Hervé Pagès
| Snapshot Date: 2025-11-02 13:40 -0500 (Sun, 02 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/GenomicAlignments |
| git_branch: devel |
| git_last_commit: 085e9df |
| git_last_commit_date: 2025-10-29 14:50:25 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-03 11:33 -0500 (Mon, 03 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4775 |
| 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 831/2321 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenomicAlignments 1.47.0 (landing page) Hervé Pagès
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the GenomicAlignments package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicAlignments.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: GenomicAlignments |
| Version: 1.47.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL GenomicAlignments |
| StartedAt: 2025-11-02 15:31:42 -0500 (Sun, 02 Nov 2025) |
| EndedAt: 2025-11-02 15:32:16 -0500 (Sun, 02 Nov 2025) |
| EllapsedTime: 33.6 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL GenomicAlignments
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘GenomicAlignments’ ...
** this is package ‘GenomicAlignments’ version ‘1.47.0’
** 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-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
In function ‘unsafe_overlap_encoding’,
inlined from ‘overlap_encoding’ at encodeOverlaps_methods.c:209:2:
encodeOverlaps_methods.c:182:9: warning: ‘out_nelt0’ may be used uninitialized [-Wmaybe-uninitialized]
182 | CharAE_delete_at(out, out_nelt0, j1 * nrow);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
encodeOverlaps_methods.c: In function ‘overlap_encoding’:
encodeOverlaps_methods.c:99:13: note: ‘out_nelt0’ was declared here
99 | int out_nelt0, i, starti, widthi, spacei, j, startj, widthj, spacej,
| ^~~~~~~~~
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o GenomicAlignments.so IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o encodeOverlaps_methods.o -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-GenomicAlignments/00new/GenomicAlignments/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (GenomicAlignments)