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Merge pull request #76 from ShawHahnLab/release-0.4.0
Release 0.4.0
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| ^.*\.Rproj$ | ||
| ^\.Rproj\.user$ | ||
| ^\.travis.yml$ | ||
| .circleci | ||
| .utils | ||
| install_linux.sh | ||
| install_windows.cmd | ||
|
|
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| # https://blog.jdblischak.com/posts/circleci-for-r-1/ | ||
| # https://blog.jdblischak.com/posts/circleci-for-r-2/ | ||
| # | ||
| # Can't get the full package check working with rocker becuase of latex/pdf | ||
| # issues. This looks like the problem: | ||
| # | ||
| # https://gitlab.irstea.fr/in-wop/airGRiwrm/-/issues/53 | ||
| # | ||
| # ...but if I switch to rocker/tidyverse it's then missing pdflatex, and if I | ||
| # stick with rocker/verse, it still can't find the font. For now I'm just | ||
| # skipping that part of the package check with --no-manual. | ||
| version: 2.1 | ||
| jobs: | ||
| build: | ||
| parameters: | ||
| rversion: | ||
| type: string | ||
| docker: | ||
| - image: rocker/verse:<<parameters.rversion>> | ||
| steps: | ||
| - checkout | ||
| - restore_cache: | ||
| keys: | ||
| - cache-{{ .Environment.CIRCLE_JOB }}-{{ checksum "DESCRIPTION" }} | ||
| - run: | ||
| name: Install package dependencies | ||
| command: R -e "devtools::install_deps(dep = TRUE)" | ||
| - save_cache: | ||
| key: cache-{{ .Environment.CIRCLE_JOB }}-{{ checksum "DESCRIPTION" }} | ||
| paths: | ||
| - "/usr/local/lib/R/site-library" | ||
| - run: | ||
| name: Check versions | ||
| command: | | ||
| which R | ||
| R --quiet -e 'installed.packages()[, "Version"]' | ||
| which pandoc | ||
| pandoc --version | ||
| - run: | ||
| name: Build package | ||
| command: R CMD build . | ||
| - run: | ||
| name: Check package | ||
| command: R CMD check --no-manual *tar.gz | ||
| - store_artifacts: | ||
| name: "Store Artifacts: 00check.log" | ||
| path: chiimp.Rcheck/00check.log | ||
| - store_artifacts: | ||
| name: "Store Artifacts: 00install.out" | ||
| path: chiimp.Rcheck/00install.out | ||
| - run: | ||
| name: "Run find_pandoc script" | ||
| command: Rscript exec/find_pandoc.R | ||
| - run: | ||
| name: "Run demo script" | ||
| command: bash exec/demo.sh $PWD/demo-files | ||
| - store_artifacts: | ||
| name: "Store Artifacts: demo: report" | ||
| path: demo-files/str-results/report.html | ||
| - store_artifacts: | ||
| name: "Store Artifacts: demo: summary" | ||
| path: demo-files/str-results/summary.csv | ||
| - run: | ||
| name: "Run demo script - empty case" | ||
| command: bash exec/demo_empty.sh $PWD/demo-empty-files | ||
| - store_artifacts: | ||
| name: "Store Artifacts: empty demo: report" | ||
| path: demo-empty-files/str-results/report.html | ||
| - store_artifacts: | ||
| name: "Store Artifacts: empty demo: summary" | ||
| path: demo-empty-files/str-results/summary.csv | ||
| - run: | ||
| name: "Run install test script" | ||
| command: bash tools/circleci_install_test.sh | ||
|
|
||
| workflows: | ||
| version: 2 | ||
| build_all: | ||
| jobs: | ||
| - build: | ||
| matrix: | ||
| parameters: | ||
| rversion: ["3.6.3", "4.2.1"] |
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| Package: chiimp | ||
| Title: Computational, High-throughput Individual Identification through Microsatellite Profiling | ||
| Version: 0.3.1 | ||
| Version: 0.4.0 | ||
| Authors@R: person("Jesse", "Connell", email = "[email protected]", role = c("aut", "cre")) | ||
| Description: An R package to analyze microsatellites in high-throughput sequencing datasets. | ||
| Depends: R (>= 3.2.3) | ||
| Depends: R (>= 3.6) | ||
| License: file LICENSE | ||
| Encoding: UTF-8 | ||
| LazyData: true | ||
| Language: en-US | ||
| biocViews: | ||
| Imports: | ||
| argparser (>= 0.4), | ||
| Biostrings (>= 2.38.4), | ||
| graphics (>= 3.6), | ||
| grDevices (>= 3.6), | ||
| methods (>= 3.6), | ||
| parallel (>= 3.6), | ||
| stats (>= 3.6), | ||
| utils (>= 3.6), | ||
| argparser (>= 0.6), | ||
| dnaplotr (>= 0.1), | ||
| dnar (>= 0.1), | ||
| devtools (>= 1.13.5), | ||
| graphics (>= 3.2.3), | ||
| grDevices (>= 3.2.3), | ||
| kableExtra (>= 0.2.1.9000), | ||
| knitr (>= 1.16), | ||
| methods (>= 3.2.3), | ||
| msa (>= 1.2.1), | ||
| openssl (>= 0.9.6), | ||
| parallel (>= 3.2.3), | ||
| pheatmap (>= 1.0.8), | ||
| rmarkdown (>= 1.6), | ||
| stats (>= 3.2.3), | ||
| stringr (>= 1.2.0), | ||
| utils (>= 3.2.3), | ||
| viridis (>= 0.4.0), | ||
| yaml (>= 2.1.14) | ||
| devtools (>= 2.3), | ||
| Biostrings (>= 2.54), | ||
| kableExtra (>= 1.1), | ||
| knitr (>= 1.28), | ||
| msa (>= 1.18), | ||
| openssl (>= 1.4), | ||
| pheatmap (>= 1.0), | ||
| rmarkdown (>= 2.1), | ||
| stringr (>= 1.4), | ||
| viridis (>= 0.5), | ||
| yaml (>= 2.2) | ||
| Remotes: | ||
| github::sherrillmix/dnar, | ||
| github::sherrillmix/dnaplotr | ||
| RoxygenNote: 6.1.1 | ||
| RoxygenNote: 7.1.1 | ||
| Suggests: | ||
| testthat, | ||
| roxygen2 |
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