BioC 2.13: CHECK report for RIPSeeker on perceval

Package: RIPSeeker

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RIPSeeker_1.2.0.tar.gz

StartedAt: 2014-04-05 03:56:22 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:03:07 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 404.7 seconds

RetCode: 0

Status:  OK

CheckDir: RIPSeeker.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/RIPSeeker.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.2.0’
* 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 ... [24s/25s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
‘library’ or ‘require’ call to ‘Rsamtools’ which was already attached by Depends.
  Please remove these calls from your code.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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:
  ‘nar.aux’, ‘SD.aux’
Please remove them from your package.
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘RIPSeeker.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [125s/153s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
mainSeek              21.863  0.195  23.630
disambiguateMultihits 19.053  0.146  19.650
selectBinSize         15.138  0.974  18.094
nbh                    6.408  0.075   7.253
plotStrandedCoverage   5.667  0.216   6.686
mainSeekSingleChrom    4.808  0.070   5.621
binCount               4.770  0.101   5.059
combineRIP             3.252  0.103  21.817
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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	0.420	0.005	0.509
addDummyProb	4.305	0.092	4.974
addPseudoAlignment	1.794	0.035	2.042
annotateRIP	0.077	0.014	0.094
binCount	4.770	0.101	5.059
combineAlignGals	1.478	0.040	1.561
combineRIP	3.252	0.103	21.817
computeLogOdd	4.590	0.063	4.857
computeRPKM	0.014	0.006	0.021
disambiguateMultihits	19.053	0.146	19.650
empiricalFDR	0.025	0.010	0.037
evalBinSize	2.765	0.107	2.970
exportGRanges	0.020	0.005	0.026
galp2gal	1.978	0.023	2.041
getAlignGal	0.687	0.025	0.720
logScoreWithControl	0.041	0.011	0.053
logScoreWithoutControl	0.030	0.010	0.039
mainSeek	21.863	0.195	23.630
mainSeekSingleChrom	4.808	0.070	5.621
nbh.GRanges	0.002	0.004	0.006
nbh	6.408	0.075	7.253
nbh.integer	0.009	0.004	0.012
nbh_chk	0.011	0.007	0.019
nbh_em	0.642	0.034	0.687
nbh_gen	0.021	0.006	0.027
nbh_init	4.272	0.036	4.801
nbh_vit	0.638	0.031	0.694
nbm_chk	0.011	0.008	0.019
nbm_em	0.645	0.023	0.679
plotCoverage	3.559	0.174	3.843
plotStrandedCoverage	5.667	0.216	6.686
randindx	0.260	0.052	0.377
ripSeek	0.046	0.021	0.074
rulebaseRIPSeek	0.025	0.014	0.043
scoreMergedBins	0.049	0.017	0.067
seekRIP	0.026	0.013	0.041
selectBinSize	15.138	0.974	18.094
statdis	0.601	0.034	0.657
viewRIP	0.025	0.018	0.045