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BioC 2.14: BUILD BIN report for GLAD on morelia

This page was generated on 2014-10-08 09:02:21 -0700 (Wed, 08 Oct 2014).

Package 350/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GLAD 2.28.1
Philippe Hupe
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/GLAD
Last Changed Rev: 89378 / Revision: 95116
Last Changed Date: 2014-04-22 17:32:41 -0700 (Tue, 22 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK [ OK ]

Summary

Package: GLAD
Version: 2.28.1
Command: rm -rf GLAD.buildbin-libdir && mkdir GLAD.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GLAD_2.28.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R GLAD.buildbin-libdir
StartedAt: 2014-10-08 02:56:46 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 02:56:57 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 10.2 seconds
RetCode: 0
Status:  OK 
PackageFile: GLAD_2.28.1.tgz
PackageFileSize: 855.8 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GLAD.buildbin-libdir && mkdir GLAD.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GLAD_2.28.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R GLAD.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=GLAD.buildbin-libdir GLAD_2.28.1.tar.gz'
>>>>>>> 

* installing *source* package ‘GLAD’ ...
checking for pkg-config... /usr/local/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
GSL has been found on the operating system
operating system: Darwin
configure: creating ./config.status
config.status: creating src/Makevars

src/Makevars file

PKG_LIBS = -L/usr/local/lib -lgsl -lgslcblas -lm  
PKG_CPPFLAGS += -DIS_MAC_OS

** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c BkpInfo.cpp -o BkpInfo.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c HaarSeg.cpp -o HaarSeg.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c MoveBkp.cpp -o MoveBkp.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c OutliersGNL.cpp -o OutliersGNL.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c chrBreakpoints.cpp -o chrBreakpoints.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c cutree.cpp -o cutree.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c daglad.cpp -o daglad.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c distance.cpp -o distance.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c filterBkp.cpp -o filterBkp.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c findCluster.cpp -o findCluster.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c glad-utils.cpp -o glad-utils.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c hclust.cpp -o hclust.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c laws.c -o laws.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c loopRemove.cpp -o loopRemove.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o GLAD.so BkpInfo.o HaarSeg.o MoveBkp.o OutliersGNL.o chrBreakpoints.o cutree.o daglad.o distance.o filterBkp.o findCluster.o glad-utils.o hclust.o laws.o loopRemove.o -L/usr/local/lib -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-bioc/meat/GLAD.buildbin-libdir/GLAD/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GLAD)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libgcc_s.1.dylib" "GLAD.buildbin-libdir/GLAD/libs//GLAD.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libgfortran.3.dylib" "GLAD.buildbin-libdir/GLAD/libs//GLAD.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libreadline.5.2.dylib" "GLAD.buildbin-libdir/GLAD/libs//GLAD.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libreadline.dylib" "GLAD.buildbin-libdir/GLAD/libs//GLAD.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libquadmath.0.dylib" "GLAD.buildbin-libdir/GLAD/libs//GLAD.so"