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 |
install for i386
* installing *source* package 'PING' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
gcc -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/src/include -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"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/src/include -IC:/GSL/i386/include -O3 -Wall -std=gnu99 -mtune=core2 -c init.c -o init.o
gcc -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/src/include -IC:/GSL/i386/include -O3 -Wall -std=gnu99 -mtune=core2 -c ping.c -o ping.o
ping.c: In function 'fitModelAllk':
ping.c:142:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
ping.c: In function 'iterEM':
ping.c:637:25: warning: unused variable 'mu' [-Wunused-variable]
ping.c: In function 'ECM1':
ping.c:882:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
ping.c:1042:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
ping.c:730:15: warning: unused variable 'k' [-Wunused-variable]
ping.c: In function 'ECM1PE':
ping.c:1290:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
ping.c:1443:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
ping.c:1078:15: warning: unused variable 'k' [-Wunused-variable]
ping.c: In function 'ECM2':
ping.c:1506:66: warning: unused variable 'ee' [-Wunused-variable]
ping.c:1506:57: warning: unused variable 'ggR' [-Wunused-variable]
ping.c:1506:52: warning: unused variable 'ggF' [-Wunused-variable]
ping.c:1506:47: warning: unused variable 'aaR' [-Wunused-variable]
ping.c:1506:42: warning: unused variable 'aaF' [-Wunused-variable]
ping.c:1506:29: warning: unused variable 'etaDiff' [-Wunused-variable]
ping.c:1506:9: warning: variable 'chiSum' set but not used [-Wunused-but-set-variable]
ping.c:1497:15: warning: unused variable 'k' [-Wunused-variable]
ping.c: In function 'ECM2PE':
ping.c:1713:66: warning: unused variable 'ee' [-Wunused-variable]
ping.c:1713:57: warning: unused variable 'ggR' [-Wunused-variable]
ping.c:1713:52: warning: unused variable 'ggF' [-Wunused-variable]
ping.c:1713:47: warning: unused variable 'aaR' [-Wunused-variable]
ping.c:1713:42: warning: unused variable 'aaF' [-Wunused-variable]
ping.c:1713:29: warning: unused variable 'etaDiff' [-Wunused-variable]
ping.c:1704:15: warning: unused variable 'k' [-Wunused-variable]
ping.c: In function 'getInfMat':
ping.c:2557:80: warning: unused variable 'PhiRw' [-Wunused-variable]
ping.c:2557:73: warning: unused variable 'PhiFw' [-Wunused-variable]
ping.c: In function 'getInfMatPE':
ping.c:3007:59: warning: unused variable 'PhiFRw' [-Wunused-variable]
ping.c: In function 'mergePeak':
ping.c:3279:20: warning: variable 'tstatMax' set but not used [-Wunused-but-set-variable]
ping.c:3268:11: warning: unused variable 'j' [-Wunused-variable]
ping.c:3268:7: warning: unused variable 'i' [-Wunused-variable]
ping.c: In function 'BIC':
ping.c:2069:6: warning: 'penalty' may be used uninitialized in this function [-Wuninitialized]
ping.c: In function 'BICPE':
ping.c:2176:6: warning: 'penalty' may be used uninitialized in this function [-Wuninitialized]
ping.c: In function 'fitModelK':
ping.c:457:18: warning: 'firstFit' may be used uninitialized in this function [-Wuninitialized]
gcc -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/src/include -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:249:7: warning: unused variable 'i' [-Wunused-variable]
segment.c: In function 'segR2':
segment.c:838:13: warning: variable 'maxLoc' set but not used [-Wunused-but-set-variable]
segment.c:838:6: warning: variable 'minLoc' set but not used [-Wunused-but-set-variable]
segment.c: In function 'getSegL':
segment.c:1294:11: warning: unused variable 'j' [-Wunused-variable]
segment.c: In function 'getDensity':
segment.c:1469:9: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1470:11: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1471:11: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1472:11: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1473:11: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1423:19: warning: variable 'chr' set but not used [-Wunused-but-set-variable]
segment.c:1419:8: warning: unused variable 'filter1' [-Wunused-variable]
segment.c:1418:11: warning: unused variable 'muFilter' [-Wunused-variable]
gcc -shared -s -static-libgcc -o PING.dll tmp.def background.o init.o ping.o segment.o -lws2_32 -LC:/GSL/i386/lib -lgsl -lgslcblas -lm -LE:/biocbld/BBS-2˜1.10-/R/bin/i386 -lR
installing to E:/biocbld/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'
install for x64
