Hervé Pagès
| Snapshot Date: 2025-10-23 14:17 -0400 (Thu, 23 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/XVector |
| git_branch: devel |
| git_last_commit: 7d24a2f |
| git_last_commit_date: 2025-09-12 22:15:39 -0400 (Fri, 12 Sep 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-24 12:04 -0400 (Fri, 24 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4898 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4688 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4634 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 2350/2359 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| XVector 0.49.1 (landing page) Hervé Pagès
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | NA | ||||||||||
|
To the developers/maintainers of the XVector package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/XVector.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: XVector |
| Version: 0.49.1 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL XVector |
| StartedAt: 2025-10-23 15:14:32 -0400 (Thu, 23 Oct 2025) |
| EndedAt: 2025-10-23 15:14:47 -0400 (Thu, 23 Oct 2025) |
| EllapsedTime: 15.0 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL XVector
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘XVector’ ...
** this is package ‘XVector’ version ‘0.49.1’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RDS_random_access.c -o RDS_random_access.o
RDS_random_access.c: In function ‘RDS_extract_subarray’:
RDS_random_access.c:796:25: warning: unused variable ‘ans’ [-Wunused-variable]
796 | SEXP subscript, ans;
| ^~~
RDS_random_access.c:793:18: warning: variable ‘x_type’ set but not used [-Wunused-but-set-variable]
793 | SEXPTYPE x_type;
| ^~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c R_init_XVector.c -o R_init_XVector.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c SharedDouble_class.c -o SharedDouble_class.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c SharedInteger_class.c -o SharedInteger_class.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c SharedRaw_class.c -o SharedRaw_class.o
SharedRaw_class.c: In function ‘SharedRaw_read_complexes_from_subscript’:
SharedRaw_class.c:396:20: warning: variable ‘src_tag’ set but not used [-Wunused-but-set-variable]
396 | SEXP dest, src_tag;
| ^~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c SharedVector_class.c -o SharedVector_class.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c XDouble_class.c -o XDouble_class.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c XInteger_class.c -o XInteger_class.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c XRawList_comparison.c -o XRawList_comparison.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c XRaw_class.c -o XRaw_class.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c XVectorList_class.c -o XVectorList_class.o
XVectorList_class.c: In function ‘_new_XRawList_from_CharAEAE’:
XVectorList_class.c:459:17: warning: ‘lkup_length’ may be used uninitialized [-Wmaybe-uninitialized]
459 | _Ocopy_bytes_to_i1i2_with_lkup(0, dest.length - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
460 | (char *) dest.ptr, dest.length,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
461 | src->elts, CharAE_get_nelt(src),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
462 | lkup0, lkup_length);
| ~~~~~~~~~~~~~~~~~~~
XVectorList_class.c:434:13: note: ‘lkup_length’ was declared here
434 | int lkup_length, nelt, i;
| ^~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c XVector_class.c -o XVector_class.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c io_utils.c -o io_utils.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c slice_methods.c -o slice_methods.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c vector_copy.c -o vector_copy.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c view_summarization_methods.c -o view_summarization_methods.o
view_summarization_methods.c: In function ‘get_which_min_from_Ints_holder’:
view_summarization_methods.c:219:45: warning: ‘cur_min’ may be used uninitialized [-Wmaybe-uninitialized]
219 | if (which_min == NA_INTEGER || x < cur_min) {
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
view_summarization_methods.c:208:19: note: ‘cur_min’ was declared here
208 | int xlen, cur_min, which_min, i, x;
| ^~~~~~~
view_summarization_methods.c: In function ‘get_which_min_from_Doubles_holder’:
view_summarization_methods.c:246:45: warning: ‘cur_min’ may be used uninitialized [-Wmaybe-uninitialized]
246 | if (which_min == NA_INTEGER || x < cur_min) {
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
view_summarization_methods.c:235:16: note: ‘cur_min’ was declared here
235 | double cur_min, x;
| ^~~~~~~
view_summarization_methods.c: In function ‘get_which_max_from_Ints_holder’:
view_summarization_methods.c:269:45: warning: ‘cur_max’ may be used uninitialized [-Wmaybe-uninitialized]
269 | if (which_max == NA_INTEGER || x > cur_max) {
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
view_summarization_methods.c:258:19: note: ‘cur_max’ was declared here
258 | int xlen, cur_max, which_max, i, x;
| ^~~~~~~
view_summarization_methods.c: In function ‘get_which_max_from_Doubles_holder’:
view_summarization_methods.c:296:45: warning: ‘cur_max’ may be used uninitialized [-Wmaybe-uninitialized]
296 | if (which_max == NA_INTEGER || x > cur_max) {
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
view_summarization_methods.c:285:16: note: ‘cur_max’ was declared here
285 | double cur_max, x;
| ^~~~~~~
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o XVector.so IRanges_stubs.o Ocopy_byteblocks.o RDS_random_access.o R_init_XVector.o S4Vectors_stubs.o SharedDouble_class.o SharedInteger_class.o SharedRaw_class.o SharedVector_class.o XDouble_class.o XInteger_class.o XRawList_comparison.o XRaw_class.o XVectorList_class.o XVector_class.o io_utils.o slice_methods.o vector_copy.o view_summarization_methods.o -lz -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-XVector/00new/XVector/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (XVector)