PICS 1.8.0
Arnaud Droit
| Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/PICS | | Last Changed Rev: 59920 / Revision: 64395 | | Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
install for i386
* installing *source* package 'PICS' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/GSL/i386/include -O3 -Wall -std=gnu99 -mtune=core2 -c background.c -o background.o
background.c: In function 'background':
background.c:44:9: warning: statement with no effect [-Wunused-value]
background.c:97:9: warning: statement with no effect [-Wunused-value]
background.c:12:10: warning: unused variable 'length' [-Wunused-variable]
background.c:10:26: warning: unused variable 'countR' [-Wunused-variable]
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/GSL/i386/include -O3 -Wall -std=gnu99 -mtune=core2 -c pics.c -o pics.o
pics.c: In function 'iterEM':
pics.c:581:25: warning: unused variable 'mu' [-Wunused-variable]
pics.c: In function 'ECM1':
pics.c:804:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
pics.c:964:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
pics.c:652:15: warning: unused variable 'k' [-Wunused-variable]
pics.c: In function 'ECM2':
pics.c:1010:66: warning: unused variable 'ee' [-Wunused-variable]
pics.c:1010:57: warning: unused variable 'ggR' [-Wunused-variable]
pics.c:1010:52: warning: unused variable 'ggF' [-Wunused-variable]
pics.c:1010:47: warning: unused variable 'aaR' [-Wunused-variable]
pics.c:1010:42: warning: unused variable 'aaF' [-Wunused-variable]
pics.c:1010:29: warning: unused variable 'etaDiff' [-Wunused-variable]
pics.c:1010:9: warning: variable 'chiSum' set but not used [-Wunused-but-set-variable]
pics.c:1001:15: warning: unused variable 'k' [-Wunused-variable]
pics.c: In function 'BIC':
pics.c:1273:96: warning: unused variable 'k' [-Wunused-variable]
pics.c: In function 'getInfMat':
pics.c:1634:76: warning: unused variable 'PhiRw' [-Wunused-variable]
pics.c:1634:69: warning: unused variable 'PhiFw' [-Wunused-variable]
pics.c: In function 'mergePeak':
pics.c:1890:11: warning: unused variable 'j' [-Wunused-variable]
pics.c:1890:7: warning: unused variable 'i' [-Wunused-variable]
pics.c: In function 'BIC':
pics.c:1308:6: warning: 'penalty' may be used uninitialized in this function [-Wuninitialized]
pics.c: In function 'fitModelK':
pics.c:421:18: warning: 'firstFit' may be used uninitialized in this function [-Wuninitialized]
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/GSL/i386/include -O3 -Wall -std=gnu99 -mtune=core2 -c segment.c -o segment.o
segment.c: In function 'segReads':
segment.c:106:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:97:45: warning: unused variable 'count' [-Wunused-variable]
segment.c: In function 'callRegions':
segment.c:248:7: warning: unused variable 'i' [-Wunused-variable]
segment.c: In function 'segR2':
segment.c:828:13: warning: variable 'maxLoc' set but not used [-Wunused-but-set-variable]
segment.c:828:6: warning: variable 'minLoc' set but not used [-Wunused-but-set-variable]
segment.c: In function 'getSegL':
segment.c:1284:11: warning: unused variable 'j' [-Wunused-variable]
segment.c: In function 'getDensity':
segment.c:1461:9: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1462:11: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1463:11: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1464:11: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1465:11: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1466:11: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1467:11: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1413:19: warning: variable 'chr' set but not used [-Wunused-but-set-variable]
segment.c:1409:8: warning: unused variable 'filter1' [-Wunused-variable]
segment.c:1408:11: warning: unused variable 'muFilter' [-Wunused-variable]
gcc -shared -s -static-libgcc -o PICS.dll tmp.def background.o pics.o segment.o -lws2_32 -LC:/GSL/i386/lib -lgsl -lgslcblas -lm -LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/PICS.buildbin-libdir/PICS/libs/i386
** R
** inst
** preparing package for lazy loading
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 generic function for 'density' from package 'stats' in package 'PICS'
