Package: RIPSeeker

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RIPSeeker_1.0.0.tar.gz

StartedAt: 2013-05-01 10:18:44 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 10:24:56 -0700 (Wed, 01 May 2013)

EllapsedTime: 372.5 seconds

RetCode: 0

Status:  OK

CheckDir: RIPSeeker.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/RIPSeeker.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'RIPSeeker/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RIPSeeker' version '1.0.0'
* 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 'RIPSeeker' can be installed ... [23s/24s] 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 ... [117s/133s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
mainSeek              20.801  0.200  21.646
disambiguateMultihits 17.287  0.200  18.094
selectBinSize         11.085  0.950  12.263
nbh                    6.805  0.071   7.153
plotStrandedCoverage   5.147  0.257   5.661
nbh_init               4.989  0.030   5.167
mainSeekSingleChrom    4.625  0.082   5.019
combineRIP             4.432  0.120  17.018
* 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
  '/Users/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
** testing if installed package can be loaded
* DONE (RIPSeeker)

name	user	system	elapsed
RIPSeeker-package	0.315	0.006	0.322
addDummyProb	3.613	0.099	3.758
addPseudoAlignment	0.971	0.053	1.054
annotateRIP	0.065	0.004	0.079
binCount	3.840	0.098	4.323
combineAlignGals	0.670	0.052	0.789
combineRIP	4.432	0.120	17.018
computeLogOdd	4.504	0.080	4.663
computeRPKM	0.013	0.009	0.024
disambiguateMultihits	17.287	0.200	18.094
empiricalFDR	0.022	0.010	0.032
evalBinSize	2.646	0.089	2.847
exportGRanges	0.013	0.007	0.019
galp2gal	1.221	0.022	1.271
getAlignGal	0.422	0.027	0.451
logScoreWithControl	0.036	0.010	0.046
logScoreWithoutControl	0.027	0.007	0.033
mainSeek	20.801	0.200	21.646
mainSeekSingleChrom	4.625	0.082	5.019
nbh.GRanges	0.008	0.004	0.013
nbh	6.805	0.071	7.153
nbh.integer	0.010	0.004	0.015
nbh_chk	0.010	0.006	0.020
nbh_em	0.725	0.025	0.761
nbh_gen	0.018	0.004	0.022
nbh_init	4.989	0.030	5.167
nbh_vit	0.719	0.026	0.753
nbm_chk	0.010	0.005	0.022
nbm_em	0.804	0.019	0.842
plotCoverage	3.476	0.182	3.786
plotStrandedCoverage	5.147	0.257	5.661
randindx	0.334	0.044	0.400
ripSeek	0.032	0.016	0.047
rulebaseRIPSeek	0.021	0.009	0.032
scoreMergedBins	0.047	0.018	0.065
seekRIP	0.033	0.012	0.045
selectBinSize	11.085	0.950	12.263
statdis	0.720	0.033	0.762
viewRIP	0.016	0.013	0.029