BioC 2.12: CHECK report for CSAR on george2

Package: CSAR

Version: 1.12.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings CSAR_1.12.0.tar.gz

StartedAt: 2013-10-09 01:11:03 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 01:15:51 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 287.7 seconds

RetCode: 0

Status:  OK

CheckDir: CSAR.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/CSAR.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 ‘CSAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CSAR’ version ‘1.12.0’
* 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 ‘CSAR’ can be installed ... [15s/15s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 ... [132s/133s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
CSAR-package           23.893  0.072  23.986
getThreshold           22.233  0.036  22.343
getPermutatedWinScores 21.641  0.040  21.904
permutatedWinScores    19.269  0.024  19.437
sigWin                  8.101  0.004   8.103
distance2Genes          7.708  0.008   7.778
genesWithPeaks          7.481  0.004   7.484
score2wig               6.436  0.004   6.463
ChIPseqScore            6.229  0.000   6.231
* 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 ‘CSAR’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c CSAR.c -o CSAR.o
gcc -std=gnu99 -shared -L/usr/local/lib -o CSAR.so CSAR.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-bioc/meat/CSAR.Rcheck/CSAR/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
No methods found in "GenomicRanges" for requests: unique
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "GenomicRanges" for requests: unique
* DONE (CSAR)

name	user	system	elapsed
CSAR-package	23.893	0.072	23.986
ChIPseqScore	6.229	0.000	6.231
distance2Genes	7.708	0.008	7.778
genesWithPeaks	7.481	0.004	7.484
getPermutatedWinScores	21.641	0.040	21.904
getThreshold	22.233	0.036	22.343
loadMappedReads	0.008	0.000	0.008
mappedReads2Nhits	2.461	0.000	2.479
permutatedWinScores	19.269	0.024	19.437
sampleSEP3_test	0.008	0.004	0.011
score2wig	6.436	0.004	6.463
sigWin	8.101	0.004	8.103