PICS 1.5.0
Arnaud Droit , Xuekui Zhang , Raphael Gottardo
| Snapshot Date: 2011-02-24 11:26:35 -0800 (Thu, 24 Feb 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/PICS | | Last Changed Rev: 50725 / Revision: 53255 | | Last Changed Date: 2010-11-06 14:29:12 -0700 (Sat, 06 Nov 2010) |
| lamb2 | Linux (openSUSE 11.2) / 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 (10.6.4) / i386 | OK | OK | [ OK ] |
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --library=PICS.buildbin-libdir PICS_1.5.0.tar.gz'
>>>>>>>
* installing *source* package 'PICS' ...
checking for pkg-config... /usr/local/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/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -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/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -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:804: warning: suggest parentheses around comparison in operand of &
pics.c:964: warning: suggest parentheses around comparison in operand of &
pics.c:652: warning: unused variable 'k'
pics.c: In function 'ECM2':
pics.c:1010: warning: unused variable 'ee'
pics.c:1010: warning: unused variable 'ggR'
pics.c:1010: warning: unused variable 'ggF'
pics.c:1010: warning: unused variable 'aaR'
pics.c:1010: warning: unused variable 'aaF'
pics.c:1010: warning: unused variable 'etaDiff'
pics.c:1001: warning: unused variable 'k'
pics.c: In function 'BIC':
pics.c:1273: warning: unused variable 'k'
pics.c: In function 'getInfMat':
pics.c:1634: warning: unused variable 'PhiRw'
pics.c:1634: warning: unused variable 'PhiFw'
pics.c: In function 'mergePeak':
pics.c:1890: warning: unused variable 'j'
pics.c:1890: warning: unused variable 'i'
pics.c: In function 'BIC':
pics.c:1276: 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/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -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:248: warning: unused variable 'i'
segment.c: In function 'getSegL':
segment.c:1284: warning: unused variable 'j'
segment.c: In function 'getDensity':
segment.c:1461: warning: suggest parentheses around comparison in operand of &
segment.c:1462: warning: suggest parentheses around comparison in operand of &
segment.c:1463: warning: suggest parentheses around comparison in operand of &
segment.c:1464: warning: suggest parentheses around comparison in operand of &
segment.c:1465: warning: suggest parentheses around comparison in operand of &
segment.c:1466: warning: suggest parentheses around comparison in operand of &
segment.c:1467: warning: suggest parentheses around comparison in operand of &
segment.c:1409: warning: unused variable 'filter1'
segment.c:1408: 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 background.o 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-2.8-bioc/meat/PICS.buildbin-libdir/PICS/libs/i386
** R
** inst
** preparing package for lazy loading
Attaching package: 'IRanges'
The following object(s) are masked from 'package:base':
Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
pmin, pmin.int, rbind, rep.int, setdiff, table, union
Loading required package: Biostrings
in method for 'as.list' with signature '"AlignedRead"': no definition for class "AlignedRead"
in method for 'coerce' with signature '"AlignedRead","GenomeData"': no definition for class "AlignedRead"
Creating a new generic function for "density" in "PICS"
Creating a new generic function for "plot" in "PICS"
** help
*** installing help indices
** building package indices ...
** 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/2.13/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/2.13/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/2.13/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/2.13/Resources/lib/libreadline.dylib" "PICS.buildbin-libdir/PICS/libs/i386/PICS.so"
>>>>>>>
>>>>>>> INSTALLATION OF ppc LIBS WITH 'R_ARCH=/ppc R CMD INSTALL --preclean --library=PICS.buildbin-libdir --libs-only PICS_1.5.0.tar.gz'
>>>>>>>
* installing *source* package 'PICS' ...
