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This page was generated on 2023-04-19 11:01:54 -0400 (Wed, 19 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnsonmacOS 13.0 Venturaarm644.2.2 (2022-10-31) -- "Innocent and Trusting" 4256
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BUILD BIN results for GenomicAlignments on kjohnson


To the developers/maintainers of the GenomicAlignments package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 782/2183HostnameOS / ArchINSTALLBUILDBUILD BIN
GenomicAlignments 1.34.1  (landing page)
Hervé Pagès
Snapshot Date: 2023-04-12 13:00:02 -0400 (Wed, 12 Apr 2023)
git_url: https://git.bioconductor.org/packages/GenomicAlignments
git_branch: RELEASE_3_16
git_last_commit: f65563c
git_last_commit_date: 2023-03-08 18:26:20 -0400 (Wed, 08 Mar 2023)
kjohnsonmacOS 13.0 Ventura / arm64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GenomicAlignments
Version: 1.34.1
Command: rm -rf GenomicAlignments.buildbin-libdir && mkdir GenomicAlignments.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GenomicAlignments_1.34.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R GenomicAlignments.buildbin-libdir
StartedAt: 2023-04-18 16:03:43 -0400 (Tue, 18 Apr 2023)
EndedAt: 2023-04-18 16:05:10 -0400 (Tue, 18 Apr 2023)
EllapsedTime: 86.8 seconds
RetCode: 0
Status:   OK  
PackageFile: GenomicAlignments_1.34.1.tgz
PackageFileSize: 2.266 MiB

Command output

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###
### Running command:
###
###   rm -rf GenomicAlignments.buildbin-libdir && mkdir GenomicAlignments.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GenomicAlignments_1.34.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R GenomicAlignments.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=GenomicAlignments.buildbin-libdir GenomicAlignments_1.34.1.tar.gz'
>>>>>>> 

* installing *source* package ‘GenomicAlignments’ ...
** using staged installation
** libs
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c cigar_utils.c -o cigar_utils.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o GenomicAlignments.so IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: -undefined dynamic_lookup may not work with chained fixups
installing to /Volumes/External/bbs-3.16-bioc-m1/meat/GenomicAlignments.buildbin-libdir/00LOCK-GenomicAlignments/00new/GenomicAlignments/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 (GenomicAlignments)


>>>>>>> 
>>>>>>> FIXING LINKS FOR GenomicAlignments.buildbin-libdir/GenomicAlignments/libs/GenomicAlignments.so
>>>>>>> 

install_name_tool -change "/opt/R/arm64/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgcc_s.1.1.dylib" "GenomicAlignments.buildbin-libdir/GenomicAlignments/libs/GenomicAlignments.so"
install_name_tool -change "/opt/R/arm64/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgfortran.5.dylib" "GenomicAlignments.buildbin-libdir/GenomicAlignments/libs/GenomicAlignments.so"
install_name_tool -change "/opt/R/arm64/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libquadmath.0.dylib" "GenomicAlignments.buildbin-libdir/GenomicAlignments/libs/GenomicAlignments.so"