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BUILD BIN report for JunctionSeq on merida1

This page was generated on 2020-04-15 12:42:57 -0400 (Wed, 15 Apr 2020).

Package 882/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
JunctionSeq 1.16.0
Stephen Hartley
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/JunctionSeq
Branch: RELEASE_3_10
Last Commit: 6792868
Last Changed Date: 2019-10-29 13:09:33 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: JunctionSeq
Version: 1.16.0
Command: rm -rf JunctionSeq.buildbin-libdir && mkdir JunctionSeq.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh JunctionSeq_1.16.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R JunctionSeq.buildbin-libdir
StartedAt: 2020-04-15 07:50:52 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 07:51:54 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 62.4 seconds
RetCode: 0
Status:  OK 
PackageFile: JunctionSeq_1.16.0.tgz
PackageFileSize: 2.318 MiB

Command output

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###
### Running command:
###
###   rm -rf JunctionSeq.buildbin-libdir && mkdir JunctionSeq.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh JunctionSeq_1.16.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R JunctionSeq.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=JunctionSeq.buildbin-libdir JunctionSeq_1.16.0.tar.gz'
>>>>>>> 

* installing *source* package ‘JunctionSeq’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c DESeq2.cpp -o DESeq2.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -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 JunctionSeq.so DESeq2.o RcppExports.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.10-bioc/meat/JunctionSeq.buildbin-libdir/00LOCK-JunctionSeq/00new/JunctionSeq/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 (JunctionSeq)


>>>>>>> 
>>>>>>> FIXING LINKS FOR JunctionSeq.buildbin-libdir/JunctionSeq/libs//JunctionSeq.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" "JunctionSeq.buildbin-libdir/JunctionSeq/libs//JunctionSeq.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "JunctionSeq.buildbin-libdir/JunctionSeq/libs//JunctionSeq.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" "JunctionSeq.buildbin-libdir/JunctionSeq/libs//JunctionSeq.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "JunctionSeq.buildbin-libdir/JunctionSeq/libs//JunctionSeq.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "JunctionSeq.buildbin-libdir/JunctionSeq/libs//JunctionSeq.so"
install_name_tool -change "/usr/local/gfortran/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "JunctionSeq.buildbin-libdir/JunctionSeq/libs//JunctionSeq.so"
install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "JunctionSeq.buildbin-libdir/JunctionSeq/libs//JunctionSeq.so"