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BioC 3.2: BUILD BIN report for IRanges on oaxaca

This page was generated on 2016-04-23 10:22:47 -0700 (Sat, 23 Apr 2016).

Package 541/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IRanges 2.4.8
Bioconductor Package Maintainer
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/IRanges
Last Changed Rev: 114030 / Revision: 116712
Last Changed Date: 2016-02-25 14:31:36 -0800 (Thu, 25 Feb 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  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: IRanges
Version: 2.4.8
Command: rm -rf IRanges.buildbin-libdir && mkdir IRanges.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh IRanges_2.4.8.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R IRanges.buildbin-libdir
StartedAt: 2016-04-23 05:48:36 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 05:48:51 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 15.8 seconds
RetCode: 0
Status:  OK 
PackageFile: IRanges_2.4.8.tgz
PackageFileSize: 1.425 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf IRanges.buildbin-libdir && mkdir IRanges.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh IRanges_2.4.8.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R IRanges.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=IRanges.buildbin-libdir IRanges_2.4.8.tar.gz'
>>>>>>> 

* installing *source* package ‘IRanges’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c CompressedList_class.c -o CompressedList_class.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c GappedRanges_class.c -o GappedRanges_class.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c Grouping_class.c -o Grouping_class.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c IRanges_class.c -o IRanges_class.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c IRanges_constructor.c -o IRanges_constructor.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c NCList.c -o NCList.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c R_init_IRanges.c -o R_init_IRanges.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c RangedData_class.c -o RangedData_class.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c Ranges_class.c -o Ranges_class.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c Ranges_comparison.c -o Ranges_comparison.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c RleViews_utils.c -o RleViews_utils.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c SimpleRangesList_class.c -o SimpleRangesList_class.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c coverage_methods.c -o coverage_methods.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c inter_range_methods.c -o inter_range_methods.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 IRanges.so CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o GappedRanges_class.o Grouping_class.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o RangedData_class.o Ranges_class.o Ranges_comparison.o RleViews_utils.o S4Vectors_stubs.o SimpleRangesList_class.o coverage_methods.o inter_range_methods.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/IRanges.buildbin-libdir/IRanges/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘window<-’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘rev’ from package ‘base’ in package ‘IRanges’
in method for ‘coerce’ with signature ‘"Hits","PartitioningByEnd"’: no definition for class “PartitioningByEnd”
in method for ‘coerce’ with signature ‘"Hits","Partitioning"’: no definition for class “Partitioning”
in method for ‘coerce’ with signature ‘"Hits","Ranges"’: no definition for class “Ranges”
in method for ‘coerce’ with signature ‘"Hits","IRanges"’: no definition for class “IRanges”
in method for ‘coerce’ with signature ‘"Hits","CompressedIntegerList"’: no definition for class “CompressedIntegerList”
in method for ‘coerce’ with signature ‘"Hits","IntegerList"’: no definition for class “IntegerList”
Creating a generic function for ‘stack’ from package ‘utils’ in package ‘IRanges’
in method for ‘!’ with signature ‘"CompressedList"’: no definition for class “CompressedList”
in method for ‘match’ with signature ‘"CompressedList","list"’: no definition for class “CompressedList”
in method for ‘match’ with signature ‘"CompressedList","vector"’: no definition for class “CompressedList”
in method for ‘duplicated’ with signature ‘"CompressedList"’: no definition for class “CompressedList”
in method for ‘unique’ with signature ‘"CompressedList"’: no definition for class “CompressedList”
in method for ‘is.na’ with signature ‘"CompressedList"’: no definition for class “CompressedList”
Creating a generic function for ‘mean’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘which.max’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘which.min’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘split<-’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘drop’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘which’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘diff’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘var’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘cov’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘cor’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘sd’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘median’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘quantile’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘chartr’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘tolower’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘toupper’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘sub’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘gsub’ from package ‘base’ in package ‘IRanges’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (IRanges)


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