BioC 3.0: CHECK report for RIPSeeker on zin1

Package: RIPSeeker

Version: 1.6.0

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings RIPSeeker_1.6.0.tar.gz

StartedAt: 2015-04-10 03:50:46 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 03:54:41 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 235.1 seconds

RetCode: 0

Status:  OK

CheckDir: RIPSeeker.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings RIPSeeker_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/RIPSeeker.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.6.0’
* 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 ... [18s/18s] 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
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 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 ... [50s/64s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
mainSeek              9.305  0.012   9.402
disambiguateMultihits 8.029  0.008   8.071
combineRIP            2.064  0.012  16.610
* 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
  ‘/home/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	0.000	0.000	0.001
addDummyProb	0.776	0.008	0.787
addPseudoAlignment	0.284	0.000	0.285
annotateRIP	0.012	0.000	0.014
binCount	1.260	0.004	1.266
combineAlignGals	0.196	0.000	0.198
combineRIP	2.064	0.012	16.610
computeLogOdd	1.464	0.004	1.476
computeRPKM	0.004	0.000	0.002
disambiguateMultihits	8.029	0.008	8.071
empiricalFDR	0.004	0.000	0.002
evalBinSize	0.660	0.000	0.659
exportGRanges	0.004	0.000	0.002
galp2gal	0.396	0.000	0.394
getAlignGal	0.128	0.004	0.130
logScoreWithControl	0.008	0.000	0.007
logScoreWithoutControl	0.000	0.004	0.004
mainSeek	9.305	0.012	9.402
mainSeekSingleChrom	1.484	0.004	1.491
nbh.GRanges	0	0	0
nbh	2.592	0.000	2.595
nbh.integer	0	0	0
nbh_chk	0.000	0.004	0.001
nbh_em	0.316	0.000	0.319
nbh_gen	0.004	0.000	0.004
nbh_init	2.116	0.000	2.117
nbh_vit	0.32	0.00	0.35
nbm_chk	0.000	0.000	0.001
nbm_em	0.456	0.000	0.459
plotCoverage	1.252	0.008	1.264
plotStrandedCoverage	2.336	0.016	2.353
randindx	0.156	0.008	0.166
ripSeek	0.008	0.000	0.008
rulebaseRIPSeek	0.004	0.000	0.003
scoreMergedBins	0.016	0.000	0.014
seekRIP	0.008	0.000	0.008
selectBinSize	4.797	0.028	4.830
statdis	0.308	0.000	0.308
viewRIP	0.008	0.000	0.005