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Package 353/609HostnameOS / ArchBUILDCHECKBUILD BIN
MANOR 1.30.0
Pierre Neuvial
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/MANOR
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: MANOR
Version: 1.30.0
Command: rm -rf MANOR.buildbin-libdir && mkdir MANOR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh MANOR_1.30.0.tar.gz /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R MANOR.buildbin-libdir
StartedAt: 2013-03-25 01:57:21 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 01:57:30 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 9.1 seconds
RetCode: 0
Status:  OK 
PackageFile: MANOR_1.30.0.tgz
PackageFileSize: 1017 KiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=MANOR.buildbin-libdir MANOR_1.30.0.tar.gz'
>>>>>>> 

* installing *source* package 'MANOR' ...
** libs
*** arch - i386
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 Rnem_arg.c -o Rnem_arg.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 Rnem_exe.c -o Rnem_exe.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 exememo.c -o exememo.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 lib_io.c -o lib_io.o
lib_io.c: In function 'CountLinesColumns':
lib_io.c:354: warning: 'mincols' may be used uninitialized in this function
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 nem_alg.c -o nem_alg.o
nem_alg.c:85:1: warning: "MAXFLOAT" redefined
In file included from /usr/include/math.h:28,
                 from nem_alg.c:73:
/usr/include/architecture/i386/math.h:542:1: warning: this is the location of the previous definition
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 nem_hlp.c -o nem_hlp.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 nem_mod.c -o nem_mod.o
nem_mod.c:51:1: warning: "MAXFLOAT" redefined
In file included from /usr/include/math.h:28,
                 from nem_mod.c:39:
/usr/include/architecture/i386/math.h:542:1: warning: this is the location of the previous definition
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 nem_nei.c -o nem_nei.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 nem_rnd.c -o nem_rnd.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 nem_ver.c -o nem_ver.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o MANOR.so Rnem_arg.o Rnem_exe.o exememo.o lib_io.o nem_alg.o nem_hlp.o nem_mod.o nem_nei.o nem_rnd.o nem_ver.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/MANOR.buildbin-libdir/MANOR/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'MANOR.Rnw' 
** testing if installed package can be loaded

* DONE (MANOR)


>>>>>>> 
>>>>>>> FIXING LINKS FOR MANOR.buildbin-libdir/MANOR/libs/i386/MANOR.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" "MANOR.buildbin-libdir/MANOR/libs/i386/MANOR.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgfortran.2.dylib" "MANOR.buildbin-libdir/MANOR/libs/i386/MANOR.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" "MANOR.buildbin-libdir/MANOR/libs/i386/MANOR.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.dylib" "MANOR.buildbin-libdir/MANOR/libs/i386/MANOR.so"


>>>>>>> 
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --no-multiarch --no-test-load --library=MANOR.buildbin-libdir --libs-only MANOR_1.30.0.tar.gz'
>>>>>>> 

* installing *source* package 'MANOR' ...
** libs
*** arch - x86_64
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 Rnem_arg.c -o Rnem_arg.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 Rnem_exe.c -o Rnem_exe.o
Rnem_exe.c: In function 'MakeErrinfo':
Rnem_exe.c:216: warning: cast from pointer to integer of different size
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 exememo.c -o exememo.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 lib_io.c -o lib_io.o
lib_io.c: In function 'CountLinesColumns':
lib_io.c:354: warning: 'mincols' may be used uninitialized in this function
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 nem_alg.c -o nem_alg.o
nem_alg.c:85:1: warning: "MAXFLOAT" redefined
In file included from /usr/include/math.h:28,
                 from nem_alg.c:73:
/usr/include/architecture/i386/math.h:542:1: warning: this is the location of the previous definition
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 nem_hlp.c -o nem_hlp.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 nem_mod.c -o nem_mod.o
nem_mod.c:51:1: warning: "MAXFLOAT" redefined
In file included from /usr/include/math.h:28,
                 from nem_mod.c:39:
/usr/include/architecture/i386/math.h:542:1: warning: this is the location of the previous definition
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 nem_nei.c -o nem_nei.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 nem_rnd.c -o nem_rnd.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 nem_ver.c -o nem_ver.o
gcc -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o MANOR.so Rnem_arg.o Rnem_exe.o exememo.o lib_io.o nem_alg.o nem_hlp.o nem_mod.o nem_nei.o nem_rnd.o nem_ver.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/MANOR.buildbin-libdir/MANOR/libs/x86_64

* DONE (MANOR)


>>>>>>> 
>>>>>>> FIXING LINKS FOR MANOR.buildbin-libdir/MANOR/libs/x86_64/MANOR.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" "MANOR.buildbin-libdir/MANOR/libs/x86_64/MANOR.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgfortran.2.dylib" "MANOR.buildbin-libdir/MANOR/libs/x86_64/MANOR.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" "MANOR.buildbin-libdir/MANOR/libs/x86_64/MANOR.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.dylib" "MANOR.buildbin-libdir/MANOR/libs/x86_64/MANOR.so"