckdb/third_party/fsst/fsst_avx512.o duckdb/third_party/fsst/libfsst.o duckdb/third_party/miniz/miniz.o duckdb/third_party/re2/re2/bitstate.o duckdb/third_party/re2/re2/compile.o duckdb/third_party/re2/re2/dfa.o duckdb/third_party/re2/re2/filtered_re2.o duckdb/third_party/re2/re2/mimics_pcre.o duckdb/third_party/re2/re2/nfa.o duckdb/third_party/re2/re2/onepass.o duckdb/third_party/re2/re2/parse.o duckdb/third_party/re2/re2/perl_groups.o duckdb/third_party/re2/re2/prefilter.o duckdb/third_party/re2/re2/prefilter_tree.o duckdb/third_party/re2/re2/prog.o duckdb/third_party/re2/re2/re2.o duckdb/third_party/re2/re2/regexp.o duckdb/third_party/re2/re2/set.o duckdb/third_party/re2/re2/simplify.o duckdb/third_party/re2/re2/stringpiece.o duckdb/third_party/re2/re2/tostring.o duckdb/third_party/re2/re2/unicode_casefold.o duckdb/third_party/re2/re2/unicode_groups.o duckdb/third_party/re2/util/rune.o duckdb/third_party/re2/util/strutil.o duckdb/third_party/hyperloglog/hyperloglog.o duckdb/third_party/hyperloglog/sds.o duckdb/third_party/skiplist/SkipList.o duckdb/third_party/fastpforlib/bitpacking.o duckdb/third_party/utf8proc/utf8proc.o duckdb/third_party/utf8proc/utf8proc_wrapper.o duckdb/third_party/libpg_query/pg_functions.o duckdb/third_party/libpg_query/postgres_parser.o duckdb/third_party/libpg_query/src_backend_nodes_list.o duckdb/third_party/libpg_query/src_backend_nodes_makefuncs.o duckdb/third_party/libpg_query/src_backend_nodes_value.o duckdb/third_party/libpg_query/src_backend_parser_gram.o duckdb/third_party/libpg_query/src_backend_parser_parser.o duckdb/third_party/libpg_query/src_backend_parser_scan.o duckdb/third_party/libpg_query/src_backend_parser_scansup.o duckdb/third_party/libpg_query/src_common_keywords.o duckdb/third_party/mbedtls/library/aes.o duckdb/third_party/mbedtls/library/aria.o duckdb/third_party/mbedtls/library/asn1parse.o duckdb/third_party/mbedtls/library/base64.o duckdb/third_party/mbedtls/library/bignum.o duckdb/third_party/mbedtls/library/camellia.o duckdb/third_party/mbedtls/library/cipher.o duckdb/third_party/mbedtls/library/cipher_wrap.o duckdb/third_party/mbedtls/library/constant_time.o duckdb/third_party/mbedtls/library/entropy.o duckdb/third_party/mbedtls/library/entropy_poll.o duckdb/third_party/mbedtls/library/gcm.o duckdb/third_party/mbedtls/library/md.o duckdb/third_party/mbedtls/library/oid.o duckdb/third_party/mbedtls/library/pem.o duckdb/third_party/mbedtls/library/pk.o duckdb/third_party/mbedtls/library/pk_wrap.o duckdb/third_party/mbedtls/library/pkparse.o duckdb/third_party/mbedtls/library/platform_util.o duckdb/third_party/mbedtls/library/rsa.o duckdb/third_party/mbedtls/library/rsa_alt_helpers.o duckdb/third_party/mbedtls/library/sha1.o duckdb/third_party/mbedtls/library/sha256.o duckdb/third_party/mbedtls/library/sha512.o duckdb/third_party/mbedtls/mbedtls_wrapper.o duckdb/extension/parquet/column_reader.o duckdb/extension/parquet/column_writer.o duckdb/extension/parquet/parquet_crypto.o duckdb/extension/parquet/parquet_extension.o duckdb/extension/parquet/parquet_metadata.o duckdb/extension/parquet/parquet_reader.o duckdb/extension/parquet/parquet_statistics.o duckdb/extension/parquet/parquet_timestamp.o duckdb/extension/parquet/parquet_writer.o duckdb/extension/parquet/serialize_parquet.o duckdb/extension/parquet/zstd_file_system.o duckdb/third_party/parquet/parquet_constants.o duckdb/third_party/parquet/parquet_types.o duckdb/third_party/thrift/thrift/protocol/TProtocol.o duckdb/third_party/thrift/thrift/transport/TTransportException.o duckdb/third_party/thrift/thrift/transport/TBufferTransports.o duckdb/third_party/snappy/snappy.o duckdb/third_party/snappy/snappy-sinksource.o duckdb/third_party/zstd/decompress/zstd_ddict.o duckdb/third_party/zstd/decompress/huf_decompress.o duckdb/third_party/zstd/decompress/zstd_decompress.o duckdb/third_party/zstd/decompress/zstd_decompress_block.o duckdb/third_party/zstd/common/entropy_common.o duckdb/third_party/zstd/common/fse_decompress.o duckdb/third_party/zstd/common/zstd_common.o duckdb/third_party/zstd/common/error_private.o duckdb/third_party/zstd/common/xxhash.o duckdb/third_party/zstd/compress/fse_compress.o duckdb/third_party/zstd/compress/hist.o duckdb/third_party/zstd/compress/huf_compress.o duckdb/third_party/zstd/compress/zstd_compress.o duckdb/third_party/zstd/compress/zstd_compress_literals.o duckdb/third_party/zstd/compress/zstd_compress_sequences.o duckdb/third_party/zstd/compress/zstd_compress_superblock.o duckdb/third_party/zstd/compress/zstd_double_fast.o duckdb/third_party/zstd/compress/zstd_fast.o duckdb/third_party/zstd/compress/zstd_lazy.o duckdb/third_party/zstd/compress/zstd_ldm.o duckdb/third_party/zstd/compress/zstd_opt.o -L/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/lib -lR + + +trying URL 'https://cloud.r-project.org/src/contrib/bslib_0.6.2.tar.gz' +Content type 'application/x-gzip' length 6060123 bytes (5.8 MB) +================================================== +downloaded 5.8 MB + +trying URL 'https://cloud.r-project.org/src/contrib/duckdb_0.10.0.tar.gz' +Content type 'application/x-gzip' length 4090561 bytes (3.9 MB) +================================================== +downloaded 3.9 MB + +... +* installing *binary* package ‘httr’ ... +* DONE (httr) +* installing *binary* package ‘jquerylib’ ... +* DONE (jquerylib) +* installing *binary* package ‘pillar’ ... +* DONE (pillar) +* installing *binary* package ‘pkgbuild’ ... +* DONE (pkgbuild) +* installing *binary* package ‘purrr’ ... +* DONE (purrr) + + +``` +### CRAN + +``` +g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_catalog.cpp -o duckdb/ub_src_catalog.o +g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_catalog_catalog_entry.cpp -o duckdb/ub_src_catalog_catalog_entry.o +g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_catalog_catalog_entry_dependency.cpp -o duckdb/ub_src_catalog_catalog_entry_dependency.o +g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_catalog_default.cpp -o duckdb/ub_src_catalog_default.o +g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_common_adbc.cpp -o duckdb/ub_src_common_adbc.o +g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_common_adbc_nanoarrow.cpp -o duckdb/ub_src_common_adbc_nanoarrow.o +g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_common.cpp -o duckdb/ub_src_common.o +g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_common_arrow_appender.cpp -o duckdb/ub_src_common_arrow_appender.o +g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_common_arrow.cpp -o duckdb/ub_src_common_arrow.o +g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_common_crypto.cpp -o duckdb/ub_src_common_crypto.o +... +g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c statement.cpp -o statement.o +g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c register.cpp -o register.o +g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include 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-Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c transform.cpp -o transform.o +g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c utils.cpp -o utils.o +g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c reltoaltrep.cpp -o reltoaltrep.o +g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c types.cpp -o types.o +g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c cpp11.cpp -o cpp11.o +g++ -std=gnu++17 -shared -L/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/lib -L/usr/local/lib64 -o duckdb.so database.o connection.o statement.o register.o relational.o scan.o transform.o utils.o reltoaltrep.o types.o cpp11.o duckdb/ub_src_catalog.o duckdb/ub_src_catalog_catalog_entry.o duckdb/ub_src_catalog_catalog_entry_dependency.o duckdb/ub_src_catalog_default.o duckdb/ub_src_common_adbc.o duckdb/ub_src_common_adbc_nanoarrow.o duckdb/ub_src_common.o duckdb/ub_src_common_arrow_appender.o duckdb/ub_src_common_arrow.o duckdb/ub_src_common_crypto.o duckdb/ub_src_common_enums.o duckdb/ub_src_common_exception.o duckdb/ub_src_common_operator.o duckdb/ub_src_common_progress_bar.o duckdb/ub_src_common_row_operations.o duckdb/ub_src_common_serializer.o duckdb/ub_src_common_sort.o duckdb/ub_src_common_types.o duckdb/ub_src_common_types_column.o duckdb/ub_src_common_types_row.o duckdb/ub_src_common_value_operations.o duckdb/src/common/vector_operations/boolean_operators.o duckdb/src/common/vector_operations/comparison_operators.o duckdb/src/common/vector_operations/generators.o duckdb/src/common/vector_operations/is_distinct_from.o duckdb/src/common/vector_operations/null_operations.o duckdb/src/common/vector_operations/numeric_inplace_operators.o duckdb/src/common/vector_operations/vector_cast.o duckdb/src/common/vector_operations/vector_copy.o duckdb/src/common/vector_operations/vector_hash.o duckdb/src/common/vector_operations/vector_storage.o duckdb/ub_src_core_functions_aggregate_algebraic.o duckdb/ub_src_core_functions_aggregate_distributive.o duckdb/ub_src_core_functions_aggregate_holistic.o duckdb/ub_src_core_functions_aggregate_nested.o duckdb/ub_src_core_functions_aggregate_regression.o duckdb/ub_src_core_functions.o duckdb/ub_src_core_functions_scalar_array.o duckdb/ub_src_core_functions_scalar_bit.o duckdb/ub_src_core_functions_scalar_blob.o duckdb/ub_src_core_functions_scalar_date.o duckdb/ub_src_core_functions_scalar_debug.o duckdb/ub_src_core_functions_scalar_enum.o duckdb/ub_src_core_functions_scalar_generic.o duckdb/ub_src_core_functions_scalar_list.o duckdb/ub_src_core_functions_scalar_map.o duckdb/ub_src_core_functions_scalar_math.o duckdb/ub_src_core_functions_scalar_operators.o duckdb/ub_src_core_functions_scalar_random.o duckdb/ub_src_core_functions_scalar_secret.o duckdb/ub_src_core_functions_scalar_string.o duckdb/ub_src_core_functions_scalar_struct.o duckdb/ub_src_core_functions_scalar_union.o duckdb/ub_src_execution.o duckdb/ub_src_execution_expression_executor.o duckdb/ub_src_execution_index_art.o duckdb/ub_src_execution_index.o duckdb/ub_src_execution_nested_loop_join.o duckdb/ub_src_execution_operator_aggregate.o duckdb/ub_src_execution_operator_csv_scanner_buffer_manager.o duckdb/ub_src_execution_operator_csv_scanner_scanner.o duckdb/ub_src_execution_operator_csv_scanner_sniffer.o duckdb/ub_src_execution_operator_csv_scanner_state_machine.o duckdb/ub_src_execution_operator_csv_scanner_table_function.o duckdb/ub_src_execution_operator_csv_scanner_util.o duckdb/ub_src_execution_operator_filter.o duckdb/ub_src_execution_operator_helper.o duckdb/ub_src_execution_operator_join.o duckdb/ub_src_execution_operator_order.o duckdb/ub_src_execution_operator_persistent.o duckdb/ub_src_execution_operator_projection.o duckdb/ub_src_execution_operator_scan.o duckdb/ub_src_execution_operator_schema.o duckdb/ub_src_execution_operator_set.o duckdb/ub_src_execution_physical_plan.o duckdb/ub_src_function_aggregate_distributive.o duckdb/ub_src_function_aggregate.o duckdb/ub_src_function.o duckdb/ub_src_function_cast.o duckdb/ub_src_function_cast_union.o duckdb/ub_src_function_pragma.o duckdb/ub_src_function_scalar_compressed_materialization.o duckdb/ub_src_function_scalar.o duckdb/ub_src_function_scalar_generic.o duckdb/ub_src_function_scalar_list.o duckdb/ub_src_function_scalar_operators.o duckdb/ub_src_function_scalar_sequence.o duckdb/ub_src_function_scalar_string.o duckdb/ub_src_function_scalar_string_regexp.o duckdb/ub_src_function_scalar_struct.o duckdb/ub_src_function_scalar_system.o duckdb/ub_src_function_table_arrow.o duckdb/ub_src_function_table.o duckdb/ub_src_function_table_system.o duckdb/ub_src_function_table_version.o duckdb/ub_src_main.o duckdb/ub_src_main_buffered_data.o duckdb/ub_src_main_capi.o duckdb/ub_src_main_capi_cast.o duckdb/ub_src_main_chunk_scan_state.o duckdb/ub_src_main_extension.o duckdb/ub_src_main_relation.o duckdb/ub_src_main_secret.o duckdb/ub_src_main_settings.o duckdb/ub_src_optimizer.o duckdb/ub_src_optimizer_compressed_materialization.o duckdb/ub_src_optimizer_join_order.o duckdb/ub_src_optimizer_matcher.o duckdb/ub_src_optimizer_pullup.o duckdb/ub_src_optimizer_pushdown.o duckdb/ub_src_optimizer_rule.o duckdb/ub_src_optimizer_statistics_expression.o duckdb/ub_src_optimizer_statistics_operator.o duckdb/ub_src_parallel.o duckdb/ub_src_parser.o duckdb/ub_src_parser_constraints.o duckdb/ub_src_parser_expression.o duckdb/ub_src_parser_parsed_data.o duckdb/ub_src_parser_query_node.o duckdb/ub_src_parser_statement.o duckdb/ub_src_parser_tableref.o duckdb/ub_src_parser_transform_constraint.o duckdb/ub_src_parser_transform_expression.o duckdb/ub_src_parser_transform_helpers.o duckdb/ub_src_parser_transform_statement.o duckdb/ub_src_parser_transform_tableref.o duckdb/ub_src_planner.o duckdb/ub_src_planner_binder_expression.o duckdb/ub_src_planner_binder_query_node.o duckdb/ub_src_planner_binder_statement.o duckdb/ub_src_planner_binder_tableref.o duckdb/ub_src_planner_expression.o duckdb/ub_src_planner_expression_binder.o duckdb/ub_src_planner_filter.o duckdb/ub_src_planner_operator.o duckdb/ub_src_planner_subquery.o duckdb/ub_src_storage.o duckdb/ub_src_storage_buffer.o duckdb/ub_src_storage_checkpoint.o duckdb/ub_src_storage_compression_alp.o duckdb/ub_src_storage_compression.o duckdb/ub_src_storage_compression_chimp.o duckdb/ub_src_storage_metadata.o duckdb/ub_src_storage_serialization.o duckdb/ub_src_storage_statistics.o duckdb/ub_src_storage_table.o duckdb/ub_src_transaction.o duckdb/src/verification/copied_statement_verifier.o duckdb/src/verification/deserialized_statement_verifier.o duckdb/src/verification/external_statement_verifier.o duckdb/src/verification/fetch_row_verifier.o duckdb/src/verification/no_operator_caching_verifier.o duckdb/src/verification/parsed_statement_verifier.o duckdb/src/verification/prepared_statement_verifier.o duckdb/src/verification/statement_verifier.o duckdb/src/verification/unoptimized_statement_verifier.o duckdb/third_party/fmt/format.o duckdb/third_party/fsst/fsst_avx512.o duckdb/third_party/fsst/libfsst.o duckdb/third_party/miniz/miniz.o duckdb/third_party/re2/re2/bitstate.o duckdb/third_party/re2/re2/compile.o duckdb/third_party/re2/re2/dfa.o duckdb/third_party/re2/re2/filtered_re2.o duckdb/third_party/re2/re2/mimics_pcre.o duckdb/third_party/re2/re2/nfa.o duckdb/third_party/re2/re2/onepass.o duckdb/third_party/re2/re2/parse.o duckdb/third_party/re2/re2/perl_groups.o duckdb/third_party/re2/re2/prefilter.o duckdb/third_party/re2/re2/prefilter_tree.o duckdb/third_party/re2/re2/prog.o duckdb/third_party/re2/re2/re2.o duckdb/third_party/re2/re2/regexp.o duckdb/third_party/re2/re2/set.o duckdb/third_party/re2/re2/simplify.o duckdb/third_party/re2/re2/stringpiece.o duckdb/third_party/re2/re2/tostring.o duckdb/third_party/re2/re2/unicode_casefold.o duckdb/third_party/re2/re2/unicode_groups.o duckdb/third_party/re2/util/rune.o duckdb/third_party/re2/util/strutil.o duckdb/third_party/hyperloglog/hyperloglog.o duckdb/third_party/hyperloglog/sds.o duckdb/third_party/skiplist/SkipList.o duckdb/third_party/fastpforlib/bitpacking.o duckdb/third_party/utf8proc/utf8proc.o duckdb/third_party/utf8proc/utf8proc_wrapper.o duckdb/third_party/libpg_query/pg_functions.o duckdb/third_party/libpg_query/postgres_parser.o duckdb/third_party/libpg_query/src_backend_nodes_list.o duckdb/third_party/libpg_query/src_backend_nodes_makefuncs.o duckdb/third_party/libpg_query/src_backend_nodes_value.o duckdb/third_party/libpg_query/src_backend_parser_gram.o duckdb/third_party/libpg_query/src_backend_parser_parser.o duckdb/third_party/libpg_query/src_backend_parser_scan.o duckdb/third_party/libpg_query/src_backend_parser_scansup.o duckdb/third_party/libpg_query/src_common_keywords.o duckdb/third_party/mbedtls/library/aes.o duckdb/third_party/mbedtls/library/aria.o duckdb/third_party/mbedtls/library/asn1parse.o duckdb/third_party/mbedtls/library/base64.o duckdb/third_party/mbedtls/library/bignum.o duckdb/third_party/mbedtls/library/camellia.o duckdb/third_party/mbedtls/library/cipher.o duckdb/third_party/mbedtls/library/cipher_wrap.o duckdb/third_party/mbedtls/library/constant_time.o duckdb/third_party/mbedtls/library/entropy.o duckdb/third_party/mbedtls/library/entropy_poll.o duckdb/third_party/mbedtls/library/gcm.o duckdb/third_party/mbedtls/library/md.o duckdb/third_party/mbedtls/library/oid.o duckdb/third_party/mbedtls/library/pem.o duckdb/third_party/mbedtls/library/pk.o duckdb/third_party/mbedtls/library/pk_wrap.o duckdb/third_party/mbedtls/library/pkparse.o duckdb/third_party/mbedtls/library/platform_util.o duckdb/third_party/mbedtls/library/rsa.o duckdb/third_party/mbedtls/library/rsa_alt_helpers.o duckdb/third_party/mbedtls/library/sha1.o duckdb/third_party/mbedtls/library/sha256.o duckdb/third_party/mbedtls/library/sha512.o duckdb/third_party/mbedtls/mbedtls_wrapper.o duckdb/extension/parquet/column_reader.o duckdb/extension/parquet/column_writer.o duckdb/extension/parquet/parquet_crypto.o duckdb/extension/parquet/parquet_extension.o duckdb/extension/parquet/parquet_metadata.o duckdb/extension/parquet/parquet_reader.o duckdb/extension/parquet/parquet_statistics.o duckdb/extension/parquet/parquet_timestamp.o duckdb/extension/parquet/parquet_writer.o duckdb/extension/parquet/serialize_parquet.o duckdb/extension/parquet/zstd_file_system.o duckdb/third_party/parquet/parquet_constants.o duckdb/third_party/parquet/parquet_types.o duckdb/third_party/thrift/thrift/protocol/TProtocol.o duckdb/third_party/thrift/thrift/transport/TTransportException.o duckdb/third_party/thrift/thrift/transport/TBufferTransports.o duckdb/third_party/snappy/snappy.o duckdb/third_party/snappy/snappy-sinksource.o duckdb/third_party/zstd/decompress/zstd_ddict.o duckdb/third_party/zstd/decompress/huf_decompress.o duckdb/third_party/zstd/decompress/zstd_decompress.o duckdb/third_party/zstd/decompress/zstd_decompress_block.o duckdb/third_party/zstd/common/entropy_common.o duckdb/third_party/zstd/common/fse_decompress.o duckdb/third_party/zstd/common/zstd_common.o duckdb/third_party/zstd/common/error_private.o duckdb/third_party/zstd/common/xxhash.o duckdb/third_party/zstd/compress/fse_compress.o duckdb/third_party/zstd/compress/hist.o duckdb/third_party/zstd/compress/huf_compress.o duckdb/third_party/zstd/compress/zstd_compress.o duckdb/third_party/zstd/compress/zstd_compress_literals.o duckdb/third_party/zstd/compress/zstd_compress_sequences.o duckdb/third_party/zstd/compress/zstd_compress_superblock.o duckdb/third_party/zstd/compress/zstd_double_fast.o duckdb/third_party/zstd/compress/zstd_fast.o duckdb/third_party/zstd/compress/zstd_lazy.o duckdb/third_party/zstd/compress/zstd_ldm.o duckdb/third_party/zstd/compress/zstd_opt.o -L/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/lib -lR + + +trying URL 'https://cloud.r-project.org/src/contrib/bslib_0.6.2.tar.gz' +Content type 'application/x-gzip' length 6060123 bytes (5.8 MB) +================================================== +downloaded 5.8 MB + +trying URL 'https://cloud.r-project.org/src/contrib/duckdb_0.10.0.tar.gz' +Content type 'application/x-gzip' length 4090561 bytes (3.9 MB) +================================================== +downloaded 3.9 MB + +... +* installing *binary* package ‘httr’ ... +* DONE (httr) +* installing *binary* package ‘jquerylib’ ... +* DONE (jquerylib) +* installing *binary* package ‘pillar’ ... +* DONE (pillar) +* installing *binary* package ‘pkgbuild’ ... +* DONE (pkgbuild) +* installing *binary* package ‘purrr’ ... +* DONE (purrr) + + +``` +# cft + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/earthlab/cft-CRAN +* Source code: https://github.com/cran/cft +* Date/Publication: 2022-10-03 07:12:18 UTC +* Number of recursive dependencies: 90 + +Run `revdep_details(, "cft")` for more info
## In both -* R CMD check timed out - +* checking whether package ‘cft’ can be installed ... ERROR + ``` + Installation failed. + See ‘/c4/home/henrik/repositories/future/revdep/checks/cft/new/cft.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel +``` +* installing *source* package ‘cft’ ... +** package ‘cft’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + there is no package called ‘ncdf4’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘cft’ +* removing ‘/c4/home/henrik/repositories/future/revdep/checks/cft/new/cft.Rcheck/cft’ + + +``` +### CRAN + +``` +* installing *source* package ‘cft’ ... +** package ‘cft’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + there is no package called ‘ncdf4’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘cft’ +* removing ‘/c4/home/henrik/repositories/future/revdep/checks/cft/old/cft.Rcheck/cft’ + + +``` +# erah + +
+ +* Version: 2.0.1 +* GitHub: https://github.com/xdomingoal/erah-devel +* Source code: https://github.com/cran/erah +* Date/Publication: 2023-12-20 10:10:02 UTC +* Number of recursive dependencies: 92 + +Run `revdep_details(, "erah")` for more info + +
+ +## In both + +* checking whether package ‘erah’ can be installed ... ERROR + ``` + Installation failed. + See ‘/c4/home/henrik/repositories/future/revdep/checks/erah/new/erah.Rcheck/00install.out’ for details. + ``` + +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘ncdf4’ + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘erah’ ... +** package ‘erah’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C compiler: ‘gcc (GCC) 10.2.1 20210130 (Red Hat 10.2.1-11)’ +gcc -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c registerDynamicSymbol.c -o registerDynamicSymbol.o +gcc -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c runfunc.c -o runfunc.o +gcc -shared -L/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/lib -L/usr/local/lib64 -o erah.so registerDynamicSymbol.o runfunc.o -L/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/lib -lR +installing to /c4/home/henrik/repositories/future/revdep/checks/erah/new/erah.Rcheck/00LOCK-erah/00new/erah/libs +** R +... +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : + there is no package called ‘ncdf4’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘erah’ +* removing ‘/c4/home/henrik/repositories/future/revdep/checks/erah/new/erah.Rcheck/erah’ + + +``` +### CRAN + +``` +* installing *source* package ‘erah’ ... +** package ‘erah’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C compiler: ‘gcc (GCC) 10.2.1 20210130 (Red Hat 10.2.1-11)’ +gcc -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c registerDynamicSymbol.c -o registerDynamicSymbol.o +gcc -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c runfunc.c -o runfunc.o +gcc -shared -L/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/lib -L/usr/local/lib64 -o erah.so registerDynamicSymbol.o runfunc.o -L/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/lib -lR +installing to /c4/home/henrik/repositories/future/revdep/checks/erah/old/erah.Rcheck/00LOCK-erah/00new/erah/libs +** R +... +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : + there is no package called ‘ncdf4’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘erah’ +* removing ‘/c4/home/henrik/repositories/future/revdep/checks/erah/old/erah.Rcheck/erah’ + + +``` +# flowml + +
+ +* Version: +* GitHub: https://github.com/HenrikBengtsson/future +* Source code: NA +* Number of recursive dependencies: 0 + +
+ +## Error before installation + +### Devel + +``` + + + +* installing *binary* package ‘abind’ ... +* DONE (abind) +* installing *binary* package ‘backports’ ... +* DONE (backports) +* installing *binary* package ‘base64enc’ ... +* DONE (base64enc) +* installing *binary* package ‘bit’ ... +* DONE (bit) +* installing *binary* package ‘bitops’ ... +* DONE (bitops) +... +* installing *binary* package ‘caret’ ... +* DONE (caret) +* installing *binary* package ‘ConsRank’ ... +* DONE (ConsRank) +* installing *binary* package ‘labelled’ ... +* DONE (labelled) +* installing *binary* package ‘nloptr’ ... +* DONE (nloptr) +* installing *binary* package ‘rrcovHD’ ... +* DONE (rrcovHD) + + +``` +### CRAN + +``` + + + +* installing *binary* package ‘abind’ ... +* DONE (abind) +* installing *binary* package ‘backports’ ... +* DONE (backports) +* installing *binary* package ‘base64enc’ ... +* DONE (base64enc) +* installing *binary* package ‘bit’ ... +* DONE (bit) +* installing *binary* package ‘bitops’ ... +* DONE (bitops) +... +* installing *binary* package ‘caret’ ... +* DONE (caret) +* installing *binary* package ‘ConsRank’ ... +* DONE (ConsRank) +* installing *binary* package ‘labelled’ ... +* DONE (labelled) +* installing *binary* package ‘nloptr’ ... +* DONE (nloptr) +* installing *binary* package ‘rrcovHD’ ... +* DONE (rrcovHD) + + +``` +# marginaleffects + +
+ +* Version: +* GitHub: https://github.com/HenrikBengtsson/future +* Source code: NA +* Number of recursive dependencies: 0 + +
+ +## Error before installation + +### Devel + +``` +Creating a generic function for ‘nrow’ from package ‘base’ in package ‘tinytable’ +Creating a generic function for ‘ncol’ from package ‘base’ in package ‘tinytable’ +Creating a generic function for ‘colnames’ from package ‘base’ in package ‘tinytable’ +Creating a generic function for ‘colnames<-’ from package ‘base’ in package ‘tinytable’ + + +trying URL 'https://cloud.r-project.org/src/contrib/fmeffects_0.1.2.tar.gz' +Content type 'application/x-gzip' length 2486200 bytes (2.4 MB) +================================================== +downloaded 2.4 MB + +trying URL 'https://cloud.r-project.org/src/contrib/ggdag_0.2.12.tar.gz' +Content type 'application/x-gzip' length 1946994 bytes (1.9 MB) +================================================== +downloaded 1.9 MB + +... +** testing if installed package can be loaded from temporary location +** testing if installed package can be loaded from final location +** testing if installed package keeps a record of temporary installation path +* DONE (mlr3fselect) +* installing *source* package ‘mlr3learners’ ... +** package ‘mlr3learners’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading + + +``` +### CRAN + +``` +Creating a generic function for ‘nrow’ from package ‘base’ in package ‘tinytable’ +Creating a generic function for ‘ncol’ from package ‘base’ in package ‘tinytable’ +Creating a generic function for ‘colnames’ from package ‘base’ in package ‘tinytable’ +Creating a generic function for ‘colnames<-’ from package ‘base’ in package ‘tinytable’ + + +trying URL 'https://cloud.r-project.org/src/contrib/fmeffects_0.1.2.tar.gz' +Content type 'application/x-gzip' length 2486200 bytes (2.4 MB) +================================================== +downloaded 2.4 MB + +trying URL 'https://cloud.r-project.org/src/contrib/ggdag_0.2.12.tar.gz' +Content type 'application/x-gzip' length 1946994 bytes (1.9 MB) +================================================== +downloaded 1.9 MB + +... +** testing if installed package can be loaded from temporary location +** testing if installed package can be loaded from final location +** testing if installed package keeps a record of temporary installation path +* DONE (mlr3fselect) +* installing *source* package ‘mlr3learners’ ... +** package ‘mlr3learners’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading + + +``` +# Prostar + +
+ +* Version: 1.34.6 +* GitHub: https://github.com/prostarproteomics/Prostar +* Source code: https://github.com/cran/Prostar +* Date/Publication: 2024-02-15 +* Number of recursive dependencies: 332 + +Run `revdep_details(, "Prostar")` for more info + +
+ +## In both + +* checking whether package ‘Prostar’ can be installed ... ERROR + ``` + Installation failed. + See ‘/c4/home/henrik/repositories/future/revdep/checks/Prostar/new/Prostar.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘Prostar’ ... +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : + there is no package called ‘ncdf4’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘Prostar’ +* removing ‘/c4/home/henrik/repositories/future/revdep/checks/Prostar/new/Prostar.Rcheck/Prostar’ + + +``` +### CRAN + +``` +* installing *source* package ‘Prostar’ ... +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : + there is no package called ‘ncdf4’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘Prostar’ +* removing ‘/c4/home/henrik/repositories/future/revdep/checks/Prostar/old/Prostar.Rcheck/Prostar’ + + +``` +# startR + +
+ +* Version: 2.3.1 +* GitHub: NA +* Source code: https://github.com/cran/startR +* Date/Publication: 2023-12-21 16:20:02 UTC +* Number of recursive dependencies: 60 + +Run `revdep_details(, "startR")` for more info + +
+ +## In both + +* checking whether package ‘startR’ can be installed ... ERROR + ``` + Installation failed. + See ‘/c4/home/henrik/repositories/future/revdep/checks/startR/new/startR.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘startR’ ... +** package ‘startR’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : + there is no package called ‘ncdf4’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘startR’ +* removing ‘/c4/home/henrik/repositories/future/revdep/checks/startR/new/startR.Rcheck/startR’ + + +``` +### CRAN + +``` +* installing *source* package ‘startR’ ... +** package ‘startR’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : + there is no package called ‘ncdf4’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘startR’ +* removing ‘/c4/home/henrik/repositories/future/revdep/checks/startR/old/startR.Rcheck/startR’ + + +``` +# TKCat + +
+ +* Version: 1.0.7 +* GitHub: https://github.com/patzaw/TKCat +* Source code: https://github.com/cran/TKCat +* Date/Publication: 2023-02-16 14:50:03 UTC +* Number of recursive dependencies: 115 + +Run `revdep_details(, "TKCat")` for more info + +
+ +## In both + +* checking whether package ‘TKCat’ can be installed ... ERROR + ``` + Installation failed. + See ‘/c4/home/henrik/repositories/future/revdep/checks/TKCat/new/TKCat.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘TKCat’ ... +** package ‘TKCat’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : + there is no package called ‘arrow’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘TKCat’ +* removing ‘/c4/home/henrik/repositories/future/revdep/checks/TKCat/new/TKCat.Rcheck/TKCat’ + + +``` +### CRAN + +``` +* installing *source* package ‘TKCat’ ... +** package ‘TKCat’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : + there is no package called ‘arrow’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘TKCat’ +* removing ‘/c4/home/henrik/repositories/future/revdep/checks/TKCat/old/TKCat.Rcheck/TKCat’ + + +``` # TriDimRegression
@@ -36,7 +603,7 @@ Run `revdep_details(, "TriDimRegression")` for more info * checking whether package ‘TriDimRegression’ can be installed ... ERROR ``` Installation failed. - See ‘/wynton/home/cbi/hb/repositories/future/revdep/checks/TriDimRegression/new/TriDimRegression.Rcheck/00install.out’ for details. + See ‘/c4/home/henrik/repositories/future/revdep/checks/TriDimRegression/new/TriDimRegression.Rcheck/00install.out’ for details. ``` ## Installation @@ -51,7 +618,7 @@ Error in loadNamespace(x) : there is no package called ‘rstantools’ Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted ERROR: configuration failed for package ‘TriDimRegression’ -* removing ‘/wynton/home/cbi/hb/repositories/future/revdep/checks/TriDimRegression/new/TriDimRegression.Rcheck/TriDimRegression’ +* removing ‘/c4/home/henrik/repositories/future/revdep/checks/TriDimRegression/new/TriDimRegression.Rcheck/TriDimRegression’ ``` @@ -65,7 +632,7 @@ Error in loadNamespace(x) : there is no package called ‘rstantools’ Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted ERROR: configuration failed for package ‘TriDimRegression’ -* removing ‘/wynton/home/cbi/hb/repositories/future/revdep/checks/TriDimRegression/old/TriDimRegression.Rcheck/TriDimRegression’ +* removing ‘/c4/home/henrik/repositories/future/revdep/checks/TriDimRegression/old/TriDimRegression.Rcheck/TriDimRegression’ ``` diff --git a/revdep/problems.md b/revdep/problems.md index 52de24ab..429f7c0a 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -6,7 +6,7 @@ * GitHub: https://github.com/yqzhong7/AIPW * Source code: https://github.com/cran/AIPW * Date/Publication: 2021-06-11 09:30:02 UTC -* Number of recursive dependencies: 102 +* Number of recursive dependencies: 100 Run `revdep_details(, "AIPW")` for more info @@ -41,17 +41,17 @@ Run `revdep_details(, "AlpsNMR")` for more info * checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: - ... --- re-building ‘Vig01-introduction-to-alpsnmr.Rmd’ using rmarkdown - Error: processing vignette 'Vig01-introduction-to-alpsnmr.Rmd' failed with diagnostics: - LaTeX failed to compile /wynton/home/cbi/hb/repositories/future/revdep/checks/AlpsNMR/new/AlpsNMR.Rcheck/vign_test/AlpsNMR/vignettes/Vig01-introduction-to-alpsnmr.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. - --- failed re-building ‘Vig01-introduction-to-alpsnmr.Rmd’ - - --- re-building ‘Vig01b-introduction-to-alpsnmr-old-api.Rmd’ using rmarkdown - Error: processing vignette 'Vig01b-introduction-to-alpsnmr-old-api.Rmd' failed with diagnostics: - LaTeX failed to compile /wynton/home/cbi/hb/repositories/future/revdep/checks/AlpsNMR/new/AlpsNMR.Rcheck/vign_test/AlpsNMR/vignettes/Vig01b-introduction-to-alpsnmr-old-api.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. + ! LuaTeX error .../texlive/texmf-dist/scripts/oberdiek/oberdiek.luatex.lua:55: b + ad argument #1 to 'insert' (table expected, got nil) + stack traceback: + [C]: in function 'insert' + .../texlive/texmf-dist/scripts/oberdiek/oberdiek.luatex.lua:55: in main chunk + [C]: in function 'dofile' + [string "\directlua "]:6: in main chunk. + l.139 } ... - LaTeX failed to compile /wynton/home/cbi/hb/repositories/future/revdep/checks/AlpsNMR/new/AlpsNMR.Rcheck/vign_test/AlpsNMR/vignettes/Vig02-handling-metadata-and-annotations.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. + LaTeX failed to compile /c4/home/henrik/repositories/future/revdep/checks/AlpsNMR/new/AlpsNMR.Rcheck/vign_test/AlpsNMR/vignettes/Vig02-handling-metadata-and-annotations.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Vig02-handling-metadata-and-annotations.log for more info. --- failed re-building ‘Vig02-handling-metadata-and-annotations.Rmd’ SUMMARY: processing the following files failed: @@ -63,15 +63,56 @@ Run `revdep_details(, "AlpsNMR")` for more info Execution halted ``` +# altdoc + +
+ +* Version: 0.3.0 +* GitHub: https://github.com/etiennebacher/altdoc +* Source code: https://github.com/cran/altdoc +* Date/Publication: 2024-02-21 16:00:06 UTC +* Number of recursive dependencies: 85 + +Run `revdep_details(, "altdoc")` for more info + +
+ +## In both + +* checking tests ... + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + ERROR + Running the tests in ‘tests/testthat.R’ failed. + Last 50 lines of output: + v Setting active project to '' + v Setting active project to '/scratch/henrik/1715415/RtmpekdtNL/testpkg221fc379b081d' + v Setting active project to '' + v Setting active project to '/scratch/henrik/1715415/RtmpekdtNL/testpkg221fc70c8fde3' + v Setting active project to '' + ... + Error in `render_docs(path = getwd())`: There were some failures when rendering vignettes. + Backtrace: + ▆ + 1. └─altdoc::render_docs(path = getwd()) at test-update.R:111:5 + 2. └─cli::cli_abort("There were some failures when rendering vignettes.") + 3. └─rlang::abort(...) + + [ FAIL 5 | WARN 0 | SKIP 7 | PASS 56 ] + Error: Test failures + Execution halted + ``` + # aroma.core
-* Version: 3.3.0 +* Version: 3.3.1 * GitHub: https://github.com/HenrikBengtsson/aroma.core * Source code: https://github.com/cran/aroma.core -* Date/Publication: 2022-11-15 18:30:13 UTC -* Number of recursive dependencies: 72 +* Date/Publication: 2024-02-19 08:40:02 UTC +* Number of recursive dependencies: 68 Run `revdep_details(, "aroma.core")` for more info @@ -85,6 +126,38 @@ Run `revdep_details(, "aroma.core")` for more info 'sfit', 'expectile', 'HaarSeg', 'mpcbs' ``` +# BAMBI + +
+ +* Version: 2.3.5 +* GitHub: https://github.com/c7rishi/BAMBI +* Source code: https://github.com/cran/BAMBI +* Date/Publication: 2023-03-08 23:10:05 UTC +* Number of recursive dependencies: 53 + +Run `revdep_details(, "BAMBI")` for more info + +
+ +## In both + +* checking whether package ‘BAMBI’ can be installed ... WARNING + ``` + Found the following significant warnings: + /c4/home/henrik/repositories/future/revdep/library/BAMBI/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/BAMBI/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/BAMBI/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + See ‘/c4/home/henrik/repositories/future/revdep/checks/BAMBI/new/BAMBI.Rcheck/00install.out’ for details. + ``` + +* checking installed package size ... NOTE + ``` + installed size is 7.3Mb + sub-directories of 1Mb or more: + libs 6.8Mb + ``` + # bamm
@@ -101,6 +174,15 @@ Run `revdep_details(, "bamm")` for more info ## In both +* checking whether package ‘bamm’ can be installed ... WARNING + ``` + Found the following significant warnings: + /c4/home/henrik/repositories/future/revdep/library/bamm/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/bamm/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/bamm/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + See ‘/c4/home/henrik/repositories/future/revdep/checks/bamm/new/bamm.Rcheck/00install.out’ for details. + ``` + * checking C++ specification ... NOTE ``` Specified C++11: please drop specification unless essential @@ -114,7 +196,7 @@ Run `revdep_details(, "bamm")` for more info * GitHub: https://github.com/mllg/batchtools * Source code: https://github.com/cran/batchtools * Date/Publication: 2023-04-20 14:20:06 UTC -* Number of recursive dependencies: 84 +* Number of recursive dependencies: 83 Run `revdep_details(, "batchtools")` for more info @@ -122,46 +204,50 @@ Run `revdep_details(, "batchtools")` for more info ## In both -* checking dependencies in R code ... NOTE +* checking package dependencies ... NOTE ``` - dev3:pid2802163: PSM3 can't open nic unit: 0 (err=23) - dev3:pid2802163.R: Unable to create send CQ of size 5080 on mlx5_0: Cannot allocate memory - dev3:pid2802163.R: Unable to initialize verbs NIC /sys/class/infiniband/mlx5_0 (unit 0:0) - dev3:pid2802163: PSM3 can't open nic unit: 0 (err=23) - dev3:pid2802163.R: Unable to create send CQ of size 5080 on mlx5_0: Cannot allocate memory - dev3:pid2802163.R: Unable to initialize verbs NIC /sys/class/infiniband/mlx5_0 (unit 0:0) - dev3:pid2802163: PSM3 can't open nic unit: 0 (err=23) - dev3:pid2802163.R: Unable to create send CQ of size 5080 on mlx5_0: Cannot allocate memory - dev3:pid2802163.R: Unable to initialize verbs NIC /sys/class/infiniband/mlx5_0 (unit 0:0) - -------------------------------------------------------------------------- - ... - dev3:pid2802163.R: Unable to create send CQ of size 5080 on mlx5_0: Cannot allocate memory - dev3:pid2802163.R: Unable to initialize verbs NIC /sys/class/infiniband/mlx5_0 (unit 0:0) - -------------------------------------------------------------------------- - Open MPI failed an OFI Libfabric library call (fi_endpoint). This is highly - unusual; your job may behave unpredictably (and/or abort) after this. - - Local host: dev3 - Location: mtl_ofi_component.c:513 - Error: Invalid argument (22) - -------------------------------------------------------------------------- + Package suggested but not available for checking: ‘doMPI’ + ``` + +* checking Rd cross-references ... NOTE + ``` + Package unavailable to check Rd xrefs: ‘Rmpi’ ``` -* checking for detritus in the temp directory ... NOTE +# bayesmove + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/joshcullen/bayesmove +* Source code: https://github.com/cran/bayesmove +* Date/Publication: 2021-10-22 08:50:09 UTC +* Number of recursive dependencies: 168 + +Run `revdep_details(, "bayesmove")` for more info + +
+ +## In both + +* checking whether package ‘bayesmove’ can be installed ... WARNING ``` - Found the following files/directories: - ‘ompi.dev3.34002’ + Found the following significant warnings: + /c4/home/henrik/repositories/future/revdep/library/bayesmove/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/bayesmove/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/bayesmove/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + See ‘/c4/home/henrik/repositories/future/revdep/checks/bayesmove/new/bayesmove.Rcheck/00install.out’ for details. ``` # BEKKs
-* Version: 1.4.3 +* Version: 1.4.4 * GitHub: NA * Source code: https://github.com/cran/BEKKs -* Date/Publication: 2023-03-26 11:00:02 UTC -* Number of recursive dependencies: 99 +* Date/Publication: 2024-01-14 15:50:09 UTC +* Number of recursive dependencies: 86 Run `revdep_details(, "BEKKs")` for more info @@ -169,17 +255,20 @@ Run `revdep_details(, "BEKKs")` for more info ## In both -* checking installed package size ... NOTE +* checking whether package ‘BEKKs’ can be installed ... WARNING ``` - installed size is 7.6Mb - sub-directories of 1Mb or more: - libs 7.3Mb + Found the following significant warnings: + /c4/home/henrik/repositories/future/revdep/library/BEKKs/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/BEKKs/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/BEKKs/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + See ‘/c4/home/henrik/repositories/future/revdep/checks/BEKKs/new/BEKKs.Rcheck/00install.out’ for details. ``` -* checking dependencies in R code ... NOTE +* checking installed package size ... NOTE ``` - Namespace in Imports field not imported from: ‘forecast’ - All declared Imports should be used. + installed size is 18.5Mb + sub-directories of 1Mb or more: + libs 17.6Mb ``` # bigDM @@ -216,7 +305,7 @@ Run `revdep_details(, "bigDM")` for more info * GitHub: https://github.com/alexander-pastukhov/bistablehistory * Source code: https://github.com/cran/bistablehistory * Date/Publication: 2023-09-13 13:20:09 UTC -* Number of recursive dependencies: 92 +* Number of recursive dependencies: 97 Run `revdep_details(, "bistablehistory")` for more info @@ -226,9 +315,9 @@ Run `revdep_details(, "bistablehistory")` for more info * checking installed package size ... NOTE ``` - installed size is 22.5Mb + installed size is 75.5Mb sub-directories of 1Mb or more: - libs 22.3Mb + libs 74.6Mb ``` * checking for GNU extensions in Makefiles ... NOTE @@ -240,10 +329,10 @@ Run `revdep_details(, "bistablehistory")` for more info
-* Version: 0.5-2 -* GitHub: NA +* Version: 0.5-3 +* GitHub: https://github.com/ecmerkle/blavaan * Source code: https://github.com/cran/blavaan -* Date/Publication: 2023-09-25 22:20:02 UTC +* Date/Publication: 2024-01-19 22:50:02 UTC * Number of recursive dependencies: 98 Run `revdep_details(, "blavaan")` for more info @@ -259,10 +348,11 @@ Run `revdep_details(, "blavaan")` for more info * checking installed package size ... NOTE ``` - installed size is 53.8Mb + installed size is 196.2Mb sub-directories of 1Mb or more: - R 1.2Mb - libs 52.6Mb + R 1.2Mb + libs 193.4Mb + testdata 1.4Mb ``` * checking for GNU extensions in Makefiles ... NOTE @@ -274,11 +364,11 @@ Run `revdep_details(, "blavaan")` for more info
-* Version: 2.20.4 +* Version: 2.21.0 * GitHub: https://github.com/paul-buerkner/brms * Source code: https://github.com/cran/brms -* Date/Publication: 2023-09-25 19:00:09 UTC -* Number of recursive dependencies: 200 +* Date/Publication: 2024-03-20 12:30:08 UTC +* Number of recursive dependencies: 201 Run `revdep_details(, "brms")` for more info @@ -291,84 +381,76 @@ Run `revdep_details(, "brms")` for more info Package suggested but not available for checking: ‘cmdstanr’ ``` -# brpop +* checking installed package size ... NOTE + ``` + installed size is 8.4Mb + sub-directories of 1Mb or more: + R 3.7Mb + doc 3.5Mb + ``` + +# ceRNAnetsim
-* Version: 0.3.0 -* GitHub: NA -* Source code: https://github.com/cran/brpop -* Date/Publication: 2023-10-24 13:20:02 UTC -* Number of recursive dependencies: 45 +* Version: 1.14.1 +* GitHub: https://github.com/selcenari/ceRNAnetsim +* Source code: https://github.com/cran/ceRNAnetsim +* Date/Publication: 2023-12-18 +* Number of recursive dependencies: 101 -Run `revdep_details(, "brpop")` for more info +Run `revdep_details(, "ceRNAnetsim")` for more info
## In both -* checking tests ... +* checking examples ... ERROR ``` - Running ‘testthat.R’ - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 50 lines of output: - Backtrace: - ▆ - 1. ├─brpop::regsaude_female_pop(type = "reg_saude_449") at test-regsaude_female_pop.R:8:3 - 2. │ └─... %>% dplyr::ungroup() - 3. ├─dplyr::ungroup(.) - 4. ├─dplyr::collect(.) + Running examples in ‘ceRNAnetsim-Ex.R’ failed + The error most likely occurred in: + + > ### Name: find_node_perturbation + > ### Title: Calculates average expression changes of all (or specified) + > ### nodes except trigger and finds the perturbed node count for all (or + > ### specified) nodes in system. + > ### Aliases: find_node_perturbation + > + > ### ** Examples ... - 7. │ └─multidplyr::cluster_assign_each(cluster, `:=`(!!name, shards)) - 8. │ └─multidplyr::cluster_assign(...) - 9. └─base::loadNamespace(x) - 10. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) - 11. └─base (local) withOneRestart(expr, restarts[[1L]]) - 12. └─base (local) doWithOneRestart(return(expr), restart) - - [ FAIL 6 | WARN 0 | SKIP 0 | PASS 6 ] - Error: Test failures - Execution halted + 23. │ └─dplyr (local) eval() + 24. └─tidygraph::map_bfs(...) + 25. └─tidygraph:::bfs_df(graph, root, mode, unreachable) + 26. └─tibble::tibble(...) + 27. └─tibble:::tibble_quos(xs, .rows, .name_repair) + 28. └─tibble:::vectbl_recycle_rows(...) + 29. └─tibble:::abort_incompatible_size(...) + 30. └─tibble:::tibble_abort(...) + 31. └─rlang::abort(x, class, ..., call = call, parent = parent, use_cli_format = TRUE) + Execution halted ``` -# campsis - -
- -* Version: 1.5.0 -* GitHub: https://github.com/Calvagone/campsis -* Source code: https://github.com/cran/campsis -* Date/Publication: 2023-10-13 13:40:02 UTC -* Number of recursive dependencies: 161 - -Run `revdep_details(, "campsis")` for more info - -
- -## In both - * checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: - comment = NA_character_), new("theta", unit = NA_character_, - name = "V2", index = 3L, value = 80, fix = FALSE, label = NA_character_, - comment = NA_character_), new("theta", unit = NA_character_, - name = "V3", index = 4L, value = 20, fix = FALSE, label = NA_character_, - comment = NA_character_), new("theta", unit = NA_character_, - name = "Q", index = 5L, value = 4, fix = FALSE, label = NA_character_, + > library(testthat) + > library(ceRNAnetsim) + Loading required package: dplyr + + Attaching package: 'dplyr' + ... - Deleting unused snapshots: - • testDefaultPlots/scatterplot-colour-scenario.svg - • testDefaultPlots/scatterplot-no-colour.svg - • testDefaultPlots/shadedplot-colour-arm-strat-wt.svg - • testDefaultPlots/shadedplot-colour-arm-wt-strat-wt.svg - • testDefaultPlots/shadedplot-colour-scenario.svg - • testDefaultPlots/spaghettiplot-colour-arm-strat-wt.svg - • testDefaultPlots/spaghettiplot-colour-scenario.svg + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test-iter_perturb.R:33:3'): Could the functions work? ──────────── + `node_efficiencies` not equal to c(NA, NA, NA, 3.18, 2.27, 3.18, NA, 32). + 2/8 mismatches (average diff: 14.9) + [5] 3.18 - 2.27 == 0.91 + [8] 3.18 - 32.00 == -28.82 + + [ FAIL 1 | WARN 35 | SKIP 0 | PASS 36 ] Error: Test failures Execution halted ``` @@ -376,49 +458,96 @@ Run `revdep_details(, "campsis")` for more info * checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: - ... - --- re-building ‘campsis.Rmd’ using rmarkdown + --- re-building ‘auxiliary_commands.Rmd’ using rmarkdown + --- finished re-building ‘auxiliary_commands.Rmd’ - Quitting from lines 43-45 [unnamed-chunk-4] (campsis.Rmd) - Error: processing vignette 'campsis.Rmd' failed with diagnostics: - ℹ In index: 1. - Caused by error: - ℹ In index: 1. - Caused by error in `loadNamespace()`: - ! there is no package called 'qs' - --- failed re-building ‘campsis.Rmd’ + --- re-building ‘basic_usage.Rmd’ using rmarkdown + --- finished re-building ‘basic_usage.Rmd’ - SUMMARY: processing the following file failed: - ‘campsis.Rmd’ + --- re-building ‘convenient_iteration.Rmd’ using rmarkdown + + Quitting from lines 226-233 [unnamed-chunk-15] (convenient_iteration.Rmd) + ... + • Size 5: Existing data. + • Size 53: Column `rank`. + ℹ Only values of size one are recycled. + --- failed re-building ‘mirtarbase_example.Rmd’ + + SUMMARY: processing the following files failed: + ‘convenient_iteration.Rmd’ ‘mirtarbase_example.Rmd’ Error: Vignette re-building failed. Execution halted ``` -# ceRNAnetsim +* checking R code for possible problems ... NOTE + ``` + simulate: no visible binding for global variable ‘avg_count_current’ + simulate: no visible binding for global variable ‘avg_count_pre’ + Undefined global functions or variables: + avg_count_current avg_count_pre + ``` + +# cft
-* Version: 1.14.1 -* GitHub: https://github.com/selcenari/ceRNAnetsim -* Source code: https://github.com/cran/ceRNAnetsim -* Date/Publication: 2023-12-18 -* Number of recursive dependencies: 101 +* Version: 1.0.0 +* GitHub: https://github.com/earthlab/cft-CRAN +* Source code: https://github.com/cran/cft +* Date/Publication: 2022-10-03 07:12:18 UTC +* Number of recursive dependencies: 90 -Run `revdep_details(, "ceRNAnetsim")` for more info +Run `revdep_details(, "cft")` for more info
## In both -* checking R code for possible problems ... NOTE +* checking whether package ‘cft’ can be installed ... ERROR ``` - simulate: no visible binding for global variable ‘avg_count_current’ - simulate: no visible binding for global variable ‘avg_count_pre’ - Undefined global functions or variables: - avg_count_current avg_count_pre + Installation failed. + See ‘/c4/home/henrik/repositories/future/revdep/checks/cft/new/cft.Rcheck/00install.out’ for details. ``` +## Installation + +### Devel + +``` +* installing *source* package ‘cft’ ... +** package ‘cft’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + there is no package called ‘ncdf4’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘cft’ +* removing ‘/c4/home/henrik/repositories/future/revdep/checks/cft/new/cft.Rcheck/cft’ + + +``` +### CRAN + +``` +* installing *source* package ‘cft’ ... +** package ‘cft’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + there is no package called ‘ncdf4’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘cft’ +* removing ‘/c4/home/henrik/repositories/future/revdep/checks/cft/old/cft.Rcheck/cft’ + + +``` # ChromSCape
@@ -427,7 +556,7 @@ Run `revdep_details(, "ceRNAnetsim")` for more info * GitHub: https://github.com/vallotlab/ChromSCape * Source code: https://github.com/cran/ChromSCape * Date/Publication: 2023-10-25 -* Number of recursive dependencies: 235 +* Number of recursive dependencies: 232 Run `revdep_details(, "ChromSCape")` for more info @@ -435,12 +564,107 @@ Run `revdep_details(, "ChromSCape")` for more info ## In both -* checking package dependencies ... ERROR +* checking dependencies in R code ... WARNING + ``` + 'library' or 'require' call not declared from: ‘dplyr’ + 'library' or 'require' call to ‘dplyr’ in package code. + Please use :: or requireNamespace() instead. + See section 'Suggested packages' in the 'Writing R Extensions' manual. ``` - Package required but not available: ‘qs’ + +* checking for code/documentation mismatches ... WARNING + ``` + Codoc mismatches from documentation object 'generate_analysis': + generate_analysis + Code: function(input_data_folder, analysis_name = "Analysis_1", + output_directory = "./", input_data_type = c("scBED", + "DenseMatrix", "SparseMatrix", "scBAM")[1], + feature_count_on = c("bins", "genebody", "peaks")[1], + feature_count_parameter = 50000, rebin_sparse_matrix = + FALSE, ref_genome = c("hg38", "mm10")[1], run = + c("filter", "CNA", "cluster", "consensus", "coverage", + "DA", "GSA", "report")[c(1, 3, 5, 6, 7, 8)], + ... + Mismatches in argument names: + Position: 5 Code: feature_count_on Docs: rebin_sparse_matrix + Position: 6 Code: feature_count_parameter Docs: feature_count_on + Position: 7 Code: rebin_sparse_matrix Docs: feature_count_parameter + Mismatches in argument default values: + Name: 'run' + Code: c("filter", "CNA", "cluster", "consensus", "coverage", "DA", + "GSA", "report")[c(1, 3, 5, 6, 7, 8)] + Docs: c("filter", "CNA", "cluster", "consensus", "peak_call", "coverage", + "DA", "GSA", "report")[c(1, 3, 6, 7, 8, 9)] + ``` + +* checking Rd \usage sections ... WARNING + ``` + Undocumented arguments in documentation object 'rebin_matrix' + ‘rebin_function’ - See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ - manual. + Functions with \usage entries need to have the appropriate \alias + entries, and all their arguments documented. + The \usage entries must correspond to syntactically valid R code. + See chapter ‘Writing R documentation files’ in the ‘Writing R + Extensions’ manual. + ``` + +* checking examples ... WARNING + ``` + Found the following significant warnings: + + Warning: 'as(, "dspMatrix")' is deprecated. + Deprecated functions may be defunct as soon as of the next release of + R. + See ?Deprecated. + ``` + +* checking for hidden files and directories ... NOTE + ``` + Found the following hidden files and directories: + .BBSoptions + These were most likely included in error. See section ‘Package + structure’ in the ‘Writing R Extensions’ manual. + ``` + +* checking installed package size ... NOTE + ``` + installed size is 8.3Mb + sub-directories of 1Mb or more: + data 1.4Mb + doc 2.9Mb + libs 1.0Mb + www 2.0Mb + ``` + +* checking R code for possible problems ... NOTE + ``` + bams_to_matrix_indexes: no visible binding for global variable + ‘files_dir_list’ + enrich_TF_ChEA3_genes: no visible binding for global variable + ‘CheA3_TF_nTargets’ + filter_correlated_cell_scExp: no visible binding for global variable + ‘run_tsne’ + generate_analysis: no visible global function definition for ‘head’ + generate_analysis: no visible binding for global variable ‘k’ + generate_analysis: no visible binding for global variable + ‘clusterConsensus’ + ... + subset_bam_call_peaks: no visible binding for global variable + ‘merged_bam’ + Undefined global functions or variables: + CheA3_TF_nTargets Component Fri_cyto Gain_or_Loss Gene TF V1 V2 + absolute_value cluster clusterConsensus cytoBand files_dir_list genes + group head k merged_bam molecule ncells new_row orientation + origin_value percent_active run_tsne sample_id total_counts + Consider adding + importFrom("utils", "head") + to your NAMESPACE file. + ``` + +* checking Rd files ... NOTE + ``` + prepare_Rd: raw_counts_to_sparse_matrix.Rd:6-8: Dropping empty section \source ``` # clickR @@ -472,7 +696,7 @@ Run `revdep_details(, "clickR")` for more info * GitHub: https://github.com/rubenarslan/codebook * Source code: https://github.com/cran/codebook * Date/Publication: 2020-06-06 23:40:03 UTC -* Number of recursive dependencies: 158 +* Number of recursive dependencies: 156 Run `revdep_details(, "codebook")` for more info @@ -519,6 +743,30 @@ Run `revdep_details(, "collinear")` for more info Note: found 1203 marked UTF-8 strings ``` +# Coxmos + +
+ +* Version: 1.0.1 +* GitHub: https://github.com/BiostatOmics/Coxmos +* Source code: https://github.com/cran/Coxmos +* Date/Publication: 2024-03-22 17:10:02 UTC +* Number of recursive dependencies: 204 + +Run `revdep_details(, "Coxmos")` for more info + +
+ +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.1Mb + sub-directories of 1Mb or more: + data 1.2Mb + doc 2.7Mb + ``` + # cSEM
@@ -564,35 +812,115 @@ Run `revdep_details(, "CSGo")` for more info All declared Imports should be used. ``` -# dispositionEffect +# deseats
-* Version: 1.0.1 -* GitHub: https://github.com/marcozanotti/dispositionEffect -* Source code: https://github.com/cran/dispositionEffect -* Date/Publication: 2022-05-30 07:50:02 UTC -* Number of recursive dependencies: 136 +* Version: 1.0.0 +* GitHub: NA +* Source code: https://github.com/cran/deseats +* Date/Publication: 2023-11-08 19:50:02 UTC +* Number of recursive dependencies: 109 -Run `revdep_details(, "dispositionEffect")` for more info +Run `revdep_details(, "deseats")` for more info
## In both -* checking tests ... +* checking whether package ‘deseats’ can be installed ... WARNING ``` - Running ‘testthat.R’ - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 50 lines of output: - ── Failure ('test-realized_duration.R:113:2'): realized_duration works (realized_only = TRUE) ── - realized_duration(...) not equal to c(...). - 1/4 mismatches - [2] 34 - 28 == 6 - ── Failure ('test-realized_duration.R:116:2'): realized_duration works (realized_only = TRUE) ── - realized_duration(...) not equal to c(...). - ... + Found the following significant warnings: + /c4/home/henrik/repositories/future/revdep/library/deseats/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/deseats/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/deseats/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + See ‘/c4/home/henrik/repositories/future/revdep/checks/deseats/new/deseats.Rcheck/00install.out’ for details. + ``` + +* checking installed package size ... NOTE + ``` + installed size is 8.3Mb + sub-directories of 1Mb or more: + libs 7.6Mb + ``` + +# dipsaus + +
+ +* Version: 0.2.8 +* GitHub: https://github.com/dipterix/dipsaus +* Source code: https://github.com/cran/dipsaus +* Date/Publication: 2023-07-03 20:00:03 UTC +* Number of recursive dependencies: 70 + +Run `revdep_details(, "dipsaus")` for more info + +
+ +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.9Mb + sub-directories of 1Mb or more: + doc 1.1Mb + libs 3.5Mb + ``` + +# disk.frame + +
+ +* Version: 0.8.3 +* GitHub: https://github.com/DiskFrame/disk.frame +* Source code: https://github.com/cran/disk.frame +* Date/Publication: 2023-08-24 16:20:10 UTC +* Number of recursive dependencies: 99 + +Run `revdep_details(, "disk.frame")` for more info + +
+ +## In both + +* checking package dependencies ... ERROR + ``` + Package required but not available: ‘arrow’ + + See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ + manual. + ``` + +# dispositionEffect + +
+ +* Version: 1.0.1 +* GitHub: https://github.com/marcozanotti/dispositionEffect +* Source code: https://github.com/cran/dispositionEffect +* Date/Publication: 2022-05-30 07:50:02 UTC +* Number of recursive dependencies: 136 + +Run `revdep_details(, "dispositionEffect")` for more info + +
+ +## In both + +* checking tests ... + ``` + Running ‘testthat.R’ + ERROR + Running the tests in ‘tests/testthat.R’ failed. + Last 50 lines of output: + ── Failure ('test-realized_duration.R:113:2'): realized_duration works (realized_only = TRUE) ── + realized_duration(...) not equal to c(...). + 1/4 mismatches + [2] 34 - 28 == 6 + ── Failure ('test-realized_duration.R:116:2'): realized_duration works (realized_only = TRUE) ── + realized_duration(...) not equal to c(...). + ... 1/4 mismatches [2] 34 - 28 == 6 ── Failure ('test-realized_duration.R:161:2'): realized_duration works (realized_only = TRUE) ── @@ -621,6 +949,31 @@ Run `revdep_details(, "dragon")` for more info ## In both +* checking tests ... + ``` + Running ‘testthat.R’ + ERROR + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(dragon) + > + > test_check("dragon") + Error in `FUN()`: + ! In path: "/c4/home/henrik/repositories/future/revdep/checks/dragon/new/dragon.Rcheck/tests/testthat/setup_test-settings.R" + ... + 10. │ └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap) + 11. │ ├─base::withCallingHandlers(...) + 12. │ └─base::eval(exprs, env) + 13. │ └─base::eval(exprs, env) + 14. │ └─igraph::read_graph("graph_by_redox.igraph", format = "ncol") at tests/testthat/setup_test-settings.R:8:1 + 15. │ └─igraph:::read.graph.ncol(file, ...) + 16. └─base::.handleSimpleError(...) + 17. └─testthat (local) h(simpleError(msg, call)) + 18. └─rlang::abort(...) + Execution halted + ``` + * checking package subdirectories ... NOTE ``` Problems with news in ‘NEWS.md’: @@ -637,11 +990,11 @@ Run `revdep_details(, "dragon")` for more info
-* Version: 7.13.8 +* Version: 7.13.9 * GitHub: https://github.com/ropensci/drake * Source code: https://github.com/cran/drake -* Date/Publication: 2023-11-06 15:40:02 UTC -* Number of recursive dependencies: 165 +* Date/Publication: 2024-03-04 15:20:02 UTC +* Number of recursive dependencies: 166 Run `revdep_details(, "drake")` for more info @@ -651,7 +1004,30 @@ Run `revdep_details(, "drake")` for more info * checking package dependencies ... NOTE ``` - Package suggested but not available for checking: ‘qs’ + Package suggested but not available for checking: ‘clustermq’ + ``` + +# DT + +
