BioC 3.4: CHECK report for RIPSeeker on zin1

Package: RIPSeeker

Version: 1.13.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings RIPSeeker_1.13.0.tar.gz

StartedAt: 2016-09-20 11:49:03 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 11:51:58 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 175.3 seconds

RetCode: 0

Status:  OK

CheckDir: RIPSeeker.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings RIPSeeker_1.13.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/RIPSeeker.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.13.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘S4Vectors’ ‘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 ... 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
annotateRIP: no visible global function definition for ‘getAnnotation’
annotateRIP: no visible global function definition for ‘getBM’
annotateRIP: no visible global function definition for ‘write.table’
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 ‘read.delim’
computeRPKM: no visible global function definition for ‘getBM’
exportGRanges: no visible global function definition for ‘write.table’
galp2gal: no visible global function definition for ‘seqlengths’
getAlignGal: no visible global function definition for ‘seqlengths<-’
getAlignGal: no visible global function definition for ‘seqlengths’
mainSeek: no visible global function definition for ‘mclapply’
mainSeekSingleChrom: no visible global function definition for
  ‘seqlengths’
plotCoverage: no visible global function definition for ‘seqlengths’
ripSeek: no visible global function definition for ‘as.roman’
ripSeek: no visible global function definition for ‘write.table’
rulebaseRIPSeek: no visible global function definition for ‘getBM’
rulebaseRIPSeek: no visible global function definition for
  ‘write.table’
selectBinSize: no visible global function definition for ‘seqlengths’
viewRIP: no visible global function definition for
  ‘GRangesForUCSCGenome’
Undefined global functions or variables:
  GRangesForUCSCGenome as.roman cdsBy exonsBy fiveUTRsByTranscript
  getAnnotation getBM intronsByTranscript mclapply read.delim
  seqlengths seqlengths<- seqlevels seqlevels<- threeUTRsByTranscript
  write.table
Consider adding
  importFrom("utils", "as.roman", "read.delim", "write.table")
to your NAMESPACE file.
* 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 ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
mainSeek              8.576  0.012   8.589
disambiguateMultihits 7.792  0.008   7.810
combineRIP            0.960  0.024  14.221
* 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-3.4-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	0	0
addDummyProb	0.376	0.016	0.393
addPseudoAlignment	0.192	0.000	0.191
annotateRIP	0.008	0.000	0.007
binCount	0.540	0.008	0.547
combineAlignGals	0.424	0.000	0.424
combineRIP	0.960	0.024	14.221
computeLogOdd	1.208	0.004	1.211
computeRPKM	0.004	0.000	0.002
disambiguateMultihits	7.792	0.008	7.810
empiricalFDR	0.000	0.000	0.002
evalBinSize	0.564	0.068	0.634
exportGRanges	0.004	0.000	0.001
galp2gal	0.144	0.004	0.149
getAlignGal	0.104	0.000	0.107
logScoreWithControl	0.004	0.000	0.004
logScoreWithoutControl	0.000	0.000	0.002
mainSeek	8.576	0.012	8.589
mainSeekSingleChrom	1.176	0.004	1.179
nbh.GRanges	0	0	0
nbh	1.924	0.008	1.935
nbh.integer	0.000	0.000	0.001
nbh_chk	0	0	0
nbh_em	0.252	0.004	0.256
nbh_gen	0.004	0.000	0.004
nbh_init	1.644	0.004	1.647
nbh_vit	0.240	0.004	0.244
nbm_chk	0.004	0.000	0.001
nbm_em	0.38	0.00	0.38
plotCoverage	0.896	0.040	0.934
plotStrandedCoverage	1.444	0.020	1.465
randindx	0.140	0.012	0.152
ripSeek	0.004	0.000	0.005
rulebaseRIPSeek	0.000	0.000	0.001
scoreMergedBins	0.008	0.000	0.008
seekRIP	0.004	0.000	0.004
selectBinSize	3.184	0.028	3.211
statdis	0.232	0.000	0.232
viewRIP	0.004	0.000	0.003