Multiple platform build/check report for BioC 3.22 - INSTALL results for GenomicRanges on taishan

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*

INSTALL results for GenomicRanges on taishan

To the developers/maintainers of the GenomicRanges package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicRanges.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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: GenomicRanges

Version: 1.61.6

Command: /home/biocbuild/R/R/bin/R CMD INSTALL GenomicRanges

StartedAt: 2025-10-23 20:34:01 -0000 (Thu, 23 Oct 2025)

EndedAt: 2025-10-23 20:34:29 -0000 (Thu, 23 Oct 2025)

EllapsedTime: 28.5 seconds

RetCode: 0

Status: OK

Command output

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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD INSTALL GenomicRanges
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘GenomicRanges’ ...
** this is package ‘GenomicRanges’ version ‘1.61.6’
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c IRanges_stubs.c -o IRanges_stubs.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/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
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c S4Vectors_stubs.c -o S4Vectors_stubs.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/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;
      |                               ^~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/site-library/00LOCK-GenomicRanges/00new/GenomicRanges/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 (GenomicRanges)