+ +* Version: 0.32 +* GitHub: https://github.com/rstudio/DT +* Source code: https://github.com/cran/DT +* Date/Publication: 2024-02-19 16:50:02 UTC +* Number of recursive dependencies: 53 + +Run `revdep_details(, "DT")` for more info + +
+ +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.4Mb + sub-directories of 1Mb or more: + htmlwidgets 4.8Mb ``` # EFAtools @@ -670,67 +1046,42 @@ Run `revdep_details(, "EFAtools")` for more info ## In both +* checking whether package ‘EFAtools’ can be installed ... WARNING + ``` + Found the following significant warnings: + /c4/home/henrik/repositories/future/revdep/library/EFAtools/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/EFAtools/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/EFAtools/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + See ‘/c4/home/henrik/repositories/future/revdep/checks/EFAtools/new/EFAtools.Rcheck/00install.out’ for details. + ``` + * checking C++ specification ... NOTE ``` Specified C++11: please drop specification unless essential ``` -* checking dependencies in R code ... NOTE +* checking installed package size ... NOTE ``` - Namespace in Imports field not imported from: ‘progress’ - All declared Imports should be used. + installed size is 7.2Mb + sub-directories of 1Mb or more: + libs 6.0Mb ``` -# EGAnet - -
- -* Version: 2.0.3 -* GitHub: https://github.com/hfgolino/EGAnet -* Source code: https://github.com/cran/EGAnet -* Date/Publication: 2023-11-17 17:30:05 UTC -* Number of recursive dependencies: 190 - -Run `revdep_details(, "EGAnet")` for more info - -
- -## In both - -* checking examples ... ERROR +* checking dependencies in R code ... NOTE ``` - Running examples in ‘EGAnet-Ex.R’ failed - The error most likely occurred in: - - > ### Name: community.detection - > ### Title: Apply a Community Detection Algorithm - > ### Aliases: community.detection - > - > ### ** Examples - > - > # Load data - ... - 1 1 1 1 1 2 2 2 3 3 2 2 3 - wmt14 wmt15 wmt16 wmt17 wmt18 - 3 2 3 2 2 - > - > # Compute Optimal (identifies maximum modularity solution) - > community.detection(network, algorithm = "optimal") - Error in (function (graph, weights = NULL) : - At core/community/optimal_modularity.c:86 : GLPK is not available, Unimplemented function call - Calls: community.detection -> do.call -> - Execution halted + Namespace in Imports field not imported from: ‘progress’ + All declared Imports should be used. ``` # envi
-* Version: 0.1.17 +* Version: 0.1.19 * GitHub: https://github.com/lance-waller-lab/envi * Source code: https://github.com/cran/envi -* Date/Publication: 2023-02-02 00:40:02 UTC -* Number of recursive dependencies: 110 +* Date/Publication: 2024-01-23 14:40:03 UTC +* Number of recursive dependencies: 153 Run `revdep_details(, "envi")` for more info @@ -742,12 +1093,7 @@ Run `revdep_details(, "envi")` for more info ``` Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available - See ‘/wynton/home/cbi/hb/repositories/future/revdep/checks/envi/new/envi.Rcheck/00install.out’ for details. - ``` - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘RStoolbox’ + See ‘/c4/home/henrik/repositories/future/revdep/checks/envi/new/envi.Rcheck/00install.out’ for details. ``` # EpiNow2 @@ -758,7 +1104,7 @@ Run `revdep_details(, "envi")` for more info * GitHub: https://github.com/epiforecasts/EpiNow2 * Source code: https://github.com/cran/EpiNow2 * Date/Publication: 2023-09-26 12:00:02 UTC -* Number of recursive dependencies: 129 +* Number of recursive dependencies: 131 Run `revdep_details(, "EpiNow2")` for more info @@ -768,9 +1114,10 @@ Run `revdep_details(, "EpiNow2")` for more info * checking installed package size ... NOTE ``` - installed size is 77.1Mb + installed size is 223.7Mb sub-directories of 1Mb or more: - libs 76.3Mb + help 2.0Mb + libs 220.8Mb ``` * checking for GNU extensions in Makefiles ... NOTE @@ -806,27 +1153,89 @@ Run `revdep_details(, "epitweetr")` for more info All declared Imports should be used. ``` -# fastRhockey +# erah
-* Version: 0.4.0 -* GitHub: https://github.com/sportsdataverse/fastRhockey -* Source code: https://github.com/cran/fastRhockey -* Date/Publication: 2022-10-25 20:55:15 UTC -* Number of recursive dependencies: 116 +* Version: 2.0.1 +* GitHub: https://github.com/xdomingoal/erah-devel +* Source code: https://github.com/cran/erah +* Date/Publication: 2023-12-20 10:10:02 UTC +* Number of recursive dependencies: 92 -Run `revdep_details(, "fastRhockey")` for more info +Run `revdep_details(, "erah")` for more info
## In both +* checking whether package ‘erah’ can be installed ... ERROR + ``` + Installation failed. + See ‘/c4/home/henrik/repositories/future/revdep/checks/erah/new/erah.Rcheck/00install.out’ for details. + ``` + * checking package dependencies ... NOTE ``` - Package suggested but not available for checking: ‘qs’ + Package suggested but not available for checking: ‘ncdf4’ ``` +## Installation + +### Devel + +``` +* installing *source* package ‘erah’ ... +** package ‘erah’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C compiler: ‘gcc (GCC) 10.2.1 20210130 (Red Hat 10.2.1-11)’ +gcc -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c registerDynamicSymbol.c -o registerDynamicSymbol.o +gcc -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c runfunc.c -o runfunc.o +gcc -shared -L/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/lib -L/usr/local/lib64 -o erah.so registerDynamicSymbol.o runfunc.o -L/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/lib -lR +installing to /c4/home/henrik/repositories/future/revdep/checks/erah/new/erah.Rcheck/00LOCK-erah/00new/erah/libs +** R +... +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : + there is no package called ‘ncdf4’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘erah’ +* removing ‘/c4/home/henrik/repositories/future/revdep/checks/erah/new/erah.Rcheck/erah’ + + +``` +### CRAN + +``` +* installing *source* package ‘erah’ ... +** package ‘erah’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C compiler: ‘gcc (GCC) 10.2.1 20210130 (Red Hat 10.2.1-11)’ +gcc -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c registerDynamicSymbol.c -o registerDynamicSymbol.o +gcc -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c runfunc.c -o runfunc.o +gcc -shared -L/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/lib -L/usr/local/lib64 -o erah.so registerDynamicSymbol.o runfunc.o -L/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/lib -lR +installing to /c4/home/henrik/repositories/future/revdep/checks/erah/old/erah.Rcheck/00LOCK-erah/00new/erah/libs +** R +... +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : + there is no package called ‘ncdf4’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘erah’ +* removing ‘/c4/home/henrik/repositories/future/revdep/checks/erah/old/erah.Rcheck/erah’ + + +``` # fdacluster
@@ -835,7 +1244,7 @@ Run `revdep_details(, "fastRhockey")` for more info * GitHub: https://github.com/astamm/fdacluster * Source code: https://github.com/cran/fdacluster * Date/Publication: 2023-07-04 15:53:04 UTC -* Number of recursive dependencies: 120 +* Number of recursive dependencies: 118 Run `revdep_details(, "fdacluster")` for more info @@ -843,12 +1252,23 @@ Run `revdep_details(, "fdacluster")` for more info ## In both +* checking whether package ‘fdacluster’ can be installed ... WARNING + ``` + Found the following significant warnings: + /c4/home/henrik/repositories/future/revdep/library/fdacluster/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/fdacluster/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/fdacluster/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + See ‘/c4/home/henrik/repositories/future/revdep/checks/fdacluster/new/fdacluster.Rcheck/00install.out’ for details. + ``` + * checking installed package size ... NOTE ``` - installed size is 9.6Mb + installed size is 22.2Mb sub-directories of 1Mb or more: - R 1.7Mb - libs 7.8Mb + R 1.8Mb + doc 1.4Mb + help 2.1Mb + libs 16.4Mb ``` # fect @@ -867,6 +1287,15 @@ Run `revdep_details(, "fect")` for more info ## In both +* checking whether package ‘fect’ can be installed ... WARNING + ``` + Found the following significant warnings: + /c4/home/henrik/repositories/future/revdep/library/fect/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/fect/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/fect/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + See ‘/c4/home/henrik/repositories/future/revdep/checks/fect/new/fect.Rcheck/00install.out’ for details. + ``` + * checking C++ specification ... NOTE ``` Specified C++11: please drop specification unless essential @@ -874,9 +1303,9 @@ Run `revdep_details(, "fect")` for more info * checking installed package size ... NOTE ``` - installed size is 7.5Mb + installed size is 13.9Mb sub-directories of 1Mb or more: - libs 6.4Mb + libs 12.6Mb ``` * checking dependencies in R code ... NOTE @@ -901,31 +1330,6 @@ Run `revdep_details(, "FLAMES")` for more info ## In both -* checking examples ... ERROR - ``` - Running examples in ‘FLAMES-Ex.R’ failed - The error most likely occurred in: - - > ### Name: sc_heatmap_expression - > ### Title: FLAMES heetmap plots - > ### Aliases: sc_heatmap_expression - > - > ### ** Examples - > - > combined_sce <- combine_sce( - ... - > sc_heatmap_expression(gene = "ENSG00000108107", multiAssay = combined_sce) - Running PCA for experiments(multiAssay)$gene_counts ... - harmonizing input: - removing 257 sampleMap rows with 'colname' not in colnames of experiments - removing 236 colData rownames not in sampleMap 'primary' - Running UMAP for experiments(multiAssay)$gene_counts ... - Error in irlba::irlba(L, nv = n, nu = 0, maxit = iters) : - function 'as_cholmod_sparse' not provided by package 'Matrix' - Calls: sc_heatmap_expression ... irlba_tsvd_normalized_laplacian_init -> irlba_spectral_tsvd - Execution halted - ``` - * checking for hidden files and directories ... NOTE ``` Found the following hidden files and directories: @@ -938,7 +1342,15 @@ Run `revdep_details(, "FLAMES")` for more info ``` Found the following notes/warnings: Non-staged installation was used - See ‘/wynton/home/cbi/hb/repositories/future/revdep/checks/FLAMES/new/FLAMES.Rcheck/00install.out’ for details. + See ‘/c4/home/henrik/repositories/future/revdep/checks/FLAMES/new/FLAMES.Rcheck/00install.out’ for details. + ``` + +* checking installed package size ... NOTE + ``` + installed size is 6.2Mb + sub-directories of 1Mb or more: + data 2.7Mb + doc 1.7Mb ``` * checking R code for possible problems ... NOTE @@ -1001,12 +1413,6 @@ Run `revdep_details(, "flowGraph")` for more info Package unavailable to check Rd xrefs: ‘doParallel’ ``` -* checking for non-standard things in the check directory ... NOTE - ``` - Found the following files/directories: - ‘temp’ ‘tmp’ - ``` - # forecastML
@@ -1029,26 +1435,119 @@ Run `revdep_details(, "forecastML")` for more info All declared Imports should be used. ``` -# future.batchtools +# genBaRcode + +
+ +* Version: 1.2.7 +* GitHub: NA +* Source code: https://github.com/cran/genBaRcode +* Date/Publication: 2023-12-11 13:10:05 UTC +* Number of recursive dependencies: 161 + +Run `revdep_details(, "genBaRcode")` for more info + +
+ +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘genBaRcode_GUI_Vignette.Rmd’ using rmarkdown + ! LaTeX Error: File `iftex.sty' not found. + + ! Emergency stop. + + + Error: processing vignette 'genBaRcode_GUI_Vignette.Rmd' failed with diagnostics: + LaTeX failed to compile /c4/home/henrik/repositories/future/revdep/checks/genBaRcode/new/genBaRcode.Rcheck/vign_test/genBaRcode/vignettes/genBaRcode_GUI_Vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See genBaRcode_GUI_Vignette.log for more info. + --- failed re-building ‘genBaRcode_GUI_Vignette.Rmd’ + ... + + Error: processing vignette 'genBaRcode_Vignette.Rmd' failed with diagnostics: + LaTeX failed to compile /c4/home/henrik/repositories/future/revdep/checks/genBaRcode/new/genBaRcode.Rcheck/vign_test/genBaRcode/vignettes/genBaRcode_Vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See genBaRcode_Vignette.log for more info. + --- failed re-building ‘genBaRcode_Vignette.Rmd’ + + SUMMARY: processing the following files failed: + ‘genBaRcode_GUI_Vignette.Rmd’ ‘genBaRcode_Vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# geocmeans + +
+ +* Version: 0.3.4 +* GitHub: https://github.com/JeremyGelb/geocmeans +* Source code: https://github.com/cran/geocmeans +* Date/Publication: 2023-09-12 03:10:02 UTC +* Number of recursive dependencies: 197 + +Run `revdep_details(, "geocmeans")` for more info + +
+ +## In both + +* checking whether package ‘geocmeans’ can be installed ... WARNING + ``` + Found the following significant warnings: + /c4/home/henrik/repositories/future/revdep/library/geocmeans/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/geocmeans/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/geocmeans/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + See ‘/c4/home/henrik/repositories/future/revdep/checks/geocmeans/new/geocmeans.Rcheck/00install.out’ for details. + ``` + +* checking installed package size ... NOTE + ``` + installed size is 13.5Mb + sub-directories of 1Mb or more: + extdata 3.0Mb + libs 8.2Mb + ``` + +# geohabnet
-* Version: 0.12.1 -* GitHub: https://github.com/HenrikBengtsson/future.batchtools -* Source code: https://github.com/cran/future.batchtools -* Date/Publication: 2023-12-20 12:20:02 UTC -* Number of recursive dependencies: 36 +* Version: 2.0.0 +* GitHub: https://github.com/GarrettLab/HabitatConnectivity +* Source code: https://github.com/cran/geohabnet +* Date/Publication: 2024-02-27 19:50:02 UTC +* Number of recursive dependencies: 134 -Run `revdep_details(, "future.batchtools")` for more info +Run `revdep_details(, "geohabnet")` for more info
## In both -* checking for non-standard things in the check directory ... NOTE +* checking re-building of vignette outputs ... ERROR ``` - Found the following files/directories: - ‘.future-set-during-startup’ + Error(s) in re-building vignettes: + --- re-building ‘LinkWeightsAnalysis.Rmd’ using rmarkdown + trying URL 'https://s3.us-east-2.amazonaws.com/earthstatdata/HarvestedAreaYield175Crops_Indvidual_Geotiff/potato_HarvAreaYield_Geotiff.zip' + Content type 'application/zip' length 10812124 bytes (10.3 MB) + ================================================== + downloaded 10.3 MB + + trying URL 'https://geohabnet.s3.us-east-2.amazonaws.com/util-rasters/ZeroRaster.tif' + Content type 'image/tiff' length 1056851 bytes (1.0 MB) + ================================================== + ... + Quitting from lines 108-109 [unnamed-chunk-5] (analysis.Rmd) + Error: processing vignette 'analysis.Rmd' failed with diagnostics: + (/c4/home/henrik/.config/R/geohabnet/parameters.yaml) Duplicate map key: 'default' + --- failed re-building ‘analysis.Rmd’ + + SUMMARY: processing the following file failed: + ‘analysis.Rmd’ + + Error: Vignette re-building failed. + Execution halted ``` # googleComputeEngineR @@ -1059,7 +1558,7 @@ Run `revdep_details(, "future.batchtools")` for more info * GitHub: https://github.com/cloudyr/googleComputeEngineR * Source code: https://github.com/cran/googleComputeEngineR * Date/Publication: 2019-05-04 22:40:02 UTC -* Number of recursive dependencies: 69 +* Number of recursive dependencies: 67 Run `revdep_details(, "googleComputeEngineR")` for more info @@ -1080,7 +1579,7 @@ Run `revdep_details(, "googleComputeEngineR")` for more info * GitHub: NA * Source code: https://github.com/cran/googleTagManageR * Date/Publication: 2022-04-16 18:12:29 UTC -* Number of recursive dependencies: 71 +* Number of recursive dependencies: 69 Run `revdep_details(, "googleTagManageR")` for more info @@ -1111,6 +1610,15 @@ Run `revdep_details(, "greed")` for more info ## In both +* checking whether package ‘greed’ can be installed ... WARNING + ``` + Found the following significant warnings: + /c4/home/henrik/repositories/future/revdep/library/greed/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/greed/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/greed/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + See ‘/c4/home/henrik/repositories/future/revdep/checks/greed/new/greed.Rcheck/00install.out’ for details. + ``` + * checking C++ specification ... NOTE ``` Specified C++11: please drop specification unless essential @@ -1118,9 +1626,9 @@ Run `revdep_details(, "greed")` for more info * checking installed package size ... NOTE ``` - installed size is 17.1Mb + installed size is 36.5Mb sub-directories of 1Mb or more: - libs 16.5Mb + libs 34.3Mb ``` * checking data for non-ASCII characters ... NOTE @@ -1144,50 +1652,25 @@ Run `revdep_details(, "gsynth")` for more info ## In both +* checking whether package ‘gsynth’ can be installed ... WARNING + ``` + Found the following significant warnings: + /c4/home/henrik/repositories/future/revdep/library/gsynth/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/gsynth/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/gsynth/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + See ‘/c4/home/henrik/repositories/future/revdep/checks/gsynth/new/gsynth.Rcheck/00install.out’ for details. + ``` + * checking C++ specification ... NOTE ``` Specified C++11: please drop specification unless essential ``` -# gtfs2gps - -
- -* Version: 2.1-1 -* GitHub: https://github.com/ipeaGIT/gtfs2gps -* Source code: https://github.com/cran/gtfs2gps -* Date/Publication: 2023-04-28 19:50:02 UTC -* Number of recursive dependencies: 90 - -Run `revdep_details(, "gtfs2gps")` for more info - -
- -## In both - -* checking tests ... +* checking installed package size ... NOTE ``` - Running ‘testthat.R’ - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(gtfs2gps) - gtfs2gps version 2.1-1 is now loaded - NOTE: All filter functions from gtfs2gps were removed - Please replace them by similar functions from gtfstools - > library(magrittr) - ... - 4. └─terra (local) .local(x, ...) - 5. ├─terra::makeValid(x) - 6. └─terra::makeValid(x) - 7. └─terra (local) .local(x, ...) - 8. └─terra:::messages(x) - 9. └─terra:::error(f, x@cpp$getError()) - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 119 ] - Error: Test failures - Execution halted + installed size is 5.2Mb + sub-directories of 1Mb or more: + libs 4.9Mb ``` # hackeRnews @@ -1198,7 +1681,7 @@ Run `revdep_details(, "gtfs2gps")` for more info * GitHub: https://github.com/szymanskir/hackeRnews * Source code: https://github.com/cran/hackeRnews * Date/Publication: 2019-12-13 13:20:05 UTC -* Number of recursive dependencies: 71 +* Number of recursive dependencies: 69 Run `revdep_details(, "hackeRnews")` for more info @@ -1211,6 +1694,57 @@ Run `revdep_details(, "hackeRnews")` for more info 'LazyData' is specified without a 'data' directory ``` +# hal9001 + +
+ +* Version: 0.4.6 +* GitHub: https://github.com/tlverse/hal9001 +* Source code: https://github.com/cran/hal9001 +* Date/Publication: 2023-11-14 15:00:02 UTC +* Number of recursive dependencies: 100 + +Run `revdep_details(, "hal9001")` for more info + +
+ +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.3Mb + sub-directories of 1Mb or more: + libs 4.9Mb + ``` + +# hbamr + +
+ +* Version: 2.2.1 +* GitHub: https://github.com/jbolstad/hbamr +* Source code: https://github.com/cran/hbamr +* Date/Publication: 2024-02-23 12:30:02 UTC +* Number of recursive dependencies: 91 + +Run `revdep_details(, "hbamr")` for more info + +
+ +## In both + +* checking installed package size ... NOTE + ``` + installed size is 353.1Mb + sub-directories of 1Mb or more: + libs 351.6Mb + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + # hero
@@ -1219,7 +1753,7 @@ Run `revdep_details(, "hackeRnews")` for more info * GitHub: NA * Source code: https://github.com/cran/hero * Date/Publication: 2023-07-15 21:10:09 UTC -* Number of recursive dependencies: 162 +* Number of recursive dependencies: 160 Run `revdep_details(, "hero")` for more info @@ -1227,56 +1761,100 @@ Run `revdep_details(, "hero")` for more info ## In both -* checking dependencies in R code ... NOTE +* checking package dependencies ... NOTE ``` - dev3:pid3635515: PSM3 can't open nic unit: 0 (err=23) - dev3:pid3635515.R: Unable to create send CQ of size 5080 on mlx5_0: Cannot allocate memory - dev3:pid3635515.R: Unable to initialize verbs NIC /sys/class/infiniband/mlx5_0 (unit 0:0) - dev3:pid3635515: PSM3 can't open nic unit: 0 (err=23) - dev3:pid3635515.R: Unable to create send CQ of size 5080 on mlx5_0: Cannot allocate memory - dev3:pid3635515.R: Unable to initialize verbs NIC /sys/class/infiniband/mlx5_0 (unit 0:0) - dev3:pid3635515: PSM3 can't open nic unit: 0 (err=23) - dev3:pid3635515.R: Unable to create send CQ of size 5080 on mlx5_0: Cannot allocate memory - dev3:pid3635515.R: Unable to initialize verbs NIC /sys/class/infiniband/mlx5_0 (unit 0:0) - -------------------------------------------------------------------------- - ... - dev3:pid3635515.R: Unable to create send CQ of size 5080 on mlx5_0: Cannot allocate memory - dev3:pid3635515.R: Unable to initialize verbs NIC /sys/class/infiniband/mlx5_0 (unit 0:0) - -------------------------------------------------------------------------- - Open MPI failed an OFI Libfabric library call (fi_endpoint). This is highly - unusual; your job may behave unpredictably (and/or abort) after this. - - Local host: dev3 - Location: mtl_ofi_component.c:513 - Error: Invalid argument (22) - -------------------------------------------------------------------------- + Package suggested but not available for checking: ‘Rmpi’ ``` -* checking for detritus in the temp directory ... NOTE +* checking Rd cross-references ... NOTE ``` - Found the following files/directories: - ‘ompi.dev3.34002’ + Package unavailable to check Rd xrefs: ‘Rmpi’ ``` -# hoopR +# heterogen
-* Version: 2.1.0 -* GitHub: https://github.com/sportsdataverse/hoopR -* Source code: https://github.com/cran/hoopR -* Date/Publication: 2023-11-25 23:40:20 UTC -* Number of recursive dependencies: 116 +* Version: 1.2.33 +* GitHub: https://github.com/patauchi/heterogen +* Source code: https://github.com/cran/heterogen +* Date/Publication: 2023-08-17 07:42:33 UTC +* Number of recursive dependencies: 56 -Run `revdep_details(, "hoopR")` for more info +Run `revdep_details(, "heterogen")` for more info
## In both -* checking package dependencies ... NOTE +* checking whether package ‘heterogen’ can be installed ... WARNING + ``` + Found the following significant warnings: + /c4/home/henrik/repositories/future/revdep/library/heterogen/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/heterogen/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/heterogen/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + See ‘/c4/home/henrik/repositories/future/revdep/checks/heterogen/new/heterogen.Rcheck/00install.out’ for details. + ``` + +* checking installed package size ... NOTE + ``` + installed size is 8.6Mb + sub-directories of 1Mb or more: + extdata 2.5Mb + libs 6.0Mb + ``` + +# httpgd + +
+ +* Version: 2.0.1 +* GitHub: https://github.com/nx10/httpgd +* Source code: https://github.com/cran/httpgd +* Date/Publication: 2024-03-11 08:00:06 UTC +* Number of recursive dependencies: 67 + +Run `revdep_details(, "httpgd")` for more info + +
+ +## In both + +* checking tests ... + ``` + Running ‘testthat.R’/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/bin/BATCH: line 60: 284845 Segmentation fault (core dumped) ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1 + + ERROR + Running the tests in ‘tests/testthat.R’ failed. + Last 50 lines of output: + 1. └─jsonlite::fromJSON(httr::content(res, as = "text")) at test-server.R:62:3 + 2. └─jsonlite:::parse_and_simplify(...) + 3. └─jsonlite:::parseJSON(txt, bigint_as_char) + 4. └─jsonlite:::parse_string(txt, bigint_as_char) + ── Error ('test-server.R:83:5'): Clear plots ─────────────────────────────────── + ... + 1/1 mismatches + [1] 503 - 404 == 99 + + [ FAIL 16 | WARN 0 | SKIP 0 | PASS 2 ] + Error: Test failures + Execution halted + + *** caught segfault *** + address (nil), cause 'unknown' + An irrecoverable exception occurred. R is aborting now ... + ``` + +* checking C++ specification ... NOTE ``` - Package suggested but not available for checking: ‘qs’ + Specified C++14: please drop specification unless essential + ``` + +* checking installed package size ... NOTE + ``` + installed size is 12.7Mb + sub-directories of 1Mb or more: + libs 12.2Mb ``` # hwep @@ -1287,7 +1865,7 @@ Run `revdep_details(, "hoopR")` for more info * GitHub: https://github.com/dcgerard/hwep * Source code: https://github.com/cran/hwep * Date/Publication: 2023-05-16 17:40:02 UTC -* Number of recursive dependencies: 110 +* Number of recursive dependencies: 116 Run `revdep_details(, "hwep")` for more info @@ -1297,9 +1875,9 @@ Run `revdep_details(, "hwep")` for more info * checking installed package size ... NOTE ``` - installed size is 28.1Mb + installed size is 84.5Mb sub-directories of 1Mb or more: - libs 27.7Mb + libs 83.9Mb ``` * checking for GNU extensions in Makefiles ... NOTE @@ -1307,6 +1885,66 @@ Run `revdep_details(, "hwep")` for more info GNU make is a SystemRequirements. ``` +# hydroloom + +
+ +* Version: 1.0.2 +* GitHub: https://github.com/DOI-USGS/hydroloom +* Source code: https://github.com/cran/hydroloom +* Date/Publication: 2024-01-15 16:20:02 UTC +* Number of recursive dependencies: 154 + +Run `revdep_details(, "hydroloom")` for more info + +
+ +## In both + +* checking examples ... ERROR + ``` + Running examples in ‘hydroloom-Ex.R’ failed + The error most likely occurred in: + + > ### Name: index_points_to_waterbodies + > ### Title: Index Points to Waterbodies + > ### Aliases: index_points_to_waterbodies + > + > ### ** Examples + > + > + > source(system.file("extdata/sample_data.R", package = "nhdplusTools")) + Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + there is no package called ‘arrow’ + Calls: source ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart + Execution halted + ``` + +* checking re-building of vignette outputs ... ERROR + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘advanced_network.Rmd’ using rmarkdown + --- finished re-building ‘advanced_network.Rmd’ + + --- re-building ‘flow-table.Rmd’ using rmarkdown + + Quitting from lines 12-32 [setup] (flow-table.Rmd) + Error: processing vignette 'flow-table.Rmd' failed with diagnostics: + there is no package called 'arrow' + ... + --- finished re-building ‘hydroloom.Rmd’ + + --- re-building ‘non-dendritic.Rmd’ using rmarkdown + --- finished re-building ‘non-dendritic.Rmd’ + + SUMMARY: processing the following file failed: + ‘flow-table.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + # infercnv
@@ -1323,6 +1961,13 @@ Run `revdep_details(, "infercnv")` for more info ## In both +* checking installed package size ... NOTE + ``` + installed size is 5.1Mb + sub-directories of 1Mb or more: + extdata 3.1Mb + ``` + * checking dependencies in R code ... NOTE ``` Unexported object imported by a ':::' call: ‘HiddenMarkov:::makedensity’ @@ -1371,11 +2016,51 @@ Run `revdep_details(, "interflex")` for more info ## In both +* checking whether package ‘interflex’ can be installed ... WARNING + ``` + Found the following significant warnings: + /c4/home/henrik/repositories/future/revdep/library/interflex/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/interflex/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/interflex/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + See ‘/c4/home/henrik/repositories/future/revdep/checks/interflex/new/interflex.Rcheck/00install.out’ for details. + ``` + * checking C++ specification ... NOTE ``` Specified C++11: please drop specification unless essential ``` +* checking installed package size ... NOTE + ``` + installed size is 5.8Mb + sub-directories of 1Mb or more: + libs 5.1Mb + ``` + +# ISAnalytics + +
+ +* Version: 1.12.0 +* GitHub: https://github.com/calabrialab/ISAnalytics +* Source code: https://github.com/cran/ISAnalytics +* Date/Publication: 2023-10-24 +* Number of recursive dependencies: 173 + +Run `revdep_details(, "ISAnalytics")` for more info + +
+ +## In both + +* checking installed package size ... NOTE + ``` + installed size is 7.2Mb + sub-directories of 1Mb or more: + data 1.4Mb + doc 3.5Mb + ``` + # ivmte
@@ -1401,10 +2086,10 @@ Run `revdep_details(, "ivmte")` for more info
-* Version: 0.5.0 +* Version: 0.5.1 * GitHub: https://github.com/keyATM/keyATM * Source code: https://github.com/cran/keyATM -* Date/Publication: 2023-05-11 07:20:03 UTC +* Date/Publication: 2024-02-04 23:30:02 UTC * Number of recursive dependencies: 107 Run `revdep_details(, "keyATM")` for more info @@ -1415,9 +2100,9 @@ Run `revdep_details(, "keyATM")` for more info * checking installed package size ... NOTE ``` - installed size is 9.3Mb + installed size is 24.7Mb sub-directories of 1Mb or more: - libs 9.1Mb + libs 24.3Mb ``` # ldsr @@ -1428,7 +2113,7 @@ Run `revdep_details(, "keyATM")` for more info * GitHub: https://github.com/ntthung/ldsr * Source code: https://github.com/cran/ldsr * Date/Publication: 2020-05-04 14:40:09 UTC -* Number of recursive dependencies: 80 +* Number of recursive dependencies: 78 Run `revdep_details(, "ldsr")` for more info @@ -1436,6 +2121,15 @@ Run `revdep_details(, "ldsr")` for more info ## In both +* checking whether package ‘ldsr’ can be installed ... WARNING + ``` + Found the following significant warnings: + /c4/home/henrik/repositories/future/revdep/library/ldsr/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/ldsr/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/ldsr/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + See ‘/c4/home/henrik/repositories/future/revdep/checks/ldsr/new/ldsr.Rcheck/00install.out’ for details. + ``` + * checking C++ specification ... NOTE ``` Specified C++11: please drop specification unless essential @@ -1445,11 +2139,11 @@ Run `revdep_details(, "ldsr")` for more info
-* Version: 4.0.4 +* Version: 4.1.1 * GitHub: https://github.com/r-lidar/lidR * Source code: https://github.com/cran/lidR -* Date/Publication: 2023-09-07 15:20:05 UTC -* Number of recursive dependencies: 155 +* Date/Publication: 2024-03-05 17:00:11 UTC +* Number of recursive dependencies: 156 Run `revdep_details(, "lidR")` for more info @@ -1457,37 +2151,44 @@ Run `revdep_details(, "lidR")` for more info ## In both -* checking installed package size ... NOTE +* checking tests ... ``` - installed size is 7.8Mb - sub-directories of 1Mb or more: - libs 6.8Mb + Running ‘testthat.R’/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/bin/BATCH: line 60: 29724 Aborted (core dumped) ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1 + + ERROR + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > Sys.setenv("R_TESTS" = "") + > + > library(testthat) + > library(lidR) + > test_check("lidR") + Tests using raster: terra + Tests using future: TRUE + Tests using OpenMP thread: 32 + OGR: Unsupported geometry type + OGR: Unsupported geometry type + Chunk 1 of 1 (100%): state ✓ + terminate called after throwing an instance of 'std::length_error' + what(): basic_string::_S_create ``` -# lightr - -
- -* Version: 1.7.0 -* GitHub: https://github.com/ropensci/lightr -* Source code: https://github.com/cran/lightr -* Date/Publication: 2022-05-14 13:50:02 UTC -* Number of recursive dependencies: 88 - -Run `revdep_details(, "lightr")` for more info - -
- -## In both - -* checking package dependencies ... NOTE +* checking whether package ‘lidR’ can be installed ... WARNING ``` - Package suggested but not available for checking: ‘pavo’ + Found the following significant warnings: + /c4/home/henrik/repositories/future/revdep/library/lidR/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/lidR/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/lidR/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + See ‘/c4/home/henrik/repositories/future/revdep/checks/lidR/new/lidR.Rcheck/00install.out’ for details. ``` -* checking Rd cross-references ... NOTE +* checking installed package size ... NOTE ``` - Package unavailable to check Rd xrefs: ‘pavo’ + installed size is 20.0Mb + sub-directories of 1Mb or more: + R 1.0Mb + extdata 1.1Mb + libs 16.3Mb ``` # MAI @@ -1513,40 +2214,144 @@ Run `revdep_details(, "MAI")` for more info is not mentioned in the DESCRIPTION file. ``` -# migraph +# manynet
-* Version: 1.2.1 -* GitHub: https://github.com/snlab-ch/migraph -* Source code: https://github.com/cran/migraph -* Date/Publication: 2023-12-17 22:30:02 UTC -* Number of recursive dependencies: 115 +* Version: 0.4.4 +* GitHub: https://github.com/stocnet/manynet +* Source code: https://github.com/cran/manynet +* Date/Publication: 2024-03-15 19:20:10 UTC +* Number of recursive dependencies: 142 -Run `revdep_details(, "migraph")` for more info +Run `revdep_details(, "manynet")` for more info
## In both -* checking examples ... ERROR +* checking package dependencies ... NOTE ``` - Running examples in ‘migraph-Ex.R’ failed - The error most likely occurred in: + Package which this enhances but not available for checking: ‘Rgraphviz’ + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 7 marked UTF-8 strings + ``` + +# matric + +
+ +* Version: 0.2.0 +* GitHub: https://github.com/cytomining/matric +* Source code: https://github.com/cran/matric +* Date/Publication: 2023-03-22 08:50:02 UTC +* Number of recursive dependencies: 107 + +Run `revdep_details(, "matric")` for more info + +
+ +## In both + +* checking package dependencies ... ERROR + ``` + Package required but not available: ‘arrow’ - > ### Name: community - > ### Title: Community partitioning algorithms - > ### Aliases: community node_optimal node_kernighanlin node_edge_betweenness - > ### node_fast_greedy node_leading_eigen node_walktrap node_infomap - > ### node_spinglass node_louvain node_leiden - > - > ### ** Examples - > - > node_optimal(ison_adolescents) - Error in igraph::cluster_optimal(manynet::as_igraph(.data)) : - At core/community/optimal_modularity.c:86 : GLPK is not available, Unimplemented function call - Calls: node_optimal -> - Execution halted + See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ + manual. + ``` + +# metabolomicsR + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/XikunHan/metabolomicsR +* Source code: https://github.com/cran/metabolomicsR +* Date/Publication: 2022-04-29 07:40:02 UTC +* Number of recursive dependencies: 182 + +Run `revdep_details(, "metabolomicsR")` for more info + +
+ +## In both + +* checking dependencies in R code ... WARNING + ``` + Missing or unexported object: ‘future::multiprocess’ + ``` + +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘genuMet’ + ``` + +# metaGE + +
+ +* Version: 1.0.3 +* GitHub: NA +* Source code: https://github.com/cran/metaGE +* Date/Publication: 2023-09-28 08:50:02 UTC +* Number of recursive dependencies: 149 + +Run `revdep_details(, "metaGE")` for more info + +
+ +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.1Mb + sub-directories of 1Mb or more: + data 4.2Mb + ``` + +# microservices + +
+ +* Version: 0.2.0 +* GitHub: https://github.com/tidylab/microservices +* Source code: https://github.com/cran/microservices +* Date/Publication: 2022-10-01 09:50:02 UTC +* Number of recursive dependencies: 72 + +Run `revdep_details(, "microservices")` for more info + +
+ +## In both + +* checking tests ... + ``` + Running ‘testthat.R’ + ERROR + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(microservices) + > test_check("microservices") + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 12 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ... + Backtrace: + ▆ + 1. ├─config::get(...) at test-endpoint-plumber-{route_name}.R:2:1 + 2. │ └─base::normalizePath(file, mustWork = FALSE) + 3. │ └─base::path.expand(path) + 4. └─base::system.file(...) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 12 ] + Error: Test failures + Execution halted ``` # MineICA @@ -1685,11 +2490,36 @@ Run `revdep_details(, "MineICA")` for more info Execution halted ``` -* checking for non-standard things in the check directory ... NOTE +# missSBM + +
+ +* Version: 1.0.4 +* GitHub: https://github.com/grossSBM/missSBM +* Source code: https://github.com/cran/missSBM +* Date/Publication: 2023-10-24 16:00:05 UTC +* Number of recursive dependencies: 114 + +Run `revdep_details(, "missSBM")` for more info + +
+ +## In both + +* checking whether package ‘missSBM’ can be installed ... WARNING + ``` + Found the following significant warnings: + /c4/home/henrik/repositories/future/revdep/library/missSBM/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/missSBM/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/missSBM/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + See ‘/c4/home/henrik/repositories/future/revdep/checks/missSBM/new/missSBM.Rcheck/00install.out’ for details. + ``` + +* checking installed package size ... NOTE ``` - Found the following files/directories: - ‘ProjByComp’ ‘carbayo’ ‘gene2MixingMatrix’ ‘myGraph.txt’ - ‘nodeInfo.txt’ ‘outputHyper_example.htm’ ‘resMineICACarbayo’ ‘toy’ + installed size is 9.8Mb + sub-directories of 1Mb or more: + libs 7.8Mb ``` # mistyR @@ -1700,7 +2530,7 @@ Run `revdep_details(, "MineICA")` for more info * GitHub: https://github.com/saezlab/mistyR * Source code: https://github.com/cran/mistyR * Date/Publication: 2023-10-24 -* Number of recursive dependencies: 156 +* Number of recursive dependencies: 155 Run `revdep_details(, "mistyR")` for more info @@ -1708,6 +2538,31 @@ Run `revdep_details(, "mistyR")` for more info ## In both +* checking tests ... + ``` + Running ‘testthat.R’ + ERROR + Running the tests in ‘tests/testthat.R’ failed. + Last 50 lines of output: + + Collecting contributions + + Collecting importances + + Aggregating + ... + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test-misty.R:212:3'): k for cv , n.bags for bagging can be changed and approx works ── + first.run < second.run is not TRUE + + `actual`: FALSE + `expected`: TRUE + + [ FAIL 1 | WARN 4 | SKIP 0 | PASS 172 ] + Error: Test failures + Execution halted + ``` + * checking R code for possible problems ... NOTE ``` aggregate_results: no visible binding for global variable ‘measure’ @@ -1733,41 +2588,72 @@ Run `revdep_details(, "mistyR")` for more info to your NAMESPACE file. ``` -* checking for non-standard things in the check directory ... NOTE +# momentuHMM + +
+ +* Version: 1.5.5 +* GitHub: https://github.com/bmcclintock/momentuHMM +* Source code: https://github.com/cran/momentuHMM +* Date/Publication: 2022-10-18 20:52:35 UTC +* Number of recursive dependencies: 145 + +Run `revdep_details(, "momentuHMM")` for more info + +
+ +## In both + +* checking whether package ‘momentuHMM’ can be installed ... WARNING ``` - Found the following files/directories: - ‘results’ + Found the following significant warnings: + /c4/home/henrik/repositories/future/revdep/library/momentuHMM/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/momentuHMM/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/momentuHMM/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + See ‘/c4/home/henrik/repositories/future/revdep/checks/momentuHMM/new/momentuHMM.Rcheck/00install.out’ for details. ``` -# mlr3resampling +* checking installed package size ... NOTE + ``` + installed size is 10.2Mb + sub-directories of 1Mb or more: + R 1.2Mb + doc 1.7Mb + libs 6.7Mb + ``` + +# MOSS
-* Version: 2023.12.20 -* GitHub: https://github.com/tdhock/mlr3resampling -* Source code: https://github.com/cran/mlr3resampling -* Date/Publication: 2023-12-21 16:40:07 UTC -* Number of recursive dependencies: 86 +* Version: 0.2.2 +* GitHub: https://github.com/agugonrey/MOSS +* Source code: https://github.com/cran/MOSS +* Date/Publication: 2022-03-25 15:50:05 UTC +* Number of recursive dependencies: 184 -Run `revdep_details(, "mlr3resampling")` for more info +Run `revdep_details(, "MOSS")` for more info
## In both -* checking re-building of vignette outputs ... ERROR +* checking re-building of vignette outputs ... WARNING ``` Error(s) in re-building vignettes: ... - --- re-building ‘Simulations.Rmd’ using rmarkdown + --- re-building ‘MOSS_working_example.Rmd’ using rmarkdown + ! LaTeX Error: File `iftex.sty' not found. + + ! Emergency stop. + - Quitting from lines 543-708 [SimulationsAnimintClassification] (Simulations.Rmd) - Error: processing vignette 'Simulations.Rmd' failed with diagnostics: - Passed a vector of type 'NULL'. Needs to be type 'character'. - --- failed re-building ‘Simulations.Rmd’ + Error: processing vignette 'MOSS_working_example.Rmd' failed with diagnostics: + LaTeX failed to compile /c4/home/henrik/repositories/future/revdep/checks/MOSS/new/MOSS.Rcheck/vign_test/MOSS/vignettes/MOSS_working_example.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See MOSS_working_example.log for more info. + --- failed re-building ‘MOSS_working_example.Rmd’ SUMMARY: processing the following file failed: - ‘Simulations.Rmd’ + ‘MOSS_working_example.Rmd’ Error: Vignette re-building failed. Execution halted @@ -1781,7 +2667,7 @@ Run `revdep_details(, "mlr3resampling")` for more info * GitHub: https://github.com/kylebaron/mrgsim.parallel * Source code: https://github.com/cran/mrgsim.parallel * Date/Publication: 2022-03-17 19:50:05 UTC -* Number of recursive dependencies: 76 +* Number of recursive dependencies: 74 Run `revdep_details(, "mrgsim.parallel")` for more info @@ -1791,18 +2677,23 @@ Run `revdep_details(, "mrgsim.parallel")` for more info * checking package dependencies ... NOTE ``` - Package suggested but not available for checking: ‘qs’ + Package suggested but not available for checking: ‘arrow’ + ``` + +* checking Rd cross-references ... NOTE + ``` + Package unavailable to check Rd xrefs: ‘arrow’ ``` # nebula
-* Version: 1.4.2 -* GitHub: NA +* Version: 1.5.3 +* GitHub: https://github.com/lhe17/nebula * Source code: https://github.com/cran/nebula -* Date/Publication: 2023-07-05 23:20:07 UTC -* Number of recursive dependencies: 74 +* Date/Publication: 2024-02-15 23:00:02 UTC +* Number of recursive dependencies: 185 Run `revdep_details(, "nebula")` for more info @@ -1812,9 +2703,9 @@ Run `revdep_details(, "nebula")` for more info * checking installed package size ... NOTE ``` - installed size is 9.5Mb + installed size is 37.4Mb sub-directories of 1Mb or more: - libs 9.3Mb + libs 35.9Mb ``` # nfl4th @@ -1837,7 +2728,7 @@ Run `revdep_details(, "nfl4th")` for more info ``` Found the following significant warnings: Warning: GitHub.com seems offline, and `options(nfl4th.keep_games)` is not set to TRUE. Deleting the games cache, and predictions may not be available without an internet connection. - See ‘/wynton/home/cbi/hb/repositories/future/revdep/checks/nfl4th/new/nfl4th.Rcheck/00install.out’ for details. + See ‘/c4/home/henrik/repositories/future/revdep/checks/nfl4th/new/nfl4th.Rcheck/00install.out’ for details. ``` * checking whether the namespace can be loaded with stated dependencies ... NOTE @@ -1851,25 +2742,28 @@ Run `revdep_details(, "nfl4th")` for more info Probably some imports need to be declared in the NAMESPACE file. ``` -# nflfastR +# nhdplusTools
-* Version: 4.6.0 -* GitHub: https://github.com/nflverse/nflfastR -* Source code: https://github.com/cran/nflfastR -* Date/Publication: 2023-10-20 15:30:07 UTC -* Number of recursive dependencies: 104 +* Version: 1.0.0 +* GitHub: https://github.com/doi-usgs/nhdplusTools +* Source code: https://github.com/cran/nhdplusTools +* Date/Publication: 2023-10-02 14:10:02 UTC +* Number of recursive dependencies: 140 -Run `revdep_details(, "nflfastR")` for more info +Run `revdep_details(, "nhdplusTools")` for more info
## In both -* checking package dependencies ... NOTE +* checking package dependencies ... ERROR ``` - Package suggested but not available for checking: ‘qs’ + Package required but not available: ‘arrow’ + + See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ + manual. ``` # oncomsm @@ -1880,7 +2774,7 @@ Run `revdep_details(, "nflfastR")` for more info * GitHub: https://github.com/Boehringer-Ingelheim/oncomsm * Source code: https://github.com/cran/oncomsm * Date/Publication: 2023-04-17 07:00:02 UTC -* Number of recursive dependencies: 125 +* Number of recursive dependencies: 127 Run `revdep_details(, "oncomsm")` for more info @@ -1890,9 +2784,10 @@ Run `revdep_details(, "oncomsm")` for more info * checking installed package size ... NOTE ``` - installed size is 19.9Mb + installed size is 67.6Mb sub-directories of 1Mb or more: - libs 19.6Mb + doc 1.0Mb + libs 65.5Mb ``` * checking for GNU extensions in Makefiles ... NOTE @@ -1916,9 +2811,22 @@ Run `revdep_details(, "onemapsgapi")` for more info ## In both -* checking package dependencies ... NOTE +* checking re-building of vignette outputs ... ERROR ``` - Package suggested but not available for checking: ‘rgdal’ + Error(s) in re-building vignettes: + ... + --- re-building ‘onemapsgapi_vignette.Rmd’ using rmarkdown + + Quitting from lines 36-37 [unnamed-chunk-4] (onemapsgapi_vignette.Rmd) + Error: processing vignette 'onemapsgapi_vignette.Rmd' failed with diagnostics: + Peer certificate cannot be authenticated with given CA certificates: [developers.onemap.sg] Peer's Certificate has expired. + --- failed re-building ‘onemapsgapi_vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘onemapsgapi_vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted ``` # OOS @@ -1971,15 +2879,15 @@ Run `revdep_details(, "pareg")` for more info > > df_genes <- data.frame( ... - [Errno 2] No such file or directory: '/wynton/home/cbi/hb/.cache/R/basilisk/1.14.1/0/envs/fallback/share/aclocal' - [Errno 2] No such file or directory: '/wynton/home/cbi/hb/.cache/R/basilisk/1.14.1/0/envs/fallback/lib/gettext' - [Errno 2] No such file or directory: '/wynton/home/cbi/hb/.cache/R/basilisk/1.14.1/0/envs/fallback/lib/pkgconfig' - [Errno 2] No such file or directory: '/wynton/home/cbi/hb/.cache/R/basilisk/1.14.1/0/envs/fallback/man/man1' - [Errno 2] No such file or directory: '/wynton/home/cbi/hb/.cache/R/basilisk/1.14.1/0/envs/fallback/share/man/man1' - [Errno 2] No such file or directory: '/wynton/home/cbi/hb/.cache/R/basilisk/1.14.1/0/envs/fallback/lib/bfd-plugins' - [Errno 2] No such file or directory: '/wynton/home/cbi/hb/.cache/R/basilisk/1.14.1/0/envs/fallback/include' - - Error: Error creating conda environment 'fallback' [exit code 1] + + ) + > fit <- pareg(df_genes, df_terms, max_iterations = 10) + Error in py_module_import(module, convert = convert) : + ImportError: /lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /c4/home/henrik/.cache/R/basilisk/1.14.3/pareg/1.6.0/pareg/lib/python3.9/site-packages/tensorflow/python/platform/_pywrap_cpu_feature_guard.so) + Run `reticulate::py_last_error()` for details. + Error in .activate_fallback(proc, testload, env = env, envpath = envpath, : + ImportError: /lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /c4/home/henrik/.cache/R/basilisk/1.14.3/pareg/1.6.0/pareg/lib/python3.9/site-packages/tensorflow/python/platform/_pywrap_cpu_feature_guard.so) + Run `reticulate::py_last_error()` for details. + Calls: pareg -> basiliskStart -> .activate_fallback Execution halted ``` @@ -1988,23 +2896,23 @@ Run `revdep_details(, "pareg")` for more info Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. - Last 50 lines of output: - pthread-stubs conda-forge/linux-64::pthread-stubs-0.4-h36c2ea0_1001 - python conda-forge/linux-64::python-3.9.18-h0755675_0_cpython - r-base conda-forge/linux-64::r-base-4.3.2-hb8ee39d_1 - r-here conda-forge/noarch::r-here-1.0.1-r43hc72bb7e_2 - r-jsonlite conda-forge/linux-64::r-jsonlite-1.8.8-r43h57805ef_0 - r-lattice conda-forge/linux-64::r-lattice-0.22_5-r43h57805ef_0 + Complete output: + > library(testthat) + > library(pareg) + Loading required package: tensorflow + Loading required package: tfprobability + + ... - done - Executing transaction: ...working... done - sh: /wynton/home/cbi/hb/.cache/R/basilisk/1.14.1/0/envs/fallback/bin/Rscript: No such file or directory - Error in makePSOCKcluster(1, rscript = rscript) : - Cluster setup failed. 1 worker of 1 failed to connect. - Calls: ... .activate_fallback -> basiliskStart -> makePSOCKcluster - In addition: Warning message: - In check_forbidden_install("Conda Environments") : - cannot install Conda Environments during R CMD check + + testload = c("tensorflow", "tensorflow_probability") + + ) + Error in py_module_import(module, convert = convert) : + ImportError: /lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /c4/home/henrik/.cache/R/basilisk/1.14.3/pareg/1.6.0/pareg/lib/python3.9/site-packages/tensorflow/python/platform/_pywrap_cpu_feature_guard.so) + Run `reticulate::py_last_error()` for details. + Error in .activate_fallback(proc, testload, env = env, envpath = envpath, : + ImportError: /lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /c4/home/henrik/.cache/R/basilisk/1.14.3/pareg/1.6.0/pareg/lib/python3.9/site-packages/tensorflow/python/platform/_pywrap_cpu_feature_guard.so) + Run `reticulate::py_last_error()` for details. + Calls: -> .activate_fallback Execution halted ``` @@ -2013,17 +2921,17 @@ Run `revdep_details(, "pareg")` for more info Error(s) in re-building vignettes: ... --- re-building ‘pareg.Rmd’ using rmarkdown - The magick package is required to crop "/wynton/home/cbi/hb/repositories/future/revdep/checks/pareg/new/pareg.Rcheck/vign_test/pareg/vignettes/pareg_files/figure-html/unnamed-chunk-4-1.png" but not available. - The magick package is required to crop "/wynton/home/cbi/hb/repositories/future/revdep/checks/pareg/new/pareg.Rcheck/vign_test/pareg/vignettes/pareg_files/figure-html/unnamed-chunk-5-1.png" but not available. - 2023-12-21 15:55:36.343997: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: SSE4.1 SSE4.2 AVX AVX2 FMA - To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags. - sh: /wynton/home/cbi/hb/.cache/R/basilisk/1.14.1/0/envs/fallback/bin/Rscript: No such file or directory + The magick package is required to crop "/c4/home/henrik/repositories/future/revdep/checks/pareg/new/pareg.Rcheck/vign_test/pareg/vignettes/pareg_files/figure-html/unnamed-chunk-4-1.png" but not available. + The magick package is required to crop "/c4/home/henrik/repositories/future/revdep/checks/pareg/new/pareg.Rcheck/vign_test/pareg/vignettes/pareg_files/figure-html/unnamed-chunk-5-1.png" but not available. Quitting from lines 145-150 [unnamed-chunk-9] (pareg.Rmd) + Error: processing vignette 'pareg.Rmd' failed with diagnostics: + ImportError: /lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /c4/home/henrik/.cache/R/basilisk/1.14.3/pareg/1.6.0/pareg/lib/python3.9/site-packages/tensorflow/python/platform/_pywrap_cpu_feature_guard.so) + Run `reticulate::py_last_error()` for details. ... --- re-building ‘pathway_similarities.Rmd’ using rmarkdown - The magick package is required to crop "/wynton/home/cbi/hb/repositories/future/revdep/checks/pareg/new/pareg.Rcheck/vign_test/pareg/vignettes/pathway_similarities_files/figure-html/unnamed-chunk-2-1.png" but not available. - The magick package is required to crop "/wynton/home/cbi/hb/repositories/future/revdep/checks/pareg/new/pareg.Rcheck/vign_test/pareg/vignettes/pathway_similarities_files/figure-html/unnamed-chunk-3-1.png" but not available. + The magick package is required to crop "/c4/home/henrik/repositories/future/revdep/checks/pareg/new/pareg.Rcheck/vign_test/pareg/vignettes/pathway_similarities_files/figure-html/unnamed-chunk-2-1.png" but not available. + The magick package is required to crop "/c4/home/henrik/repositories/future/revdep/checks/pareg/new/pareg.Rcheck/vign_test/pareg/vignettes/pathway_similarities_files/figure-html/unnamed-chunk-3-1.png" but not available. --- finished re-building ‘pathway_similarities.Rmd’ SUMMARY: processing the following file failed: @@ -2062,17 +2970,39 @@ Run `revdep_details(, "pareg")` for more info ``` Found the following notes/warnings: Non-staged installation was used - See ‘/wynton/home/cbi/hb/repositories/future/revdep/checks/pareg/new/pareg.Rcheck/00install.out’ for details. + See ‘/c4/home/henrik/repositories/future/revdep/checks/pareg/new/pareg.Rcheck/00install.out’ for details. + ``` + +# parseRPDR + +
+ +* Version: 1.1.0 +* GitHub: https://github.com/martonkolossvary/parseRPDR +* Source code: https://github.com/cran/parseRPDR +* Date/Publication: 2024-01-09 12:10:02 UTC +* Number of recursive dependencies: 89 + +Run `revdep_details(, "parseRPDR")` for more info + +
+ +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘doParallel’ + All declared Imports should be used. ``` # partR2
-* Version: 0.9.1 +* Version: 0.9.2 * GitHub: https://github.com/mastoffel/partR2 * Source code: https://github.com/cran/partR2 -* Date/Publication: 2021-01-18 16:30:04 UTC +* Date/Publication: 2024-03-04 13:20:02 UTC * Number of recursive dependencies: 94 Run `revdep_details(, "partR2")` for more info @@ -2107,7 +3037,12 @@ Run `revdep_details(, "pavo")` for more info ``` Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available - See ‘/wynton/home/cbi/hb/repositories/future/revdep/checks/pavo/new/pavo.Rcheck/00install.out’ for details. + See ‘/c4/home/henrik/repositories/future/revdep/checks/pavo/new/pavo.Rcheck/00install.out’ for details. + ``` + +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘imager’ ``` # PCRedux @@ -2118,7 +3053,7 @@ Run `revdep_details(, "pavo")` for more info * GitHub: https://github.com/PCRuniversum/PCRedux * Source code: https://github.com/cran/PCRedux * Date/Publication: 2022-05-11 11:40:02 UTC -* Number of recursive dependencies: 155 +* Number of recursive dependencies: 153 Run `revdep_details(, "PCRedux")` for more info @@ -2126,56 +3061,27 @@ Run `revdep_details(, "PCRedux")` for more info ## In both -* checking examples ... ERROR +* checking re-building of vignette outputs ... WARNING ``` - Running examples in ‘PCRedux-Ex.R’ failed - The error most likely occurred in: + Error(s) in re-building vignettes: + ... + --- re-building ‘PCRedux.Rmd’ using rmarkdown + ! LaTeX Error: File `iftex.sty' not found. - > ### Name: encu - > ### Title: A function to calculate numerous features from amplification - > ### curve data from a quantitative PCR experiment. - > ### Aliases: encu - > ### Keywords: intercept normalization preprocessing slope - > - > ### ** Examples - ... - Loading required package: MASS - Loading required package: minpack.lm - Loading required package: rgl - Loading required package: robustbase - Loading required package: Matrix - > res_encu <- encu(testdat[, 1:3]) - Error in validObject(.Object) : - invalid class “der” object: superclass "mMatrix" not defined in the environment of the object's class - Calls: encu ... initialize -> initialize -> initMatrix -> validObject + ! Emergency stop. + + + Error: processing vignette 'PCRedux.Rmd' failed with diagnostics: + LaTeX failed to compile /c4/home/henrik/repositories/future/revdep/checks/PCRedux/new/PCRedux.Rcheck/vign_test/PCRedux/vignettes/PCRedux.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See PCRedux.log for more info. + --- failed re-building ‘PCRedux.Rmd’ + + SUMMARY: processing the following file failed: + ‘PCRedux.Rmd’ + + Error: Vignette re-building failed. Execution halted ``` -* checking tests ... - ``` - Running ‘spelling.R’ - Running ‘testthat.R’ - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 50 lines of output: - 8. ├─chipPCR::bg.max(x, y) - 9. └─chipPCR::bg.max(x, y) - 10. ├─chipPCR::inder(x, y, smooth.method = "supsmu") - 11. └─chipPCR::inder(x, y, smooth.method = "supsmu") - 12. └─methods::new("der", .Data = dat, method = smooth.method) - ... - 11. └─chipPCR::inder(x, y, smooth.method = "supsmu") - 12. └─methods::new("der", .Data = dat, method = smooth.method) - 13. ├─methods::initialize(value, ...) - 14. └─methods::initialize(value, ...) - 15. └─methods (local) initMatrix(.Object, ...) - 16. └─methods::validObject(.Object) - - [ FAIL 4 | WARN 4 | SKIP 0 | PASS 37 ] - Error: Test failures - Execution halted - ``` - # photosynthesis
@@ -2184,7 +3090,7 @@ Run `revdep_details(, "PCRedux")` for more info * GitHub: https://github.com/cdmuir/photosynthesis * Source code: https://github.com/cran/photosynthesis * Date/Publication: 2023-08-15 07:20:05 UTC -* Number of recursive dependencies: 144 +* Number of recursive dependencies: 122 Run `revdep_details(, "photosynthesis")` for more info @@ -2192,6 +3098,13 @@ Run `revdep_details(, "photosynthesis")` for more info ## In both +* checking installed package size ... NOTE + ``` + installed size is 7.1Mb + sub-directories of 1Mb or more: + doc 6.0Mb + ``` + * checking data for non-ASCII characters ... NOTE ``` Note: found 13 marked UTF-8 strings @@ -2227,11 +3140,11 @@ Run `revdep_details(, "phylolm")` for more info
-* Version: 1.0.4 +* Version: 1.2.0 * GitHub: https://github.com/pln-team/PLNmodels * Source code: https://github.com/cran/PLNmodels -* Date/Publication: 2023-08-24 15:10:02 UTC -* Number of recursive dependencies: 150 +* Date/Publication: 2024-03-05 15:50:03 UTC +* Number of recursive dependencies: 151 Run `revdep_details(, "PLNmodels")` for more info @@ -2239,22 +3152,59 @@ Run `revdep_details(, "PLNmodels")` for more info ## In both +* checking whether package ‘PLNmodels’ can be installed ... WARNING + ``` + Found the following significant warnings: + /c4/home/henrik/repositories/future/revdep/library/PLNmodels/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/PLNmodels/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/PLNmodels/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + See ‘/c4/home/henrik/repositories/future/revdep/checks/PLNmodels/new/PLNmodels.Rcheck/00install.out’ for details. + ``` + * checking installed package size ... NOTE ``` - installed size is 8.7Mb + installed size is 27.5Mb sub-directories of 1Mb or more: - libs 7.8Mb + data 1.4Mb + doc 2.0Mb + libs 22.4Mb + ``` + +# plumber + +
+ +* Version: 1.2.1 +* GitHub: https://github.com/rstudio/plumber +* Source code: https://github.com/cran/plumber +* Date/Publication: 2022-09-06 19:10:02 UTC +* Number of recursive dependencies: 104 + +Run `revdep_details(, "plumber")` for more info + +
+ +## In both + +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘arrow’ + ``` + +* checking Rd cross-references ... NOTE + ``` + Package unavailable to check Rd xrefs: ‘arrow’ ``` # portvine
-* Version: 1.0.2 +* Version: 1.0.3 * GitHub: https://github.com/EmanuelSommer/portvine * Source code: https://github.com/cran/portvine -* Date/Publication: 2023-01-06 09:40:04 UTC -* Number of recursive dependencies: 132 +* Date/Publication: 2024-01-18 16:30:02 UTC +* Number of recursive dependencies: 130 Run `revdep_details(, "portvine")` for more info @@ -2262,16 +3212,50 @@ Run `revdep_details(, "portvine")` for more info ## In both -* checking C++ specification ... NOTE +* checking installed package size ... NOTE ``` - Specified C++11: please drop specification unless essential + installed size is 52.9Mb + sub-directories of 1Mb or more: + libs 51.9Mb + ``` + +# ProFAST + +
+ +* Version: 1.4 +* GitHub: https://github.com/feiyoung/ProFAST +* Source code: https://github.com/cran/ProFAST +* Date/Publication: 2024-03-18 08:10:06 UTC +* Number of recursive dependencies: 253 + +Run `revdep_details(, "ProFAST")` for more info + +
+ +## In both + +* checking whether package ‘ProFAST’ can be installed ... WARNING + ``` + Found the following significant warnings: + /c4/home/henrik/repositories/future/revdep/library/ProFAST/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/ProFAST/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/ProFAST/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + See ‘/c4/home/henrik/repositories/future/revdep/checks/ProFAST/new/ProFAST.Rcheck/00install.out’ for details. ``` * checking installed package size ... NOTE ``` - installed size is 17.7Mb + installed size is 23.8Mb sub-directories of 1Mb or more: - libs 17.4Mb + data 2.2Mb + libs 21.1Mb + ``` + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘Rcpp’ + All declared Imports should be used. ``` # projpred @@ -2290,20 +3274,37 @@ Run `revdep_details(, "projpred")` for more info ## In both +* checking whether package ‘projpred’ can be installed ... WARNING + ``` + Found the following significant warnings: + /c4/home/henrik/repositories/future/revdep/library/projpred/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/projpred/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/projpred/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + See ‘/c4/home/henrik/repositories/future/revdep/checks/projpred/new/projpred.Rcheck/00install.out’ for details. + ``` + * checking package dependencies ... NOTE ``` Package suggested but not available for checking: ‘cmdstanr’ ``` +* checking installed package size ... NOTE + ``` + installed size is 5.9Mb + sub-directories of 1Mb or more: + doc 1.4Mb + libs 3.6Mb + ``` + # Prostar
