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BUILD BIN report for VariantFiltering on merida2

This page was generated on 2019-04-09 13:29:35 -0400 (Tue, 09 Apr 2019).

Package 1670/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VariantFiltering 1.19.0
Robert Castelo
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/VariantFiltering
Branch: master
Last Commit: b46d294
Last Changed Date: 2018-10-30 11:54:32 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  ERROR  skipped  skipped 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK [ OK ]

Summary

Package: VariantFiltering
Version: 1.19.0
Command: rm -rf VariantFiltering.buildbin-libdir && mkdir VariantFiltering.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh VariantFiltering_1.19.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R VariantFiltering.buildbin-libdir
StartedAt: 2019-04-09 06:44:00 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 06:45:11 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 71.1 seconds
RetCode: 0
Status:  OK 
PackageFile: VariantFiltering_1.19.0.tgz
PackageFileSize: 3.834 MiB

Command output

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### Running command:
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###   rm -rf VariantFiltering.buildbin-libdir && mkdir VariantFiltering.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh VariantFiltering_1.19.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R VariantFiltering.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=VariantFiltering.buildbin-libdir VariantFiltering_1.19.0.tar.gz'
>>>>>>> 

* installing *source* package ‘VariantFiltering’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Biostrings/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c Biostrings_stubs.c -o Biostrings_stubs.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Biostrings/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_init_VariantFiltering.c -o R_init_VariantFiltering.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Biostrings/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c methods-WeightMatrix.c -o methods-WeightMatrix.o
clang -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 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-3.9-bioc/meat/VariantFiltering.buildbin-libdir/VariantFiltering/libs
** R
** inst
** byte-compile and prepare package for lazy loading
in method for 'annotateVariants' with signature 'annObj="MafDb"': no definition for class "MafDb"
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (VariantFiltering)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgcc_s.1.dylib" "VariantFiltering.buildbin-libdir/VariantFiltering/libs//VariantFiltering.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "VariantFiltering.buildbin-libdir/VariantFiltering/libs//VariantFiltering.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.5.2.dylib" "VariantFiltering.buildbin-libdir/VariantFiltering/libs//VariantFiltering.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "VariantFiltering.buildbin-libdir/VariantFiltering/libs//VariantFiltering.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "VariantFiltering.buildbin-libdir/VariantFiltering/libs//VariantFiltering.so"