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BUILD BIN report for chimera on celaya2

This page was generated on 2019-10-16 12:51:07 -0400 (Wed, 16 Oct 2019).

Package 254/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chimera 1.26.0
Raffaele A Calogero
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/chimera
Branch: RELEASE_3_9
Last Commit: dfcad86
Last Changed Date: 2019-05-02 11:53:41 -0400 (Thu, 02 May 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  ERROR  skipped  skipped 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: chimera
Version: 1.26.0
Command: rm -rf chimera.buildbin-libdir && mkdir chimera.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh chimera_1.26.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R chimera.buildbin-libdir
StartedAt: 2019-10-16 08:19:10 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 08:20:10 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 59.5 seconds
RetCode: 0
Status:  OK 
PackageFile: chimera_1.26.0.tgz
PackageFileSize: 2.544 MiB

Command output

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###
### Running command:
###
###   rm -rf chimera.buildbin-libdir && mkdir chimera.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh chimera_1.26.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R chimera.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=chimera.buildbin-libdir chimera_1.26.0.tar.gz'
>>>>>>> 

* installing *source* package ‘chimera’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c StarParser.cpp -o StarParser.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 chimera.so StarParser.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/chimera.buildbin-libdir/00LOCK-chimera/00new/chimera/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 (chimera)


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