BioC 3.0: CHECK report for RIPSeeker on perceval

Package: RIPSeeker

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RIPSeeker_1.6.0.tar.gz

StartedAt: 2015-04-10 05:45:31 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 05:52:01 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 390.3 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_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/RIPSeeker.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.6.0’
* 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 ... [28s/30s] 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.
'library' or 'require' calls in package code:
  ‘biomaRt’ ‘ChIPpeakAnno’ ‘GenomicFeatures’ ‘parallel’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in 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 ... NOTE
addDummyProb: no visible global function definition for ‘metadata<-’
addPseudoAlignment: no visible global function definition for ‘Rle’
annotateRIP: no visible global function definition for ‘getAnnotation’
annotateRIP: no visible global function definition for ‘getBM’
binCount: no visible global function definition for ‘runValue’
binCount: no visible global function definition for ‘seqlengths’
combineRIP: no visible global function definition for ‘seqlengths<-’
combineRIP: no visible global function definition for ‘seqlengths’
computeRPKM: no visible global function definition for ‘exonsBy’
computeRPKM: no visible global function definition for ‘cdsBy’
computeRPKM: no visible global function definition for
  ‘intronsByTranscript’
computeRPKM: no visible global function definition for
  ‘fiveUTRsByTranscript’
computeRPKM: no visible global function definition for
  ‘threeUTRsByTranscript’
computeRPKM: no visible global function definition for ‘seqlevels<-’
computeRPKM: no visible global function definition for ‘seqlevels’
computeRPKM: no visible global function definition for ‘SimpleList’
computeRPKM: no visible global function definition for ‘getBM’
galp2gal: no visible global function definition for ‘seqlengths’
getAlignGal: no visible global function definition for ‘seqlengths<-’
getAlignGal: no visible global function definition for ‘seqlengths’
getAlignGal: no visible global function definition for ‘runValue’
getAlignGal: no visible global function definition for ‘metadata<-’
getAlignGal: no visible global function definition for ‘Rle’
mainSeek: no visible global function definition for ‘mclapply’
mainSeekSingleChrom: no visible global function definition for
  ‘runValue’
mainSeekSingleChrom: no visible global function definition for
  ‘seqlengths’
nbh.GRanges: no visible global function definition for ‘metadata<-’
plotCoverage: no visible global function definition for ‘runValue’
plotCoverage: no visible global function definition for ‘seqlengths’
rulebaseRIPSeek: no visible global function definition for ‘getBM’
seekRIP: no visible global function definition for ‘runValue’
selectBinSize: no visible global function definition for ‘seqlengths’
viewRIP: no visible global function definition for ‘runValue’
viewRIP: no visible global function definition for
  ‘GRangesForUCSCGenome’
* 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 ... [88s/106s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
mainSeek              17.667  0.057  17.800
disambiguateMultihits 14.821  0.059  14.946
selectBinSize          8.598  0.562   9.194
combineRIP             3.035  0.110  20.660
* 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
* DONE

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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	1.558	0.029	1.589
addPseudoAlignment	1.185	0.020	1.206
annotateRIP	0.028	0.002	0.029
binCount	2.271	0.053	2.328
combineAlignGals	0.729	0.019	0.749
combineRIP	3.035	0.110	20.660
computeLogOdd	2.554	0.047	2.612
computeRPKM	0.005	0.000	0.005
disambiguateMultihits	14.821	0.059	14.946
empiricalFDR	0.002	0.000	0.002
evalBinSize	1.354	0.029	1.383
exportGRanges	0.003	0.000	0.004
galp2gal	0.500	0.016	0.517
getAlignGal	0.540	0.012	0.553
logScoreWithControl	0.014	0.001	0.014
logScoreWithoutControl	0.007	0.000	0.007
mainSeek	17.667	0.057	17.800
mainSeekSingleChrom	2.867	0.018	2.886
nbh.GRanges	0.001	0.000	0.000
nbh	3.725	0.019	3.747
nbh.integer	0	0	0
nbh_chk	0.002	0.000	0.001
nbh_em	0.460	0.006	0.466
nbh_gen	0.006	0.000	0.007
nbh_init	2.824	0.009	2.836
nbh_vit	0.444	0.006	0.457
nbm_chk	0.001	0.000	0.001
nbm_em	0.594	0.005	0.600
plotCoverage	1.737	0.076	1.824
plotStrandedCoverage	3.763	0.154	4.065
randindx	0.230	0.027	0.297
ripSeek	0.016	0.000	0.016
rulebaseRIPSeek	0.005	0.000	0.005
scoreMergedBins	0.028	0.001	0.029
seekRIP	0.015	0.000	0.015
selectBinSize	8.598	0.562	9.194
statdis	0.455	0.012	0.472
viewRIP	0.010	0.000	0.011