BioC 3.5: CHECK report for RIPSeeker on oaxaca

Package: RIPSeeker

Version: 1.15.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RIPSeeker_1.15.0.tar.gz

StartedAt: 2017-03-04 08:15:07 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 08:19:46 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 278.9 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_1.15.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/RIPSeeker.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.15.0’
* 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 loading without being on the library search path ... 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’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
mainSeek              10.985  0.049  11.039
disambiguateMultihits 10.702  0.056  10.766
combineRIP             4.295  0.069  32.454
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-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	0.001	0.001
addDummyProb	1.792	0.035	1.828
addPseudoAlignment	1.135	0.047	1.183
annotateRIP	0.018	0.001	0.019
binCount	0.579	0.030	0.609
combineAlignGals	0.277	0.022	0.300
combineRIP	4.295	0.069	32.454
computeLogOdd	1.346	0.028	1.373
computeRPKM	0.004	0.000	0.004
disambiguateMultihits	10.702	0.056	10.766
empiricalFDR	0.002	0.000	0.003
evalBinSize	0.412	0.033	0.446
exportGRanges	0.001	0.000	0.002
galp2gal	0.434	0.010	0.943
getAlignGal	0.143	0.007	0.150
logScoreWithControl	0.011	0.000	0.012
logScoreWithoutControl	0.006	0.001	0.006
mainSeek	10.985	0.049	11.039
mainSeekSingleChrom	1.406	0.019	1.426
nbh.GRanges	0	0	0
nbh	1.905	0.021	1.927
nbh.integer	0.000	0.000	0.001
nbh_chk	0.001	0.000	0.001
nbh_em	0.218	0.001	0.220
nbh_gen	0.031	0.000	0.031
nbh_init	1.975	0.017	1.993
nbh_vit	0.190	0.002	0.191
nbm_chk	0.001	0.000	0.001
nbm_em	0.479	0.005	0.485
plotCoverage	0.680	0.054	0.735
plotStrandedCoverage	1.091	0.073	1.184
randindx	0.148	0.014	0.189
ripSeek	0.007	0.000	0.008
rulebaseRIPSeek	0.003	0.000	0.003
scoreMergedBins	0.013	0.000	0.013
seekRIP	0.006	0.000	0.007
selectBinSize	3.214	0.237	3.451
statdis	0.176	0.004	0.179
viewRIP	0.005	0.000	0.005