[R-pkg-devel] R CMD build segfault (r88038)

[Josiah Parry]

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Josiah Parry reacted via Gmail
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On Mon, Mar 24, 2025 at 9:48 AM Dirk Eddelbuettel <edd using debian.org> wrote:

>
> On 24 March 2025 at 09:10, Josiah Parry wrote:
> | In trying to address new WARNINGs on R-devel I'm trying to rebuild my
> | package environment on R 4.6 (r88038) so I can try and remediate.
> However,
> | I'm encountering a segfault when doing so which doesn't occur for R 4.5.0
> | alpha (2025-03-18 r87991).
> |
> | Is there a known change to building using R CMD build that we have to
> | address?
> |
> | rextendr ⚡ R CMD build .
> | * checking for file ‘./DESCRIPTION’ ... OK
> | * preparing ‘rextendr’:
> | * checking DESCRIPTION meta-information ... OK
> | * installing the package to build vignettes
> |       -----------------------------------
> | * installing *source* package ‘rextendr’ ...
> | ** this is package ‘rextendr’ version ‘0.3.1.9001’
> | ** using staged installation
> | ** R
> | ** inst
> | ** byte-compile and prepare package for lazy loading
> | sh: line 1: 20659 Segmentation fault: 11  R_TESTS=
> | '/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/bin/R'
> | --no-save --no-restore --no-echo 2>&1 <
> |
> '/var/folders/wd/xq999jjj3bx2w8cpg7lkfxlm0000gn/T//RtmpkyfWsl/file50adcb72e68'
>
> It's been a while since I have seen such a segfault, but I have encountered
> plenty in both the earlier days of Rcpp, or when working with for example
> the
> geospatial satck. And it almost always traced back to different (binary,
> i.e. 'native' code containing) packages requiring a rebuild.  While I
> haven't
> seen it lately, my suggestion would still be to see if it persists if you
> rebuild everything touched by that package / if it happens for subsets of
> these packages. Subsetting to the other native packages may suffice. From a
> quick check (see below) that is still 16 packages.
>
> Dirk
>
> > db <- data.table(tools::CRAN_package_db())
> > pkgs <- data.table(Package=tools::package_dependencies("rextendr",
> db=db, recursive=TRUE)[[1]])
> > pkgs[,Package]
>  [1] "brio"       "callr"      "cli"        "desc"       "dplyr"
>  [6] "glue"       "jsonlite"   "pkgbuild"   "processx"   "purrr"
> [11] "rlang"      "rprojroot"  "stringi"    "tibble"     "vctrs"
> [16] "withr"      "R6"         "utils"      "generics"   "lifecycle"
> [21] "magrittr"   "methods"    "pillar"     "tidyselect" "ps"
> [26] "tools"      "stats"      "fansi"      "pkgconfig"  "graphics"
> [31] "grDevices"  "utf8"
> > db[pkgs, on="Package"][NeedsCompilation=="yes", Package]
>  [1] "brio"       "cli"        "dplyr"      "glue"       "jsonlite"
>  [6] "processx"   "purrr"      "rlang"      "stringi"    "tibble"
> [11] "vctrs"      "magrittr"   "tidyselect" "ps"         "fansi"
> [16] "utf8"
> >
>
> --
> dirk.eddelbuettel.com | @eddelbuettel | edd using debian.org
>