BioC 2.12: CHECK report for RIPSeeker on george2

Package: RIPSeeker

Version: 1.0.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings RIPSeeker_1.0.0.tar.gz

StartedAt: 2013-10-09 04:33:42 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 04:41:34 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 472.0 seconds

RetCode: 0

Status:  OK

CheckDir: RIPSeeker.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/RIPSeeker.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 ‘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 ... [29s/29s] 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 ... [144s/176s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
mainSeek              27.525  0.020  31.718
disambiguateMultihits 23.421  0.032  24.822
selectBinSize         15.673  0.048  15.739
nbh                    8.396  0.016  11.336
plotStrandedCoverage   6.868  0.060   6.930
computeLogOdd          5.321  0.024   5.438
addDummyProb           5.241  0.040   5.558
nbh_init               5.237  0.004   5.621
mainSeekSingleChrom    5.097  0.012   5.309
combineRIP             4.748  0.032  21.346
binCount               4.532  0.028   6.101
* 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
  ‘/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
** testing if installed package can be loaded
* DONE (RIPSeeker)

name	user	system	elapsed
RIPSeeker-package	0.020	0.004	0.023
addDummyProb	5.241	0.040	5.558
addPseudoAlignment	1.876	0.008	2.167
annotateRIP	0.068	0.004	0.139
binCount	4.532	0.028	6.101
combineAlignGals	0.616	0.004	0.622
combineRIP	4.748	0.032	21.346
computeLogOdd	5.321	0.024	5.438
computeRPKM	0.024	0.000	0.024
disambiguateMultihits	23.421	0.032	24.822
empiricalFDR	0.036	0.000	0.035
evalBinSize	2.992	0.012	3.005
exportGRanges	0.036	0.000	0.037
galp2gal	1.181	0.004	1.184
getAlignGal	0.324	0.008	0.334
logScoreWithControl	0.044	0.000	0.042
logScoreWithoutControl	0.032	0.000	0.032
mainSeek	27.525	0.020	31.718
mainSeekSingleChrom	5.097	0.012	5.309
nbh.GRanges	0.008	0.000	0.005
nbh	8.396	0.016	11.336
nbh.integer	0.008	0.000	0.007
nbh_chk	0.020	0.004	0.033
nbh_em	0.828	0.012	0.942
nbh_gen	0.024	0.000	0.025
nbh_init	5.237	0.004	5.621
nbh_vit	0.808	0.004	0.811
nbm_chk	0.016	0.000	0.017
nbm_em	0.876	0.004	0.882
plotCoverage	4.460	0.060	4.523
plotStrandedCoverage	6.868	0.060	6.930
randindx	0.272	0.028	0.301
ripSeek	0.052	0.000	0.053
rulebaseRIPSeek	0.024	0.000	0.022
scoreMergedBins	0.060	0.000	0.058
seekRIP	0.040	0.000	0.043
selectBinSize	15.673	0.048	15.739
statdis	0.760	0.008	0.767
viewRIP	0.040	0.004	0.042