-* Version: 1.34.3 +* Version: 1.34.6 * GitHub: https://github.com/prostarproteomics/Prostar * Source code: https://github.com/cran/Prostar -* Date/Publication: 2023-11-27 -* Number of recursive dependencies: 331 +* Date/Publication: 2024-02-15 +* Number of recursive dependencies: 332 Run `revdep_details(, "Prostar")` for more info @@ -2311,37 +3312,48 @@ Run `revdep_details(, "Prostar")` for more info ## In both -* checking re-building of vignette outputs ... ERROR +* checking whether package ‘Prostar’ can be installed ... ERROR ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘Prostar_UserManual.Rmd’ using rmarkdown - ! Undefined control sequence. - dataset\textquotesingle - {{}}\textquotesingle {{}}, - l.556 ...textquotesingle{}\textquotesingle{}, one} - imputed dataset'\,' and so... - - Error: processing vignette 'Prostar_UserManual.Rmd' failed with diagnostics: - LaTeX failed to compile /wynton/home/cbi/hb/repositories/future/revdep/checks/Prostar/new/Prostar.Rcheck/vign_test/Prostar/vignettes/Prostar_UserManual.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Prostar_UserManual.log for more info. - --- failed re-building ‘Prostar_UserManual.Rmd’ - - SUMMARY: processing the following file failed: - ‘Prostar_UserManual.Rmd’ - - Error: Vignette re-building failed. - Execution halted + Installation failed. + See ‘/c4/home/henrik/repositories/future/revdep/checks/Prostar/new/Prostar.Rcheck/00install.out’ for details. ``` -* checking dependencies in R code ... WARNING - ``` - '::' or ':::' import not declared from: ‘Biobase’ - Namespaces in Imports field not imported from: - ‘DT’ ‘R.utils’ ‘RColorBrewer’ ‘XML’ ‘colourpicker’ ‘gtools’ ‘knitr’ - ‘rclipboard’ ‘sass’ ‘shinyTree’ ‘shinyWidgets’ - All declared Imports should be used. - ``` +## Installation + +### Devel + +``` +* installing *source* package ‘Prostar’ ... +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : + there is no package called ‘ncdf4’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘Prostar’ +* removing ‘/c4/home/henrik/repositories/future/revdep/checks/Prostar/new/Prostar.Rcheck/Prostar’ + + +``` +### CRAN + +``` +* installing *source* package ‘Prostar’ ... +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : + there is no package called ‘ncdf4’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘Prostar’ +* removing ‘/c4/home/henrik/repositories/future/revdep/checks/Prostar/old/Prostar.Rcheck/Prostar’ + +``` # pseudohouseholds
@@ -2371,7 +3383,7 @@ Run `revdep_details(, "pseudohouseholds")` for more info * GitHub: https://github.com/ccagc/QDNAseq * Source code: https://github.com/cran/QDNAseq * Date/Publication: 2023-10-24 -* Number of recursive dependencies: 93 +* Number of recursive dependencies: 89 Run `revdep_details(, "QDNAseq")` for more info @@ -2379,17 +3391,39 @@ Run `revdep_details(, "QDNAseq")` for more info ## In both -* R CMD check timed out +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘QDNAseq.Rnw’ using Sweave + EM algorithm started ... + + Warning in allprior/tot : + Recycling array of length 1 in vector-array arithmetic is deprecated. + Use c() or as.vector() instead. + + Warning in allprior/tot : + Recycling array of length 1 in vector-array arithmetic is deprecated. + ... + l.196 \RequirePackage + {parnotes}^^M + ! ==> Fatal error occurred, no output PDF file produced! + --- failed re-building ‘QDNAseq.Rnw’ + + SUMMARY: processing the following file failed: + ‘QDNAseq.Rnw’ + Error: Vignette re-building failed. + Execution halted + ``` # RAINBOWR
-* Version: 0.1.33 +* Version: 0.1.35 * GitHub: NA * Source code: https://github.com/cran/RAINBOWR -* Date/Publication: 2023-09-12 05:40:02 UTC +* Date/Publication: 2024-03-03 09:12:36 UTC * Number of recursive dependencies: 167 Run `revdep_details(, "RAINBOWR")` for more info @@ -2400,77 +3434,82 @@ Run `revdep_details(, "RAINBOWR")` for more info * checking installed package size ... NOTE ``` - installed size is 11.7Mb + installed size is 45.2Mb sub-directories of 1Mb or more: - libs 10.8Mb + libs 43.9Mb ``` -# regmedint +# receptiviti
-* Version: 1.0.0 -* GitHub: https://github.com/kaz-yos/regmedint -* Source code: https://github.com/cran/regmedint -* Date/Publication: 2022-04-06 20:20:02 UTC -* Number of recursive dependencies: 155 +* Version: 0.1.7 +* GitHub: https://github.com/Receptiviti/receptiviti-r +* Source code: https://github.com/cran/receptiviti +* Date/Publication: 2024-02-23 23:50:05 UTC +* Number of recursive dependencies: 67 -Run `revdep_details(, "regmedint")` for more info +Run `revdep_details(, "receptiviti")` for more info
## In both -* checking dependencies in R code ... NOTE +* checking tests ... ``` - Namespace in Imports field not imported from: ‘Deriv’ - All declared Imports should be used. + Running ‘testthat.R’ + ERROR + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(receptiviti) + > + > test_check("receptiviti") + Status: ERROR + Message: 400 + ... + 7. └─receptiviti::receptiviti(...) + ── Failure ('test-receptiviti_status.R:5:3'): failures works ─────────────────── + receptiviti_status(...) is not NULL + + `actual` is a list + `expected` is NULL + + [ FAIL 2 | WARN 0 | SKIP 2 | PASS 6 ] + Error: Test failures + Execution halted + ``` + +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘arrow’ + ``` + +* checking Rd cross-references ... NOTE + ``` + Package unavailable to check Rd xrefs: ‘arrow’ ``` -# reproducible +# regmedint
-* Version: 2.0.10 -* GitHub: https://github.com/PredictiveEcology/reproducible -* Source code: https://github.com/cran/reproducible -* Date/Publication: 2023-11-22 04:40:02 UTC -* Number of recursive dependencies: 103 +* Version: 1.0.1 +* GitHub: https://github.com/kaz-yos/regmedint +* Source code: https://github.com/cran/regmedint +* Date/Publication: 2024-01-13 00:50:02 UTC +* Number of recursive dependencies: 154 -Run `revdep_details(, "reproducible")` for more info +Run `revdep_details(, "regmedint")` for more info
## In both -* checking tests ... - ``` - Running ‘test-all.R’ - ERROR - Running the tests in ‘tests/test-all.R’ failed. - Last 50 lines of output: - 'test-preProcessWorks.R:315:3', 'test-preProcessWorks.R:328:3', - 'test-preProcessWorks.R:348:3', 'test-preProcessWorks.R:361:3', - 'test-preProcessWorks.R:374:3', 'test-preProcessWorks.R:391:3', - 'test-preProcessWorks.R:409:3', 'test-preProcessWorks.R:438:3', - 'test-preProcessWorks.R:459:3', 'test-preProcessWorks.R:487:3', - 'test-preProcessWorks.R:543:3', 'test-preProcessWorks.R:569:3', - ... - 4. └─reproducible:::makeVal(x) - 5. ├─terra::makeValid(x) - 6. └─terra::makeValid(x) - 7. └─terra (local) .local(x, ...) - 8. └─terra:::messages(x) - 9. └─terra:::error(f, x@cpp$getError()) - - [ FAIL 2 | WARN 7 | SKIP 92 | PASS 389 ] - Error: Test failures - Execution halted - ``` - -* checking package dependencies ... NOTE +* checking dependencies in R code ... NOTE ``` - Package suggested but not available for checking: ‘qs’ + Namespace in Imports field not imported from: ‘Deriv’ + All declared Imports should be used. ``` # rgee @@ -2481,7 +3520,7 @@ Run `revdep_details(, "reproducible")` for more info * GitHub: https://github.com/r-spatial/rgee * Source code: https://github.com/cran/rgee * Date/Publication: 2023-09-27 08:30:02 UTC -* Number of recursive dependencies: 146 +* Number of recursive dependencies: 144 Run `revdep_details(, "rgee")` for more info @@ -2489,9 +3528,11 @@ Run `revdep_details(, "rgee")` for more info ## In both -* checking package dependencies ... NOTE +* checking installed package size ... NOTE ``` - Package suggested but not available for checking: ‘geojsonio’ + installed size is 8.2Mb + sub-directories of 1Mb or more: + doc 6.9Mb ``` # robotstxt @@ -2537,11 +3578,20 @@ Run `revdep_details(, "rpm")` for more info ## In both +* checking whether package ‘rpm’ can be installed ... WARNING + ``` + Found the following significant warnings: + /c4/home/henrik/repositories/future/revdep/library/rpm/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/rpm/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/rpm/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + See ‘/c4/home/henrik/repositories/future/revdep/checks/rpm/new/rpm.Rcheck/00install.out’ for details. + ``` + * checking installed package size ... NOTE ``` - installed size is 6.0Mb + installed size is 11.6Mb sub-directories of 1Mb or more: - libs 5.6Mb + libs 11.1Mb ``` # sapfluxnetr @@ -2565,6 +3615,48 @@ Run `revdep_details(, "sapfluxnetr")` for more info Note: found 4 marked UTF-8 strings ``` +# SCArray.sat + +
+ +* Version: 1.2.1 +* GitHub: https://github.com/AbbVie-ComputationalGenomics/SCArray +* Source code: https://github.com/cran/SCArray.sat +* Date/Publication: 2024-01-16 +* Number of recursive dependencies: 181 + +Run `revdep_details(, "SCArray.sat")` for more info + +
+ +## In both + +* checking S3 generic/method consistency ... WARNING + ``` + SetAssayData: + function(object, layer, new.data, slot, ...) + SetAssayData.SCArrayAssay: + function(object, slot, new.data, ...) + + CreateSeuratObject: + function(counts, assay, names.field, names.delim, meta.data, project, + ...) + CreateSeuratObject.DelayedMatrix: + function(counts, project, assay, names.field, names.delim, meta.data, + min.cells, min.features, row.names, ...) + See section ‘Generic functions and methods’ in the ‘Writing R + Extensions’ manual. + ``` + +* checking dependencies in R code ... NOTE + ``` + Unexported objects imported by ':::' calls: + ‘Seurat:::DEmethods_counts’ ‘Seurat:::DEmethods_nocorrect’ + ‘Seurat:::FastExpMean’ ‘Seurat:::FastLogVMR’ ‘Seurat:::NBResiduals’ + ‘Seurat:::UpdateKey’ ‘Seurat:::ValidateDataForMerge’ + See the note in ?`:::` about the use of this operator. + ``` + # sctransform
@@ -2581,6 +3673,15 @@ Run `revdep_details(, "sctransform")` for more info ## In both +* checking whether package ‘sctransform’ can be installed ... WARNING + ``` + Found the following significant warnings: + /c4/home/henrik/repositories/future/revdep/library/sctransform/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/sctransform/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/sctransform/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + See ‘/c4/home/henrik/repositories/future/revdep/checks/sctransform/new/sctransform.Rcheck/00install.out’ for details. + ``` + * checking package dependencies ... NOTE ``` Package which this enhances but not available for checking: ‘glmGamPoi’ @@ -2594,7 +3695,7 @@ Run `revdep_details(, "sctransform")` for more info * GitHub: https://github.com/Abson-dev/sdmApp * Source code: https://github.com/cran/sdmApp * Date/Publication: 2021-07-07 08:30:02 UTC -* Number of recursive dependencies: 177 +* Number of recursive dependencies: 176 Run `revdep_details(, "sdmApp")` for more info @@ -2602,11 +3703,6 @@ Run `revdep_details(, "sdmApp")` for more info ## In both -* checking package dependencies ... NOTE - ``` - Packages suggested but not available for checking: 'rgdal', 'rgeos' - ``` - * checking dependencies in R code ... NOTE ``` Namespace in Imports field not imported from: ‘sp’ @@ -2617,11 +3713,11 @@ Run `revdep_details(, "sdmApp")` for more info
-* Version: 0.4.1 +* Version: 0.4.3 * GitHub: https://github.com/pbs-assess/sdmTMB * Source code: https://github.com/cran/sdmTMB -* Date/Publication: 2023-11-03 07:20:02 UTC -* Number of recursive dependencies: 117 +* Date/Publication: 2024-02-29 01:40:02 UTC +* Number of recursive dependencies: 116 Run `revdep_details(, "sdmTMB")` for more info @@ -2629,11 +3725,36 @@ Run `revdep_details(, "sdmTMB")` for more info ## In both +* checking tests ... + ``` + Running ‘testthat.R’ + ERROR + Running the tests in ‘tests/testthat.R’ failed. + Last 50 lines of output: + 'test-deprecated-args.R:2:3', 'test-deprecated-args.R:67:3', + 'test-dharma.R:3:3', 'test-extra-optimization.R:2:3', + 'test-extra-time.R:3:3', 'test-extra-time.R:42:3', 'test-extra-time.R:116:3', + 'test-factor-levels.R:2:3', 'test-factor-levels.R:37:3', + 'test-factor-levels.R:91:3', 'test-forecasting.R:2:3', 'test-index.R:3:3', + 'test-link-prediction.R:5:3', 'test-link-prediction.R:67:3', + ... + [6] -0.37427778 - -0.37427783 [6] + [7] -0.01713492 - -0.01713497 [7] + [8] 0.14953175 - 0.14953169 [8] + [9] -0.51713492 - -0.51713497 [9] + [10] 0.08286508 - 0.08286503 [10] + ... ... ... and 290 more ... + + [ FAIL 1 | WARN 0 | SKIP 146 | PASS 151 ] + Error: Test failures + Execution halted + ``` + * checking installed package size ... NOTE ``` - installed size is 31.4Mb + installed size is 105.4Mb sub-directories of 1Mb or more: - libs 30.9Mb + libs 103.7Mb ``` # sentopics @@ -2652,6 +3773,23 @@ Run `revdep_details(, "sentopics")` for more info ## In both +* checking whether package ‘sentopics’ can be installed ... WARNING + ``` + Found the following significant warnings: + /c4/home/henrik/repositories/future/revdep/library/sentopics/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/sentopics/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/sentopics/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + See ‘/c4/home/henrik/repositories/future/revdep/checks/sentopics/new/sentopics.Rcheck/00install.out’ for details. + ``` + +* checking installed package size ... NOTE + ``` + installed size is 8.1Mb + sub-directories of 1Mb or more: + data 1.2Mb + libs 6.2Mb + ``` + * checking Rd cross-references ... NOTE ``` Package unavailable to check Rd xrefs: ‘lexicon’ @@ -2666,11 +3804,11 @@ Run `revdep_details(, "sentopics")` for more info
-* Version: 5.0.1 +* Version: 5.0.3 * GitHub: https://github.com/satijalab/seurat * Source code: https://github.com/cran/Seurat -* Date/Publication: 2023-11-17 23:10:06 UTC -* Number of recursive dependencies: 264 +* Date/Publication: 2024-03-18 23:40:02 UTC +* Number of recursive dependencies: 267 Run `revdep_details(, "Seurat")` for more info @@ -2685,10 +3823,10 @@ Run `revdep_details(, "Seurat")` for more info * checking installed package size ... NOTE ``` - installed size is 6.8Mb + installed size is 16.0Mb sub-directories of 1Mb or more: - R 1.6Mb - libs 5.0Mb + R 1.7Mb + libs 13.5Mb ``` * checking Rd cross-references ... NOTE @@ -2704,7 +3842,7 @@ Run `revdep_details(, "Seurat")` for more info * GitHub: https://github.com/mojaveazure/seurat-object * Source code: https://github.com/cran/SeuratObject * Date/Publication: 2023-11-17 22:40:16 UTC -* Number of recursive dependencies: 105 +* Number of recursive dependencies: 103 Run `revdep_details(, "SeuratObject")` for more info @@ -2719,11 +3857,69 @@ Run `revdep_details(, "SeuratObject")` for more info Package which this enhances but not available for checking: ‘Seurat’ ``` +* checking installed package size ... NOTE + ``` + installed size is 5.4Mb + sub-directories of 1Mb or more: + R 1.5Mb + libs 3.2Mb + ``` + * checking Rd cross-references ... NOTE ``` Package unavailable to check Rd xrefs: ‘plotly’ ``` +# sharp + +
+ +* Version: 1.4.6 +* GitHub: https://github.com/barbarabodinier/sharp +* Source code: https://github.com/cran/sharp +* Date/Publication: 2024-02-03 17:30:02 UTC +* Number of recursive dependencies: 157 + +Run `revdep_details(, "sharp")` for more info + +
+ +## In both + +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘rCOSA’ + ``` + +* checking Rd cross-references ... NOTE + ``` + Package unavailable to check Rd xrefs: ‘rCOSA’ + ``` + +# shiny + +
+ +* Version: 1.8.0 +* GitHub: https://github.com/rstudio/shiny +* Source code: https://github.com/cran/shiny +* Date/Publication: 2023-11-17 23:40:02 UTC +* Number of recursive dependencies: 90 + +Run `revdep_details(, "shiny")` for more info + +
+ +## In both + +* checking installed package size ... NOTE + ``` + installed size is 11.4Mb + sub-directories of 1Mb or more: + R 1.4Mb + www 8.9Mb + ``` + # shiny.worker
@@ -2752,6 +3948,30 @@ Run `revdep_details(, "shiny.worker")` for more info 'LazyData' is specified without a 'data' directory ``` +# sigminer + +
+ +* Version: 2.3.0 +* GitHub: https://github.com/ShixiangWang/sigminer +* Source code: https://github.com/cran/sigminer +* Date/Publication: 2023-12-12 11:50:03 UTC +* Number of recursive dependencies: 205 + +Run `revdep_details(, "sigminer")` for more info + +
+ +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.9Mb + sub-directories of 1Mb or more: + help 1.7Mb + libs 1.4Mb + ``` + # Signac
@@ -2760,7 +3980,7 @@ Run `revdep_details(, "shiny.worker")` for more info * GitHub: https://github.com/stuart-lab/signac * Source code: https://github.com/cran/Signac * Date/Publication: 2023-11-08 09:30:02 UTC -* Number of recursive dependencies: 251 +* Number of recursive dependencies: 254 Run `revdep_details(, "Signac")` for more info @@ -2768,14 +3988,12 @@ Run `revdep_details(, "Signac")` for more info ## In both -* checking package dependencies ... NOTE - ``` - Packages suggested but not available for checking: 'ggseqlogo', 'qlcMatrix' - ``` - -* checking Rd cross-references ... NOTE +* checking installed package size ... NOTE ``` - Unknown package ‘ggseqlogo’ in Rd xrefs + installed size is 5.1Mb + sub-directories of 1Mb or more: + R 1.1Mb + libs 2.9Mb ``` # signeR @@ -2794,11 +4012,28 @@ Run `revdep_details(, "signeR")` for more info ## In both +* checking whether package ‘signeR’ can be installed ... WARNING + ``` + Found the following significant warnings: + /c4/home/henrik/repositories/future/revdep/library/signeR/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/signeR/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/signeR/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + See ‘/c4/home/henrik/repositories/future/revdep/checks/signeR/new/signeR.Rcheck/00install.out’ for details. + ``` + * checking C++ specification ... NOTE ``` Specified C++11: please drop specification unless essential ``` +* checking installed package size ... NOTE + ``` + installed size is 6.6Mb + sub-directories of 1Mb or more: + R 1.2Mb + doc 4.5Mb + ``` + * checking R code for possible problems ... NOTE ``` covariate: no visible binding for global variable ‘.’ @@ -2839,10 +4074,32 @@ Run `revdep_details(, "signeR")` for more info prepare_Rd: tcga_tumors.Rd:27-28: Dropping empty section \examples ``` -* checking for non-standard things in the check directory ... NOTE +# SimDesign + +
+ +* Version: 2.14 +* GitHub: https://github.com/philchalmers/SimDesign +* Source code: https://github.com/cran/SimDesign +* Date/Publication: 2024-01-09 09:10:11 UTC +* Number of recursive dependencies: 124 + +Run `revdep_details(, "SimDesign")` for more info + +
+ +## In both + +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘doMPI’ + ``` + +* checking installed package size ... NOTE ``` - Found the following files/directories: - ‘tmp.pdf’ + installed size is 5.8Mb + sub-directories of 1Mb or more: + doc 5.2Mb ``` # sits @@ -2861,22 +4118,32 @@ Run `revdep_details(, "sits")` for more info ## In both +* checking whether package ‘sits’ can be installed ... WARNING + ``` + Found the following significant warnings: + /c4/home/henrik/repositories/future/revdep/library/sits/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/sits/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/sits/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + See ‘/c4/home/henrik/repositories/future/revdep/checks/sits/new/sits.Rcheck/00install.out’ for details. + ``` + * checking installed package size ... NOTE ``` - installed size is 5.9Mb + installed size is 13.2Mb sub-directories of 1Mb or more: - R 1.1Mb - libs 4.6Mb + R 1.1Mb + extdata 1.5Mb + libs 9.9Mb ``` # skpr
-* Version: 1.6.1 +* Version: 1.6.2 * GitHub: https://github.com/tylermorganwall/skpr * Source code: https://github.com/cran/skpr -* Date/Publication: 2023-12-07 16:50:02 UTC +* Date/Publication: 2024-02-06 19:50:02 UTC * Number of recursive dependencies: 149 Run `revdep_details(, "skpr")` for more info @@ -2887,20 +4154,20 @@ Run `revdep_details(, "skpr")` for more info * checking installed package size ... NOTE ``` - installed size is 20.8Mb + installed size is 63.3Mb sub-directories of 1Mb or more: - libs 20.3Mb + libs 62.8Mb ``` # SmCCNet
-* Version: 2.0.1 +* Version: 2.0.2 * GitHub: https://github.com/KechrisLab/SmCCNet * Source code: https://github.com/cran/SmCCNet -* Date/Publication: 2023-10-03 21:50:16 UTC -* Number of recursive dependencies: 163 +* Date/Publication: 2024-01-13 21:50:17 UTC +* Number of recursive dependencies: 162 Run `revdep_details(, "SmCCNet")` for more info @@ -2908,21 +4175,21 @@ Run `revdep_details(, "SmCCNet")` for more info ## In both -* checking re-building of vignette outputs ... WARNING +* checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: --- re-building ‘SmCCNet_Vignette_AutoSmCCNet.Rmd’ using rmarkdown - ! LaTeX Error: File `ucharcat.sty' not found. - - ! Emergency stop. - + ! kpathsea: Running mktexfmt xelatex.fmt Error: processing vignette 'SmCCNet_Vignette_AutoSmCCNet.Rmd' failed with diagnostics: - LaTeX failed to compile /wynton/home/cbi/hb/repositories/future/revdep/checks/SmCCNet/new/SmCCNet.Rcheck/vign_test/SmCCNet/vignettes/SmCCNet_Vignette_AutoSmCCNet.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See SmCCNet_Vignette_AutoSmCCNet.log for more info. + LaTeX failed to compile /c4/home/henrik/repositories/future/revdep/checks/SmCCNet/new/SmCCNet.Rcheck/vign_test/SmCCNet/vignettes/SmCCNet_Vignette_AutoSmCCNet.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See SmCCNet_Vignette_AutoSmCCNet.log for more info. --- failed re-building ‘SmCCNet_Vignette_AutoSmCCNet.Rmd’ + + --- re-building ‘SmCCNet_Vignette_MultiOmics.Rmd’ using rmarkdown + ! kpathsea: Running mktexfmt xelatex.fmt ... Error: processing vignette 'SmCCNet_Vignette_SingleOmics.Rmd' failed with diagnostics: - LaTeX failed to compile /wynton/home/cbi/hb/repositories/future/revdep/checks/SmCCNet/new/SmCCNet.Rcheck/vign_test/SmCCNet/vignettes/SmCCNet_Vignette_SingleOmics.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See SmCCNet_Vignette_SingleOmics.log for more info. + LaTeX failed to compile /c4/home/henrik/repositories/future/revdep/checks/SmCCNet/new/SmCCNet.Rcheck/vign_test/SmCCNet/vignettes/SmCCNet_Vignette_SingleOmics.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See SmCCNet_Vignette_SingleOmics.log for more info. --- failed re-building ‘SmCCNet_Vignette_SingleOmics.Rmd’ SUMMARY: processing the following files failed: @@ -2933,6 +4200,31 @@ Run `revdep_details(, "SmCCNet")` for more info Execution halted ``` +# smoots + +
+ +* Version: 1.1.4 +* GitHub: NA +* Source code: https://github.com/cran/smoots +* Date/Publication: 2023-09-11 08:50:02 UTC +* Number of recursive dependencies: 76 + +Run `revdep_details(, "smoots")` for more info + +
+ +## In both + +* checking whether package ‘smoots’ can be installed ... WARNING + ``` + Found the following significant warnings: + /c4/home/henrik/repositories/future/revdep/library/smoots/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/smoots/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/smoots/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + See ‘/c4/home/henrik/repositories/future/revdep/checks/smoots/new/smoots.Rcheck/00install.out’ for details. + ``` + # solitude
@@ -2964,7 +4256,7 @@ Run `revdep_details(, "solitude")` for more info * GitHub: https://github.com/PredictiveEcology/SpaDES.core * Source code: https://github.com/cran/SpaDES.core * Date/Publication: 2023-11-10 10:20:02 UTC -* Number of recursive dependencies: 139 +* Number of recursive dependencies: 137 Run `revdep_details(, "SpaDES.core")` for more info @@ -2972,14 +4264,16 @@ Run `revdep_details(, "SpaDES.core")` for more info ## In both -* checking package dependencies ... ERROR +* checking package dependencies ... NOTE ``` - Package required but not available: ‘qs’ - Package suggested but not available for checking: ‘NLMR’ - - See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ - manual. + ``` + +* checking installed package size ... NOTE + ``` + installed size is 6.2Mb + sub-directories of 1Mb or more: + R 4.7Mb ``` # spaMM @@ -3000,8 +4294,7 @@ Run `revdep_details(, "spaMM")` for more info * checking package dependencies ... NOTE ``` - Packages suggested but not available for checking: - 'IsoriX', 'ROI.plugin.glpk' + Packages suggested but not available for checking: 'Infusion', 'blackbox' Packages which this enhances but not available for checking: 'multcomp', 'RLRsim', 'lmerTest' @@ -3009,20 +4302,20 @@ Run `revdep_details(, "spaMM")` for more info * checking installed package size ... NOTE ``` - installed size is 21.3Mb + installed size is 56.9Mb sub-directories of 1Mb or more: - R 2.6Mb - libs 18.2Mb + R 2.7Mb + libs 52.9Mb ``` # sparrpowR
-* Version: 0.2.7 +* Version: 0.2.8 * GitHub: https://github.com/machiela-lab/sparrpowR * Source code: https://github.com/cran/sparrpowR -* Date/Publication: 2023-02-02 01:00:02 UTC +* Date/Publication: 2024-01-23 15:20:02 UTC * Number of recursive dependencies: 130 Run `revdep_details(, "sparrpowR")` for more info @@ -3035,7 +4328,7 @@ Run `revdep_details(, "sparrpowR")` for more info ``` Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available - See ‘/wynton/home/cbi/hb/repositories/future/revdep/checks/sparrpowR/new/sparrpowR.Rcheck/00install.out’ for details. + See ‘/c4/home/henrik/repositories/future/revdep/checks/sparrpowR/new/sparrpowR.Rcheck/00install.out’ for details. ``` # SPARSEMODr @@ -3077,6 +4370,15 @@ Run `revdep_details(, "spatialwarnings")` for more info ## In both +* checking whether package ‘spatialwarnings’ can be installed ... WARNING + ``` + Found the following significant warnings: + /c4/home/henrik/repositories/future/revdep/library/spatialwarnings/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/spatialwarnings/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/spatialwarnings/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + See ‘/c4/home/henrik/repositories/future/revdep/checks/spatialwarnings/new/spatialwarnings.Rcheck/00install.out’ for details. + ``` + * checking Rd cross-references ... WARNING ``` Missing link or links in documentation object 'indictest.Rd': @@ -3085,6 +4387,13 @@ Run `revdep_details(, "spatialwarnings")` for more info See section 'Cross-references' in the 'Writing R Extensions' manual. ``` +* checking installed package size ... NOTE + ``` + installed size is 7.0Mb + sub-directories of 1Mb or more: + libs 6.0Mb + ``` + # sphunif
@@ -3093,7 +4402,7 @@ Run `revdep_details(, "spatialwarnings")` for more info * GitHub: https://github.com/egarpor/sphunif * Source code: https://github.com/cran/sphunif * Date/Publication: 2023-12-04 19:50:02 UTC -* Number of recursive dependencies: 79 +* Number of recursive dependencies: 77 Run `revdep_details(, "sphunif")` for more info @@ -3101,11 +4410,20 @@ Run `revdep_details(, "sphunif")` for more info ## In both +* checking whether package ‘sphunif’ can be installed ... WARNING + ``` + Found the following significant warnings: + /c4/home/henrik/repositories/future/revdep/library/sphunif/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/sphunif/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/sphunif/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + See ‘/c4/home/henrik/repositories/future/revdep/checks/sphunif/new/sphunif.Rcheck/00install.out’ for details. + ``` + * checking installed package size ... NOTE ``` - installed size is 10.1Mb + installed size is 24.7Mb sub-directories of 1Mb or more: - libs 9.8Mb + libs 23.7Mb ``` * checking data for non-ASCII characters ... NOTE @@ -3121,7 +4439,7 @@ Run `revdep_details(, "sphunif")` for more info * GitHub: https://github.com/JeremyGelb/spNetwork * Source code: https://github.com/cran/spNetwork * Date/Publication: 2023-08-24 11:20:05 UTC -* Number of recursive dependencies: 149 +* Number of recursive dependencies: 146 Run `revdep_details(, "spNetwork")` for more info @@ -3129,80 +4447,250 @@ Run `revdep_details(, "spNetwork")` for more info ## In both +* checking whether package ‘spNetwork’ can be installed ... WARNING + ``` + Found the following significant warnings: + /c4/home/henrik/repositories/future/revdep/library/spNetwork/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/spNetwork/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/spNetwork/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + See ‘/c4/home/henrik/repositories/future/revdep/checks/spNetwork/new/spNetwork.Rcheck/00install.out’ for details. + ``` + * checking installed package size ... NOTE ``` - installed size is 9.2Mb + installed size is 25.5Mb sub-directories of 1Mb or more: - libs 8.8Mb + doc 1.0Mb + extdata 2.6Mb + libs 20.5Mb ``` # squat
-* Version: 0.2.1 +* Version: 0.3.0 * GitHub: https://github.com/LMJL-Alea/squat * Source code: https://github.com/cran/squat -* Date/Publication: 2023-07-09 09:10:05 UTC -* Number of recursive dependencies: 133 +* Date/Publication: 2024-01-10 15:40:02 UTC +* Number of recursive dependencies: 143 + +Run `revdep_details(, "squat")` for more info + +
+ +## In both + +* checking whether package ‘squat’ can be installed ... WARNING + ``` + Found the following significant warnings: + /c4/home/henrik/repositories/future/revdep/library/squat/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/squat/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/squat/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + See ‘/c4/home/henrik/repositories/future/revdep/checks/squat/new/squat.Rcheck/00install.out’ for details. + ``` + +* checking installed package size ... NOTE + ``` + installed size is 20.4Mb + sub-directories of 1Mb or more: + data 1.1Mb + help 1.1Mb + libs 18.0Mb + ``` + +# ssdtools + +
+ +* Version: 1.0.6 +* GitHub: https://github.com/bcgov/ssdtools +* Source code: https://github.com/cran/ssdtools +* Date/Publication: 2023-09-07 14:10:02 UTC +* Number of recursive dependencies: 120 + +Run `revdep_details(, "ssdtools")` for more info + +
+ +## In both + +* checking installed package size ... NOTE + ``` + installed size is 42.1Mb + sub-directories of 1Mb or more: + doc 1.2Mb + libs 39.6Mb + ``` + +# stars + +
+ +* Version: 0.6-4 +* GitHub: https://github.com/r-spatial/stars +* Source code: https://github.com/cran/stars +* Date/Publication: 2023-09-11 11:50:02 UTC +* Number of recursive dependencies: 164 + +Run `revdep_details(, "stars")` for more info + +
+ +## Newly broken + +* checking examples ...sh: line 1: 76201 Aborted (core dumped) LANGUAGE=en _R_CHECK_INTERNALS2_=1 '/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/bin/R' --vanilla --encoding=UTF-8 > 'stars-Ex.Rout' 2>&1 < 'stars-Ex.R' + ``` + ERROR + Running examples in ‘stars-Ex.R’ failed + The error most likely occurred in: + + > ### Name: mdim + > ### Title: Read or write data using GDAL's multidimensional array API + > ### Aliases: mdim read_mdim write_mdim + > + > ### ** Examples + > + ... + dmalloc: no + Packages w/ extra debug output: none + API tracing: no + Using memory checker: no + Memory allocation sanity checks: no + Function stack tracing: no + Use file locking: best-effort + Strict file format checks: no + Optimization instrumentation: no + Bye... + ``` + +## Newly fixed + +* checking examples ...sh: line 1: 76251 Aborted (core dumped) LANGUAGE=en _R_CHECK_INTERNALS2_=1 '/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/bin/R' --vanilla --encoding=UTF-8 > 'stars-Ex.Rout' 2>&1 < 'stars-Ex.R' + ``` + ERROR + Running examples in ‘stars-Ex.R’ failed + The error most likely occurred in: + + > ### Name: mdim + > ### Title: Read or write data using GDAL's multidimensional array API + > ### Aliases: mdim read_mdim write_mdim + > + > ### ** Examples + > + ... + dmalloc: no + Packages w/ extra debug output: none + API tracing: no + Using memory checker: no + Memory allocation sanity checks: no + Function stack tracing: no + Use file locking: best-effort + Strict file format checks: no + Optimization instrumentation: no + Bye... + ``` -Run `revdep_details(, "squat")` for more info +## In both -
+* checking tests ... + ``` + Running ‘aggregate.R’ + Comparing ‘aggregate.Rout’ to ‘aggregate.Rout.save’ ...4c4 + < Linking to GEOS 3.11.2, GDAL 3.6.4, PROJ 8.2.1; sf_use_s2() is TRUE + --- + > Linking to GEOS 3.11.2, GDAL 3.6.2, PROJ 9.2.0; sf_use_s2() is TRUE + Running ‘align.R’ + Comparing ‘align.Rout’ to ‘align.Rout.save’ ... OK + Running ‘area.R’ + Comparing ‘area.Rout’ to ‘area.Rout.save’ ... OK + Running ‘crop.R’ + ... + dmalloc: no + Packages w/ extra debug output: none + API tracing: no + Using memory checker: no + Memory allocation sanity checks: no + Function stack tracing: no + Use file locking: best-effort + Strict file format checks: no + Optimization instrumentation: no + Bye... + ``` -## In both +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘starsdata’ + ``` * checking installed package size ... NOTE ``` - installed size is 6.2Mb + installed size is 6.1Mb sub-directories of 1Mb or more: - libs 6.1Mb + doc 2.4Mb + nc 1.7Mb ``` -# ssdtools +# startR
-* Version: 1.0.6 -* GitHub: https://github.com/bcgov/ssdtools -* Source code: https://github.com/cran/ssdtools -* Date/Publication: 2023-09-07 14:10:02 UTC -* Number of recursive dependencies: 120 +* Version: 2.3.1 +* GitHub: NA +* Source code: https://github.com/cran/startR +* Date/Publication: 2023-12-21 16:20:02 UTC +* Number of recursive dependencies: 60 -Run `revdep_details(, "ssdtools")` for more info +Run `revdep_details(, "startR")` for more info
## In both -* checking installed package size ... NOTE +* checking whether package ‘startR’ can be installed ... ERROR ``` - installed size is 10.3Mb - sub-directories of 1Mb or more: - libs 10.0Mb + Installation failed. + See ‘/c4/home/henrik/repositories/future/revdep/checks/startR/new/startR.Rcheck/00install.out’ for details. ``` -# stars +## Installation -
+### Devel -* Version: 0.6-4 -* GitHub: https://github.com/r-spatial/stars -* Source code: https://github.com/cran/stars -* Date/Publication: 2023-09-11 11:50:02 UTC -* Number of recursive dependencies: 163 +``` +* installing *source* package ‘startR’ ... +** package ‘startR’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : + there is no package called ‘ncdf4’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘startR’ +* removing ‘/c4/home/henrik/repositories/future/revdep/checks/startR/new/startR.Rcheck/startR’ -Run `revdep_details(, "stars")` for more info -
+``` +### CRAN -## In both +``` +* installing *source* package ‘startR’ ... +** package ‘startR’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : + there is no package called ‘ncdf4’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘startR’ +* removing ‘/c4/home/henrik/repositories/future/revdep/checks/startR/old/startR.Rcheck/startR’ -* checking package dependencies ... NOTE - ``` - Packages suggested but not available for checking: 'ncdfgeom', 'starsdata' - ``` +``` # stppSim
@@ -3211,7 +4699,7 @@ Run `revdep_details(, "stars")` for more info * GitHub: https://github.com/Manalytics/stppSim * Source code: https://github.com/cran/stppSim * Date/Publication: 2023-10-29 21:20:02 UTC -* Number of recursive dependencies: 134 +* Number of recursive dependencies: 133 Run `revdep_details(, "stppSim")` for more info @@ -3223,17 +4711,52 @@ Run `revdep_details(, "stppSim")` for more info ``` Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available - See ‘/wynton/home/cbi/hb/repositories/future/revdep/checks/stppSim/new/stppSim.Rcheck/00install.out’ for details. + See ‘/c4/home/henrik/repositories/future/revdep/checks/stppSim/new/stppSim.Rcheck/00install.out’ for details. + ``` + +# survstan + +
+ +* Version: 0.0.7 +* GitHub: https://github.com/fndemarqui/survstan +* Source code: https://github.com/cran/survstan +* Date/Publication: 2024-03-20 23:00:02 UTC +* Number of recursive dependencies: 127 + +Run `revdep_details(, "survstan")` for more info + +
+ +## In both + +* checking installed package size ... NOTE + ``` + installed size is 90.6Mb + sub-directories of 1Mb or more: + libs 90.1Mb + ``` + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘RcppParallel’ ‘rstantools’ + All declared Imports should be used. + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. ``` # synergyfinder
-* Version: 3.10.0 +* Version: 3.10.3 * GitHub: NA * Source code: https://github.com/cran/synergyfinder -* Date/Publication: 2023-10-24 +* Date/Publication: 2024-01-22 * Number of recursive dependencies: 202 Run `revdep_details(, "synergyfinder")` for more info @@ -3250,6 +4773,13 @@ Run `revdep_details(, "synergyfinder")` for more info All declared Imports should be used. ``` +* checking installed package size ... NOTE + ``` + installed size is 6.0Mb + sub-directories of 1Mb or more: + doc 5.7Mb + ``` + * checking R code for possible problems ... NOTE ``` .Extract2DrugPlotData: no visible binding for global variable @@ -3263,14 +4793,14 @@ Run `revdep_details(, "synergyfinder")` for more info .Extract2DrugPlotData: no visible binding for global variable ‘conc2’ .Extract2DrugPlotData: no visible binding for global variable ‘text’ ... - response_mean response_origin response_origin_CI95 + response_CI95 response_mean response_origin response_origin_CI95 response_origin_mean response_origin_sd response_origin_sem response_sd response_sem right start synergy t.test text theta value x y Consider adding importFrom("grDevices", "dev.list", "dev.off") importFrom("graphics", "text") - importFrom("stats", "end", "start", "t.test") + importFrom("stats", "end", "predict", "start", "t.test") importFrom("utils", "data", "head") to your NAMESPACE file. ``` @@ -3305,11 +4835,11 @@ Run `revdep_details(, "tableschema.r")` for more info
-* Version: 0.4 +* Version: 0.5 * GitHub: https://github.com/kkholst/targeted * Source code: https://github.com/cran/targeted -* Date/Publication: 2023-12-19 22:50:02 UTC -* Number of recursive dependencies: 100 +* Date/Publication: 2024-02-22 10:00:21 UTC +* Number of recursive dependencies: 98 Run `revdep_details(, "targeted")` for more info @@ -3317,21 +4847,31 @@ Run `revdep_details(, "targeted")` for more info ## In both +* checking whether package ‘targeted’ can be installed ... WARNING + ``` + Found the following significant warnings: + /c4/home/henrik/repositories/future/revdep/library/targeted/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/targeted/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/targeted/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + See ‘/c4/home/henrik/repositories/future/revdep/checks/targeted/new/targeted.Rcheck/00install.out’ for details. + ``` + * checking installed package size ... NOTE ``` - installed size is 9.6Mb + installed size is 22.4Mb sub-directories of 1Mb or more: - libs 9.3Mb + doc 1.1Mb + libs 20.9Mb ``` # targets
-* Version: 1.4.0 +* Version: 1.6.0 * GitHub: https://github.com/ropensci/targets * Source code: https://github.com/cran/targets -* Date/Publication: 2023-12-11 17:00:02 UTC +* Date/Publication: 2024-03-13 16:30:02 UTC * Number of recursive dependencies: 166 Run `revdep_details(, "targets")` for more info @@ -3342,18 +4882,18 @@ Run `revdep_details(, "targets")` for more info * checking package dependencies ... NOTE ``` - Package suggested but not available for checking: ‘qs’ + Package suggested but not available for checking: ‘clustermq’ ``` # text
-* Version: 1.0 +* Version: 1.2.0 * GitHub: https://github.com/OscarKjell/text * Source code: https://github.com/cran/text -* Date/Publication: 2023-08-09 16:40:05 UTC -* Number of recursive dependencies: 155 +* Date/Publication: 2024-02-13 20:51:36 UTC +* Number of recursive dependencies: 161 Run `revdep_details(, "text")` for more info @@ -3366,6 +4906,119 @@ Run `revdep_details(, "text")` for more info Note: found 3 marked UTF-8 strings ``` +# tglkmeans + +
+ +* Version: 0.5.4 +* GitHub: https://github.com/tanaylab/tglkmeans +* Source code: https://github.com/cran/tglkmeans +* Date/Publication: 2024-01-09 14:10:02 UTC +* Number of recursive dependencies: 89 + +Run `revdep_details(, "tglkmeans")` for more info + +
+ +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.2Mb + sub-directories of 1Mb or more: + libs 5.0Mb + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# TKCat + +
+ +* Version: 1.0.7 +* GitHub: https://github.com/patzaw/TKCat +* Source code: https://github.com/cran/TKCat +* Date/Publication: 2023-02-16 14:50:03 UTC +* Number of recursive dependencies: 115 + +Run `revdep_details(, "TKCat")` for more info + +
+ +## In both + +* checking whether package ‘TKCat’ can be installed ... ERROR + ``` + Installation failed. + See ‘/c4/home/henrik/repositories/future/revdep/checks/TKCat/new/TKCat.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘TKCat’ ... +** package ‘TKCat’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : + there is no package called ‘arrow’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘TKCat’ +* removing ‘/c4/home/henrik/repositories/future/revdep/checks/TKCat/new/TKCat.Rcheck/TKCat’ + + +``` +### CRAN + +``` +* installing *source* package ‘TKCat’ ... +** package ‘TKCat’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : + there is no package called ‘arrow’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘TKCat’ +* removing ‘/c4/home/henrik/repositories/future/revdep/checks/TKCat/old/TKCat.Rcheck/TKCat’ + + +``` +# TreeSearch + +
+ +* Version: 1.4.0 +* GitHub: https://github.com/ms609/TreeSearch +* Source code: https://github.com/cran/TreeSearch +* Date/Publication: 2023-08-26 04:50:02 UTC +* Number of recursive dependencies: 126 + +Run `revdep_details(, "TreeSearch")` for more info + +
+ +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.9Mb + sub-directories of 1Mb or more: + datasets 1.6Mb + doc 1.2Mb + libs 2.5Mb + ``` + # TriDimRegression
@@ -3385,7 +5038,7 @@ Run `revdep_details(, "TriDimRegression")` for more info * checking whether package ‘TriDimRegression’ can be installed ... ERROR ``` Installation failed. - See ‘/wynton/home/cbi/hb/repositories/future/revdep/checks/TriDimRegression/new/TriDimRegression.Rcheck/00install.out’ for details. + See ‘/c4/home/henrik/repositories/future/revdep/checks/TriDimRegression/new/TriDimRegression.Rcheck/00install.out’ for details. ``` ## Installation @@ -3400,7 +5053,7 @@ Error in loadNamespace(x) : there is no package called ‘rstantools’ Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted ERROR: configuration failed for package ‘TriDimRegression’ -* removing ‘/wynton/home/cbi/hb/repositories/future/revdep/checks/TriDimRegression/new/TriDimRegression.Rcheck/TriDimRegression’ +* removing ‘/c4/home/henrik/repositories/future/revdep/checks/TriDimRegression/new/TriDimRegression.Rcheck/TriDimRegression’ ``` @@ -3414,10 +5067,58 @@ Error in loadNamespace(x) : there is no package called ‘rstantools’ Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted ERROR: configuration failed for package ‘TriDimRegression’ -* removing ‘/wynton/home/cbi/hb/repositories/future/revdep/checks/TriDimRegression/old/TriDimRegression.Rcheck/TriDimRegression’ +* removing ‘/c4/home/henrik/repositories/future/revdep/checks/TriDimRegression/old/TriDimRegression.Rcheck/TriDimRegression’ ``` +# tsdistributions + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/tsmodels/tsdistributions +* Source code: https://github.com/cran/tsdistributions +* Date/Publication: 2024-03-17 09:10:05 UTC +* Number of recursive dependencies: 72 + +Run `revdep_details(, "tsdistributions")` for more info + +
+ +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘estimation_demo.Rmd’ using rmarkdown + --- finished re-building ‘estimation_demo.Rmd’ + + --- re-building ‘location_scale_distributions.Rmd’ using rmarkdown + ! LaTeX Error: File `iftex.sty' not found. + + ! Emergency stop. + + ... + --- failed re-building ‘location_scale_distributions.Rmd’ + + --- re-building ‘profile_demo.Rmd’ using rmarkdown + --- finished re-building ‘profile_demo.Rmd’ + + SUMMARY: processing the following file failed: + ‘location_scale_distributions.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +* checking installed package size ... NOTE + ``` + installed size is 42.4Mb + sub-directories of 1Mb or more: + libs 41.8Mb + ``` + # txshift
@@ -3439,6 +5140,63 @@ Run `revdep_details(, "txshift")` for more info Package which this enhances but not available for checking: ‘sl3’ ``` +# UCSCXenaShiny + +
+ +* Version: 2.0.0 +* GitHub: https://github.com/openbiox/UCSCXenaShiny +* Source code: https://github.com/cran/UCSCXenaShiny +* Date/Publication: 2024-03-14 03:20:09 UTC +* Number of recursive dependencies: 199 + +Run `revdep_details(, "UCSCXenaShiny")` for more info + +
+ +## In both + +* checking installed package size ... NOTE + ``` + installed size is 7.8Mb + sub-directories of 1Mb or more: + data 1.1Mb + doc 1.4Mb + shinyapp 4.6Mb + ``` + +# updog + +
+ +* Version: 2.1.5 +* GitHub: https://github.com/dcgerard/updog +* Source code: https://github.com/cran/updog +* Date/Publication: 2023-11-29 15:50:02 UTC +* Number of recursive dependencies: 151 + +Run `revdep_details(, "updog")` for more info + +
+ +## In both + +* checking whether package ‘updog’ can be installed ... WARNING + ``` + Found the following significant warnings: + /c4/home/henrik/repositories/future/revdep/library/updog/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/updog/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/updog/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + See ‘/c4/home/henrik/repositories/future/revdep/checks/updog/new/updog.Rcheck/00install.out’ for details. + ``` + +* checking installed package size ... NOTE + ``` + installed size is 8.0Mb + sub-directories of 1Mb or more: + libs 7.3Mb + ``` + # vmeasur
@@ -3455,11 +5213,12 @@ Run `revdep_details(, "vmeasur")` for more info ## In both -* checking whether package ‘vmeasur’ can be installed ... WARNING +* checking package dependencies ... ERROR ``` - Found the following significant warnings: - Warning: no DISPLAY variable so Tk is not available - See ‘/wynton/home/cbi/hb/repositories/future/revdep/checks/vmeasur/new/vmeasur.Rcheck/00install.out’ for details. + Package required but not available: ‘imager’ + + See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ + manual. ``` # WeightedCluster @@ -3485,19 +5244,19 @@ Run `revdep_details(, "WeightedCluster")` for more info --- finished re-building ‘WeightedCluster.Rnw’ --- re-building ‘WeightedClusterFR.Rnw’ using knitr - Error: processing vignette 'WeightedClusterFR.Rnw' failed with diagnostics: - Running 'texi2dvi' on 'WeightedClusterFR.tex' failed. - LaTeX errors: - ! Package babel Error: Unknown option `frenchb'. Either you misspelled it - (babel) or the language definition file frenchb.ldf was not foun + --- finished re-building ‘WeightedClusterFR.Rnw’ + + --- re-building ‘WeightedClusterPreview.Rnw’ using knitr + Error: processing vignette 'WeightedClusterPreview.Rnw' failed with diagnostics: + Running 'texi2dvi' on 'WeightedClusterPreview.tex' failed. ... l.85 \usepackage {tikz}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘WeightedClusterPreview.Rnw’ - SUMMARY: processing the following files failed: - ‘WeightedClusterFR.Rnw’ ‘WeightedClusterPreview.Rnw’ + SUMMARY: processing the following file failed: + ‘WeightedClusterPreview.Rnw’ Error: Vignette re-building failed. Execution halted @@ -3507,11 +5266,11 @@ Run `revdep_details(, "WeightedCluster")` for more info
-* Version: 1.0.1 +* Version: 3.0.1 * GitHub: https://github.com/kosukeimai/wru * Source code: https://github.com/cran/wru -* Date/Publication: 2022-10-21 17:30:02 UTC -* Number of recursive dependencies: 89 +* Date/Publication: 2024-02-28 04:20:02 UTC +* Number of recursive dependencies: 96 Run `revdep_details(, "wru")` for more info @@ -3519,14 +5278,28 @@ Run `revdep_details(, "wru")` for more info ## In both -* checking C++ specification ... NOTE +* checking whether package ‘wru’ can be installed ... WARNING ``` - Specified C++11: please drop specification unless essential + Found the following significant warnings: + /c4/home/henrik/repositories/future/revdep/library/wru/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/wru/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + /c4/home/henrik/repositories/future/revdep/library/wru/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] + See ‘/c4/home/henrik/repositories/future/revdep/checks/wru/new/wru.Rcheck/00install.out’ for details. + ``` + +* checking installed package size ... NOTE + ``` + installed size is 7.5Mb + sub-directories of 1Mb or more: + data 3.5Mb + help 1.9Mb + libs 2.0Mb ``` * checking dependencies in R code ... NOTE ``` - Namespace in Imports field not imported from: ‘future’ + Namespaces in Imports field not imported from: + ‘future’ ‘tidyr’ All declared Imports should be used. ``` @@ -3569,6 +5342,14 @@ Run `revdep_details(, "XNAString")` for more info Specified C++11: please drop specification unless essential ``` +* checking installed package size ... NOTE + ``` + installed size is 11.2Mb + sub-directories of 1Mb or more: + doc 1.0Mb + libs 9.5Mb + ``` + * checking top-level files ... NOTE ``` File From 762a9bad7fc93e582de923f8b6c69e86e0c993bc Mon Sep 17 00:00:00 2001 From: Henrik Bengtsson Date: Tue, 26 Mar 2024 11:19:19 -0700 Subject: [PATCH 02/25] Bump develop version [ci skip] --- DESCRIPTION | 2 +- NEWS.md | 5 +++++ 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index dd4cadd6..0b0de97d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: future -Version: 1.33.2 +Version: 1.33.2-9000 Title: Unified Parallel and Distributed Processing in R for Everyone Imports: digest, diff --git a/NEWS.md b/NEWS.md index 19d584c9..07377bf1 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,8 @@ +# Version (development version) + + * ... + + # Version 1.33.2 [2024-03-23] ## Performance From a83c9b8d279d68c29d3773054e28bbb80f393cde Mon Sep 17 00:00:00 2001 From: Henrik Bengtsson Date: Wed, 27 Mar 2024 15:08:52 -0700 Subject: [PATCH 03/25] docs fix [ci skip] --- vignettes/future-4-non-exportable-objects.md.rsp | 1 + 1 file changed, 1 insertion(+) diff --git a/vignettes/future-4-non-exportable-objects.md.rsp b/vignettes/future-4-non-exportable-objects.md.rsp index 26be3f1e..8af7bc9e 100644 --- a/vignettes/future-4-non-exportable-objects.md.rsp +++ b/vignettes/future-4-non-exportable-objects.md.rsp @@ -1143,6 +1143,7 @@ str(e) [data.table]: https://cran.r-project.org/package=data.table [arrow]: https://cran.r-project.org/package=arrow +[bigmemory]: https://cran.r-project.org/package=bigmemory [cpp11]: https://cran.r-project.org/package=cpp11 [DBI]: https://cran.r-project.org/package=DBI [inline]: https://cran.r-project.org/package=inline From 6744ed88f424c5341c982b6870b949fba9e8bb4a Mon Sep 17 00:00:00 2001 From: Marcin <133694481+m7pr@users.noreply.github.com> Date: Wed, 22 May 2024 21:29:58 +0200 Subject: [PATCH 04/25] typo in multisession.R documentation --- R/multisession.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/multisession.R b/R/multisession.R index 83347e3f..733ac355 100644 --- a/R/multisession.R +++ b/R/multisession.R @@ -37,7 +37,7 @@ #' #' @return #' A \link{MultisessionFuture}. -#' If `workers == 1`, then all processing using done in the +#' If `workers == 1`, then all processing is done in the #' current/main \R session and we therefore fall back to using a #' lazy future. To override this fallback, use `workers = I(1)`. #' From eaa6d480771d985dc75ee1f4ae2fcb562b2657e3 Mon Sep 17 00:00:00 2001 From: Henrik Bengtsson Date: Tue, 28 May 2024 08:03:38 -0700 Subject: [PATCH 05/25] refresh --- pkgdown/_pkgdown.yml | 14 +++++++------- pkgdown/_pkgdown.yml.rsp | 8 +++++--- 2 files changed, 12 insertions(+), 10 deletions(-) diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml index d3eaedbb..d0254da8 100644 --- a/pkgdown/_pkgdown.yml +++ b/pkgdown/_pkgdown.yml @@ -19,18 +19,20 @@ navbar: pkgs: text: Packages menu: - - text: doFuture + - text: doFuture (map-reduce) href: https://doFuture.futureverse.org - - text: furrr + - text: furrr (map-reduce) href: https://furrr.futureverse.org - text: future href: https://future.futureverse.org - - text: future.apply + - text: future.apply (map-reduce) href: https://future.apply.futureverse.org - - text: future.batchtools + - text: future.batchtools (backend) href: https://future.batchtools.futureverse.org - - text: future.callr + - text: future.callr (backend) href: https://future.callr.futureverse.org + - text: future.mirai (backend) + href: https://future.mirai.futureverse.org - text: future.tests href: https://future.tests.futureverse.org - text: globals @@ -45,8 +47,6 @@ navbar: href: https://BiocParallel.FutureParam.futureverse.org - text: future.tools (experimental) href: https://future.tools.futureverse.org - - text: future.mirai (experimental) - href: https://future.mirai.futureverse.org - text: future.mapreduce (experimental) href: https://future.mapreduce.futureverse.org - text: marshal (experimental) diff --git a/pkgdown/_pkgdown.yml.rsp b/pkgdown/_pkgdown.yml.rsp index 6d931ca0..fc1792a5 100644 --- a/pkgdown/_pkgdown.yml.rsp +++ b/pkgdown/_pkgdown.yml.rsp @@ -1,6 +1,8 @@ <% -pkgs <- c("globals", "listenv", "parallelly", "future", "future.apply", "furrr", "future.tests", "future.callr", "future.batchtools", "doFuture", "progressr") -pkgs_extra <- c("BiocParallel.FutureParam", "future.tools", "future.mirai", "future.mapreduce", "marshal") +pkgs_mapreduce <- c("future.apply", "doFuture", "furrr") +pkgs_backend <- c("future.batchtools", "future.callr", "future.mirai") +pkgs <- c("globals", "listenv", "parallelly", "future", "future.tests", "progressr", pkgs_mapreduce, pkgs_backend) +pkgs_extra <- c("BiocParallel.FutureParam", "future.tools", "future.mapreduce", "marshal") pkgs <- c(sort(pkgs), pkgs_extra) urls <- sprintf("https://%s.futureverse.org", pkgs) names(urls) <- pkgs @@ -33,7 +35,7 @@ navbar: text: Packages menu: <% for (name in names(urls)) { %> - - text: <%= name %> <% if (name %in% pkgs_extra) { %>(experimental)<% } %> + - text: <%= name %> <% if (name %in% pkgs_extra) { %>(experimental)<% } else if (name %in% pkgs_backend) { %>(backend)<% } else if (name %in% pkgs_mapreduce) { %>(map-reduce)<% } %> href: <%= urls[name] %> <% } %> cran: From 99f8dda360b6a7e444ef3b91b1c33ea88d0a559c Mon Sep 17 00:00:00 2001 From: Henrik Bengtsson Date: Tue, 28 May 2024 08:03:43 -0700 Subject: [PATCH 06/25] resolved() for ClusterFuture:s would produce Error: 'inherits(future, "Future")' is not TRUE [#723] --- DESCRIPTION | 2 +- NEWS.md | 7 ++++++- R/ClusterFuture-class.R | 4 ++-- 3 files changed, 9 insertions(+), 4 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 0b0de97d..cd67f309 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: future -Version: 1.33.2-9000 +Version: 1.33.2-9001 Title: Unified Parallel and Distributed Processing in R for Everyone Imports: digest, diff --git a/NEWS.md b/NEWS.md index 07377bf1..7d6a17e4 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,11 @@ # Version (development version) - * ... +## Bug Fixes + + * `resolved()` for `ClusterFuture`:s would produce `Error: + 'inherits(future, "Future")' is not TRUE` instead of an intended, + informative error message that the connection to the parallel + worker is broken. # Version 1.33.2 [2024-03-23] diff --git a/R/ClusterFuture-class.R b/R/ClusterFuture-class.R index 53923ce2..83f1caee 100644 --- a/R/ClusterFuture-class.R +++ b/R/ClusterFuture-class.R @@ -280,8 +280,8 @@ resolved.ClusterFuture <- function(x, run = TRUE, timeout = NULL, ...) { isValid <- isConnectionValid(con) if (!isValid) { ex <- simpleError("Connection to the worker is corrupt") - msg <- post_mortem_cluster_failure(ex, when = "checking resolved from", node = node, future = future) - stop(FutureError(msg, future = future)) + msg <- post_mortem_cluster_failure(ex, when = "checking resolved from", node = node, future = x) + stop(FutureError(msg, future = x)) } if (is.null(timeout)) { From 9cc64fa25d53d184d048f172952117fc5f87d93a Mon Sep 17 00:00:00 2001 From: Henrik Bengtsson Date: Wed, 29 May 2024 14:28:25 -0700 Subject: [PATCH 07/25] Added support for backend maintainers to specify "cleanup" hook functions [#719] --- DESCRIPTION | 2 +- NEWS.md | 7 +++++++ R/cluster.R | 3 +++ R/multisession.R | 3 +++ R/zzz.plan.R | 18 +++++++++++++----- man/future.options.Rd | 4 ++-- man/multisession.Rd | 2 +- 7 files changed, 30 insertions(+), 9 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index cd67f309..ff41d7d7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: future -Version: 1.33.2-9001 +Version: 1.33.2-9002 Title: Unified Parallel and Distributed Processing in R for Everyone Imports: digest, diff --git a/NEWS.md b/NEWS.md index 7d6a17e4..9010fa95 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,12 @@ # Version (development version) +## New Features + + * Added support for backend maintainers to specify "cleanup" hook + functions on future strategies, which are called when switching + future plan. These hook functions are specified via the optional + `cleanup` attribute, cf. `attr(cluster, "cleanup")`. + ## Bug Fixes * `resolved()` for `ClusterFuture`:s would produce `Error: diff --git a/R/cluster.R b/R/cluster.R index f9f1cb7e..01e28cc6 100644 --- a/R/cluster.R +++ b/R/cluster.R @@ -46,4 +46,7 @@ cluster <- function(..., persistent = FALSE, workers = availableWorkers(), envir } class(cluster) <- c("cluster", "multiprocess", "future", "function") attr(cluster, "init") <- TRUE +attr(cluster, "cleanup") <- function() { + ClusterRegistry(action = "stop") +} attr(cluster, "tweakable") <- quote(c(makeClusterPSOCK_args(), "persistent")) diff --git a/R/multisession.R b/R/multisession.R index 733ac355..1e6ce5f3 100644 --- a/R/multisession.R +++ b/R/multisession.R @@ -81,4 +81,7 @@ multisession <- function(..., workers = availableCores(), lazy = FALSE, rscript_ } class(multisession) <- c("multisession", "cluster", "multiprocess", "future", "function") attr(multisession, "init") <- TRUE +attr(multisession, "cleanup") <- function() { + ClusterRegistry(action = "stop") +} attr(multisession, "untweakable") <- c("persistent") diff --git a/R/zzz.plan.R b/R/zzz.plan.R index c9795f11..dc2d18a1 100644 --- a/R/zzz.plan.R +++ b/R/zzz.plan.R @@ -177,7 +177,16 @@ plan <- local({ }) plan_cleanup <- function() { - ClusterRegistry(action = "stop") + evaluator <- stack[[1L]] + + cleanup <- attr(evaluator, "cleanup", exact = TRUE) + if (!is.null(cleanup)) { + if (is.function(cleanup)) { + cleanup() + } else { + stop(FutureError(sprintf("Unknown type of 'cleanup' attribute on current future strategy: %s", sQuote(paste(class(cleanup), collapse = ", "))))) + } + } } plan_init <- function() { @@ -266,11 +275,11 @@ plan <- local({ ## Warn about 'multicore' on certain systems warn_about_multicore(newStack) - stack <<- newStack - - ## Stop any (implicitly started) clusters? + ## Stop/cleanup any previously registered backends? if (cleanup) plan_cleanup() + stack <<- newStack + ## Initiate future workers? if (init) plan_init() @@ -575,4 +584,3 @@ resetWorkers.multicore <- function(x, ...) { FutureRegistry(reg, action = "collect-all", earlySignal = FALSE) stop_if_not(usedCores() == 0L) } - diff --git a/man/future.options.Rd b/man/future.options.Rd index 7a533cdb..d606ba80 100644 --- a/man/future.options.Rd +++ b/man/future.options.Rd @@ -188,9 +188,9 @@ All of the above \R \option{future.*} options can be set by corresponding environment variable \env{R_FUTURE_*} \emph{when the \pkg{future} package is loaded}. This means that those environment variables must be set before the \pkg{future} package is loaded in order to have an effect. -For example, if \code{R_FUTURE_RNG_ONMISUSE = "ignore"}, then option +For example, if \code{R_FUTURE_RNG_ONMISUSE="ignore"}, then option \option{future.rng.onMisuse} is set to \code{"ignore"} (character string). -Similarly, if \code{R_FUTURE_GLOBALS_MAXSIZE = "50000000"}, then option +Similarly, if \code{R_FUTURE_GLOBALS_MAXSIZE="50000000"}, then option \option{future.globals.maxSize} is set to \code{50000000} (numeric). } diff --git a/man/multisession.Rd b/man/multisession.Rd index 1dd50bc5..c309d638 100644 --- a/man/multisession.Rd +++ b/man/multisession.Rd @@ -37,7 +37,7 @@ identified.