BioC 2.14: CHECK report for RIPSeeker on zin2

Package: RIPSeeker

Version: 1.4.0

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings RIPSeeker_1.4.0.tar.gz

StartedAt: 2014-10-08 02:24:12 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 02:28:09 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 237.0 seconds

RetCode: 0

Status:  OK

CheckDir: RIPSeeker.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings RIPSeeker_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/RIPSeeker.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (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 ... [17s/17s] 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 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 ... [61s/78s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
mainSeek              12.041  0.004  12.081
disambiguateMultihits 10.217  0.008  10.284
selectBinSize          5.032  0.008   5.045
combineRIP             2.204  0.032  18.500
* 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
  ‘/home/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	0.000	0.000	0.002
addDummyProb	1.148	0.012	1.163
addPseudoAlignment	0.648	0.012	0.662
annotateRIP	0.016	0.000	0.013
binCount	1.324	0.000	1.328
combineAlignGals	0.556	0.008	0.566
combineRIP	2.204	0.032	18.500
computeLogOdd	2.244	0.004	2.249
computeRPKM	0.000	0.004	0.003
disambiguateMultihits	10.217	0.008	10.284
empiricalFDR	0.000	0.000	0.001
evalBinSize	0.928	0.004	0.933
exportGRanges	0.004	0.000	0.002
galp2gal	1.788	0.008	1.834
getAlignGal	0.192	0.004	0.200
logScoreWithControl	0.008	0.000	0.008
logScoreWithoutControl	0.004	0.000	0.004
mainSeek	12.041	0.004	12.081
mainSeekSingleChrom	2.064	0.004	2.072
nbh.GRanges	0	0	0
nbh	3.664	0.000	3.673
nbh.integer	0.004	0.000	0.000
nbh_chk	0.000	0.000	0.001
nbh_em	0.388	0.000	0.386
nbh_gen	0.004	0.000	0.004
nbh_init	2.765	0.000	2.800
nbh_vit	0.388	0.000	0.388
nbm_chk	0	0	0
nbm_em	0.412	0.000	0.414
plotCoverage	1.812	0.004	1.823
plotStrandedCoverage	2.508	0.012	2.524
randindx	0.160	0.008	0.169
ripSeek	0.008	0.000	0.008
rulebaseRIPSeek	0.000	0.000	0.003
scoreMergedBins	0.012	0.000	0.013
seekRIP	0.008	0.000	0.006
selectBinSize	5.032	0.008	5.045
statdis	0.388	0.000	0.390
viewRIP	0.004	0.000	0.005