h5vc 2.4.0
Paul Theodor Pyl
| Snapshot Date: 2015-11-05 16:24:12 -0800 (Thu, 05 Nov 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/h5vc | | Last Changed Rev: 109589 / Revision: 110379 | | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | [ OK ] | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf h5vc.buildbin-libdir && mkdir h5vc.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh h5vc_2.4.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R h5vc.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=h5vc.buildbin-libdir h5vc_2.4.0.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-3.2-bioc/meat/h5vc.buildbin-libdir/h5vc/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* 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"