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Package 404/553HostnameOS / ArchBUILDCHECKBUILD BIN
PING 1.0.0
Xuekui Zhang
Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/PING
Last Changed Rev: 64678 / Revision: 69725
Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012)
lamb2 Linux (openSUSE 11.4) / 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: PING
Version: 1.0.0
Command: rm -rf PING.buildbin-libdir && mkdir PING.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh PING_1.0.0.tar.gz /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R PING.buildbin-libdir
StartedAt: 2012-09-24 02:23:52 -0700 (Mon, 24 Sep 2012)
EndedAt: 2012-09-24 02:24:30 -0700 (Mon, 24 Sep 2012)
EllapsedTime: 37.2 seconds
RetCode: 0
Status:  OK 
PackageFile: PING_1.0.0.tgz
PackageFileSize: 1.124 MiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=PING.buildbin-libdir PING_1.0.0.tar.gz'
>>>>>>> 

* installing *source* package 'PING' ...
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/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c background.c -o background.o
background.c: In function 'background':
background.c:44: warning: statement with no effect
background.c:97: warning: statement with no effect
background.c:12: warning: unused variable 'length'
background.c:10: warning: unused variable 'countR'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c init.c -o init.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c ping.c -o ping.o
ping.c: In function 'fitModelAllk':
ping.c:142: warning: suggest parentheses around comparison in operand of &
ping.c: In function 'iterEM':
ping.c:637: warning: unused variable 'mu'
ping.c: In function 'ECM1':
ping.c:882: warning: suggest parentheses around comparison in operand of &
ping.c:1042: warning: suggest parentheses around comparison in operand of &
ping.c:730: warning: unused variable 'k'
ping.c: In function 'ECM1PE':
ping.c:1290: warning: suggest parentheses around comparison in operand of &
ping.c:1443: warning: suggest parentheses around comparison in operand of &
ping.c:1078: warning: unused variable 'k'
ping.c: In function 'ECM2':
ping.c:1506: warning: unused variable 'ee'
ping.c:1506: warning: unused variable 'ggR'
ping.c:1506: warning: unused variable 'ggF'
ping.c:1506: warning: unused variable 'aaR'
ping.c:1506: warning: unused variable 'aaF'
ping.c:1506: warning: unused variable 'etaDiff'
ping.c:1497: warning: unused variable 'k'
ping.c: In function 'ECM2PE':
ping.c:1713: warning: unused variable 'ee'
ping.c:1713: warning: unused variable 'ggR'
ping.c:1713: warning: unused variable 'ggF'
ping.c:1713: warning: unused variable 'aaR'
ping.c:1713: warning: unused variable 'aaF'
ping.c:1713: warning: unused variable 'etaDiff'
ping.c:1704: warning: unused variable 'k'
ping.c: In function 'getInfMat':
ping.c:2557: warning: unused variable 'PhiRw'
ping.c:2557: warning: unused variable 'PhiFw'
ping.c: In function 'getInfMatPE':
ping.c:3007: warning: unused variable 'PhiFRw'
ping.c: In function 'mergePeak':
ping.c:3268: warning: unused variable 'j'
ping.c:3268: warning: unused variable 'i'
ping.c: In function 'BICPE':
ping.c:2133: warning: 'penalty' may be used uninitialized in this function
ping.c: In function 'BIC':
ping.c:2026: warning: 'penalty' may be used uninitialized in this function
ping.c: In function 'fitModelK':
ping.c:457: warning: 'firstFit' may be used uninitialized in this function
ping.c:457: warning: 'ans' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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:106: warning: suggest parentheses around comparison in operand of &
segment.c:97: warning: unused variable 'count'
segment.c: In function 'callRegions':
segment.c:249: warning: unused variable 'i'
segment.c: In function 'getSegL':
segment.c:1294: warning: unused variable 'j'
segment.c: In function 'getDensity':
segment.c:1469: warning: suggest parentheses around comparison in operand of &
segment.c:1470: warning: suggest parentheses around comparison in operand of &
segment.c:1471: warning: suggest parentheses around comparison in operand of &
segment.c:1472: warning: suggest parentheses around comparison in operand of &
segment.c:1473: warning: suggest parentheses around comparison in operand of &
segment.c:1419: warning: unused variable 'filter1'
segment.c:1418: 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 PING.so background.o init.o ping.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-2.10-bioc/meat/PING.buildbin-libdir/PING/libs/i386
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import 'show' when loading 'GenomeGraphs'
Creating a new generic function for 'map' in package 'PING'
Creating a generic function for 'plot' from package 'graphics' in package 'PING'
** help
*** installing help indices
** building package indices
** installing vignettes
   'PING.Rnw' 
** testing if installed package can be loaded
Warning: replacing previous import 'show' when loading 'GenomeGraphs'

