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BUILD BIN report for ORFik on celaya2

This page was generated on 2019-10-16 13:02:33 -0400 (Wed, 16 Oct 2019).

Package 1150/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ORFik 1.4.1
Kornel Labun
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/ORFik
Branch: RELEASE_3_9
Last Commit: 3ae9f3b
Last Changed Date: 2019-06-06 08:36:37 -0400 (Thu, 06 Jun 2019)
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  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: ORFik
Version: 1.4.1
Command: rm -rf ORFik.buildbin-libdir && mkdir ORFik.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ORFik_1.4.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R ORFik.buildbin-libdir
StartedAt: 2019-10-16 09:05:09 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 09:06:37 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 88.1 seconds
RetCode: 0
Status:  OK 
PackageFile: ORFik_1.4.1.tgz
PackageFileSize: 1.359 MiB

Command output

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###
### Running command:
###
###   rm -rf ORFik.buildbin-libdir && mkdir ORFik.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ORFik_1.4.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R ORFik.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=ORFik.buildbin-libdir ORFik_1.4.1.tar.gz'
>>>>>>> 

* installing *source* package ‘ORFik’ ...
** 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" -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 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c findORFsHelpers.cpp -o findORFsHelpers.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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c findOrfs.cpp -o findOrfs.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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c findOrfsFasta.cpp -o findOrfsFasta.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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c pmapFromTranscripts.cpp -o pmapFromTranscripts.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 ORFik.so RcppExports.o findORFsHelpers.o findOrfs.o findOrfsFasta.o pmapFromTranscripts.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/ORFik.buildbin-libdir/00LOCK-ORFik/00new/ORFik/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 (ORFik)


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