BioC 2.9: CHECK report for PICS on wilson2

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/PICS.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-15 r56138)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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
  ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/PICS.Rcheck/00check.log’
for details

* installing *source* package ‘PICS’ ...
checking for pkg-config... /usr/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
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -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 -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -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 -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -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 -std=gnu99 -shared -L/usr/local/lib64 -o PICS.so background.o pics.o segment.o -lgsl -lgslcblas -lm -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/PICS.Rcheck/PICS/libs
** 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 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

* DONE (PICS)

name	user	system	elapsed
makeRangedDataOutput	0	0	0
pics-class	0	0	0
picsError-class	0.000	0.000	0.001
picsFDR	0	0	0
picsList-class	0.004	0.000	0.001
segmentReads	3.932	0.036	3.970
setParaEM	0.000	0.000	0.001
setParaPrior	0	0	0

Summary

Command output