* DONE (PING)


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


>>>>>>> 
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --no-multiarch --no-test-load --library=PING.buildbin-libdir --libs-only PING_1.0.0.tar.gz'
>>>>>>> 

* installing *source* package 'PING' ...
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/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c background.c -o background.o
background.c: In function 'background':
background.c:44: warning: statement with no effect
background.c:97: warning: statement with no effect
background.c:12: warning: unused variable 'length'
background.c:10: warning: unused variable 'countR'
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c init.c -o init.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c ping.c -o ping.o
ping.c: In function 'fitModelAllk':
ping.c:142: warning: suggest parentheses around comparison in operand of &
ping.c: In function 'iterEM':
ping.c:637: warning: unused variable 'mu'
ping.c: In function 'ECM1':
ping.c:882: warning: suggest parentheses around comparison in operand of &
ping.c:1042: warning: suggest parentheses around comparison in operand of &
ping.c:730: warning: unused variable 'k'
ping.c: In function 'ECM1PE':
ping.c:1290: warning: suggest parentheses around comparison in operand of &
ping.c:1443: warning: suggest parentheses around comparison in operand of &
ping.c:1078: warning: unused variable 'k'
ping.c: In function 'ECM2':
ping.c:1506: warning: unused variable 'ee'
ping.c:1506: warning: unused variable 'ggR'
ping.c:1506: warning: unused variable 'ggF'
ping.c:1506: warning: unused variable 'aaR'
ping.c:1506: warning: unused variable 'aaF'
ping.c:1506: warning: unused variable 'etaDiff'
ping.c:1497: warning: unused variable 'k'
ping.c: In function 'ECM2PE':
ping.c:1713: warning: unused variable 'ee'
ping.c:1713: warning: unused variable 'ggR'
ping.c:1713: warning: unused variable 'ggF'
ping.c:1713: warning: unused variable 'aaR'
ping.c:1713: warning: unused variable 'aaF'
ping.c:1713: warning: unused variable 'etaDiff'
ping.c:1704: warning: unused variable 'k'
ping.c: In function 'getInfMat':
ping.c:2557: warning: unused variable 'PhiRw'
ping.c:2557: warning: unused variable 'PhiFw'
ping.c: In function 'getInfMatPE':
ping.c:3007: warning: unused variable 'PhiFRw'
ping.c: In function 'mergePeak':
ping.c:3268: warning: unused variable 'j'
ping.c:3268: warning: unused variable 'i'
ping.c: In function 'BICPE':
ping.c:2133: warning: 'penalty' may be used uninitialized in this function
ping.c: In function 'BIC':
ping.c:2026: warning: 'penalty' may be used uninitialized in this function
ping.c: In function 'fitModelK':
ping.c:457: warning: 'firstFit' may be used uninitialized in this function
ping.c:457: warning: 'ans' may be used uninitialized in this function
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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:106: warning: suggest parentheses around comparison in operand of &
segment.c:97: warning: unused variable 'count'
segment.c: In function 'callRegions':
segment.c:249: warning: unused variable 'i'
segment.c: In function 'getSegL':
segment.c:1294: warning: unused variable 'j'
segment.c: In function 'getDensity':
segment.c:1469: warning: suggest parentheses around comparison in operand of &
segment.c:1470: warning: suggest parentheses around comparison in operand of &
segment.c:1471: warning: suggest parentheses around comparison in operand of &
segment.c:1472: warning: suggest parentheses around comparison in operand of &
segment.c:1473: warning: suggest parentheses around comparison in operand of &
segment.c:1419: warning: unused variable 'filter1'
segment.c:1418: 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 PING.so background.o init.o ping.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-2.10-bioc/meat/PING.buildbin-libdir/PING/libs/x86_64

* DONE (PING)


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