Segfault with NULLs #438

muschellij2 · 2022-02-02T03:38:25Z

I don't know why I get a segault here exactly, but I boiled it down to the case where you have a URL and NULL for credentials and repo. I ran into this when using remotes::install_bioc test.

Libgit2 version

git2r::libgit2_version()
#> $major
#> [1] 0
#> 
#> $minor
#> [1] 27
#> 
#> $rev
#> [1] 7
git2r::libgit2_features()
#> $threads
#> [1] TRUE
#> 
#> $https
#> [1] TRUE
#> 
#> $ssh
#> [1] TRUE

^{Created on 2022-02-10 by the reprex package (v2.0.1)}

Session info

sessioninfo::session_info()
#> Warning in system("timedatectl", intern = TRUE): running command 'timedatectl'
#> had status 1
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.1.2 (2021-11-01)
#>  os       Debian GNU/Linux 10 (buster)
#>  system   x86_64, linux-gnu
#>  ui       X11
#>  language (EN)
#>  collate  C.UTF-8
#>  ctype    C.UTF-8
#>  tz       Etc/UTC
#>  date     2022-02-10
#>  pandoc   2.14.0.3 @ /usr/lib/rstudio-server/bin/pandoc/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version    date (UTC) lib source
#>  cli           3.1.1.9000 2022-02-09 [1] Github (r-lib/cli@00d1770)
#>  digest        0.6.29     2021-12-01 [1] CRAN (R 4.1.2)
#>  evaluate      0.14       2019-05-28 [1] CRAN (R 4.1.2)
#>  fastmap       1.1.0      2021-01-25 [1] CRAN (R 4.1.2)
#>  fs            1.5.2      2021-12-08 [1] CRAN (R 4.1.2)
#>  git2r         0.29.0     2021-11-22 [1] CRAN (R 4.1.2)
#>  glue          1.6.1      2022-01-22 [1] CRAN (R 4.1.2)
#>  highr         0.9        2021-04-16 [1] CRAN (R 4.1.2)
#>  htmltools     0.5.2      2021-08-25 [1] CRAN (R 4.1.0)
#>  knitr         1.37       2021-12-16 [1] CRAN (R 4.1.2)
#>  lifecycle     1.0.1      2021-09-24 [1] CRAN (R 4.1.0)
#>  magrittr      2.0.2      2022-01-26 [1] CRAN (R 4.1.2)
#>  reprex        2.0.1      2021-08-05 [1] CRAN (R 4.1.0)
#>  rlang         1.0.1      2022-02-03 [1] CRAN (R 4.1.2)
#>  rmarkdown     2.11       2021-09-14 [1] CRAN (R 4.1.0)
#>  rstudioapi    0.13       2020-11-12 [1] CRAN (R 4.1.2)
#>  sessioninfo   1.2.2.9000 2022-02-10 [1] Github (r-lib/sessioninfo@6c683ac)
#>  stringi       1.7.6      2021-11-29 [1] CRAN (R 4.1.0)
#>  stringr       1.4.0.9000 2021-12-14 [1] xgit ([email protected]:tidyverse/stringr.git@dd909b7)
#>  vctrs         0.3.8      2021-04-29 [1] CRAN (R 4.1.2)
#>  withr         2.4.3      2021-11-30 [1] CRAN (R 4.1.0)
#>  xfun          0.29       2021-12-14 [1] CRAN (R 4.1.2)
#>  yaml          2.2.2      2022-01-25 [1] CRAN (R 4.1.2)
#> 
#>  [1] /home/jupyter/.R/library
#>  [2] /usr/local/lib/R/site-library
#>  [3] /usr/lib/R/site-library
#>  [4] /usr/lib/R/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────

Code that segfaults

url <- "https://git.bioconductor.org/packages/MeasurementError.cor"
res <- git2r::remote_ls(url)

Output of Segfault

This reprex appears to crash R.
See standard output and standard error for more details.

Standard output and error

x Install the styler package in order to use `style = TRUE`.

