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BioC 3.1: BUILD BIN report for chromDraw on petty

This page was generated on 2015-10-09 09:37:12 -0700 (Fri, 09 Oct 2015).

Package 166/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chromDraw 1.0.0
Jan Janecka
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/chromDraw
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  WARNINGS UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS [ OK ]UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: chromDraw
Version: 1.0.0
Command: rm -rf chromDraw.buildbin-libdir && mkdir chromDraw.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh chromDraw_1.0.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R chromDraw.buildbin-libdir
StartedAt: 2015-10-09 03:03:18 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 03:04:01 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 42.5 seconds
RetCode: 0
Status:  OK 
PackageFile: chromDraw_1.0.0.tgz
PackageFileSize: 601.3 KiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf chromDraw.buildbin-libdir && mkdir chromDraw.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh chromDraw_1.0.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R chromDraw.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=chromDraw.buildbin-libdir chromDraw_1.0.0.tar.gz'
>>>>>>> 

* installing *source* package ‘chromDraw’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c chromDraw.cpp -o chromDraw.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c RcppExports.cpp -o RcppExports.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c libBoard/src/Board.cpp -o libBoard/src/Board.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c libBoard/src/Color.cpp -o libBoard/src/Color.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c libBoard/src/PSFonts.cpp -o libBoard/src/PSFonts.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c libBoard/src/Path.cpp -o libBoard/src/Path.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c libBoard/src/Rect.cpp -o libBoard/src/Rect.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c libBoard/src/ShapeList.cpp -o libBoard/src/ShapeList.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c libBoard/src/Shapes.cpp -o libBoard/src/Shapes.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c libBoard/src/Tools.cpp -o libBoard/src/Tools.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c libBoard/src/Transforms.cpp -o libBoard/src/Transforms.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c chromDrawCPP/canvas.cpp -o chromDrawCPP/canvas.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c chromDrawCPP/chBlock.cpp -o chromDrawCPP/chBlock.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c chromDrawCPP/chCentromere.cpp -o chromDrawCPP/chCentromere.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c chromDrawCPP/chdrawer.cpp -o chromDrawCPP/chdrawer.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c chromDrawCPP/chromosome.cpp -o chromDrawCPP/chromosome.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c chromDrawCPP/chromosomeElement.cpp -o chromDrawCPP/chromosomeElement.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c chromDrawCPP/color.cpp -o chromDrawCPP/color.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c chromDrawCPP/colorPalette.cpp -o chromDrawCPP/colorPalette.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c chromDrawCPP/getOpts.cpp -o chromDrawCPP/getOpts.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c chromDrawCPP/ideogram.cpp -o chromDrawCPP/ideogram.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c chromDrawCPP/karyotype.cpp -o chromDrawCPP/karyotype.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c chromDrawCPP/parameters.cpp -o chromDrawCPP/parameters.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c R_init_chromDraw.cpp -o R_init_chromDraw.o
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 chromDraw.so chromDraw.o RcppExports.o ./libBoard/src/Board.o ./libBoard/src/Color.o ./libBoard/src/PSFonts.o ./libBoard/src/Path.o ./libBoard/src/Rect.o ./libBoard/src/ShapeList.o ./libBoard/src/Shapes.o ./libBoard/src/Tools.o ./libBoard/src/Transforms.o ./chromDrawCPP/canvas.o ./chromDrawCPP/chBlock.o ./chromDrawCPP/chCentromere.o ./chromDrawCPP/chdrawer.o ./chromDrawCPP/chromosome.o ./chromDrawCPP/chromosomeElement.o ./chromDrawCPP/color.o ./chromDrawCPP/colorPalette.o ./chromDrawCPP/getOpts.o ./chromDrawCPP/ideogram.o ./chromDrawCPP/karyotype.o ./chromDrawCPP/parameters.o ./R_init_chromDraw.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-bioc/meat/chromDraw.buildbin-libdir/chromDraw/libs
** R
** 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 (chromDraw)


>>>>>>> 
>>>>>>> FIXING LINKS FOR chromDraw.buildbin-libdir/chromDraw/libs//chromDraw.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" "chromDraw.buildbin-libdir/chromDraw/libs//chromDraw.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgfortran.2.dylib" "chromDraw.buildbin-libdir/chromDraw/libs//chromDraw.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" "chromDraw.buildbin-libdir/chromDraw/libs//chromDraw.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.dylib" "chromDraw.buildbin-libdir/chromDraw/libs//chromDraw.so"