BioC 2.14: CHECK report for RIPSeeker on petty

Package: RIPSeeker

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RIPSeeker_1.4.0.tar.gz

StartedAt: 2014-10-07 23:50:48 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:59:32 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 524.1 seconds

RetCode: 0

Status:  OK

CheckDir: RIPSeeker.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RIPSeeker_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/RIPSeeker.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.4.0’
* 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 ... [36s/37s] 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’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following files look like leftovers/mistakes:
  ‘nar.aux’, ‘SD.aux’
Please remove them from your package.
* checking examples ... [138s/156s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
mainSeek              26.341  0.077  26.884
disambiguateMultihits 21.078  0.060  21.255
selectBinSize         10.300  0.413  10.733
nbh                    8.663  0.033   9.046
nbh_init               6.162  0.012   6.201
plotStrandedCoverage   5.458  0.159   5.732
mainSeekSingleChrom    5.427  0.029   5.817
combineRIP             5.241  0.099  21.620
* 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 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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	0.003	0.001	0.003
addDummyProb	3.128	0.040	3.173
addPseudoAlignment	2.569	0.021	2.594
annotateRIP	0.043	0.001	0.043
binCount	3.215	0.037	3.253
combineAlignGals	1.933	0.027	1.962
combineRIP	5.241	0.099	21.620
computeLogOdd	4.519	0.028	4.549
computeRPKM	0.008	0.001	0.009
disambiguateMultihits	21.078	0.060	21.255
empiricalFDR	0.003	0.000	0.004
evalBinSize	2.616	0.036	2.673
exportGRanges	0.005	0.000	0.005
galp2gal	3.775	0.018	3.820
getAlignGal	1.058	0.015	1.082
logScoreWithControl	0.020	0.000	0.021
logScoreWithoutControl	0.012	0.000	0.013
mainSeek	26.341	0.077	26.884
mainSeekSingleChrom	5.427	0.029	5.817
nbh.GRanges	0.001	0.000	0.001
nbh	8.663	0.033	9.046
nbh.integer	0.001	0.000	0.002
nbh_chk	0.002	0.000	0.003
nbh_em	0.903	0.005	0.913
nbh_gen	0.011	0.001	0.011
nbh_init	6.162	0.012	6.201
nbh_vit	0.883	0.005	0.901
nbm_chk	0.002	0.000	0.002
nbm_em	0.892	0.003	0.897
plotCoverage	3.581	0.095	3.721
plotStrandedCoverage	5.458	0.159	5.732
randindx	0.341	0.031	0.388
ripSeek	0.024	0.001	0.026
rulebaseRIPSeek	0.007	0.001	0.007
scoreMergedBins	0.044	0.001	0.045
seekRIP	0.020	0.001	0.020
selectBinSize	10.300	0.413	10.733
statdis	0.853	0.010	0.865
viewRIP	0.016	0.000	0.017