BioC 2.14: CHECK report for RIPSeeker on morelia

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: 2014-10-08 01:13:18 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 01:18:16 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 298.1 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-darwin13.1.0 (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 ... [20s/20s] 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 loading without being on the library search path ... 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:
  ‘SD.aux’, ‘nar.aux’
Please remove them from your package.
* checking examples ... [72s/88s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
mainSeek              13.551  0.040  13.616
disambiguateMultihits 11.651  0.035  11.701
selectBinSize          6.123  0.216   6.351
combineRIP             3.738  0.054  18.727
* 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	0.002	0.000	0.002
addDummyProb	1.581	0.025	1.607
addPseudoAlignment	0.921	0.011	0.932
annotateRIP	0.021	0.001	0.023
binCount	1.887	0.021	1.912
combineAlignGals	0.741	0.013	0.755
combineRIP	3.738	0.054	18.727
computeLogOdd	2.555	0.018	2.579
computeRPKM	0.003	0.000	0.002
disambiguateMultihits	11.651	0.035	11.701
empiricalFDR	0.002	0.001	0.002
evalBinSize	1.105	0.017	1.124
exportGRanges	0.003	0.000	0.003
galp2gal	2.027	0.012	2.040
getAlignGal	0.255	0.009	0.265
logScoreWithControl	0.008	0.000	0.008
logScoreWithoutControl	0.004	0.000	0.005
mainSeek	13.551	0.040	13.616
mainSeekSingleChrom	2.431	0.014	2.683
nbh.GRanges	0.001	0.000	0.001
nbh	4.121	0.012	4.138
nbh.integer	0.001	0.000	0.001
nbh_chk	0.002	0.000	0.002
nbh_em	0.479	0.003	0.487
nbh_gen	0.005	0.000	0.005
nbh_init	3.128	0.007	3.140
nbh_vit	0.420	0.003	0.423
nbm_chk	0.001	0.000	0.001
nbm_em	0.453	0.008	0.462
plotCoverage	1.579	0.039	1.620
plotStrandedCoverage	2.703	0.067	2.801
randindx	0.168	0.013	0.208
ripSeek	0.011	0.001	0.011
rulebaseRIPSeek	0.004	0.000	0.005
scoreMergedBins	0.02	0.00	0.02
seekRIP	0.009	0.001	0.010
selectBinSize	6.123	0.216	6.351
statdis	0.477	0.004	0.482
viewRIP	0.008	0.000	0.009