} } \value{ A \link{MultisessionFuture}. -If \code{workers == 1}, then all processing using done in the +If \code{workers == 1}, then all processing is done in the current/main \R session and we therefore fall back to using a lazy future. To override this fallback, use \code{workers = I(1)}. } From d4b460d18e14663fcf7c4481f7f60e9dd444af2e Mon Sep 17 00:00:00 2001 From: Henrik Bengtsson Date: Wed, 29 May 2024 14:55:53 -0700 Subject: [PATCH 08/25] Backward compatibility: Call ClusterRegistry(action = "stop") for now, if nothing is specified [#719] --- DESCRIPTION | 2 +- R/zzz.plan.R | 3 +++ 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index ff41d7d7..8f135950 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: future -Version: 1.33.2-9002 +Version: 1.33.2-9003 Title: Unified Parallel and Distributed Processing in R for Everyone Imports: digest, diff --git a/R/zzz.plan.R b/R/zzz.plan.R index dc2d18a1..d803e79f 100644 --- a/R/zzz.plan.R +++ b/R/zzz.plan.R @@ -186,6 +186,9 @@ plan <- local({ } else { stop(FutureError(sprintf("Unknown type of 'cleanup' attribute on current future strategy: %s", sQuote(paste(class(cleanup), collapse = ", "))))) } + } else { + ## Backward compatibility for future (<= 1.33.2) + ClusterRegistry(action = "stop") } } From 070e487b78973218db884346b8bac29c0eaf0cda Mon Sep 17 00:00:00 2001 From: Henrik Bengtsson Date: Wed, 29 May 2024 15:25:33 -0700 Subject: [PATCH 09/25] Update plan("reset") to call the "cleanup" hook functions before changing the stack [#719] --- DESCRIPTION | 2 +- R/zzz.plan.R | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 8f135950..b1629cda 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: future -Version: 1.33.2-9003 +Version: 1.33.2-9004 Title: Unified Parallel and Distributed Processing in R for Everyone Imports: digest, diff --git a/R/zzz.plan.R b/R/zzz.plan.R index d803e79f..0c07a2ed 100644 --- a/R/zzz.plan.R +++ b/R/zzz.plan.R @@ -188,7 +188,7 @@ plan <- local({ } } else { ## Backward compatibility for future (<= 1.33.2) - ClusterRegistry(action = "stop") + ## ClusterRegistry(action = "stop") } } @@ -320,10 +320,10 @@ plan <- local({ ## List stack of future strategies? return(stack) } else if (identical(strategy, "reset")) { - ## Reset stack of future strategies? - stack <<- defaultStack ## Stop any (implicitly started) clusters? if (.cleanup) plan_cleanup() + ## Reset stack of future strategies? + stack <<- defaultStack return(stack) } else if (identical(strategy, "pop")) { ## Pop strategy stack and return old stack From b25ac791cf40f1e3ee4763949d2f6579a5870e25 Mon Sep 17 00:00:00 2001 From: Henrik Bengtsson Date: Thu, 30 May 2024 00:15:25 -0700 Subject: [PATCH 10/25] Fix one detritus issue --- DESCRIPTION | 2 +- R/zzz.plan.R | 8 ++++---- tests/multisession.R | 6 ++++++ 3 files changed, 11 insertions(+), 5 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index b1629cda..f0998e8a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: future -Version: 1.33.2-9004 +Version: 1.33.2-9005 Title: Unified Parallel and Distributed Processing in R for Everyone Imports: digest, diff --git a/R/zzz.plan.R b/R/zzz.plan.R index 0c07a2ed..6bf5fe43 100644 --- a/R/zzz.plan.R +++ b/R/zzz.plan.R @@ -190,7 +190,7 @@ plan <- local({ ## Backward compatibility for future (<= 1.33.2) ## ClusterRegistry(action = "stop") } - } + } ## plan_cleanup() plan_init <- function() { evaluator <- stack[[1L]] @@ -238,7 +238,7 @@ plan <- local({ paste(sQuote(class(evaluator)), collapse = ", ")) } } - } + } ## plan_init() equal_strategy_stacks <- function(stack, other) { @@ -295,7 +295,7 @@ plan <- local({ !is.na(nbrOfWorkers), nbrOfWorkers >= 1L) invisible(oldStack) - } + } ## plan_set() ## Main function @@ -320,7 +320,7 @@ plan <- local({ ## List stack of future strategies? return(stack) } else if (identical(strategy, "reset")) { - ## Stop any (implicitly started) clusters? + ## Stop/cleanup any previously registered backends? if (.cleanup) plan_cleanup() ## Reset stack of future strategies? stack <<- defaultStack diff --git a/tests/multisession.R b/tests/multisession.R index dfe1f252..f932ab35 100644 --- a/tests/multisession.R +++ b/tests/multisession.R @@ -159,6 +159,7 @@ stopifnot(v == yTruth) message("*** multisession(..., workers = 1L) ... DONE") + message("*** multisession(..., gc = TRUE) ...") plan(multisession, workers = 2L) @@ -189,6 +190,11 @@ message("*** multisession(...) - stopping with plan() change ...") plan(multisession, workers = 2L) f <- future(1L) + +## Collect value, to speep up the stopping of the parallel workers, +## and to make sure we're not leaving any stray processes behind. +v <- value(f) + cl <- ClusterRegistry("get") stopifnot(inherits(cl, "cluster"), length(cl) >= 1L) From 28956546c4178b8a4e391dd00bdf402a7d43c38f Mon Sep 17 00:00:00 2001 From: Henrik Bengtsson Date: Thu, 30 May 2024 00:29:41 -0700 Subject: [PATCH 11/25] Fix another detritus issue --- tests/multisession.R | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/tests/multisession.R b/tests/multisession.R index f932ab35..4c057d15 100644 --- a/tests/multisession.R +++ b/tests/multisession.R @@ -100,6 +100,10 @@ for (cores in 1:availCores) { ## https://github.com/HenrikBengtsson/Wishlist-for-R/issues/57 ## stopifnot(inherits(res, "MyError")) + ## Make sure to stop these cluster processes to avoid triggering + ## checking for detritus in the temp directory ... NOTE + ClusterRegistry(action = "stop") + message(sprintf("Testing with %d cores ... DONE", cores)) } ## for (cores ...) From 74ebf91136839e4529b57c5a9627dfe17bff597d Mon Sep 17 00:00:00 2001 From: Henrik Bengtsson Date: Thu, 30 May 2024 08:23:42 -0700 Subject: [PATCH 12/25] Fix a few more detritus issues [#719] --- DESCRIPTION | 2 +- tests/Future-class.R | 7 +++++-- tests/globals,NSE.R | 4 ++++ 3 files changed, 10 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index f0998e8a..f039e9ad 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: future -Version: 1.33.2-9005 +Version: 1.33.2-9006 Title: Unified Parallel and Distributed Processing in R for Everyone Imports: digest, diff --git a/tests/Future-class.R b/tests/Future-class.R index b58bbf76..7911ee7f 100644 --- a/tests/Future-class.R +++ b/tests/Future-class.R @@ -25,11 +25,11 @@ stopifnot(is.call(expr)) clazzes <- list( sequential = SequentialFuture, - multisession = function(...) MultisessionFuture(..., workers = 2L), + multisession = function(...) MultisessionFuture(..., workers = I(1L)), sequential = SequentialFuture ) if (supportsMulticore()) { - clazzes$multicore = function(...) MulticoreFuture(..., workers = 2L) + clazzes$multicore = function(...) MulticoreFuture(..., workers = I(1L)) } for (clazz in clazzes) { @@ -48,6 +48,9 @@ for (clazz in clazzes) { v <- value(f) print(v) stopifnot(v == 42L) + + ## To avoid 'multisession' from leaving stray workers behind + ClusterRegistry(action = "stop") } message("*** Future class - exception ... DONE") diff --git a/tests/globals,NSE.R b/tests/globals,NSE.R index cc9546fc..ad60d6a9 100644 --- a/tests/globals,NSE.R +++ b/tests/globals,NSE.R @@ -40,6 +40,10 @@ for (strategy in supportedStrategies()) { } %lazy% TRUE stopifnot(identical(v3, v0)) + ## Make sure to shut down nested parallel workers + void %<-% { plan(sequential) } + print(void) + message(sprintf("- Strategy: %s ... DONE", strategy)) } From 8dbc510058fb993f208a49c96285814c4a5df3bc Mon Sep 17 00:00:00 2001 From: Henrik Bengtsson Date: Thu, 30 May 2024 08:33:34 -0700 Subject: [PATCH 13/25] Add option 'future.plan.cleanup.legacy' for a while [#719] --- DESCRIPTION | 2 +- R/options.R | 3 +++ R/zzz.plan.R | 4 +++- vignettes/future-8-how-future-is-validated.md.rsp | 2 +- 4 files changed, 8 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index f039e9ad..b68d5e75 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: future -Version: 1.33.2-9006 +Version: 1.33.2-9007 Title: Unified Parallel and Distributed Processing in R for Everyone Imports: digest, diff --git a/R/options.R b/R/options.R index 889ba50a..f778c360 100644 --- a/R/options.R +++ b/R/options.R @@ -356,4 +356,7 @@ update_package_options <- function(debug = FALSE) { ## SETTINGS USED FOR DEPRECATING FEATURES ## future 1.22.0: update_package_option("future.globals.keepWhere", mode = "logical", debug = debug) + + ## future 1.34.0: + update_package_option("future.plan.cleanup.legacy", mode = "logical", debug = debug) } diff --git a/R/zzz.plan.R b/R/zzz.plan.R index 6bf5fe43..5c82c9b1 100644 --- a/R/zzz.plan.R +++ b/R/zzz.plan.R @@ -188,7 +188,9 @@ plan <- local({ } } else { ## Backward compatibility for future (<= 1.33.2) - ## ClusterRegistry(action = "stop") + if (getOption("future.plan.cleanup.legacy", FALSE)) { + ClusterRegistry(action = "stop") + } } } ## plan_cleanup() diff --git a/vignettes/future-8-how-future-is-validated.md.rsp b/vignettes/future-8-how-future-is-validated.md.rsp index 8273e701..55e96224 100644 --- a/vignettes/future-8-how-future-is-validated.md.rsp +++ b/vignettes/future-8-how-future-is-validated.md.rsp @@ -91,4 +91,4 @@ of the _Future API_ and the future ecosystem at large. [revdepcheck]: https://github.com/r-lib/revdepcheck [GitHub Actions]: https://github.com/features/actions -[R-hub]: https://builder.r-hub.io/ +[R-hub]: https://r-hub.github.io/rhub/ From 8935f1b370fea9c95530d35cb6370dbf82335da4 Mon Sep 17 00:00:00 2001 From: Henrik Bengtsson Date: Sun, 30 Jun 2024 18:57:11 +0200 Subject: [PATCH 14/25] GA: Modernize covr job --- .github/workflows/covr.yaml | 47 +++++++++++++++---------------------- 1 file changed, 19 insertions(+), 28 deletions(-) diff --git a/.github/workflows/covr.yaml b/.github/workflows/covr.yaml index 84489f69..81af6c74 100644 --- a/.github/workflows/covr.yaml +++ b/.github/workflows/covr.yaml @@ -8,7 +8,7 @@ jobs: timeout-minutes: 45 - runs-on: ubuntu-22.04 + runs-on: ubuntu-latest name: covr @@ -17,48 +17,39 @@ jobs: env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - RSPM: https://packagemanager.rstudio.com/cran/__linux__/jammy/latest + R_KEEP_PKG_SOURCE: yes R_REMOTES_NO_ERRORS_FROM_WARNINGS: true + ## Test in other locale (optional) + LANGUAGE: ${{ matrix.config.language }} ## R CMD check + _R_CHECK_CRAN_INCOMING_: false _R_CHECK_LENGTH_1_CONDITION_: true _R_CHECK_LENGTH_1_LOGIC2_: true _R_CHECK_MATRIX_DATA_: true - _R_CHECK_CRAN_INCOMING_: false + _R_CHECK_SUGGESTS_ONLY_: true + _R_CHECK_THINGS_IN_TEMP_DIR_: true + RCMDCHECK_ERROR_ON: note + ## Specific to futures + R_FUTURE_RNG_ONMISUSE: error steps: - uses: actions/checkout@v4 - - uses: r-lib/actions/setup-pandoc@v2 - - uses: r-lib/actions/setup-r@v2 with: - r-version: release - - - name: Query dependencies - run: | - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") - shell: Rscript {0} + use-public-rspm: true - - name: Cache R packages - uses: actions/cache@v3 + - uses: r-lib/actions/setup-r-dependencies@v2 with: - path: ${{ env.R_LIBS_USER }} - key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} - restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- - - - name: Install system dependencies - env: - RHUB_PLATFORM: linux-x86_64-ubuntu-gcc - run: | - Rscript -e "remotes::install_github('r-hub/sysreqs')" - sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))") - sudo -s eval "$sysreqs" + extra-packages: | + any::rcmdcheck + any::remotes + any::sessioninfo + any::covr + needs: check - name: Install dependencies run: | - install.packages(c("covr", "sessioninfo")) remotes::install_deps(dependencies = TRUE) install.packages(".", repos=NULL, type="source") shell: Rscript {0} @@ -76,7 +67,7 @@ jobs: ## https://app.codecov.io/gh///settings ## 2. Set 'CODECOV_TOKEN' in GitHub Secrets: ## https://github.com///settings/environments/ - coverage <- covr::package_coverage() + coverage <- covr::package_coverage(quiet = FALSE) print(coverage) covr::codecov(coverage = coverage, token="${{secrets.CODECOV_TOKEN}}") shell: Rscript {0} From 97eaf427de07fc9346e587ca91b11b1039319a9a Mon Sep 17 00:00:00 2001 From: Henrik Bengtsson Date: Sun, 30 Jun 2024 18:57:23 +0200 Subject: [PATCH 15/25] Vignette: Use I(.) for manually tested clusters [#725] --- DESCRIPTION | 4 ++-- pkgdown/_pkgdown.yml.rsp | 2 +- vignettes/future-3-topologies.md.rsp | 12 ++++++------ 3 files changed, 9 insertions(+), 9 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index b68d5e75..eb645326 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: future -Version: 1.33.2-9007 +Version: 1.33.2-9008 Title: Unified Parallel and Distributed Processing in R for Everyone Imports: digest, @@ -40,5 +40,5 @@ ByteCompile: TRUE URL: https://future.futureverse.org, https://github.com/HenrikBengtsson/future BugReports: https://github.com/HenrikBengtsson/future/issues Encoding: UTF-8 -RoxygenNote: 7.3.1 +RoxygenNote: 7.3.2 Roxygen: list(markdown = TRUE) diff --git a/pkgdown/_pkgdown.yml.rsp b/pkgdown/_pkgdown.yml.rsp index fc1792a5..fe85ef54 100644 --- a/pkgdown/_pkgdown.yml.rsp +++ b/pkgdown/_pkgdown.yml.rsp @@ -18,7 +18,7 @@ url: https://<%= pkg %>.futureverse.org home: links: - text: Roadmap/Milestones - href: https://github.com/HenrikBengtsson/<%= pkg %>/milestones + href: https://github.com/<%= gsub("(^.*:|[.]git$)", "", subset(gert::git_remote_list(), name == "origin")$url) %>/milestones - text: The Futureverse Project href: https://www.futureverse.org/ - text: Futureverse User Forum diff --git a/vignettes/future-3-topologies.md.rsp b/vignettes/future-3-topologies.md.rsp index 070268dd..739e8145 100644 --- a/vignettes/future-3-topologies.md.rsp +++ b/vignettes/future-3-topologies.md.rsp @@ -102,15 +102,15 @@ Although this does not give an error, we will find that the inner layer of futur Now, we could imagine that we process the outer layer with, say, two parallel futures, and then the inner layer with four parallel futures. In that case, we would end up running on at most eight cores (= 2 * 4). This can be achieved by forcing a fixed number of workers at each layer: ```r -plan(list(tweak(multisession, workers = 2), tweak(multisession, workers = 4))) +plan(list(tweak(multisession, workers = 2), tweak(multisession, workers = I(4)))) ``` -When using this approach, there is a risk of setting up too many concurrent workers. To make sure the setup respects `availableCores()`, use something like: +When using this approach, there is a risk of setting up too many concurrent workers. Because Futureverse has a built-in protection, we need to declare nested workers using the As-Is `I(.)` function, which basically tells the parallel framework "trust us, we know what we are doing". To minimize the risk of mistakes and to make sure our setup respects `availableCores()`, use something like: ```r plan(list( tweak(multisession, workers = availableCores() %/% 4), - tweak(multisession, workers = 4) + tweak(multisession, workers = I(4)) )) ``` @@ -134,7 +134,7 @@ One possible downside to the above setup is that we might not utilize all availa nodes <- rep(c("n1", "n2", "n3"), each = 8) plan(list( tweak(cluster, workers = nodes), - tweak(multisession, workers = 2) + tweak(multisession, workers = I(2)) )) ``` @@ -229,7 +229,7 @@ tweaking the `multisession` plan by passing a function to `workers`; halfCores <- function() { max(1, round(0.5 * availableCores())) plan(list( tweak(cluster, workers = nodes), - tweak(multisession, workers = halfCores) + tweak(multisession, workers = I(halfCores)) )) ``` @@ -250,7 +250,7 @@ customWorkers <- function() { } plan(list( tweak(cluster, workers = nodes), - tweak(multisession, workers = customWorkers) + tweak(multisession, workers = I(customWorkers)) )) ``` From 639a09458f71b88e685c7ecd705c9dd0d2ad40f4 Mon Sep 17 00:00:00 2001 From: Henrik Bengtsson Date: Sun, 30 Jun 2024 19:28:19 +0200 Subject: [PATCH 16/25] GA: modernize --- .github/workflows/covr.yaml | 1 + .github/workflows/future_tests.yaml | 42 +++++++++++--------------- .github/workflows/revdepcheck-top.yaml | 35 ++++++--------------- 3 files changed, 28 insertions(+), 50 deletions(-) diff --git a/.github/workflows/covr.yaml b/.github/workflows/covr.yaml index 81af6c74..3ac1bc6b 100644 --- a/.github/workflows/covr.yaml +++ b/.github/workflows/covr.yaml @@ -71,3 +71,4 @@ jobs: print(coverage) covr::codecov(coverage = coverage, token="${{secrets.CODECOV_TOKEN}}") shell: Rscript {0} + diff --git a/.github/workflows/future_tests.yaml b/.github/workflows/future_tests.yaml index 788d520e..6f7efb37 100644 --- a/.github/workflows/future_tests.yaml +++ b/.github/workflows/future_tests.yaml @@ -8,7 +8,7 @@ jobs: timeout-minutes: 30 - runs-on: ubuntu-22.04 + runs-on: ubuntu-latest name: future.plan=${{ matrix.future.plan }} @@ -26,7 +26,6 @@ jobs: env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - RSPM: https://packagemanager.rstudio.com/cran/__linux__/jammy/latest R_REMOTES_NO_ERRORS_FROM_WARNINGS: true ## R CMD check _R_CHECK_LENGTH_1_LOGIC2_: true @@ -42,35 +41,28 @@ jobs: - uses: r-lib/actions/setup-r@v2 with: - r-version: release + use-public-rspm: true - - name: Query R package dependencies - run: | - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") - shell: Rscript {0} - - - name: Cache R packages - uses: actions/cache@v3 + - uses: r-lib/actions/setup-r-dependencies@v2 with: - path: ${{ env.R_LIBS_USER }} - key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} - restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- + extra-packages: | + any::rcmdcheck + any::remotes + any::sessioninfo + any::covr + needs: check - - name: Install R package system dependencies (Linux) - if: runner.os == 'Linux' - env: - RHUB_PLATFORM: linux-x86_64-ubuntu-gcc + - name: Install dependencies run: | - Rscript -e "remotes::install_github('r-hub/sysreqs')" - sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))") - sudo -s eval "$sysreqs" + remotes::install_deps(dependencies = TRUE) + install.packages(".", repos=NULL, type="source") + shell: Rscript {0} - - name: Install R package dependencies + - name: Session info run: | - remotes::install_deps(dependencies = TRUE) - install.packages(".", repos=NULL, type="source") ## needed by parallel workers + options(width = 100) + pkgs <- installed.packages()[, "Package"] + sessioninfo::session_info(pkgs, include_base = TRUE) shell: Rscript {0} - name: Install 'future.tests' and any backend R packages diff --git a/.github/workflows/revdepcheck-top.yaml b/.github/workflows/revdepcheck-top.yaml index d3a9d55d..1c70317d 100644 --- a/.github/workflows/revdepcheck-top.yaml +++ b/.github/workflows/revdepcheck-top.yaml @@ -8,7 +8,7 @@ jobs: timeout-minutes: 30 - runs-on: ubuntu-22.04 + runs-on: ubuntu-latest name: ${{ matrix.config.pkg }} (${{ matrix.config.r }}) ${{ matrix.config.label }} @@ -51,36 +51,21 @@ jobs: - uses: r-lib/actions/setup-r@v2 with: r-version: ${{ matrix.config.r }} + use-public-rspm: true - - name: Query dependencies - run: | - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") - shell: Rscript {0} - - - name: Cache R packages - if: runner.os != 'Windows' - uses: actions/cache@v3 + - uses: r-lib/actions/setup-r-dependencies@v2 with: - path: ${{ env.R_LIBS_USER }} - key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} - restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- - - - name: Install system dependencies (Linux) - if: runner.os == 'Linux' - env: - RHUB_PLATFORM: linux-x86_64-ubuntu-gcc - run: | - Rscript -e "remotes::install_github('r-hub/sysreqs')" - sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))") - sudo -s eval "$sysreqs" + extra-packages: | + any::rcmdcheck + any::remotes + any::sessioninfo + any::covr + needs: check - name: Install dependencies run: | remotes::install_deps(dependencies = TRUE) - remotes::install_cran("rcmdcheck") - install.packages(".", repos=NULL, type="source") ## needed by parallel workers + install.packages(".", repos=NULL, type="source") install.packages("${{ matrix.config.pkg }}", dependencies=TRUE) shell: Rscript {0} From 12738e2e950d68ba26b90e5d8be506239a74d575 Mon Sep 17 00:00:00 2001 From: Henrik Bengtsson Date: Sun, 30 Jun 2024 20:27:42 +0200 Subject: [PATCH 17/25] GA: exdend run-time --- .github/workflows/covr.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/covr.yaml b/.github/workflows/covr.yaml index 3ac1bc6b..29c6796d 100644 --- a/.github/workflows/covr.yaml +++ b/.github/workflows/covr.yaml @@ -6,7 +6,7 @@ jobs: covr: if: "! contains(github.event.head_commit.message, '[ci skip]')" - timeout-minutes: 45 + timeout-minutes: 60 runs-on: ubuntu-latest From 424212fad4a718655a9d5a0163ffd4e6cf6fa5a1 Mon Sep 17 00:00:00 2001 From: Henrik Bengtsson Date: Sat, 27 Jul 2024 14:58:32 +0200 Subject: [PATCH 18/25] Moved objectSize() to separate file [#736] --- R/utils-objectSize.R | 130 ++++++++++++++++++++++++++++++++++++++++++ R/utils.R | 132 ------------------------------------------- 2 files changed, 130 insertions(+), 132 deletions(-) create mode 100644 R/utils-objectSize.R diff --git a/R/utils-objectSize.R b/R/utils-objectSize.R new file mode 100644 index 00000000..7c6f7a4c --- /dev/null +++ b/R/utils-objectSize.R @@ -0,0 +1,130 @@ +## A *rough* estimate of size of an object + its environment. +#' @keywords internal +#' @importFrom utils object.size +objectSize <- function(x, depth = 3L, enclosure = getOption("future.globals.objectSize.enclosure", FALSE)) { + # Nothing to do? + if (isNamespace(x)) return(0) + if (depth <= 0) return(0) + + if (!is.list(x) && !is.environment(x)) { + size <- unclass(object.size(x)) + ## Issue #176 is because of this + if (enclosure) x <- environment(x) + } else { + size <- 0 + } + + ## Nothing more to do? + if (depth == 1) return(size) + + .scannedEnvs <- new.env() + scanned <- function(e) { + for (name in names(.scannedEnvs)) + if (identical(e, .scannedEnvs[[name]])) return(TRUE) + FALSE + } + + objectSize_list <- function(x, depth) { + ## Nothing to do? + if (depth <= 0) return(0) + + if (inherits(x, "FutureGlobals")) { + size <- attr(x, "total_size", exact = TRUE) + if (!is.na(size)) return(size) + } + + depth <- depth - 1L + size <- 0 + + ## Use the true length that corresponds to what .subset2() uses + nx <- .length(x) + + for (kk in seq_len(nx)) { + ## NOTE: Use non-class dispatching subsetting to avoid infinite loop, + ## e.g. x <- packageVersion("future") gives x[[1]] == x. + x_kk <- .subset2(x, kk) + if (missing(x_kk)) { + ## e.g. x <- alist(a=) + } else if (is.list(x_kk)) { + size <- size + objectSize_list(x_kk, depth = depth) + } else if (is.environment(x_kk)) { + if (!scanned(x_kk)) size <- size + objectSize_env(x_kk, depth = depth) + } else { + size <- size + unclass(object.size(x_kk)) + } + } + size + } ## objectSize_list() + + objectSize_env <- function(x, depth) { + # Nothing to do? + if (depth <= 0) return(0) + depth <- depth - 1L + if (isNamespace(x)) return(0) +## if (inherits(x, "Future")) return(0) + + size <- 0 + + ## Get all objects in the environment + elements <- ls(envir = x, all.names = TRUE) + if (length(elements) == 0) return(0) + + ## Skip variables that are future promises in order + ## to avoid inspecting promises that are already + ## under investigation. + skip <- grep("^.future_", elements, value = TRUE) + if (length(skip) > 0) { + skip <- gsub("^.future_", "", elements) + elements <- setdiff(elements, skip) + if (length(elements) == 0) return(0) + } + + ## Avoid scanning the current environment again + name <- sprintf("env_%d", length(.scannedEnvs)) + .scannedEnvs[[name]] <- x + + for (element in elements) { + ## FIXME: Some elements may not exist, although ls() returns them + ## and exists() say they do exist, cf. Issue #161 /HB 2017-08-24 + ## NOTE: Hmm... is it possible to test for the existence or are + ## we doomed to have to use of tryCatch() here? + res <- tryCatch({ + x_kk <- .subset2(x, element) + NULL ## So that 'x_kk' is not returned, which may be missing() + }, error = identity) + + ## A promise that cannot be resolved? This could be a false positive, + ## e.g. an expression not to be resolved, cf. Issue #161 /HB 2017-08-24 + if (inherits(res, "error")) next + + ## Nothing to do? + if (missing(x_kk)) next + + if (is.list(x_kk)) { + size <- size + objectSize_list(x_kk, depth = depth) + } else if (is.environment(x_kk)) { +## if (!inherits(x_kk, "Future") && !scanned(x_kk)) { + if (!scanned(x_kk)) { + size <- size + objectSize_env(x_kk, depth = depth) + } + } else { + size <- size + unclass(object.size(x_kk)) + } + } + + size + } ## objectSize_env() + + ## Suppress "Warning message: + ## In doTryCatch(return(expr), name, parentenv, handler) : + ## restarting interrupted promise evaluation" + suppressWarnings({ + if (is.list(x)) { + size <- size + objectSize_list(x, depth = depth - 1L) + } else if (is.environment(x)) { + size <- size + objectSize_env(x, depth = depth - 1L) + } + }) + + size +} diff --git a/R/utils.R b/R/utils.R index 4e7cd32e..0287abee 100644 --- a/R/utils.R +++ b/R/utils.R @@ -323,138 +323,6 @@ parseCmdArgs <- function() { } # parseCmdArgs() -## A *rough* estimate of size of an object + its environment. -#' @keywords internal -#' @importFrom utils object.size -objectSize <- function(x, depth = 3L, enclosure = getOption("future.globals.objectSize.enclosure", FALSE)) { - # Nothing to do? - if (isNamespace(x)) return(0) - if (depth <= 0) return(0) - - if (!is.list(x) && !is.environment(x)) { - size <- unclass(object.size(x)) - ## Issue #176 is because of this - if (enclosure) x <- environment(x) - } else { - size <- 0 - } - - ## Nothing more to do? - if (depth == 1) return(size) - - .scannedEnvs <- new.env() - scanned <- function(e) { - for (name in names(.scannedEnvs)) - if (identical(e, .scannedEnvs[[name]])) return(TRUE) - FALSE - } - - objectSize_list <- function(x, depth) { - ## Nothing to do? - if (depth <= 0) return(0) - - if (inherits(x, "FutureGlobals")) { - size <- attr(x, "total_size", exact = TRUE) - if (!is.na(size)) return(size) - } - - depth <- depth - 1L - size <- 0 - - ## Use the true length that corresponds to what .subset2() uses - nx <- .length(x) - - for (kk in seq_len(nx)) { - ## NOTE: Use non-class dispatching subsetting to avoid infinite loop, - ## e.g. x <- packageVersion("future") gives x[[1]] == x. - x_kk <- .subset2(x, kk) - if (missing(x_kk)) { - ## e.g. x <- alist(a=) - } else if (is.list(x_kk)) { - size <- size + objectSize_list(x_kk, depth = depth) - } else if (is.environment(x_kk)) { - if (!scanned(x_kk)) size <- size + objectSize_env(x_kk, depth = depth) - } else { - size <- size + unclass(object.size(x_kk)) - } - } - size - } ## objectSize_list() - - objectSize_env <- function(x, depth) { - # Nothing to do? - if (depth <= 0) return(0) - depth <- depth - 1L - if (isNamespace(x)) return(0) -## if (inherits(x, "Future")) return(0) - - size <- 0 - - ## Get all objects in the environment - elements <- ls(envir = x, all.names = TRUE) - if (length(elements) == 0) return(0) - - ## Skip variables that are future promises in order - ## to avoid inspecting promises that are already - ## under investigation. - skip <- grep("^.future_", elements, value = TRUE) - if (length(skip) > 0) { - skip <- gsub("^.future_", "", elements) - elements <- setdiff(elements, skip) - if (length(elements) == 0) return(0) - } - - ## Avoid scanning the current environment again - name <- sprintf("env_%d", length(.scannedEnvs)) - .scannedEnvs[[name]] <- x - - for (element in elements) { - ## FIXME: Some elements may not exist, although ls() returns them - ## and exists() say they do exist, cf. Issue #161 /HB 2017-08-24 - ## NOTE: Hmm... is it possible to test for the existence or are - ## we doomed to have to use of tryCatch() here? - res <- tryCatch({ - x_kk <- .subset2(x, element) - NULL ## So that 'x_kk' is not returned, which may be missing() - }, error = identity) - - ## A promise that cannot be resolved? This could be a false positive, - ## e.g. an expression not to be resolved, cf. Issue #161 /HB 2017-08-24 - if (inherits(res, "error")) next - - ## Nothing to do? - if (missing(x_kk)) next - - if (is.list(x_kk)) { - size <- size + objectSize_list(x_kk, depth = depth) - } else if (is.environment(x_kk)) { -## if (!inherits(x_kk, "Future") && !scanned(x_kk)) { - if (!scanned(x_kk)) { - size <- size + objectSize_env(x_kk, depth = depth) - } - } else { - size <- size + unclass(object.size(x_kk)) - } - } - - size - } ## objectSize_env() - - ## Suppress "Warning message: - ## In doTryCatch(return(expr), name, parentenv, handler) : - ## restarting interrupted promise evaluation" - suppressWarnings({ - if (is.list(x)) { - size <- size + objectSize_list(x, depth = depth - 1L) - } else if (is.environment(x)) { - size <- size + objectSize_env(x, depth = depth - 1L) - } - }) - - size -} - - #' Gets the length of an object without dispatching #' #' @param x Any \R object. From 2f50f72e1cc5788f500dc5e375bd9c3e94b74f8f Mon Sep 17 00:00:00 2001 From: Henrik Bengtsson Date: Sat, 27 Jul 2024 15:52:05 +0200 Subject: [PATCH 19/25] Size calculation of globals is now done using the much faster parallelly::serializedSize(), if parallelly (>= 1.38.0) is installed [#736] --- DESCRIPTION | 2 +- NEWS.md | 6 ++++++ R/options.R | 9 +++++++++ R/utils-objectSize.R | 13 +++++++++++++ man/future.options.Rd | 2 ++ tests/cluster.R | 33 --------------------------------- tests/globals,toolarge.R | 21 +++++++++++---------- tests/multisession.R | 38 -------------------------------------- 8 files changed, 42 insertions(+), 82 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index eb645326..bcefcdb1 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: future -Version: 1.33.2-9008 +Version: 1.33.2-9009 Title: Unified Parallel and Distributed Processing in R for Everyone Imports: digest, diff --git a/NEWS.md b/NEWS.md index 9010fa95..97f9de29 100644 --- a/NEWS.md +++ b/NEWS.md @@ -7,6 +7,12 @@ future plan. These hook functions are specified via the optional `cleanup` attribute, cf. `attr(cluster, "cleanup")`. +## Performance + + * Size calculation of globals is now done using the much faster + `parallelly::serializedSize()`, if **parallelly** (>= 1.38.0) is + installed. + ## Bug Fixes * `resolved()` for `ClusterFuture`:s would produce `Error: diff --git a/R/options.R b/R/options.R index f778c360..37738f99 100644 --- a/R/options.R +++ b/R/options.R @@ -188,6 +188,8 @@ #' R_FUTURE_OUTPUT_WINDOWS_REENCODE #' future.journal #' R_FUTURE_JOURNAL +#' R_FUTURE_GLOBALS_OBJECTSIZE_METHOD +#' future.globals.objectSize.method #' #' @name future.options NULL @@ -358,5 +360,12 @@ update_package_options <- function(debug = FALSE) { update_package_option("future.globals.keepWhere", mode = "logical", debug = debug) ## future 1.34.0: + update_package_option("future.globals.objectSize.method", mode = "character", debug = debug) + if (is.null(getOption("future.globals.objectSize.method"))) { + if (exists("serializedSize", envir = getNamespace("parallelly"), inherits = FALSE)) { + options(future.globals.objectSize.method = "serializedSize") + } + } + update_package_option("future.plan.cleanup.legacy", mode = "logical", debug = debug) } diff --git a/R/utils-objectSize.R b/R/utils-objectSize.R index 7c6f7a4c..cf19e3ce 100644 --- a/R/utils-objectSize.R +++ b/R/utils-objectSize.R @@ -5,6 +5,19 @@ objectSize <- function(x, depth = 3L, enclosure = getOption("future.globals.obje # Nothing to do? if (isNamespace(x)) return(0) if (depth <= 0) return(0) + + method <- getOption("future.globals.objectSize.method", "objectSize") + if (method == "serializedSize") { + ns <- getNamespace("parallelly") + if (!exists("serializedSize", envir = ns, inherits = FALSE)) { + stop("Option 'future.globals.objectSize.method' supports \"serializedSize\" only for parallelly (>= 1.38.0)") + } + serializedSize <- get("serializedSize", envir = ns, inherits = FALSE) + size <- serializedSize(x) + return(size) + } else if (method != "objectSize") { + stop(paste("Unknown value on option 'future.globals.objectSize.method':", sQuote(method))) + } if (!is.list(x) && !is.environment(x)) { size <- unclass(object.size(x)) diff --git a/man/future.options.Rd b/man/future.options.Rd index d606ba80..05c9c790 100644 --- a/man/future.options.Rd +++ b/man/future.options.Rd @@ -45,6 +45,8 @@ \alias{R_FUTURE_OUTPUT_WINDOWS_REENCODE} \alias{future.journal} \alias{R_FUTURE_JOURNAL} +\alias{R_FUTURE_GLOBALS_OBJECTSIZE_METHOD} +\alias{future.globals.objectSize.method} \title{Options used for futures} \description{ Below are the \R options and environment variables that are used by the diff --git a/tests/cluster.R b/tests/cluster.R index b9f59161..e44d3ba4 100644 --- a/tests/cluster.R +++ b/tests/cluster.R @@ -141,39 +141,6 @@ for (type in types) { res <- tryCatch(value(f), error = identity) stopifnot(inherits(res, "error"), inherits(res, "MyError")) - message("*** cluster() - too large globals ...") - ooptsT <- options(future.globals.maxSize = object.size(1:1014)) - - limit <- getOption("future.globals.maxSize") - cat(sprintf("Max total size of globals: %g bytes\n", limit)) - - ## A large object - a <- 1:1014 - yTruth <- sum(a) - size <- object.size(a) - cat(sprintf("a: %g bytes\n", size)) - f <- future({ sum(a) }) - print(f) - rm(list = "a") - v <- value(f) - print(v) - stopifnot(v == yTruth) - - - ## A too large object - a <- 1:1015 - yTruth <- sum(a) - size <- object.size(a) - cat(sprintf("a: %g bytes\n", size)) - res <- tryCatch(f <- future({ sum(a) }), error = identity) - rm(list = "a") - stopifnot(inherits(res, "error")) - - ## Undo options changed in this test - options(ooptsT) - - message("*** cluster() - too large globals ... DONE") - message("*** cluster() - installed libraries ...") f <- try(cluster({ list( diff --git a/tests/globals,toolarge.R b/tests/globals,toolarge.R index 82da9978..7b6718cb 100644 --- a/tests/globals,toolarge.R +++ b/tests/globals,toolarge.R @@ -3,25 +3,26 @@ library("listenv") message("*** Globals - too large ...") -ooptsT <- options(future.globals.maxSize = object.size(1:1000) - 1L) +a <- integer(length = 1000) +ooptsT <- options(future.globals.maxSize = object.size(a) - 100L) limit <- getOption("future.globals.maxSize") cat(sprintf("Max total size of globals: %g bytes\n", limit)) plan(multisession) exprs <- list( - A = substitute({ a }, env = list()), - B = substitute({ a * b }, env = list()), - C = substitute({ a * b * c }, env = list()), - D = substitute({ a * b * c * d }, env = list()), + A = substitute({ a }, env = list()), + B = substitute({ a * b }, env = list()), + C = substitute({ a * b * c }, env = list()), + D = substitute({ a * b * c * d }, env = list()), E = substitute({ a * b * c * d * e }, env = list()) ) -a <- 1:1000 -b <- 1:900 -c <- 1:800 -d <- 1:700 -e <- 1 +a <- integer(length = 1000) +b <- integer(length = 900) +c <- integer(length = 800) +d <- integer(length = 700) +e <- integer(length = 1) for (name in names(exprs)) { message(sprintf("Expression %s:", name)) diff --git a/tests/multisession.R b/tests/multisession.R index 4c057d15..947c70d0 100644 --- a/tests/multisession.R +++ b/tests/multisession.R @@ -108,44 +108,6 @@ for (cores in 1:availCores) { } ## for (cores ...) -message("*** multisession() - too large globals ...") -ooptsT <- options(future.globals.maxSize = object.size(1:1014)) - -limit <- getOption("future.globals.maxSize") -cat(sprintf("Max total size of globals: %g bytes\n", limit)) - -for (workers in unique(c(1L, availableCores()))) { - ## Speed up CRAN checks: Skip on CRAN Windows 32-bit - if (!fullTest && isWin32) next - - message("Max number of sessions: ", workers) - - ## A large object - a <- 1:1014 - yTruth <- sum(a) - size <- object.size(a) - cat(sprintf("a: %g bytes\n", size)) - f <- multisession({ sum(a) }, globals = TRUE, workers = workers) - print(f) - rm(list = "a") - v <- value(f) - print(v) - stopifnot(v == yTruth) - - - ## A too large object - a <- 1:1015 - yTruth <- sum(a) - size <- object.size(a) - cat(sprintf("a: %g bytes\n", size)) - res <- try(f <- multisession({ sum(a) }, globals = TRUE, workers = workers), silent = TRUE) - rm(list = "a") - stopifnot(inherits(res, "try-error")) -} ## for (workers in ...) - -## Undo options changed in this test -options(ooptsT) - message("*** multisession() - too large globals ... DONE") message("*** multisession(..., workers = 1L) ...") From af7055d905401501a44b5ad04a7b0c7584d458dc Mon Sep 17 00:00:00 2001 From: Henrik Bengtsson Date: Sun, 28 Jul 2024 14:41:40 +0200 Subject: [PATCH 20/25] Require parallelly (>= 1.38.0) so we can use parallelly::serializedSize() [#736] --- DESCRIPTION | 4 ++-- NAMESPACE | 1 + NEWS.md | 3 +-- R/utils-objectSize.R | 6 +----- 4 files changed, 5 insertions(+), 9 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index bcefcdb1..e4a67120 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,12 +1,12 @@ Package: future -Version: 1.33.2-9009 +Version: 1.33.2-9010 Title: Unified Parallel and Distributed Processing in R for Everyone Imports: digest, globals (>= 0.16.1), listenv (>= 0.8.0), parallel, - parallelly (>= 1.34.0), + parallelly (>= 1.38.0), utils Suggests: methods, diff --git a/NAMESPACE b/NAMESPACE index 253b394f..ac88a601 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -180,6 +180,7 @@ importFrom(parallelly,isNodeAlive) importFrom(parallelly,makeClusterMPI) importFrom(parallelly,makeClusterPSOCK) importFrom(parallelly,makeNodePSOCK) +importFrom(parallelly,serializedSize) importFrom(parallelly,supportsMulticore) importFrom(utils,capture.output) importFrom(utils,file_test) diff --git a/NEWS.md b/NEWS.md index 97f9de29..2b3eaf0b 100644 --- a/NEWS.md +++ b/NEWS.md @@ -10,8 +10,7 @@ ## Performance * Size calculation of globals is now done using the much faster - `parallelly::serializedSize()`, if **parallelly** (>= 1.38.0) is - installed. + `parallelly::serializedSize()`. ## Bug Fixes diff --git a/R/utils-objectSize.R b/R/utils-objectSize.R index cf19e3ce..fb3e2d50 100644 --- a/R/utils-objectSize.R +++ b/R/utils-objectSize.R @@ -1,6 +1,7 @@ ## A *rough* estimate of size of an object + its environment. #' @keywords internal #' @importFrom utils object.size +#' @importFrom parallelly serializedSize objectSize <- function(x, depth = 3L, enclosure = getOption("future.globals.objectSize.enclosure", FALSE)) { # Nothing to do? if (isNamespace(x)) return(0) @@ -8,11 +9,6 @@ objectSize <- function(x, depth = 3L, enclosure = getOption("future.globals.obje method <- getOption("future.globals.objectSize.method", "objectSize") if (method == "serializedSize") { - ns <- getNamespace("parallelly") - if (!exists("serializedSize", envir = ns, inherits = FALSE)) { - stop("Option 'future.globals.objectSize.method' supports \"serializedSize\" only for parallelly (>= 1.38.0)") - } - serializedSize <- get("serializedSize", envir = ns, inherits = FALSE) size <- serializedSize(x) return(size) } else if (method != "objectSize") { From 21fe894988e4539c0c38b764f7840e06b2196ef1 Mon Sep 17 00:00:00 2001 From: Henrik Bengtsson Date: Sun, 28 Jul 2024 14:43:42 +0200 Subject: [PATCH 21/25] Default to 'serializedSize' [#736] --- DESCRIPTION | 2 +- R/options.R | 6 ------ R/utils-objectSize.R | 2 +- 3 files changed, 2 insertions(+), 8 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index e4a67120..2312035a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: future -Version: 1.33.2-9010 +Version: 1.33.2-9011 Title: Unified Parallel and Distributed Processing in R for Everyone Imports: digest, diff --git a/R/options.R b/R/options.R index 37738f99..9272c859 100644 --- a/R/options.R +++ b/R/options.R @@ -361,11 +361,5 @@ update_package_options <- function(debug = FALSE) { ## future 1.34.0: update_package_option("future.globals.objectSize.method", mode = "character", debug = debug) - if (is.null(getOption("future.globals.objectSize.method"))) { - if (exists("serializedSize", envir = getNamespace("parallelly"), inherits = FALSE)) { - options(future.globals.objectSize.method = "serializedSize") - } - } - update_package_option("future.plan.cleanup.legacy", mode = "logical", debug = debug) } diff --git a/R/utils-objectSize.R b/R/utils-objectSize.R index fb3e2d50..de9fac99 100644 --- a/R/utils-objectSize.R +++ b/R/utils-objectSize.R @@ -7,7 +7,7 @@ objectSize <- function(x, depth = 3L, enclosure = getOption("future.globals.obje if (isNamespace(x)) return(0) if (depth <= 0) return(0) - method <- getOption("future.globals.objectSize.method", "objectSize") + method <- getOption("future.globals.objectSize.method", "serializedSize") if (method == "serializedSize") { size <- serializedSize(x) return(size) From adf32b81763e34cdb981b6f4c4f8db880668d770 Mon Sep 17 00:00:00 2001 From: Henrik Bengtsson Date: Mon, 29 Jul 2024 06:54:58 -0700 Subject: [PATCH 22/25] REVDEP: Checked 376 packages [ci skip] --- revdep/README.md | 794 ++++----- revdep/cran.md | 23 +- revdep/failures.md | 590 +------ revdep/problems.md | 3874 +++++++++++++++++++++++--------------------- 4 files changed, 2463 insertions(+), 2818 deletions(-) diff --git a/revdep/README.md b/revdep/README.md index e0a69f60..d5430d4d 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,412 +1,424 @@ # Platform -|field |value | -|:--------|:---------------------------------------------------------------| -|version |R version 4.3.3 (2024-02-29) | -|os |CentOS Linux 7 (Core) | -|system |x86_64, linux-gnu | -|ui |X11 | -|language |en | -|collate |en_US.UTF-8 | -|ctype |en_US.UTF-8 | -|tz |America/Los_Angeles | -|date |2024-03-22 | -|pandoc |3.1.11.1 @ /software/c4/cbi/software/pandoc-3.1.11.1/bin/pandoc | +|field |value | +|:--------|:---------------------------------------------------------| +|version |R version 4.4.1 (2024-06-14) | +|os |Rocky Linux 8.10 (Green Obsidian) | +|system |x86_64, linux-gnu | +|ui |X11 | +|language |en | +|collate |en_US.UTF-8 | +|ctype |en_US.UTF-8 | +|tz |America/Los_Angeles | +|date |2024-07-29 | +|pandoc |3.2.1 @ /software/c4/cbi/software/pandoc-3.2.1/bin/pandoc | # Dependencies |package |old |new |Δ | |:----------|:------|:-----------|:--| -|future |1.33.1 |1.33.1-9009 |* | -|codetools |0.2-19 |0.2-19 | | -|digest |0.6.35 |0.6.35 | | +|future |1.33.2 |1.33.2-9011 |* | +|codetools |0.2-20 |0.2-20 | | +|digest |0.6.36 |0.6.36 | | |globals |0.16.3 |0.16.3 | | |listenv |0.9.1 |0.9.1 | | -|parallelly |1.37.1 |1.37.1 | | +|parallelly |1.38.0 |1.38.0 | | # Revdeps -## Failed to check (9) +## Failed to check (1) |package |version |error |warning |note | |:----------------|:-------|:-----|:-------|:----| -|arkdb |? | | | | -|[cft](failures.md#cft)|1.0.0 |1 | | | -|[erah](failures.md#erah)|2.0.1 |1 | |1 | -|flowml |? | | | | -|marginaleffects |? | | | | -|[Prostar](failures.md#prostar)|1.34.6 |1 | | | -|[startR](failures.md#startr)|2.3.1 |1 | | | -|[TKCat](failures.md#tkcat)|1.0.7 |1 | | | |[TriDimRegression](failures.md#tridimregression)|1.0.2 |1 | | | -## New problems (1) +## New problems (4) -|package |version |error |warning |note | -|:-------|:-------|:-----------|:-------|:----| -|[stars](problems.md#stars)|0.6-4 |1 -1 __+1__ | |2 | +|package |version |error |warning |note | +|:--------------------|:-------|:-----|:-------|:--------| +|[googleComputeEngineR](problems.md#googlecomputeenginer)|0.3.0 | | |2 __+1__ | +|[modelsummary](problems.md#modelsummary)|2.1.1 | | |__+1__ | +|[Rcurvep](problems.md#rcurvep)|1.3.1 | | |__+1__ | +|[SPARSEMODr](problems.md#sparsemodr)|1.2.0 | | |1 __+1__ | -## All (359) +## All (376) -|package |version |error |warning |note | -|:--------------------------|:----------|:-----------|:-------|:----| -|adestr |0.5.0 | | | | -|AICcPermanova |0.0.2 | | | | -|[AIPW](problems.md#aipw) |0.6.3.2 | | |1 | -|ale |0.3.0 | | | | -|alookr |0.3.9 | | | | -|alphaci |1.0.1 | | | | -|[AlpsNMR](problems.md#alpsnmr)|4.4.0 |1 | | | -|[altdoc](problems.md#altdoc)|0.3.0 |1 | | | -|antaresEditObject |0.6.1 | | | | -|arkdb |? | | | | -|aroma.affymetrix |3.2.2 | | | | -|aroma.cn |1.7.1 | | | | -|[aroma.core](problems.md#aromacore)|3.3.1 | | |1 | -|ARPALData |1.5.2 | | | | -|[BAMBI](problems.md#bambi) |2.3.5 | |1 |1 | -|[bamm](problems.md#bamm) |0.4.3 | |1 |1 | -|baseballr |1.6.0 | | | | -|BatchGetSymbols |2.6.4 | | | | -|[batchtools](problems.md#batchtools)|0.9.17 | | |2 | -|bayesian |0.0.9 | | | | -|[bayesmove](problems.md#bayesmove)|0.2.1 | |1 | | -|bbknnR |1.1.1 | | | | -|bcmaps |2.2.0 | | | | -|[BEKKs](problems.md#bekks) |1.4.4 | |1 |1 | -|bhmbasket |0.9.5 | | | | -|[bigDM](problems.md#bigdm) |0.5.3 | | |2 | -|[bistablehistory](problems.md#bistablehistory)|1.1.2 | | |2 | -|bkmrhat |1.1.3 | | | | -|[blavaan](problems.md#blavaan)|0.5-3 | | |3 | -|bolasso |0.2.0 | | | | -|[brms](problems.md#brms) |2.21.0 | | |2 | -|brpop |0.3.0 | | | | -|bsitar |0.2.1 | | | | -|bspcov |1.0.0 | | | | -|calmr |0.6.1 | | | | -|campsis |1.5.1 | | | | -|canaper |1.0.1 | | | | -|[ceRNAnetsim](problems.md#cernanetsim)|1.14.1 |3 | |1 | -|[cft](failures.md#cft) |1.0.0 |1 | | | -|chatAI4R |0.2.10 | | | | -|[ChromSCape](problems.md#chromscape)|1.12.0 | |4 |4 | -|civis |3.1.2 | | | | -|[clickR](problems.md#clickr)|0.9.39 | | |1 | -|Clustering |1.7.7 | | | | -|ClustIRR |1.0.0 | | | | -|codalm |0.1.2 | | | | -|[codebook](problems.md#codebook)|0.9.2 | | |3 | -|[collinear](problems.md#collinear)|1.1.1 | | |1 | -|conformalInference.fd |1.1.1 | | | | -|conformalInference.multi |1.1.1 | | | | -|[Coxmos](problems.md#coxmos)|1.0.1 | | |1 | -|crossmap |0.4.0 | | | | -|CSCNet |0.1.2 | | | | -|[cSEM](problems.md#csem) |0.5.0 | | |1 | -|[CSGo](problems.md#csgo) |0.6.7 | | |1 | -|cvCovEst |1.2.2 | | | | -|dagHMM |0.1.0 | | | | -|dataquieR |2.0.1 | | | | -|DeclareDesign |1.0.8 | | | | -|delayed |0.4.0 | | | | -|[deseats](problems.md#deseats)|1.0.0 | |1 |1 | -|[dipsaus](problems.md#dipsaus)|0.2.8 | | |1 | -|[disk.frame](problems.md#diskframe)|0.8.3 |1 | | | -|[dispositionEffect](problems.md#dispositioneffect)|1.0.1 |1 | | | -|doFuture |1.0.1 | | | | -|DQAstats |0.3.3 | | | | -|[dragon](problems.md#dragon)|1.2.1 |1 | |2 | -|[drake](problems.md#drake) |7.13.9 | | |1 | -|drimmR |1.0.1 | | | | -|drtmle |1.1.2 | | | | -|dsos |0.1.2 | | | | -|[DT](problems.md#dt) |0.32 | | |1 | -|easyalluvial |0.3.2 | | | | -|ecic |0.0.3 | | | | -|eCV |0.0.2 | | | | -|[EFAtools](problems.md#efatools)|0.4.4 | |1 |3 | -|EGAnet |2.0.5 | | | | -|elevatr |0.99.0 | | | | -|[envi](problems.md#envi) |0.1.19 | |1 | | -|epe4md |0.1.4 | | | | -|EpiForsk |0.1.1 | | | | -|[EpiNow2](problems.md#epinow2)|1.4.0 | | |2 | -|[epitweetr](problems.md#epitweetr)|2.2.16 | | |2 | -|epwshiftr |0.1.4 | | | | -|[erah](failures.md#erah) |2.0.1 |1 | |1 | -|ezcox |1.0.4 | | | | -|fabletools |0.4.1 | | | | -|FAMoS |0.3.0 | | | | -|fastRhockey |0.4.0 | | | | -|[fdacluster](problems.md#fdacluster)|0.3.0 | |1 |1 | -|fdWasserstein |1.0 | | | | -|[fect](problems.md#fect) |1.0.0 | |1 |3 | -|fiery |1.2.1 | | | | -|finbif |0.9.5 | | | | -|fitlandr |0.1.0 | | | | -|[FLAMES](problems.md#flames)|1.8.0 | | |5 | -|[flowGraph](problems.md#flowgraph)|1.10.0 | | |2 | -|flowml |? | | | | -|[forecastML](problems.md#forecastml)|0.9.0 | | |1 | -|fst4pg |1.0.0 | | | | -|fundiversity |1.1.1 | | | | -|funGp |0.3.2 | | | | -|furrr |0.3.1 | | | | -|future.apply |1.11.1 | | | | -|future.batchtools |0.12.1 | | | | -|future.callr |0.8.2 | | | | -|future.tests |0.7.0 | | | | -|fxTWAPLS |0.1.2 | | | | -|[genBaRcode](problems.md#genbarcode)|1.2.7 | |1 | | -|[geocmeans](problems.md#geocmeans)|0.3.4 | |1 |1 | -|[geohabnet](problems.md#geohabnet)|2.0.0 |1 | | | -|GetBCBData |0.7.0 | | | | -|[googleComputeEngineR](problems.md#googlecomputeenginer)|0.3.0 | | |1 | -|googlePubsubR |0.0.4 | | | | -|[googleTagManageR](problems.md#googletagmanager)|0.2.0 | | |1 | -|greatR |1.1.0 | | | | -|[greed](problems.md#greed) |0.6.1 | |1 |3 | -|greta |0.4.5 | | | | -|gsdensity |0.1.2 | | | | -|gstat |2.1-1 | | | | -|GSVA |1.50.1 | | | | -|[gsynth](problems.md#gsynth)|1.2.1 | |1 |2 | -|gtfs2emis |0.1.0 | | | | -|gtfs2gps |2.1-1 | | | | -|gWQS |3.0.5 | | | | -|[hackeRnews](problems.md#hackernews)|0.1.0 | | |1 | -|hacksig |0.1.2 | | | | -|[hal9001](problems.md#hal9001)|0.4.6 | | |1 | -|haldensify |0.2.3 | | | | -|[hbamr](problems.md#hbamr) |2.2.1 | | |2 | -|[hero](problems.md#hero) |0.6 | | |2 | -|[heterogen](problems.md#heterogen)|1.2.33 | |1 |1 | -|hoopR |2.1.0 | | | | -|[httpgd](problems.md#httpgd)|2.0.1 |1 | |2 | -|[hwep](problems.md#hwep) |2.0.2 | | |2 | -|[hydroloom](problems.md#hydroloom)|1.0.2 |2 | | | -|idmodelr |0.4.0 | | | | -|imagefluency |0.2.5 | | | | -|iml |0.11.1 | | | | -|incubate |1.2.1 | | | | -|iNEXT.beta3D |1.0.0 | | | | -|[infercnv](problems.md#infercnv)|1.18.1 | | |2 | -|inlinedocs |2023.9.4 | | | | -|[InPAS](problems.md#inpas) |2.10.0 | | |1 | -|[interflex](problems.md#interflex)|1.2.6 | |1 |2 | -|ipc |0.1.4 | | | | -|[ISAnalytics](problems.md#isanalytics)|1.12.0 | | |1 | -|isopam |2.0 | | | | -|ivDiag |1.0.6 | | | | -|[ivmte](problems.md#ivmte) |1.4.0 | | |1 | -|jlmerclusterperm |1.1.3 | | | | -|JointAI |1.0.5 | | | | -|jstor |0.3.11 | | | | -|JuliaConnectoR |1.1.3 | | | | -|kernelboot |0.1.10 | | | | -|[keyATM](problems.md#keyatm)|0.5.1 | | |1 | -|LandComp |0.0.5 | | | | -|latentcor |2.0.1 | | | | -|lava |1.8.0 | | | | -|ldaPrototype |0.3.1 | | | | -|[ldsr](problems.md#ldsr) |0.0.2 | |1 |1 | -|lemna |1.0.1 | | | | -|LexFindR |1.0.2 | | | | -|lgr |0.4.4 | | | | -|[lidR](problems.md#lidr) |4.1.1 |1 |1 |1 | -|lightr |1.7.1 | | | | -|lmtp |1.3.2 | | | | -|LTFHPlus |2.1.1 | | | | -|LWFBrook90R |0.5.3 | | | | -|[MAI](problems.md#mai) |1.8.0 | | |1 | -|malariaAtlas |1.5.1 | | | | -|MAMS |2.0.1 | | | | -|[manynet](problems.md#manynet)|0.4.4 | | |2 | -|mapme.biodiversity |0.5.0 | | | | -|marginaleffects |? | | | | -|[matric](problems.md#matric)|0.2.0 |1 | | | -|mbbe |0.1.0 | | | | -|mcmcensemble |3.1.0 | | | | -|mcp |0.3.4 | | | | -|merTools |0.6.2 | | | | -|[metabolomicsR](problems.md#metabolomicsr)|1.0.0 | |1 |1 | -|[metaGE](problems.md#metage)|1.0.3 | | |1 | -|mice |3.16.0 | | | | -|[microservices](problems.md#microservices)|0.2.0 |1 | | | -|migraph |1.3.4 | | | | -|mikropml |1.6.1 | | | | -|[MineICA](problems.md#mineica)|1.42.0 | |3 |4 | -|[missSBM](problems.md#misssbm)|1.0.4 | |1 |1 | -|[mistyR](problems.md#mistyr)|1.10.0 |1 | |1 | -|mlr3 |0.18.0 | | | | -|mlr3db |0.5.2 | | | | -|mlr3pipelines |0.5.0-2 | | | | -|mlr3resampling |2024.1.23 | | | | -|mlr3spatial |0.5.0 | | | | -|modelsummary |1.4.5 | | | | -|[momentuHMM](problems.md#momentuhmm)|1.5.5 | |1 |1 | -|[MOSS](problems.md#moss) |0.2.2 | |1 | | -|mplusParallel.automation |0.0.1.1 | | | | -|[mrgsim.parallel](problems.md#mrgsimparallel)|0.2.1 | | |2 | -|mslp |1.4.0 | | | | -|multilevelmediation |0.3.1 | | | | -|multitool |0.1.4 | | | | -|multiverse |0.6.1 | | | | -|[nebula](problems.md#nebula)|1.5.3 | | |1 | -|netShiny |1.0 | | | | -|NetSimR |0.1.5 | | | | -|[nfl4th](problems.md#nfl4th)|1.0.4 | |1 |1 | -|nflfastR |4.6.1 | | | | -|nflseedR |1.2.0 | | | | -|[nhdplusTools](problems.md#nhdplustools)|1.0.0 |1 | | | -|nncc |2.0.0 | | | | -|[oncomsm](problems.md#oncomsm)|0.1.4 | | |2 | -|[onemapsgapi](problems.md#onemapsgapi)|1.1.0 |1 | | | -|[OOS](problems.md#oos) |1.0.0 | | |1 | -|optic |1.0.1 | | | | -|OptimalGoldstandardDesigns |1.0.1 | | | | -|optimLanduse |1.2.1 | | | | -|origami |1.0.7 | | | | -|paramsim |0.1.0 | | | | -|[pareg](problems.md#pareg) |1.6.0 |3 | |2 | -|[parseRPDR](problems.md#parserpdr)|1.1.0 | | |1 | -|[partR2](problems.md#partr2)|0.9.2 | | |1 | -|[pavo](problems.md#pavo) |2.9.0 | |1 |1 | -|pbapply |1.7-2 | | | | -|[PCRedux](problems.md#pcredux)|1.1-2 | |1 | | -|PeakSegDisk |2023.11.27 | | | | -|penaltyLearning |2024.1.25 | | | | -|pGRN |0.3.5 | | | | -|[photosynthesis](problems.md#photosynthesis)|2.1.4 | | |2 | -|[phylolm](problems.md#phylolm)|2.6.2 | | |2 | -|phylopath |1.2.1 | | | | -|PINstimation |0.1.2 | | | | -|[PLNmodels](problems.md#plnmodels)|1.2.0 | |1 |1 | -|[plumber](problems.md#plumber)|1.2.1 | | |2 | -|polle |1.3 | | | | -|POMADE |0.2.0 | | | | -|[portvine](problems.md#portvine)|1.0.3 | | |1 | -|powRICLPM |0.1.1 | | | | -|[ProFAST](problems.md#profast)|1.4 | |1 |2 | -|progressr |0.14.0 | | | | -|[projpred](problems.md#projpred)|2.8.0 | |1 |2 | -|promises |1.2.1 | | | | -|[Prostar](failures.md#prostar)|1.34.6 |1 | | | -|proteus |1.1.4 | | | | -|protti |0.7.0 | | | | -|PSCBS |0.67.0 | | | | -|[pseudohouseholds](problems.md#pseudohouseholds)|0.1.1 | | |1 | -|PUMP |1.0.3 | | | | -|qape |2.1 | | | | -|[QDNAseq](problems.md#qdnaseq)|1.38.0 | | |1 | -|qgcomp |2.15.2 | | | | -|qgcompint |0.7.0 | | | | -|[RAINBOWR](problems.md#rainbowr)|0.1.35 | | |1 | -|rangeMapper |2.0.3 | | | | -|rBiasCorrection |0.3.4 | | | | -|Rcurvep |1.3.1 | | | | -|[receptiviti](problems.md#receptiviti)|0.1.7 |1 | |2 | -|refineR |1.6.1 | | | | -|[regmedint](problems.md#regmedint)|1.0.1 | | |1 | -|remiod |1.0.2 | | | | -|reproducible |2.0.10 | | | | -|reval |3.1-0 | | | | -|[rgee](problems.md#rgee) |1.1.7 | | |1 | -|rkeops |2.2.2 | | | | -|[robotstxt](problems.md#robotstxt)|0.7.13 | | |2 | -|robust2sls |0.2.2 | | | | -|[rpm](problems.md#rpm) |0.7-1 | |1 |1 | -|rsi |0.1.2 | | | | -|RTransferEntropy |0.2.21 | | | | -|s3fs |0.1.5 | | | | -|saeczi |0.1.1 | | | | -|[sapfluxnetr](problems.md#sapfluxnetr)|0.1.4 | | |1 | -|[SCArray.sat](problems.md#scarraysat)|1.2.1 | |1 |1 | -|scBubbletree |1.4.0 | | | | -|scDiffCom |1.0.0 | | | | -|[sctransform](problems.md#sctransform)|0.4.1 | |1 |1 | -|[sdmApp](problems.md#sdmapp)|0.0.2 | | |1 | -|[sdmTMB](problems.md#sdmtmb)|0.4.3 |1 | |1 | -|seer |1.1.8 | | | | -|semPower |2.1.0 | | | | -|semTests |0.5.0 | | | | -|semtree |0.9.19 | | | | -|[sentopics](problems.md#sentopics)|0.7.2 | |1 |3 | -|[Seurat](problems.md#seurat)|5.0.3 | | |3 | -|[SeuratObject](problems.md#seuratobject)|5.0.1 | | |3 | -|[sharp](problems.md#sharp) |1.4.6 | | |2 | -|[shiny](problems.md#shiny) |1.8.0 | | |1 | -|[shiny.worker](problems.md#shinyworker)|0.0.1 | | |2 | -|[sigminer](problems.md#sigminer)|2.3.0 | | |1 | -|[Signac](problems.md#signac)|1.12.0 | | |1 | -|[signeR](problems.md#signer)|2.4.0 | |1 |4 | -|[SimDesign](problems.md#simdesign)|2.14 | | |2 | -|simglm |0.8.9 | | | | -|simhelpers |0.2.1 | | | | -|simIDM |0.1.0 | | | | -|sims |0.0.3 | | | | -|simtrial |0.3.2 | | | | -|[sits](problems.md#sits) |1.4.2-1 | |1 |1 | -|skewlmm |1.1.0 | | | | -|[skpr](problems.md#skpr) |1.6.2 | | |1 | -|[SmCCNet](problems.md#smccnet)|2.0.2 |1 | | | -|[smoots](problems.md#smoots)|1.1.4 | |1 | | -|sNPLS |1.0.27 | | | | -|[solitude](problems.md#solitude)|1.1.3 | | |1 | -|sovereign |1.2.1 | | | | -|[SpaDES.core](problems.md#spadescore)|2.0.3 | | |2 | -|[spaMM](problems.md#spamm) |4.4.16 | | |2 | -|[sparrpowR](problems.md#sparrpowr)|0.2.8 | |1 | | -|[SPARSEMODr](problems.md#sparsemodr)|1.2.0 | | |1 | -|spatialTIME |1.3.4-3 | | | | -|[spatialwarnings](problems.md#spatialwarnings)|3.0.3 | |2 |1 | -|spdesign |0.0.3 | | | | -|specr |1.0.0 | | | | -|sperrorest |3.0.5 | | | | -|spFSR |2.0.4 | | | | -|[sphunif](problems.md#sphunif)|1.3.0 | |1 |2 | -|[spNetwork](problems.md#spnetwork)|0.4.3.8 | |1 |1 | -|[squat](problems.md#squat) |0.3.0 | |1 |1 | -|[ssdtools](problems.md#ssdtools)|1.0.6 | | |1 | -|stacks |1.0.4 | | | | -|[stars](problems.md#stars) |0.6-4 |1 -1 __+1__ | |2 | -|[startR](failures.md#startr)|2.3.1 |1 | | | -|steps |1.3.0 | | | | -|[stppSim](problems.md#stppsim)|1.3.2 | |1 | | -|supercells |1.0.0 | | | | -|[survstan](problems.md#survstan)|0.0.7 | | |3 | -|[synergyfinder](problems.md#synergyfinder)|3.10.3 | |1 |3 | -|[tableschema.r](problems.md#tableschemar)|1.1.2 | | |1 | -|[targeted](problems.md#targeted)|0.5 | |1 |1 | -|[targets](problems.md#targets)|1.6.0 | | |1 | -|TaxaNorm |2.4 | | | | -|tealeaves |1.0.6 | | | | -|templr |0.2-0 | | | | -|[text](problems.md#text) |1.2.0 | | |1 | -|[tglkmeans](problems.md#tglkmeans)|0.5.4 | | |2 | -|tidyMC |1.0.0 | | | | -|tidyqwi |0.1.2 | | | | -|tidySEM |0.2.6 | | | | -|tipmap |0.5.2 | | | | -|[TKCat](failures.md#tkcat) |1.0.7 |1 | | | -|[TreeSearch](problems.md#treesearch)|1.4.0 | | |1 | -|[TriDimRegression](failures.md#tridimregression)|1.0.2 |1 | | | -|[tsdistributions](problems.md#tsdistributions)|1.0.0 | |1 |1 | -|tsfeatures |1.1.1 | | | | -|tune |1.2.0 | | | | -|[txshift](problems.md#txshift)|0.3.8 | | |1 | -|uci |0.3.0 | | | | -|[UCSCXenaShiny](problems.md#ucscxenashiny)|2.0.0 | | |1 | -|[updog](problems.md#updog) |2.1.5 | |1 |1 | -|[vmeasur](problems.md#vmeasur)|0.1.4 |1 | | | -|webdeveloper |1.0.5 | | | | -|[WeightedCluster](problems.md#weightedcluster)|1.6-4 | |1 | | -|whitewater |0.1.3 | | | | -|wildmeta |0.3.2 | | | | -|wingen |2.1.1 | | | | -|[wru](problems.md#wru) |3.0.1 | |1 |2 | -|xegaPopulation |1.0.0.0 | | | | -|[XNAString](problems.md#xnastring)|1.10.0 | |1 |3 | -|yfR |1.1.0 | | | | +|package |version |error |warning |note | +|:--------------------------|:----------|:-----|:-------|:--------| +|adestr |1.0.0 | | | | +|AICcPermanova |0.0.2 | | | | +|[AIPW](problems.md#aipw) |0.6.3.2 | | |1 | +|ale |0.3.0 | | | | +|alookr |0.3.9 | | | | +|alphaci |1.0.1 | | | | +|[AlpsNMR](problems.md#alpsnmr)|4.6.0 |1 | | | +|[altdoc](problems.md#altdoc)|0.4.0 |1 | | | +|ao |1.1.0 | | | | +|[apsimx](problems.md#apsimx)|2.7.7 | | |1 | +|arkdb |0.0.18 | | | | +|[aroma.affymetrix](problems.md#aromaaffymetrix)|3.2.2 | | |1 | +|aroma.cn |1.7.1 | | | | +|[aroma.core](problems.md#aromacore)|3.3.1 | | |1 | +|ARPALData |1.5.2 | | | | +|[BAMBI](problems.md#bambi) |2.3.5 | | |2 | +|[bamm](problems.md#bamm) |0.5.0 | | |2 | +|baseballr |1.6.0 | | | | +|BatchGetSymbols |2.6.4 | | | | +|[batchtools](problems.md#batchtools)|0.9.17 | | |3 | +|bayesian |1.0.1 | | | | +|[bayesmove](problems.md#bayesmove)|0.2.1 | | |1 | +|[bbknnR](problems.md#bbknnr)|1.1.1 | | |1 | +|bcmaps |2.2.0 | | | | +|[BEKKs](problems.md#bekks) |1.4.4 | | |1 | +|bhmbasket |0.9.5 | | | | +|[bigDM](problems.md#bigdm) |0.5.4 | | |2 | +|[bistablehistory](problems.md#bistablehistory)|1.1.2 | | |2 | +|bkmrhat |1.1.3 | | | | +|[blavaan](problems.md#blavaan)|0.5-5 | | |3 | +|bolasso |0.2.0 | | | | +|[brms](problems.md#brms) |2.21.0 | | |2 | +|brpop |0.3.0 | | | | +|bsitar |0.2.1 | | | | +|[bslib](problems.md#bslib) |0.7.0 | | |1 | +|bspcov |1.0.0 | | | | +|calmr |0.6.1 | | | | +|campsis |1.5.3 | | | | +|canaper |1.0.1 | | | | +|[ceRNAnetsim](problems.md#cernanetsim)|1.16.0 | | |1 | +|cft |1.0.0 | | | | +|chatAI4R |0.2.10 | | | | +|[ChromSCape](problems.md#chromscape)|1.14.0 | |3 |4 | +|[civis](problems.md#civis) |3.1.2 | | |1 | +|[clickR](problems.md#clickr)|0.9.39 | | |1 | +|Clustering |1.7.10 | | | | +|[codalm](problems.md#codalm)|0.1.2 | | |1 | +|[codebook](problems.md#codebook)|0.9.2 | | |3 | +|[collinear](problems.md#collinear)|1.1.1 | | |1 | +|conformalInference.fd |1.1.1 | | | | +|conformalInference.multi |1.1.1 | | | | +|[Coxmos](problems.md#coxmos)|1.0.2 | | |1 | +|crossmap |0.4.0 | | | | +|CSCNet |0.1.2 | | | | +|[cSEM](problems.md#csem) |0.5.0 | | |2 | +|[CSGo](problems.md#csgo) |0.6.7 | | |1 | +|cvasi |1.1.3 | | | | +|cvCovEst |1.2.2 | | | | +|[dar](problems.md#dar) |1.0.0 | | |1 | +|dartR.popgen |1.0.0 | | | | +|dataquieR |2.1.0 | | | | +|DeclareDesign |1.0.10 | | | | +|delayed |0.5.0 | | | | +|[deseats](problems.md#deseats)|1.1.0 | | |1 | +|[dipsaus](problems.md#dipsaus)|0.2.9 | | |1 | +|[disk.frame](problems.md#diskframe)|0.8.3 | | |1 | +|[dispositionEffect](problems.md#dispositioneffect)|1.0.1 |1 | | | +|doFuture |1.0.1 | | | | +|DQAstats |0.3.5 | | | | +|drake |7.13.10 | | | | +|drimmR |1.0.1 | | | | +|drtmle |1.1.2 | | | | +|dsos |0.1.2 | | | | +|[DT](problems.md#dt) |0.33 | | |1 | +|easyalluvial |0.3.2 | | | | +|ecic |0.0.3 | | | | +|eCV |0.0.2 | | | | +|[EFAtools](problems.md#efatools)|0.4.4 | | |3 | +|EGAnet |2.0.6 | | | | +|elevatr |0.99.0 | | | | +|[envi](problems.md#envi) |0.1.19 | |1 | | +|epe4md |0.1.4 | | |-1 | +|EpiForsk |0.1.1 | | | | +|[EpiNow2](problems.md#epinow2)|1.5.2 | | |4 | +|[epitweetr](problems.md#epitweetr)|2.2.16 | | |2 | +|epwshiftr |0.1.4 | | | | +|[erah](problems.md#erah) |2.0.1 | | |1 | +|esemifar |2.0.1 | | | | +|ezcox |1.0.4 | | | | +|[fabletools](problems.md#fabletools)|0.4.2 | | |1 | +|FAMoS |0.3.0 | | | | +|[fastRhockey](problems.md#fastrhockey)|0.4.0 | | |1 | +|[fdacluster](problems.md#fdacluster)|0.3.0 | | |1 | +|fdWasserstein |1.0 | | | | +|[fect](problems.md#fect) |1.0.0 | | |3 | +|ferrn |0.1.0 | | | | +|fiery |1.2.1 | | | | +|finbif |0.9.7 | | | | +|fitlandr |0.1.0 | | | | +|[FLAMES](problems.md#flames)|1.10.0 | | |8 | +|[flowGraph](problems.md#flowgraph)|1.12.0 | | |3 | +|flowml |0.1.3 | | | | +|fmeffects |0.1.3 | | | | +|[forecastML](problems.md#forecastml)|0.9.0 | | |1 | +|fst4pg |1.0.0 | | | | +|fundiversity |1.1.1 | | | | +|funGp |1.0.0 | | | | +|furrr |0.3.1 | | | | +|future.apply |1.11.2 | | | | +|future.batchtools |0.12.1 | | | | +|future.callr |0.8.2 | | | | +|future.mirai |0.2.2 | | | | +|future.tests |0.7.0 | | | | +|futureverse |0.1.0 | | | | +|fxTWAPLS |0.1.3 | | | | +|[GeDS](problems.md#geds) |0.2.3 | |1 | | +|genBaRcode |1.2.7 | | | | +|[geocmeans](problems.md#geocmeans)|0.3.4 | | |1 | +|geohabnet |2.1.3 | | | | +|[GeoModels](problems.md#geomodels)|2.0.4 | | |1 | +|GetBCBData |0.7.0 | | | | +|[googleComputeEngineR](problems.md#googlecomputeenginer)|0.3.0 | | |2 __+1__ | +|googlePubsubR |0.0.4 | | | | +|[googleTagManageR](problems.md#googletagmanager)|0.2.0 | | |1 | +|greatR |2.0.0 | | | | +|[greed](problems.md#greed) |0.6.1 | | |3 | +|greta |0.4.5 | | | | +|[gstat](problems.md#gstat) |2.1-1 | | |1 | +|GSVA |1.52.3 | | | | +|[gsynth](problems.md#gsynth)|1.2.1 | | |2 | +|gtfs2emis |0.1.0 | | | | +|[gtfs2gps](problems.md#gtfs2gps)|2.1-1 |1 | | | +|gWQS |3.0.5 | | | | +|[hackeRnews](problems.md#hackernews)|0.1.0 | | |1 | +|hacksig |0.1.2 | | | | +|[hal9001](problems.md#hal9001)|0.4.6 | | |1 | +|haldensify |0.2.3 | | | | +|[hbamr](problems.md#hbamr) |2.3.1 | | |2 | +|[hero](problems.md#hero) |0.6 | | |3 | +|[heterogen](problems.md#heterogen)|1.2.33 | | |1 | +|hoopR |2.1.0 | | | | +|[httpgd](problems.md#httpgd)|2.0.2 |1 | |2 | +|[hwep](problems.md#hwep) |2.0.2 | | |3 | +|[hydroloom](problems.md#hydroloom)|1.0.2 |2 | |1 | +|idmodelr |0.4.0 | | | | +|imagefluency |0.2.5 | | | | +|iml |0.11.3 | | | | +|incubate |1.2.1 | | | | +|iNEXT.beta3D |1.0.2 | | | | +|[infercnv](problems.md#infercnv)|1.20.0 | | |3 | +|inlinedocs |2023.9.4 | | | | +|[InPAS](problems.md#inpas) |2.12.0 | |1 |2 | +|[interflex](problems.md#interflex)|1.2.6 | | |2 | +|ipc |0.1.4 | | | | +|[ISAnalytics](problems.md#isanalytics)|1.14.0 | | |2 | +|isopam |2.0 | | | | +|ivDiag |1.0.6 | | | | +|[ivmte](problems.md#ivmte) |1.4.0 | | |2 | +|jlmerclusterperm |1.1.4 | | | | +|JointAI |1.0.6 | | | | +|jstor |0.3.11 | | | | +|JuliaConnectoR |1.1.3 | | | | +|kernelboot |0.1.10 | | | | +|[keyATM](problems.md#keyatm)|0.5.2 | | |1 | +|LandComp |0.0.5 | | | | +|[latentcor](problems.md#latentcor)|2.0.1 | | |1 | +|[lava](problems.md#lava) |1.8.0 | | |1 | +|ldaPrototype |0.3.1 | | | | +|[ldsr](problems.md#ldsr) |0.0.2 | | |2 | +|lemna |1.0.1 | | | | +|LexFindR |1.1.0 | | | | +|lgr |0.4.4 | | | | +|[lidR](problems.md#lidr) |4.1.2 |-1 | |1 | +|[lightr](problems.md#lightr)|1.7.1 | | |2 | +|lmtp |1.4.0 | | | | +|LTFHPlus |2.1.1 | | | | +|LWFBrook90R |0.5.3 | | | | +|[MAI](problems.md#mai) |1.10.0 | | |1 | +|malariaAtlas |1.6.1 | | | | +|MAMS |2.0.2 | | | | +|[manynet](problems.md#manynet)|1.0.2 | | |2 | +|[mapme.biodiversity](problems.md#mapmebiodiversity)|0.8.0 |1 | | | +|marginaleffects |0.21.0 | | | | +|mbbe |0.1.0 | | | | +|mcmcensemble |3.1.0 | | | | +|mcp |0.3.4 | | | | +|merTools |0.6.2 | | | | +|[metaGE](problems.md#metage)|1.0.3 | | |1 | +|[mice](problems.md#mice) |3.16.0 | | |3 | +|migraph |1.4.1 | | | | +|[mikropml](problems.md#mikropml)|1.6.1 | | |1 | +|[MineICA](problems.md#mineica)|1.44.0 | |4 |4 | +|[missSBM](problems.md#misssbm)|1.0.4 | | |1 | +|[mistyR](problems.md#mistyr)|1.12.0 | | |2 | +|mlr3 |0.20.1 | | | | +|mlr3db |0.5.2 | | | | +|mlr3pipelines |0.6.0 | | | | +|mlr3resampling |2024.7.7 | | | | +|mlr3spatial |0.5.0 | | | | +|mlr3summary |0.1.0 | | | | +|mlr3torch |0.1.0 | | | | +|mlr3tuning |1.0.0 | | | | +|[modelsummary](problems.md#modelsummary)|2.1.1 | | |__+1__ | +|[momentuHMM](problems.md#momentuhmm)|1.5.5 | | |1 | +|[MOSS](problems.md#moss) |0.2.2 | | |1 | +|mplusParallel.automation |0.0.1.1 | | | | +|mrgsim.parallel |0.2.1 | | | | +|mslp |1.6.0 | | | | +|[multilevelcoda](problems.md#multilevelcoda)|1.3.0.2 | | |2 | +|multilevelmediation |0.3.1 | | | | +|[multitool](problems.md#multitool)|0.1.4 | | |1 | +|[multiverse](problems.md#multiverse)|0.6.1 | | |1 | +|[nebula](problems.md#nebula)|1.5.3 | | |1 | +|netShiny |1.0 | | | | +|NetSimR |0.1.5 | | | | +|nfl4th |1.0.4 | | | | +|nflfastR |4.6.1 | | | | +|[nflseedR](problems.md#nflseedr)|1.2.0 | | |1 | +|[nhdplusTools](problems.md#nhdplustools)|1.2.1 | | |1 | +|nncc |2.0.0 | | | | +|[oncomsm](problems.md#oncomsm)|0.1.4 | | |2 | +|[OOS](problems.md#oos) |1.0.0 | | |1 | +|optic |1.0.1 | | | | +|[OptimalGoldstandardDesigns](problems.md#optimalgoldstandarddesigns)|1.0.1 | | |1 | +|optimLanduse |1.2.1 | | | | +|origami |1.0.7 | | | | +|paramsim |0.1.0 | | | | +|[pareg](problems.md#pareg) |1.8.0 |3 | |2 | +|parseRPDR |1.1.1 | | | | +|[partR2](problems.md#partr2)|0.9.2 | | |1 | +|[pavo](problems.md#pavo) |2.9.0 | |1 | | +|pbapply |1.7-2 | | | | +|PeakSegDisk |2023.11.27 | | | | +|penaltyLearning |2024.1.25 | | | | +|pGRN |0.3.5 | | | | +|[photosynthesis](problems.md#photosynthesis)|2.1.4 | | |2 | +|[phylolm](problems.md#phylolm)|2.6.2 | | |2 | +|phylopath |1.3.0 | | | | +|PINstimation |0.1.2 | | | | +|[PLNmodels](problems.md#plnmodels)|1.2.0 | | |1 | +|plumber |1.2.2 | | | | +|polle |1.4 | | | | +|POMADE |0.2.0 | | | | +|[portvine](problems.md#portvine)|1.0.3 | | |1 | +|powRICLPM |0.1.1 | | | | +|[ProFAST](problems.md#profast)|1.4 | | |2 | +|progressr |0.14.0 | | | | +|[projpred](problems.md#projpred)|2.8.0 | | |2 | +|promises |1.3.0 | | | | +|[Prostar](problems.md#prostar)|1.36.2 | |1 |1 | +|proteus |1.1.4 | | | | +|protti |0.9.0 | | | | +|[psborrow2](problems.md#psborrow2)|0.0.3.4 | | |1 | +|PSCBS |0.67.0 | | | | +|[pseudohouseholds](problems.md#pseudohouseholds)|0.1.1 | | |1 -1 | +|PUMP |1.0.3 | | | | +|[qape](problems.md#qape) |2.1 | | |1 | +|[QDNAseq](problems.md#qdnaseq)|1.40.0 | |1 |1 | +|[qgcomp](problems.md#qgcomp)|2.15.2 | | |1 | +|qgcompint |0.7.0 | | | | +|[RAINBOWR](problems.md#rainbowr)|0.1.35 | | |1 | +|rangeMapper |2.0.3 | | | | +|rBiasCorrection |0.3.4 | | | | +|[Rcurvep](problems.md#rcurvep)|1.3.1 | | |__+1__ | +|readsdr |0.3.0 | | | | +|[receptiviti](problems.md#receptiviti)|0.1.8 |1 | | | +|rechaRge |1.0.0 | | | | +|refineR |1.6.1 | | | | +|[regmedint](problems.md#regmedint)|1.0.1 | | |1 | +|remiod |1.0.2 | | | | +|[reproducible](problems.md#reproducible)|2.1.0 |1 | | | +|reval |3.1-0 | | | | +|[rgee](problems.md#rgee) |1.1.7 | | |3 | +|[robotstxt](problems.md#robotstxt)|0.7.13 | | |2 | +|robust2sls |0.2.2 | | | | +|[rpm](problems.md#rpm) |0.7-3 | | |1 | +|rsi |0.2.1 | | | | +|RTransferEntropy |0.2.21 | | | | +|rTwig |1.0.2 | | | | +|s3fs |0.1.6 | | | | +|saeczi |0.2.0 | | | | +|[sampcompR](problems.md#sampcompr)|0.2.1 | | |1 | +|[sapfluxnetr](problems.md#sapfluxnetr)|0.1.4 | | |1 | +|[SCArray.sat](problems.md#scarraysat)|1.4.0 | | |1 | +|scBubbletree |1.6.0 | | | | +|SCdeconR |1.0.0 | | | | +|scDiffCom |1.0.0 | | | | +|SCtools |0.3.3 | | | | +|[sctransform](problems.md#sctransform)|0.4.1 | | |1 | +|[sdmTMB](problems.md#sdmtmb)|0.6.0 | | |1 | +|seer |1.1.8 | | | | +|semPower |2.1.0 | | | | +|semTests |0.5.0 | | | | +|semtree |0.9.20 | | | | +|[sentopics](problems.md#sentopics)|0.7.3 | | |3 | +|[Seurat](problems.md#seurat)|5.1.0 | | |3 | +|[SeuratObject](problems.md#seuratobject)|5.0.2 | | |3 | +|[sharp](problems.md#sharp) |1.4.6 | | |2 | +|[shiny](problems.md#shiny) |1.8.1.1 | | |1 | +|[shiny.worker](problems.md#shinyworker)|0.0.1 | | |2 | +|[sigminer](problems.md#sigminer)|2.3.1 | | |1 | +|[Signac](problems.md#signac)|1.13.0 | | |1 | +|[signeR](problems.md#signer)|2.6.0 | | |4 | +|[SimDesign](problems.md#simdesign)|2.16 | | |1 | +|simglm |0.8.9 | | | | +|simhelpers |0.2.1 | | | | +|simIDM |0.1.0 | | | | +|sims |0.0.3 | | | | +|simtrial |0.4.1 | | | | +|[sits](problems.md#sits) |1.5.0 | | |2 | +|skewlmm |1.1.0 | | | | +|[skpr](problems.md#skpr) |1.7.1 | | |1 | +|[SmCCNet](problems.md#smccnet)|2.0.3 | |1 | | +|[smoots](problems.md#smoots)|1.1.4 | | |1 | +|sNPLS |1.0.27 | | | | +|[solitude](problems.md#solitude)|1.1.3 | | |1 | +|sovereign |1.2.1 | | | | +|[SpaDES.core](problems.md#spadescore)|2.1.0 | | |2 | +|[spaMM](problems.md#spamm) |4.5.0 | | |2 | +|[sparrpowR](problems.md#sparrpowr)|0.2.8 | |1 | | +|[SPARSEMODr](problems.md#sparsemodr)|1.2.0 | | |1 __+1__ | +|spatialTIME |1.3.4-5 | | | | +|[spatialwarnings](problems.md#spatialwarnings)|3.0.3 | |1 |2 | +|spdesign |0.0.4 | | | | +|specr |1.0.0 | | | | +|[sperrorest](problems.md#sperrorest)|3.0.5 | | |1 | +|spFSR |2.0.4 | | | | +|[sphunif](problems.md#sphunif)|1.4.0 | | |2 | +|[spNetwork](problems.md#spnetwork)|0.4.4.3 | | |1 | +|[squat](problems.md#squat) |0.3.0 | | |1 | +|[ssdtools](problems.md#ssdtools)|1.0.6 | | |1 | +|stacks |1.0.5 | | | | +|[stars](problems.md#stars) |0.6-6 |1 | |2 | +|startR |2.3.1 | | | | +|steps |1.3.0 | | | | +|[stppSim](problems.md#stppsim)|1.3.4 | |1 | | +|supercells |1.0.0 | | | | +|[survstan](problems.md#survstan)|0.0.7.1 | | |3 | +|[synergyfinder](problems.md#synergyfinder)|3.12.0 | |1 |3 | +|[tableschema.r](problems.md#tableschemar)|1.1.2 | | |2 | +|[targeted](problems.md#targeted)|0.5 | | |1 | +|targets |1.7.1 | | | | +|TaxaNorm |2.4 | | | | +|tealeaves |1.0.6 | | | | +|templr |0.2-0 | | | | +|[tenm](problems.md#tenm) |0.5.1 | | |1 | +|[text](problems.md#text) |1.2.1 | | |1 | +|[tglkmeans](problems.md#tglkmeans)|0.5.5 | | |3 | +|tidyMC |1.0.0 | | | | +|tidySEM |0.2.7 | | | | +|tipmap |0.5.2 | | | | +|TKCat |1.1.11 | | | | +|[TreeMineR](problems.md#treeminer)|1.0.1 | | |1 | +|[TreeSearch](problems.md#treesearch)|1.5.1 | | |1 | +|[TriDimRegression](failures.md#tridimregression)|1.0.2 |1 | | | +|[tsdistributions](problems.md#tsdistributions)|1.0.1 |1 | |1 | +|tsfeatures |1.1.1 | | | | +|[tsgarch](problems.md#tsgarch)|1.0.2 | | |1 | +|tune |1.2.1 | | | | +|[txshift](problems.md#txshift)|0.3.8 | | |2 | +|uci |0.3.0 | | | | +|[UCSCXenaShiny](problems.md#ucscxenashiny)|2.1.0 | | |1 | +|[updog](problems.md#updog) |2.1.5 | | |1 | +|[vital](problems.md#vital) |1.1.0 | | |1 | +|[vmeasur](problems.md#vmeasur)|0.1.4 | |1 | | +|webdeveloper |1.0.5 | | | | +|[WeightedCluster](problems.md#weightedcluster)|1.6-4 | |1 | | +|whitewater |0.1.3 | | | | +|wildmeta |0.3.2 | | | | +|wingen |2.1.2 | | | | +|[winputall](problems.md#winputall)|1.0.1 | | |2 | +|[wru](problems.md#wru) |3.0.3 | | |2 | +|xegaPopulation |1.0.0.0 | | | | +|[XNAString](problems.md#xnastring)|1.12.0 | |1 |3 | +|ycevo |0.2.1 | | | | +|yfR |1.1.0 | | | | diff --git a/revdep/cran.md b/revdep/cran.md index 08bdce77..68f598d6 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,22 +1,27 @@ ## revdepcheck results -We checked 359 reverse dependencies (334 from CRAN + 25 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. +We checked 376 reverse dependencies (354 from CRAN + 22 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. - * We saw 1 new problems - * We failed to check 5 packages + * We saw 4 new problems + * We failed to check 1 packages Issues with CRAN packages are summarised below. ### New problems (This reports the first line of each new failure) -* stars - checking examples ...sh: line 1: 76201 Aborted (core dumped) LANGUAGE=en _R_CHECK_INTERNALS2_=1 '/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/bin/R' --vanilla --encoding=UTF-8 > 'stars-Ex.Rout' 2>&1 < 'stars-Ex.R' +* googleComputeEngineR + checking installed package size ... NOTE + +* modelsummary + checking installed package size ... NOTE + +* Rcurvep + checking installed package size ... NOTE + +* SPARSEMODr + checking installed package size ... NOTE ### Failed to check -* cft (NA) -* erah (NA) -* startR (NA) -* TKCat (NA) * TriDimRegression (NA) diff --git a/revdep/failures.md b/revdep/failures.md index 366c1a40..88c0dd6c 100644 --- a/revdep/failures.md +++ b/revdep/failures.md @@ -1,589 +1,3 @@ -# arkdb - -
- -* Version: -* GitHub: https://github.com/HenrikBengtsson/future -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` -g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_catalog.cpp -o duckdb/ub_src_catalog.o -g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_catalog_catalog_entry.cpp -o duckdb/ub_src_catalog_catalog_entry.o -g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_catalog_catalog_entry_dependency.cpp -o duckdb/ub_src_catalog_catalog_entry_dependency.o -g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_catalog_default.cpp -o duckdb/ub_src_catalog_default.o -g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_common_adbc.cpp -o duckdb/ub_src_common_adbc.o -g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_common_adbc_nanoarrow.cpp -o duckdb/ub_src_common_adbc_nanoarrow.o -g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_common.cpp -o duckdb/ub_src_common.o -g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_common_arrow_appender.cpp -o duckdb/ub_src_common_arrow_appender.o -g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_common_arrow.cpp -o duckdb/ub_src_common_arrow.o -g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_common_crypto.cpp -o duckdb/ub_src_common_crypto.o -... -g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c statement.cpp -o statement.o -g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c register.cpp -o register.o -g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib 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-Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c scan.cpp -o scan.o -g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c transform.cpp -o transform.o -g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c utils.cpp -o utils.o -g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c reltoaltrep.cpp -o reltoaltrep.o -g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c types.cpp -o types.o -g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c cpp11.cpp -o cpp11.o -g++ -std=gnu++17 -shared -L/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/lib -L/usr/local/lib64 -o duckdb.so database.o connection.o statement.o register.o relational.o scan.o transform.o utils.o reltoaltrep.o types.o cpp11.o duckdb/ub_src_catalog.o duckdb/ub_src_catalog_catalog_entry.o duckdb/ub_src_catalog_catalog_entry_dependency.o duckdb/ub_src_catalog_default.o duckdb/ub_src_common_adbc.o duckdb/ub_src_common_adbc_nanoarrow.o duckdb/ub_src_common.o duckdb/ub_src_common_arrow_appender.o duckdb/ub_src_common_arrow.o duckdb/ub_src_common_crypto.o duckdb/ub_src_common_enums.o duckdb/ub_src_common_exception.o duckdb/ub_src_common_operator.o duckdb/ub_src_common_progress_bar.o duckdb/ub_src_common_row_operations.o duckdb/ub_src_common_serializer.o duckdb/ub_src_common_sort.o duckdb/ub_src_common_types.o duckdb/ub_src_common_types_column.o duckdb/ub_src_common_types_row.o duckdb/ub_src_common_value_operations.o duckdb/src/common/vector_operations/boolean_operators.o duckdb/src/common/vector_operations/comparison_operators.o duckdb/src/common/vector_operations/generators.o duckdb/src/common/vector_operations/is_distinct_from.o duckdb/src/common/vector_operations/null_operations.o duckdb/src/common/vector_operations/numeric_inplace_operators.o duckdb/src/common/vector_operations/vector_cast.o duckdb/src/common/vector_operations/vector_copy.o duckdb/src/common/vector_operations/vector_hash.o duckdb/src/common/vector_operations/vector_storage.o duckdb/ub_src_core_functions_aggregate_algebraic.o duckdb/ub_src_core_functions_aggregate_distributive.o duckdb/ub_src_core_functions_aggregate_holistic.o duckdb/ub_src_core_functions_aggregate_nested.o duckdb/ub_src_core_functions_aggregate_regression.o duckdb/ub_src_core_functions.o duckdb/ub_src_core_functions_scalar_array.o duckdb/ub_src_core_functions_scalar_bit.o duckdb/ub_src_core_functions_scalar_blob.o duckdb/ub_src_core_functions_scalar_date.o duckdb/ub_src_core_functions_scalar_debug.o duckdb/ub_src_core_functions_scalar_enum.o duckdb/ub_src_core_functions_scalar_generic.o duckdb/ub_src_core_functions_scalar_list.o duckdb/ub_src_core_functions_scalar_map.o duckdb/ub_src_core_functions_scalar_math.o duckdb/ub_src_core_functions_scalar_operators.o duckdb/ub_src_core_functions_scalar_random.o duckdb/ub_src_core_functions_scalar_secret.o duckdb/ub_src_core_functions_scalar_string.o duckdb/ub_src_core_functions_scalar_struct.o duckdb/ub_src_core_functions_scalar_union.o duckdb/ub_src_execution.o duckdb/ub_src_execution_expression_executor.o duckdb/ub_src_execution_index_art.o duckdb/ub_src_execution_index.o duckdb/ub_src_execution_nested_loop_join.o duckdb/ub_src_execution_operator_aggregate.o duckdb/ub_src_execution_operator_csv_scanner_buffer_manager.o duckdb/ub_src_execution_operator_csv_scanner_scanner.o duckdb/ub_src_execution_operator_csv_scanner_sniffer.o duckdb/ub_src_execution_operator_csv_scanner_state_machine.o duckdb/ub_src_execution_operator_csv_scanner_table_function.o duckdb/ub_src_execution_operator_csv_scanner_util.o duckdb/ub_src_execution_operator_filter.o duckdb/ub_src_execution_operator_helper.o duckdb/ub_src_execution_operator_join.o duckdb/ub_src_execution_operator_order.o duckdb/ub_src_execution_operator_persistent.o duckdb/ub_src_execution_operator_projection.o duckdb/ub_src_execution_operator_scan.o duckdb/ub_src_execution_operator_schema.o duckdb/ub_src_execution_operator_set.o duckdb/ub_src_execution_physical_plan.o duckdb/ub_src_function_aggregate_distributive.o duckdb/ub_src_function_aggregate.o duckdb/ub_src_function.o duckdb/ub_src_function_cast.o duckdb/ub_src_function_cast_union.o duckdb/ub_src_function_pragma.o duckdb/ub_src_function_scalar_compressed_materialization.o duckdb/ub_src_function_scalar.o duckdb/ub_src_function_scalar_generic.o duckdb/ub_src_function_scalar_list.o duckdb/ub_src_function_scalar_operators.o duckdb/ub_src_function_scalar_sequence.o duckdb/ub_src_function_scalar_string.o duckdb/ub_src_function_scalar_string_regexp.o duckdb/ub_src_function_scalar_struct.o duckdb/ub_src_function_scalar_system.o duckdb/ub_src_function_table_arrow.o duckdb/ub_src_function_table.o duckdb/ub_src_function_table_system.o duckdb/ub_src_function_table_version.o duckdb/ub_src_main.o duckdb/ub_src_main_buffered_data.o duckdb/ub_src_main_capi.o duckdb/ub_src_main_capi_cast.o duckdb/ub_src_main_chunk_scan_state.o duckdb/ub_src_main_extension.o duckdb/ub_src_main_relation.o duckdb/ub_src_main_secret.o duckdb/ub_src_main_settings.o duckdb/ub_src_optimizer.o duckdb/ub_src_optimizer_compressed_materialization.o duckdb/ub_src_optimizer_join_order.o duckdb/ub_src_optimizer_matcher.o duckdb/ub_src_optimizer_pullup.o duckdb/ub_src_optimizer_pushdown.o duckdb/ub_src_optimizer_rule.o duckdb/ub_src_optimizer_statistics_expression.o duckdb/ub_src_optimizer_statistics_operator.o duckdb/ub_src_parallel.o duckdb/ub_src_parser.o duckdb/ub_src_parser_constraints.o duckdb/ub_src_parser_expression.o duckdb/ub_src_parser_parsed_data.o duckdb/ub_src_parser_query_node.o duckdb/ub_src_parser_statement.o duckdb/ub_src_parser_tableref.o duckdb/ub_src_parser_transform_constraint.o duckdb/ub_src_parser_transform_expression.o duckdb/ub_src_parser_transform_helpers.o duckdb/ub_src_parser_transform_statement.o duckdb/ub_src_parser_transform_tableref.o duckdb/ub_src_planner.o duckdb/ub_src_planner_binder_expression.o duckdb/ub_src_planner_binder_query_node.o duckdb/ub_src_planner_binder_statement.o duckdb/ub_src_planner_binder_tableref.o duckdb/ub_src_planner_expression.o duckdb/ub_src_planner_expression_binder.o duckdb/ub_src_planner_filter.o duckdb/ub_src_planner_operator.o duckdb/ub_src_planner_subquery.o duckdb/ub_src_storage.o duckdb/ub_src_storage_buffer.o duckdb/ub_src_storage_checkpoint.o duckdb/ub_src_storage_compression_alp.o duckdb/ub_src_storage_compression.o duckdb/ub_src_storage_compression_chimp.o duckdb/ub_src_storage_metadata.o duckdb/ub_src_storage_serialization.o duckdb/ub_src_storage_statistics.o duckdb/ub_src_storage_table.o duckdb/ub_src_transaction.o duckdb/src/verification/copied_statement_verifier.o duckdb/src/verification/deserialized_statement_verifier.o duckdb/src/verification/external_statement_verifier.o duckdb/src/verification/fetch_row_verifier.o duckdb/src/verification/no_operator_caching_verifier.o duckdb/src/verification/parsed_statement_verifier.o duckdb/src/verification/prepared_statement_verifier.o duckdb/src/verification/statement_verifier.o duckdb/src/verification/unoptimized_statement_verifier.o duckdb/third_party/fmt/format.o duckdb/third_party/fsst/fsst_avx512.o duckdb/third_party/fsst/libfsst.o duckdb/third_party/miniz/miniz.o duckdb/third_party/re2/re2/bitstate.o duckdb/third_party/re2/re2/compile.o duckdb/third_party/re2/re2/dfa.o duckdb/third_party/re2/re2/filtered_re2.o duckdb/third_party/re2/re2/mimics_pcre.o duckdb/third_party/re2/re2/nfa.o duckdb/third_party/re2/re2/onepass.o duckdb/third_party/re2/re2/parse.o duckdb/third_party/re2/re2/perl_groups.o duckdb/third_party/re2/re2/prefilter.o duckdb/third_party/re2/re2/prefilter_tree.o duckdb/third_party/re2/re2/prog.o duckdb/third_party/re2/re2/re2.o duckdb/third_party/re2/re2/regexp.o duckdb/third_party/re2/re2/set.o duckdb/third_party/re2/re2/simplify.o duckdb/third_party/re2/re2/stringpiece.o duckdb/third_party/re2/re2/tostring.o duckdb/third_party/re2/re2/unicode_casefold.o duckdb/third_party/re2/re2/unicode_groups.o duckdb/third_party/re2/util/rune.o duckdb/third_party/re2/util/strutil.o duckdb/third_party/hyperloglog/hyperloglog.o duckdb/third_party/hyperloglog/sds.o duckdb/third_party/skiplist/SkipList.o duckdb/third_party/fastpforlib/bitpacking.o duckdb/third_party/utf8proc/utf8proc.o duckdb/third_party/utf8proc/utf8proc_wrapper.o duckdb/third_party/libpg_query/pg_functions.o duckdb/third_party/libpg_query/postgres_parser.o duckdb/third_party/libpg_query/src_backend_nodes_list.o duckdb/third_party/libpg_query/src_backend_nodes_makefuncs.o duckdb/third_party/libpg_query/src_backend_nodes_value.o duckdb/third_party/libpg_query/src_backend_parser_gram.o duckdb/third_party/libpg_query/src_backend_parser_parser.o duckdb/third_party/libpg_query/src_backend_parser_scan.o duckdb/third_party/libpg_query/src_backend_parser_scansup.o duckdb/third_party/libpg_query/src_common_keywords.o duckdb/third_party/mbedtls/library/aes.o duckdb/third_party/mbedtls/library/aria.o duckdb/third_party/mbedtls/library/asn1parse.o duckdb/third_party/mbedtls/library/base64.o duckdb/third_party/mbedtls/library/bignum.o duckdb/third_party/mbedtls/library/camellia.o duckdb/third_party/mbedtls/library/cipher.o duckdb/third_party/mbedtls/library/cipher_wrap.o duckdb/third_party/mbedtls/library/constant_time.o duckdb/third_party/mbedtls/library/entropy.o duckdb/third_party/mbedtls/library/entropy_poll.o duckdb/third_party/mbedtls/library/gcm.o duckdb/third_party/mbedtls/library/md.o duckdb/third_party/mbedtls/library/oid.o duckdb/third_party/mbedtls/library/pem.o duckdb/third_party/mbedtls/library/pk.o duckdb/third_party/mbedtls/library/pk_wrap.o duckdb/third_party/mbedtls/library/pkparse.o duckdb/third_party/mbedtls/library/platform_util.o duckdb/third_party/mbedtls/library/rsa.o duckdb/third_party/mbedtls/library/rsa_alt_helpers.o duckdb/third_party/mbedtls/library/sha1.o duckdb/third_party/mbedtls/library/sha256.o duckdb/third_party/mbedtls/library/sha512.o duckdb/third_party/mbedtls/mbedtls_wrapper.o duckdb/extension/parquet/column_reader.o duckdb/extension/parquet/column_writer.o duckdb/extension/parquet/parquet_crypto.o duckdb/extension/parquet/parquet_extension.o duckdb/extension/parquet/parquet_metadata.o duckdb/extension/parquet/parquet_reader.o duckdb/extension/parquet/parquet_statistics.o duckdb/extension/parquet/parquet_timestamp.o duckdb/extension/parquet/parquet_writer.o duckdb/extension/parquet/serialize_parquet.o duckdb/extension/parquet/zstd_file_system.o duckdb/third_party/parquet/parquet_constants.o duckdb/third_party/parquet/parquet_types.o duckdb/third_party/thrift/thrift/protocol/TProtocol.o duckdb/third_party/thrift/thrift/transport/TTransportException.o duckdb/third_party/thrift/thrift/transport/TBufferTransports.o duckdb/third_party/snappy/snappy.o duckdb/third_party/snappy/snappy-sinksource.o duckdb/third_party/zstd/decompress/zstd_ddict.o duckdb/third_party/zstd/decompress/huf_decompress.o duckdb/third_party/zstd/decompress/zstd_decompress.o duckdb/third_party/zstd/decompress/zstd_decompress_block.o duckdb/third_party/zstd/common/entropy_common.o duckdb/third_party/zstd/common/fse_decompress.o duckdb/third_party/zstd/common/zstd_common.o duckdb/third_party/zstd/common/error_private.o duckdb/third_party/zstd/common/xxhash.o duckdb/third_party/zstd/compress/fse_compress.o duckdb/third_party/zstd/compress/hist.o duckdb/third_party/zstd/compress/huf_compress.o duckdb/third_party/zstd/compress/zstd_compress.o duckdb/third_party/zstd/compress/zstd_compress_literals.o duckdb/third_party/zstd/compress/zstd_compress_sequences.o duckdb/third_party/zstd/compress/zstd_compress_superblock.o duckdb/third_party/zstd/compress/zstd_double_fast.o duckdb/third_party/zstd/compress/zstd_fast.o duckdb/third_party/zstd/compress/zstd_lazy.o duckdb/third_party/zstd/compress/zstd_ldm.o duckdb/third_party/zstd/compress/zstd_opt.o -L/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/lib -lR - - -trying URL 'https://cloud.r-project.org/src/contrib/bslib_0.6.2.tar.gz' -Content type 'application/x-gzip' length 6060123 bytes (5.8 MB) -================================================== -downloaded 5.8 MB - -trying URL 'https://cloud.r-project.org/src/contrib/duckdb_0.10.0.tar.gz' -Content type 'application/x-gzip' length 4090561 bytes (3.9 MB) -================================================== -downloaded 3.9 MB - -... -* installing *binary* package ‘httr’ ... -* DONE (httr) -* installing *binary* package ‘jquerylib’ ... -* DONE (jquerylib) -* installing *binary* package ‘pillar’ ... -* DONE (pillar) -* installing *binary* package ‘pkgbuild’ ... -* DONE (pkgbuild) -* installing *binary* package ‘purrr’ ... -* DONE (purrr) - - -``` -### CRAN - -``` -g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_catalog.cpp -o duckdb/ub_src_catalog.o -g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_catalog_catalog_entry.cpp -o duckdb/ub_src_catalog_catalog_entry.o -g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_catalog_catalog_entry_dependency.cpp -o duckdb/ub_src_catalog_catalog_entry_dependency.o -g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_catalog_default.cpp -o duckdb/ub_src_catalog_default.o -g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_common_adbc.cpp -o duckdb/ub_src_common_adbc.o -g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_common_adbc_nanoarrow.cpp -o duckdb/ub_src_common_adbc_nanoarrow.o -g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_common.cpp -o duckdb/ub_src_common.o -g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_common_arrow_appender.cpp -o duckdb/ub_src_common_arrow_appender.o -g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_common_arrow.cpp -o duckdb/ub_src_common_arrow.o -g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c duckdb/ub_src_common_crypto.cpp -o duckdb/ub_src_common_crypto.o -... -g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include 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-I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include 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-Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c utils.cpp -o utils.o -g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c reltoaltrep.cpp -o reltoaltrep.o -g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c types.cpp -o types.o -g++ -std=gnu++17 -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -Iduckdb/src/include -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/re2 -Iduckdb/third_party/miniz -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/utf8proc -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/skiplist -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/tdigest -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/libpg_query -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/pcg -Iduckdb/third_party/httplib -Iduckdb/third_party/fast_float -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c cpp11.cpp -o cpp11.o -g++ -std=gnu++17 -shared -L/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/lib -L/usr/local/lib64 -o duckdb.so database.o connection.o statement.o register.o relational.o scan.o transform.o utils.o reltoaltrep.o types.o cpp11.o duckdb/ub_src_catalog.o duckdb/ub_src_catalog_catalog_entry.o duckdb/ub_src_catalog_catalog_entry_dependency.o duckdb/ub_src_catalog_default.o duckdb/ub_src_common_adbc.o duckdb/ub_src_common_adbc_nanoarrow.o duckdb/ub_src_common.o duckdb/ub_src_common_arrow_appender.o duckdb/ub_src_common_arrow.o duckdb/ub_src_common_crypto.o duckdb/ub_src_common_enums.o duckdb/ub_src_common_exception.o duckdb/ub_src_common_operator.o duckdb/ub_src_common_progress_bar.o duckdb/ub_src_common_row_operations.o duckdb/ub_src_common_serializer.o duckdb/ub_src_common_sort.o duckdb/ub_src_common_types.o duckdb/ub_src_common_types_column.o duckdb/ub_src_common_types_row.o duckdb/ub_src_common_value_operations.o duckdb/src/common/vector_operations/boolean_operators.o duckdb/src/common/vector_operations/comparison_operators.o duckdb/src/common/vector_operations/generators.o duckdb/src/common/vector_operations/is_distinct_from.o duckdb/src/common/vector_operations/null_operations.o duckdb/src/common/vector_operations/numeric_inplace_operators.o duckdb/src/common/vector_operations/vector_cast.o duckdb/src/common/vector_operations/vector_copy.o duckdb/src/common/vector_operations/vector_hash.o duckdb/src/common/vector_operations/vector_storage.o duckdb/ub_src_core_functions_aggregate_algebraic.o duckdb/ub_src_core_functions_aggregate_distributive.o duckdb/ub_src_core_functions_aggregate_holistic.o duckdb/ub_src_core_functions_aggregate_nested.o duckdb/ub_src_core_functions_aggregate_regression.o duckdb/ub_src_core_functions.o duckdb/ub_src_core_functions_scalar_array.o duckdb/ub_src_core_functions_scalar_bit.o duckdb/ub_src_core_functions_scalar_blob.o duckdb/ub_src_core_functions_scalar_date.o duckdb/ub_src_core_functions_scalar_debug.o duckdb/ub_src_core_functions_scalar_enum.o duckdb/ub_src_core_functions_scalar_generic.o duckdb/ub_src_core_functions_scalar_list.o duckdb/ub_src_core_functions_scalar_map.o duckdb/ub_src_core_functions_scalar_math.o duckdb/ub_src_core_functions_scalar_operators.o duckdb/ub_src_core_functions_scalar_random.o duckdb/ub_src_core_functions_scalar_secret.o duckdb/ub_src_core_functions_scalar_string.o duckdb/ub_src_core_functions_scalar_struct.o duckdb/ub_src_core_functions_scalar_union.o duckdb/ub_src_execution.o duckdb/ub_src_execution_expression_executor.o duckdb/ub_src_execution_index_art.o duckdb/ub_src_execution_index.o duckdb/ub_src_execution_nested_loop_join.o duckdb/ub_src_execution_operator_aggregate.o duckdb/ub_src_execution_operator_csv_scanner_buffer_manager.o duckdb/ub_src_execution_operator_csv_scanner_scanner.o duckdb/ub_src_execution_operator_csv_scanner_sniffer.o duckdb/ub_src_execution_operator_csv_scanner_state_machine.o duckdb/ub_src_execution_operator_csv_scanner_table_function.o duckdb/ub_src_execution_operator_csv_scanner_util.o duckdb/ub_src_execution_operator_filter.o duckdb/ub_src_execution_operator_helper.o duckdb/ub_src_execution_operator_join.o duckdb/ub_src_execution_operator_order.o duckdb/ub_src_execution_operator_persistent.o duckdb/ub_src_execution_operator_projection.o duckdb/ub_src_execution_operator_scan.o duckdb/ub_src_execution_operator_schema.o duckdb/ub_src_execution_operator_set.o duckdb/ub_src_execution_physical_plan.o duckdb/ub_src_function_aggregate_distributive.o duckdb/ub_src_function_aggregate.o duckdb/ub_src_function.o duckdb/ub_src_function_cast.o duckdb/ub_src_function_cast_union.o duckdb/ub_src_function_pragma.o duckdb/ub_src_function_scalar_compressed_materialization.o duckdb/ub_src_function_scalar.o duckdb/ub_src_function_scalar_generic.o duckdb/ub_src_function_scalar_list.o duckdb/ub_src_function_scalar_operators.o duckdb/ub_src_function_scalar_sequence.o duckdb/ub_src_function_scalar_string.o duckdb/ub_src_function_scalar_string_regexp.o duckdb/ub_src_function_scalar_struct.o duckdb/ub_src_function_scalar_system.o duckdb/ub_src_function_table_arrow.o duckdb/ub_src_function_table.o duckdb/ub_src_function_table_system.o duckdb/ub_src_function_table_version.o duckdb/ub_src_main.o duckdb/ub_src_main_buffered_data.o duckdb/ub_src_main_capi.o duckdb/ub_src_main_capi_cast.o duckdb/ub_src_main_chunk_scan_state.o duckdb/ub_src_main_extension.o duckdb/ub_src_main_relation.o duckdb/ub_src_main_secret.o duckdb/ub_src_main_settings.o duckdb/ub_src_optimizer.o duckdb/ub_src_optimizer_compressed_materialization.o duckdb/ub_src_optimizer_join_order.o duckdb/ub_src_optimizer_matcher.o duckdb/ub_src_optimizer_pullup.o duckdb/ub_src_optimizer_pushdown.o duckdb/ub_src_optimizer_rule.o duckdb/ub_src_optimizer_statistics_expression.o duckdb/ub_src_optimizer_statistics_operator.o duckdb/ub_src_parallel.o duckdb/ub_src_parser.o duckdb/ub_src_parser_constraints.o duckdb/ub_src_parser_expression.o duckdb/ub_src_parser_parsed_data.o duckdb/ub_src_parser_query_node.o duckdb/ub_src_parser_statement.o duckdb/ub_src_parser_tableref.o duckdb/ub_src_parser_transform_constraint.o duckdb/ub_src_parser_transform_expression.o duckdb/ub_src_parser_transform_helpers.o duckdb/ub_src_parser_transform_statement.o duckdb/ub_src_parser_transform_tableref.o duckdb/ub_src_planner.o duckdb/ub_src_planner_binder_expression.o duckdb/ub_src_planner_binder_query_node.o duckdb/ub_src_planner_binder_statement.o duckdb/ub_src_planner_binder_tableref.o duckdb/ub_src_planner_expression.o duckdb/ub_src_planner_expression_binder.o duckdb/ub_src_planner_filter.o duckdb/ub_src_planner_operator.o duckdb/ub_src_planner_subquery.o duckdb/ub_src_storage.o duckdb/ub_src_storage_buffer.o duckdb/ub_src_storage_checkpoint.o duckdb/ub_src_storage_compression_alp.o duckdb/ub_src_storage_compression.o duckdb/ub_src_storage_compression_chimp.o duckdb/ub_src_storage_metadata.o duckdb/ub_src_storage_serialization.o duckdb/ub_src_storage_statistics.o duckdb/ub_src_storage_table.o duckdb/ub_src_transaction.o duckdb/src/verification/copied_statement_verifier.o duckdb/src/verification/deserialized_statement_verifier.o duckdb/src/verification/external_statement_verifier.o duckdb/src/verification/fetch_row_verifier.o duckdb/src/verification/no_operator_caching_verifier.o duckdb/src/verification/parsed_statement_verifier.o duckdb/src/verification/prepared_statement_verifier.o duckdb/src/verification/statement_verifier.o duckdb/src/verification/unoptimized_statement_verifier.o duckdb/third_party/fmt/format.o duckdb/third_party/fsst/fsst_avx512.o duckdb/third_party/fsst/libfsst.o duckdb/third_party/miniz/miniz.o duckdb/third_party/re2/re2/bitstate.o duckdb/third_party/re2/re2/compile.o duckdb/third_party/re2/re2/dfa.o duckdb/third_party/re2/re2/filtered_re2.o duckdb/third_party/re2/re2/mimics_pcre.o duckdb/third_party/re2/re2/nfa.o duckdb/third_party/re2/re2/onepass.o duckdb/third_party/re2/re2/parse.o duckdb/third_party/re2/re2/perl_groups.o duckdb/third_party/re2/re2/prefilter.o duckdb/third_party/re2/re2/prefilter_tree.o duckdb/third_party/re2/re2/prog.o duckdb/third_party/re2/re2/re2.o duckdb/third_party/re2/re2/regexp.o duckdb/third_party/re2/re2/set.o duckdb/third_party/re2/re2/simplify.o duckdb/third_party/re2/re2/stringpiece.o duckdb/third_party/re2/re2/tostring.o duckdb/third_party/re2/re2/unicode_casefold.o duckdb/third_party/re2/re2/unicode_groups.o duckdb/third_party/re2/util/rune.o duckdb/third_party/re2/util/strutil.o duckdb/third_party/hyperloglog/hyperloglog.o duckdb/third_party/hyperloglog/sds.o duckdb/third_party/skiplist/SkipList.o duckdb/third_party/fastpforlib/bitpacking.o duckdb/third_party/utf8proc/utf8proc.o duckdb/third_party/utf8proc/utf8proc_wrapper.o duckdb/third_party/libpg_query/pg_functions.o duckdb/third_party/libpg_query/postgres_parser.o duckdb/third_party/libpg_query/src_backend_nodes_list.o duckdb/third_party/libpg_query/src_backend_nodes_makefuncs.o duckdb/third_party/libpg_query/src_backend_nodes_value.o duckdb/third_party/libpg_query/src_backend_parser_gram.o duckdb/third_party/libpg_query/src_backend_parser_parser.o duckdb/third_party/libpg_query/src_backend_parser_scan.o duckdb/third_party/libpg_query/src_backend_parser_scansup.o duckdb/third_party/libpg_query/src_common_keywords.o duckdb/third_party/mbedtls/library/aes.o duckdb/third_party/mbedtls/library/aria.o duckdb/third_party/mbedtls/library/asn1parse.o duckdb/third_party/mbedtls/library/base64.o duckdb/third_party/mbedtls/library/bignum.o duckdb/third_party/mbedtls/library/camellia.o duckdb/third_party/mbedtls/library/cipher.o duckdb/third_party/mbedtls/library/cipher_wrap.o duckdb/third_party/mbedtls/library/constant_time.o duckdb/third_party/mbedtls/library/entropy.o duckdb/third_party/mbedtls/library/entropy_poll.o duckdb/third_party/mbedtls/library/gcm.o duckdb/third_party/mbedtls/library/md.o duckdb/third_party/mbedtls/library/oid.o duckdb/third_party/mbedtls/library/pem.o duckdb/third_party/mbedtls/library/pk.o duckdb/third_party/mbedtls/library/pk_wrap.o duckdb/third_party/mbedtls/library/pkparse.o duckdb/third_party/mbedtls/library/platform_util.o duckdb/third_party/mbedtls/library/rsa.o duckdb/third_party/mbedtls/library/rsa_alt_helpers.o duckdb/third_party/mbedtls/library/sha1.o duckdb/third_party/mbedtls/library/sha256.o duckdb/third_party/mbedtls/library/sha512.o duckdb/third_party/mbedtls/mbedtls_wrapper.o duckdb/extension/parquet/column_reader.o duckdb/extension/parquet/column_writer.o duckdb/extension/parquet/parquet_crypto.o duckdb/extension/parquet/parquet_extension.o duckdb/extension/parquet/parquet_metadata.o duckdb/extension/parquet/parquet_reader.o duckdb/extension/parquet/parquet_statistics.o duckdb/extension/parquet/parquet_timestamp.o duckdb/extension/parquet/parquet_writer.o duckdb/extension/parquet/serialize_parquet.o duckdb/extension/parquet/zstd_file_system.o duckdb/third_party/parquet/parquet_constants.o duckdb/third_party/parquet/parquet_types.o duckdb/third_party/thrift/thrift/protocol/TProtocol.o duckdb/third_party/thrift/thrift/transport/TTransportException.o duckdb/third_party/thrift/thrift/transport/TBufferTransports.o duckdb/third_party/snappy/snappy.o duckdb/third_party/snappy/snappy-sinksource.o duckdb/third_party/zstd/decompress/zstd_ddict.o duckdb/third_party/zstd/decompress/huf_decompress.o duckdb/third_party/zstd/decompress/zstd_decompress.o duckdb/third_party/zstd/decompress/zstd_decompress_block.o duckdb/third_party/zstd/common/entropy_common.o duckdb/third_party/zstd/common/fse_decompress.o duckdb/third_party/zstd/common/zstd_common.o duckdb/third_party/zstd/common/error_private.o duckdb/third_party/zstd/common/xxhash.o duckdb/third_party/zstd/compress/fse_compress.o duckdb/third_party/zstd/compress/hist.o duckdb/third_party/zstd/compress/huf_compress.o duckdb/third_party/zstd/compress/zstd_compress.o duckdb/third_party/zstd/compress/zstd_compress_literals.o duckdb/third_party/zstd/compress/zstd_compress_sequences.o duckdb/third_party/zstd/compress/zstd_compress_superblock.o duckdb/third_party/zstd/compress/zstd_double_fast.o duckdb/third_party/zstd/compress/zstd_fast.o duckdb/third_party/zstd/compress/zstd_lazy.o duckdb/third_party/zstd/compress/zstd_ldm.o duckdb/third_party/zstd/compress/zstd_opt.o -L/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/lib -lR - - -trying URL 'https://cloud.r-project.org/src/contrib/bslib_0.6.2.tar.gz' -Content type 'application/x-gzip' length 6060123 bytes (5.8 MB) -================================================== -downloaded 5.8 MB - -trying URL 'https://cloud.r-project.org/src/contrib/duckdb_0.10.0.tar.gz' -Content type 'application/x-gzip' length 4090561 bytes (3.9 MB) -================================================== -downloaded 3.9 MB - -... -* installing *binary* package ‘httr’ ... -* DONE (httr) -* installing *binary* package ‘jquerylib’ ... -* DONE (jquerylib) -* installing *binary* package ‘pillar’ ... -* DONE (pillar) -* installing *binary* package ‘pkgbuild’ ... -* DONE (pkgbuild) -* installing *binary* package ‘purrr’ ... -* DONE (purrr) - - -``` -# cft - -
- -* Version: 1.0.0 -* GitHub: https://github.com/earthlab/cft-CRAN -* Source code: https://github.com/cran/cft -* Date/Publication: 2022-10-03 07:12:18 UTC -* Number of recursive dependencies: 90 - -Run `revdep_details(, "cft")` for more info - -
- -## In both - -* checking whether package ‘cft’ can be installed ... ERROR - ``` - Installation failed. - See ‘/c4/home/henrik/repositories/future/revdep/checks/cft/new/cft.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘cft’ ... -** package ‘cft’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - there is no package called ‘ncdf4’ -Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart -Execution halted -ERROR: lazy loading failed for package ‘cft’ -* removing ‘/c4/home/henrik/repositories/future/revdep/checks/cft/new/cft.Rcheck/cft’ - - -``` -### CRAN - -``` -* installing *source* package ‘cft’ ... -** package ‘cft’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - there is no package called ‘ncdf4’ -Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart -Execution halted -ERROR: lazy loading failed for package ‘cft’ -* removing ‘/c4/home/henrik/repositories/future/revdep/checks/cft/old/cft.Rcheck/cft’ - - -``` -# erah - -
- -* Version: 2.0.1 -* GitHub: https://github.com/xdomingoal/erah-devel -* Source code: https://github.com/cran/erah -* Date/Publication: 2023-12-20 10:10:02 UTC -* Number of recursive dependencies: 92 - -Run `revdep_details(, "erah")` for more info - -
- -## In both - -* checking whether package ‘erah’ can be installed ... ERROR - ``` - Installation failed. - See ‘/c4/home/henrik/repositories/future/revdep/checks/erah/new/erah.Rcheck/00install.out’ for details. - ``` - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘ncdf4’ - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘erah’ ... -** package ‘erah’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C compiler: ‘gcc (GCC) 10.2.1 20210130 (Red Hat 10.2.1-11)’ -gcc -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c registerDynamicSymbol.c -o registerDynamicSymbol.o -gcc -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c runfunc.c -o runfunc.o -gcc -shared -L/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/lib -L/usr/local/lib64 -o erah.so registerDynamicSymbol.o runfunc.o -L/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/lib -lR -installing to /c4/home/henrik/repositories/future/revdep/checks/erah/new/erah.Rcheck/00LOCK-erah/00new/erah/libs -** R -... -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : - there is no package called ‘ncdf4’ -Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart -Execution halted -ERROR: lazy loading failed for package ‘erah’ -* removing ‘/c4/home/henrik/repositories/future/revdep/checks/erah/new/erah.Rcheck/erah’ - - -``` -### CRAN - -``` -* installing *source* package ‘erah’ ... -** package ‘erah’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C compiler: ‘gcc (GCC) 10.2.1 20210130 (Red Hat 10.2.1-11)’ -gcc -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c registerDynamicSymbol.c -o registerDynamicSymbol.o -gcc -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c runfunc.c -o runfunc.o -gcc -shared -L/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/lib -L/usr/local/lib64 -o erah.so registerDynamicSymbol.o runfunc.o -L/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/lib -lR -installing to /c4/home/henrik/repositories/future/revdep/checks/erah/old/erah.Rcheck/00LOCK-erah/00new/erah/libs -** R -... -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : - there is no package called ‘ncdf4’ -Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart -Execution halted -ERROR: lazy loading failed for package ‘erah’ -* removing ‘/c4/home/henrik/repositories/future/revdep/checks/erah/old/erah.Rcheck/erah’ - - -``` -# flowml - -
- -* Version: -* GitHub: https://github.com/HenrikBengtsson/future -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - -* installing *binary* package ‘abind’ ... -* DONE (abind) -* installing *binary* package ‘backports’ ... -* DONE (backports) -* installing *binary* package ‘base64enc’ ... -* DONE (base64enc) -* installing *binary* package ‘bit’ ... -* DONE (bit) -* installing *binary* package ‘bitops’ ... -* DONE (bitops) -... -* installing *binary* package ‘caret’ ... -* DONE (caret) -* installing *binary* package ‘ConsRank’ ... -* DONE (ConsRank) -* installing *binary* package ‘labelled’ ... -* DONE (labelled) -* installing *binary* package ‘nloptr’ ... -* DONE (nloptr) -* installing *binary* package ‘rrcovHD’ ... -* DONE (rrcovHD) - - -``` -### CRAN - -``` - - - -* installing *binary* package ‘abind’ ... -* DONE (abind) -* installing *binary* package ‘backports’ ... -* DONE (backports) -* installing *binary* package ‘base64enc’ ... -* DONE (base64enc) -* installing *binary* package ‘bit’ ... -* DONE (bit) -* installing *binary* package ‘bitops’ ... -* DONE (bitops) -... -* installing *binary* package ‘caret’ ... -* DONE (caret) -* installing *binary* package ‘ConsRank’ ... -* DONE (ConsRank) -* installing *binary* package ‘labelled’ ... -* DONE (labelled) -* installing *binary* package ‘nloptr’ ... -* DONE (nloptr) -* installing *binary* package ‘rrcovHD’ ... -* DONE (rrcovHD) - - -``` -# marginaleffects - -
- -* Version: -* GitHub: https://github.com/HenrikBengtsson/future -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` -Creating a generic function for ‘nrow’ from package ‘base’ in package ‘tinytable’ -Creating a generic function for ‘ncol’ from package ‘base’ in package ‘tinytable’ -Creating a generic function for ‘colnames’ from package ‘base’ in package ‘tinytable’ -Creating a generic function for ‘colnames<-’ from package ‘base’ in package ‘tinytable’ - - -trying URL 'https://cloud.r-project.org/src/contrib/fmeffects_0.1.2.tar.gz' -Content type 'application/x-gzip' length 2486200 bytes (2.4 MB) -================================================== -downloaded 2.4 MB - -trying URL 'https://cloud.r-project.org/src/contrib/ggdag_0.2.12.tar.gz' -Content type 'application/x-gzip' length 1946994 bytes (1.9 MB) -================================================== -downloaded 1.9 MB - -... -** testing if installed package can be loaded from temporary location -** testing if installed package can be loaded from final location -** testing if installed package keeps a record of temporary installation path -* DONE (mlr3fselect) -* installing *source* package ‘mlr3learners’ ... -** package ‘mlr3learners’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading - - -``` -### CRAN - -``` -Creating a generic function for ‘nrow’ from package ‘base’ in package ‘tinytable’ -Creating a generic function for ‘ncol’ from package ‘base’ in package ‘tinytable’ -Creating a generic function for ‘colnames’ from package ‘base’ in package ‘tinytable’ -Creating a generic function for ‘colnames<-’ from package ‘base’ in package ‘tinytable’ - - -trying URL 'https://cloud.r-project.org/src/contrib/fmeffects_0.1.2.tar.gz' -Content type 'application/x-gzip' length 2486200 bytes (2.4 MB) -================================================== -downloaded 2.4 MB - -trying URL 'https://cloud.r-project.org/src/contrib/ggdag_0.2.12.tar.gz' -Content type 'application/x-gzip' length 1946994 bytes (1.9 MB) -================================================== -downloaded 1.9 MB - -... -** testing if installed package can be loaded from temporary location -** testing if installed package can be loaded from final location -** testing if installed package keeps a record of temporary installation path -* DONE (mlr3fselect) -* installing *source* package ‘mlr3learners’ ... -** package ‘mlr3learners’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading - - -``` -# Prostar - -
- -* Version: 1.34.6 -* GitHub: https://github.com/prostarproteomics/Prostar -* Source code: https://github.com/cran/Prostar -* Date/Publication: 2024-02-15 -* Number of recursive dependencies: 332 - -Run `revdep_details(, "Prostar")` for more info - -
- -## In both - -* checking whether package ‘Prostar’ can be installed ... ERROR - ``` - Installation failed. - See ‘/c4/home/henrik/repositories/future/revdep/checks/Prostar/new/Prostar.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘Prostar’ ... -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : - there is no package called ‘ncdf4’ -Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart -Execution halted -ERROR: lazy loading failed for package ‘Prostar’ -* removing ‘/c4/home/henrik/repositories/future/revdep/checks/Prostar/new/Prostar.Rcheck/Prostar’ - - -``` -### CRAN - -``` -* installing *source* package ‘Prostar’ ... -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : - there is no package called ‘ncdf4’ -Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart -Execution halted -ERROR: lazy loading failed for package ‘Prostar’ -* removing ‘/c4/home/henrik/repositories/future/revdep/checks/Prostar/old/Prostar.Rcheck/Prostar’ - - -``` -# startR - -
- -* Version: 2.3.1 -* GitHub: NA -* Source code: https://github.com/cran/startR -* Date/Publication: 2023-12-21 16:20:02 UTC -* Number of recursive dependencies: 60 - -Run `revdep_details(, "startR")` for more info - -
- -## In both - -* checking whether package ‘startR’ can be installed ... ERROR - ``` - Installation failed. - See ‘/c4/home/henrik/repositories/future/revdep/checks/startR/new/startR.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘startR’ ... -** package ‘startR’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : - there is no package called ‘ncdf4’ -Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart -Execution halted -ERROR: lazy loading failed for package ‘startR’ -* removing ‘/c4/home/henrik/repositories/future/revdep/checks/startR/new/startR.Rcheck/startR’ - - -``` -### CRAN - -``` -* installing *source* package ‘startR’ ... -** package ‘startR’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : - there is no package called ‘ncdf4’ -Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart -Execution halted -ERROR: lazy loading failed for package ‘startR’ -* removing ‘/c4/home/henrik/repositories/future/revdep/checks/startR/old/startR.Rcheck/startR’ - - -``` -# TKCat - -
- -* Version: 1.0.7 -* GitHub: https://github.com/patzaw/TKCat -* Source code: https://github.com/cran/TKCat -* Date/Publication: 2023-02-16 14:50:03 UTC -* Number of recursive dependencies: 115 - -Run `revdep_details(, "TKCat")` for more info - -
- -## In both - -* checking whether package ‘TKCat’ can be installed ... ERROR - ``` - Installation failed. - See ‘/c4/home/henrik/repositories/future/revdep/checks/TKCat/new/TKCat.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘TKCat’ ... -** package ‘TKCat’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : - there is no package called ‘arrow’ -Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart -Execution halted -ERROR: lazy loading failed for package ‘TKCat’ -* removing ‘/c4/home/henrik/repositories/future/revdep/checks/TKCat/new/TKCat.Rcheck/TKCat’ - - -``` -### CRAN - -``` -* installing *source* package ‘TKCat’ ... -** package ‘TKCat’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : - there is no package called ‘arrow’ -Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart -Execution halted -ERROR: lazy loading failed for package ‘TKCat’ -* removing ‘/c4/home/henrik/repositories/future/revdep/checks/TKCat/old/TKCat.Rcheck/TKCat’ - - -``` # TriDimRegression
@@ -592,9 +6,9 @@ ERROR: lazy loading failed for package ‘TKCat’ * GitHub: https://github.com/alexander-pastukhov/tridim-regression * Source code: https://github.com/cran/TriDimRegression * Date/Publication: 2023-09-13 14:10:03 UTC -* Number of recursive dependencies: 100 +* Number of recursive dependencies: 99 -Run `revdep_details(, "TriDimRegression")` for more info +Run `revdepcheck::revdep_details(, "TriDimRegression")` for more info
diff --git a/revdep/problems.md b/revdep/problems.md index 429f7c0a..7dae2adc 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -6,9 +6,9 @@ * GitHub: https://github.com/yqzhong7/AIPW * Source code: https://github.com/cran/AIPW * Date/Publication: 2021-06-11 09:30:02 UTC -* Number of recursive dependencies: 100 +* Number of recursive dependencies: 99 -Run `revdep_details(, "AIPW")` for more info +Run `revdepcheck::revdep_details(, "AIPW")` for more info
@@ -26,13 +26,13 @@ Run `revdep_details(, "AIPW")` for more info
-* Version: 4.4.0 +* Version: 4.6.0 * GitHub: https://github.com/sipss/AlpsNMR * Source code: https://github.com/cran/AlpsNMR -* Date/Publication: 2023-10-24 -* Number of recursive dependencies: 187 +* Date/Publication: 2024-04-30 +* Number of recursive dependencies: 185 -Run `revdep_details(, "AlpsNMR")` for more info +Run `revdepcheck::revdep_details(, "AlpsNMR")` for more info
@@ -41,17 +41,17 @@ Run `revdep_details(, "AlpsNMR")` for more info * checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: + ... --- re-building ‘Vig01-introduction-to-alpsnmr.Rmd’ using rmarkdown - ! LuaTeX error .../texlive/texmf-dist/scripts/oberdiek/oberdiek.luatex.lua:55: b - ad argument #1 to 'insert' (table expected, got nil) - stack traceback: - [C]: in function 'insert' - .../texlive/texmf-dist/scripts/oberdiek/oberdiek.luatex.lua:55: in main chunk - [C]: in function 'dofile' - [string "\directlua "]:6: in main chunk. - l.139 } + Error: processing vignette 'Vig01-introduction-to-alpsnmr.Rmd' failed with diagnostics: + LaTeX failed to compile /c4/home/henrik/repositories/future/revdep/checks/AlpsNMR/new/AlpsNMR.Rcheck/vign_test/AlpsNMR/vignettes/Vig01-introduction-to-alpsnmr.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. + --- failed re-building ‘Vig01-introduction-to-alpsnmr.Rmd’ + + --- re-building ‘Vig01b-introduction-to-alpsnmr-old-api.Rmd’ using rmarkdown + Error: processing vignette 'Vig01b-introduction-to-alpsnmr-old-api.Rmd' failed with diagnostics: + LaTeX failed to compile /c4/home/henrik/repositories/future/revdep/checks/AlpsNMR/new/AlpsNMR.Rcheck/vign_test/AlpsNMR/vignettes/Vig01b-introduction-to-alpsnmr-old-api.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. ... - LaTeX failed to compile /c4/home/henrik/repositories/future/revdep/checks/AlpsNMR/new/AlpsNMR.Rcheck/vign_test/AlpsNMR/vignettes/Vig02-handling-metadata-and-annotations.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Vig02-handling-metadata-and-annotations.log for more info. + LaTeX failed to compile /c4/home/henrik/repositories/future/revdep/checks/AlpsNMR/new/AlpsNMR.Rcheck/vign_test/AlpsNMR/vignettes/Vig02-handling-metadata-and-annotations.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. --- failed re-building ‘Vig02-handling-metadata-and-annotations.Rmd’ SUMMARY: processing the following files failed: @@ -67,13 +67,13 @@ Run `revdep_details(, "AlpsNMR")` for more info
-* Version: 0.3.0 +* Version: 0.4.0 * GitHub: https://github.com/etiennebacher/altdoc * Source code: https://github.com/cran/altdoc -* Date/Publication: 2024-02-21 16:00:06 UTC +* Date/Publication: 2024-07-23 21:10:02 UTC * Number of recursive dependencies: 85 -Run `revdep_details(, "altdoc")` for more info +Run `revdepcheck::revdep_details(, "altdoc")` for more info
@@ -86,24 +86,72 @@ Run `revdep_details(, "altdoc")` for more info ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: - v Setting active project to '' - v Setting active project to '/scratch/henrik/1715415/RtmpekdtNL/testpkg221fc379b081d' - v Setting active project to '' - v Setting active project to '/scratch/henrik/1715415/RtmpekdtNL/testpkg221fc70c8fde3' - v Setting active project to '' + 5. │ │ └─base::withCallingHandlers(...) + 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 7. └─altdoc::render_docs(path = getwd()) + 8. └─altdoc:::.import_vignettes(...) + 9. └─base::vapply(...) ... - Error in `render_docs(path = getwd())`: There were some failures when rendering vignettes. - Backtrace: - ▆ - 1. └─altdoc::render_docs(path = getwd()) at test-update.R:111:5 - 2. └─cli::cli_abort("There were some failures when rendering vignettes.") - 3. └─rlang::abort(...) + 2. └─altdoc:::.import_vignettes(...) + 3. └─base::vapply(...) + 4. └─altdoc (local) FUN(X[[i]], ...) + 5. └─altdoc:::.render_one_vignette(...) + 6. └─altdoc:::.qmd2md(origin, tar_dir, verbose = verbose, preamble = pre) + 7. └─base::cat(out[[2]]) - [ FAIL 5 | WARN 0 | SKIP 7 | PASS 56 ] + [ FAIL 8 | WARN 0 | SKIP 8 | PASS 55 ] Error: Test failures Execution halted ``` +# apsimx + +
+ +* Version: 2.7.7 +* GitHub: https://github.com/femiguez/apsimx +* Source code: https://github.com/cran/apsimx +* Date/Publication: 2024-05-06 18:20:03 UTC +* Number of recursive dependencies: 194 + +Run `revdepcheck::revdep_details(, "apsimx")` for more info + +
+ +## In both + +* checking installed package size ... NOTE + ``` + installed size is 7.1Mb + sub-directories of 1Mb or more: + extdata 5.5Mb + ``` + +# aroma.affymetrix + +
+ +* Version: 3.2.2 +* GitHub: https://github.com/HenrikBengtsson/aroma.affymetrix +* Source code: https://github.com/cran/aroma.affymetrix +* Date/Publication: 2024-02-18 20:40:03 UTC +* Number of recursive dependencies: 85 + +Run `revdepcheck::revdep_details(, "aroma.affymetrix")` for more info + +
+ +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.6Mb + sub-directories of 1Mb or more: + R 2.5Mb + help 1.1Mb + testScripts 1.1Mb + ``` + # aroma.core
@@ -112,9 +160,9 @@ Run `revdep_details(, "altdoc")` for more info * GitHub: https://github.com/HenrikBengtsson/aroma.core * Source code: https://github.com/cran/aroma.core * Date/Publication: 2024-02-19 08:40:02 UTC -* Number of recursive dependencies: 68 +* Number of recursive dependencies: 67 -Run `revdep_details(, "aroma.core")` for more info +Run `revdepcheck::revdep_details(, "aroma.core")` for more info
@@ -136,56 +184,66 @@ Run `revdep_details(, "aroma.core")` for more info * Date/Publication: 2023-03-08 23:10:05 UTC * Number of recursive dependencies: 53 -Run `revdep_details(, "BAMBI")` for more info +Run `revdepcheck::revdep_details(, "BAMBI")` for more info
## In both -* checking whether package ‘BAMBI’ can be installed ... WARNING +* checking installed package size ... NOTE ``` - Found the following significant warnings: - /c4/home/henrik/repositories/future/revdep/library/BAMBI/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/BAMBI/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/BAMBI/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - See ‘/c4/home/henrik/repositories/future/revdep/checks/BAMBI/new/BAMBI.Rcheck/00install.out’ for details. + installed size is 7.9Mb + sub-directories of 1Mb or more: + libs 7.4Mb ``` -* checking installed package size ... NOTE +* checking Rd files ... NOTE ``` - installed size is 7.3Mb - sub-directories of 1Mb or more: - libs 6.8Mb + checkRd: (-1) contour.angmcmc.Rd:48: Lost braces; missing escapes or markup? + 48 | Ignored if {show.data == FALSE}.} + | ^ + checkRd: (-1) contour.angmcmc.Rd:51: Lost braces; missing escapes or markup? + 51 | Ignored if {show.data == FALSE}.} + | ^ + checkRd: (-1) fit_incremental_angmix.Rd:104: Lost braces; missing escapes or markup? + 104 | \item{alpha}{significance level used in the test H_{0K}: expected log predictive density (elpd) for the fitted model with K components >= elpd for the fitted model + | ^ + checkRd: (-1) fit_incremental_angmix.Rd:148: Lost braces; missing escapes or markup? + 148 | H_{0K}: expected log predictive density (elpd) for the fitted model with K components >= elpd for the fitted model + | ^ + checkRd: (-1) fit_incremental_angmix.Rd:163: Lost braces; missing escapes or markup? + 163 | The incremental fitting stops if H_{0K} cannot be rejected + | ^ ``` # bamm
-* Version: 0.4.3 +* Version: 0.5.0 * GitHub: https://github.com/luismurao/bamm * Source code: https://github.com/cran/bamm -* Date/Publication: 2022-12-20 11:10:05 UTC -* Number of recursive dependencies: 109 +* Date/Publication: 2024-07-06 20:22:11 UTC +* Number of recursive dependencies: 104 -Run `revdep_details(, "bamm")` for more info +Run `revdepcheck::revdep_details(, "bamm")` for more info
