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BioC 3.1: BUILD BIN report for h5vc on petty

This page was generated on 2015-10-09 09:36:08 -0700 (Fri, 09 Oct 2015).

Package 453/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
h5vc 2.2.0
Paul Theodor Pyl
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/h5vc
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: h5vc
Version: 2.2.0
Command: rm -rf h5vc.buildbin-libdir && mkdir h5vc.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh h5vc_2.2.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R h5vc.buildbin-libdir
StartedAt: 2015-10-09 03:11:48 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 03:12:11 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 22.6 seconds
RetCode: 0
Status:  OK 
PackageFile: h5vc_2.2.0.tgz
PackageFileSize: 826.7 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf h5vc.buildbin-libdir && mkdir h5vc.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh h5vc_2.2.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R h5vc.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=h5vc.buildbin-libdir h5vc_2.2.0.tar.gz'
>>>>>>> 

* installing *source* package ‘h5vc’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c tallyBAM.cpp -o tallyBAM.o
tallyBAM.cpp: In function ‘int pileup_func_old(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)’:
tallyBAM.cpp:47: warning: unused variable ‘len’
tallyBAM.cpp: In function ‘int pileup_func(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)’:
tallyBAM.cpp:96: warning: unused variable ‘len’
tallyBAM.cpp: In function ‘int _tallyBAM(char**, char**, int*, int*, int*, int*, int*, int*, int*, int*)’:
tallyBAM.cpp:141: warning: unused variable ‘c’
tallyBAM.cpp: At global scope:
tallyBAM.cpp:43: warning: ‘int pileup_func_old(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)’ defined but not used
llvm-g++-4.2 -arch x86_64 -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 -L/usr/local/lib -o h5vc.so tallyBAM.o /Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/usrlib//libbam.a /Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/usrlib//libbcf.a /Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/usrlib//libtabix.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-bioc/meat/h5vc.buildbin-libdir/h5vc/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (h5vc)


>>>>>>> 
>>>>>>> FIXING LINKS FOR h5vc.buildbin-libdir/h5vc/libs//h5vc.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgcc_s.1.dylib" "h5vc.buildbin-libdir/h5vc/libs//h5vc.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgfortran.2.dylib" "h5vc.buildbin-libdir/h5vc/libs//h5vc.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.5.2.dylib" "h5vc.buildbin-libdir/h5vc/libs//h5vc.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.dylib" "h5vc.buildbin-libdir/h5vc/libs//h5vc.so"