Package: RIPSeeker

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RIPSeeker.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RIPSeeker_1.22.0.tar.gz

StartedAt: 2019-04-16 02:23:30 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 02:27:58 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 267.4 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 --install=check:RIPSeeker.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RIPSeeker_1.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/RIPSeeker.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.22.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
mainSeek              15.233  0.073  15.403
disambiguateMultihits 14.673  0.076  14.840
combineRIP             1.544  0.081  12.748
* 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-3.8-bioc/meat/RIPSeeker.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RIPSeeker
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘RIPSeeker’ ...
** R
** inst
** byte-compile and prepare 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	0.002
addDummyProb	0.947	0.034	0.996
addPseudoAlignment	0.943	0.013	0.975
annotateRIP	0.016	0.001	0.017
binCount	0.495	0.031	0.539
combineAlignGals	0.284	0.020	0.306
combineRIP	1.544	0.081	12.748
computeLogOdd	1.886	0.048	1.965
computeRPKM	0.004	0.000	0.004
disambiguateMultihits	14.673	0.076	14.840
empiricalFDR	0.001	0.000	0.001
evalBinSize	0.343	0.044	0.388
exportGRanges	0.001	0.000	0.002
galp2gal	0.263	0.003	0.268
getAlignGal	0.137	0.005	0.144
logScoreWithControl	0.006	0.000	0.007
logScoreWithoutControl	0.003	0.000	0.003
mainSeek	15.233	0.073	15.403
mainSeekSingleChrom	1.607	0.016	1.636
nbh.GRanges	0.000	0.000	0.001
nbh	2.328	0.024	2.364
nbh.integer	0.000	0.000	0.001
nbh_chk	0.000	0.001	0.001
nbh_em	0.396	0.002	0.401
nbh_gen	0.005	0.000	0.004
nbh_init	1.955	0.006	1.993
nbh_vit	0.279	0.003	0.285
nbm_chk	0.000	0.000	0.001
nbm_em	0.418	0.003	0.427
plotCoverage	0.621	0.055	0.680
plotStrandedCoverage	1.100	0.105	1.219
randindx	0.185	0.013	0.204
ripSeek	0.011	0.001	0.011
rulebaseRIPSeek	0.002	0.000	0.002
scoreMergedBins	0.018	0.001	0.019
seekRIP	0.008	0.000	0.009
selectBinSize	3.133	0.286	3.445
statdis	0.268	0.003	0.272
viewRIP	0.006	0.001	0.007