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BioC 3.2: BUILD BIN report for chromDraw on oaxaca

This page was generated on 2015-10-27 17:42:01 -0400 (Tue, 27 Oct 2015).

Package 174/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chromDraw 1.2.0
Jan Janecka
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/chromDraw
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: chromDraw
Version: 1.2.0
Command: rm -rf chromDraw.buildbin-libdir && mkdir chromDraw.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh chromDraw_1.2.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R chromDraw.buildbin-libdir
StartedAt: 2015-10-27 09:32:50 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 09:33:35 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 44.7 seconds
RetCode: 0
Status:  OK 
PackageFile: chromDraw_1.2.0.tgz
PackageFileSize: 604.3 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_1.2.0.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_1.2.0.tar.gz'
>>>>>>> 

* installing *source* package ‘chromDraw’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c chromDraw.cpp -o chromDraw.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c libBoard/src/Board.cpp -o libBoard/src/Board.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c libBoard/src/Color.cpp -o libBoard/src/Color.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c libBoard/src/PSFonts.cpp -o libBoard/src/PSFonts.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c libBoard/src/Path.cpp -o libBoard/src/Path.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c libBoard/src/Rect.cpp -o libBoard/src/Rect.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c libBoard/src/ShapeList.cpp -o libBoard/src/ShapeList.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c libBoard/src/Shapes.cpp -o libBoard/src/Shapes.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c libBoard/src/Tools.cpp -o libBoard/src/Tools.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c libBoard/src/Transforms.cpp -o libBoard/src/Transforms.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c chromDrawCPP/canvas.cpp -o chromDrawCPP/canvas.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c chromDrawCPP/chBlock.cpp -o chromDrawCPP/chBlock.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c chromDrawCPP/chCentromere.cpp -o chromDrawCPP/chCentromere.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c chromDrawCPP/chdrawer.cpp -o chromDrawCPP/chdrawer.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c chromDrawCPP/chromosome.cpp -o chromDrawCPP/chromosome.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c chromDrawCPP/chromosomeElement.cpp -o chromDrawCPP/chromosomeElement.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c chromDrawCPP/color.cpp -o chromDrawCPP/color.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c chromDrawCPP/colorPalette.cpp -o chromDrawCPP/colorPalette.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c chromDrawCPP/getOpts.cpp -o chromDrawCPP/getOpts.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c chromDrawCPP/ideogram.cpp -o chromDrawCPP/ideogram.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c chromDrawCPP/karyotype.cpp -o chromDrawCPP/karyotype.o
chromDrawCPP/karyotype.cpp:265:7: warning: delete called on 'chBlock' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
                                                delete block;
                                                ^
chromDrawCPP/karyotype.cpp:273:6: warning: delete called on 'chBlock' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
                                        delete block;
                                        ^
chromDrawCPP/karyotype.cpp:312:6: warning: delete called on 'chCentromere' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
                                        delete centromere;
                                        ^
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c chromDrawCPP/parameters.cpp -o chromDrawCPP/parameters.o
chromDrawCPP/parameters.cpp:58:21: warning: extra tokens at end of #ifdef directive [-Wextra-tokens]
                                                #ifdef _WIN32 || _WIN64
                                                              ^
                                                              //
chromDrawCPP/parameters.cpp:123:15: warning: extra tokens at end of #ifdef directive [-Wextra-tokens]
#ifdef _WIN32 || _WIN64
              ^
              //
chromDrawCPP/parameters.cpp:135:15: warning: extra tokens at end of #ifdef directive [-Wextra-tokens]
#ifdef _WIN32 || _WIN64
              ^
              //
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c R_init_chromDraw.cpp -o R_init_chromDraw.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 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-3.2-bioc/meat/chromDraw.buildbin-libdir/chromDraw/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* 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.3.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgfortran.3.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"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libquadmath.0.dylib" "chromDraw.buildbin-libdir/chromDraw/libs//chromDraw.so"