* installing *source* package 'PING' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
gcc -m64 -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/src/include -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"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/src/include -IC:/GSL/x64/include -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c init.c -o init.o
gcc -m64 -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/src/include -IC:/GSL/x64/include -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c ping.c -o ping.o
ping.c: In function 'fitModelAllk':
ping.c:142:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
ping.c: In function 'iterEM':
ping.c:637:25: warning: unused variable 'mu' [-Wunused-variable]
ping.c: In function 'ECM1':
ping.c:882:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
ping.c:1042:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
ping.c:730:15: warning: unused variable 'k' [-Wunused-variable]
ping.c: In function 'ECM1PE':
ping.c:1290:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
ping.c:1443:3: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
ping.c:1078:15: warning: unused variable 'k' [-Wunused-variable]
ping.c: In function 'ECM2':
ping.c:1506:66: warning: unused variable 'ee' [-Wunused-variable]
ping.c:1506:57: warning: unused variable 'ggR' [-Wunused-variable]
ping.c:1506:52: warning: unused variable 'ggF' [-Wunused-variable]
ping.c:1506:47: warning: unused variable 'aaR' [-Wunused-variable]
ping.c:1506:42: warning: unused variable 'aaF' [-Wunused-variable]
ping.c:1506:29: warning: unused variable 'etaDiff' [-Wunused-variable]
ping.c:1506:9: warning: variable 'chiSum' set but not used [-Wunused-but-set-variable]
ping.c:1497:15: warning: unused variable 'k' [-Wunused-variable]
ping.c: In function 'ECM2PE':
ping.c:1713:66: warning: unused variable 'ee' [-Wunused-variable]
ping.c:1713:57: warning: unused variable 'ggR' [-Wunused-variable]
ping.c:1713:52: warning: unused variable 'ggF' [-Wunused-variable]
ping.c:1713:47: warning: unused variable 'aaR' [-Wunused-variable]
ping.c:1713:42: warning: unused variable 'aaF' [-Wunused-variable]
ping.c:1713:29: warning: unused variable 'etaDiff' [-Wunused-variable]
ping.c:1704:15: warning: unused variable 'k' [-Wunused-variable]
ping.c: In function 'getInfMat':
ping.c:2557:80: warning: unused variable 'PhiRw' [-Wunused-variable]
ping.c:2557:73: warning: unused variable 'PhiFw' [-Wunused-variable]
ping.c: In function 'getInfMatPE':
ping.c:3007:59: warning: unused variable 'PhiFRw' [-Wunused-variable]
ping.c: In function 'mergePeak':
ping.c:3279:20: warning: variable 'tstatMax' set but not used [-Wunused-but-set-variable]
ping.c:3268:11: warning: unused variable 'j' [-Wunused-variable]
ping.c:3268:7: warning: unused variable 'i' [-Wunused-variable]
ping.c: In function 'BIC':
ping.c:2069:6: warning: 'penalty' may be used uninitialized in this function [-Wuninitialized]
ping.c: In function 'BICPE':
ping.c:2176:6: warning: 'penalty' may be used uninitialized in this function [-Wuninitialized]
ping.c: In function 'fitModelK':
ping.c:457:18: warning: 'firstFit' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/src/include -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:249:7: warning: unused variable 'i' [-Wunused-variable]
segment.c: In function 'segR2':
segment.c:838:13: warning: variable 'maxLoc' set but not used [-Wunused-but-set-variable]
segment.c:838:6: warning: variable 'minLoc' set but not used [-Wunused-but-set-variable]
segment.c: In function 'getSegL':
segment.c:1294:11: warning: unused variable 'j' [-Wunused-variable]
segment.c: In function 'getDensity':
segment.c:1469:9: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1470:11: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1471:11: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1472:11: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1473:11: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
segment.c:1423:19: warning: variable 'chr' set but not used [-Wunused-but-set-variable]
segment.c:1419:8: warning: unused variable 'filter1' [-Wunused-variable]
segment.c:1418:11: warning: unused variable 'muFilter' [-Wunused-variable]
gcc -m64 -shared -s -static-libgcc -o PING.dll tmp.def background.o init.o ping.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 -LE:/biocbld/BBS-2~1.10-/R/bin/x64 -lR
installing to E:/biocbld/bbs-2.10-bioc/meat/PING.buildbin-libdir/PING/libs/x64
** testing if installed package can be loaded
Warning: replacing previous import 'show' when loading 'GenomeGraphs'
* MD5 sums
packaged installation of 'PING' as PING_1.0.0.zip
* DONE (PING)