BioC 3.2: CHECK report for RIPSeeker on linux1.bioconductor.org

Package: RIPSeeker

Version: 1.10.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings RIPSeeker_1.10.0.tar.gz

StartedAt: 2015-10-27 07:33:35 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 07:37:16 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 221.6 seconds

RetCode: 0

Status:  OK

CheckDir: RIPSeeker.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings RIPSeeker_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/RIPSeeker.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-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 ‘1.10.0’
* 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 ... [15s/15s] 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’
* 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 ... [44s/79s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
disambiguateMultihits 9.445  0.008   9.467
mainSeek              8.373  0.028   8.402
combineRIP            1.451  0.008  36.861
* 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
  ‘/home/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	0.000
addDummyProb	0.459	0.008	0.468
addPseudoAlignment	0.508	0.000	0.509
annotateRIP	0.014	0.000	0.013
binCount	0.744	0.004	0.755
combineAlignGals	0.273	0.000	0.273
combineRIP	1.451	0.008	36.861
computeLogOdd	1.685	0.004	1.692
computeRPKM	0.003	0.000	0.003
disambiguateMultihits	9.445	0.008	9.467
empiricalFDR	0.002	0.000	0.002
evalBinSize	0.422	0.012	0.433
exportGRanges	0.001	0.000	0.001
galp2gal	0.275	0.000	0.276
getAlignGal	0.110	0.000	0.109
logScoreWithControl	0.003	0.000	0.004
logScoreWithoutControl	0.002	0.000	0.002
mainSeek	8.373	0.028	8.402
mainSeekSingleChrom	1.307	0.004	1.315
nbh.GRanges	0.000	0.000	0.001
nbh	2.022	0.008	2.033
nbh.integer	0.001	0.000	0.001
nbh_chk	0.000	0.000	0.001
nbh_em	0.200	0.004	0.204
nbh_gen	0.003	0.000	0.003
nbh_init	1.450	0.000	1.453
nbh_vit	0.193	0.000	0.193
nbm_chk	0	0	0
nbm_em	0.295	0.000	0.294
plotCoverage	1.146	0.008	1.155
plotStrandedCoverage	1.685	0.000	1.690
randindx	0.137	0.008	0.146
ripSeek	0.004	0.000	0.004
rulebaseRIPSeek	0.002	0.000	0.002
scoreMergedBins	0.007	0.000	0.007
seekRIP	0.004	0.000	0.004
selectBinSize	3.586	0.012	3.602
statdis	0.377	0.000	0.377
viewRIP	0.006	0.000	0.005