 *** caught segfault ***
address 0xc800010009, cause 'memory not mapped'

Traceback:
 1: git2r::remote_ls(url)
 2: eval(expr, envir, enclos)
 3: eval(expr, envir, enclos)
 4: withVisible(eval(expr, envir, enclos))
 5: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,     error = eHandler, message = mHandler)
 6: doTryCatch(return(expr), name, parentenv, handler)
 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8: tryCatchList(expr, classes, parentenv, handlers)
 9: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
10: try(f, silent = TRUE)
11: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,     enclos)), warning = wHandler, error = eHandler, message = mHandler))
12: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,     envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
13: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,     debug = debug, last = i == length(out), use_try = stop_on_error !=         2L, keep_warning = keep_warning, keep_message = keep_message,     output_handler = output_handler, include_timing = include_timing)
14: evaluate::evaluate(...)
15: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),     keep_message = !isFALSE(options$message), stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options))
16: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,     keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options)))
17: eng_r(options)
18: block_exec(params)
19: call_block(x)
20: process_group.block(group)
21: process_group(group)
22: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        setwd(wd)        cat(res, sep = "\n", file = output %n% "")        message("Quitting from lines ", paste(current_lines(i),             collapse = "-"), " (", knit_concord$get("infile"),             ") ")    })
23: process_file(text, output)
24: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
25: rmarkdown::render(input, quiet = TRUE, envir = globalenv(), encoding = "UTF-8")
26: (function (input) {    rmarkdown::render(input, quiet = TRUE, envir = globalenv(),         encoding = "UTF-8")})(input = base::quote("grave-cobra_reprex.R"))
27: (function (what, args, quote = FALSE, envir = parent.frame()) {    if (!is.list(args))         stop("second argument must be a list")    if (quote)         args <- lapply(args, enquote)    .Internal(do.call(what, args, envir))})(base::quote(function (input) {    rmarkdown::render(input, quiet = TRUE, envir = globalenv(),         encoding = "UTF-8")}), base::quote(list(input = "grave-cobra_reprex.R")), envir = base::quote(<environment>),     quote = base::quote(TRUE))
28: do.call(do.call, c(readRDS("/tmp/Rtmpv9dmjG/callr-fun-5e4c4c920ef4"),     list(envir = .GlobalEnv, quote = TRUE)), envir = .GlobalEnv,     quote = TRUE)
29: saveRDS(do.call(do.call, c(readRDS("/tmp/Rtmpv9dmjG/callr-fun-5e4c4c920ef4"),     list(envir = .GlobalEnv, quote = TRUE)), envir = .GlobalEnv,     quote = TRUE), file = "/tmp/Rtmpv9dmjG/callr-res-5e4c1d5e941")
30: withCallingHandlers({    NULL    saveRDS(do.call(do.call, c(readRDS("/tmp/Rtmpv9dmjG/callr-fun-5e4c4c920ef4"),         list(envir = .GlobalEnv, quote = TRUE)), envir = .GlobalEnv,         quote = TRUE), file = "/tmp/Rtmpv9dmjG/callr-res-5e4c1d5e941")    flush(stdout())    flush(stderr())    NULL    invisible()}, error = function(e) {    {        callr_data <- as.environment("tools:callr")$`__callr_data__`        err <- callr_data$err        assign(".Traceback", .traceback(4), envir = callr_data)        dump.frames("__callr_dump__")        assign(".Last.dump", .GlobalEnv$`__callr_dump__`, envir = callr_data)        rm("__callr_dump__", envir = .GlobalEnv)        e$call <- deparse(conditionCall(e), nlines = 6)        e2 <- err$new_error(conditionMessage(e), call. = conditionCall(e))        class(e2) <- c("callr_remote_error", class(e2))        e2$error <- e        calls <- sys.calls()        dcframe <- which(vapply(calls, function(x) length(x) >=             1 && identical(x[[1]], quote(do.call)), logical(1)))[1]        if (!is.na(dcframe))             e2$`_ignore` <- list(c(1, dcframe + 1L))        e2$`_pid` <- Sys.getpid()        e2$`_timestamp` <- Sys.time()        if (inherits(e, "rlib_error_2_0"))             e2$parent <- e$parent        e2 <- err$add_trace_back(e2, embed = FALSE)        saveRDS(list("error", e2), file = paste0("/tmp/Rtmpv9dmjG/callr-res-5e4c1d5e941",             ".error"))    }}, interrupt = function(e) {    {        callr_data <- as.environment("tools:callr")$`__callr_data__`        err <- callr_data$err        assign(".Traceback", .traceback(4), envir = callr_data)        dump.frames("__callr_dump__")        assign(".Last.dump", .GlobalEnv$`__callr_dump__`, envir = callr_data)        rm("__callr_dump__", envir = .GlobalEnv)        e$call <- deparse(conditionCall(e), nlines = 6)        e2 <- err$new_error(conditionMessage(e), call. = conditionCall(e))        class(e2) <- c("callr_remote_error", class(e2))        e2$error <- e        calls <- sys.calls()        dcframe <- which(vapply(calls, function(x) length(x) >=             1 && identical(x[[1]], quote(do.call)), logical(1)))[1]        if (!is.na(dcframe))             e2$`_ignore` <- list(c(1, dcframe + 1L))        e2$`_pid` <- Sys.getpid()        e2$`_timestamp` <- Sys.time()        if (inherits(e, "rlib_error_2_0"))             e2$parent <- e$parent        e2 <- err$add_trace_back(e2, embed = FALSE)        saveRDS(list("error", e2), file = paste0("/tmp/Rtmpv9dmjG/callr-res-5e4c1d5e941",             ".error"))    }}, callr_message = function(e) {    try(signalCondition(e))})
31: doTryCatch(return(expr), name, parentenv, handler)
32: tryCatchOne(expr, names, parentenv, handlers[[1L]])
33: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
34: doTryCatch(return(expr), name, parentenv, handler)
35: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
36: tryCatchList(expr, classes, parentenv, handlers)
37: tryCatch(withCallingHandlers({    NULL    saveRDS(do.call(do.call, c(readRDS("/tmp/Rtmpv9dmjG/callr-fun-5e4c4c920ef4"),         list(envir = .GlobalEnv, quote = TRUE)), envir = .GlobalEnv,         quote = TRUE), file = "/tmp/Rtmpv9dmjG/callr-res-5e4c1d5e941")    flush(stdout())    flush(stderr())    NULL    invisible()}, error = function(e) {    {        callr_data <- as.environment("tools:callr")$`__callr_data__`        err <- callr_data$err        assign(".Traceback", .traceback(4), envir = callr_data)        dump.frames("__callr_dump__")        assign(".Last.dump", .GlobalEnv$`__callr_dump__`, envir = callr_data)        rm("__callr_dump__", envir = .GlobalEnv)        e$call <- deparse(conditionCall(e), nlines = 6)        e2 <- err$new_error(conditionMessage(e), call. = conditionCall(e))        class(e2) <- c("callr_remote_error", class(e2))        e2$error <- e        calls <- sys.calls()        dcframe <- which(vapply(calls, function(x) length(x) >=             1 && identical(x[[1]], quote(do.call)), logical(1)))[1]        if (!is.na(dcframe))             e2$`_ignore` <- list(c(1, dcframe + 1L))        e2$`_pid` <- Sys.getpid()        e2$`_timestamp` <- Sys.time()        if (inherits(e, "rlib_error_2_0"))             e2$parent <- e$parent        e2 <- err$add_trace_back(e2, embed = FALSE)        saveRDS(list("error", e2), file = paste0("/tmp/Rtmpv9dmjG/callr-res-5e4c1d5e941",             ".error"))    }}, interrupt = function(e) {    {        callr_data <- as.environment("tools:callr")$`__callr_data__`        err <- callr_data$err        assign(".Traceback", .traceback(4), envir = callr_data)        dump.frames("__callr_dump__")        assign(".Last.dump", .GlobalEnv$`__callr_dump__`, envir = callr_data)        rm("__callr_dump__", envir = .GlobalEnv)        e$call <- deparse(conditionCall(e), nlines = 6)        e2 <- err$new_error(conditionMessage(e), call. = conditionCall(e))        class(e2) <- c("callr_remote_error", class(e2))        e2$error <- e        calls <- sys.calls()        dcframe <- which(vapply(calls, function(x) length(x) >=             1 && identical(x[[1]], quote(do.call)), logical(1)))[1]        if (!is.na(dcframe))             e2$`_ignore` <- list(c(1, dcframe + 1L))        e2$`_pid` <- Sys.getpid()        e2$`_timestamp` <- Sys.time()        if (inherits(e, "rlib_error_2_0"))             e2$parent <- e$parent        e2 <- err$add_trace_back(e2, embed = FALSE)        saveRDS(list("error", e2), file = paste0("/tmp/Rtmpv9dmjG/callr-res-5e4c1d5e941",             ".error"))    }}, callr_message = function(e) {    try(signalCondition(e))}), error = function(e) {    NULL    try(stop(e))}, interrupt = function(e) {    NULL    e})
An irrecoverable exception occurred. R is aborting now ...