## In both -* checking whether package ‘bamm’ can be installed ... WARNING +* checking installed package size ... NOTE ``` - Found the following significant warnings: - /c4/home/henrik/repositories/future/revdep/library/bamm/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/bamm/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/bamm/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - See ‘/c4/home/henrik/repositories/future/revdep/checks/bamm/new/bamm.Rcheck/00install.out’ for details. + installed size is 5.0Mb + sub-directories of 1Mb or more: + libs 2.9Mb ``` -* checking C++ specification ... NOTE +* checking dependencies in R code ... NOTE ``` - Specified C++11: please drop specification unless essential + Namespaces in Imports field not imported from: + ‘crosstalk’ ‘plotly’ + All declared Imports should be used. ``` # batchtools @@ -196,9 +254,9 @@ Run `revdep_details(, "bamm")` for more info * GitHub: https://github.com/mllg/batchtools * Source code: https://github.com/cran/batchtools * Date/Publication: 2023-04-20 14:20:06 UTC -* Number of recursive dependencies: 83 +* Number of recursive dependencies: 82 -Run `revdep_details(, "batchtools")` for more info +Run `revdepcheck::revdep_details(, "batchtools")` for more info
@@ -209,6 +267,16 @@ Run `revdep_details(, "batchtools")` for more info Package suggested but not available for checking: ‘doMPI’ ``` +* checking Rd files ... NOTE + ``` + checkRd: (-1) JobCollection.Rd:41: Lost braces + 41 | \item{namespaces}{code{character} with required packages to load via \code{\link[base]{requireNamespace}}.} + | ^ + checkRd: (-1) addAlgorithm.Rd:31: Lost braces + 31 | Algorithms are functions which get the code{data} part as well as the problem instance (the return value of the + | ^ + ``` + * checking Rd cross-references ... NOTE ``` Package unavailable to check Rd xrefs: ‘Rmpi’ @@ -224,19 +292,41 @@ Run `revdep_details(, "batchtools")` for more info * Date/Publication: 2021-10-22 08:50:09 UTC * Number of recursive dependencies: 168 -Run `revdep_details(, "bayesmove")` for more info +Run `revdepcheck::revdep_details(, "bayesmove")` for more info
## In both -* checking whether package ‘bayesmove’ can be installed ... WARNING +* checking Rd files ... NOTE ``` - Found the following significant warnings: - /c4/home/henrik/repositories/future/revdep/library/bayesmove/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/bayesmove/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/bayesmove/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - See ‘/c4/home/henrik/repositories/future/revdep/checks/bayesmove/new/bayesmove.Rcheck/00install.out’ for details. + checkRd: (-1) insert_NAs.Rd:22: Lost braces; missing escapes or markup? + 22 | A data frame where new rows have been inserted to regularize the \code{date} column. This results in values provided for \code{id}, \code{date}, and {dt} while inserting NAs for all other columns. Additionally, observations with duplicate date-times are removed. + | ^ + ``` + +# bbknnR + +
+ +* Version: 1.1.1 +* GitHub: https://github.com/ycli1995/bbknnR +* Source code: https://github.com/cran/bbknnR +* Date/Publication: 2024-02-13 10:20:03 UTC +* Number of recursive dependencies: 163 + +Run `revdepcheck::revdep_details(, "bbknnR")` for more info + +
+ +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.0Mb + sub-directories of 1Mb or more: + data 3.0Mb + libs 1.6Mb ``` # BEKKs @@ -249,39 +339,30 @@ Run `revdep_details(, "bayesmove")` for more info * Date/Publication: 2024-01-14 15:50:09 UTC * Number of recursive dependencies: 86 -Run `revdep_details(, "BEKKs")` for more info +Run `revdepcheck::revdep_details(, "BEKKs")` for more info
## In both -* checking whether package ‘BEKKs’ can be installed ... WARNING - ``` - Found the following significant warnings: - /c4/home/henrik/repositories/future/revdep/library/BEKKs/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/BEKKs/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/BEKKs/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - See ‘/c4/home/henrik/repositories/future/revdep/checks/BEKKs/new/BEKKs.Rcheck/00install.out’ for details. - ``` - * checking installed package size ... NOTE ``` - installed size is 18.5Mb + installed size is 18.7Mb sub-directories of 1Mb or more: - libs 17.6Mb + libs 17.8Mb ``` # bigDM
-* Version: 0.5.3 +* Version: 0.5.4 * GitHub: https://github.com/spatialstatisticsupna/bigDM * Source code: https://github.com/cran/bigDM -* Date/Publication: 2023-10-17 12:50:02 UTC -* Number of recursive dependencies: 135 +* Date/Publication: 2024-05-30 15:20:10 UTC +* Number of recursive dependencies: 128 -Run `revdep_details(, "bigDM")` for more info +Run `revdepcheck::revdep_details(, "bigDM")` for more info
@@ -305,9 +386,9 @@ Run `revdep_details(, "bigDM")` for more info * GitHub: https://github.com/alexander-pastukhov/bistablehistory * Source code: https://github.com/cran/bistablehistory * Date/Publication: 2023-09-13 13:20:09 UTC -* Number of recursive dependencies: 97 +* Number of recursive dependencies: 96 -Run `revdep_details(, "bistablehistory")` for more info +Run `revdepcheck::revdep_details(, "bistablehistory")` for more info
@@ -315,9 +396,9 @@ Run `revdep_details(, "bistablehistory")` for more info * checking installed package size ... NOTE ``` - installed size is 75.5Mb + installed size is 72.0Mb sub-directories of 1Mb or more: - libs 74.6Mb + libs 71.0Mb ``` * checking for GNU extensions in Makefiles ... NOTE @@ -329,13 +410,13 @@ Run `revdep_details(, "bistablehistory")` for more info
-* Version: 0.5-3 +* Version: 0.5-5 * GitHub: https://github.com/ecmerkle/blavaan * Source code: https://github.com/cran/blavaan -* Date/Publication: 2024-01-19 22:50:02 UTC -* Number of recursive dependencies: 98 +* Date/Publication: 2024-06-09 21:00:02 UTC +* Number of recursive dependencies: 97 -Run `revdep_details(, "blavaan")` for more info +Run `revdepcheck::revdep_details(, "blavaan")` for more info
@@ -348,10 +429,10 @@ Run `revdep_details(, "blavaan")` for more info * checking installed package size ... NOTE ``` - installed size is 196.2Mb + installed size is 187.8Mb sub-directories of 1Mb or more: R 1.2Mb - libs 193.4Mb + libs 184.9Mb testdata 1.4Mb ``` @@ -368,9 +449,9 @@ Run `revdep_details(, "blavaan")` for more info * GitHub: https://github.com/paul-buerkner/brms * Source code: https://github.com/cran/brms * Date/Publication: 2024-03-20 12:30:08 UTC -* Number of recursive dependencies: 201 +* Number of recursive dependencies: 200 -Run `revdep_details(, "brms")` for more info +Run `revdepcheck::revdep_details(, "brms")` for more info
@@ -383,182 +464,77 @@ Run `revdep_details(, "brms")` for more info * checking installed package size ... NOTE ``` - installed size is 8.4Mb + installed size is 8.7Mb sub-directories of 1Mb or more: R 3.7Mb - doc 3.5Mb + doc 3.6Mb ``` -# ceRNAnetsim +# bslib
-* Version: 1.14.1 -* GitHub: https://github.com/selcenari/ceRNAnetsim -* Source code: https://github.com/cran/ceRNAnetsim -* Date/Publication: 2023-12-18 -* Number of recursive dependencies: 101 +* Version: 0.7.0 +* GitHub: https://github.com/rstudio/bslib +* Source code: https://github.com/cran/bslib +* Date/Publication: 2024-03-29 01:00:03 UTC +* Number of recursive dependencies: 79 -Run `revdep_details(, "ceRNAnetsim")` for more info +Run `revdepcheck::revdep_details(, "bslib")` for more info
## In both -* checking examples ... ERROR - ``` - Running examples in ‘ceRNAnetsim-Ex.R’ failed - The error most likely occurred in: - - > ### Name: find_node_perturbation - > ### Title: Calculates average expression changes of all (or specified) - > ### nodes except trigger and finds the perturbed node count for all (or - > ### specified) nodes in system. - > ### Aliases: find_node_perturbation - > - > ### ** Examples - ... - 23. │ └─dplyr (local) eval() - 24. └─tidygraph::map_bfs(...) - 25. └─tidygraph:::bfs_df(graph, root, mode, unreachable) - 26. └─tibble::tibble(...) - 27. └─tibble:::tibble_quos(xs, .rows, .name_repair) - 28. └─tibble:::vectbl_recycle_rows(...) - 29. └─tibble:::abort_incompatible_size(...) - 30. └─tibble:::tibble_abort(...) - 31. └─rlang::abort(x, class, ..., call = call, parent = parent, use_cli_format = TRUE) - Execution halted - ``` - -* checking tests ... - ``` - Running ‘testthat.R’ - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 50 lines of output: - > library(testthat) - > library(ceRNAnetsim) - Loading required package: dplyr - - Attaching package: 'dplyr' - - ... - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Failure ('test-iter_perturb.R:33:3'): Could the functions work? ──────────── - `node_efficiencies` not equal to c(NA, NA, NA, 3.18, 2.27, 3.18, NA, 32). - 2/8 mismatches (average diff: 14.9) - [5] 3.18 - 2.27 == 0.91 - [8] 3.18 - 32.00 == -28.82 - - [ FAIL 1 | WARN 35 | SKIP 0 | PASS 36 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... ERROR - ``` - Error(s) in re-building vignettes: - --- re-building ‘auxiliary_commands.Rmd’ using rmarkdown - --- finished re-building ‘auxiliary_commands.Rmd’ - - --- re-building ‘basic_usage.Rmd’ using rmarkdown - --- finished re-building ‘basic_usage.Rmd’ - - --- re-building ‘convenient_iteration.Rmd’ using rmarkdown - - Quitting from lines 226-233 [unnamed-chunk-15] (convenient_iteration.Rmd) - ... - • Size 5: Existing data. - • Size 53: Column `rank`. - ℹ Only values of size one are recycled. - --- failed re-building ‘mirtarbase_example.Rmd’ - - SUMMARY: processing the following files failed: - ‘convenient_iteration.Rmd’ ‘mirtarbase_example.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -* checking R code for possible problems ... NOTE +* checking installed package size ... NOTE ``` - simulate: no visible binding for global variable ‘avg_count_current’ - simulate: no visible binding for global variable ‘avg_count_pre’ - Undefined global functions or variables: - avg_count_current avg_count_pre + installed size is 11.7Mb + sub-directories of 1Mb or more: + components 1.0Mb + fonts 2.8Mb + lib 5.2Mb ``` -# cft +# ceRNAnetsim
-* Version: 1.0.0 -* GitHub: https://github.com/earthlab/cft-CRAN -* Source code: https://github.com/cran/cft -* Date/Publication: 2022-10-03 07:12:18 UTC -* Number of recursive dependencies: 90 +* Version: 1.16.0 +* GitHub: https://github.com/selcenari/ceRNAnetsim +* Source code: https://github.com/cran/ceRNAnetsim +* Date/Publication: 2024-04-30 +* Number of recursive dependencies: 100 -Run `revdep_details(, "cft")` for more info +Run `revdepcheck::revdep_details(, "ceRNAnetsim")` for more info
## In both -* checking whether package ‘cft’ can be installed ... ERROR +* checking R code for possible problems ... NOTE ``` - Installation failed. - See ‘/c4/home/henrik/repositories/future/revdep/checks/cft/new/cft.Rcheck/00install.out’ for details. + find_node_perturbation: no visible binding for global variable + ‘perturbation_efficiency’ + find_node_perturbation: no visible binding for global variable + ‘perturbed_count’ + simulate: no visible binding for global variable ‘avg_count_current’ + simulate: no visible binding for global variable ‘avg_count_pre’ + Undefined global functions or variables: + avg_count_current avg_count_pre perturbation_efficiency + perturbed_count ``` -## Installation - -### Devel - -``` -* installing *source* package ‘cft’ ... -** package ‘cft’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - there is no package called ‘ncdf4’ -Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart -Execution halted -ERROR: lazy loading failed for package ‘cft’ -* removing ‘/c4/home/henrik/repositories/future/revdep/checks/cft/new/cft.Rcheck/cft’ - - -``` -### CRAN - -``` -* installing *source* package ‘cft’ ... -** package ‘cft’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - there is no package called ‘ncdf4’ -Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart -Execution halted -ERROR: lazy loading failed for package ‘cft’ -* removing ‘/c4/home/henrik/repositories/future/revdep/checks/cft/old/cft.Rcheck/cft’ - - -``` # ChromSCape
-* Version: 1.12.0 +* Version: 1.14.0 * GitHub: https://github.com/vallotlab/ChromSCape * Source code: https://github.com/cran/ChromSCape -* Date/Publication: 2023-10-25 +* Date/Publication: 2024-04-30 * Number of recursive dependencies: 232 -Run `revdep_details(, "ChromSCape")` for more info +Run `revdepcheck::revdep_details(, "ChromSCape")` for more info
@@ -574,7 +550,7 @@ Run `revdep_details(, "ChromSCape")` for more info * checking for code/documentation mismatches ... WARNING ``` - Codoc mismatches from documentation object 'generate_analysis': + Codoc mismatches from Rd file 'generate_analysis.Rd': generate_analysis Code: function(input_data_folder, analysis_name = "Analysis_1", output_directory = "./", input_data_type = c("scBED", @@ -599,7 +575,7 @@ Run `revdep_details(, "ChromSCape")` for more info * checking Rd \usage sections ... WARNING ``` - Undocumented arguments in documentation object 'rebin_matrix' + Undocumented arguments in Rd file 'rebin_matrix.Rd' ‘rebin_function’ Functions with \usage entries need to have the appropriate \alias @@ -609,16 +585,6 @@ Run `revdep_details(, "ChromSCape")` for more info Extensions’ manual. ``` -* checking examples ... WARNING - ``` - Found the following significant warnings: - - Warning: 'as(, "dspMatrix")' is deprecated. - Deprecated functions may be defunct as soon as of the next release of - R. - See ?Deprecated. - ``` - * checking for hidden files and directories ... NOTE ``` Found the following hidden files and directories: @@ -629,12 +595,12 @@ Run `revdep_details(, "ChromSCape")` for more info * checking installed package size ... NOTE ``` - installed size is 8.3Mb + installed size is 8.6Mb sub-directories of 1Mb or more: - data 1.4Mb + data 1.5Mb doc 2.9Mb - libs 1.0Mb - www 2.0Mb + libs 1.1Mb + www 2.1Mb ``` * checking R code for possible problems ... NOTE @@ -667,6 +633,47 @@ Run `revdep_details(, "ChromSCape")` for more info prepare_Rd: raw_counts_to_sparse_matrix.Rd:6-8: Dropping empty section \source ``` +# civis + +
+ +* Version: 3.1.2 +* GitHub: https://github.com/civisanalytics/civis-r +* Source code: https://github.com/cran/civis +* Date/Publication: 2023-03-31 08:00:03 UTC +* Number of recursive dependencies: 89 + +Run `revdepcheck::revdep_details(, "civis")` for more info + +
+ +## In both + +* checking Rd files ... NOTE + ``` + checkRd: (-1) enhancements_get_civis_data_match.Rd:60: Lost braces; missing escapes or markup? + 60 | \item{inputFieldMapping}{list, The field (i.e., column) mapping for the input table. See https://api.civisanalytics.com/enhancements/field-mapping for a list of valid field types and descriptions. Each field type should be mapped to a string specifying a column name in the input table. For field types that support multiple values (e.g., the "phone" field), a list of column names can be provided (e.g., {"phone": ["home_phone", "mobile_phone"], ...}).} + | ^ + checkRd: (-1) enhancements_patch_civis_data_match.Rd:53: Lost braces; missing escapes or markup? + 53 | \item{input_field_mapping}{list optional. The field (i.e., column) mapping for the input table. See https://api.civisanalytics.com/enhancements/field-mapping for a list of valid field types and descriptions. Each field type should be mapped to a string specifying a column name in the input table. For field types that support multiple values (e.g., the "phone" field), a list of column names can be provided (e.g., {"phone": ["home_phone", "mobile_phone"], ...}).} + | ^ + checkRd: (-1) enhancements_patch_civis_data_match.Rd:125: Lost braces; missing escapes or markup? + 125 | \item{inputFieldMapping}{list, The field (i.e., column) mapping for the input table. See https://api.civisanalytics.com/enhancements/field-mapping for a list of valid field types and descriptions. Each field type should be mapped to a string specifying a column name in the input table. For field types that support multiple values (e.g., the "phone" field), a list of column names can be provided (e.g., {"phone": ["home_phone", "mobile_phone"], ...}).} + | ^ + checkRd: (-1) enhancements_post_civis_data_match.Rd:24: Lost braces; missing escapes or markup? + ... + | ^ + checkRd: (-1) templates_patch_scripts.Rd:42: Lost braces; missing escapes or markup? + 42 | \item allowedValues array, The possible values this parameter can take, effectively making this an enumerable parameter. Allowed values is an array of hashes of the following format: `{label: 'Import', 'value': 'import'}` + | ^ + checkRd: (-1) templates_post_scripts.Rd:45: Lost braces; missing escapes or markup? + 45 | \item allowedValues array, The possible values this parameter can take, effectively making this an enumerable parameter. Allowed values is an array of hashes of the following format: `{label: 'Import', 'value': 'import'}` + | ^ + checkRd: (-1) templates_put_scripts.Rd:42: Lost braces; missing escapes or markup? + 42 | \item allowedValues array, The possible values this parameter can take, effectively making this an enumerable parameter. Allowed values is an array of hashes of the following format: `{label: 'Import', 'value': 'import'}` + | ^ + ``` + # clickR
@@ -677,7 +684,7 @@ Run `revdep_details(, "ChromSCape")` for more info * Date/Publication: 2023-08-07 17:40:06 UTC * Number of recursive dependencies: 9 -Run `revdep_details(, "clickR")` for more info +Run `revdepcheck::revdep_details(, "clickR")` for more info
@@ -688,6 +695,33 @@ Run `revdep_details(, "clickR")` for more info Note: found 1 marked UTF-8 string ``` +# codalm + +
+ +* Version: 0.1.2 +* GitHub: https://github.com/jfiksel/codalm +* Source code: https://github.com/cran/codalm +* Date/Publication: 2021-07-26 18:40:02 UTC +* Number of recursive dependencies: 57 + +Run `revdepcheck::revdep_details(, "codalm")` for more info + +
+ +## In both + +* checking Rd files ... NOTE + ``` + checkRd: (-1) educFM.Rd:22: Lost braces in \itemize; meant \describe ? + checkRd: (-1) educFM.Rd:23: Lost braces in \itemize; meant \describe ? + checkRd: (-1) educFM.Rd:24: Lost braces in \itemize; meant \describe ? + checkRd: (-1) educFM.Rd:25: Lost braces in \itemize; meant \describe ? + checkRd: (-1) educFM.Rd:26: Lost braces in \itemize; meant \describe ? + checkRd: (-1) educFM.Rd:27: Lost braces in \itemize; meant \describe ? + checkRd: (-1) educFM.Rd:28: Lost braces in \itemize; meant \describe ? + ``` + # codebook
@@ -696,9 +730,9 @@ Run `revdep_details(, "clickR")` for more info * GitHub: https://github.com/rubenarslan/codebook * Source code: https://github.com/cran/codebook * Date/Publication: 2020-06-06 23:40:03 UTC -* Number of recursive dependencies: 156 +* Number of recursive dependencies: 155 -Run `revdep_details(, "codebook")` for more info +Run `revdepcheck::revdep_details(, "codebook")` for more info
@@ -731,7 +765,7 @@ Run `revdep_details(, "codebook")` for more info * Date/Publication: 2023-12-08 08:50:02 UTC * Number of recursive dependencies: 55 -Run `revdep_details(, "collinear")` for more info +Run `revdepcheck::revdep_details(, "collinear")` for more info
@@ -747,13 +781,13 @@ Run `revdep_details(, "collinear")` for more info
-* Version: 1.0.1 +* Version: 1.0.2 * GitHub: https://github.com/BiostatOmics/Coxmos * Source code: https://github.com/cran/Coxmos -* Date/Publication: 2024-03-22 17:10:02 UTC -* Number of recursive dependencies: 204 +* Date/Publication: 2024-03-25 20:32:38 UTC +* Number of recursive dependencies: 194 -Run `revdep_details(, "Coxmos")` for more info +Run `revdepcheck::revdep_details(, "Coxmos")` for more info
@@ -761,10 +795,11 @@ Run `revdep_details(, "Coxmos")` for more info * checking installed package size ... NOTE ``` - installed size is 5.1Mb + installed size is 5.6Mb sub-directories of 1Mb or more: + R 1.0Mb data 1.2Mb - doc 2.7Mb + doc 2.9Mb ``` # cSEM @@ -777,7 +812,7 @@ Run `revdep_details(, "Coxmos")` for more info * Date/Publication: 2022-11-24 17:50:05 UTC * Number of recursive dependencies: 128 -Run `revdep_details(, "cSEM")` for more info +Run `revdepcheck::revdep_details(, "cSEM")` for more info
@@ -789,6 +824,13 @@ Run `revdep_details(, "cSEM")` for more info All declared Imports should be used. ``` +* checking Rd files ... NOTE + ``` + checkRd: (-1) calculateEffects.Rd:24: Lost braces; missing escapes or markup? + 24 | equals (I-B)^{-1}Gamma. The indirect effect equals the difference between + | ^ + ``` + # CSGo
@@ -797,9 +839,9 @@ Run `revdep_details(, "cSEM")` for more info * GitHub: https://github.com/adsoncostanzifilho/CSGo * Source code: https://github.com/cran/CSGo * Date/Publication: 2021-05-07 18:50:02 UTC -* Number of recursive dependencies: 77 +* Number of recursive dependencies: 76 -Run `revdep_details(, "CSGo")` for more info +Run `revdepcheck::revdep_details(, "CSGo")` for more info
@@ -812,49 +854,63 @@ Run `revdep_details(, "CSGo")` for more info All declared Imports should be used. ``` -# deseats +# dar
* Version: 1.0.0 -* GitHub: NA -* Source code: https://github.com/cran/deseats -* Date/Publication: 2023-11-08 19:50:02 UTC -* Number of recursive dependencies: 109 +* GitHub: https://github.com/MicrobialGenomics-IrsicaixaOrg/dar +* Source code: https://github.com/cran/dar +* Date/Publication: 2024-04-30 +* Number of recursive dependencies: 378 -Run `revdep_details(, "deseats")` for more info +Run `revdepcheck::revdep_details(, "dar")` for more info
## In both -* checking whether package ‘deseats’ can be installed ... WARNING +* checking installed package size ... NOTE ``` - Found the following significant warnings: - /c4/home/henrik/repositories/future/revdep/library/deseats/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/deseats/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/deseats/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - See ‘/c4/home/henrik/repositories/future/revdep/checks/deseats/new/deseats.Rcheck/00install.out’ for details. + installed size is 5.6Mb + sub-directories of 1Mb or more: + doc 4.2Mb ``` +# deseats + +
+ +* Version: 1.1.0 +* GitHub: NA +* Source code: https://github.com/cran/deseats +* Date/Publication: 2024-07-12 10:50:15 UTC +* Number of recursive dependencies: 115 + +Run `revdepcheck::revdep_details(, "deseats")` for more info + +
+ +## In both + * checking installed package size ... NOTE ``` - installed size is 8.3Mb + installed size is 8.5Mb sub-directories of 1Mb or more: - libs 7.6Mb + libs 7.8Mb ``` # dipsaus
-* Version: 0.2.8 +* Version: 0.2.9 * GitHub: https://github.com/dipterix/dipsaus * Source code: https://github.com/cran/dipsaus -* Date/Publication: 2023-07-03 20:00:03 UTC -* Number of recursive dependencies: 70 +* Date/Publication: 2024-06-27 11:10:01 UTC +* Number of recursive dependencies: 69 -Run `revdep_details(, "dipsaus")` for more info +Run `revdepcheck::revdep_details(, "dipsaus")` for more info
@@ -862,10 +918,10 @@ Run `revdep_details(, "dipsaus")` for more info * checking installed package size ... NOTE ``` - installed size is 5.9Mb + installed size is 6.7Mb sub-directories of 1Mb or more: doc 1.1Mb - libs 3.5Mb + libs 4.2Mb ``` # disk.frame @@ -876,20 +932,22 @@ Run `revdep_details(, "dipsaus")` for more info * GitHub: https://github.com/DiskFrame/disk.frame * Source code: https://github.com/cran/disk.frame * Date/Publication: 2023-08-24 16:20:10 UTC -* Number of recursive dependencies: 99 +* Number of recursive dependencies: 98 -Run `revdep_details(, "disk.frame")` for more info +Run `revdepcheck::revdep_details(, "disk.frame")` for more info
## In both -* checking package dependencies ... ERROR +* checking Rd files ... NOTE ``` - Package required but not available: ‘arrow’ - - See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ - manual. + checkRd: (-1) csv_to_disk.frame.Rd:56: Lost braces; missing escapes or markup? + 56 | strings, and you are encouraged to use {fasttime} to convert the strings to + | ^ + checkRd: (-1) purrr_as_mapper.Rd:10: Lost braces; missing escapes or markup? + 10 | \item{.f}{a normal function or purrr syntax function i.e. `~{ ...code...}`} + | ^ ``` # dispositionEffect @@ -902,7 +960,7 @@ Run `revdep_details(, "disk.frame")` for more info * Date/Publication: 2022-05-30 07:50:02 UTC * Number of recursive dependencies: 136 -Run `revdep_details(, "dispositionEffect")` for more info +Run `revdepcheck::revdep_details(, "dispositionEffect")` for more info
@@ -933,101 +991,27 @@ Run `revdep_details(, "dispositionEffect")` for more info Execution halted ``` -# dragon +# DT
-* Version: 1.2.1 -* GitHub: https://github.com/sjspielman/dragon -* Source code: https://github.com/cran/dragon -* Date/Publication: 2022-04-08 08:42:33 UTC -* Number of recursive dependencies: 131 +* Version: 0.33 +* GitHub: https://github.com/rstudio/DT +* Source code: https://github.com/cran/DT +* Date/Publication: 2024-04-04 05:03:17 UTC +* Number of recursive dependencies: 52 -Run `revdep_details(, "dragon")` for more info +Run `revdepcheck::revdep_details(, "DT")` for more info
## In both -* checking tests ... +* checking installed package size ... NOTE ``` - Running ‘testthat.R’ - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(dragon) - > - > test_check("dragon") - Error in `FUN()`: - ! In path: "/c4/home/henrik/repositories/future/revdep/checks/dragon/new/dragon.Rcheck/tests/testthat/setup_test-settings.R" - ... - 10. │ └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap) - 11. │ ├─base::withCallingHandlers(...) - 12. │ └─base::eval(exprs, env) - 13. │ └─base::eval(exprs, env) - 14. │ └─igraph::read_graph("graph_by_redox.igraph", format = "ncol") at tests/testthat/setup_test-settings.R:8:1 - 15. │ └─igraph:::read.graph.ncol(file, ...) - 16. └─base::.handleSimpleError(...) - 17. └─testthat (local) h(simpleError(msg, call)) - 18. └─rlang::abort(...) - Execution halted - ``` - -* checking package subdirectories ... NOTE - ``` - Problems with news in ‘NEWS.md’: - No news entries found. - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘htmltools’ - All declared Imports should be used. - ``` - -# drake - -
- -* Version: 7.13.9 -* GitHub: https://github.com/ropensci/drake -* Source code: https://github.com/cran/drake -* Date/Publication: 2024-03-04 15:20:02 UTC -* Number of recursive dependencies: 166 - -Run `revdep_details(, "drake")` for more info - -
- -## In both - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘clustermq’ - ``` - -# DT - -
- -* Version: 0.32 -* GitHub: https://github.com/rstudio/DT -* Source code: https://github.com/cran/DT -* Date/Publication: 2024-02-19 16:50:02 UTC -* Number of recursive dependencies: 53 - -Run `revdep_details(, "DT")` for more info - -
- -## In both - -* checking installed package size ... NOTE - ``` - installed size is 5.4Mb + installed size is 6.4Mb sub-directories of 1Mb or more: - htmlwidgets 4.8Mb + htmlwidgets 5.5Mb ``` # EFAtools @@ -1038,23 +1022,14 @@ Run `revdep_details(, "DT")` for more info * GitHub: https://github.com/mdsteiner/EFAtools * Source code: https://github.com/cran/EFAtools * Date/Publication: 2023-01-06 14:50:40 UTC -* Number of recursive dependencies: 94 +* Number of recursive dependencies: 93 -Run `revdep_details(, "EFAtools")` for more info +Run `revdepcheck::revdep_details(, "EFAtools")` for more info
## In both -* checking whether package ‘EFAtools’ can be installed ... WARNING - ``` - Found the following significant warnings: - /c4/home/henrik/repositories/future/revdep/library/EFAtools/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/EFAtools/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/EFAtools/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - See ‘/c4/home/henrik/repositories/future/revdep/checks/EFAtools/new/EFAtools.Rcheck/00install.out’ for details. - ``` - * checking C++ specification ... NOTE ``` Specified C++11: please drop specification unless essential @@ -1062,9 +1037,9 @@ Run `revdep_details(, "EFAtools")` for more info * checking installed package size ... NOTE ``` - installed size is 7.2Mb + installed size is 7.5Mb sub-directories of 1Mb or more: - libs 6.0Mb + libs 6.2Mb ``` * checking dependencies in R code ... NOTE @@ -1083,7 +1058,7 @@ Run `revdep_details(, "EFAtools")` for more info * Date/Publication: 2024-01-23 14:40:03 UTC * Number of recursive dependencies: 153 -Run `revdep_details(, "envi")` for more info +Run `revdepcheck::revdep_details(, "envi")` for more info
@@ -1100,24 +1075,35 @@ Run `revdep_details(, "envi")` for more info
-* Version: 1.4.0 +* Version: 1.5.2 * GitHub: https://github.com/epiforecasts/EpiNow2 * Source code: https://github.com/cran/EpiNow2 -* Date/Publication: 2023-09-26 12:00:02 UTC -* Number of recursive dependencies: 131 +* Date/Publication: 2024-05-16 22:50:06 UTC +* Number of recursive dependencies: 132 -Run `revdep_details(, "EpiNow2")` for more info +Run `revdepcheck::revdep_details(, "EpiNow2")` for more info
## In both +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘cmdstanr’ + ``` + * checking installed package size ... NOTE ``` - installed size is 223.7Mb + installed size is 227.1Mb sub-directories of 1Mb or more: - help 2.0Mb - libs 220.8Mb + doc 1.8Mb + extdata 2.3Mb + libs 221.6Mb + ``` + +* checking Rd cross-references ... NOTE + ``` + Package unavailable to check Rd xrefs: ‘cmdstanr’ ``` * checking for GNU extensions in Makefiles ... NOTE @@ -1133,9 +1119,9 @@ Run `revdep_details(, "EpiNow2")` for more info * GitHub: https://github.com/EU-ECDC/epitweetr * Source code: https://github.com/cran/epitweetr * Date/Publication: 2023-11-15 09:30:08 UTC -* Number of recursive dependencies: 149 +* Number of recursive dependencies: 148 -Run `revdep_details(, "epitweetr")` for more info +Run `revdepcheck::revdep_details(, "epitweetr")` for more info
@@ -1161,81 +1147,64 @@ Run `revdep_details(, "epitweetr")` for more info * GitHub: https://github.com/xdomingoal/erah-devel * Source code: https://github.com/cran/erah * Date/Publication: 2023-12-20 10:10:02 UTC -* Number of recursive dependencies: 92 +* Number of recursive dependencies: 91 -Run `revdep_details(, "erah")` for more info +Run `revdepcheck::revdep_details(, "erah")` for more info
## In both -* checking whether package ‘erah’ can be installed ... ERROR +* checking package dependencies ... NOTE ``` - Installation failed. - See ‘/c4/home/henrik/repositories/future/revdep/checks/erah/new/erah.Rcheck/00install.out’ for details. + Package suggested but not available for checking: ‘mzR’ ``` +# fabletools + +
+ +* Version: 0.4.2 +* GitHub: https://github.com/tidyverts/fabletools +* Source code: https://github.com/cran/fabletools +* Date/Publication: 2024-04-22 11:22:41 UTC +* Number of recursive dependencies: 106 + +Run `revdepcheck::revdep_details(, "fabletools")` for more info + +
+ +## In both + * checking package dependencies ... NOTE ``` - Package suggested but not available for checking: ‘ncdf4’ + Package suggested but not available for checking: ‘fable’ ``` -## Installation +# fastRhockey -### Devel +
-``` -* installing *source* package ‘erah’ ... -** package ‘erah’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C compiler: ‘gcc (GCC) 10.2.1 20210130 (Red Hat 10.2.1-11)’ -gcc -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c registerDynamicSymbol.c -o registerDynamicSymbol.o -gcc -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c runfunc.c -o runfunc.o -gcc -shared -L/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/lib -L/usr/local/lib64 -o erah.so registerDynamicSymbol.o runfunc.o -L/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/lib -lR -installing to /c4/home/henrik/repositories/future/revdep/checks/erah/new/erah.Rcheck/00LOCK-erah/00new/erah/libs -** R -... -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : - there is no package called ‘ncdf4’ -Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart -Execution halted -ERROR: lazy loading failed for package ‘erah’ -* removing ‘/c4/home/henrik/repositories/future/revdep/checks/erah/new/erah.Rcheck/erah’ +* Version: 0.4.0 +* GitHub: https://github.com/sportsdataverse/fastRhockey +* Source code: https://github.com/cran/fastRhockey +* Date/Publication: 2022-10-25 20:55:15 UTC +* Number of recursive dependencies: 116 +Run `revdepcheck::revdep_details(, "fastRhockey")` for more info -``` -### CRAN +
-``` -* installing *source* package ‘erah’ ... -** package ‘erah’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C compiler: ‘gcc (GCC) 10.2.1 20210130 (Red Hat 10.2.1-11)’ -gcc -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c registerDynamicSymbol.c -o registerDynamicSymbol.o -gcc -I"/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c runfunc.c -o runfunc.o -gcc -shared -L/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/lib -L/usr/local/lib64 -o erah.so registerDynamicSymbol.o runfunc.o -L/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/lib -lR -installing to /c4/home/henrik/repositories/future/revdep/checks/erah/old/erah.Rcheck/00LOCK-erah/00new/erah/libs -** R -... -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : - there is no package called ‘ncdf4’ -Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart -Execution halted -ERROR: lazy loading failed for package ‘erah’ -* removing ‘/c4/home/henrik/repositories/future/revdep/checks/erah/old/erah.Rcheck/erah’ +## In both +* checking Rd files ... NOTE + ``` + checkRd: (-1) update_nhl_db.Rd:51-53: Lost braces in \itemize; meant \describe ? + checkRd: (-1) update_nhl_db.Rd:54-57: Lost braces in \itemize; meant \describe ? + checkRd: (-1) update_phf_db.Rd:51-53: Lost braces in \itemize; meant \describe ? + checkRd: (-1) update_phf_db.Rd:54-57: Lost braces in \itemize; meant \describe ? + ``` -``` # fdacluster
@@ -1244,31 +1213,22 @@ ERROR: lazy loading failed for package ‘erah’ * GitHub: https://github.com/astamm/fdacluster * Source code: https://github.com/cran/fdacluster * Date/Publication: 2023-07-04 15:53:04 UTC -* Number of recursive dependencies: 118 +* Number of recursive dependencies: 127 -Run `revdep_details(, "fdacluster")` for more info +Run `revdepcheck::revdep_details(, "fdacluster")` for more info
## In both -* checking whether package ‘fdacluster’ can be installed ... WARNING - ``` - Found the following significant warnings: - /c4/home/henrik/repositories/future/revdep/library/fdacluster/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/fdacluster/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/fdacluster/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - See ‘/c4/home/henrik/repositories/future/revdep/checks/fdacluster/new/fdacluster.Rcheck/00install.out’ for details. - ``` - * checking installed package size ... NOTE ``` - installed size is 22.2Mb + installed size is 22.7Mb sub-directories of 1Mb or more: R 1.8Mb - doc 1.4Mb + doc 1.5Mb help 2.1Mb - libs 16.4Mb + libs 16.8Mb ``` # fect @@ -1279,23 +1239,14 @@ Run `revdep_details(, "fdacluster")` for more info * GitHub: NA * Source code: https://github.com/cran/fect * Date/Publication: 2022-10-14 09:52:32 UTC -* Number of recursive dependencies: 81 +* Number of recursive dependencies: 80 -Run `revdep_details(, "fect")` for more info +Run `revdepcheck::revdep_details(, "fect")` for more info
## In both -* checking whether package ‘fect’ can be installed ... WARNING - ``` - Found the following significant warnings: - /c4/home/henrik/repositories/future/revdep/library/fect/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/fect/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/fect/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - See ‘/c4/home/henrik/repositories/future/revdep/checks/fect/new/fect.Rcheck/00install.out’ for details. - ``` - * checking C++ specification ... NOTE ``` Specified C++11: please drop specification unless essential @@ -1303,9 +1254,9 @@ Run `revdep_details(, "fect")` for more info * checking installed package size ... NOTE ``` - installed size is 13.9Mb + installed size is 14.7Mb sub-directories of 1Mb or more: - libs 12.6Mb + libs 13.4Mb ``` * checking dependencies in R code ... NOTE @@ -1318,13 +1269,13 @@ Run `revdep_details(, "fect")` for more info
-* Version: 1.8.0 -* GitHub: https://github.com/OliverVoogd/FLAMES +* Version: 1.10.0 +* GitHub: https://github.com/mritchielab/FLAMES * Source code: https://github.com/cran/FLAMES -* Date/Publication: 2023-10-24 -* Number of recursive dependencies: 255 +* Date/Publication: 2024-04-30 +* Number of recursive dependencies: 259 -Run `revdep_details(, "FLAMES")` for more info +Run `revdepcheck::revdep_details(, "FLAMES")` for more info
@@ -1347,35 +1298,74 @@ Run `revdep_details(, "FLAMES")` for more info * checking installed package size ... NOTE ``` - installed size is 6.2Mb + installed size is 7.6Mb sub-directories of 1Mb or more: data 2.7Mb doc 1.7Mb + libs 1.5Mb + ``` + +* checking DESCRIPTION meta-information ... NOTE + ``` + Package listed in more than one of Depends, Imports, Suggests, Enhances: + ‘txdbmaker’ + A package should be listed in only one of these fields. + ``` + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: 'IRanges' + All declared Imports should be used. ``` * checking R code for possible problems ... NOTE ``` - annotation_to_fasta: no visible global function definition for - 'write.table' + find_variants_grange: no visible binding for global variable + 'which_label' + find_variants_grange: no visible binding for global variable + 'nucleotide' + find_variants_grange: no visible binding for global variable 'pos' + find_variants_grange: no visible binding for global variable 'count' + find_variants_grange: no visible binding for global variable + 'counts_no_ins' + find_variants_grange: no visible binding for global variable 'ref' generate_sc_sce: no visible binding for global variable 'FSM_match' - plot_coverage: no visible binding for global variable 'x' - plot_coverage: no visible binding for global variable 'transcript' - plot_coverage: no visible binding for global variable 'length_bin' - plot_demultiplex: no visible binding for global variable 'Freq' - plot_demultiplex: no visible binding for global variable '.' - plot_demultiplex: no visible binding for global variable 'x' - plot_demultiplex: no visible binding for global variable ... - sc_umap_expression : plot_idx: no visible binding for global variable - 'y' - transcript_coverage: no visible binding for global variable 'mat' + variant_count_tb: no visible binding for global variable 'barcode' + variant_count_tb: no visible binding for global variable 'allele_count' + variant_count_tb: no visible binding for global variable + 'cell_total_reads' Undefined global functions or variables: - . BarcodeEditDist FSM_match FlankEditDist Freq all_vars cell_id cnt - everything gene_id heatmap_annotation_colors label length_bin mat n - name tr_id transcript transcript_id value write.table x y - Consider adding - importFrom("utils", "write.table") - to your NAMESPACE file. + . BarcodeEditDist FSM_match FlankEditDist Freq all_vars allele_count + bam_index barcode cell_id cell_total_reads cnt count counts_no_ins + everything gene_id heatmap_annotation_colors label length_bin mat + mutation_index n name nucleotide pct pos ref tr_id transcript + transcript_id value which_label x y + ``` + +* checking Rd files ... NOTE + ``` + checkRd: (-1) bulk_long_pipeline.Rd:80-81: Lost braces in \itemize; meant \describe ? + checkRd: (-1) bulk_long_pipeline.Rd:82-83: Lost braces in \itemize; meant \describe ? + checkRd: (-1) bulk_long_pipeline.Rd:84-86: Lost braces in \itemize; meant \describe ? + checkRd: (-1) bulk_long_pipeline.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) bulk_long_pipeline.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) bulk_long_pipeline.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) bulk_long_pipeline.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) bulk_long_pipeline.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) bulk_long_pipeline.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) create_config.Rd:14: Lost braces in \itemize; meant \describe ? + ... + checkRd: (-1) sc_long_multisample_pipeline.Rd:92-94: Lost braces in \itemize; meant \describe ? + checkRd: (-1) sc_long_pipeline.Rd:94-95: Lost braces in \itemize; meant \describe ? + checkRd: (-1) sc_long_pipeline.Rd:96-97: Lost braces in \itemize; meant \describe ? + checkRd: (-1) sc_long_pipeline.Rd:98-100: Lost braces in \itemize; meant \describe ? + checkRd: (-1) sc_long_pipeline.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) sc_long_pipeline.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) sc_long_pipeline.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) sc_long_pipeline.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) sc_long_pipeline.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) sc_long_pipeline.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly ``` * checking for GNU extensions in Makefiles ... NOTE @@ -1387,13 +1377,13 @@ Run `revdep_details(, "FLAMES")` for more info
-* Version: 1.10.0 +* Version: 1.12.0 * GitHub: https://github.com/aya49/flowGraph * Source code: https://github.com/cran/flowGraph -* Date/Publication: 2023-10-24 -* Number of recursive dependencies: 94 +* Date/Publication: 2024-04-30 +* Number of recursive dependencies: 93 -Run `revdep_details(, "flowGraph")` for more info +Run `revdepcheck::revdep_details(, "flowGraph")` for more info
@@ -1408,6 +1398,16 @@ Run `revdep_details(, "flowGraph")` for more info meta no_cores ``` +* checking Rd files ... NOTE + ``` + checkRd: (-1) fg_get_graph.Rd:13: Lost braces + 13 | A list containing two data frames (\code{v} and ]code{e}) + | ^ + checkRd: (-1) ggdf.Rd:22: Lost braces + 22 | code{ggdf} adds to the data frames \code{v} and \code{e} in slot + | ^ + ``` + * checking Rd cross-references ... NOTE ``` Package unavailable to check Rd xrefs: ‘doParallel’ @@ -1421,9 +1421,9 @@ Run `revdep_details(, "flowGraph")` for more info * GitHub: https://github.com/nredell/forecastML * Source code: https://github.com/cran/forecastML * Date/Publication: 2020-05-07 15:10:17 UTC -* Number of recursive dependencies: 105 +* Number of recursive dependencies: 104 -Run `revdep_details(, "forecastML")` for more info +Run `revdepcheck::revdep_details(, "forecastML")` for more info
@@ -1435,45 +1435,27 @@ Run `revdep_details(, "forecastML")` for more info All declared Imports should be used. ``` -# genBaRcode +# GeDS
-* Version: 1.2.7 -* GitHub: NA -* Source code: https://github.com/cran/genBaRcode -* Date/Publication: 2023-12-11 13:10:05 UTC -* Number of recursive dependencies: 161 +* Version: 0.2.3 +* GitHub: https://github.com/emilioluissaenzguillen/GeDS +* Source code: https://github.com/cran/GeDS +* Date/Publication: 2024-07-19 14:30:02 UTC +* Number of recursive dependencies: 33 -Run `revdep_details(, "genBaRcode")` for more info +Run `revdepcheck::revdep_details(, "GeDS")` for more info
## In both -* checking re-building of vignette outputs ... WARNING +* checking whether package ‘GeDS’ can be installed ... WARNING ``` - Error(s) in re-building vignettes: - --- re-building ‘genBaRcode_GUI_Vignette.Rmd’ using rmarkdown - ! LaTeX Error: File `iftex.sty' not found. - - ! Emergency stop. - - - Error: processing vignette 'genBaRcode_GUI_Vignette.Rmd' failed with diagnostics: - LaTeX failed to compile /c4/home/henrik/repositories/future/revdep/checks/genBaRcode/new/genBaRcode.Rcheck/vign_test/genBaRcode/vignettes/genBaRcode_GUI_Vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See genBaRcode_GUI_Vignette.log for more info. - --- failed re-building ‘genBaRcode_GUI_Vignette.Rmd’ - ... - - Error: processing vignette 'genBaRcode_Vignette.Rmd' failed with diagnostics: - LaTeX failed to compile /c4/home/henrik/repositories/future/revdep/checks/genBaRcode/new/genBaRcode.Rcheck/vign_test/genBaRcode/vignettes/genBaRcode_Vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See genBaRcode_Vignette.log for more info. - --- failed re-building ‘genBaRcode_Vignette.Rmd’ - - SUMMARY: processing the following files failed: - ‘genBaRcode_GUI_Vignette.Rmd’ ‘genBaRcode_Vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted + Found the following significant warnings: + Warning: no DISPLAY variable so Tk is not available + See ‘/c4/home/henrik/repositories/future/revdep/checks/GeDS/new/GeDS.Rcheck/00install.out’ for details. ``` # geocmeans @@ -1484,70 +1466,45 @@ Run `revdep_details(, "genBaRcode")` for more info * GitHub: https://github.com/JeremyGelb/geocmeans * Source code: https://github.com/cran/geocmeans * Date/Publication: 2023-09-12 03:10:02 UTC -* Number of recursive dependencies: 197 +* Number of recursive dependencies: 200 -Run `revdep_details(, "geocmeans")` for more info +Run `revdepcheck::revdep_details(, "geocmeans")` for more info
## In both -* checking whether package ‘geocmeans’ can be installed ... WARNING - ``` - Found the following significant warnings: - /c4/home/henrik/repositories/future/revdep/library/geocmeans/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/geocmeans/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/geocmeans/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - See ‘/c4/home/henrik/repositories/future/revdep/checks/geocmeans/new/geocmeans.Rcheck/00install.out’ for details. - ``` - * checking installed package size ... NOTE ``` - installed size is 13.5Mb + installed size is 14.3Mb sub-directories of 1Mb or more: extdata 3.0Mb - libs 8.2Mb + libs 9.0Mb ``` -# geohabnet +# GeoModels
-* Version: 2.0.0 -* GitHub: https://github.com/GarrettLab/HabitatConnectivity -* Source code: https://github.com/cran/geohabnet -* Date/Publication: 2024-02-27 19:50:02 UTC -* Number of recursive dependencies: 134 +* Version: 2.0.4 +* GitHub: https://github.com/vmoprojs/GeoModels +* Source code: https://github.com/cran/GeoModels +* Date/Publication: 2024-07-09 14:50:12 UTC +* Number of recursive dependencies: 54 -Run `revdep_details(, "geohabnet")` for more info +Run `revdepcheck::revdep_details(, "GeoModels")` for more info
## In both -* checking re-building of vignette outputs ... ERROR +* checking installed package size ... NOTE ``` - Error(s) in re-building vignettes: - --- re-building ‘LinkWeightsAnalysis.Rmd’ using rmarkdown - trying URL 'https://s3.us-east-2.amazonaws.com/earthstatdata/HarvestedAreaYield175Crops_Indvidual_Geotiff/potato_HarvAreaYield_Geotiff.zip' - Content type 'application/zip' length 10812124 bytes (10.3 MB) - ================================================== - downloaded 10.3 MB - - trying URL 'https://geohabnet.s3.us-east-2.amazonaws.com/util-rasters/ZeroRaster.tif' - Content type 'image/tiff' length 1056851 bytes (1.0 MB) - ================================================== - ... - Quitting from lines 108-109 [unnamed-chunk-5] (analysis.Rmd) - Error: processing vignette 'analysis.Rmd' failed with diagnostics: - (/c4/home/henrik/.config/R/geohabnet/parameters.yaml) Duplicate map key: 'default' - --- failed re-building ‘analysis.Rmd’ - - SUMMARY: processing the following file failed: - ‘analysis.Rmd’ - - Error: Vignette re-building failed. - Execution halted + installed size is 6.1Mb + sub-directories of 1Mb or more: + R 1.0Mb + data 1.9Mb + libs 2.8Mb ``` # googleComputeEngineR @@ -1558,14 +1515,48 @@ Run `revdep_details(, "geohabnet")` for more info * GitHub: https://github.com/cloudyr/googleComputeEngineR * Source code: https://github.com/cran/googleComputeEngineR * Date/Publication: 2019-05-04 22:40:02 UTC -* Number of recursive dependencies: 67 +* Number of recursive dependencies: 66 -Run `revdep_details(, "googleComputeEngineR")` for more info +Run `revdepcheck::revdep_details(, "googleComputeEngineR")` for more info
+## Newly broken + +* checking installed package size ... NOTE + ``` + installed size is 5.2Mb + sub-directories of 1Mb or more: + doc 4.5Mb + ``` + ## In both +* checking Rd files ... NOTE + ``` + checkRd: (-1) docker_cmd.gce_instance.Rd:21: Lost braces; missing escapes or markup? + 21 | \item{nvidia}{If true will use \code{nvidia-docker} instead of {docker}} + | ^ + checkRd: (-1) gce_list_disks.Rd:11: Lost braces; missing escapes or markup? + 11 | \item{filter}{Sets a filter expression for filtering listed resources, in the form filter={expression}} + | ^ + checkRd: (-1) gce_list_disks_all.Rd:11: Lost braces; missing escapes or markup? + 11 | \item{filter}{Sets a filter expression for filtering listed resources, in the form filter={expression}} + | ^ + checkRd: (-1) gce_list_firewall_rules.Rd:11: Lost braces; missing escapes or markup? + ... + | ^ + checkRd: (-1) gce_list_networks.Rd:11: Lost braces; missing escapes or markup? + 11 | \item{filter}{Sets a filter expression for filtering listed resources, in the form filter={expression}} + | ^ + checkRd: (-1) gce_list_zone_op.Rd:11: Lost braces; missing escapes or markup? + 11 | \item{filter}{Sets a filter expression for filtering listed resources, in the form filter={expression}} + | ^ + checkRd: (-1) gce_list_zones.Rd:13: Lost braces; missing escapes or markup? + 13 | \item{filter}{Sets a filter expression for filtering listed resources, in the form filter={expression}} + | ^ + ``` + * checking LazyData ... NOTE ``` 'LazyData' is specified without a 'data' directory @@ -1579,9 +1570,9 @@ Run `revdep_details(, "googleComputeEngineR")` for more info * GitHub: NA * Source code: https://github.com/cran/googleTagManageR * Date/Publication: 2022-04-16 18:12:29 UTC -* Number of recursive dependencies: 69 +* Number of recursive dependencies: 68 -Run `revdep_details(, "googleTagManageR")` for more info +Run `revdepcheck::revdep_details(, "googleTagManageR")` for more info
@@ -1602,23 +1593,14 @@ Run `revdep_details(, "googleTagManageR")` for more info * GitHub: https://github.com/comeetie/greed * Source code: https://github.com/cran/greed * Date/Publication: 2022-10-03 22:00:05 UTC -* Number of recursive dependencies: 98 +* Number of recursive dependencies: 97 -Run `revdep_details(, "greed")` for more info +Run `revdepcheck::revdep_details(, "greed")` for more info
## In both -* checking whether package ‘greed’ can be installed ... WARNING - ``` - Found the following significant warnings: - /c4/home/henrik/repositories/future/revdep/library/greed/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/greed/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/greed/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - See ‘/c4/home/henrik/repositories/future/revdep/checks/greed/new/greed.Rcheck/00install.out’ for details. - ``` - * checking C++ specification ... NOTE ``` Specified C++11: please drop specification unless essential @@ -1626,9 +1608,9 @@ Run `revdep_details(, "greed")` for more info * checking installed package size ... NOTE ``` - installed size is 36.5Mb + installed size is 38.4Mb sub-directories of 1Mb or more: - libs 34.3Mb + libs 36.1Mb ``` * checking data for non-ASCII characters ... NOTE @@ -1636,6 +1618,47 @@ Run `revdep_details(, "greed")` for more info Note: found 989 marked UTF-8 strings ``` +# gstat + +
+ +* Version: 2.1-1 +* GitHub: https://github.com/r-spatial/gstat +* Source code: https://github.com/cran/gstat +* Date/Publication: 2023-04-06 10:32:40 UTC +* Number of recursive dependencies: 39 + +Run `revdepcheck::revdep_details(, "gstat")` for more info + +
+ +## In both + +* checking Rd files ... NOTE + ``` + checkRd: (-1) jura.Rd:29: Lost braces; missing escapes or markup? + 29 | \item{Cd}{ mg cadmium kg^{-1} topsoil } + | ^ + checkRd: (-1) jura.Rd:30: Lost braces; missing escapes or markup? + 30 | \item{Co}{ mg cobalt kg^{-1} topsoil } + | ^ + checkRd: (-1) jura.Rd:31: Lost braces; missing escapes or markup? + 31 | \item{Cr}{ mg chromium kg^{-1} topsoil } + | ^ + checkRd: (-1) jura.Rd:32: Lost braces; missing escapes or markup? + ... + | ^ + checkRd: (-1) jura.Rd:35: Lost braces; missing escapes or markup? + 35 | \item{Zn}{ mg zinc kg^{-1} topsoil } + | ^ + checkRd: (-1) variogramST.Rd:49: Lost braces; missing escapes or markup? + 49 | time lag $t$, the pseudo cross variogram $(Z_i(s)-Z_{i+t}(s+h))^2$ is averaged over all time + | ^ + checkRd: (-1) variogramST.Rd:50: Lost braces; missing escapes or markup? + 50 | lagged observation sets $Z_i$ and $Z_{i+t}$ available (weighted by the number of pairs involved). + | ^ + ``` + # gsynth
@@ -1644,23 +1667,14 @@ Run `revdep_details(, "greed")` for more info * GitHub: NA * Source code: https://github.com/cran/gsynth * Date/Publication: 2021-08-06 07:50:05 UTC -* Number of recursive dependencies: 77 +* Number of recursive dependencies: 76 -Run `revdep_details(, "gsynth")` for more info +Run `revdepcheck::revdep_details(, "gsynth")` for more info
## In both -* checking whether package ‘gsynth’ can be installed ... WARNING - ``` - Found the following significant warnings: - /c4/home/henrik/repositories/future/revdep/library/gsynth/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/gsynth/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/gsynth/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - See ‘/c4/home/henrik/repositories/future/revdep/checks/gsynth/new/gsynth.Rcheck/00install.out’ for details. - ``` - * checking C++ specification ... NOTE ``` Specified C++11: please drop specification unless essential @@ -1668,9 +1682,50 @@ Run `revdep_details(, "gsynth")` for more info * checking installed package size ... NOTE ``` - installed size is 5.2Mb + installed size is 5.6Mb sub-directories of 1Mb or more: - libs 4.9Mb + libs 5.2Mb + ``` + +# gtfs2gps + +
+ +* Version: 2.1-1 +* GitHub: https://github.com/ipeaGIT/gtfs2gps +* Source code: https://github.com/cran/gtfs2gps +* Date/Publication: 2023-04-28 19:50:02 UTC +* Number of recursive dependencies: 87 + +Run `revdepcheck::revdep_details(, "gtfs2gps")` for more info + +
+ +## In both + +* checking tests ... + ``` + Running ‘testthat.R’ + ERROR + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(gtfs2gps) + gtfs2gps version 2.1-1 is now loaded + NOTE: All filter functions from gtfs2gps were removed + Please replace them by similar functions from gtfstools + > library(magrittr) + ... + 4. └─terra (local) .local(x, ...) + 5. ├─terra::makeValid(x) + 6. └─terra::makeValid(x) + 7. └─terra (local) .local(x, ...) + 8. └─terra:::messages(x) + 9. └─terra:::error(f, x@ptr$getError()) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 119 ] + Error: Test failures + Execution halted ``` # hackeRnews @@ -1681,9 +1736,9 @@ Run `revdep_details(, "gsynth")` for more info * GitHub: https://github.com/szymanskir/hackeRnews * Source code: https://github.com/cran/hackeRnews * Date/Publication: 2019-12-13 13:20:05 UTC -* Number of recursive dependencies: 69 +* Number of recursive dependencies: 68 -Run `revdep_details(, "hackeRnews")` for more info +Run `revdepcheck::revdep_details(, "hackeRnews")` for more info
@@ -1702,9 +1757,9 @@ Run `revdep_details(, "hackeRnews")` for more info * GitHub: https://github.com/tlverse/hal9001 * Source code: https://github.com/cran/hal9001 * Date/Publication: 2023-11-14 15:00:02 UTC -* Number of recursive dependencies: 100 +* Number of recursive dependencies: 99 -Run `revdep_details(, "hal9001")` for more info +Run `revdepcheck::revdep_details(, "hal9001")` for more info
@@ -1721,13 +1776,13 @@ Run `revdep_details(, "hal9001")` for more info
-* Version: 2.2.1 +* Version: 2.3.1 * GitHub: https://github.com/jbolstad/hbamr * Source code: https://github.com/cran/hbamr -* Date/Publication: 2024-02-23 12:30:02 UTC -* Number of recursive dependencies: 91 +* Date/Publication: 2024-06-04 15:50:06 UTC +* Number of recursive dependencies: 90 -Run `revdep_details(, "hbamr")` for more info +Run `revdepcheck::revdep_details(, "hbamr")` for more info
@@ -1735,9 +1790,9 @@ Run `revdep_details(, "hbamr")` for more info * checking installed package size ... NOTE ``` - installed size is 353.1Mb + installed size is 342.1Mb sub-directories of 1Mb or more: - libs 351.6Mb + libs 340.5Mb ``` * checking for GNU extensions in Makefiles ... NOTE @@ -1753,9 +1808,9 @@ Run `revdep_details(, "hbamr")` for more info * GitHub: NA * Source code: https://github.com/cran/hero * Date/Publication: 2023-07-15 21:10:09 UTC -* Number of recursive dependencies: 160 +* Number of recursive dependencies: 159 -Run `revdep_details(, "hero")` for more info +Run `revdepcheck::revdep_details(, "hero")` for more info
@@ -1766,6 +1821,16 @@ Run `revdep_details(, "hero")` for more info Package suggested but not available for checking: ‘Rmpi’ ``` +* checking Rd files ... NOTE + ``` + checkRd: (-1) hero.Rd:67-68: Lost braces + 67 | then \code{\link[pbapply]{pblapply}} is used. If code{package == + | ^ + checkRd: (-1) hero.Rd:69: Lost braces + 69 | code{package == "Rmpi"}, then \code{\link[Rmpi]{mpi.applyLB}} is used.} + | ^ + ``` + * checking Rd cross-references ... NOTE ``` Package unavailable to check Rd xrefs: ‘Rmpi’ @@ -1779,28 +1844,19 @@ Run `revdep_details(, "hero")` for more info * GitHub: https://github.com/patauchi/heterogen * Source code: https://github.com/cran/heterogen * Date/Publication: 2023-08-17 07:42:33 UTC -* Number of recursive dependencies: 56 +* Number of recursive dependencies: 55 -Run `revdep_details(, "heterogen")` for more info +Run `revdepcheck::revdep_details(, "heterogen")` for more info
## In both -* checking whether package ‘heterogen’ can be installed ... WARNING - ``` - Found the following significant warnings: - /c4/home/henrik/repositories/future/revdep/library/heterogen/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/heterogen/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/heterogen/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - See ‘/c4/home/henrik/repositories/future/revdep/checks/heterogen/new/heterogen.Rcheck/00install.out’ for details. - ``` - * checking installed package size ... NOTE ``` - installed size is 8.6Mb + installed size is 8.8Mb sub-directories of 1Mb or more: - extdata 2.5Mb + extdata 2.6Mb libs 6.0Mb ``` @@ -1808,13 +1864,13 @@ Run `revdep_details(, "heterogen")` for more info
-* Version: 2.0.1 +* Version: 2.0.2 * GitHub: https://github.com/nx10/httpgd * Source code: https://github.com/cran/httpgd -* Date/Publication: 2024-03-11 08:00:06 UTC -* Number of recursive dependencies: 67 +* Date/Publication: 2024-06-05 21:40:27 UTC +* Number of recursive dependencies: 66 -Run `revdep_details(, "httpgd")` for more info +Run `revdepcheck::revdep_details(, "httpgd")` for more info
@@ -1822,7 +1878,7 @@ Run `revdep_details(, "httpgd")` for more info * checking tests ... ``` - Running ‘testthat.R’/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/bin/BATCH: line 60: 284845 Segmentation fault (core dumped) ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1 + Running ‘testthat.R’/software/c4/cbi/software/_rocky8/R-4.4.1-gcc13/lib64/R/bin/BATCH: line 60: 1026404 Segmentation fault (core dumped) ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1 ERROR Running the tests in ‘tests/testthat.R’ failed. @@ -1841,7 +1897,7 @@ Run `revdep_details(, "httpgd")` for more info Execution halted *** caught segfault *** - address (nil), cause 'unknown' + address 0x4adfdb0, cause 'invalid permissions' An irrecoverable exception occurred. R is aborting now ... ``` @@ -1852,9 +1908,9 @@ Run `revdep_details(, "httpgd")` for more info * checking installed package size ... NOTE ``` - installed size is 12.7Mb + installed size is 12.5Mb sub-directories of 1Mb or more: - libs 12.2Mb + libs 11.9Mb ``` # hwep @@ -1865,9 +1921,9 @@ Run `revdep_details(, "httpgd")` for more info * GitHub: https://github.com/dcgerard/hwep * Source code: https://github.com/cran/hwep * Date/Publication: 2023-05-16 17:40:02 UTC -* Number of recursive dependencies: 116 +* Number of recursive dependencies: 115 -Run `revdep_details(, "hwep")` for more info +Run `revdepcheck::revdep_details(, "hwep")` for more info
@@ -1875,9 +1931,16 @@ Run `revdep_details(, "hwep")` for more info * checking installed package size ... NOTE ``` - installed size is 84.5Mb + installed size is 80.5Mb sub-directories of 1Mb or more: - libs 83.9Mb + libs 79.9Mb + ``` + +* checking Rd files ... NOTE + ``` + checkRd: (-1) simgl.Rd:50: Lost braces; missing escapes or markup? + 50 | Uses the {updog} R package for simulating read counts and generating + | ^ ``` * checking for GNU extensions in Makefiles ... NOTE @@ -1893,9 +1956,9 @@ Run `revdep_details(, "hwep")` for more info * GitHub: https://github.com/DOI-USGS/hydroloom * Source code: https://github.com/cran/hydroloom * Date/Publication: 2024-01-15 16:20:02 UTC -* Number of recursive dependencies: 154 +* Number of recursive dependencies: 145 -Run `revdep_details(, "hydroloom")` for more info +Run `revdepcheck::revdep_details(, "hydroloom")` for more info
