BioC 3.3: CHECK report for RIPSeeker on morelia

Package: RIPSeeker

Version: 1.11.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RIPSeeker_1.11.0.tar.gz

StartedAt: 2015-10-22 10:34:48 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 10:38:01 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 193.7 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_1.11.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/RIPSeeker.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.11.0’
* 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 ... [13s/13s] 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:
  ‘ChIPpeakAnno’ ‘GenomicFeatures’ ‘biomaRt’ ‘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’
Undefined global functions or variables:
  GRangesForUCSCGenome Rle cdsBy exonsBy fiveUTRsByTranscript
  getAnnotation getBM intronsByTranscript mclapply metadata runValue
  seqlengths seqlengths<- seqlevels seqlevels<- threeUTRsByTranscript
* 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 ... [38s/65s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
mainSeek              7.421  0.035   7.488
disambiguateMultihits 7.063  0.059   7.210
combineRIP            1.424  0.060  28.420
* 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-3.3-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	0.001
addDummyProb	0.734	0.015	0.749
addPseudoAlignment	0.510	0.011	0.520
annotateRIP	0.021	0.000	0.022
binCount	0.910	0.020	0.931
combineAlignGals	0.259	0.020	0.282
combineRIP	1.424	0.060	28.420
computeLogOdd	1.347	0.034	1.382
computeRPKM	0.003	0.000	0.002
disambiguateMultihits	7.063	0.059	7.210
empiricalFDR	0.001	0.000	0.001
evalBinSize	0.323	0.019	0.343
exportGRanges	0.003	0.000	0.003
galp2gal	0.357	0.012	0.392
getAlignGal	0.148	0.009	0.157
logScoreWithControl	0.009	0.000	0.010
logScoreWithoutControl	0.004	0.000	0.003
mainSeek	7.421	0.035	7.488
mainSeekSingleChrom	1.019	0.016	1.036
nbh.GRanges	0	0	0
nbh	1.709	0.011	1.721
nbh.integer	0.001	0.000	0.001
nbh_chk	0.001	0.000	0.000
nbh_em	0.186	0.002	0.190
nbh_gen	0.003	0.000	0.003
nbh_init	1.505	0.002	1.509
nbh_vit	0.226	0.002	0.228
nbm_chk	0.000	0.000	0.001
nbm_em	0.277	0.004	0.281
plotCoverage	0.542	0.052	0.594
plotStrandedCoverage	1.455	0.061	1.545
randindx	0.125	0.011	0.163
ripSeek	0.008	0.000	0.008
rulebaseRIPSeek	0.003	0.001	0.003
scoreMergedBins	0.013	0.000	0.014
seekRIP	0.007	0.000	0.007
selectBinSize	2.621	0.192	3.042
statdis	0.303	0.005	0.309
viewRIP	0.006	0.000	0.006