BioC 2.12: CHECK report for RIPSeeker on petty

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: 2013-10-08 23:42:42 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:50:24 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 462.3 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 3.0.1 (2013-05-16)
* 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 ... [27s/28s] 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 sizes of PDF files under 'inst/doc' ... 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 ... [136s/171s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
mainSeek              23.882  0.180  24.604
disambiguateMultihits 19.627  0.162  19.888
selectBinSize         11.919  0.826  15.983
nbh                    9.695  0.065  10.070
nbh_init               7.009  0.032   7.224
plotStrandedCoverage   6.115  0.229  10.362
combineRIP             5.798  0.124  19.003
mainSeekSingleChrom    5.605  0.069   6.014
computeLogOdd          5.396  0.078   5.698
addDummyProb           4.324  0.090   7.322
plotCoverage           3.958  0.157   5.499
binCount               3.978  0.094   5.407
* 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	0.010	0.004	0.030
addDummyProb	4.324	0.090	7.322
addPseudoAlignment	1.604	0.034	2.798
annotateRIP	0.041	0.009	0.087
binCount	3.978	0.094	5.407
combineAlignGals	1.267	0.058	1.903
combineRIP	5.798	0.124	19.003
computeLogOdd	5.396	0.078	5.698
computeRPKM	0.012	0.007	0.019
disambiguateMultihits	19.627	0.162	19.888
empiricalFDR	0.019	0.009	0.028
evalBinSize	2.587	0.073	2.684
exportGRanges	0.014	0.005	0.018
galp2gal	1.556	0.020	1.604
getAlignGal	0.489	0.028	0.522
logScoreWithControl	0.036	0.006	0.042
logScoreWithoutControl	0.023	0.005	0.029
mainSeek	23.882	0.180	24.604
mainSeekSingleChrom	5.605	0.069	6.014
nbh.GRanges	0.008	0.004	0.012
nbh	9.695	0.065	10.070
nbh.integer	0.006	0.004	0.009
nbh_chk	0.009	0.006	0.016
nbh_em	1.010	0.026	1.062
nbh_gen	0.014	0.004	0.017
nbh_init	7.009	0.032	7.224
nbh_vit	1.009	0.024	1.074
nbm_chk	0.010	0.007	0.018
nbm_em	0.982	0.016	1.033
plotCoverage	3.958	0.157	5.499
plotStrandedCoverage	6.115	0.229	10.362
randindx	0.365	0.039	0.739
ripSeek	0.025	0.014	0.042
rulebaseRIPSeek	0.012	0.009	0.022
scoreMergedBins	0.034	0.017	0.080
seekRIP	0.024	0.011	0.051
selectBinSize	11.919	0.826	15.983
statdis	1.021	0.025	1.608
viewRIP	0.023	0.012	0.057