Back to Mac ARM64 build report for BioC 3.16
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This page was generated on 2023-04-19 11:01:58 -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 sigPathway on kjohnson


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

raw results

Package 1872/2183HostnameOS / ArchINSTALLBUILDBUILD BIN
sigPathway 1.66.2  (landing page)
Weil Lai
Snapshot Date: 2023-04-12 13:00:02 -0400 (Wed, 12 Apr 2023)
git_url: https://git.bioconductor.org/packages/sigPathway
git_branch: RELEASE_3_16
git_last_commit: 0351ca6
git_last_commit_date: 2023-01-19 11:18:33 -0400 (Thu, 19 Jan 2023)
kjohnsonmacOS 13.0 Ventura / arm64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: sigPathway
Version: 1.66.2
Command: rm -rf sigPathway.buildbin-libdir && mkdir sigPathway.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh sigPathway_1.66.2.tar.gz /Library/Frameworks/R.framework/Resources/bin/R sigPathway.buildbin-libdir
StartedAt: 2023-04-18 19:35:42 -0400 (Tue, 18 Apr 2023)
EndedAt: 2023-04-18 19:35:57 -0400 (Tue, 18 Apr 2023)
EllapsedTime: 14.3 seconds
RetCode: 0
Status:   OK  
PackageFile: sigPathway_1.66.2.tgz
PackageFileSize: 781.3 KiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf sigPathway.buildbin-libdir && mkdir sigPathway.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh sigPathway_1.66.2.tar.gz /Library/Frameworks/R.framework/Resources/bin/R sigPathway.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=sigPathway.buildbin-libdir sigPathway_1.66.2.tar.gz'
>>>>>>> 

* installing *source* package ‘sigPathway’ ...
** using staged installation
** libs
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c calc_gene_set_internal.c -o calc_gene_set_internal.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c calc_gene_set_stat.c -o calc_gene_set_stat.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c calc_probe_stat.c -o calc_probe_stat.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c calc_weights.c -o calc_weights.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c matrix_fn.c -o matrix_fn.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c permute.c -o permute.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c shuffle.c -o shuffle.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c sigPathway.c -o sigPathway.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 sigPathway.so calc_gene_set_internal.o calc_gene_set_stat.o calc_probe_stat.o calc_weights.o matrix_fn.o permute.o shuffle.o sigPathway.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: -undefined dynamic_lookup may not work with chained fixups
ld: warning: could not create compact unwind for ___emutls_get_address: registers 23 and 24 not saved contiguously in frame
installing to /Volumes/External/bbs-3.16-bioc-m1/meat/sigPathway.buildbin-libdir/00LOCK-sigPathway/00new/sigPathway/libs
** R
** data
** 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 (sigPathway)


>>>>>>> 
>>>>>>> FIXING LINKS FOR sigPathway.buildbin-libdir/sigPathway/libs/sigPathway.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" "sigPathway.buildbin-libdir/sigPathway/libs/sigPathway.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" "sigPathway.buildbin-libdir/sigPathway/libs/sigPathway.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" "sigPathway.buildbin-libdir/sigPathway/libs/sigPathway.so"
install_name_tool -change "/opt/R/arm64/gfortran/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgfortran.5.dylib" "sigPathway.buildbin-libdir/sigPathway/libs/sigPathway.so"
install_name_tool -change "/opt/R/arm64/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libquadmath.0.dylib" "sigPathway.buildbin-libdir/sigPathway/libs/sigPathway.so"