checking for pkg-config... /usr/local/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 - ppc
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 -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 ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -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:804: warning: suggest parentheses around comparison in operand of &
pics.c:964: warning: suggest parentheses around comparison in operand of &
pics.c:652: warning: unused variable 'k'
pics.c: In function 'ECM2':
pics.c:1010: warning: unused variable 'ee'
pics.c:1010: warning: unused variable 'ggR'
pics.c:1010: warning: unused variable 'ggF'
pics.c:1010: warning: unused variable 'aaR'
pics.c:1010: warning: unused variable 'aaF'
pics.c:1010: warning: unused variable 'etaDiff'
pics.c:1001: warning: unused variable 'k'
pics.c: In function 'BIC':
pics.c:1273: warning: unused variable 'k'
pics.c: In function 'getInfMat':
pics.c:1634: warning: unused variable 'PhiRw'
pics.c:1634: warning: unused variable 'PhiFw'
pics.c: In function 'mergePeak':
pics.c:1890: warning: unused variable 'j'
pics.c:1890: warning: unused variable 'i'
pics.c: In function 'BIC':
pics.c:1276: 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 ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -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:248: warning: unused variable 'i'
segment.c: In function 'getSegL':
segment.c:1284: warning: unused variable 'j'
segment.c: In function 'getDensity':
segment.c:1461: warning: suggest parentheses around comparison in operand of &
segment.c:1462: warning: suggest parentheses around comparison in operand of &
segment.c:1463: warning: suggest parentheses around comparison in operand of &
segment.c:1464: warning: suggest parentheses around comparison in operand of &
segment.c:1465: warning: suggest parentheses around comparison in operand of &
segment.c:1466: warning: suggest parentheses around comparison in operand of &
segment.c:1467: warning: suggest parentheses around comparison in operand of &
segment.c:1409: warning: unused variable 'filter1'
segment.c:1408: warning: unused variable 'muFilter'
gcc -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o PICS.so background.o 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-2.8-bioc/meat/PICS.buildbin-libdir/PICS/libs/ppc
* DONE (PICS)
>>>>>>>
>>>>>>> FIXING LINKS FOR PICS.buildbin-libdir/PICS/libs/ppc/PICS.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" "PICS.buildbin-libdir/PICS/libs/ppc/PICS.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgfortran.2.dylib" "PICS.buildbin-libdir/PICS/libs/ppc/PICS.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" "PICS.buildbin-libdir/PICS/libs/ppc/PICS.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.dylib" "PICS.buildbin-libdir/PICS/libs/ppc/PICS.so"
>>>>>>>
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --library=PICS.buildbin-libdir --libs-only PICS_1.5.0.tar.gz'
>>>>>>>
* installing *source* package 'PICS' ...
checking for pkg-config... /usr/local/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/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -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/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -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:804: warning: suggest parentheses around comparison in operand of &
pics.c:964: warning: suggest parentheses around comparison in operand of &
pics.c:652: warning: unused variable 'k'
pics.c: In function 'ECM2':
pics.c:1010: warning: unused variable 'ee'
pics.c:1010: warning: unused variable 'ggR'
pics.c:1010: warning: unused variable 'ggF'
pics.c:1010: warning: unused variable 'aaR'
pics.c:1010: warning: unused variable 'aaF'
pics.c:1010: warning: unused variable 'etaDiff'
pics.c:1001: warning: unused variable 'k'
pics.c: In function 'BIC':
pics.c:1273: warning: unused variable 'k'
pics.c: In function 'getInfMat':
pics.c:1634: warning: unused variable 'PhiRw'
pics.c:1634: warning: unused variable 'PhiFw'
pics.c: In function 'mergePeak':
pics.c:1890: warning: unused variable 'j'
pics.c:1890: warning: unused variable 'i'
pics.c: In function 'BIC':
pics.c:1276: 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/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -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:248: warning: unused variable 'i'
segment.c: In function 'getSegL':
segment.c:1284: warning: unused variable 'j'
segment.c: In function 'getDensity':
segment.c:1461: warning: suggest parentheses around comparison in operand of &
segment.c:1462: warning: suggest parentheses around comparison in operand of &
segment.c:1463: warning: suggest parentheses around comparison in operand of &
segment.c:1464: warning: suggest parentheses around comparison in operand of &
segment.c:1465: warning: suggest parentheses around comparison in operand of &
segment.c:1466: warning: suggest parentheses around comparison in operand of &
segment.c:1467: warning: suggest parentheses around comparison in operand of &
segment.c:1409: warning: unused variable 'filter1'
segment.c:1408: 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 background.o 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-2.8-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/2.13/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/2.13/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/2.13/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/2.13/Resources/lib/libreadline.dylib" "PICS.buildbin-libdir/PICS/libs/x86_64/PICS.so"