BioC 2.13: CHECK report for RIPSeeker on zin1

Package: RIPSeeker

Version: 1.2.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings RIPSeeker_1.2.0.tar.gz

StartedAt: 2014-04-05 03:35:21 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:39:08 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 226.4 seconds

RetCode: 0

Status:  OK

CheckDir: RIPSeeker.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/RIPSeeker.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.2.0’
* 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 ... [14s/14s] 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’ ... NOTE
The following files look like leftovers/mistakes:
  ‘SD.aux’, ‘nar.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 ... [69s/88s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
mainSeek              11.905  0.000  11.988
disambiguateMultihits  9.984  0.004  10.027
selectBinSize          7.149  0.048   7.263
combineRIP             2.504  0.008  22.087
* 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
  ‘/home/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	0.188	0.004	0.190
addDummyProb	2.052	0.004	2.060
addPseudoAlignment	0.652	0.004	0.660
annotateRIP	0.208	0.000	0.209
binCount	1.984	0.016	2.004
combineAlignGals	0.548	0.004	0.555
combineRIP	2.504	0.008	22.087
computeLogOdd	2.621	0.000	2.630
computeRPKM	0.008	0.000	0.006
disambiguateMultihits	9.984	0.004	10.027
empiricalFDR	0.004	0.000	0.005
evalBinSize	1.388	0.004	1.393
exportGRanges	0.000	0.004	0.006
galp2gal	1.428	0.000	1.430
getAlignGal	0.404	0.000	0.406
logScoreWithControl	0.008	0.000	0.011
logScoreWithoutControl	0.008	0.000	0.006
mainSeek	11.905	0.000	11.988
mainSeekSingleChrom	2.884	0.004	2.893
nbh.GRanges	0.004	0.000	0.003
nbh	4.617	0.000	4.629
nbh.integer	0.000	0.000	0.001
nbh_chk	0.004	0.000	0.004
nbh_em	0.504	0.004	0.508
nbh_gen	0.008	0.000	0.009
nbh_init	3.316	0.000	3.320
nbh_vit	0.440	0.004	0.443
nbm_chk	0.000	0.000	0.003
nbm_em	0.492	0.000	0.489
plotCoverage	2.276	0.024	2.310
plotStrandedCoverage	3.340	0.016	3.362
randindx	0.184	0.008	0.191
ripSeek	0.016	0.000	0.014
rulebaseRIPSeek	0.008	0.000	0.008
scoreMergedBins	0.020	0.000	0.022
seekRIP	0.008	0.000	0.012
selectBinSize	7.149	0.048	7.263
statdis	0.480	0.000	0.479
viewRIP	0.008	0.000	0.008