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Package 603/609HostnameOS / ArchBUILDCHECKBUILD BIN
xcms 1.34.0
Ralf Tautenhahn
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/xcms
Last Changed Rev: 70050 / Revision: 74773
Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK  OK [ OK ]

Summary

Package: xcms
Version: 1.34.0
Command: rm -rf xcms.buildbin-libdir && mkdir xcms.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh xcms_1.34.0.tar.gz /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R xcms.buildbin-libdir
StartedAt: 2013-03-25 02:11:37 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 02:12:24 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 46.6 seconds
RetCode: 0
Status:  OK 
PackageFile: xcms_1.34.0.tgz
PackageFileSize: 1.743 MiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=xcms.buildbin-libdir xcms_1.34.0.tar.gz'
>>>>>>> 

* installing *source* package 'xcms' ...
** libs
*** arch - i386
rm -f massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o util.o xcms.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
massifquant/xcms_massifquant.cpp: In function 'SEXPREC* massifquant(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
massifquant/xcms_massifquant.cpp:107: warning: deprecated conversion from string constant to 'char*'
massifquant/xcms_massifquant.cpp:107: warning: deprecated conversion from string constant to 'char*'
massifquant/xcms_massifquant.cpp:107: warning: deprecated conversion from string constant to 'char*'
massifquant/xcms_massifquant.cpp:107: warning: deprecated conversion from string constant to 'char*'
massifquant/xcms_massifquant.cpp:107: warning: deprecated conversion from string constant to 'char*'
massifquant/xcms_massifquant.cpp:107: warning: deprecated conversion from string constant to 'char*'
massifquant/xcms_massifquant.cpp:107: warning: deprecated conversion from string constant to 'char*'
massifquant/xcms_massifquant.cpp:116: warning: unused variable 'scanLength'
massifquant/xcms_massifquant.cpp:33: warning: unused variable 'vstcenter'
massifquant/xcms_massifquant.cpp:33: warning: unused variable 'vintenmax'
massifquant/xcms_massifquant.cpp:70: warning: unused variable 'maxScanNums'
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c massifquant/Tracker.cpp -o massifquant/Tracker.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c massifquant/SegProc.cpp -o massifquant/SegProc.o
massifquant/SegProc.cpp: In member function 'double SegProc::Rf_pt(double, double, int, int)':
massifquant/SegProc.cpp:361: warning: deprecated conversion from string constant to 'char*'
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c obiwarp/mat.cpp -o obiwarp/mat.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c obiwarp/vec.cpp -o obiwarp/vec.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o
obiwarp/xcms_dynprog.cpp: In member function 'void DynProg::score_mutual_info(VEC::MatF&, VEC::MatF&, VEC::MatF&, int)':
obiwarp/xcms_dynprog.cpp:732: warning: unused variable 'cols'
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c xcms_obiwarp.cpp -o xcms_obiwarp.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c fastMatch.c -o fastMatch.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c mzClust_hclust.c -o mzClust_hclust.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c mzROI.c -o mzROI.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c util.c -o util.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c xcms.c -o xcms.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o xcms.so massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o util.o xcms.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/xcms.buildbin-libdir/xcms/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'xcmsDirect.Rnw' 
   'xcmsInstall.Rnw' 
   'xcmsMSn.Rnw' 
   'xcmsPreprocess.Rnw' 
** testing if installed package can be loaded

* DONE (xcms)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgcc_s.1.dylib" "xcms.buildbin-libdir/xcms/libs/i386/xcms.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgfortran.2.dylib" "xcms.buildbin-libdir/xcms/libs/i386/xcms.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.5.2.dylib" "xcms.buildbin-libdir/xcms/libs/i386/xcms.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.dylib" "xcms.buildbin-libdir/xcms/libs/i386/xcms.so"


>>>>>>> 
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --no-multiarch --no-test-load --library=xcms.buildbin-libdir --libs-only xcms_1.34.0.tar.gz'
>>>>>>> 

* installing *source* package 'xcms' ...
** libs
*** arch - x86_64
rm -f massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o util.o xcms.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
massifquant/xcms_massifquant.cpp: In function 'SEXPREC* massifquant(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
massifquant/xcms_massifquant.cpp:107: warning: deprecated conversion from string constant to 'char*'
massifquant/xcms_massifquant.cpp:107: warning: deprecated conversion from string constant to 'char*'
massifquant/xcms_massifquant.cpp:107: warning: deprecated conversion from string constant to 'char*'
massifquant/xcms_massifquant.cpp:107: warning: deprecated conversion from string constant to 'char*'
massifquant/xcms_massifquant.cpp:107: warning: deprecated conversion from string constant to 'char*'
massifquant/xcms_massifquant.cpp:107: warning: deprecated conversion from string constant to 'char*'
massifquant/xcms_massifquant.cpp:107: warning: deprecated conversion from string constant to 'char*'
massifquant/xcms_massifquant.cpp:116: warning: unused variable 'scanLength'
massifquant/xcms_massifquant.cpp:33: warning: unused variable 'vstcenter'
massifquant/xcms_massifquant.cpp:33: warning: unused variable 'vintenmax'
massifquant/xcms_massifquant.cpp:70: warning: unused variable 'maxScanNums'
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c massifquant/Tracker.cpp -o massifquant/Tracker.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c massifquant/SegProc.cpp -o massifquant/SegProc.o
massifquant/SegProc.cpp: In member function 'double SegProc::Rf_pt(double, double, int, int)':
massifquant/SegProc.cpp:361: warning: deprecated conversion from string constant to 'char*'
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c obiwarp/mat.cpp -o obiwarp/mat.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c obiwarp/vec.cpp -o obiwarp/vec.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o
obiwarp/xcms_dynprog.cpp: In member function 'void DynProg::score_mutual_info(VEC::MatF&, VEC::MatF&, VEC::MatF&, int)':
obiwarp/xcms_dynprog.cpp:732: warning: unused variable 'cols'
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c xcms_obiwarp.cpp -o xcms_obiwarp.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c fastMatch.c -o fastMatch.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c mzClust_hclust.c -o mzClust_hclust.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c mzROI.c -o mzROI.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c util.c -o util.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c xcms.c -o xcms.o
g++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o xcms.so massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o util.o xcms.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/xcms.buildbin-libdir/xcms/libs/x86_64

* DONE (xcms)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgcc_s.1.dylib" "xcms.buildbin-libdir/xcms/libs/x86_64/xcms.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgfortran.2.dylib" "xcms.buildbin-libdir/xcms/libs/x86_64/xcms.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.5.2.dylib" "xcms.buildbin-libdir/xcms/libs/x86_64/xcms.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.dylib" "xcms.buildbin-libdir/xcms/libs/x86_64/xcms.so"