Package: RIPSeeker

Version: 0.99.8

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings RIPSeeker_0.99.8.tar.gz

StartedAt: 2013-01-16 05:55:38 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 06:00:33 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 295.4 seconds

RetCode: 0

Status:  OK

CheckDir: RIPSeeker.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/RIPSeeker.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RIPSeeker/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RIPSeeker’ version ‘0.99.8’
* 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 ‘RIPSeeker’ can be installed ... 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 installed files from ‘inst/doc’ ... NOTE
The following files look like leftovers/mistakes:
  ‘SD.aux’, ‘nar.aux’
Please remove them from your package.
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
mainSeek              18.417  0.004  18.436
disambiguateMultihits 16.093  0.008  16.102
selectBinSize         10.325  0.040  10.369
nbh                    5.724  0.004   5.750
combineRIP             3.128  0.008   6.340
* 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

NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/RIPSeeker.Rcheck/00check.log’
for details.

* installing *source* package ‘RIPSeeker’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘RIPSeeker.Rnw’ 
** testing if installed package can be loaded

* DONE (RIPSeeker)

name	user	system	elapsed
RIPSeeker-package	0.008	0.004	0.011
addDummyProb	2.660	0.024	2.681
addPseudoAlignment	1.108	0.004	1.113
annotateRIP	0.048	0.004	0.053
binCount	3.469	0.004	3.472
combineAlignGals	0.908	0.008	0.920
combineRIP	3.128	0.008	6.340
computeLogOdd	3.908	0.004	3.915
computeRPKM	0.012	0.000	0.016
disambiguateMultihits	16.093	0.008	16.102
empiricalFDR	0.024	0.000	0.023
evalBinSize	1.888	0.016	1.902
exportGRanges	0.020	0.000	0.019
galp2gal	1.028	0.004	1.056
getAlignGal	0.284	0.004	0.286
logScoreWithControl	0.408	0.000	0.405
logScoreWithoutControl	0.016	0.000	0.015
mainSeek	18.417	0.004	18.436
mainSeekSingleChrom	3.525	0.004	3.547
nbh.GRanges	0.008	0.000	0.008
nbh	5.724	0.004	5.750
nbh.integer	0.004	0.000	0.002
nbh_chk	0.012	0.000	0.009
nbh_em	0.600	0.000	0.603
nbh_gen	0.016	0.000	0.017
nbh_init	4.032	0.000	4.037
nbh_vit	0.632	0.000	0.631
nbm_chk	0.012	0.000	0.013
nbm_em	0.692	0.008	0.698
plotCoverage	3.153	0.036	3.189
plotStrandedCoverage	4.404	0.048	4.451
randindx	0.228	0.016	0.240
ripSeek	0.032	0.000	0.031
rulebaseRIPSeek	0.016	0.000	0.016
scoreMergedBins	0.044	0.000	0.042
seekRIP	0.036	0.000	0.035
selectBinSize	10.325	0.040	10.369
statdis	0.580	0.012	0.593
viewRIP	0.024	0.000	0.023