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Back toMultiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-12-15 12:06 -0500 (Mon, 15 Dec 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble"4882
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble"4673
kjohnson1macOS 13.7.5 Venturaarm644.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"4607
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six"4671
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

Package182/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Bioc.gff 1.0.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2025-12-11 13:45 -0500 (Thu, 11 Dec 2025)
git_url: https://git.bioconductor.org/packages/Bioc.gff
git_branch: RELEASE_3_22
git_last_commit: 5bbebde
git_last_commit_date: 2025-10-29 11:37:35 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

BUILD BIN results for Bioc.gff on merida1

To the developers/maintainers of the Bioc.gff package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Bioc.gff.git to reflect on this report. SeeTroubleshooting Build Report for more information.
- Use the followingRenviron 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. SeeRenviron.bioc for more information.

raw results


Summary

Package: Bioc.gff
Version: 1.0.0
Command: rm -rf Bioc.gff.buildbin-libdir && mkdir Bioc.gff.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Bioc.gff_1.0.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Bioc.gff.buildbin-libdir
StartedAt: 2025-12-12 14:25:09 -0500 (Fri, 12 Dec 2025)
EndedAt: 2025-12-12 14:25:41 -0500 (Fri, 12 Dec 2025)
EllapsedTime: 32.5 seconds
RetCode: 0
Status:  OK  
PackageFile: Bioc.gff_1.0.0.tgz
PackageFileSize: 369.4KiB

Command output

################################################################################################################################################################## Running command:######   rm -rf Bioc.gff.buildbin-libdir && mkdir Bioc.gff.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Bioc.gff_1.0.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Bioc.gff.buildbin-libdir###############################################################################################################################################################>>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Bioc.gff.buildbin-libdir Bioc.gff_1.0.0.tar.gz'>>>>>>> * installing *source* package ‘Bioc.gff’ ...** this is package ‘Bioc.gff’ version ‘1.0.0’** using staged installation** libsusing C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’using SDK: ‘MacOSX11.3.1.sdk’clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c R_init_Bioc_gff.c -o R_init_Bioc_gff.oclang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.oclang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c XVector_stubs.c -o XVector_stubs.oclang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c readGFF.c -o readGFF.oclang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c utils.c -o utils.oclang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o Bioc.gff.so R_init_Bioc_gff.o S4Vectors_stubs.o XVector_stubs.o readGFF.o utils.o -F/Library/Frameworks/R.framework/.. -framework Rinstalling to /Users/biocbuild/bbs-3.22-bioc/meat/Bioc.gff.buildbin-libdir/00LOCK-Bioc.gff/00new/Bioc.gff/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 (Bioc.gff)>>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR Bioc.gff.buildbin-libdir/Bioc.gff/libs/Bioc.gff.so>>>>>>> >>>>>>> Paths before fix:Bioc.gff.buildbin-libdir/Bioc.gff/libs/Bioc.gff.so:Bioc.gff.so (compatibility version 0.0.0, current version 0.0.0)/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.2)/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)>>>>>>> Fix with install_name_tool:install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgcc_s.1.1.dylib" "Bioc.gff.buildbin-libdir/Bioc.gff/libs/Bioc.gff.so"install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib" "Bioc.gff.buildbin-libdir/Bioc.gff/libs/Bioc.gff.so"install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib" "Bioc.gff.buildbin-libdir/Bioc.gff/libs/Bioc.gff.so">>>>>>> Paths after fix:Bioc.gff.buildbin-libdir/Bioc.gff/libs/Bioc.gff.so:Bioc.gff.so (compatibility version 0.0.0, current version 0.0.0)/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.2)/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
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