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Package 474/658HostnameOS / ArchBUILDCHECKBUILD BIN
PICS 2.1.01
Renan Sauteraud
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/PICS
Last Changed Rev: 74018 / Revision: 74774
Last Changed Date: 2013-03-07 10:03:41 -0800 (Thu, 07 Mar 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK [ OK ]

Summary

Package: PICS
Version: 2.1.01
Command: rm -rf PICS.buildbin-libdir && mkdir PICS.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh PICS_2.1.01.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R PICS.buildbin-libdir
StartedAt: 2013-03-25 05:36:53 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 05:37:17 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 24.1 seconds
RetCode: 0
Status:  OK 
PackageFile: PICS_2.1.01.tgz
PackageFileSize: 1.376 MiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=PICS.buildbin-libdir PICS_2.1.01.tar.gz'
>>>>>>> 

* installing *source* package 'PICS' ...
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
configure: creating ./config.status
config.status: creating src/Makevars
** 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 pics.c -o pics.o
pics.c: In function 'iterEM':
pics.c:581: warning: unused variable 'mu'
pics.c: In function 'ECM1':
pics.c:803: warning: suggest parentheses around comparison in operand of &
pics.c:963: warning: suggest parentheses around comparison in operand of &
pics.c:651: warning: unused variable 'k'
pics.c: In function 'ECM2':
pics.c:1009: warning: unused variable 'ee'
pics.c:1009: warning: unused variable 'ggR'
pics.c:1009: warning: unused variable 'ggF'
pics.c:1009: warning: unused variable 'aaR'
pics.c:1009: warning: unused variable 'aaF'
pics.c:1009: warning: unused variable 'etaDiff'
pics.c:1000: warning: unused variable 'k'
pics.c: In function 'BIC':
pics.c:1272: warning: unused variable 'k'
pics.c: In function 'getInfMat':
pics.c:1633: warning: unused variable 'PhiRw'
pics.c:1633: warning: unused variable 'PhiFw'
pics.c: In function 'mergePeak':
pics.c:1889: warning: unused variable 'j'
pics.c:1889: warning: unused variable 'i'
pics.c: In function 'BIC':
pics.c:1275: warning: 'penalty' may be used uninitialized in this function
pics.c: In function 'fitModelK':
pics.c:421: warning: 'firstFit' may be used uninitialized in this function
pics.c:421: warning: 'ans' 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 segment.c -o segment.o
segment.c: In function 'segReads':
segment.c:123: warning: suggest parentheses around comparison in operand of &
segment.c:114: warning: unused variable 'count'
segment.c: In function 'callRegions':
segment.c:308: warning: unused variable 'i'
segment.c: In function 'getSegL':
segment.c:1364: warning: unused variable 'j'
segment.c: In function 'getDensity':
segment.c:1543: warning: suggest parentheses around comparison in operand of &
segment.c:1544: warning: suggest parentheses around comparison in operand of &
segment.c:1545: warning: suggest parentheses around comparison in operand of &
segment.c:1546: warning: suggest parentheses around comparison in operand of &
segment.c:1547: warning: suggest parentheses around comparison in operand of &
segment.c:1548: warning: suggest parentheses around comparison in operand of &
segment.c:1549: warning: suggest parentheses around comparison in operand of &
segment.c:1490: warning: unused variable 'filter1'
segment.c:1489: warning: unused variable 'muFilter'
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o PICS.so pics.o segment.o -L/usr/local/lib -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/PICS.buildbin-libdir/PICS/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'PICS.Rnw' 
** testing if installed package can be loaded
* DONE (PICS)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgcc_s.1.dylib" "PICS.buildbin-libdir/PICS/libs/i386/PICS.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "PICS.buildbin-libdir/PICS/libs/i386/PICS.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.5.2.dylib" "PICS.buildbin-libdir/PICS/libs/i386/PICS.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "PICS.buildbin-libdir/PICS/libs/i386/PICS.so"


>>>>>>> 
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --no-multiarch --no-test-load --library=PICS.buildbin-libdir --libs-only PICS_2.1.01.tar.gz'
>>>>>>> 

* installing *source* package 'PICS' ...
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
configure: creating ./config.status
config.status: creating src/Makevars
** 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 pics.c -o pics.o
pics.c: In function 'iterEM':
pics.c:581: warning: unused variable 'mu'
pics.c: In function 'ECM1':
pics.c:803: warning: suggest parentheses around comparison in operand of &
pics.c:963: warning: suggest parentheses around comparison in operand of &
pics.c:651: warning: unused variable 'k'
pics.c: In function 'ECM2':
pics.c:1009: warning: unused variable 'ee'
pics.c:1009: warning: unused variable 'ggR'
pics.c:1009: warning: unused variable 'ggF'
pics.c:1009: warning: unused variable 'aaR'
pics.c:1009: warning: unused variable 'aaF'
pics.c:1009: warning: unused variable 'etaDiff'
pics.c:1000: warning: unused variable 'k'
pics.c: In function 'BIC':
pics.c:1272: warning: unused variable 'k'
pics.c: In function 'getInfMat':
pics.c:1633: warning: unused variable 'PhiRw'
pics.c:1633: warning: unused variable 'PhiFw'
pics.c: In function 'mergePeak':
pics.c:1889: warning: unused variable 'j'
pics.c:1889: warning: unused variable 'i'
pics.c: In function 'BIC':
pics.c:1275: warning: 'penalty' may be used uninitialized in this function
pics.c: In function 'fitModelK':
pics.c:421: warning: 'firstFit' may be used uninitialized in this function
pics.c:421: warning: 'ans' 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 segment.c -o segment.o
segment.c: In function 'segReads':
segment.c:123: warning: suggest parentheses around comparison in operand of &
segment.c:114: warning: unused variable 'count'
segment.c: In function 'callRegions':
segment.c:308: warning: unused variable 'i'
segment.c: In function 'getSegL':
segment.c:1364: warning: unused variable 'j'
segment.c: In function 'getDensity':
segment.c:1543: warning: suggest parentheses around comparison in operand of &
segment.c:1544: warning: suggest parentheses around comparison in operand of &
segment.c:1545: warning: suggest parentheses around comparison in operand of &
segment.c:1546: warning: suggest parentheses around comparison in operand of &
segment.c:1547: warning: suggest parentheses around comparison in operand of &
segment.c:1548: warning: suggest parentheses around comparison in operand of &
segment.c:1549: warning: suggest parentheses around comparison in operand of &
segment.c:1490: warning: unused variable 'filter1'
segment.c:1489: warning: unused variable 'muFilter'
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 PICS.so pics.o segment.o -L/usr/local/lib -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/PICS.buildbin-libdir/PICS/libs/x86_64
* DONE (PICS)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgcc_s.1.dylib" "PICS.buildbin-libdir/PICS/libs/x86_64/PICS.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "PICS.buildbin-libdir/PICS/libs/x86_64/PICS.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.5.2.dylib" "PICS.buildbin-libdir/PICS/libs/x86_64/PICS.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "PICS.buildbin-libdir/PICS/libs/x86_64/PICS.so"