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BioC 3.2: BUILD BIN report for genoset on oaxaca

This page was generated on 2015-08-24 10:56:37 -0700 (Mon, 24 Aug 2015).

Package 416/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genoset 1.23.5
Peter M. Haverty
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/genoset
Last Changed Rev: 106677 / Revision: 107696
Last Changed Date: 2015-07-22 20:15:59 -0700 (Wed, 22 Jul 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: genoset
Version: 1.23.5
Command: rm -rf genoset.buildbin-libdir && mkdir genoset.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh genoset_1.23.5.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R genoset.buildbin-libdir
StartedAt: 2015-08-24 05:12:01 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 05:12:23 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 21.8 seconds
RetCode: 0
Status:  OK 
PackageFile: genoset_1.23.5.tgz
PackageFileSize: 505.2 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf genoset.buildbin-libdir && mkdir genoset.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh genoset_1.23.5.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R genoset.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=genoset.buildbin-libdir genoset_1.23.5.tar.gz'
>>>>>>> 

* installing *source* package ‘genoset’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c bounds.c -o bounds.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c init.c -o init.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c rangeSummaries.c -o rangeSummaries.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c utils.c -o utils.o
clang -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 genoset.so bounds.o init.o rangeSummaries.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/genoset.buildbin-libdir/genoset/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: subclass "GNCList" of class "GenomicRanges" is not local and cannot be updated for new inheritance information; consider setClassUnion()
Warning: subclass "GIntervalTree" of class "GenomicRanges" is not local and cannot be updated for new inheritance information; consider setClassUnion()
** help
Warning: bad markup (extra space?) at GenoSet.Rd:15:56
Warning: bad markup (extra space?) at baf2mbaf.Rd:10:61
Warning: bad markup (extra space?) at calcGC.Rd:10:58
Warning: bad markup (extra space?) at calcGC.Rd:13:59
Warning: bad markup (extra space?) at do_rledf_views.Rd:17:56
Warning: bad markup (extra space?) at gcCorrect.Rd:12:60
Warning: bad markup (extra space?) at genoPlot-methods.Rd:23:56
Warning: bad markup (extra space?) at genoPlot-methods.Rd:56:56
Warning: bad markup (extra space?) at genomeAxis.Rd:13:59
Warning: bad markup (extra space?) at runCBS.Rd:17:63
Warning: bad markup (extra space?) at segs2Rle.Rd:11:56
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (genoset)


>>>>>>> 
>>>>>>> FIXING LINKS FOR genoset.buildbin-libdir/genoset/libs//genoset.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" "genoset.buildbin-libdir/genoset/libs//genoset.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgfortran.3.dylib" "genoset.buildbin-libdir/genoset/libs//genoset.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" "genoset.buildbin-libdir/genoset/libs//genoset.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.dylib" "genoset.buildbin-libdir/genoset/libs//genoset.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libquadmath.0.dylib" "genoset.buildbin-libdir/genoset/libs//genoset.so"