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 |
* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/PICS.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PICS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PICS' version '1.8.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'multicore'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'PICS' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File 'D:/biocbld/bbs-2.9-bioc/meat/PICS.buildbin-libdir/PICS/libs/i386/PICS.dll':
Found 'puts', possibly from 'printf' (C), 'puts' (C)
Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console. The detected symbols
are linked into the code but might come from libraries and not actually
be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... 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)