BioC 3.1: CHECK report for RIPSeeker on moscato2

Package: RIPSeeker

Version: 1.8.0

Command: rm -rf RIPSeeker.buildbin-libdir RIPSeeker.Rcheck && mkdir RIPSeeker.buildbin-libdir RIPSeeker.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RIPSeeker.buildbin-libdir RIPSeeker_1.8.0.tar.gz >RIPSeeker.Rcheck\00install.out 2>&1 && cp RIPSeeker.Rcheck\00install.out RIPSeeker-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=RIPSeeker.buildbin-libdir --install="check:RIPSeeker-install.out" --force-multiarch --no-vignettes --timings RIPSeeker_1.8.0.tar.gz

StartedAt: 2015-10-09 05:37:29 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 05:42:54 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 324.8 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 && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RIPSeeker.buildbin-libdir RIPSeeker_1.8.0.tar.gz >RIPSeeker.Rcheck\00install.out 2>&1 && cp RIPSeeker.Rcheck\00install.out RIPSeeker-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=RIPSeeker.buildbin-libdir --install="check:RIPSeeker-install.out" --force-multiarch --no-vignettes --timings RIPSeeker_1.8.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/RIPSeeker.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '1.8.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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
addDummyProb: no visible global function definition for 'metadata<-'
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 'SimpleList'
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 'metadata<-'
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'
nbh.GRanges: no visible global function definition for 'metadata<-'
plotCoverage: no visible global function definition for 'runValue'
plotCoverage: no visible global function definition for 'seqlengths'
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' ... [60s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
mainSeek              7.36   0.00    7.36
disambiguateMultihits 7.25   0.00    7.30
combineRIP            2.58   0.03   17.33
** running examples for arch 'x64' ... [71s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
mainSeek              10.25   0.03   10.28
disambiguateMultihits 10.10   0.00   10.09
combineRIP             3.15   0.05   19.59
* 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
  'E:/biocbld/bbs-3.1-bioc/meat/RIPSeeker.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'RIPSeeker' ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'RIPSeeker' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'RIPSeeker' as RIPSeeker_1.8.0.zip
* DONE (RIPSeeker)

name	user	system	elapsed
RIPSeeker-package	0	0	0
addDummyProb	0.60	0.00	0.61
addPseudoAlignment	0.86	0.00	0.85
annotateRIP	0.02	0.00	0.02
binCount	0.92	0.00	0.92
combineAlignGals	0.65	0.00	0.66
combineRIP	2.58	0.03	17.33
computeLogOdd	1.35	0.00	1.34
computeRPKM	0	0	0
disambiguateMultihits	7.25	0.00	7.30
empiricalFDR	0	0	0
evalBinSize	0.59	0.00	0.59
exportGRanges	0	0	0
galp2gal	0.33	0.03	0.64
getAlignGal	0.17	0.00	0.17
logScoreWithControl	0	0	0
logScoreWithoutControl	0.02	0.00	0.02
mainSeek	7.36	0.00	7.36
mainSeekSingleChrom	1.39	0.00	1.39
nbh.GRanges	0	0	0
nbh	2.40	0.02	2.42
nbh.integer	0	0	0
nbh_chk	0.02	0.00	0.02
nbh_em	0.26	0.01	0.28
nbh_gen	0	0	0
nbh_init	2.43	0.00	2.44
nbh_vit	0.28	0.00	0.28
nbm_chk	0	0	0
nbm_em	0.39	0.00	0.39
plotCoverage	1.20	0.02	1.22
plotStrandedCoverage	2.29	0.04	2.34
randindx	0.22	0.02	0.23
ripSeek	0	0	0
rulebaseRIPSeek	0	0	0
scoreMergedBins	0.01	0.00	0.01
seekRIP	0	0	0
selectBinSize	3.03	0.11	3.14
statdis	0.28	0.00	0.28
viewRIP	0	0	0

name	user	system	elapsed
RIPSeeker-package	0	0	0
addDummyProb	0.88	0.00	0.88
addPseudoAlignment	0.32	0.00	0.32
annotateRIP	0.02	0.00	0.02
binCount	0.93	0.00	0.93
combineAlignGals	0.32	0.00	0.32
combineRIP	3.15	0.05	19.59
computeLogOdd	2.73	0.00	2.73
computeRPKM	0.01	0.00	0.02
disambiguateMultihits	10.10	0.00	10.09
empiricalFDR	0	0	0
evalBinSize	0.45	0.00	0.45
exportGRanges	0	0	0
galp2gal	0.42	0.00	0.42
getAlignGal	0.17	0.00	0.17
logScoreWithControl	0	0	0
logScoreWithoutControl	0	0	0
mainSeek	10.25	0.03	10.28
mainSeekSingleChrom	1.73	0.01	1.75
nbh.GRanges	0	0	0
nbh	3.44	0.00	3.45
nbh.integer	0	0	0
nbh_chk	0	0	0
nbh_em	0.34	0.00	0.34
nbh_gen	0	0	0
nbh_init	2.29	0.00	2.30
nbh_vit	0.33	0.00	0.32
nbm_chk	0	0	0
nbm_em	0.40	0.00	0.41
plotCoverage	1.28	0.03	1.31
plotStrandedCoverage	2.7	0.0	2.7
randindx	0.22	0.02	0.24
ripSeek	0.01	0.00	0.02
rulebaseRIPSeek	0	0	0
scoreMergedBins	0.02	0.00	0.02
seekRIP	0	0	0
selectBinSize	4.21	0.25	4.46
statdis	0.64	0.00	0.64
viewRIP	0	0	0