The text was updated successfully, but these errors were encountered:

muschellij2 · 2022-02-02T03:41:27Z

This may have to do with the fact I'm running on a docker image, so I think when credentials queries the SSH agent, there may be some odd stuff going on or permissions issues.

muschellij2 · 2022-02-10T17:24:00Z

Same as #264

muschellij2 · 2022-02-10T17:43:46Z

Fixed in libgit2 1.3.0 via (shell):

wget https://github.com/libgit2/libgit2/archive/refs/tags/v1.3.0.tar.gz
mkdir build && cd build
cmake ..
cmake --build .
sudo make install
R -e 'install.packages("git2r", type = "source")'

path is set to a repo:

path = "~/targets-minimal-original/"
git2r::libgit2_features()
#> $threads
#> [1] TRUE
#> 
#> $https
#> [1] TRUE
#> 
#> $ssh
#> [1] TRUE
git2r::libgit2_version()
#> $major
#> [1] 1
#> 
#> $minor
#> [1] 3
#> 
#> $rev
#> [1] 0
ssh_cred = git2r::cred_ssh_key()
repo = git2r::init(path = path)
git2r::remote_ls("origin", repo = repo)
#>                                       HEAD 
#> "f699789c97a350c1106a661a524672fc6816a4c2" 
#>                            refs/heads/main 
#> "f699789c97a350c1106a661a524672fc6816a4c2" 
#>                    refs/heads/targets-runs 
#> "00c523c790332bfd9ebf3690889cc2e124e653f5" 
#>                           refs/pull/5/head 
#> "d358f04517b2a2b66a7d39c1f798515359e6b98c" 
#>                           refs/pull/6/head 
#> "aa0b0e7f34bd16479065e524b571f84107aff006" 
#>                            refs/tags/0.0.1 
#> "3a2269f707a9dbfeb9ff8eddd41b63efcf643b15"

^{Created on 2022-02-10 by the reprex package (v2.0.1)}

Session info

sessioninfo::session_info()
#> Warning in system("timedatectl", intern = TRUE): running command 'timedatectl'
#> had status 1
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.1.2 (2021-11-01)
#>  os       Debian GNU/Linux 10 (buster)
#>  system   x86_64, linux-gnu
#>  ui       X11
#>  language (EN)
#>  collate  C.UTF-8
#>  ctype    C.UTF-8
#>  tz       Etc/UTC
#>  date     2022-02-10
#>  pandoc   2.14.0.3 @ /usr/lib/rstudio-server/bin/pandoc/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version    date (UTC) lib source
#>  cli           3.1.1.9000 2022-02-09 [1] Github (r-lib/cli@00d1770)
#>  digest        0.6.29     2021-12-01 [1] CRAN (R 4.1.2)
#>  evaluate      0.14       2019-05-28 [1] CRAN (R 4.1.2)
#>  fastmap       1.1.0      2021-01-25 [1] CRAN (R 4.1.2)
#>  fs            1.5.2      2021-12-08 [1] CRAN (R 4.1.2)
#>  git2r         0.29.0     2021-11-22 [1] CRAN (R 4.1.2)
#>  glue          1.6.1      2022-01-22 [1] CRAN (R 4.1.2)
#>  highr         0.9        2021-04-16 [1] CRAN (R 4.1.2)
#>  htmltools     0.5.2      2021-08-25 [1] CRAN (R 4.1.0)
#>  knitr         1.37       2021-12-16 [1] CRAN (R 4.1.2)
#>  lifecycle     1.0.1      2021-09-24 [1] CRAN (R 4.1.0)
#>  magrittr      2.0.2      2022-01-26 [1] CRAN (R 4.1.2)
#>  reprex        2.0.1      2021-08-05 [1] CRAN (R 4.1.0)
#>  rlang         1.0.1      2022-02-03 [1] CRAN (R 4.1.2)
#>  rmarkdown     2.11       2021-09-14 [1] CRAN (R 4.1.0)
#>  rstudioapi    0.13       2020-11-12 [1] CRAN (R 4.1.2)
#>  sessioninfo   1.2.2.9000 2022-02-10 [1] Github (r-lib/sessioninfo@6c683ac)
#>  stringi       1.7.6      2021-11-29 [1] CRAN (R 4.1.0)
#>  stringr       1.4.0.9000 2021-12-14 [1] xgit ([email protected]:tidyverse/stringr.git@dd909b7)
#>  vctrs         0.3.8      2021-04-29 [1] CRAN (R 4.1.2)
#>  withr         2.4.3      2021-11-30 [1] CRAN (R 4.1.0)
#>  xfun          0.29       2021-12-14 [1] CRAN (R 4.1.2)
#>  yaml          2.2.2      2022-01-25 [1] CRAN (R 4.1.2)
#> 
#>  [1] /home/jupyter/.R/library
#>  [2] /usr/local/lib/R/site-library
#>  [3] /usr/lib/R/site-library
#>  [4] /usr/lib/R/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────

muschellij2 closed this as completed Feb 10, 2022

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Segfault with NULLs #438

Segfault with NULLs #438

muschellij2 commented Feb 2, 2022 •

edited

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muschellij2 commented Feb 2, 2022

muschellij2 commented Feb 10, 2022

muschellij2 commented Feb 10, 2022

Segfault with NULLs #438

Segfault with NULLs #438

Comments

muschellij2 commented Feb 2, 2022 • edited Loading

Libgit2 version

Code that segfaults

Output of Segfault

Standard output and error

muschellij2 commented Feb 2, 2022

muschellij2 commented Feb 10, 2022

muschellij2 commented Feb 10, 2022

muschellij2 commented Feb 2, 2022 •

edited

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