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Package 186/444HostnameOS / ArchBUILDCHECKBUILD BIN
GLAD 2.13.5
Philippe Hupe
Snapshot Date: 2011-03-17 11:16:30 -0700 (Thu, 17 Mar 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GLAD
Last Changed Rev: 53302 / Revision: 53825
Last Changed Date: 2011-02-28 05:29:48 -0800 (Mon, 28 Feb 2011)
lamb1 Linux (openSUSE 11.3) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.6) / i386  OK  OK [ OK ]

Summary

Package: GLAD
Version: 2.13.5
Command: /Users/biocbuild/BBS/utils/build-universal.sh GLAD_2.13.5.tar.gz /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R GLAD.buildbin-libdir
StartedAt: 2011-03-17 17:59:38 -0700 (Thu, 17 Mar 2011)
EndedAt: 2011-03-17 18:00:08 -0700 (Thu, 17 Mar 2011)
EllapsedTime: 30.0 seconds
RetCode: 0
Status:  OK 
PackageFile: GLAD_2.13.5.tgz
PackageFileSize: 1.481 MiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --library=GLAD.buildbin-libdir GLAD_2.13.5.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
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c BkpInfo.cpp -o BkpInfo.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c HaarSeg.cpp -o HaarSeg.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c MoveBkp.cpp -o MoveBkp.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c OutliersGNL.cpp -o OutliersGNL.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c chrBreakpoints.cpp -o chrBreakpoints.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c cutree.cpp -o cutree.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c daglad.cpp -o daglad.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c distance.cpp -o distance.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c filterBkp.cpp -o filterBkp.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c findCluster.cpp -o findCluster.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c glad-utils.cpp -o glad-utils.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c hclust.cpp -o hclust.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c laws.c -o laws.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c loopRemove.cpp -o loopRemove.o
g++ -arch i386 -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-2.8-bioc/meat/GLAD.buildbin-libdir/GLAD/libs/i386
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (GLAD)


>>>>>>> 
>>>>>>> FIXING LINKS FOR GLAD.buildbin-libdir/GLAD/libs/i386/GLAD.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgcc_s.1.dylib" "GLAD.buildbin-libdir/GLAD/libs/i386/GLAD.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgfortran.2.dylib" "GLAD.buildbin-libdir/GLAD/libs/i386/GLAD.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.5.2.dylib" "GLAD.buildbin-libdir/GLAD/libs/i386/GLAD.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.dylib" "GLAD.buildbin-libdir/GLAD/libs/i386/GLAD.so"


>>>>>>> 
>>>>>>> INSTALLATION OF ppc LIBS WITH 'R_ARCH=/ppc R CMD INSTALL --preclean --library=GLAD.buildbin-libdir --libs-only GLAD_2.13.5.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
*** arch - ppc
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c BkpInfo.cpp -o BkpInfo.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c HaarSeg.cpp -o HaarSeg.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c MoveBkp.cpp -o MoveBkp.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c OutliersGNL.cpp -o OutliersGNL.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c chrBreakpoints.cpp -o chrBreakpoints.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c cutree.cpp -o cutree.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c daglad.cpp -o daglad.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c distance.cpp -o distance.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c filterBkp.cpp -o filterBkp.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c findCluster.cpp -o findCluster.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c glad-utils.cpp -o glad-utils.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c hclust.cpp -o hclust.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c laws.c -o laws.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c loopRemove.cpp -o loopRemove.o
g++ -arch ppc -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-2.8-bioc/meat/GLAD.buildbin-libdir/GLAD/libs/ppc

* DONE (GLAD)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgcc_s.1.dylib" "GLAD.buildbin-libdir/GLAD/libs/ppc/GLAD.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgfortran.2.dylib" "GLAD.buildbin-libdir/GLAD/libs/ppc/GLAD.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.5.2.dylib" "GLAD.buildbin-libdir/GLAD/libs/ppc/GLAD.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.dylib" "GLAD.buildbin-libdir/GLAD/libs/ppc/GLAD.so"


>>>>>>> 
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --library=GLAD.buildbin-libdir --libs-only GLAD_2.13.5.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
*** arch - x86_64
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c BkpInfo.cpp -o BkpInfo.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c HaarSeg.cpp -o HaarSeg.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c MoveBkp.cpp -o MoveBkp.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c OutliersGNL.cpp -o OutliersGNL.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c chrBreakpoints.cpp -o chrBreakpoints.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c cutree.cpp -o cutree.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c daglad.cpp -o daglad.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c distance.cpp -o distance.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c filterBkp.cpp -o filterBkp.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c findCluster.cpp -o findCluster.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c glad-utils.cpp -o glad-utils.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c hclust.cpp -o hclust.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c laws.c -o laws.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c loopRemove.cpp -o loopRemove.o
g++ -arch x86_64 -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-2.8-bioc/meat/GLAD.buildbin-libdir/GLAD/libs/x86_64

* DONE (GLAD)


>>>>>>> 
>>>>>>> FIXING LINKS FOR GLAD.buildbin-libdir/GLAD/libs/x86_64/GLAD.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgcc_s.1.dylib" "GLAD.buildbin-libdir/GLAD/libs/x86_64/GLAD.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgfortran.2.dylib" "GLAD.buildbin-libdir/GLAD/libs/x86_64/GLAD.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.5.2.dylib" "GLAD.buildbin-libdir/GLAD/libs/x86_64/GLAD.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.dylib" "GLAD.buildbin-libdir/GLAD/libs/x86_64/GLAD.so"