@@ -1914,9 +1977,8 @@ Run `revdep_details(, "hydroloom")` for more info > > > source(system.file("extdata/sample_data.R", package = "nhdplusTools")) - Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - there is no package called ‘arrow’ - Calls: source ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart + Error in source(system.file("extdata/sample_data.R", package = "nhdplusTools")) : + empty file/url name Execution halted ``` @@ -1931,7 +1993,7 @@ Run `revdep_details(, "hydroloom")` for more info Quitting from lines 12-32 [setup] (flow-table.Rmd) Error: processing vignette 'flow-table.Rmd' failed with diagnostics: - there is no package called 'arrow' + there is no package called 'nhdplusTools' ... --- finished re-building ‘hydroloom.Rmd’ @@ -1945,17 +2007,22 @@ Run `revdep_details(, "hydroloom")` for more info Execution halted ``` +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘nhdplusTools’ + ``` + # infercnv
-* Version: 1.18.1 +* Version: 1.20.0 * GitHub: https://github.com/broadinstitute/inferCNV * Source code: https://github.com/cran/infercnv -* Date/Publication: 2023-12-01 +* Date/Publication: 2024-04-30 * Number of recursive dependencies: 205 -Run `revdep_details(, "infercnv")` for more info +Run `revdepcheck::revdep_details(, "infercnv")` for more info
@@ -1974,22 +2041,40 @@ Run `revdep_details(, "infercnv")` for more info See the note in ?`:::` about the use of this operator. ``` +* checking Rd files ... NOTE + ``` + checkRd: (-1) run.Rd:268: Lost braces; missing escapes or markup? + 268 | \item{require_DE_all_normals}{If mask_nonDE_genes is set, those genes will be masked only if they are are found as DE according to test.use and mask_nonDE_pval in each of the comparisons to normal cells options: {"any", "most", "all"} (default: "any") + | ^ + ``` + # InPAS
-* Version: 2.10.0 +* Version: 2.12.0 * GitHub: NA * Source code: https://github.com/cran/InPAS -* Date/Publication: 2023-10-24 -* Number of recursive dependencies: 172 +* Date/Publication: 2024-04-30 +* Number of recursive dependencies: 165 -Run `revdep_details(, "InPAS")` for more info +Run `revdepcheck::revdep_details(, "InPAS")` for more info
## In both +* checking Rd cross-references ... WARNING + ``` + Missing link or links in Rd file 'get_ssRleCov.Rd': + ‘[BSgenome:BSgenomeForge]{BSgenome::forgeBSgenomeDataPkg()}’ + + Missing link or links in Rd file 'set_globals.Rd': + ‘[BSgenome:BSgenomeForge]{BSgenome::forgeBSgenomeDataPkg()}’ + + See section 'Cross-references' in the 'Writing R Extensions' manual. + ``` + * checking dependencies in R code ... NOTE ``` There are ::: calls to the package's namespace in its code. A package @@ -2000,6 +2085,18 @@ Run `revdep_details(, "InPAS")` for more info ‘search_distalCPs’ ‘search_proximalCPs’ ``` +* checking Rd \usage sections ... NOTE + ``` + Documented arguments not in \usage in Rd file 'get_UTR3TotalCov.Rd': + ‘gcCompensationensation’ + + Functions with \usage entries need to have the appropriate \alias + entries, and all their arguments documented. + The \usage entries must correspond to syntactically valid R code. + See chapter ‘Writing R documentation files’ in the ‘Writing R + Extensions’ manual. + ``` + # interflex
@@ -2008,23 +2105,14 @@ Run `revdep_details(, "InPAS")` for more info * GitHub: NA * Source code: https://github.com/cran/interflex * Date/Publication: 2021-05-18 11:40:02 UTC -* Number of recursive dependencies: 103 +* Number of recursive dependencies: 91 -Run `revdep_details(, "interflex")` for more info +Run `revdepcheck::revdep_details(, "interflex")` for more info
## In both -* checking whether package ‘interflex’ can be installed ... WARNING - ``` - Found the following significant warnings: - /c4/home/henrik/repositories/future/revdep/library/interflex/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/interflex/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/interflex/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - See ‘/c4/home/henrik/repositories/future/revdep/checks/interflex/new/interflex.Rcheck/00install.out’ for details. - ``` - * checking C++ specification ... NOTE ``` Specified C++11: please drop specification unless essential @@ -2032,22 +2120,22 @@ Run `revdep_details(, "interflex")` for more info * checking installed package size ... NOTE ``` - installed size is 5.8Mb + installed size is 6.0Mb sub-directories of 1Mb or more: - libs 5.1Mb + libs 5.3Mb ``` # ISAnalytics
-* Version: 1.12.0 +* Version: 1.14.0 * GitHub: https://github.com/calabrialab/ISAnalytics * Source code: https://github.com/cran/ISAnalytics -* Date/Publication: 2023-10-24 -* Number of recursive dependencies: 173 +* Date/Publication: 2024-04-30 +* Number of recursive dependencies: 179 -Run `revdep_details(, "ISAnalytics")` for more info +Run `revdepcheck::revdep_details(, "ISAnalytics")` for more info
@@ -2055,10 +2143,18 @@ Run `revdep_details(, "ISAnalytics")` for more info * checking installed package size ... NOTE ``` - installed size is 7.2Mb + installed size is 7.6Mb sub-directories of 1Mb or more: + R 1.0Mb data 1.4Mb - doc 3.5Mb + doc 3.6Mb + ``` + +* checking Rd files ... NOTE + ``` + checkRd: (-1) refGenes_hg19.Rd:21: Lost braces; missing escapes or markup? + 21 | \item Download from {http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/} + | ^ ``` # ivmte @@ -2069,9 +2165,9 @@ Run `revdep_details(, "ISAnalytics")` for more info * GitHub: NA * Source code: https://github.com/cran/ivmte * Date/Publication: 2021-09-17 12:20:07 UTC -* Number of recursive dependencies: 112 +* Number of recursive dependencies: 116 -Run `revdep_details(, "ivmte")` for more info +Run `revdepcheck::revdep_details(, "ivmte")` for more info
@@ -2082,17 +2178,27 @@ Run `revdep_details(, "ivmte")` for more info Packages suggested but not available for checking: 'gurobi', 'cplexAPI' ``` +* checking Rd files ... NOTE + ``` + checkRd: (-1) sTsls.Rd:17: Lost braces; missing escapes or markup? + 17 | \item{pi}{the matrix E[XZ']E[ZZ']^{-1}} + | ^ + checkRd: (-1) sTslsSplines.Rd:20: Lost braces; missing escapes or markup? + 20 | \item{pi}{matrix, corresponds to E[XZ']E[ZZ']^{-1}, the first stage + | ^ + ``` + # keyATM
-* Version: 0.5.1 +* Version: 0.5.2 * GitHub: https://github.com/keyATM/keyATM * Source code: https://github.com/cran/keyATM -* Date/Publication: 2024-02-04 23:30:02 UTC -* Number of recursive dependencies: 107 +* Date/Publication: 2024-04-24 14:50:06 UTC +* Number of recursive dependencies: 102 -Run `revdep_details(, "keyATM")` for more info +Run `revdepcheck::revdep_details(, "keyATM")` for more info
@@ -2100,9 +2206,71 @@ Run `revdep_details(, "keyATM")` for more info * checking installed package size ... NOTE ``` - installed size is 24.7Mb + installed size is 25.4Mb sub-directories of 1Mb or more: - libs 24.3Mb + libs 24.9Mb + ``` + +# latentcor + +
+ +* Version: 2.0.1 +* GitHub: NA +* Source code: https://github.com/cran/latentcor +* Date/Publication: 2022-09-05 20:50:02 UTC +* Number of recursive dependencies: 143 + +Run `revdepcheck::revdep_details(, "latentcor")` for more info + +
+ +## In both + +* checking Rd files ... NOTE + ``` + checkRd: (-1) evaluation.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) evaluation.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) evaluation.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) evaluation.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) evaluation.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) evaluation.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) evaluation.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) evaluation.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) evaluation.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) evaluation.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly + ... + checkRd: (-1) gen_data.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) gen_data.Rd:36-37: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) get_types.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) interpolation.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) interpolation.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) latentcor.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) latentcor.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) latentcor.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) latentcor.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) latentcor.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly + ``` + +# lava + +
+ +* Version: 1.8.0 +* GitHub: https://github.com/kkholst/lava +* Source code: https://github.com/cran/lava +* Date/Publication: 2024-03-05 13:00:02 UTC +* Number of recursive dependencies: 131 + +Run `revdepcheck::revdep_details(, "lava")` for more info + +
+ +## In both + +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘lavaSearch2’ ``` # ldsr @@ -2113,48 +2281,45 @@ Run `revdep_details(, "keyATM")` for more info * GitHub: https://github.com/ntthung/ldsr * Source code: https://github.com/cran/ldsr * Date/Publication: 2020-05-04 14:40:09 UTC -* Number of recursive dependencies: 78 +* Number of recursive dependencies: 77 -Run `revdep_details(, "ldsr")` for more info +Run `revdepcheck::revdep_details(, "ldsr")` for more info
## In both -* checking whether package ‘ldsr’ can be installed ... WARNING +* checking C++ specification ... NOTE ``` - Found the following significant warnings: - /c4/home/henrik/repositories/future/revdep/library/ldsr/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/ldsr/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/ldsr/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - See ‘/c4/home/henrik/repositories/future/revdep/checks/ldsr/new/ldsr.Rcheck/00install.out’ for details. + Specified C++11: please drop specification unless essential ``` -* checking C++ specification ... NOTE +* checking installed package size ... NOTE ``` - Specified C++11: please drop specification unless essential + installed size is 7.5Mb + sub-directories of 1Mb or more: + libs 7.0Mb ``` # lidR
-* Version: 4.1.1 +* Version: 4.1.2 * GitHub: https://github.com/r-lidar/lidR * Source code: https://github.com/cran/lidR -* Date/Publication: 2024-03-05 17:00:11 UTC -* Number of recursive dependencies: 156 +* Date/Publication: 2024-07-09 08:40:02 UTC +* Number of recursive dependencies: 147 -Run `revdep_details(, "lidR")` for more info +Run `revdepcheck::revdep_details(, "lidR")` for more info
-## In both +## Newly fixed * checking tests ... ``` - Running ‘testthat.R’/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/bin/BATCH: line 60: 29724 Aborted (core dumped) ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1 - + Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: @@ -2164,44 +2329,68 @@ Run `revdep_details(, "lidR")` for more info > library(lidR) > test_check("lidR") Tests using raster: terra - Tests using future: TRUE - Tests using OpenMP thread: 32 - OGR: Unsupported geometry type - OGR: Unsupported geometry type - Chunk 1 of 1 (100%): state ✓ - terminate called after throwing an instance of 'std::length_error' - what(): basic_string::_S_create + ... + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test-locate_trees.R:36:3'): find_trees is backward compatible ───── + dim(ttops) not equal to c(177, 2). + 1/2 mismatches + [1] 178 - 177 == 1 + + [ FAIL 1 | WARN 0 | SKIP 43 | PASS 1303 ] + Error: Test failures + Execution halted ``` -* checking whether package ‘lidR’ can be installed ... WARNING - ``` - Found the following significant warnings: - /c4/home/henrik/repositories/future/revdep/library/lidR/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/lidR/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/lidR/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - See ‘/c4/home/henrik/repositories/future/revdep/checks/lidR/new/lidR.Rcheck/00install.out’ for details. - ``` +## In both * checking installed package size ... NOTE ``` - installed size is 20.0Mb + installed size is 19.1Mb sub-directories of 1Mb or more: R 1.0Mb - extdata 1.1Mb - libs 16.3Mb + doc 1.0Mb + extdata 1.2Mb + libs 15.4Mb + ``` + +# lightr + +
+ +* Version: 1.7.1 +* GitHub: https://github.com/ropensci/lightr +* Source code: https://github.com/cran/lightr +* Date/Publication: 2024-03-21 21:50:10 UTC +* Number of recursive dependencies: 92 + +Run `revdepcheck::revdep_details(, "lightr")` for more info + +
+ +## In both + +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘pavo’ + ``` + +* checking Rd cross-references ... NOTE + ``` + Package unavailable to check Rd xrefs: ‘pavo’ ``` # MAI
-* Version: 1.8.0 +* Version: 1.10.0 * GitHub: https://github.com/KechrisLab/MAI * Source code: https://github.com/cran/MAI -* Date/Publication: 2023-10-24 -* Number of recursive dependencies: 178 +* Date/Publication: 2024-04-30 +* Number of recursive dependencies: 176 -Run `revdep_details(, "MAI")` for more info +Run `revdepcheck::revdep_details(, "MAI")` for more info
@@ -2218,13 +2407,13 @@ Run `revdep_details(, "MAI")` for more info
-* Version: 0.4.4 +* Version: 1.0.2 * GitHub: https://github.com/stocnet/manynet * Source code: https://github.com/cran/manynet -* Date/Publication: 2024-03-15 19:20:10 UTC -* Number of recursive dependencies: 142 +* Date/Publication: 2024-07-22 07:50:02 UTC +* Number of recursive dependencies: 152 -Run `revdep_details(, "manynet")` for more info +Run `revdepcheck::revdep_details(, "manynet")` for more info
@@ -2232,6 +2421,8 @@ Run `revdep_details(, "manynet")` for more info * checking package dependencies ... NOTE ``` + Package suggested but not available for checking: ‘migraph’ + Package which this enhances but not available for checking: ‘Rgraphviz’ ``` @@ -2240,131 +2431,161 @@ Run `revdep_details(, "manynet")` for more info Note: found 7 marked UTF-8 strings ``` -# matric +# mapme.biodiversity
-* Version: 0.2.0 -* GitHub: https://github.com/cytomining/matric -* Source code: https://github.com/cran/matric -* Date/Publication: 2023-03-22 08:50:02 UTC -* Number of recursive dependencies: 107 +* Version: 0.8.0 +* GitHub: https://github.com/mapme-initiative/mapme.biodiversity +* Source code: https://github.com/cran/mapme.biodiversity +* Date/Publication: 2024-07-03 05:30:02 UTC +* Number of recursive dependencies: 106 -Run `revdep_details(, "matric")` for more info +Run `revdepcheck::revdep_details(, "mapme.biodiversity")` for more info
## In both -* checking package dependencies ... ERROR +* checking tests ... ``` - Package required but not available: ‘arrow’ - - See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ - manual. + Running ‘testthat.R’ + ERROR + Running the tests in ‘tests/testthat.R’ failed. + Last 50 lines of output: + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test-calc_deforestation_drivers.R:13:3'): deforestation drivers works ── + + Error: crs not found: is it missing? + Backtrace: + ▆ + ... + 12. │ └─jsonlite:::parseJSON(txt, bigint_as_char) + 13. │ └─jsonlite:::parse_string(txt, bigint_as_char) + 14. └─base::.handleSimpleError(...) + 15. └─purrr (local) h(simpleError(msg, call)) + 16. └─cli::cli_abort(...) + 17. └─rlang::abort(...) + + [ FAIL 3 | WARN 1 | SKIP 33 | PASS 298 ] + Error: Test failures + Execution halted ``` -# metabolomicsR +# metaGE
-* Version: 1.0.0 -* GitHub: https://github.com/XikunHan/metabolomicsR -* Source code: https://github.com/cran/metabolomicsR -* Date/Publication: 2022-04-29 07:40:02 UTC -* Number of recursive dependencies: 182 +* Version: 1.0.3 +* GitHub: NA +* Source code: https://github.com/cran/metaGE +* Date/Publication: 2023-09-28 08:50:02 UTC +* Number of recursive dependencies: 148 -Run `revdep_details(, "metabolomicsR")` for more info +Run `revdepcheck::revdep_details(, "metaGE")` for more info
## In both -* checking dependencies in R code ... WARNING - ``` - Missing or unexported object: ‘future::multiprocess’ - ``` - -* checking package dependencies ... NOTE +* checking installed package size ... NOTE ``` - Package suggested but not available for checking: ‘genuMet’ + installed size is 5.2Mb + sub-directories of 1Mb or more: + data 4.2Mb ``` -# metaGE +# mice
-* Version: 1.0.3 -* GitHub: NA -* Source code: https://github.com/cran/metaGE -* Date/Publication: 2023-09-28 08:50:02 UTC -* Number of recursive dependencies: 149 +* Version: 3.16.0 +* GitHub: https://github.com/amices/mice +* Source code: https://github.com/cran/mice +* Date/Publication: 2023-06-05 14:40:02 UTC +* Number of recursive dependencies: 131 -Run `revdep_details(, "metaGE")` for more info +Run `revdepcheck::revdep_details(, "mice")` for more info
## In both -* checking installed package size ... NOTE +* checking package dependencies ... NOTE ``` - installed size is 5.1Mb - sub-directories of 1Mb or more: - data 4.2Mb + Package suggested but not available for checking: ‘miceadds’ + ``` + +* checking Rd files ... NOTE + ``` + checkRd: (-1) ampute.Rd:143: Lost braces + 143 | we refer to \doi{10.1177/0049124118799376}{Schouten and Vink, 2018}. + | ^ + checkRd: (-1) ampute.Rd:188: Lost braces + 188 | \doi{10.1080/00949655.2018.1491577}{Schouten, Lugtig and Vink, 2018}. + | ^ + checkRd: (-1) ampute.Rd:223: Lost braces + 223 | Schouten, R.M. and Vink, G. (2018){The Dance of the Mechanisms: How Observed Information Influences the Validity of Missingness Assumptions}. + | ^ + checkRd: (-1) mice.Rd:348: Lost braces; missing escapes or markup? + 348 | The \pkg{mice} software was published in the {Journal of Statistical Software} (Van Buuren and Groothuis-Oudshoorn, 2011). \doi{10.18637/jss.v045.i03} + | ^ + checkRd: (-1) mice.impute.pmm.Rd:87: Lost braces; missing escapes or markup? + 87 | \item{Construct \eqn{n_0} sets \eqn{Z_j}, each containing \eqn{d} candidate donors, from Y_{obs} such that \eqn{\sum_d\dot\eta(i,j)} is minimum for all \eqn{j=1,\dots,n_0}. Break ties randomly.} + | ^ + ``` + +* checking Rd cross-references ... NOTE + ``` + Package unavailable to check Rd xrefs: ‘miceadds’ ``` -# microservices +# mikropml
-* Version: 0.2.0 -* GitHub: https://github.com/tidylab/microservices -* Source code: https://github.com/cran/microservices -* Date/Publication: 2022-10-01 09:50:02 UTC -* Number of recursive dependencies: 72 +* Version: 1.6.1 +* GitHub: https://github.com/SchlossLab/mikropml +* Source code: https://github.com/cran/mikropml +* Date/Publication: 2023-08-21 15:10:05 UTC +* Number of recursive dependencies: 130 -Run `revdep_details(, "microservices")` for more info +Run `revdepcheck::revdep_details(, "mikropml")` for more info
## In both -* checking tests ... +* checking Rd files ... NOTE ``` - Running ‘testthat.R’ - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(microservices) - > test_check("microservices") - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 12 ] - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ... - Backtrace: - ▆ - 1. ├─config::get(...) at test-endpoint-plumber-{route_name}.R:2:1 - 2. │ └─base::normalizePath(file, mustWork = FALSE) - 3. │ └─base::path.expand(path) - 4. └─base::system.file(...) - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 12 ] - Error: Test failures - Execution halted + checkRd: (-1) create_grouped_data_partition.Rd:60: Lost braces; missing escapes or markup? + 60 | Zena Lapp, {zenalapp@umich.edu} + | ^ + checkRd: (-1) create_grouped_data_partition.Rd:62: Lost braces; missing escapes or markup? + 62 | Kelly Sovacool, {sovacool@umich.edu} + | ^ + checkRd: (-1) create_grouped_k_multifolds.Rd:30: Lost braces; missing escapes or markup? + 30 | Zena Lapp, {zenalapp@umich.edu} + | ^ + checkRd: (-1) get_partition_indices.Rd:58: Lost braces; missing escapes or markup? + 58 | Kelly Sovacool, {sovacool@umich.edu} + | ^ + checkRd: (-1) set_hparams_glmnet.Rd:16: Lost braces; missing escapes or markup? + 16 | Zena Lapp, {zenalapp@umich.edu} + | ^ ``` # MineICA
-* Version: 1.42.0 +* Version: 1.44.0 * GitHub: NA * Source code: https://github.com/cran/MineICA -* Date/Publication: 2023-10-24 -* Number of recursive dependencies: 216 +* Date/Publication: 2024-04-30 +* Number of recursive dependencies: 217 -Run `revdep_details(, "MineICA")` for more info +Run `revdepcheck::revdep_details(, "MineICA")` for more info
@@ -2392,19 +2613,19 @@ Run `revdep_details(, "MineICA")` for more info * checking Rd cross-references ... WARNING ``` - Missing link or links in documentation object 'Alist.Rd': + Missing link or links in Rd file 'Alist.Rd': ‘class-IcaSet’ - Missing link or links in documentation object 'Slist.Rd': + Missing link or links in Rd file 'Slist.Rd': ‘class-IcaSet’ - Missing link or links in documentation object 'class-IcaSet.Rd': + Missing link or links in Rd file 'class-IcaSet.Rd': ‘class-IcaSet’ - Missing link or links in documentation object 'getComp.Rd': + Missing link or links in Rd file 'getComp.Rd': ‘class-IcaSet’ - Missing link or links in documentation object 'runAn.Rd': + Missing link or links in Rd file 'runAn.Rd': ‘[Category:class-GOHyperGParams]{GOHyperGParams}’ See section 'Cross-references' in the 'Writing R Extensions' manual. @@ -2420,6 +2641,31 @@ Run `revdep_details(, "MineICA")` for more info Extensions’ manual. ``` +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘MineICA.Rnw’ using Sweave + Loading required package: BiocGenerics + + Attaching package: ‘BiocGenerics’ + + The following objects are masked from ‘package:stats’: + + IQR, mad, sd, var, xtabs + + ... + l.23 \usepackage + {subfig}^^M + ! ==> Fatal error occurred, no output PDF file produced! + --- failed re-building ‘MineICA.Rnw’ + + SUMMARY: processing the following file failed: + ‘MineICA.Rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + * checking package dependencies ... NOTE ``` Package which this enhances but not available for checking: ‘doMC’ @@ -2465,29 +2711,29 @@ Run `revdep_details(, "MineICA")` for more info contains 'methods'). ``` -* checking re-building of vignette outputs ... NOTE +* checking Rd files ... NOTE ``` - Error(s) in re-building vignettes: - --- re-building ‘MineICA.Rnw’ using Sweave - Loading required package: BiocGenerics - - Attaching package: ‘BiocGenerics’ - - The following objects are masked from ‘package:stats’: - - IQR, mad, sd, var, xtabs - + checkRd: (-1) clusterFastICARuns.Rd:47: Lost braces + 47 | \item{...}{Additional parameters for code{funClus}} + | ^ + checkRd: (-1) clusterFastICARuns.Rd:52: Lost braces + 52 | item{W}{the estimated unmixing matrix}, \item{Iq}{Iq + | ^ + checkRd: (-1) clusterFastICARuns.Rd:52: Lost braces + 52 | item{W}{the estimated unmixing matrix}, \item{Iq}{Iq + | ^ + checkRd: (-1) plotDensOneAnnotInAllComp.Rd:104: Lost braces ... - l.23 \usepackage - {subfig}^^M - ! ==> Fatal error occurred, no output PDF file produced! - --- failed re-building ‘MineICA.Rnw’ - - SUMMARY: processing the following file failed: - ‘MineICA.Rnw’ - - Error: Vignette re-building failed. - Execution halted + | ^ + checkRd: (-1) runICA.Rd:44: Lost braces + 44 | item{W}{the estimated unmixing matrix}} + | ^ + checkRd: (-1) runICA.Rd:44: Lost braces + 44 | item{W}{the estimated unmixing matrix}} + | ^ + checkRd: (-1) writeProjByComp.Rd:38: Lost braces + 38 | their annotations, please remember to modify code{genesPath(params)}, or + | ^ ``` # missSBM @@ -2498,71 +2744,38 @@ Run `revdep_details(, "MineICA")` for more info * GitHub: https://github.com/grossSBM/missSBM * Source code: https://github.com/cran/missSBM * Date/Publication: 2023-10-24 16:00:05 UTC -* Number of recursive dependencies: 114 +* Number of recursive dependencies: 113 -Run `revdep_details(, "missSBM")` for more info +Run `revdepcheck::revdep_details(, "missSBM")` for more info
## In both -* checking whether package ‘missSBM’ can be installed ... WARNING +* checking installed package size ... NOTE ``` - Found the following significant warnings: - /c4/home/henrik/repositories/future/revdep/library/missSBM/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/missSBM/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/missSBM/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - See ‘/c4/home/henrik/repositories/future/revdep/checks/missSBM/new/missSBM.Rcheck/00install.out’ for details. - ``` - -* checking installed package size ... NOTE - ``` - installed size is 9.8Mb + installed size is 10.1Mb sub-directories of 1Mb or more: - libs 7.8Mb + R 1.0Mb + libs 7.9Mb ``` # mistyR
-* Version: 1.10.0 +* Version: 1.12.0 * GitHub: https://github.com/saezlab/mistyR * Source code: https://github.com/cran/mistyR -* Date/Publication: 2023-10-24 -* Number of recursive dependencies: 155 +* Date/Publication: 2024-05-01 +* Number of recursive dependencies: 153 -Run `revdep_details(, "mistyR")` for more info +Run `revdepcheck::revdep_details(, "mistyR")` for more info
## In both -* checking tests ... - ``` - Running ‘testthat.R’ - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 50 lines of output: - - Collecting contributions - - Collecting importances - - Aggregating - ... - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Failure ('test-misty.R:212:3'): k for cv , n.bags for bagging can be changed and approx works ── - first.run < second.run is not TRUE - - `actual`: FALSE - `expected`: TRUE - - [ FAIL 1 | WARN 4 | SKIP 0 | PASS 172 ] - Error: Test failures - Execution halted - ``` - * checking R code for possible problems ... NOTE ``` aggregate_results: no visible binding for global variable ‘measure’ @@ -2588,6 +2801,37 @@ Run `revdep_details(, "mistyR")` for more info to your NAMESPACE file. ``` +* checking Rd files ... NOTE + ``` + checkRd: (-1) collect_results.Rd:32: Lost braces; missing escapes or markup? + 32 | for all performance measures for each {target} over all samples.} + | ^ + ``` + +# modelsummary + +
+ +* Version: 2.1.1 +* GitHub: https://github.com/vincentarelbundock/modelsummary +* Source code: https://github.com/cran/modelsummary +* Date/Publication: 2024-06-14 14:20:06 UTC +* Number of recursive dependencies: 300 + +Run `revdepcheck::revdep_details(, "modelsummary")` for more info + +
+ +## Newly broken + +* checking installed package size ... NOTE + ``` + installed size is 5.9Mb + sub-directories of 1Mb or more: + help 3.8Mb + tinytest 1.7Mb + ``` + # momentuHMM
@@ -2596,30 +2840,21 @@ Run `revdep_details(, "mistyR")` for more info * GitHub: https://github.com/bmcclintock/momentuHMM * Source code: https://github.com/cran/momentuHMM * Date/Publication: 2022-10-18 20:52:35 UTC -* Number of recursive dependencies: 145 +* Number of recursive dependencies: 149 -Run `revdep_details(, "momentuHMM")` for more info +Run `revdepcheck::revdep_details(, "momentuHMM")` for more info
## In both -* checking whether package ‘momentuHMM’ can be installed ... WARNING - ``` - Found the following significant warnings: - /c4/home/henrik/repositories/future/revdep/library/momentuHMM/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/momentuHMM/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/momentuHMM/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - See ‘/c4/home/henrik/repositories/future/revdep/checks/momentuHMM/new/momentuHMM.Rcheck/00install.out’ for details. - ``` - * checking installed package size ... NOTE ``` - installed size is 10.2Mb + installed size is 11.0Mb sub-directories of 1Mb or more: - R 1.2Mb + R 1.5Mb doc 1.7Mb - libs 6.7Mb + libs 7.1Mb ``` # MOSS @@ -2630,46 +2865,35 @@ Run `revdep_details(, "momentuHMM")` for more info * GitHub: https://github.com/agugonrey/MOSS * Source code: https://github.com/cran/MOSS * Date/Publication: 2022-03-25 15:50:05 UTC -* Number of recursive dependencies: 184 +* Number of recursive dependencies: 182 -Run `revdep_details(, "MOSS")` for more info +Run `revdepcheck::revdep_details(, "MOSS")` for more info
## In both -* checking re-building of vignette outputs ... WARNING +* checking Rd files ... NOTE ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘MOSS_working_example.Rmd’ using rmarkdown - ! LaTeX Error: File `iftex.sty' not found. - - ! Emergency stop. - - - Error: processing vignette 'MOSS_working_example.Rmd' failed with diagnostics: - LaTeX failed to compile /c4/home/henrik/repositories/future/revdep/checks/MOSS/new/MOSS.Rcheck/vign_test/MOSS/vignettes/MOSS_working_example.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See MOSS_working_example.log for more info. - --- failed re-building ‘MOSS_working_example.Rmd’ - - SUMMARY: processing the following file failed: - ‘MOSS_working_example.Rmd’ - - Error: Vignette re-building failed. - Execution halted + checkRd: (-1) ssvdEN_sol_path.Rd:58: Lost braces; missing escapes or markup? + 58 | \item{tol}{Convergence is determined when ||U_j - U_{j-1}||_F < tol, + | ^ + checkRd: (-1) ssvdEN_sol_path_par.Rd:59: Lost braces; missing escapes or markup? + 59 | \item{tol}{Convergence is determined when ||U_j - U_{j-1}||_F < tol, + | ^ ``` -# mrgsim.parallel +# multilevelcoda
-* Version: 0.2.1 -* GitHub: https://github.com/kylebaron/mrgsim.parallel -* Source code: https://github.com/cran/mrgsim.parallel -* Date/Publication: 2022-03-17 19:50:05 UTC -* Number of recursive dependencies: 74 +* Version: 1.3.0.2 +* GitHub: https://github.com/florale/multilevelcoda +* Source code: https://github.com/cran/multilevelcoda +* Date/Publication: 2024-07-09 14:50:02 UTC +* Number of recursive dependencies: 171 -Run `revdep_details(, "mrgsim.parallel")` for more info +Run `revdepcheck::revdep_details(, "multilevelcoda")` for more info
@@ -2677,12 +2901,66 @@ Run `revdep_details(, "mrgsim.parallel")` for more info * checking package dependencies ... NOTE ``` - Package suggested but not available for checking: ‘arrow’ + Package suggested but not available for checking: ‘cmdstanr’ ``` -* checking Rd cross-references ... NOTE +* checking installed package size ... NOTE + ``` + installed size is 7.9Mb + sub-directories of 1Mb or more: + doc 6.4Mb + ``` + +# multitool + +
+ +* Version: 0.1.4 +* GitHub: https://github.com/ethan-young/multitool +* Source code: https://github.com/cran/multitool +* Date/Publication: 2024-02-08 17:40:02 UTC +* Number of recursive dependencies: 161 + +Run `revdepcheck::revdep_details(, "multitool")` for more info + +
+ +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.0Mb + sub-directories of 1Mb or more: + doc 4.3Mb + ``` + +# multiverse + +
+ +* Version: 0.6.1 +* GitHub: https://github.com/MUCollective/multiverse +* Source code: https://github.com/cran/multiverse +* Date/Publication: 2022-07-04 13:20:02 UTC +* Number of recursive dependencies: 133 + +Run `revdepcheck::revdep_details(, "multiverse")` for more info + +
+ +## In both + +* checking Rd files ... NOTE ``` - Package unavailable to check Rd xrefs: ‘arrow’ + checkRd: (-1) durante.Rd:60-61: Lost braces + 60 | in their study, \doi{10.1177/0956797612466416}{\emph{The + | ^ + checkRd: (-1) hurricane.Rd:34: Lost braces + 34 | in their study, \doi{10.1073/pnas.1402786111}{\emph{Female hurricanes are deadlier than male hurricanes}}. + | ^ + checkRd: (-1) userlogs.Rd:33: Lost braces + 33 | \doi{10.1145/2470654.2481359}{Evaluating the Efficiency of Physical Visualizations} + | ^ ``` # nebula @@ -2693,9 +2971,9 @@ Run `revdep_details(, "mrgsim.parallel")` for more info * GitHub: https://github.com/lhe17/nebula * Source code: https://github.com/cran/nebula * Date/Publication: 2024-02-15 23:00:02 UTC -* Number of recursive dependencies: 185 +* Number of recursive dependencies: 173 -Run `revdep_details(, "nebula")` for more info +Run `revdepcheck::revdep_details(, "nebula")` for more info
@@ -2703,67 +2981,62 @@ Run `revdep_details(, "nebula")` for more info * checking installed package size ... NOTE ``` - installed size is 37.4Mb + installed size is 35.4Mb sub-directories of 1Mb or more: - libs 35.9Mb + libs 33.7Mb ``` -# nfl4th +# nflseedR
-* Version: 1.0.4 -* GitHub: https://github.com/nflverse/nfl4th -* Source code: https://github.com/cran/nfl4th -* Date/Publication: 2023-08-21 09:32:33 UTC -* Number of recursive dependencies: 111 +* Version: 1.2.0 +* GitHub: https://github.com/nflverse/nflseedR +* Source code: https://github.com/cran/nflseedR +* Date/Publication: 2023-01-05 21:50:31 UTC +* Number of recursive dependencies: 87 -Run `revdep_details(, "nfl4th")` for more info +Run `revdepcheck::revdep_details(, "nflseedR")` for more info
## In both -* checking whether package ‘nfl4th’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: GitHub.com seems offline, and `options(nfl4th.keep_games)` is not set to TRUE. Deleting the games cache, and predictions may not be available without an internet connection. - See ‘/c4/home/henrik/repositories/future/revdep/checks/nfl4th/new/nfl4th.Rcheck/00install.out’ for details. - ``` - -* checking whether the namespace can be loaded with stated dependencies ... NOTE +* checking Rd files ... NOTE ``` - Warning: GitHub.com seems offline, and `options(nfl4th.keep_games)` is not set to TRUE. Deleting the games cache, and predictions may not be available without an internet connection. - - A namespace must be able to be loaded with just the base namespace - loaded: otherwise if the namespace gets loaded by a saved object, the - session will be unable to start. - - Probably some imports need to be declared in the NAMESPACE file. + checkRd: (-1) load_schedules.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) load_schedules.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) load_schedules.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) load_schedules.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) load_schedules.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) load_schedules.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) load_schedules.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) load_schedules.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) load_schedules.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly ``` # nhdplusTools
-* Version: 1.0.0 +* Version: 1.2.1 * GitHub: https://github.com/doi-usgs/nhdplusTools * Source code: https://github.com/cran/nhdplusTools -* Date/Publication: 2023-10-02 14:10:02 UTC -* Number of recursive dependencies: 140 +* Date/Publication: 2024-06-05 18:20:02 UTC +* Number of recursive dependencies: 138 -Run `revdep_details(, "nhdplusTools")` for more info +Run `revdepcheck::revdep_details(, "nhdplusTools")` for more info
## In both -* checking package dependencies ... ERROR +* checking installed package size ... NOTE ``` - Package required but not available: ‘arrow’ - - See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ - manual. + installed size is 6.5Mb + sub-directories of 1Mb or more: + data 1.6Mb + doc 4.2Mb ``` # oncomsm @@ -2774,9 +3047,9 @@ Run `revdep_details(, "nhdplusTools")` for more info * GitHub: https://github.com/Boehringer-Ingelheim/oncomsm * Source code: https://github.com/cran/oncomsm * Date/Publication: 2023-04-17 07:00:02 UTC -* Number of recursive dependencies: 127 +* Number of recursive dependencies: 126 -Run `revdep_details(, "oncomsm")` for more info +Run `revdepcheck::revdep_details(, "oncomsm")` for more info
@@ -2784,10 +3057,10 @@ Run `revdep_details(, "oncomsm")` for more info * checking installed package size ... NOTE ``` - installed size is 67.6Mb + installed size is 64.2Mb sub-directories of 1Mb or more: - doc 1.0Mb - libs 65.5Mb + doc 1.1Mb + libs 62.0Mb ``` * checking for GNU extensions in Makefiles ... NOTE @@ -2795,72 +3068,64 @@ Run `revdep_details(, "oncomsm")` for more info GNU make is a SystemRequirements. ``` -# onemapsgapi +# OOS
-* Version: 1.1.0 -* GitHub: NA -* Source code: https://github.com/cran/onemapsgapi -* Date/Publication: 2022-11-29 08:00:03 UTC -* Number of recursive dependencies: 71 +* Version: 1.0.0 +* GitHub: https://github.com/tylerJPike/OOS +* Source code: https://github.com/cran/OOS +* Date/Publication: 2021-03-17 13:20:20 UTC +* Number of recursive dependencies: 136 -Run `revdep_details(, "onemapsgapi")` for more info +Run `revdepcheck::revdep_details(, "OOS")` for more info
## In both -* checking re-building of vignette outputs ... ERROR +* checking LazyData ... NOTE ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘onemapsgapi_vignette.Rmd’ using rmarkdown - - Quitting from lines 36-37 [unnamed-chunk-4] (onemapsgapi_vignette.Rmd) - Error: processing vignette 'onemapsgapi_vignette.Rmd' failed with diagnostics: - Peer certificate cannot be authenticated with given CA certificates: [developers.onemap.sg] Peer's Certificate has expired. - --- failed re-building ‘onemapsgapi_vignette.Rmd’ - - SUMMARY: processing the following file failed: - ‘onemapsgapi_vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted + 'LazyData' is specified without a 'data' directory ``` -# OOS +# OptimalGoldstandardDesigns
-* Version: 1.0.0 -* GitHub: https://github.com/tylerJPike/OOS -* Source code: https://github.com/cran/OOS -* Date/Publication: 2021-03-17 13:20:20 UTC -* Number of recursive dependencies: 137 +* Version: 1.0.1 +* GitHub: https://github.com/jan-imbi/OptimalGoldstandardDesigns +* Source code: https://github.com/cran/OptimalGoldstandardDesigns +* Date/Publication: 2023-09-11 10:40:05 UTC +* Number of recursive dependencies: 72 -Run `revdep_details(, "OOS")` for more info +Run `revdepcheck::revdep_details(, "OptimalGoldstandardDesigns")` for more info
## In both -* checking LazyData ... NOTE +* checking Rd files ... NOTE ``` - 'LazyData' is specified without a 'data' directory + checkRd: (-1) calc_n_from_c.Rd:5: Lost braces; missing escapes or markup? + 5 | \title{Helper function to calculate other n's given n_{1,T} and allocation ratios} + | ^ + checkRd: (-1) calc_n_from_c.Rd:15: Lost braces; missing escapes or markup? + 15 | Helper function to calculate other n's given n_{1,T} and allocation ratios + | ^ ``` # pareg
-* Version: 1.6.0 +* Version: 1.8.0 * GitHub: https://github.com/cbg-ethz/pareg * Source code: https://github.com/cran/pareg -* Date/Publication: 2023-10-24 -* Number of recursive dependencies: 320 +* Date/Publication: 2024-04-30 +* Number of recursive dependencies: 317 -Run `revdep_details(, "pareg")` for more info +Run `revdepcheck::revdep_details(, "pareg")` for more info
@@ -2879,15 +3144,15 @@ Run `revdep_details(, "pareg")` for more info > > df_genes <- data.frame( ... - + ) - > fit <- pareg(df_genes, df_terms, max_iterations = 10) - Error in py_module_import(module, convert = convert) : - ImportError: /lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /c4/home/henrik/.cache/R/basilisk/1.14.3/pareg/1.6.0/pareg/lib/python3.9/site-packages/tensorflow/python/platform/_pywrap_cpu_feature_guard.so) - Run `reticulate::py_last_error()` for details. - Error in .activate_fallback(proc, testload, env = env, envpath = envpath, : - ImportError: /lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /c4/home/henrik/.cache/R/basilisk/1.14.3/pareg/1.6.0/pareg/lib/python3.9/site-packages/tensorflow/python/platform/_pywrap_cpu_feature_guard.so) + Failed to load the native TensorFlow runtime. + See https://www.tensorflow.org/install/errors for some common causes and solutions. + If you need help, create an issue at https://github.com/tensorflow/tensorflow/issues and include the entire stack trace above this error message. Run `reticulate::py_last_error()` for details. - Calls: pareg -> basiliskStart -> .activate_fallback + Warning in serverSocket(port = port) : + unable to load shared object '/software/c4/cbi/software/_rocky8/R-4.4.1-gcc13/lib64/R/modules//internet.so': + /lib64/libk5crypto.so.3: undefined symbol: EVP_KDF_ctrl, version OPENSSL_1_1_1b + Error in serverSocket(port = port) : internet routines cannot be loaded + Calls: pareg ... .activate_fallback -> basiliskStart -> makePSOCKcluster -> serverSocket Execution halted ``` @@ -2904,15 +3169,15 @@ Run `revdep_details(, "pareg")` for more info ... - + testload = c("tensorflow", "tensorflow_probability") - + ) - Error in py_module_import(module, convert = convert) : - ImportError: /lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /c4/home/henrik/.cache/R/basilisk/1.14.3/pareg/1.6.0/pareg/lib/python3.9/site-packages/tensorflow/python/platform/_pywrap_cpu_feature_guard.so) - Run `reticulate::py_last_error()` for details. - Error in .activate_fallback(proc, testload, env = env, envpath = envpath, : - ImportError: /lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /c4/home/henrik/.cache/R/basilisk/1.14.3/pareg/1.6.0/pareg/lib/python3.9/site-packages/tensorflow/python/platform/_pywrap_cpu_feature_guard.so) + See https://www.tensorflow.org/install/errors for some common causes and solutions. + If you need help, create an issue at https://github.com/tensorflow/tensorflow/issues and include the entire stack trace above this error message. Run `reticulate::py_last_error()` for details. - Calls: -> .activate_fallback + Error in serverSocket(port = port) : internet routines cannot be loaded + Calls: ... .activate_fallback -> basiliskStart -> makePSOCKcluster -> serverSocket + In addition: Warning message: + In serverSocket(port = port) : + unable to load shared object '/software/c4/cbi/software/_rocky8/R-4.4.1-gcc13/lib64/R/modules//internet.so': + /lib64/libk5crypto.so.3: undefined symbol: EVP_KDF_ctrl, version OPENSSL_1_1_1b Execution halted ``` @@ -2923,11 +3188,11 @@ Run `revdep_details(, "pareg")` for more info --- re-building ‘pareg.Rmd’ using rmarkdown The magick package is required to crop "/c4/home/henrik/repositories/future/revdep/checks/pareg/new/pareg.Rcheck/vign_test/pareg/vignettes/pareg_files/figure-html/unnamed-chunk-4-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/future/revdep/checks/pareg/new/pareg.Rcheck/vign_test/pareg/vignettes/pareg_files/figure-html/unnamed-chunk-5-1.png" but not available. + 2024-07-29 06:07:21.892909: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: SSE4.1 SSE4.2 AVX AVX2 FMA + To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags. Quitting from lines 145-150 [unnamed-chunk-9] (pareg.Rmd) Error: processing vignette 'pareg.Rmd' failed with diagnostics: - ImportError: /lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /c4/home/henrik/.cache/R/basilisk/1.14.3/pareg/1.6.0/pareg/lib/python3.9/site-packages/tensorflow/python/platform/_pywrap_cpu_feature_guard.so) - Run `reticulate::py_last_error()` for details. ... --- re-building ‘pathway_similarities.Rmd’ using rmarkdown The magick package is required to crop "/c4/home/henrik/repositories/future/revdep/checks/pareg/new/pareg.Rcheck/vign_test/pareg/vignettes/pathway_similarities_files/figure-html/unnamed-chunk-2-1.png" but not available. @@ -2973,28 +3238,6 @@ Run `revdep_details(, "pareg")` for more info See ‘/c4/home/henrik/repositories/future/revdep/checks/pareg/new/pareg.Rcheck/00install.out’ for details. ``` -# parseRPDR - -
- -* Version: 1.1.0 -* GitHub: https://github.com/martonkolossvary/parseRPDR -* Source code: https://github.com/cran/parseRPDR -* Date/Publication: 2024-01-09 12:10:02 UTC -* Number of recursive dependencies: 89 - -Run `revdep_details(, "parseRPDR")` for more info - -
- -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘doParallel’ - All declared Imports should be used. - ``` - # partR2
@@ -3003,9 +3246,9 @@ Run `revdep_details(, "parseRPDR")` for more info * GitHub: https://github.com/mastoffel/partR2 * Source code: https://github.com/cran/partR2 * Date/Publication: 2024-03-04 13:20:02 UTC -* Number of recursive dependencies: 94 +* Number of recursive dependencies: 93 -Run `revdep_details(, "partR2")` for more info +Run `revdepcheck::revdep_details(, "partR2")` for more info
@@ -3025,9 +3268,9 @@ Run `revdep_details(, "partR2")` for more info * GitHub: https://github.com/rmaia/pavo * Source code: https://github.com/cran/pavo * Date/Publication: 2023-09-24 10:10:02 UTC -* Number of recursive dependencies: 104 +* Number of recursive dependencies: 103 -Run `revdep_details(, "pavo")` for more info +Run `revdepcheck::revdep_details(, "pavo")` for more info
@@ -3040,48 +3283,6 @@ Run `revdep_details(, "pavo")` for more info See ‘/c4/home/henrik/repositories/future/revdep/checks/pavo/new/pavo.Rcheck/00install.out’ for details. ``` -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘imager’ - ``` - -# PCRedux - -
- -* Version: 1.1-2 -* GitHub: https://github.com/PCRuniversum/PCRedux -* Source code: https://github.com/cran/PCRedux -* Date/Publication: 2022-05-11 11:40:02 UTC -* Number of recursive dependencies: 153 - -Run `revdep_details(, "PCRedux")` for more info - -
- -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘PCRedux.Rmd’ using rmarkdown - ! LaTeX Error: File `iftex.sty' not found. - - ! Emergency stop. - - - Error: processing vignette 'PCRedux.Rmd' failed with diagnostics: - LaTeX failed to compile /c4/home/henrik/repositories/future/revdep/checks/PCRedux/new/PCRedux.Rcheck/vign_test/PCRedux/vignettes/PCRedux.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See PCRedux.log for more info. - --- failed re-building ‘PCRedux.Rmd’ - - SUMMARY: processing the following file failed: - ‘PCRedux.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - # photosynthesis
@@ -3090,9 +3291,9 @@ Run `revdep_details(, "PCRedux")` for more info * GitHub: https://github.com/cdmuir/photosynthesis * Source code: https://github.com/cran/photosynthesis * Date/Publication: 2023-08-15 07:20:05 UTC -* Number of recursive dependencies: 122 +* Number of recursive dependencies: 121 -Run `revdep_details(, "photosynthesis")` for more info +Run `revdepcheck::revdep_details(, "photosynthesis")` for more info
@@ -3100,9 +3301,9 @@ Run `revdep_details(, "photosynthesis")` for more info * checking installed package size ... NOTE ``` - installed size is 7.1Mb + installed size is 7.2Mb sub-directories of 1Mb or more: - doc 6.0Mb + doc 6.1Mb ``` * checking data for non-ASCII characters ... NOTE @@ -3120,7 +3321,7 @@ Run `revdep_details(, "photosynthesis")` for more info * Date/Publication: 2020-06-22 05:10:08 UTC * Number of recursive dependencies: 41 -Run `revdep_details(, "phylolm")` for more info +Run `revdepcheck::revdep_details(, "phylolm")` for more info
@@ -3144,58 +3345,24 @@ Run `revdep_details(, "phylolm")` for more info * GitHub: https://github.com/pln-team/PLNmodels * Source code: https://github.com/cran/PLNmodels * Date/Publication: 2024-03-05 15:50:03 UTC -* Number of recursive dependencies: 151 +* Number of recursive dependencies: 155 -Run `revdep_details(, "PLNmodels")` for more info +Run `revdepcheck::revdep_details(, "PLNmodels")` for more info
## In both -* checking whether package ‘PLNmodels’ can be installed ... WARNING - ``` - Found the following significant warnings: - /c4/home/henrik/repositories/future/revdep/library/PLNmodels/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/PLNmodels/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/PLNmodels/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - See ‘/c4/home/henrik/repositories/future/revdep/checks/PLNmodels/new/PLNmodels.Rcheck/00install.out’ for details. - ``` - * checking installed package size ... NOTE ``` - installed size is 27.5Mb + installed size is 27.7Mb sub-directories of 1Mb or more: + R 1.0Mb data 1.4Mb - doc 2.0Mb + doc 2.1Mb libs 22.4Mb ``` -# plumber - -
- -* Version: 1.2.1 -* GitHub: https://github.com/rstudio/plumber -* Source code: https://github.com/cran/plumber -* Date/Publication: 2022-09-06 19:10:02 UTC -* Number of recursive dependencies: 104 - -Run `revdep_details(, "plumber")` for more info - -
- -## In both - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘arrow’ - ``` - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘arrow’ - ``` - # portvine
@@ -3204,9 +3371,9 @@ Run `revdep_details(, "plumber")` for more info * GitHub: https://github.com/EmanuelSommer/portvine * Source code: https://github.com/cran/portvine * Date/Publication: 2024-01-18 16:30:02 UTC -* Number of recursive dependencies: 130 +* Number of recursive dependencies: 129 -Run `revdep_details(, "portvine")` for more info +Run `revdepcheck::revdep_details(, "portvine")` for more info
@@ -3214,9 +3381,9 @@ Run `revdep_details(, "portvine")` for more info * checking installed package size ... NOTE ``` - installed size is 52.9Mb + installed size is 50.2Mb sub-directories of 1Mb or more: - libs 51.9Mb + libs 49.1Mb ``` # ProFAST @@ -3227,29 +3394,20 @@ Run `revdep_details(, "portvine")` for more info * GitHub: https://github.com/feiyoung/ProFAST * Source code: https://github.com/cran/ProFAST * Date/Publication: 2024-03-18 08:10:06 UTC -* Number of recursive dependencies: 253 +* Number of recursive dependencies: 245 -Run `revdep_details(, "ProFAST")` for more info +Run `revdepcheck::revdep_details(, "ProFAST")` for more info
## In both -* checking whether package ‘ProFAST’ can be installed ... WARNING - ``` - Found the following significant warnings: - /c4/home/henrik/repositories/future/revdep/library/ProFAST/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/ProFAST/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/ProFAST/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - See ‘/c4/home/henrik/repositories/future/revdep/checks/ProFAST/new/ProFAST.Rcheck/00install.out’ for details. - ``` - * checking installed package size ... NOTE ``` - installed size is 23.8Mb + installed size is 24.5Mb sub-directories of 1Mb or more: data 2.2Mb - libs 21.1Mb + libs 21.8Mb ``` * checking dependencies in R code ... NOTE @@ -3266,23 +3424,14 @@ Run `revdep_details(, "ProFAST")` for more info * GitHub: https://github.com/stan-dev/projpred * Source code: https://github.com/cran/projpred * Date/Publication: 2023-12-15 00:00:02 UTC -* Number of recursive dependencies: 158 +* Number of recursive dependencies: 157 -Run `revdep_details(, "projpred")` for more info +Run `revdepcheck::revdep_details(, "projpred")` for more info
## In both -* checking whether package ‘projpred’ can be installed ... WARNING - ``` - Found the following significant warnings: - /c4/home/henrik/repositories/future/revdep/library/projpred/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/projpred/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/projpred/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - See ‘/c4/home/henrik/repositories/future/revdep/checks/projpred/new/projpred.Rcheck/00install.out’ for details. - ``` - * checking package dependencies ... NOTE ``` Package suggested but not available for checking: ‘cmdstanr’ @@ -3290,7 +3439,7 @@ Run `revdep_details(, "projpred")` for more info * checking installed package size ... NOTE ``` - installed size is 5.9Mb + installed size is 6.0Mb sub-directories of 1Mb or more: doc 1.4Mb libs 3.6Mb @@ -3300,98 +3449,138 @@ Run `revdep_details(, "projpred")` for more info
-* Version: 1.34.6 +* Version: 1.36.2 * GitHub: https://github.com/prostarproteomics/Prostar * Source code: https://github.com/cran/Prostar -* Date/Publication: 2024-02-15 -* Number of recursive dependencies: 332 +* Date/Publication: 2024-06-12 +* Number of recursive dependencies: 191 -Run `revdep_details(, "Prostar")` for more info +Run `revdepcheck::revdep_details(, "Prostar")` for more info
## In both -* checking whether package ‘Prostar’ can be installed ... ERROR +* checking re-building of vignette outputs ... WARNING ``` - Installation failed. - See ‘/c4/home/henrik/repositories/future/revdep/checks/Prostar/new/Prostar.Rcheck/00install.out’ for details. + Error(s) in re-building vignettes: + ... + --- re-building ‘Prostar_UserManual.Rmd’ using rmarkdown + ! LaTeX Error: File `titling.sty' not found. + + ! Emergency stop. + + + Error: processing vignette 'Prostar_UserManual.Rmd' failed with diagnostics: + LaTeX failed to compile /c4/home/henrik/repositories/future/revdep/checks/Prostar/new/Prostar.Rcheck/vign_test/Prostar/vignettes/Prostar_UserManual.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Prostar_UserManual.log for more info. + --- failed re-building ‘Prostar_UserManual.Rmd’ + + SUMMARY: processing the following file failed: + ‘Prostar_UserManual.Rmd’ + + Error: Vignette re-building failed. + Execution halted ``` -## Installation +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘DT’ ‘R.utils’ ‘RColorBrewer’ ‘XML’ ‘colourpicker’ ‘gtools’ + ‘markdown’ ‘rclipboard’ ‘sass’ ‘shinyTree’ ‘shinyWidgets’ + All declared Imports should be used. + ``` -### Devel +# psborrow2 -``` -* installing *source* package ‘Prostar’ ... -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : - there is no package called ‘ncdf4’ -Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart -Execution halted -ERROR: lazy loading failed for package ‘Prostar’ -* removing ‘/c4/home/henrik/repositories/future/revdep/checks/Prostar/new/Prostar.Rcheck/Prostar’ +
+* Version: 0.0.3.4 +* GitHub: https://github.com/Genentech/psborrow2 +* Source code: https://github.com/cran/psborrow2 +* Date/Publication: 2024-04-30 21:30:02 UTC +* Number of recursive dependencies: 152 -``` -### CRAN +Run `revdepcheck::revdep_details(, "psborrow2")` for more info -``` -* installing *source* package ‘Prostar’ ... -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : - there is no package called ‘ncdf4’ -Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart -Execution halted -ERROR: lazy loading failed for package ‘Prostar’ -* removing ‘/c4/home/henrik/repositories/future/revdep/checks/Prostar/old/Prostar.Rcheck/Prostar’ +
+ +## In both + +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘cmdstanr’ + ``` + +# pseudohouseholds + +
+ +* Version: 0.1.1 +* GitHub: https://github.com/chris31415926535/pseudohouseholds +* Source code: https://github.com/cran/pseudohouseholds +* Date/Publication: 2023-07-19 09:30:02 UTC +* Number of recursive dependencies: 104 + +Run `revdepcheck::revdep_details(, "pseudohouseholds")` for more info +
+ +## Newly fixed + +* checking installed package size ... NOTE + ``` + installed size is 5.3Mb + sub-directories of 1Mb or more: + data 5.0Mb + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 596 marked UTF-8 strings + ``` -``` -# pseudohouseholds +# qape
-* Version: 0.1.1 -* GitHub: https://github.com/chris31415926535/pseudohouseholds -* Source code: https://github.com/cran/pseudohouseholds -* Date/Publication: 2023-07-19 09:30:02 UTC -* Number of recursive dependencies: 105 +* Version: 2.1 +* GitHub: NA +* Source code: https://github.com/cran/qape +* Date/Publication: 2023-08-21 14:10:12 UTC +* Number of recursive dependencies: 39 -Run `revdep_details(, "pseudohouseholds")` for more info +Run `revdepcheck::revdep_details(, "qape")` for more info
## In both -* checking data for non-ASCII characters ... NOTE +* checking Rd files ... NOTE ``` - Note: found 596 marked UTF-8 strings + checkRd: (-1) srswrRe.Rd:10: Lost braces + 10 | \item{listRanef}{{\emph{ranef(model)}} object where {\emph{model}} is an { \emph{lmer}} object.} + | ^ ``` # QDNAseq
-* Version: 1.38.0 +* Version: 1.40.0 * GitHub: https://github.com/ccagc/QDNAseq * Source code: https://github.com/cran/QDNAseq -* Date/Publication: 2023-10-24 -* Number of recursive dependencies: 89 +* Date/Publication: 2024-04-30 +* Number of recursive dependencies: 94 -Run `revdep_details(, "QDNAseq")` for more info +Run `revdepcheck::revdep_details(, "QDNAseq")` for more info
## In both -* checking re-building of vignette outputs ... NOTE +* checking re-building of vignette outputs ... WARNING ``` Error(s) in re-building vignettes: --- re-building ‘QDNAseq.Rnw’ using Sweave @@ -3400,11 +3589,11 @@ Run `revdep_details(, "QDNAseq")` for more info Warning in allprior/tot : Recycling array of length 1 in vector-array arithmetic is deprecated. Use c() or as.vector() instead. - Warning in allprior/tot : Recycling array of length 1 in vector-array arithmetic is deprecated. + Use c() or as.vector() instead. ... - l.196 \RequirePackage + l.197 \RequirePackage {parnotes}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘QDNAseq.Rnw’ @@ -3416,6 +3605,37 @@ Run `revdep_details(, "QDNAseq")` for more info Execution halted ``` +* checking Rd files ... NOTE + ``` + checkRd: (-1) exportBins.Rd:41: Lost braces + 41 | \code{"bed"}. This argument is ignored if code{type = "calls"}.} + | ^ + ``` + +# qgcomp + +
+ +* Version: 2.15.2 +* GitHub: https://github.com/alexpkeil1/qgcomp +* Source code: https://github.com/cran/qgcomp +* Date/Publication: 2023-08-10 09:10:06 UTC +* Number of recursive dependencies: 156 + +Run `revdepcheck::revdep_details(, "qgcomp")` for more info + +
+ +## In both + +* checking Rd files ... NOTE + ``` + checkRd: (-1) qgcomp.survcurve.boot.Rd:17-19: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) qgcomp.survcurve.boot.Rd:20-21: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) qgcomp.survcurve.boot.Rd:22-23: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) qgcomp.survcurve.boot.Rd:24-25: Lost braces in \itemize; \value handles \item{}{} directly + ``` + # RAINBOWR
@@ -3424,9 +3644,9 @@ Run `revdep_details(, "QDNAseq")` for more info * GitHub: NA * Source code: https://github.com/cran/RAINBOWR * Date/Publication: 2024-03-03 09:12:36 UTC -* Number of recursive dependencies: 167 +* Number of recursive dependencies: 154 -Run `revdep_details(, "RAINBOWR")` for more info +Run `revdepcheck::revdep_details(, "RAINBOWR")` for more info
@@ -3434,22 +3654,46 @@ Run `revdep_details(, "RAINBOWR")` for more info * checking installed package size ... NOTE ``` - installed size is 45.2Mb + installed size is 42.9Mb + sub-directories of 1Mb or more: + libs 41.5Mb + ``` + +# Rcurvep + +
+ +* Version: 1.3.1 +* GitHub: https://github.com/moggces/Rcurvep +* Source code: https://github.com/cran/Rcurvep +* Date/Publication: 2024-01-09 08:20:32 UTC +* Number of recursive dependencies: 112 + +Run `revdepcheck::revdep_details(, "Rcurvep")` for more info + +
+ +## Newly broken + +* checking installed package size ... NOTE + ``` + installed size is 5.8Mb sub-directories of 1Mb or more: - libs 43.9Mb + data 1.2Mb + java 4.0Mb ``` # receptiviti
-* Version: 0.1.7 +* Version: 0.1.8 * GitHub: https://github.com/Receptiviti/receptiviti-r * Source code: https://github.com/cran/receptiviti -* Date/Publication: 2024-02-23 23:50:05 UTC -* Number of recursive dependencies: 67 +* Date/Publication: 2024-03-29 18:00:03 UTC +* Number of recursive dependencies: 66 -Run `revdep_details(, "receptiviti")` for more info +Run `revdepcheck::revdep_details(, "receptiviti")` for more info
@@ -3480,16 +3724,6 @@ Run `revdep_details(, "receptiviti")` for more info Execution halted ``` -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘arrow’ - ``` - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘arrow’ - ``` - # regmedint
@@ -3498,9 +3732,9 @@ Run `revdep_details(, "receptiviti")` for more info * GitHub: https://github.com/kaz-yos/regmedint * Source code: https://github.com/cran/regmedint * Date/Publication: 2024-01-13 00:50:02 UTC -* Number of recursive dependencies: 154 +* Number of recursive dependencies: 153 -Run `revdep_details(, "regmedint")` for more info +Run `revdepcheck::revdep_details(, "regmedint")` for more info
@@ -3512,6 +3746,47 @@ Run `revdep_details(, "regmedint")` for more info All declared Imports should be used. ``` +# reproducible + +
+ +* Version: 2.1.0 +* GitHub: https://github.com/PredictiveEcology/reproducible +* Source code: https://github.com/cran/reproducible +* Date/Publication: 2024-05-30 00:20:02 UTC +* Number of recursive dependencies: 104 + +Run `revdepcheck::revdep_details(, "reproducible")` for more info + +
+ +## In both + +* checking tests ... + ``` + Running ‘test-all.R’ + ERROR + Running the tests in ‘tests/test-all.R’ failed. + Last 50 lines of output: + 'test-preProcessWorks.R:315:3', 'test-preProcessWorks.R:328:3', + 'test-preProcessWorks.R:348:3', 'test-preProcessWorks.R:361:3', + 'test-preProcessWorks.R:374:3', 'test-preProcessWorks.R:391:3', + 'test-preProcessWorks.R:409:3', 'test-preProcessWorks.R:438:3', + 'test-preProcessWorks.R:459:3', 'test-preProcessWorks.R:487:3', + 'test-preProcessWorks.R:543:3', 'test-preProcessWorks.R:569:3', + ... + 4. └─reproducible:::makeVal(x) + 5. ├─terra::makeValid(x) + 6. └─terra::makeValid(x) + 7. └─terra (local) .local(x, ...) + 8. └─terra:::messages(x) + 9. └─terra:::error(f, x@ptr$getError()) + + [ FAIL 2 | WARN 0 | SKIP 91 | PASS 412 ] + Error: Test failures + Execution halted + ``` + # rgee
@@ -3520,21 +3795,51 @@ Run `revdep_details(, "regmedint")` for more info * GitHub: https://github.com/r-spatial/rgee * Source code: https://github.com/cran/rgee * Date/Publication: 2023-09-27 08:30:02 UTC -* Number of recursive dependencies: 144 +* Number of recursive dependencies: 136 -Run `revdep_details(, "rgee")` for more info +Run `revdepcheck::revdep_details(, "rgee")` for more info
