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: 2017-10-18 02:34:40 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 02:41:33 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 412.8 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 3.4.2 Patched (2017-10-07 r73498)
* 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              11.32   0.00   11.33
disambiguateMultihits  8.86   0.02    8.87
combineRIP             3.34   0.11   33.12
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
mainSeek              18.90   0.00   18.91
disambiguateMultihits 18.79   0.00   18.80
combineRIP             4.41   0.07   23.46
* 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	1.12	0.02	1.14
addPseudoAlignment	0.66	0.00	0.65
annotateRIP	0.01	0.00	0.02
binCount	0.50	0.03	0.53
combineAlignGals	0.25	0.00	0.25
combineRIP	3.34	0.11	33.12
computeLogOdd	1.28	0.01	1.30
computeRPKM	0	0	0
disambiguateMultihits	8.86	0.02	8.87
empiricalFDR	0	0	0
evalBinSize	0.56	0.03	0.60
exportGRanges	0	0	0
galp2gal	0.28	0.00	0.28
getAlignGal	0.11	0.00	0.11
logScoreWithControl	0.02	0.00	0.02
logScoreWithoutControl	0	0	0
mainSeek	11.32	0.00	11.33
mainSeekSingleChrom	1.00	0.02	1.01
nbh.GRanges	0	0	0
nbh	1.36	0.01	1.38
nbh.integer	0	0	0
nbh_chk	0	0	0
nbh_em	0.18	0.00	0.17
nbh_gen	0.03	0.00	0.03
nbh_init	0.90	0.00	0.91
nbh_vit	0.16	0.02	0.17
nbm_chk	0	0	0
nbm_em	0.29	0.00	0.28
plotCoverage	0.76	0.01	0.79
plotStrandedCoverage	2.52	0.02	2.53
randindx	0.15	0.01	0.17
ripSeek	0	0	0
rulebaseRIPSeek	0	0	0
scoreMergedBins	0	0	0
seekRIP	0	0	0
selectBinSize	2.86	0.22	3.08
statdis	0.14	0.02	0.16
viewRIP	0	0	0

name	user	system	elapsed
RIPSeeker-package	0	0	0
addDummyProb	2.38	0.00	2.37
addPseudoAlignment	1.25	0.00	1.25
annotateRIP	0	0	0
binCount	0.53	0.01	0.55
combineAlignGals	0.22	0.00	0.22
combineRIP	4.41	0.07	23.46
computeLogOdd	1.97	0.00	1.97
computeRPKM	0	0	0
disambiguateMultihits	18.79	0.00	18.80
empiricalFDR	0	0	0
evalBinSize	1.19	0.00	1.19
exportGRanges	0	0	0
galp2gal	0.56	0.00	0.57
getAlignGal	0.23	0.00	0.24
logScoreWithControl	0.02	0.00	0.01
logScoreWithoutControl	0	0	0
mainSeek	18.90	0.00	18.91
mainSeekSingleChrom	1.83	0.01	1.84
nbh.GRanges	0	0	0
nbh	1.97	0.03	2.00
nbh.integer	0	0	0
nbh_chk	0	0	0
nbh_em	0.44	0.00	0.44
nbh_gen	0.04	0.00	0.05
nbh_init	1.69	0.00	1.68
nbh_vit	0.31	0.03	0.35
nbm_chk	0	0	0
nbm_em	0.32	0.00	0.31
plotCoverage	0.70	0.00	0.71
plotStrandedCoverage	1.41	0.08	1.48
randindx	0.18	0.01	0.21
ripSeek	0.02	0.00	0.01
rulebaseRIPSeek	0	0	0
scoreMergedBins	0	0	0
seekRIP	0	0	0
selectBinSize	4.14	0.10	4.23
statdis	0.19	0.00	0.19
viewRIP	0	0	0