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: 2013-03-24 09:44:10 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 09:50:23 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 373.0 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 beta (2013-03-21 r62346)
* 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 '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 ... [24s/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 ... [116s/131s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
mainSeek              20.858  0.191  21.317
disambiguateMultihits 18.067  0.190  18.563
selectBinSize         10.964  0.977  12.477
nbh                    7.046  0.070   7.207
nbh_init               5.192  0.034   5.312
plotStrandedCoverage   4.787  0.274   5.204
combineRIP             4.275  0.104  15.786
* 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	0.012	0.005	0.017
addDummyProb	3.644	0.109	3.822
addPseudoAlignment	1.309	0.032	1.384
annotateRIP	0.041	0.014	0.054
binCount	3.599	0.112	3.874
combineAlignGals	0.637	0.057	0.764
combineRIP	4.275	0.104	15.786
computeLogOdd	4.649	0.062	4.964
computeRPKM	0.015	0.010	0.026
disambiguateMultihits	18.067	0.190	18.563
empiricalFDR	0.020	0.011	0.030
evalBinSize	2.224	0.093	2.335
exportGRanges	0.012	0.008	0.020
galp2gal	1.213	0.024	1.283
getAlignGal	0.758	0.035	0.798
logScoreWithControl	0.023	0.017	0.041
logScoreWithoutControl	0.014	0.011	0.024
mainSeek	20.858	0.191	21.317
mainSeekSingleChrom	4.740	0.087	4.889
nbh.GRanges	0.002	0.004	0.007
nbh	7.046	0.070	7.207
nbh.integer	0.002	0.003	0.006
nbh_chk	0.010	0.007	0.017
nbh_em	0.759	0.028	0.790
nbh_gen	0.012	0.006	0.018
nbh_init	5.192	0.034	5.312
nbh_vit	0.777	0.032	0.811
nbm_chk	0.012	0.009	0.021
nbm_em	1.221	0.040	1.270
plotCoverage	3.095	0.190	3.362
plotStrandedCoverage	4.787	0.274	5.204
randindx	0.339	0.055	0.417
ripSeek	0.027	0.021	0.050
rulebaseRIPSeek	0.016	0.014	0.030
scoreMergedBins	0.035	0.024	0.059
seekRIP	0.026	0.016	0.043
selectBinSize	10.964	0.977	12.477
statdis	0.774	0.038	0.825
viewRIP	0.017	0.016	0.033