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This page was generated on 2025-03-24 12:36 -0400 (Mon, 24 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 870
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Package 97/217HostnameOS / ArchINSTALLBUILDCHECK
GenomicRanges 1.59.1  (landing page)
Hervé Pagès
Snapshot Date: 2025-03-24 12:00 -0400 (Mon, 24 Mar 2025)
git_url: https://git.bioconductor.org/packages/GenomicRanges
git_branch: devel
git_last_commit: efa80fa
git_last_commit_date: 2024-11-15 06:05:50 -0400 (Fri, 15 Nov 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  ERROR    ERROR  skipped

BUILD results for GenomicRanges on teran2

To the developers/maintainers of the GenomicRanges package:
- 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.

raw results


Summary

Package: GenomicRanges
Version: 1.59.1
Command: /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD build --keep-empty-dirs --no-resave-data GenomicRanges
StartedAt: 2025-03-24 12:22:28 -0400 (Mon, 24 Mar 2025)
EndedAt: 2025-03-24 12:22:30 -0400 (Mon, 24 Mar 2025)
EllapsedTime: 2.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
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###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD build --keep-empty-dirs --no-resave-data GenomicRanges
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* checking for file ‘GenomicRanges/DESCRIPTION’ ... OK
* preparing ‘GenomicRanges’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
      -----------------------------------
* installing *source* package ‘GenomicRanges’ ...
** this is package ‘GenomicRanges’ version ‘1.59.1’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/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 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/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 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c transcript_utils.c -o transcript_utils.o
In function ‘tloc2rloc’,
    inlined from ‘tlocs2rlocs’ at transcript_utils.c:208:26:
transcript_utils.c:143:45: warning: ‘start’ may be used uninitialized [-Wmaybe-uninitialized]
  143 |         return on_minus_strand ? end - tloc : start + tloc;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
transcript_utils.c: In function ‘tlocs2rlocs’:
transcript_utils.c:120:24: note: ‘start’ was declared here
  120 |         int nexons, j, start, end, width;
      |                        ^~~~~
In function ‘tloc2rloc’,
    inlined from ‘tlocs2rlocs’ at transcript_utils.c:208:26:
transcript_utils.c:143:45: warning: ‘end’ may be used uninitialized [-Wmaybe-uninitialized]
  143 |         return on_minus_strand ? end - tloc : start + tloc;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
transcript_utils.c: In function ‘tlocs2rlocs’:
transcript_utils.c:120:31: note: ‘end’ was declared here
  120 |         int nexons, j, start, end, width;
      |                               ^~~
gcc -shared -L/usr/local/lib -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o
installing to /tmp/RtmpclJ4uO/Rinst22a7664d0452a9/00LOCK-GenomicRanges/00new/GenomicRanges/libs
** R
** inst
Warning in file.append(to[okay], from[okay]) :
  write error during file append
Warning in file.append(to[okay], from[okay]) :
  write error during file append
Warning in file.append(to[okay], from[okay]) :
  write error during file append
Warning in file.append(to[okay], from[okay]) :
  write error during file append
Warning in file.append(to[okay], from[okay]) :
  write error during file append
Warning in file.append(to[okay], from[okay]) :
  write error during file append
Warning in file.append(to[okay], from[okay]) :
  write error during file append
Warning in file.append(to[okay], from[okay]) :
  write error during file append
** byte-compile and prepare package for lazy loading
Fatal error: cannot create 'R_TempDir'
ERROR: lazy loading failed for package ‘GenomicRanges’
* removing ‘/tmp/RtmpclJ4uO/Rinst22a7664d0452a9/GenomicRanges’
      -----------------------------------
ERROR: package installation failed