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This page was generated on 2025-03-10 12:12 -0400 (Mon, 10 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4670
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4355
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4446
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4439
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4306
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 1441/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
oligo 1.70.1  (landing page)
Benilton Carvalho
Snapshot Date: 2025-03-06 13:00 -0500 (Thu, 06 Mar 2025)
git_url: https://git.bioconductor.org/packages/oligo
git_branch: RELEASE_3_20
git_last_commit: c68cfae
git_last_commit_date: 2025-03-04 09:34:58 -0500 (Tue, 04 Mar 2025)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  YES
palomino8Windows Server 2022 Datacenter / x64  ERROR    ERROR  skippedskipped
merida1macOS 12.7.5 Monterey / x86_64  ERROR    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  ERROR    ERROR  skippedskipped
taishanLinux (openEuler 24.03 LTS) / aarch64  ERROR    ERROR  skipped

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: 2025-03-07 02:49:02 -0000 (Fri, 07 Mar 2025)
EndedAt: 2025-03-07 02:49:04 -0000 (Fri, 07 Mar 2025)
EllapsedTime: 2.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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


* 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/RtmpYAaNLj/Rinst1c41c954160451/oligo’
      -----------------------------------
ERROR: package installation failed