Package: RIPSeeker

Version: 0.99.9

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RIPSeeker_0.99.9.tar.gz

StartedAt: 2013-03-25 04:26:54 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 04:32:34 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 340.3 seconds

RetCode: 0

Status:  OK

CheckDir: RIPSeeker.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/RIPSeeker.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'RIPSeeker/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RIPSeeker' version '0.99.9'
* 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 ... [22s/23s] 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 ... [103s/118s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
mainSeek              16.680  0.405  17.102
disambiguateMultihits 15.865  0.507  16.792
selectBinSize          7.470  1.359   8.887
nbh                    6.283  0.184   6.476
nbh_init               5.411  0.095   5.512
plotStrandedCoverage   4.890  0.491   5.480
combineRIP             3.270  0.114  17.473
* 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
   'RIPSeeker.Rnw' 
** testing if installed package can be loaded
* DONE (RIPSeeker)

name	user	system	elapsed
RIPSeeker-package	0.007	0.007	0.013
addDummyProb	2.424	0.140	2.567
addPseudoAlignment	0.884	0.088	0.977
annotateRIP	0.205	0.025	0.231
binCount	2.732	0.187	2.925
combineAlignGals	0.736	0.071	0.810
combineRIP	3.270	0.114	17.473
computeLogOdd	4.385	0.165	4.595
computeRPKM	0.014	0.018	0.051
disambiguateMultihits	15.865	0.507	16.792
empiricalFDR	0.023	0.019	0.043
evalBinSize	2.682	0.199	2.895
exportGRanges	0.024	0.016	0.039
galp2gal	1.459	0.028	1.497
getAlignGal	0.468	0.051	0.521
logScoreWithControl	0.017	0.017	0.036
logScoreWithoutControl	0.014	0.015	0.030
mainSeek	16.680	0.405	17.102
mainSeekSingleChrom	4.803	0.183	4.997
nbh.GRanges	0.002	0.004	0.006
nbh	6.283	0.184	6.476
nbh.integer	0.003	0.005	0.008
nbh_chk	0.012	0.011	0.025
nbh_em	0.981	0.042	1.024
nbh_gen	0.014	0.009	0.023
nbh_init	5.411	0.095	5.512
nbh_vit	0.995	0.048	1.045
nbm_chk	0.008	0.012	0.019
nbm_em	1.093	0.100	1.195
plotCoverage	3.095	0.304	3.433
plotStrandedCoverage	4.890	0.491	5.480
randindx	0.351	0.051	0.411
ripSeek	0.021	0.021	0.043
rulebaseRIPSeek	0.012	0.013	0.026
scoreMergedBins	0.024	0.024	0.048
seekRIP	0.018	0.018	0.036
selectBinSize	7.470	1.359	8.887
statdis	0.626	0.037	0.663
viewRIP	0.012	0.016	0.028