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October 11, 2024 11:55
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triggers segfault on ubuntu 24.04 under R 4.4.1, when compiled with rmarkdown::render
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| --- | |
| title: "Triggers a curl/httr segfault during R CMD build" | |
| author: Hervé Pagès | |
| output: | |
| BiocStyle::html_document: | |
| toc: true | |
| toc_depth: 2 | |
| vignette: > | |
| %\VignetteEngine{knitr::rmarkdown} | |
| %\VignetteEncoding{UTF-8} | |
| --- | |
| This vignette triggers a curl segfault when built with | |
| `R CMD build curlminitest` on Ubuntu 24.04 and Intel Mac. | |
| The segfault typically occurs inside `curl::curl_fetch_disk()`. | |
| ```{r} | |
| library(httr) | |
| url1 <- "https://en.wikipedia.org/wiki/Bioconductor" | |
| response1 <- GET(url1) | |
| url2 <- "ftp://ftp.ensembl.org/pub/release-71/gtf/caenorhabditis_elegans/Caenorhabditis_elegans.WBcel235.71.gtf.gz" | |
| response2a <- GET(url2, write_disk(tempfile())) | |
| response2b <- GET(url2, write_disk(tempfile())) | |
| ``` |
Without gdb we see
> rmarkdown::render("curlminitest.Rmd")
processing file: curlminitest.Rmd
|................................... | 67% [unnamed-chunk-1]
*** caught segfault ***
address (nil), cause 'unknown'
Traceback:
1: curl::curl_fetch_disk(url, x$path, handle = handle)
2: request_fetch.write_disk(req$output, req$url, handle)
3: request_fetch(req$output, req$url, handle)
4: request_perform(req, hu$handle$handle)
5: GET(url2, write_disk(tempfile()))
6: eval(expr, envir)
7: eval(expr, envir)
8: withVisible(eval(expr, envir))
9: withCallingHandlers(code, message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push
(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2
|| getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call
(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watc
her$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"),
stop = invokeRestart("eval_stop"), error = invokeRestart("eval_error", cnd))})
10: eval(call)
11: eval(call)
12: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() w
atcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
13: doWithOneRestart(return(expr), restart)
14: withOneRestart(expr, restarts[[1L]])
> sessionInfo()
R version 4.4.1 Patched (2024-09-30 r87215)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.1 LTS
Matrix products: default
BLAS: /usr/local/lib/R/lib/libRblas.so
LAPACK: /usr/local/lib/R/lib/libRlapack.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] httr_1.4.7 BiocStyle_2.32.1
loaded via a namespace (and not attached):
[1] digest_0.6.37 R6_2.5.1 bookdown_0.40
[4] fastmap_1.2.0 xfun_0.48 cachem_1.1.0
[7] knitr_1.48 htmltools_0.5.8.1 rmarkdown_2.28
[10] lifecycle_1.0.4 cli_3.6.3 sass_0.4.9
[13] jquerylib_0.1.4 compiler_4.4.1 tools_4.4.1
[16] curl_5.2.3 evaluate_1.0.1 bslib_0.8.0
[19] yaml_2.3.10 BiocManager_1.30.25 jsonlite_1.8.9
[22] rlang_1.1.4
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under R -d gdb