BioC 3.2: CHECK report for RIPSeeker on perceval

Package: RIPSeeker

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RIPSeeker_1.10.0.tar.gz

StartedAt: 2015-11-10 08:57:49 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 09:02:08 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 259.3 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 RIPSeeker_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/RIPSeeker.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* 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 ‘1.10.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘IRanges’ ‘GenomicRanges’ ‘SummarizedExperiment’ ‘Rsamtools’
  ‘GenomicAlignments’ ‘rtracklayer’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ... [18s/19s] 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
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 ‘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 ‘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’
plotCoverage: no visible global function definition for ‘runValue’
plotCoverage: no visible global function definition for ‘seqlengths’
rulebaseRIPSeek: no visible global function definition for ‘metadata’
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 ... [61s/76s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
mainSeek              12.177  0.018  12.195
disambiguateMultihits 10.744  0.023  10.768
combineRIP             1.834  0.107  16.956
* 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

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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	0.001	0.000	0.002
addDummyProb	1.056	0.027	1.083
addPseudoAlignment	0.765	0.008	0.773
annotateRIP	0.026	0.000	0.027
binCount	1.496	0.021	1.517
combineAlignGals	0.751	0.012	0.762
combineRIP	1.834	0.107	16.956
computeLogOdd	2.099	0.015	2.113
computeRPKM	0.005	0.000	0.005
disambiguateMultihits	10.744	0.023	10.768
empiricalFDR	0.001	0.001	0.002
evalBinSize	0.885	0.021	0.906
exportGRanges	0.003	0.000	0.004
galp2gal	0.448	0.009	0.457
getAlignGal	0.588	0.008	0.595
logScoreWithControl	0.014	0.000	0.015
logScoreWithoutControl	0.007	0.001	0.007
mainSeek	12.177	0.018	12.195
mainSeekSingleChrom	2.076	0.014	2.089
nbh.GRanges	0.001	0.000	0.001
nbh	3.288	0.013	3.370
nbh.integer	0	0	0
nbh_chk	0.002	0.000	0.001
nbh_em	0.340	0.003	0.342
nbh_gen	0.005	0.000	0.006
nbh_init	2.309	0.003	2.313
nbh_vit	0.344	0.003	0.348
nbm_chk	0.001	0.000	0.001
nbm_em	0.409	0.003	0.411
plotCoverage	1.486	0.049	1.536
plotStrandedCoverage	2.646	0.095	2.838
randindx	0.241	0.020	0.274
ripSeek	0.015	0.001	0.015
rulebaseRIPSeek	0.005	0.000	0.005
scoreMergedBins	0.027	0.000	0.027
seekRIP	0.013	0.000	0.014
selectBinSize	4.385	0.317	4.703
statdis	0.347	0.004	0.351
viewRIP	0.009	0.001	0.010