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BioC 3.4: BUILD BIN report for Cardinal on morelia

This page was generated on 2017-04-15 16:26:14 -0400 (Sat, 15 Apr 2017).

Package 163/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Cardinal 1.6.0
Kylie A. Bemis
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/Cardinal
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: Cardinal
Version: 1.6.0
Command: rm -rf Cardinal.buildbin-libdir && mkdir Cardinal.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Cardinal_1.6.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Cardinal.buildbin-libdir
StartedAt: 2017-04-15 09:44:30 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 09:44:53 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 22.9 seconds
RetCode: 0
Status:  OK 
PackageFile: Cardinal_1.6.0.tgz
PackageFileSize: 2.484 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Cardinal.buildbin-libdir && mkdir Cardinal.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Cardinal_1.6.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Cardinal.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Cardinal.buildbin-libdir Cardinal_1.6.0.tar.gz'
>>>>>>> 

* installing *source* package ‘Cardinal’ ...
** 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 dynamicAlign.c -o dynamicAlign.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 fastmap.c -o fastmap.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 localMaxima.c -o localMaxima.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 pugixml.cpp -o pugixml.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 readAnalyze.cpp -o readAnalyze.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 readImzML.cpp -o readImzML.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 smooth.c -o smooth.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 spatial.c -o spatial.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.cpp -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 Cardinal.so dynamicAlign.o fastmap.o localMaxima.o pugixml.o readAnalyze.o readImzML.o smooth.o spatial.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.4-bioc/meat/Cardinal.buildbin-libdir/Cardinal/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 (Cardinal)


>>>>>>> 
>>>>>>> FIXING LINKS FOR Cardinal.buildbin-libdir/Cardinal/libs//Cardinal.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libgcc_s.1.dylib" "Cardinal.buildbin-libdir/Cardinal/libs//Cardinal.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libgfortran.3.dylib" "Cardinal.buildbin-libdir/Cardinal/libs//Cardinal.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libreadline.5.2.dylib" "Cardinal.buildbin-libdir/Cardinal/libs//Cardinal.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libreadline.dylib" "Cardinal.buildbin-libdir/Cardinal/libs//Cardinal.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libquadmath.0.dylib" "Cardinal.buildbin-libdir/Cardinal/libs//Cardinal.so"