BioC 3.2: CHECK report for RIPSeeker on moscato1

Package: RIPSeeker

Version: 1.10.0

Command: rm -rf RIPSeeker.buildbin-libdir RIPSeeker.Rcheck && mkdir RIPSeeker.buildbin-libdir RIPSeeker.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RIPSeeker.buildbin-libdir RIPSeeker_1.10.0.tar.gz >RIPSeeker.Rcheck\00install.out 2>&1 && cp RIPSeeker.Rcheck\00install.out RIPSeeker-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=RIPSeeker.buildbin-libdir --install="check:RIPSeeker-install.out" --force-multiarch --no-vignettes --timings RIPSeeker_1.10.0.tar.gz

StartedAt: 2016-04-23 06:49:32 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 06:57:15 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 462.8 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 && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RIPSeeker.buildbin-libdir RIPSeeker_1.10.0.tar.gz >RIPSeeker.Rcheck\00install.out 2>&1 && cp RIPSeeker.Rcheck\00install.out RIPSeeker-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=RIPSeeker.buildbin-libdir --install="check:RIPSeeker-install.out" --force-multiarch --no-vignettes --timings RIPSeeker_1.10.0.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/RIPSeeker.Rcheck'
* using R version 3.2.4 (2016-03-10)
* 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 '1.10.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  '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
* 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 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
addPseudoAlignment: no visible global function definition for 'Rle'
annotateRIP: no visible global function definition for 'getAnnotation'
annotateRIP: no visible global function definition for 'getBM'
binCount: no visible global function definition for 'runValue'
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 'getBM'
galp2gal: no visible global function definition for 'seqlengths'
getAlignGal: no visible global function definition for 'seqlengths<-'
getAlignGal: no visible global function definition for 'seqlengths'
getAlignGal: no visible global function definition for 'runValue'
getAlignGal: no visible global function definition for 'Rle'
mainSeek: no visible global function definition for 'mclapply'
mainSeekSingleChrom: no visible global function definition for
  'runValue'
mainSeekSingleChrom: no visible global function definition for
  'seqlengths'
plotCoverage: no visible global function definition for 'runValue'
plotCoverage: no visible global function definition for 'seqlengths'
rulebaseRIPSeek: no visible global function definition for 'metadata'
rulebaseRIPSeek: no visible global function definition for 'getBM'
seekRIP: no visible global function definition for 'runValue'
selectBinSize: no visible global function definition for 'seqlengths'
viewRIP: no visible global function definition for 'runValue'
viewRIP: no visible global function definition for
  'GRangesForUCSCGenome'
* 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' ... NOTE
The following files look like leftovers/mistakes:
  'SD.aux', 'nar.aux'
Please remove them from your package.
* checking examples ...
** running examples for arch 'i386' ... [81s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
disambiguateMultihits 11.42   0.00   11.42
mainSeek              11.25   0.00   11.25
combineRIP             1.65   0.02   21.14
** running examples for arch 'x64' ... [88s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
mainSeek              14.04   0.01   14.05
disambiguateMultihits 12.14   0.00   12.14
selectBinSize          4.61   0.17    5.37
combineRIP             2.09   0.06   19.52
* 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
  'D:/biocbld/bbs-3.2-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_1.10.0.zip
* DONE (RIPSeeker)

name	user	system	elapsed
RIPSeeker-package	0	0	0
addDummyProb	0.81	0.02	0.82
addPseudoAlignment	0.47	0.00	0.47
annotateRIP	0.02	0.00	0.02
binCount	1.06	0.01	1.07
combineAlignGals	0.34	0.00	0.35
combineRIP	1.65	0.02	21.14
computeLogOdd	1.80	0.00	1.79
computeRPKM	0	0	0
disambiguateMultihits	11.42	0.00	11.42
empiricalFDR	0.01	0.00	0.01
evalBinSize	0.44	0.00	0.44
exportGRanges	0	0	0
galp2gal	0.41	0.00	0.41
getAlignGal	0.23	0.00	0.23
logScoreWithControl	0	0	0
logScoreWithoutControl	0.01	0.00	0.01
mainSeek	11.25	0.00	11.25
mainSeekSingleChrom	2.30	0.02	2.31
nbh.GRanges	0	0	0
nbh	4.16	0.00	4.16
nbh.integer	0	0	0
nbh_chk	0	0	0
nbh_em	0.48	0.01	0.50
nbh_gen	0	0	0
nbh_init	2.62	0.00	2.62
nbh_vit	0.50	0.00	0.49
nbm_chk	0	0	0
nbm_em	0.43	0.00	0.44
plotCoverage	1.80	0.04	2.03
plotStrandedCoverage	3.48	0.03	3.51
randindx	0.32	0.01	0.34
ripSeek	0	0	0
rulebaseRIPSeek	0	0	0
scoreMergedBins	0.02	0.00	0.02
seekRIP	0	0	0
selectBinSize	4.43	0.24	4.67
statdis	0.32	0.00	0.31
viewRIP	0	0	0

name	user	system	elapsed
RIPSeeker-package	0	0	0
addDummyProb	0.70	0.02	0.72
addPseudoAlignment	0.31	0.00	0.31
annotateRIP	0.02	0.00	0.02
binCount	1.59	0.00	1.59
combineAlignGals	0.36	0.00	0.36
combineRIP	2.09	0.06	19.52
computeLogOdd	2.35	0.00	2.38
computeRPKM	0	0	0
disambiguateMultihits	12.14	0.00	12.14
empiricalFDR	0	0	0
evalBinSize	0.49	0.00	0.49
exportGRanges	0	0	0
galp2gal	0.53	0.00	0.66
getAlignGal	0.26	0.00	0.27
logScoreWithControl	0.02	0.00	0.02
logScoreWithoutControl	0	0	0
mainSeek	14.04	0.01	14.05
mainSeekSingleChrom	1.79	0.00	1.80
nbh.GRanges	0	0	0
nbh	3.74	0.00	3.75
nbh.integer	0	0	0
nbh_chk	0	0	0
nbh_em	0.47	0.01	0.48
nbh_gen	0	0	0
nbh_init	2.74	0.00	2.74
nbh_vit	0.47	0.02	0.49
nbm_chk	0	0	0
nbm_em	0.45	0.00	0.45
plotCoverage	1.59	0.00	1.59
plotStrandedCoverage	3.00	0.06	3.15
randindx	0.24	0.02	1.88
ripSeek	0	0	0
rulebaseRIPSeek	0	0	0
scoreMergedBins	0.02	0.00	0.02
seekRIP	0	0	0
selectBinSize	4.61	0.17	5.37
statdis	0.61	0.00	1.09
viewRIP	0	0	0