BioC 2.12: CHECK report for ChIPseqR on george2

Package: ChIPseqR

Version: 1.14.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings ChIPseqR_1.14.0.tar.gz

StartedAt: 2013-10-09 00:50:44 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 00:59:57 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 552.9 seconds

RetCode: 0

Status:  OK

CheckDir: ChIPseqR.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/ChIPseqR.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPseqR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPseqR’ version ‘1.14.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ChIPseqR’ can be installed ... [37s/42s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 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 use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [155s/165s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
alignFeature       36.062  1.376  39.010
BindScore          36.102  0.336  38.689
simpleNucCall      21.349  0.064  21.973
callBindingSites   21.270  0.076  24.464
RLEBindScore-class 19.637  0.064  20.786
* 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

* installing *source* package ‘ChIPseqR’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c startScore.c -o startScore.o
startScore.c: In function ‘_ratioStat_pois’:
startScore.c:66:15: warning: unused variable ‘tmp_stat’ [-Wunused-variable]
gcc -std=gnu99 -shared -L/usr/local/lib -o ChIPseqR.so startScore.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-bioc/meat/ChIPseqR.Rcheck/ChIPseqR/libs
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘image’ when loading ‘graphics’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘image’ when loading ‘graphics’
* DONE (ChIPseqR)

name	user	system	elapsed
BindScore	36.102	0.336	38.689
ChIPseqR-package	0.000	0.004	0.004
RLEBindScore-class	19.637	0.064	20.786
RLEReadCounts-class	0.036	0.000	0.036
ReadCounts	0.052	0.000	0.053
alignFeature	36.062	1.376	39.010
callBindingSites	21.270	0.076	24.464
pos2gff	0.048	0.000	0.048
simpleNucCall	21.349	0.064	21.973
strandPileup	0.820	0.008	0.829
windowCounts	0.080	0.000	0.079