Multiple platform build/check report for BioC 3.20 - BUILD results for oligo on taishan

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4764
palomino8	Windows Server 2022 Datacenter	x64	4.4.3 (2025-02-28 ucrt) -- "Trophy Case"	4495
merida1	macOS 12.7.5 Monterey	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4522
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.3 (2025-02-28) -- "Trophy Case"	4449
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.3 (2025-02-28) -- "Trophy Case"	4426
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*

BUILD results for oligo on taishan

To the developers/maintainers of the oligo package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/oligo.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: oligo

Version: 1.70.1

Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data oligo

StartedAt: 2025-04-01 01:15:07 -0000 (Tue, 01 Apr 2025)

EndedAt: 2025-04-01 01:15:09 -0000 (Tue, 01 Apr 2025)

EllapsedTime: 2.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data oligo
###
##############################################################################
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* checking for file ‘oligo/DESCRIPTION’ ... OK
* preparing ‘oligo’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running ‘cleanup’
* installing the package to build vignettes
      -----------------------------------
* installing *source* package ‘oligo’ ...
** 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 -I"/home/biocbuild/R/R-4.4.3/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.3/site-library/preprocessCore/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c DABG.c -o DABG.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R-4.4.3/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.3/site-library/preprocessCore/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c ParserGzXYS.c -o ParserGzXYS.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R-4.4.3/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.3/site-library/preprocessCore/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c ParserXYS.c -o ParserXYS.o
ParserXYS.c: In function ‘xys_header_field’:
ParserXYS.c:148:5: error: implicit declaration of function ‘error’; did you mean ‘perror’? [-Wimplicit-function-declaration]
  148 |     error("Error reading from %s.\n", currentFile);
      |     ^~~~~
      |     perror
make: *** [/home/biocbuild/R/R-4.4.3/etc/Makeconf:195: ParserXYS.o] Error 1
ERROR: compilation failed for package ‘oligo’
* removing ‘/home/biocbuild/tmp/RtmpehEVqr/Rinst13c2356cf4480/oligo’
      -----------------------------------
ERROR: package installation failed