PICS 1.7.0
Arnaud Droit , Xuekui Zhang , Raphael Gottardo
| Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/PICS | | Last Changed Rev: 54811 / Revision: 55359 | | Last Changed Date: 2011-04-13 18:45:05 -0700 (Wed, 13 Apr 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | [ WARNINGS ] | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | WARNINGS | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/PICS.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* 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 '1.7.0'
* checking package name space 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 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
* 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... NOTE
PICS: no visible global function definition for 'mclapply'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Functions/methods with usage in documentation object 'pics' but not in code:
pics
Functions/methods with usage in documentation object 'segReadsList' but not in code:
new
Functions/methods with usage in documentation object 'segReads' but not in code:
new
* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'segReadsList':
'new'
Objects in \usage without \alias in documentation object 'segReads':
'new'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 examples ... 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
WARNING: There were 2 warnings, see
'E:/biocbld/bbs-2.9-bioc/meat/PICS.Rcheck/00check.log'
for details
* installing *source* package 'PICS' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/gsl/include -O3 -Wall -std=gnu99 -c background.c -o background.o
background.c: In function 'background':
background.c:44:9: warning: statement with no effect
background.c:97:9: warning: statement with no effect
background.c:12:10: warning: unused variable 'length'
background.c:10:26: warning: unused variable 'countR'
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/gsl/include -O3 -Wall -std=gnu99 -c pics.c -o pics.o
pics.c: In function 'iterEM':
pics.c:581:25: warning: unused variable 'mu'
pics.c: In function 'ECM1':
pics.c:804:3: warning: suggest parentheses around comparison in operand of '&'
pics.c:964:3: warning: suggest parentheses around comparison in operand of '&'
pics.c:652:15: warning: unused variable 'k'
pics.c: In function 'ECM2':
pics.c:1010:66: warning: unused variable 'ee'
pics.c:1010:57: warning: unused variable 'ggR'
pics.c:1010:52: warning: unused variable 'ggF'
pics.c:1010:47: warning: unused variable 'aaR'
pics.c:1010:42: warning: unused variable 'aaF'
pics.c:1010:29: warning: unused variable 'etaDiff'
pics.c:1001:15: warning: unused variable 'k'
pics.c: In function 'BIC':
pics.c:1273:96: warning: unused variable 'k'
pics.c: In function 'getInfMat':
pics.c:1634:76: warning: unused variable 'PhiRw'
pics.c:1634:69: warning: unused variable 'PhiFw'
pics.c: In function 'mergePeak':
pics.c:1890:11: warning: unused variable 'j'
pics.c:1890:7: warning: unused variable 'i'
pics.c: In function 'BIC':
pics.c:1276:35: warning: 'penalty' may be used uninitialized in this function
pics.c: In function 'fitModelK':
pics.c:421:7: warning: 'ans' may be used uninitialized in this function
pics.c:421:18: warning: 'firstFit' may be used uninitialized in this function
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/gsl/include -O3 -Wall -std=gnu99 -c segment.c -o segment.o
segment.c: In function 'segReads':
segment.c:106:3: warning: suggest parentheses around comparison in operand of '&'
segment.c:97:45: warning: unused variable 'count'
segment.c: In function 'callRegions':
segment.c:248:7: warning: unused variable 'i'
segment.c: In function 'getSegL':
segment.c:1284:11: warning: unused variable 'j'
segment.c: In function 'getDensity':
segment.c:1461:9: warning: suggest parentheses around comparison in operand of '&'
segment.c:1462:11: warning: suggest parentheses around comparison in operand of '&'
segment.c:1463:11: warning: suggest parentheses around comparison in operand of '&'
segment.c:1464:11: warning: suggest parentheses around comparison in operand of '&'
segment.c:1465:11: warning: suggest parentheses around comparison in operand of '&'
segment.c:1466:11: warning: suggest parentheses around comparison in operand of '&'
segment.c:1467:11: warning: suggest parentheses around comparison in operand of '&'
segment.c:1409:8: warning: unused variable 'filter1'
segment.c:1408:11: warning: unused variable 'muFilter'
gcc -shared -s -static-libgcc -o PICS.dll tmp.def background.o pics.o segment.o -lws2_32 -LC:/gsl/bin -lgsl -lgslcblas -lm -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/PICS.Rcheck/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 ...
*** tangling vignette sources ...
'PICS.Rnw'
** testing if installed package can be loaded
* DONE (PICS)