Back to Mac ARM64 build report for BioC 3.17
ABCDEFGHIJKLMNOPQRSTU[V]WXYZ

This page was generated on 2023-10-20 09:38:14 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 2182/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VariantFiltering 1.36.1  (landing page)
Robert Castelo
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/VariantFiltering
git_branch: RELEASE_3_17
git_last_commit: f9846cf
git_last_commit_date: 2023-06-26 07:54:10 -0400 (Mon, 26 Jun 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

BUILD BIN results for VariantFiltering on kjohnson2


To the developers/maintainers of the VariantFiltering package:
- 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.

raw results

Summary

Package: VariantFiltering
Version: 1.36.1
Command: rm -rf VariantFiltering.buildbin-libdir && mkdir VariantFiltering.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh VariantFiltering_1.36.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R VariantFiltering.buildbin-libdir
StartedAt: 2023-10-19 18:04:31 -0400 (Thu, 19 Oct 2023)
EndedAt: 2023-10-19 18:07:20 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 168.7 seconds
RetCode: 0
Status:   OK  
PackageFile: VariantFiltering_1.36.1.tgz
PackageFileSize: 4.157 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf VariantFiltering.buildbin-libdir && mkdir VariantFiltering.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh VariantFiltering_1.36.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R VariantFiltering.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=VariantFiltering.buildbin-libdir VariantFiltering_1.36.1.tar.gz'
>>>>>>> 

* installing *source* package ‘VariantFiltering’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/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  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c R_init_VariantFiltering.c -o R_init_VariantFiltering.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c methods-WeightMatrix.c -o methods-WeightMatrix.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 VariantFiltering.so Biostrings_stubs.o R_init_VariantFiltering.o methods-WeightMatrix.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/VariantFiltering.buildbin-libdir/00LOCK-VariantFiltering/00new/VariantFiltering/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 (VariantFiltering)


>>>>>>> 
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR VariantFiltering.buildbin-libdir/VariantFiltering/libs/VariantFiltering.so
>>>>>>> 

>>>>>>> Paths before fix:
VariantFiltering.buildbin-libdir/VariantFiltering/libs/VariantFiltering.so:
	VariantFiltering.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/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/4.3-arm64/Resources/lib/libgcc_s.1.1.dylib" "VariantFiltering.buildbin-libdir/VariantFiltering/libs/VariantFiltering.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "VariantFiltering.buildbin-libdir/VariantFiltering/libs/VariantFiltering.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "VariantFiltering.buildbin-libdir/VariantFiltering/libs/VariantFiltering.so"

>>>>>>> Paths after fix:

VariantFiltering.buildbin-libdir/VariantFiltering/libs/VariantFiltering.so:
	VariantFiltering.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)