BioC 3.5: CHECK report for RIPSeeker on tokay2

Package: RIPSeeker

Version: 1.16.0

Command: rm -rf RIPSeeker.buildbin-libdir RIPSeeker.Rcheck && mkdir RIPSeeker.buildbin-libdir RIPSeeker.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RIPSeeker.buildbin-libdir RIPSeeker_1.16.0.tar.gz >RIPSeeker.Rcheck\00install.out 2>&1 && cp RIPSeeker.Rcheck\00install.out RIPSeeker-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=RIPSeeker.buildbin-libdir --install="check:RIPSeeker-install.out" --force-multiarch --no-vignettes --timings RIPSeeker_1.16.0.tar.gz

StartedAt: 2017-08-16 02:28:28 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:34:56 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 388.1 seconds

RetCode: 0

Status:  OK

CheckDir: RIPSeeker.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf RIPSeeker.buildbin-libdir RIPSeeker.Rcheck && mkdir RIPSeeker.buildbin-libdir RIPSeeker.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RIPSeeker.buildbin-libdir RIPSeeker_1.16.0.tar.gz >RIPSeeker.Rcheck\00install.out 2>&1 && cp RIPSeeker.Rcheck\00install.out RIPSeeker-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=RIPSeeker.buildbin-libdir --install="check:RIPSeeker-install.out" --force-multiarch --no-vignettes --timings RIPSeeker_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/RIPSeeker.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RIPSeeker/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RIPSeeker' version '1.16.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
mainSeek              12.55   0.00   12.55
disambiguateMultihits 11.25   0.01   11.28
combineRIP             3.15   0.10   21.66
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
mainSeek              14.78   0.00   14.78
disambiguateMultihits 13.75   0.02   13.76
combineRIP             4.03   0.03   21.35
* 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/RIPSeeker.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'RIPSeeker' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RIPSeeker' as RIPSeeker_1.16.0.zip
* DONE (RIPSeeker)

name	user	system	elapsed
RIPSeeker-package	0	0	0
addDummyProb	1.13	0.10	1.22
addPseudoAlignment	0.66	0.01	0.67
annotateRIP	0	0	0
binCount	0.43	0.00	0.44
combineAlignGals	0.18	0.00	0.17
combineRIP	3.15	0.10	21.66
computeLogOdd	1.64	0.00	1.64
computeRPKM	0	0	0
disambiguateMultihits	11.25	0.01	11.28
empiricalFDR	0	0	0
evalBinSize	0.33	0.00	0.33
exportGRanges	0	0	0
galp2gal	0.29	0.00	0.30
getAlignGal	0.13	0.00	0.12
logScoreWithControl	0	0	0
logScoreWithoutControl	0	0	0
mainSeek	12.55	0.00	12.55
mainSeekSingleChrom	1.22	0.00	1.21
nbh.GRanges	0	0	0
nbh	1.34	0.00	1.35
nbh.integer	0	0	0
nbh_chk	0	0	0
nbh_em	0.21	0.00	0.20
nbh_gen	0.03	0.00	0.03
nbh_init	0.92	0.00	0.92
nbh_vit	0.14	0.00	0.15
nbm_chk	0.02	0.00	0.01
nbm_em	0.26	0.00	0.27
plotCoverage	0.81	0.10	0.90
plotStrandedCoverage	2.43	0.04	2.47
randindx	0.15	0.02	0.17
ripSeek	0	0	0
rulebaseRIPSeek	0	0	0
scoreMergedBins	0	0	0
seekRIP	0	0	0
selectBinSize	3.44	0.18	3.63
statdis	0.14	0.00	0.14
viewRIP	0.01	0.00	0.02

name	user	system	elapsed
RIPSeeker-package	0.01	0.00	0.02
addDummyProb	1.35	0.00	1.34
addPseudoAlignment	0.83	0.00	0.83
annotateRIP	0	0	0
binCount	1.29	0.05	1.35
combineAlignGals	0.32	0.01	0.32
combineRIP	4.03	0.03	21.35
computeLogOdd	1.95	0.00	1.95
computeRPKM	0.02	0.00	0.02
disambiguateMultihits	13.75	0.02	13.76
empiricalFDR	0	0	0
evalBinSize	0.26	0.01	0.28
exportGRanges	0.02	0.00	0.02
galp2gal	0.89	0.00	0.89
getAlignGal	0.17	0.00	0.17
logScoreWithControl	0.02	0.00	0.02
logScoreWithoutControl	0	0	0
mainSeek	14.78	0.00	14.78
mainSeekSingleChrom	1.68	0.02	1.70
nbh.GRanges	0	0	0
nbh	1.61	0.02	1.63
nbh.integer	0	0	0
nbh_chk	0	0	0
nbh_em	0.24	0.00	0.23
nbh_gen	0.03	0.00	0.03
nbh_init	1.62	0.00	1.63
nbh_vit	0.29	0.00	0.28
nbm_chk	0	0	0
nbm_em	0.44	0.00	0.44
plotCoverage	1.06	0.01	1.08
plotStrandedCoverage	1.45	0.10	1.55
randindx	0.19	0.01	0.20
ripSeek	0.02	0.00	0.01
rulebaseRIPSeek	0	0	0
scoreMergedBins	0	0	0
seekRIP	0	0	0
selectBinSize	3.85	0.22	4.06
statdis	0.17	0.00	0.17
viewRIP	0	0	0