Creating a generic function for 'plot' from package 'graphics' in package 'PICS'
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
'PICS.Rnw'
** testing if installed package can be loaded
add DLL for x64
* installing *source* package 'PICS' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/GSL/x64/include -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c background.c -o background.o
background.c: In function 'background':
background.c:44:9: warning: statement with no effect [-Wunused-value]
background.c:97:9: warning: statement with no effect [-Wunused-value]
background.c:12:10: warning: unused variable 'length' [-Wunused-variable]
background.c:10:26: warning: unused variable 'countR' [-Wunused-variable]
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/GSL/x64/include -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c pics.c -o pics.o
pics.c: In function 'iterEM':
pics.c:581:25: warning: unused variable 'mu' [-Wunused-variable]
pics.c: In function 'ECM1':
pics.c:804:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
pics.c:964:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
pics.c:652:15: warning: unused variable 'k' [-Wunused-variable]
pics.c: In function 'ECM2':
pics.c:1010:66: warning: unused variable 'ee' [-Wunused-variable]
pics.c:1010:57: warning: unused variable 'ggR' [-Wunused-variable]
pics.c:1010:52: warning: unused variable 'ggF' [-Wunused-variable]
pics.c:1010:47: warning: unused variable 'aaR' [-Wunused-variable]
pics.c:1010:42: warning: unused variable 'aaF' [-Wunused-variable]
pics.c:1010:29: warning: unused variable 'etaDiff' [-Wunused-variable]
pics.c:1010:9: warning: variable 'chiSum' set but not used [-Wunused-but-set-variable]
pics.c:1001:15: warning: unused variable 'k' [-Wunused-variable]
pics.c: In function 'BIC':
pics.c:1273:96: warning: unused variable 'k' [-Wunused-variable]
pics.c: In function 'getInfMat':
pics.c:1634:76: warning: unused variable 'PhiRw' [-Wunused-variable]
pics.c:1634:69: warning: unused variable 'PhiFw' [-Wunused-variable]
pics.c: In function 'mergePeak':
pics.c:1890:11: warning: unused variable 'j' [-Wunused-variable]
pics.c:1890:7: warning: unused variable 'i' [-Wunused-variable]
pics.c: In function 'BIC':
pics.c:1308:6: warning: 'penalty' may be used uninitialized in this function [-Wuninitialized]
pics.c: In function 'fitModelK':
pics.c:421:18: warning: 'firstFit' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/GSL/x64/include -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c segment.c -o segment.o
segment.c: In function 'segReads':
segment.c:106:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:97:45: warning: unused variable 'count' [-Wunused-variable]
segment.c: In function 'callRegions':
segment.c:248:7: warning: unused variable 'i' [-Wunused-variable]
segment.c: In function 'segR2':
segment.c:828:13: warning: variable 'maxLoc' set but not used [-Wunused-but-set-variable]
segment.c:828:6: warning: variable 'minLoc' set but not used [-Wunused-but-set-variable]
segment.c: In function 'getSegL':
segment.c:1284:11: warning: unused variable 'j' [-Wunused-variable]
segment.c: In function 'getDensity':
segment.c:1461:9: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1462:11: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1463:11: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1464:11: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1465:11: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1466:11: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1467:11: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1413:19: warning: variable 'chr' set but not used [-Wunused-but-set-variable]
segment.c:1409:8: warning: unused variable 'filter1' [-Wunused-variable]
segment.c:1408:11: warning: unused variable 'muFilter' [-Wunused-variable]
gcc -m64 -shared -s -static-libgcc -o PICS.dll tmp.def background.o pics.o segment.o -lws2_32 -LC:/GSL/x64/lib -lgsl -lgslcblas -lm -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/PICS.buildbin-libdir/PICS/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PICS' as PICS_1.8.0.zip
* DONE (PICS)