Back to Multiple platform build/check report for BioC 3.12
ABCDEFG[H]IJKLMNOPQRSTUVWXYZ

BUILD BIN report for hapFabia on merida1

This page was generated on 2021-05-06 12:35:13 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the hapFabia package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 813/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hapFabia 1.32.0  (landing page)
Andreas Mitterecker
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/hapFabia
Branch: RELEASE_3_12
Last Commit: 83cb41e
Last Changed Date: 2020-10-27 10:47:06 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: hapFabia
Version: 1.32.0
Command: rm -rf hapFabia.buildbin-libdir && mkdir hapFabia.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh hapFabia_1.32.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R hapFabia.buildbin-libdir
StartedAt: 2021-05-06 08:52:31 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 08:53:27 -0400 (Thu, 06 May 2021)
EllapsedTime: 55.5 seconds
RetCode: 0
Status:   OK  
PackageFile: hapFabia_1.32.0.tgz
PackageFileSize: 1.752 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf hapFabia.buildbin-libdir && mkdir hapFabia.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh hapFabia_1.32.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R hapFabia.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=hapFabia.buildbin-libdir hapFabia_1.32.0.tar.gz'
>>>>>>> 

* installing *source* package ‘hapFabia’ ...
** using staged installation
rmdir: inst/commandLine/i386: No such file or directory
rmdir: inst/commandLine/x86_64: No such file or directory
rmdir: inst/commandLine/ppc: No such file or directory
rmdir: inst/commandLine/ppc64: No such file or directory
rmdir: inst/commandLine: No such file or directory
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c interfaceR.c -o interfaceR.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c split_sparse_matrixB.c -o split_sparse_matrixB.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c vcftoFABIAB.c -o vcftoFABIAB.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o hapFabia.so interfaceR.o split_sparse_matrixB.o vcftoFABIAB.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang -mmacosx-version-min=10.13 -c ./commandLine/split_sparse_matrix.c -o ./commandLine/split_sparse_matrix.o -Wall -g -O2 
clang -mmacosx-version-min=10.13 -c split_sparse_matrixB.c -o ./commandLine/split_sparse_matrixB.o -Wall -g -O2 
clang -mmacosx-version-min=10.13 ./commandLine/split_sparse_matrix.o ./commandLine/split_sparse_matrixB.o -o ./commandLine/split_sparse_matrix
mv ./commandLine/split_sparse_matrix ../inst/commandLine/
clang -mmacosx-version-min=10.13 -c ./commandLine/vcftoFABIA.c -o ./commandLine/vcftoFABIA.o -Wall -g -O2 
clang -mmacosx-version-min=10.13 -c vcftoFABIAB.c -o ./commandLine/vcftoFABIAB.o -Wall -g -O2 
clang -mmacosx-version-min=10.13 ./commandLine/vcftoFABIA.o ./commandLine/vcftoFABIAB.o -o ./commandLine/vcftoFABIA
mv ./commandLine/vcftoFABIA ../inst/commandLine/
installing to /Users/biocbuild/bbs-3.12-bioc/meat/hapFabia.buildbin-libdir/00LOCK-hapFabia/00new/hapFabia/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 (hapFabia)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgcc_s.1.dylib" "hapFabia.buildbin-libdir/hapFabia/libs/hapFabia.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.5.dylib" "hapFabia.buildbin-libdir/hapFabia/libs/hapFabia.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "hapFabia.buildbin-libdir/hapFabia/libs/hapFabia.so"