## In both +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘geojsonio’ + ``` + * checking installed package size ... NOTE ``` - installed size is 8.2Mb + installed size is 8.4Mb sub-directories of 1Mb or more: doc 6.9Mb ``` +* checking Rd files ... NOTE + ``` + checkRd: (-1) ee_Authenticate.Rd:40: Lost braces in \itemize; meant \describe ? + checkRd: (-1) ee_Authenticate.Rd:41: Lost braces in \itemize; meant \describe ? + checkRd: (-1) ee_Authenticate.Rd:42: Lost braces in \itemize; meant \describe ? + checkRd: (-1) ee_Authenticate.Rd:43: Lost braces in \itemize; meant \describe ? + checkRd: (-1) ee_Authenticate.Rd:44: Lost braces in \itemize; meant \describe ? + checkRd: (-1) ee_Initialize.Rd:49: Lost braces in \itemize; meant \describe ? + checkRd: (-1) ee_Initialize.Rd:50: Lost braces in \itemize; meant \describe ? + checkRd: (-1) ee_Initialize.Rd:51: Lost braces in \itemize; meant \describe ? + checkRd: (-1) ee_Initialize.Rd:52: Lost braces in \itemize; meant \describe ? + checkRd: (-1) ee_Initialize.Rd:53: Lost braces in \itemize; meant \describe ? + ... + checkRd: (-1) ee_imagecollection_to_local.Rd:105: Lost braces in \itemize; meant \describe ? + checkRd: (-1) ee_imagecollection_to_local.Rd:106: Lost braces in \itemize; meant \describe ? + checkRd: (-1) ee_imagecollection_to_local.Rd:107: Lost braces in \itemize; meant \describe ? + checkRd: (-1) ee_imagecollection_to_local.Rd:108: Lost braces in \itemize; meant \describe ? + checkRd: (-1) ee_install.Rd:35-37: Lost braces in \itemize; meant \describe ? + checkRd: (-1) ee_install.Rd:38-39: Lost braces in \itemize; meant \describe ? + checkRd: (-1) ee_install.Rd:40: Lost braces in \itemize; meant \describe ? + checkRd: (-1) ee_install.Rd:41-44: Lost braces in \itemize; meant \describe ? + checkRd: (-1) ee_install.Rd:45: Lost braces in \itemize; meant \describe ? + checkRd: (-1) ee_install.Rd:46: Lost braces in \itemize; meant \describe ? + ``` + # robotstxt
@@ -3543,9 +3848,9 @@ Run `revdep_details(, "rgee")` for more info * GitHub: https://github.com/ropensci/robotstxt * Source code: https://github.com/cran/robotstxt * Date/Publication: 2020-09-03 19:30:02 UTC -* Number of recursive dependencies: 70 +* Number of recursive dependencies: 69 -Run `revdep_details(, "robotstxt")` for more info +Run `revdepcheck::revdep_details(, "robotstxt")` for more info
@@ -3566,32 +3871,44 @@ Run `revdep_details(, "robotstxt")` for more info
-* Version: 0.7-1 +* Version: 0.7-3 * GitHub: https://github.com/handcock/rpm * Source code: https://github.com/cran/rpm -* Date/Publication: 2023-04-21 23:30:02 UTC +* Date/Publication: 2024-04-18 08:20:03 UTC * Number of recursive dependencies: 66 -Run `revdep_details(, "rpm")` for more info +Run `revdepcheck::revdep_details(, "rpm")` for more info
## In both -* checking whether package ‘rpm’ can be installed ... WARNING +* checking installed package size ... NOTE ``` - Found the following significant warnings: - /c4/home/henrik/repositories/future/revdep/library/rpm/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/rpm/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/rpm/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - See ‘/c4/home/henrik/repositories/future/revdep/checks/rpm/new/rpm.Rcheck/00install.out’ for details. + installed size is 13.4Mb + sub-directories of 1Mb or more: + libs 12.8Mb ``` -* checking installed package size ... NOTE +# sampcompR + +
+ +* Version: 0.2.1 +* GitHub: NA +* Source code: https://github.com/cran/sampcompR +* Date/Publication: 2024-07-15 19:11:15 UTC +* Number of recursive dependencies: 182 + +Run `revdepcheck::revdep_details(, "sampcompR")` for more info + +
+ +## In both + +* checking Rd cross-references ... NOTE ``` - installed size is 11.6Mb - sub-directories of 1Mb or more: - libs 11.1Mb + Package unavailable to check Rd xrefs: ‘stargazer’ ``` # sapfluxnetr @@ -3602,9 +3919,9 @@ Run `revdep_details(, "rpm")` for more info * GitHub: https://github.com/sapfluxnet/sapfluxnetr * Source code: https://github.com/cran/sapfluxnetr * Date/Publication: 2023-01-25 15:30:02 UTC -* Number of recursive dependencies: 83 +* Number of recursive dependencies: 82 -Run `revdep_details(, "sapfluxnetr")` for more info +Run `revdepcheck::revdep_details(, "sapfluxnetr")` for more info
@@ -3619,35 +3936,18 @@ Run `revdep_details(, "sapfluxnetr")` for more info
-* Version: 1.2.1 +* Version: 1.4.0 * GitHub: https://github.com/AbbVie-ComputationalGenomics/SCArray * Source code: https://github.com/cran/SCArray.sat -* Date/Publication: 2024-01-16 +* Date/Publication: 2024-04-30 * Number of recursive dependencies: 181 -Run `revdep_details(, "SCArray.sat")` for more info +Run `revdepcheck::revdep_details(, "SCArray.sat")` for more info
## In both -* checking S3 generic/method consistency ... WARNING - ``` - SetAssayData: - function(object, layer, new.data, slot, ...) - SetAssayData.SCArrayAssay: - function(object, slot, new.data, ...) - - CreateSeuratObject: - function(counts, assay, names.field, names.delim, meta.data, project, - ...) - CreateSeuratObject.DelayedMatrix: - function(counts, project, assay, names.field, names.delim, meta.data, - min.cells, min.features, row.names, ...) - See section ‘Generic functions and methods’ in the ‘Writing R - Extensions’ manual. - ``` - * checking dependencies in R code ... NOTE ``` Unexported objects imported by ':::' calls: @@ -3667,124 +3967,59 @@ Run `revdep_details(, "SCArray.sat")` for more info * Date/Publication: 2023-10-19 04:40:02 UTC * Number of recursive dependencies: 68 -Run `revdep_details(, "sctransform")` for more info +Run `revdepcheck::revdep_details(, "sctransform")` for more info
## In both -* checking whether package ‘sctransform’ can be installed ... WARNING - ``` - Found the following significant warnings: - /c4/home/henrik/repositories/future/revdep/library/sctransform/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/sctransform/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/sctransform/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - See ‘/c4/home/henrik/repositories/future/revdep/checks/sctransform/new/sctransform.Rcheck/00install.out’ for details. - ``` - * checking package dependencies ... NOTE ``` Package which this enhances but not available for checking: ‘glmGamPoi’ ``` -# sdmApp - -
- -* Version: 0.0.2 -* GitHub: https://github.com/Abson-dev/sdmApp -* Source code: https://github.com/cran/sdmApp -* Date/Publication: 2021-07-07 08:30:02 UTC -* Number of recursive dependencies: 176 - -Run `revdep_details(, "sdmApp")` for more info - -
- -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘sp’ - All declared Imports should be used. - ``` - # sdmTMB
-* Version: 0.4.3 +* Version: 0.6.0 * GitHub: https://github.com/pbs-assess/sdmTMB * Source code: https://github.com/cran/sdmTMB -* Date/Publication: 2024-02-29 01:40:02 UTC -* Number of recursive dependencies: 116 +* Date/Publication: 2024-05-30 00:00:02 UTC +* Number of recursive dependencies: 149 -Run `revdep_details(, "sdmTMB")` for more info +Run `revdepcheck::revdep_details(, "sdmTMB")` for more info
## In both -* checking tests ... - ``` - Running ‘testthat.R’ - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 50 lines of output: - 'test-deprecated-args.R:2:3', 'test-deprecated-args.R:67:3', - 'test-dharma.R:3:3', 'test-extra-optimization.R:2:3', - 'test-extra-time.R:3:3', 'test-extra-time.R:42:3', 'test-extra-time.R:116:3', - 'test-factor-levels.R:2:3', 'test-factor-levels.R:37:3', - 'test-factor-levels.R:91:3', 'test-forecasting.R:2:3', 'test-index.R:3:3', - 'test-link-prediction.R:5:3', 'test-link-prediction.R:67:3', - ... - [6] -0.37427778 - -0.37427783 [6] - [7] -0.01713492 - -0.01713497 [7] - [8] 0.14953175 - 0.14953169 [8] - [9] -0.51713492 - -0.51713497 [9] - [10] 0.08286508 - 0.08286503 [10] - ... ... ... and 290 more ... - - [ FAIL 1 | WARN 0 | SKIP 146 | PASS 151 ] - Error: Test failures - Execution halted - ``` - * checking installed package size ... NOTE ``` - installed size is 105.4Mb + installed size is 98.5Mb sub-directories of 1Mb or more: - libs 103.7Mb + libs 96.6Mb ``` # sentopics
-* Version: 0.7.2 +* Version: 0.7.3 * GitHub: https://github.com/odelmarcelle/sentopics * Source code: https://github.com/cran/sentopics -* Date/Publication: 2023-05-28 09:50:02 UTC -* Number of recursive dependencies: 173 +* Date/Publication: 2024-04-18 13:12:38 UTC +* Number of recursive dependencies: 172 -Run `revdep_details(, "sentopics")` for more info +Run `revdepcheck::revdep_details(, "sentopics")` for more info
## In both -* checking whether package ‘sentopics’ can be installed ... WARNING - ``` - Found the following significant warnings: - /c4/home/henrik/repositories/future/revdep/library/sentopics/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/sentopics/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/sentopics/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - See ‘/c4/home/henrik/repositories/future/revdep/checks/sentopics/new/sentopics.Rcheck/00install.out’ for details. - ``` - * checking installed package size ... NOTE ``` - installed size is 8.1Mb + installed size is 8.2Mb sub-directories of 1Mb or more: data 1.2Mb libs 6.2Mb @@ -3804,13 +4039,13 @@ Run `revdep_details(, "sentopics")` for more info
-* Version: 5.0.3 +* Version: 5.1.0 * GitHub: https://github.com/satijalab/seurat * Source code: https://github.com/cran/Seurat -* Date/Publication: 2024-03-18 23:40:02 UTC +* Date/Publication: 2024-05-10 17:23:17 UTC * Number of recursive dependencies: 267 -Run `revdep_details(, "Seurat")` for more info +Run `revdepcheck::revdep_details(, "Seurat")` for more info
@@ -3818,14 +4053,16 @@ Run `revdep_details(, "Seurat")` for more info * checking package dependencies ... NOTE ``` - Packages suggested but not available for checking: 'BPCells', 'presto' + Packages suggested but not available for checking: + 'BPCells', 'hdf5r', 'presto' ``` * checking installed package size ... NOTE ``` - installed size is 16.0Mb + installed size is 16.8Mb sub-directories of 1Mb or more: - R 1.7Mb + R 2.0Mb + help 1.0Mb libs 13.5Mb ``` @@ -3838,13 +4075,13 @@ Run `revdep_details(, "Seurat")` for more info
-* Version: 5.0.1 -* GitHub: https://github.com/mojaveazure/seurat-object +* Version: 5.0.2 +* GitHub: https://github.com/satijalab/seurat-object * Source code: https://github.com/cran/SeuratObject -* Date/Publication: 2023-11-17 22:40:16 UTC -* Number of recursive dependencies: 103 +* Date/Publication: 2024-05-08 13:40:06 UTC +* Number of recursive dependencies: 102 -Run `revdep_details(, "SeuratObject")` for more info +Run `revdepcheck::revdep_details(, "SeuratObject")` for more info
@@ -3859,7 +4096,7 @@ Run `revdep_details(, "SeuratObject")` for more info * checking installed package size ... NOTE ``` - installed size is 5.4Mb + installed size is 5.5Mb sub-directories of 1Mb or more: R 1.5Mb libs 3.2Mb @@ -3878,9 +4115,9 @@ Run `revdep_details(, "SeuratObject")` for more info * GitHub: https://github.com/barbarabodinier/sharp * Source code: https://github.com/cran/sharp * Date/Publication: 2024-02-03 17:30:02 UTC -* Number of recursive dependencies: 157 +* Number of recursive dependencies: 156 -Run `revdep_details(, "sharp")` for more info +Run `revdepcheck::revdep_details(, "sharp")` for more info
@@ -3900,13 +4137,13 @@ Run `revdep_details(, "sharp")` for more info
-* Version: 1.8.0 +* Version: 1.8.1.1 * GitHub: https://github.com/rstudio/shiny * Source code: https://github.com/cran/shiny -* Date/Publication: 2023-11-17 23:40:02 UTC -* Number of recursive dependencies: 90 +* Date/Publication: 2024-04-02 17:22:03 UTC +* Number of recursive dependencies: 92 -Run `revdep_details(, "shiny")` for more info +Run `revdepcheck::revdep_details(, "shiny")` for more info
@@ -3914,10 +4151,10 @@ Run `revdep_details(, "shiny")` for more info * checking installed package size ... NOTE ``` - installed size is 11.4Mb + installed size is 13.2Mb sub-directories of 1Mb or more: - R 1.4Mb - www 8.9Mb + R 1.5Mb + www 10.2Mb ``` # shiny.worker @@ -3928,9 +4165,9 @@ Run `revdep_details(, "shiny")` for more info * GitHub: NA * Source code: https://github.com/cran/shiny.worker * Date/Publication: 2021-01-21 11:00:02 UTC -* Number of recursive dependencies: 65 +* Number of recursive dependencies: 64 -Run `revdep_details(, "shiny.worker")` for more info +Run `revdepcheck::revdep_details(, "shiny.worker")` for more info
@@ -3952,13 +4189,13 @@ Run `revdep_details(, "shiny.worker")` for more info
-* Version: 2.3.0 +* Version: 2.3.1 * GitHub: https://github.com/ShixiangWang/sigminer * Source code: https://github.com/cran/sigminer -* Date/Publication: 2023-12-12 11:50:03 UTC -* Number of recursive dependencies: 205 +* Date/Publication: 2024-05-11 08:50:02 UTC +* Number of recursive dependencies: 209 -Run `revdep_details(, "sigminer")` for more info +Run `revdepcheck::revdep_details(, "sigminer")` for more info
@@ -3966,23 +4203,24 @@ Run `revdep_details(, "sigminer")` for more info * checking installed package size ... NOTE ``` - installed size is 5.9Mb + installed size is 6.7Mb sub-directories of 1Mb or more: - help 1.7Mb - libs 1.4Mb + extdata 1.0Mb + help 1.7Mb + libs 1.6Mb ``` # Signac
-* Version: 1.12.0 +* Version: 1.13.0 * GitHub: https://github.com/stuart-lab/signac * Source code: https://github.com/cran/Signac -* Date/Publication: 2023-11-08 09:30:02 UTC -* Number of recursive dependencies: 254 +* Date/Publication: 2024-04-04 02:42:57 UTC +* Number of recursive dependencies: 247 -Run `revdep_details(, "Signac")` for more info +Run `revdepcheck::revdep_details(, "Signac")` for more info
@@ -4000,27 +4238,18 @@ Run `revdep_details(, "Signac")` for more info
-* Version: 2.4.0 +* Version: 2.6.0 * GitHub: https://github.com/TojalLab/signeR * Source code: https://github.com/cran/signeR -* Date/Publication: 2023-10-24 -* Number of recursive dependencies: 244 +* Date/Publication: 2024-04-30 +* Number of recursive dependencies: 234 -Run `revdep_details(, "signeR")` for more info +Run `revdepcheck::revdep_details(, "signeR")` for more info
## In both -* checking whether package ‘signeR’ can be installed ... WARNING - ``` - Found the following significant warnings: - /c4/home/henrik/repositories/future/revdep/library/signeR/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/signeR/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/signeR/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - See ‘/c4/home/henrik/repositories/future/revdep/checks/signeR/new/signeR.Rcheck/00install.out’ for details. - ``` - * checking C++ specification ... NOTE ``` Specified C++11: please drop specification unless essential @@ -4078,75 +4307,66 @@ Run `revdep_details(, "signeR")` for more info
-* Version: 2.14 +* Version: 2.16 * GitHub: https://github.com/philchalmers/SimDesign * Source code: https://github.com/cran/SimDesign -* Date/Publication: 2024-01-09 09:10:11 UTC -* Number of recursive dependencies: 124 +* Date/Publication: 2024-07-08 16:20:02 UTC +* Number of recursive dependencies: 135 -Run `revdep_details(, "SimDesign")` for more info +Run `revdepcheck::revdep_details(, "SimDesign")` for more info
## In both -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘doMPI’ - ``` - * checking installed package size ... NOTE ``` - installed size is 5.8Mb + installed size is 7.2Mb sub-directories of 1Mb or more: - doc 5.2Mb + doc 6.5Mb ``` # sits
-* Version: 1.4.2-1 +* Version: 1.5.0 * GitHub: https://github.com/e-sensing/sits * Source code: https://github.com/cran/sits -* Date/Publication: 2023-11-02 15:10:02 UTC -* Number of recursive dependencies: 221 +* Date/Publication: 2024-05-09 19:00:03 UTC +* Number of recursive dependencies: 228 -Run `revdep_details(, "sits")` for more info +Run `revdepcheck::revdep_details(, "sits")` for more info
## In both -* checking whether package ‘sits’ can be installed ... WARNING +* checking package dependencies ... NOTE ``` - Found the following significant warnings: - /c4/home/henrik/repositories/future/revdep/library/sits/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/sits/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/sits/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - See ‘/c4/home/henrik/repositories/future/revdep/checks/sits/new/sits.Rcheck/00install.out’ for details. + Package suggested but not available for checking: ‘gdalcubes’ ``` * checking installed package size ... NOTE ``` - installed size is 13.2Mb + installed size is 15.8Mb sub-directories of 1Mb or more: - R 1.1Mb - extdata 1.5Mb - libs 9.9Mb + R 1.5Mb + extdata 1.2Mb + libs 12.4Mb ``` # skpr
-* Version: 1.6.2 +* Version: 1.7.1 * GitHub: https://github.com/tylermorganwall/skpr * Source code: https://github.com/cran/skpr -* Date/Publication: 2024-02-06 19:50:02 UTC -* Number of recursive dependencies: 149 +* Date/Publication: 2024-03-26 01:30:02 UTC +* Number of recursive dependencies: 152 -Run `revdep_details(, "skpr")` for more info +Run `revdepcheck::revdep_details(, "skpr")` for more info
@@ -4154,39 +4374,39 @@ Run `revdep_details(, "skpr")` for more info * checking installed package size ... NOTE ``` - installed size is 63.3Mb + installed size is 59.6Mb sub-directories of 1Mb or more: - libs 62.8Mb + libs 59.0Mb ``` # SmCCNet
-* Version: 2.0.2 +* Version: 2.0.3 * GitHub: https://github.com/KechrisLab/SmCCNet * Source code: https://github.com/cran/SmCCNet -* Date/Publication: 2024-01-13 21:50:17 UTC -* Number of recursive dependencies: 162 +* Date/Publication: 2024-04-16 05:20:02 UTC +* Number of recursive dependencies: 161 -Run `revdep_details(, "SmCCNet")` for more info +Run `revdepcheck::revdep_details(, "SmCCNet")` for more info
## In both -* checking re-building of vignette outputs ... ERROR +* checking re-building of vignette outputs ... WARNING ``` Error(s) in re-building vignettes: --- re-building ‘SmCCNet_Vignette_AutoSmCCNet.Rmd’ using rmarkdown - ! kpathsea: Running mktexfmt xelatex.fmt + ! LaTeX Error: File `ucharcat.sty' not found. - Error: processing vignette 'SmCCNet_Vignette_AutoSmCCNet.Rmd' failed with diagnostics: - LaTeX failed to compile /c4/home/henrik/repositories/future/revdep/checks/SmCCNet/new/SmCCNet.Rcheck/vign_test/SmCCNet/vignettes/SmCCNet_Vignette_AutoSmCCNet.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See SmCCNet_Vignette_AutoSmCCNet.log for more info. - --- failed re-building ‘SmCCNet_Vignette_AutoSmCCNet.Rmd’ + ! Emergency stop. + - --- re-building ‘SmCCNet_Vignette_MultiOmics.Rmd’ using rmarkdown ! kpathsea: Running mktexfmt xelatex.fmt + ! mktexfmt: mktexfmt is using the following fmtutil.cnf files (in precedence order): + ! mktexfmt: /usr/share/texlive/texmf-dist/web2c/fmtutil.cnf ... Error: processing vignette 'SmCCNet_Vignette_SingleOmics.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/future/revdep/checks/SmCCNet/new/SmCCNet.Rcheck/vign_test/SmCCNet/vignettes/SmCCNet_Vignette_SingleOmics.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See SmCCNet_Vignette_SingleOmics.log for more info. @@ -4208,21 +4428,19 @@ Run `revdep_details(, "SmCCNet")` for more info * GitHub: NA * Source code: https://github.com/cran/smoots * Date/Publication: 2023-09-11 08:50:02 UTC -* Number of recursive dependencies: 76 +* Number of recursive dependencies: 75 -Run `revdep_details(, "smoots")` for more info +Run `revdepcheck::revdep_details(, "smoots")` for more info
## In both -* checking whether package ‘smoots’ can be installed ... WARNING +* checking installed package size ... NOTE ``` - Found the following significant warnings: - /c4/home/henrik/repositories/future/revdep/library/smoots/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/smoots/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/smoots/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - See ‘/c4/home/henrik/repositories/future/revdep/checks/smoots/new/smoots.Rcheck/00install.out’ for details. + installed size is 7.3Mb + sub-directories of 1Mb or more: + libs 6.5Mb ``` # solitude @@ -4235,7 +4453,7 @@ Run `revdep_details(, "smoots")` for more info * Date/Publication: 2021-07-29 20:00:02 UTC * Number of recursive dependencies: 131 -Run `revdep_details(, "solitude")` for more info +Run `revdepcheck::revdep_details(, "solitude")` for more info @@ -4252,13 +4470,13 @@ Run `revdep_details(, "solitude")` for more info
-* Version: 2.0.3 +* Version: 2.1.0 * GitHub: https://github.com/PredictiveEcology/SpaDES.core * Source code: https://github.com/cran/SpaDES.core -* Date/Publication: 2023-11-10 10:20:02 UTC -* Number of recursive dependencies: 137 +* Date/Publication: 2024-06-02 11:02:47 UTC +* Number of recursive dependencies: 136 -Run `revdep_details(, "SpaDES.core")` for more info +Run `revdepcheck::revdep_details(, "SpaDES.core")` for more info
@@ -4271,22 +4489,22 @@ Run `revdep_details(, "SpaDES.core")` for more info * checking installed package size ... NOTE ``` - installed size is 6.2Mb + installed size is 6.7Mb sub-directories of 1Mb or more: - R 4.7Mb + R 5.0Mb ``` # spaMM
-* Version: 4.4.16 +* Version: 4.5.0 * GitHub: NA * Source code: https://github.com/cran/spaMM -* Date/Publication: 2023-12-20 13:50:02 UTC -* Number of recursive dependencies: 102 +* Date/Publication: 2024-06-09 22:20:02 UTC +* Number of recursive dependencies: 103 -Run `revdep_details(, "spaMM")` for more info +Run `revdepcheck::revdep_details(, "spaMM")` for more info
@@ -4294,7 +4512,8 @@ Run `revdep_details(, "spaMM")` for more info * checking package dependencies ... NOTE ``` - Packages suggested but not available for checking: 'Infusion', 'blackbox' + Packages suggested but not available for checking: + 'Infusion', 'IsoriX', 'blackbox' Packages which this enhances but not available for checking: 'multcomp', 'RLRsim', 'lmerTest' @@ -4302,10 +4521,10 @@ Run `revdep_details(, "spaMM")` for more info * checking installed package size ... NOTE ``` - installed size is 56.9Mb + installed size is 54.6Mb sub-directories of 1Mb or more: - R 2.7Mb - libs 52.9Mb + R 3.1Mb + libs 50.2Mb ``` # sparrpowR @@ -4316,9 +4535,9 @@ Run `revdep_details(, "spaMM")` for more info * GitHub: https://github.com/machiela-lab/sparrpowR * Source code: https://github.com/cran/sparrpowR * Date/Publication: 2024-01-23 15:20:02 UTC -* Number of recursive dependencies: 130 +* Number of recursive dependencies: 131 -Run `revdep_details(, "sparrpowR")` for more info +Run `revdepcheck::revdep_details(, "sparrpowR")` for more info @@ -4339,12 +4558,22 @@ Run `revdep_details(, "sparrpowR")` for more info * GitHub: https://github.com/NAU-CCL/SPARSEMODr * Source code: https://github.com/cran/SPARSEMODr * Date/Publication: 2022-07-19 20:50:02 UTC -* Number of recursive dependencies: 127 +* Number of recursive dependencies: 126 -Run `revdep_details(, "SPARSEMODr")` for more info +Run `revdepcheck::revdep_details(, "SPARSEMODr")` for more info +## Newly broken + +* checking installed package size ... NOTE + ``` + installed size is 5.4Mb + sub-directories of 1Mb or more: + doc 1.2Mb + libs 4.0Mb + ``` + ## In both * checking dependencies in R code ... NOTE @@ -4354,76 +4583,124 @@ Run `revdep_details(, "SPARSEMODr")` for more info All declared Imports should be used. ``` -# spatialwarnings +# spatialwarnings + +
+ +* Version: 3.0.3 +* GitHub: https://github.com/spatial-ews/spatialwarnings +* Source code: https://github.com/cran/spatialwarnings +* Date/Publication: 2022-03-21 13:00:02 UTC +* Number of recursive dependencies: 97 + +Run `revdepcheck::revdep_details(, "spatialwarnings")` for more info + +
+ +## In both + +* checking Rd cross-references ... WARNING + ``` + Missing link or links in Rd file 'indictest.Rd': + ‘mgcv’ + + See section 'Cross-references' in the 'Writing R Extensions' manual. + ``` + +* checking installed package size ... NOTE + ``` + installed size is 7.3Mb + sub-directories of 1Mb or more: + libs 6.2Mb + ``` + +* checking Rd files ... NOTE + ``` + checkRd: (-1) pl_fit.Rd:75: Lost braces in \itemize; meant \describe ? + checkRd: (-1) pl_fit.Rd:76-77: Lost braces in \itemize; meant \describe ? + checkRd: (-1) pl_fit.Rd:78-79: Lost braces in \itemize; meant \describe ? + checkRd: (-1) pl_fit.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) pl_fit.Rd:29-30: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) pl_fit.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) pl_fit.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) pl_fit.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) pl_fit.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) pl_fit.Rd:40-41: Lost braces in \itemize; \value handles \item{}{} directly + ... + checkRd: (-1) simple_sews.Rd:60: Lost braces in \itemize; meant \describe ? + checkRd: (-1) simple_sews.Rd:61: Lost braces in \itemize; meant \describe ? + checkRd: (-1) simple_sews.Rd:62-64: Lost braces in \itemize; meant \describe ? + checkRd: (-1) simple_sews.Rd:65-67: Lost braces in \itemize; meant \describe ? + checkRd: (-1) simple_sews.Rd:68-69: Lost braces in \itemize; meant \describe ? + checkRd: (-1) simple_sews.Rd:70-71: Lost braces in \itemize; meant \describe ? + checkRd: (-1) simple_sews.Rd:72-73: Lost braces in \itemize; meant \describe ? + checkRd: (-1) simple_sews.Rd:74: Lost braces in \itemize; meant \describe ? + checkRd: (-1) simple_sews.Rd:75-76: Lost braces in \itemize; meant \describe ? + checkRd: (-1) simple_sews.Rd:77-79: Lost braces in \itemize; meant \describe ? + ``` + +# sperrorest
-* Version: 3.0.3 -* GitHub: https://github.com/spatial-ews/spatialwarnings -* Source code: https://github.com/cran/spatialwarnings -* Date/Publication: 2022-03-21 13:00:02 UTC -* Number of recursive dependencies: 97 +* Version: 3.0.5 +* GitHub: https://github.com/giscience-fsu/sperrorest +* Source code: https://github.com/cran/sperrorest +* Date/Publication: 2022-10-16 12:50:02 UTC +* Number of recursive dependencies: 74 -Run `revdep_details(, "spatialwarnings")` for more info +Run `revdepcheck::revdep_details(, "sperrorest")` for more info
## In both -* checking whether package ‘spatialwarnings’ can be installed ... WARNING - ``` - Found the following significant warnings: - /c4/home/henrik/repositories/future/revdep/library/spatialwarnings/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/spatialwarnings/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/spatialwarnings/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - See ‘/c4/home/henrik/repositories/future/revdep/checks/spatialwarnings/new/spatialwarnings.Rcheck/00install.out’ for details. - ``` - -* checking Rd cross-references ... WARNING - ``` - Missing link or links in documentation object 'indictest.Rd': - ‘mgcv’ - - See section 'Cross-references' in the 'Writing R Extensions' manual. - ``` - -* checking installed package size ... NOTE +* checking Rd files ... NOTE ``` - installed size is 7.0Mb - sub-directories of 1Mb or more: - libs 6.0Mb + checkRd: (-1) partition_cv.Rd:36: Lost braces; missing escapes or markup? + 36 | if \code{TRUE} (used internally by other {sperrorest} functions), return a + | ^ + checkRd: (-1) partition_cv_strat.Rd:28: Lost braces; missing escapes or markup? + 28 | if \code{TRUE} (used internally by other {sperrorest} functions), return a + | ^ + checkRd: (-1) partition_factor.Rd:28: Lost braces; missing escapes or markup? + 28 | if \code{TRUE} (used internally by other {sperrorest} functions), return a + | ^ + checkRd: (-1) partition_factor_cv.Rd:43: Lost braces; missing escapes or markup? + ... + | ^ + checkRd: (-1) sperrorest.Rd:148: Lost braces; missing escapes or markup? + 148 | information about the {sperrorest} package version + | ^ + checkRd: (-1) summary.sperroresterror.Rd:5: Lost braces; missing escapes or markup? + 5 | \title{Summarize error statistics obtained by {sperrorest}} + | ^ + checkRd: (-1) summary.sperrorestimportance.Rd:5: Lost braces; missing escapes or markup? + 5 | \title{Summarize variable importance statistics obtained by {sperrorest}} + | ^ ``` # sphunif
-* Version: 1.3.0 +* Version: 1.4.0 * GitHub: https://github.com/egarpor/sphunif * Source code: https://github.com/cran/sphunif -* Date/Publication: 2023-12-04 19:50:02 UTC -* Number of recursive dependencies: 77 +* Date/Publication: 2024-05-24 21:50:01 UTC +* Number of recursive dependencies: 75 -Run `revdep_details(, "sphunif")` for more info +Run `revdepcheck::revdep_details(, "sphunif")` for more info
## In both -* checking whether package ‘sphunif’ can be installed ... WARNING - ``` - Found the following significant warnings: - /c4/home/henrik/repositories/future/revdep/library/sphunif/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/sphunif/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/sphunif/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - See ‘/c4/home/henrik/repositories/future/revdep/checks/sphunif/new/sphunif.Rcheck/00install.out’ for details. - ``` - * checking installed package size ... NOTE ``` - installed size is 24.7Mb + installed size is 25.1Mb sub-directories of 1Mb or more: - libs 23.7Mb + libs 23.9Mb ``` * checking data for non-ASCII characters ... NOTE @@ -4435,34 +4712,24 @@ Run `revdep_details(, "sphunif")` for more info
-* Version: 0.4.3.8 +* Version: 0.4.4.3 * GitHub: https://github.com/JeremyGelb/spNetwork * Source code: https://github.com/cran/spNetwork -* Date/Publication: 2023-08-24 11:20:05 UTC -* Number of recursive dependencies: 146 +* Date/Publication: 2024-06-21 21:40:02 UTC +* Number of recursive dependencies: 143 -Run `revdep_details(, "spNetwork")` for more info +Run `revdepcheck::revdep_details(, "spNetwork")` for more info
## In both -* checking whether package ‘spNetwork’ can be installed ... WARNING - ``` - Found the following significant warnings: - /c4/home/henrik/repositories/future/revdep/library/spNetwork/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/spNetwork/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/spNetwork/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - See ‘/c4/home/henrik/repositories/future/revdep/checks/spNetwork/new/spNetwork.Rcheck/00install.out’ for details. - ``` - * checking installed package size ... NOTE ``` - installed size is 25.5Mb + installed size is 27.6Mb sub-directories of 1Mb or more: - doc 1.0Mb extdata 2.6Mb - libs 20.5Mb + libs 22.6Mb ``` # squat @@ -4473,30 +4740,21 @@ Run `revdep_details(, "spNetwork")` for more info * GitHub: https://github.com/LMJL-Alea/squat * Source code: https://github.com/cran/squat * Date/Publication: 2024-01-10 15:40:02 UTC -* Number of recursive dependencies: 143 +* Number of recursive dependencies: 141 -Run `revdep_details(, "squat")` for more info +Run `revdepcheck::revdep_details(, "squat")` for more info ## In both -* checking whether package ‘squat’ can be installed ... WARNING - ``` - Found the following significant warnings: - /c4/home/henrik/repositories/future/revdep/library/squat/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/squat/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/squat/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - See ‘/c4/home/henrik/repositories/future/revdep/checks/squat/new/squat.Rcheck/00install.out’ for details. - ``` - * checking installed package size ... NOTE ``` - installed size is 20.4Mb + installed size is 19.9Mb sub-directories of 1Mb or more: data 1.1Mb help 1.1Mb - libs 18.0Mb + libs 17.5Mb ``` # ssdtools @@ -4507,9 +4765,9 @@ Run `revdep_details(, "squat")` for more info * GitHub: https://github.com/bcgov/ssdtools * Source code: https://github.com/cran/ssdtools * Date/Publication: 2023-09-07 14:10:02 UTC -* Number of recursive dependencies: 120 +* Number of recursive dependencies: 119 -Run `revdep_details(, "ssdtools")` for more info +Run `revdepcheck::revdep_details(, "ssdtools")` for more info @@ -4517,191 +4775,78 @@ Run `revdep_details(, "ssdtools")` for more info * checking installed package size ... NOTE ``` - installed size is 42.1Mb + installed size is 39.9Mb sub-directories of 1Mb or more: doc 1.2Mb - libs 39.6Mb + help 1.0Mb + libs 37.3Mb ``` # stars
-* Version: 0.6-4 +* Version: 0.6-6 * GitHub: https://github.com/r-spatial/stars * Source code: https://github.com/cran/stars -* Date/Publication: 2023-09-11 11:50:02 UTC -* Number of recursive dependencies: 164 +* Date/Publication: 2024-07-16 09:40:02 UTC +* Number of recursive dependencies: 166 -Run `revdep_details(, "stars")` for more info +Run `revdepcheck::revdep_details(, "stars")` for more info
-## Newly broken - -* checking examples ...sh: line 1: 76201 Aborted (core dumped) LANGUAGE=en _R_CHECK_INTERNALS2_=1 '/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/bin/R' --vanilla --encoding=UTF-8 > 'stars-Ex.Rout' 2>&1 < 'stars-Ex.R' - ``` - ERROR - Running examples in ‘stars-Ex.R’ failed - The error most likely occurred in: - - > ### Name: mdim - > ### Title: Read or write data using GDAL's multidimensional array API - > ### Aliases: mdim read_mdim write_mdim - > - > ### ** Examples - > - ... - dmalloc: no - Packages w/ extra debug output: none - API tracing: no - Using memory checker: no - Memory allocation sanity checks: no - Function stack tracing: no - Use file locking: best-effort - Strict file format checks: no - Optimization instrumentation: no - Bye... - ``` - -## Newly fixed - -* checking examples ...sh: line 1: 76251 Aborted (core dumped) LANGUAGE=en _R_CHECK_INTERNALS2_=1 '/software/c4/cbi/software/_centos7/R-4.3.3-gcc10/lib64/R/bin/R' --vanilla --encoding=UTF-8 > 'stars-Ex.Rout' 2>&1 < 'stars-Ex.R' - ``` - ERROR - Running examples in ‘stars-Ex.R’ failed - The error most likely occurred in: - - > ### Name: mdim - > ### Title: Read or write data using GDAL's multidimensional array API - > ### Aliases: mdim read_mdim write_mdim - > - > ### ** Examples - > - ... - dmalloc: no - Packages w/ extra debug output: none - API tracing: no - Using memory checker: no - Memory allocation sanity checks: no - Function stack tracing: no - Use file locking: best-effort - Strict file format checks: no - Optimization instrumentation: no - Bye... - ``` - ## In both * checking tests ... ``` Running ‘aggregate.R’ - Comparing ‘aggregate.Rout’ to ‘aggregate.Rout.save’ ...4c4 - < Linking to GEOS 3.11.2, GDAL 3.6.4, PROJ 8.2.1; sf_use_s2() is TRUE - --- - > Linking to GEOS 3.11.2, GDAL 3.6.2, PROJ 9.2.0; sf_use_s2() is TRUE + Comparing ‘aggregate.Rout’ to ‘aggregate.Rout.save’ ... OK Running ‘align.R’ Comparing ‘align.Rout’ to ‘align.Rout.save’ ... OK Running ‘area.R’ Comparing ‘area.Rout’ to ‘area.Rout.save’ ... OK Running ‘crop.R’ + Comparing ‘crop.Rout’ to ‘crop.Rout.save’ ... OK + Running ‘curvilinear.R’ + Comparing ‘curvilinear.Rout’ to ‘curvilinear.Rout.save’ ... OK ... - dmalloc: no - Packages w/ extra debug output: none - API tracing: no - Using memory checker: no - Memory allocation sanity checks: no - Function stack tracing: no - Use file locking: best-effort - Strict file format checks: no - Optimization instrumentation: no - Bye... + > + > s = st_set_dimensions(s, st_dimensions(s), xy = NULL) + > sfc = st_sfc(st_point(0:1), st_point(3:2)) + > s = st_set_dimensions(s, 1, sfc) |> st_set_crs(4326) + > tm = as.POSIXct("2023-03-04 12:35") + c(0, 3600) + > s = st_set_dimensions(s, 2, tm) + > f = tempfile(fileext = ".nc") + > write_mdim(s, f, as_float = FALSE) + Error: requires GDAL >= 3.1.0 and 64-bit + Execution halted ``` * checking package dependencies ... NOTE ``` - Package suggested but not available for checking: ‘starsdata’ + Packages suggested but not available for checking: 'ncdfgeom', 'starsdata' ``` * checking installed package size ... NOTE ``` - installed size is 6.1Mb + installed size is 6.4Mb sub-directories of 1Mb or more: doc 2.4Mb nc 1.7Mb ``` -# startR - -
- -* Version: 2.3.1 -* GitHub: NA -* Source code: https://github.com/cran/startR -* Date/Publication: 2023-12-21 16:20:02 UTC -* Number of recursive dependencies: 60 - -Run `revdep_details(, "startR")` for more info - -
- -## In both - -* checking whether package ‘startR’ can be installed ... ERROR - ``` - Installation failed. - See ‘/c4/home/henrik/repositories/future/revdep/checks/startR/new/startR.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘startR’ ... -** package ‘startR’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : - there is no package called ‘ncdf4’ -Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart -Execution halted -ERROR: lazy loading failed for package ‘startR’ -* removing ‘/c4/home/henrik/repositories/future/revdep/checks/startR/new/startR.Rcheck/startR’ - - -``` -### CRAN - -``` -* installing *source* package ‘startR’ ... -** package ‘startR’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : - there is no package called ‘ncdf4’ -Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart -Execution halted -ERROR: lazy loading failed for package ‘startR’ -* removing ‘/c4/home/henrik/repositories/future/revdep/checks/startR/old/startR.Rcheck/startR’ - - -``` # stppSim
-* Version: 1.3.2 +* Version: 1.3.4 * GitHub: https://github.com/Manalytics/stppSim * Source code: https://github.com/cran/stppSim -* Date/Publication: 2023-10-29 21:20:02 UTC -* Number of recursive dependencies: 133 +* Date/Publication: 2024-07-24 13:30:02 UTC +* Number of recursive dependencies: 131 -Run `revdep_details(, "stppSim")` for more info +Run `revdepcheck::revdep_details(, "stppSim")` for more info
@@ -4718,13 +4863,13 @@ Run `revdep_details(, "stppSim")` for more info
-* Version: 0.0.7 +* Version: 0.0.7.1 * GitHub: https://github.com/fndemarqui/survstan * Source code: https://github.com/cran/survstan -* Date/Publication: 2024-03-20 23:00:02 UTC -* Number of recursive dependencies: 127 +* Date/Publication: 2024-04-12 16:50:02 UTC +* Number of recursive dependencies: 126 -Run `revdep_details(, "survstan")` for more info +Run `revdepcheck::revdep_details(, "survstan")` for more info
@@ -4732,9 +4877,9 @@ Run `revdep_details(, "survstan")` for more info * checking installed package size ... NOTE ``` - installed size is 90.6Mb + installed size is 85.7Mb sub-directories of 1Mb or more: - libs 90.1Mb + libs 85.1Mb ``` * checking dependencies in R code ... NOTE @@ -4753,13 +4898,13 @@ Run `revdep_details(, "survstan")` for more info
-* Version: 3.10.3 +* Version: 3.12.0 * GitHub: NA * Source code: https://github.com/cran/synergyfinder -* Date/Publication: 2024-01-22 -* Number of recursive dependencies: 202 +* Date/Publication: 2024-04-30 +* Number of recursive dependencies: 196 -Run `revdep_details(, "synergyfinder")` for more info +Run `revdepcheck::revdep_details(, "synergyfinder")` for more info
@@ -4775,9 +4920,9 @@ Run `revdep_details(, "synergyfinder")` for more info * checking installed package size ... NOTE ``` - installed size is 6.0Mb + installed size is 7.5Mb sub-directories of 1Mb or more: - doc 5.7Mb + doc 7.1Mb ``` * checking R code for possible problems ... NOTE @@ -4807,7 +4952,22 @@ Run `revdep_details(, "synergyfinder")` for more info * checking Rd files ... NOTE ``` + checkRd: (-1) FitDoseResponse.Rd:54: Lost braces + 54 | href{https://onlinelibrary.wiley.com/doi/book/10.1002/0471725315}{Nonlinear + | ^ + checkRd: (-1) FitDoseResponse.Rd:54-55: Lost braces + 54 | href{https://onlinelibrary.wiley.com/doi/book/10.1002/0471725315}{Nonlinear + | ^ checkRd: (-1) FitDoseResponse.Rd:55: Escaped LaTeX specials: \& + checkRd: (-1) PlotBarometer.Rd:118: Lost braces + 118 | href{https://www.frontiersin.org/articles/10.3389/fphar.2015.00181/full}{What + | ^ + checkRd: (-1) PlotBarometer.Rd:118-119: Lost braces + 118 | href{https://www.frontiersin.org/articles/10.3389/fphar.2015.00181/full}{What + | ^ + checkRd: (-1) PlotDoseResponseCurve.Rd:84: Lost braces + 84 | link[drc]{plot.drc} function. For example, use xlim = c(0.5, 500) or + | ^ ``` # tableschema.r @@ -4820,12 +4980,37 @@ Run `revdep_details(, "synergyfinder")` for more info * Date/Publication: 2022-09-29 20:00:03 UTC * Number of recursive dependencies: 66 -Run `revdep_details(, "tableschema.r")` for more info +Run `revdepcheck::revdep_details(, "tableschema.r")` for more info ## In both +* checking Rd files ... NOTE + ``` + checkRd: (-1) Field.Rd:69: Lost braces in \itemize; meant \describe ? + checkRd: (-1) Field.Rd:70: Lost braces in \itemize; meant \describe ? + checkRd: (-1) Field.Rd:71: Lost braces in \itemize; meant \describe ? + checkRd: (-1) Field.Rd:72: Lost braces in \itemize; meant \describe ? + checkRd: (-1) Field.Rd:77: Lost braces in \itemize; meant \describe ? + checkRd: (-1) Field.Rd:78-80: Lost braces in \itemize; meant \describe ? + checkRd: (-1) Field.Rd:81: Lost braces in \itemize; meant \describe ? + checkRd: (-1) Field.Rd:82: Lost braces in \itemize; meant \describe ? + checkRd: (-1) Field.Rd:88: Lost braces in \itemize; meant \describe ? + checkRd: (-1) Field.Rd:89: Lost braces in \itemize; meant \describe ? + ... + checkRd: (-1) Table.Rd:85: Lost braces in \itemize; meant \describe ? + checkRd: (-1) tableschema.r-package.Rd:174: Lost braces + 174 | in the resources array of a href{http://frictionlessdata.io/specs/data-package/}{Data Package}. + | ^ + checkRd: (-1) tableschema.r-package.Rd:174: Lost braces + 174 | in the resources array of a href{http://frictionlessdata.io/specs/data-package/}{Data Package}. + | ^ + checkRd: (-1) types.castDate.Rd:14: Lost braces in \itemize; meant \describe ? + checkRd: (-1) types.castDate.Rd:15: Lost braces in \itemize; meant \describe ? + checkRd: (-1) types.castDate.Rd:16: Lost braces in \itemize; meant \describe ? + ``` + * checking Rd cross-references ... NOTE ``` Package unavailable to check Rd xrefs: ‘parsedate’ @@ -4839,63 +5024,56 @@ Run `revdep_details(, "tableschema.r")` for more info * GitHub: https://github.com/kkholst/targeted * Source code: https://github.com/cran/targeted * Date/Publication: 2024-02-22 10:00:21 UTC -* Number of recursive dependencies: 98 +* Number of recursive dependencies: 97 -Run `revdep_details(, "targeted")` for more info +Run `revdepcheck::revdep_details(, "targeted")` for more info ## In both -* checking whether package ‘targeted’ can be installed ... WARNING - ``` - Found the following significant warnings: - /c4/home/henrik/repositories/future/revdep/library/targeted/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/targeted/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/targeted/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - See ‘/c4/home/henrik/repositories/future/revdep/checks/targeted/new/targeted.Rcheck/00install.out’ for details. - ``` - * checking installed package size ... NOTE ``` - installed size is 22.4Mb + installed size is 22.9Mb sub-directories of 1Mb or more: doc 1.1Mb - libs 20.9Mb + libs 21.2Mb ``` -# targets +# tenm
-* Version: 1.6.0 -* GitHub: https://github.com/ropensci/targets -* Source code: https://github.com/cran/targets -* Date/Publication: 2024-03-13 16:30:02 UTC -* Number of recursive dependencies: 166 +* Version: 0.5.1 +* GitHub: https://github.com/luismurao/tenm +* Source code: https://github.com/cran/tenm +* Date/Publication: 2024-07-23 00:30:01 UTC +* Number of recursive dependencies: 79 -Run `revdep_details(, "targets")` for more info +Run `revdepcheck::revdep_details(, "tenm")` for more info
## In both -* checking package dependencies ... NOTE +* checking installed package size ... NOTE ``` - Package suggested but not available for checking: ‘clustermq’ + installed size is 5.9Mb + sub-directories of 1Mb or more: + extdata 5.0Mb ``` # text
-* Version: 1.2.0 +* Version: 1.2.1 * GitHub: https://github.com/OscarKjell/text * Source code: https://github.com/cran/text -* Date/Publication: 2024-02-13 20:51:36 UTC -* Number of recursive dependencies: 161 +* Date/Publication: 2024-04-23 00:00:03 UTC +* Number of recursive dependencies: 168 -Run `revdep_details(, "text")` for more info +Run `revdepcheck::revdep_details(, "text")` for more info
@@ -4910,13 +5088,13 @@ Run `revdep_details(, "text")` for more info
-* Version: 0.5.4 +* Version: 0.5.5 * GitHub: https://github.com/tanaylab/tglkmeans * Source code: https://github.com/cran/tglkmeans -* Date/Publication: 2024-01-09 14:10:02 UTC -* Number of recursive dependencies: 89 +* Date/Publication: 2024-05-15 08:40:02 UTC +* Number of recursive dependencies: 90 -Run `revdep_details(, "tglkmeans")` for more info +Run `revdepcheck::revdep_details(, "tglkmeans")` for more info
@@ -4924,9 +5102,15 @@ Run `revdep_details(, "tglkmeans")` for more info * checking installed package size ... NOTE ``` - installed size is 5.2Mb + installed size is 5.4Mb sub-directories of 1Mb or more: - libs 5.0Mb + libs 5.2Mb + ``` + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘doRNG’ + All declared Imports should be used. ``` * checking for GNU extensions in Makefiles ... NOTE @@ -4934,77 +5118,38 @@ Run `revdep_details(, "tglkmeans")` for more info GNU make is a SystemRequirements. ``` -# TKCat +# TreeMineR
-* Version: 1.0.7 -* GitHub: https://github.com/patzaw/TKCat -* Source code: https://github.com/cran/TKCat -* Date/Publication: 2023-02-16 14:50:03 UTC -* Number of recursive dependencies: 115 +* Version: 1.0.1 +* GitHub: NA +* Source code: https://github.com/cran/TreeMineR +* Date/Publication: 2024-04-02 10:00:02 UTC +* Number of recursive dependencies: 49 -Run `revdep_details(, "TKCat")` for more info +Run `revdepcheck::revdep_details(, "TreeMineR")` for more info
## In both -* checking whether package ‘TKCat’ can be installed ... ERROR +* checking data for non-ASCII characters ... NOTE ``` - Installation failed. - See ‘/c4/home/henrik/repositories/future/revdep/checks/TKCat/new/TKCat.Rcheck/00install.out’ for details. + Note: found 3 marked UTF-8 strings ``` -## Installation - -### Devel - -``` -* installing *source* package ‘TKCat’ ... -** package ‘TKCat’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : - there is no package called ‘arrow’ -Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart -Execution halted -ERROR: lazy loading failed for package ‘TKCat’ -* removing ‘/c4/home/henrik/repositories/future/revdep/checks/TKCat/new/TKCat.Rcheck/TKCat’ - - -``` -### CRAN - -``` -* installing *source* package ‘TKCat’ ... -** package ‘TKCat’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : - there is no package called ‘arrow’ -Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart -Execution halted -ERROR: lazy loading failed for package ‘TKCat’ -* removing ‘/c4/home/henrik/repositories/future/revdep/checks/TKCat/old/TKCat.Rcheck/TKCat’ - - -``` # TreeSearch
-* Version: 1.4.0 +* Version: 1.5.1 * GitHub: https://github.com/ms609/TreeSearch * Source code: https://github.com/cran/TreeSearch -* Date/Publication: 2023-08-26 04:50:02 UTC -* Number of recursive dependencies: 126 +* Date/Publication: 2024-05-23 13:40:03 UTC +* Number of recursive dependencies: 125 -Run `revdep_details(, "TreeSearch")` for more info +Run `revdepcheck::revdep_details(, "TreeSearch")` for more info
@@ -5012,11 +5157,11 @@ Run `revdep_details(, "TreeSearch")` for more info * checking installed package size ... NOTE ``` - installed size is 6.9Mb + installed size is 7.7Mb sub-directories of 1Mb or more: datasets 1.6Mb - doc 1.2Mb - libs 2.5Mb + doc 1.3Mb + libs 3.1Mb ``` # TriDimRegression @@ -5027,9 +5172,9 @@ Run `revdep_details(, "TreeSearch")` for more info * GitHub: https://github.com/alexander-pastukhov/tridim-regression * Source code: https://github.com/cran/TriDimRegression * Date/Publication: 2023-09-13 14:10:03 UTC -* Number of recursive dependencies: 100 +* Number of recursive dependencies: 99 -Run `revdep_details(, "TriDimRegression")` for more info +Run `revdepcheck::revdep_details(, "TriDimRegression")` for more info @@ -5075,19 +5220,19 @@ ERROR: configuration failed for package ‘TriDimRegression’
-* Version: 1.0.0 +* Version: 1.0.1 * GitHub: https://github.com/tsmodels/tsdistributions * Source code: https://github.com/cran/tsdistributions -* Date/Publication: 2024-03-17 09:10:05 UTC -* Number of recursive dependencies: 72 +* Date/Publication: 2024-05-13 09:10:02 UTC +* Number of recursive dependencies: 79 -Run `revdep_details(, "tsdistributions")` for more info +Run `revdepcheck::revdep_details(, "tsdistributions")` for more info
## In both -* checking re-building of vignette outputs ... WARNING +* checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... @@ -5095,16 +5240,16 @@ Run `revdep_details(, "tsdistributions")` for more info --- finished re-building ‘estimation_demo.Rmd’ --- re-building ‘location_scale_distributions.Rmd’ using rmarkdown - ! LaTeX Error: File `iftex.sty' not found. + ! Undefined control sequence. + l.60 \NewDocumentCommand + \citeproctext{}{} - ! Emergency stop. - ... - --- failed re-building ‘location_scale_distributions.Rmd’ - - --- re-building ‘profile_demo.Rmd’ using rmarkdown --- finished re-building ‘profile_demo.Rmd’ + --- re-building ‘spd_demo.Rmd’ using rmarkdown + --- finished re-building ‘spd_demo.Rmd’ + SUMMARY: processing the following file failed: ‘location_scale_distributions.Rmd’ @@ -5114,9 +5259,32 @@ Run `revdep_details(, "tsdistributions")` for more info * checking installed package size ... NOTE ``` - installed size is 42.4Mb + installed size is 40.2Mb + sub-directories of 1Mb or more: + libs 39.6Mb + ``` + +# tsgarch + +
+ +* Version: 1.0.2 +* GitHub: https://github.com/tsmodels/tsgarch +* Source code: https://github.com/cran/tsgarch +* Date/Publication: 2024-05-08 12:50:02 UTC +* Number of recursive dependencies: 113 + +Run `revdepcheck::revdep_details(, "tsgarch")` for more info + +
+ +## In both + +* checking installed package size ... NOTE + ``` + installed size is 138.0Mb sub-directories of 1Mb or more: - libs 41.8Mb + libs 136.8Mb ``` # txshift @@ -5127,9 +5295,9 @@ Run `revdep_details(, "tsdistributions")` for more info * GitHub: https://github.com/nhejazi/txshift * Source code: https://github.com/cran/txshift * Date/Publication: 2022-02-09 22:30:02 UTC -* Number of recursive dependencies: 113 +* Number of recursive dependencies: 112 -Run `revdep_details(, "txshift")` for more info +Run `revdepcheck::revdep_details(, "txshift")` for more info @@ -5140,17 +5308,30 @@ Run `revdep_details(, "txshift")` for more info Package which this enhances but not available for checking: ‘sl3’ ``` +* checking Rd files ... NOTE + ``` + checkRd: (-1) est_g_exp.Rd:55: Lost braces; missing escapes or markup? + 55 | {A - delta}, {A + delta}, and {A + 2 * delta}). + | ^ + checkRd: (-1) est_g_exp.Rd:55: Lost braces; missing escapes or markup? + 55 | {A - delta}, {A + delta}, and {A + 2 * delta}). + | ^ + checkRd: (-1) est_g_exp.Rd:55: Lost braces; missing escapes or markup? + 55 | {A - delta}, {A + delta}, and {A + 2 * delta}). + | ^ + ``` + # UCSCXenaShiny
-* Version: 2.0.0 +* Version: 2.1.0 * GitHub: https://github.com/openbiox/UCSCXenaShiny * Source code: https://github.com/cran/UCSCXenaShiny -* Date/Publication: 2024-03-14 03:20:09 UTC -* Number of recursive dependencies: 199 +* Date/Publication: 2024-05-15 14:10:06 UTC +* Number of recursive dependencies: 203 -Run `revdep_details(, "UCSCXenaShiny")` for more info +Run `revdepcheck::revdep_details(, "UCSCXenaShiny")` for more info
@@ -5158,11 +5339,11 @@ Run `revdep_details(, "UCSCXenaShiny")` for more info * checking installed package size ... NOTE ``` - installed size is 7.8Mb + installed size is 7.9Mb sub-directories of 1Mb or more: data 1.1Mb doc 1.4Mb - shinyapp 4.6Mb + shinyapp 4.9Mb ``` # updog @@ -5173,28 +5354,43 @@ Run `revdep_details(, "UCSCXenaShiny")` for more info * GitHub: https://github.com/dcgerard/updog * Source code: https://github.com/cran/updog * Date/Publication: 2023-11-29 15:50:02 UTC -* Number of recursive dependencies: 151 +* Number of recursive dependencies: 138 -Run `revdep_details(, "updog")` for more info +Run `revdepcheck::revdep_details(, "updog")` for more info ## In both -* checking whether package ‘updog’ can be installed ... WARNING +* checking installed package size ... NOTE ``` - Found the following significant warnings: - /c4/home/henrik/repositories/future/revdep/library/updog/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/updog/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/updog/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - See ‘/c4/home/henrik/repositories/future/revdep/checks/updog/new/updog.Rcheck/00install.out’ for details. + installed size is 8.9Mb + sub-directories of 1Mb or more: + libs 8.0Mb ``` +# vital + +
+ +* Version: 1.1.0 +* GitHub: https://github.com/robjhyndman/vital +* Source code: https://github.com/cran/vital +* Date/Publication: 2024-06-21 08:00:02 UTC +* Number of recursive dependencies: 201 + +Run `revdepcheck::revdep_details(, "vital")` for more info + +
+ +## In both + * checking installed package size ... NOTE ``` - installed size is 8.0Mb + installed size is 6.0Mb sub-directories of 1Mb or more: - libs 7.3Mb + data 4.4Mb + help 1.3Mb ``` # vmeasur @@ -5205,20 +5401,19 @@ Run `revdep_details(, "updog")` for more info * GitHub: NA * Source code: https://github.com/cran/vmeasur * Date/Publication: 2021-11-11 19:00:02 UTC -* Number of recursive dependencies: 119 +* Number of recursive dependencies: 106 -Run `revdep_details(, "vmeasur")` for more info +Run `revdepcheck::revdep_details(, "vmeasur")` for more info ## In both -* checking package dependencies ... ERROR +* checking whether package ‘vmeasur’ can be installed ... WARNING ``` - Package required but not available: ‘imager’ - - See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ - manual. + Found the following significant warnings: + Warning: no DISPLAY variable so Tk is not available + See ‘/c4/home/henrik/repositories/future/revdep/checks/vmeasur/new/vmeasur.Rcheck/00install.out’ for details. ``` # WeightedCluster @@ -5231,7 +5426,7 @@ Run `revdep_details(, "vmeasur")` for more info * Date/Publication: 2023-07-07 07:50:02 UTC * Number of recursive dependencies: 43 -Run `revdep_details(, "WeightedCluster")` for more info +Run `revdepcheck::revdep_details(, "WeightedCluster")` for more info @@ -5241,59 +5436,78 @@ Run `revdep_details(, "WeightedCluster")` for more info ``` Error(s) in re-building vignettes: --- re-building ‘WeightedCluster.Rnw’ using knitr + Warning in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : + texi2dvi script/program not available, using emulation --- finished re-building ‘WeightedCluster.Rnw’ --- re-building ‘WeightedClusterFR.Rnw’ using knitr - --- finished re-building ‘WeightedClusterFR.Rnw’ - - --- re-building ‘WeightedClusterPreview.Rnw’ using knitr - Error: processing vignette 'WeightedClusterPreview.Rnw' failed with diagnostics: - Running 'texi2dvi' on 'WeightedClusterPreview.tex' failed. + Warning in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : + texi2dvi script/program not available, using emulation + Error: processing vignette 'WeightedClusterFR.Rnw' failed with diagnostics: ... l.85 \usepackage {tikz}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘WeightedClusterPreview.Rnw’ - SUMMARY: processing the following file failed: - ‘WeightedClusterPreview.Rnw’ + SUMMARY: processing the following files failed: + ‘WeightedClusterFR.Rnw’ ‘WeightedClusterPreview.Rnw’ Error: Vignette re-building failed. Execution halted ``` +# winputall + +
+ +* Version: 1.0.1 +* GitHub: NA +* Source code: https://github.com/cran/winputall +* Date/Publication: 2024-06-07 14:40:02 UTC +* Number of recursive dependencies: 103 + +Run `revdepcheck::revdep_details(, "winputall")` for more info + +
+ +## In both + +* checking installed package size ... NOTE + ``` + installed size is 103.9Mb + sub-directories of 1Mb or more: + libs 103.5Mb + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + # wru
-* Version: 3.0.1 +* Version: 3.0.3 * GitHub: https://github.com/kosukeimai/wru * Source code: https://github.com/cran/wru -* Date/Publication: 2024-02-28 04:20:02 UTC +* Date/Publication: 2024-05-24 18:00:02 UTC * Number of recursive dependencies: 96 -Run `revdep_details(, "wru")` for more info +Run `revdepcheck::revdep_details(, "wru")` for more info
## In both -* checking whether package ‘wru’ can be installed ... WARNING - ``` - Found the following significant warnings: - /c4/home/henrik/repositories/future/revdep/library/wru/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/wru/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - /c4/home/henrik/repositories/future/revdep/library/wru/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat arma::reshape(const arma::Base&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations] - See ‘/c4/home/henrik/repositories/future/revdep/checks/wru/new/wru.Rcheck/00install.out’ for details. - ``` - * checking installed package size ... NOTE ``` installed size is 7.5Mb sub-directories of 1Mb or more: data 3.5Mb help 1.9Mb - libs 2.0Mb + libs 1.9Mb ``` * checking dependencies in R code ... NOTE @@ -5307,13 +5521,13 @@ Run `revdep_details(, "wru")` for more info
-* Version: 1.10.0 +* Version: 1.12.0 * GitHub: NA * Source code: https://github.com/cran/XNAString -* Date/Publication: 2023-10-24 -* Number of recursive dependencies: 106 +* Date/Publication: 2024-04-30 +* Number of recursive dependencies: 112 -Run `revdep_details(, "XNAString")` for more info +Run `revdepcheck::revdep_details(, "XNAString")` for more info
@@ -5344,7 +5558,7 @@ Run `revdep_details(, "XNAString")` for more info * checking installed package size ... NOTE ``` - installed size is 11.2Mb + installed size is 11.3Mb sub-directories of 1Mb or more: doc 1.0Mb libs 9.5Mb From 12a8079e6fc48fa40cd6ae3ce101139f29c000d9 Mon Sep 17 00:00:00 2001 From: Henrik Bengtsson Date: Mon, 29 Jul 2024 16:05:47 +0200 Subject: [PATCH 23/25] GA: increase run-time for covr --- .github/workflows/covr.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/covr.yaml b/.github/workflows/covr.yaml index 29c6796d..372ac983 100644 --- a/.github/workflows/covr.yaml +++ b/.github/workflows/covr.yaml @@ -6,7 +6,7 @@ jobs: covr: if: "! contains(github.event.head_commit.message, '[ci skip]')" - timeout-minutes: 60 + timeout-minutes: 120 runs-on: ubuntu-latest From 8fcc54a4b1fea64d2e3670870337a460f52c5ea9 Mon Sep 17 00:00:00 2001 From: Henrik Bengtsson Date: Mon, 29 Jul 2024 16:05:17 +0200 Subject: [PATCH 24/25] future 1.34.0 --- DESCRIPTION | 2 +- NEWS.md | 2 +- cran-comments.md | 27 +++++++++++---------------- 3 files changed, 13 insertions(+), 18 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 2312035a..81204d68 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: future -Version: 1.33.2-9011 +Version: 1.34.0 Title: Unified Parallel and Distributed Processing in R for Everyone Imports: digest, diff --git a/NEWS.md b/NEWS.md index 2b3eaf0b..98c8ba8e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# Version (development version) +# Version 1.34.0 [2024-07-29] ## New Features diff --git a/cran-comments.md b/cran-comments.md index d24fd378..4f9ad96c 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,10 +1,10 @@ -# CRAN submission future 1.33.2 +# CRAN submission future 1.34.0 -on 2024-03-23 +on 2024-07-29 -## Notes sent to CRAN +I've verified this submission has no negative impact on any of the 376 reverse package dependencies available on CRAN (n = 354) and Bioconductor (n = 22). -Thanks in advance +Thank you ## Notes not sent to CRAN @@ -13,17 +13,12 @@ Thanks in advance The package has been verified using `R CMD check --as-cran` on: -| R version | GitHub | R-hub | mac/win-builder | -| --------- | ------ | ----- | --------------- | -| 3.5.x | L | | | -| 4.1.x | L | | | -| 4.2.x | L M W | . . | | -| 4.3.x | L M W | . . | M1 W | -| devel | L M W | . | W | +| R version | GitHub | mac/win-builder | +| --------- | ------ | --------------- | +| 3.5.x | L | | +| 4.2.x | L | | +| 4.3.x | L M W | | +| 4.4.x | L M W | M1 W | +| devel | L M1 W | W | _Legend: OS: L = Linux, M = macOS, M1 = macOS M1, W = Windows_ - - -R-hub checks: - -Skipped. From e7399dea4b9d16a41d05002d2d57ba3e97d9f645 Mon Sep 17 00:00:00 2001 From: Henrik Bengtsson Date: Mon, 29 Jul 2024 16:19:40 +0200 Subject: [PATCH 25/25] spelling --- inst/WORDLIST | 4 ++++ vignettes/future-4-non-exportable-objects.md.rsp | 2 +- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/inst/WORDLIST b/inst/WORDLIST index 089960b3..51559aeb 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -34,6 +34,7 @@ FutureRegistry FutureResult FutureStrategy FutureStrategyList +Futureverse FutureWarning Globals HB @@ -169,6 +170,7 @@ baseenv batchtools bc bfr +bigmemory bioconductor calc callr @@ -332,6 +334,7 @@ nbrOfWorkers nc ncdf ncid +ncol ncores ncvar nd @@ -391,6 +394,7 @@ resignal resignaled reticulate revdepcheck +rhub rng rnorm roundtrip diff --git a/vignettes/future-4-non-exportable-objects.md.rsp b/vignettes/future-4-non-exportable-objects.md.rsp index 8af7bc9e..3331a72a 100644 --- a/vignettes/future-4-non-exportable-objects.md.rsp +++ b/vignettes/future-4-non-exportable-objects.md.rsp @@ -215,7 +215,7 @@ print(x[1,1]) #> [1] 42 ``` -Note how `x` was updated in-place. This is achived by `big.matrix` +Note how `x` was updated in-place. This is achieved by `big.matrix` objects holds an external pointer to where the matrix data is stored; ```r