Back to Mac ARM64 build report for BioC 3.16
ABCDEFGHIJKLMNOPQRSTU[V]WXYZ

This page was generated on 2023-04-19 11:01:59 -0400 (Wed, 19 Apr 2023).

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


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

raw results

Package 2133/2183HostnameOS / ArchINSTALLBUILDBUILD BIN
VariantAnnotation 1.44.1  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2023-04-12 13:00:02 -0400 (Wed, 12 Apr 2023)
git_url: https://git.bioconductor.org/packages/VariantAnnotation
git_branch: RELEASE_3_16
git_last_commit: 2c52839
git_last_commit_date: 2023-02-14 16:02:56 -0400 (Tue, 14 Feb 2023)
kjohnsonmacOS 13.0 Ventura / arm64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: VariantAnnotation
Version: 1.44.1
Command: rm -rf VariantAnnotation.buildbin-libdir && mkdir VariantAnnotation.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh VariantAnnotation_1.44.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R VariantAnnotation.buildbin-libdir
StartedAt: 2023-04-18 20:23:33 -0400 (Tue, 18 Apr 2023)
EndedAt: 2023-04-18 20:25:48 -0400 (Tue, 18 Apr 2023)
EllapsedTime: 135.3 seconds
RetCode: 0
Status:   OK  
PackageFile: VariantAnnotation_1.44.1.tgz
PackageFileSize: 3.914 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf VariantAnnotation.buildbin-libdir && mkdir VariantAnnotation.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh VariantAnnotation_1.44.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R VariantAnnotation.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=VariantAnnotation.buildbin-libdir VariantAnnotation_1.44.1.tar.gz'
>>>>>>> 

* installing *source* package ‘VariantAnnotation’ ...
** using staged installation
** libs
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -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'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c Biostrings_stubs.c -o Biostrings_stubs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -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'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib/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 -D_FILE_OFFSET_BITS=64 -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'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -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'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c XVector_stubs.c -o XVector_stubs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -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'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c dna_hash.c -o dna_hash.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -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'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c rle.c -o rle.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -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'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c strhash.c -o strhash.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -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'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c utilities.c -o utilities.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -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'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c vcffile.c -o vcffile.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -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'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c vcftype.c -o vcftype.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -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'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c writevcf.c -o writevcf.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 VariantAnnotation.so Biostrings_stubs.o IRanges_stubs.o R_init_VariantAnnotation.o XVector_stubs.o dna_hash.o rle.o strhash.o utilities.o vcffile.o vcftype.o writevcf.o /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -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/VariantAnnotation.buildbin-libdir/00LOCK-VariantAnnotation/00new/VariantAnnotation/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘tabulate’ in package ‘VariantAnnotation’
** 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 (VariantAnnotation)


>>>>>>> 
>>>>>>> FIXING LINKS FOR VariantAnnotation.buildbin-libdir/VariantAnnotation/libs/VariantAnnotation.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" "VariantAnnotation.buildbin-libdir/VariantAnnotation/libs/VariantAnnotation.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" "VariantAnnotation.buildbin-libdir/VariantAnnotation/libs/VariantAnnotation.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" "VariantAnnotation.buildbin-libdir/VariantAnnotation/libs/VariantAnnotation.so"