BioC 3.0: CHECK report for RIPSeeker on moscato1

Package: RIPSeeker

Version: 1.6.0

Command: rm -rf RIPSeeker.buildbin-libdir RIPSeeker.Rcheck && mkdir RIPSeeker.buildbin-libdir RIPSeeker.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RIPSeeker.buildbin-libdir RIPSeeker_1.6.0.tar.gz >RIPSeeker.Rcheck\00install.out 2>&1 && cp RIPSeeker.Rcheck\00install.out RIPSeeker-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=RIPSeeker.buildbin-libdir --install="check:RIPSeeker-install.out" --force-multiarch --no-vignettes --timings RIPSeeker_1.6.0.tar.gz

StartedAt: 2015-04-10 05:02:25 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 05:09:39 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 434.0 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-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RIPSeeker.buildbin-libdir RIPSeeker_1.6.0.tar.gz >RIPSeeker.Rcheck\00install.out 2>&1 && cp RIPSeeker.Rcheck\00install.out RIPSeeker-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=RIPSeeker.buildbin-libdir --install="check:RIPSeeker-install.out" --force-multiarch --no-vignettes --timings RIPSeeker_1.6.0.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/RIPSeeker.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-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 '1.6.0'
* 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' ... [71s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
mainSeek              8.99   0.01    9.06
disambiguateMultihits 8.16   0.01    8.18
selectBinSize         4.91   0.17    5.08
combineRIP            2.34   0.05   18.08
** running examples for arch 'x64' ... [80s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
mainSeek              11.65   0.02   11.67
disambiguateMultihits  9.75   0.00    9.78
selectBinSize          5.26   0.25    5.51
combineRIP             2.96   0.08   19.65
* 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

NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-3.0-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_1.6.0.zip
* DONE (RIPSeeker)

name	user	system	elapsed
RIPSeeker-package	0	0	0
addDummyProb	1.06	0.00	1.06
addPseudoAlignment	0.5	0.0	0.5
annotateRIP	0	0	0
binCount	1.26	0.00	1.27
combineAlignGals	0.41	0.00	0.40
combineRIP	2.34	0.05	18.08
computeLogOdd	2.2	0.0	2.2
computeRPKM	0	0	0
disambiguateMultihits	8.16	0.01	8.18
empiricalFDR	0	0	0
evalBinSize	0.72	0.02	0.73
exportGRanges	0	0	0
galp2gal	0.59	0.01	1.23
getAlignGal	0.16	0.00	0.15
logScoreWithControl	0	0	0
logScoreWithoutControl	0	0	0
mainSeek	8.99	0.01	9.06
mainSeekSingleChrom	1.59	0.00	1.60
nbh.GRanges	0	0	0
nbh	2.79	0.00	2.80
nbh.integer	0	0	0
nbh_chk	0	0	0
nbh_em	0.33	0.00	0.32
nbh_gen	0.01	0.00	0.02
nbh_init	2.2	0.0	2.2
nbh_vit	0.33	0.00	0.33
nbm_chk	0	0	0
nbm_em	0.40	0.00	0.41
plotCoverage	1.64	0.04	1.67
plotStrandedCoverage	2.51	0.04	2.56
randindx	0.22	0.03	0.24
ripSeek	0	0	0
rulebaseRIPSeek	0.02	0.00	0.02
scoreMergedBins	0	0	0
seekRIP	0.01	0.00	0.02
selectBinSize	4.91	0.17	5.08
statdis	0.35	0.00	0.34
viewRIP	0	0	0

name	user	system	elapsed
RIPSeeker-package	0	0	0
addDummyProb	0.95	0.00	0.95
addPseudoAlignment	0.36	0.00	0.36
annotateRIP	0.02	0.00	0.01
binCount	1.43	0.00	1.44
combineAlignGals	0.27	0.00	0.26
combineRIP	2.96	0.08	19.65
computeLogOdd	1.95	0.01	1.96
computeRPKM	0	0	0
disambiguateMultihits	9.75	0.00	9.78
empiricalFDR	0	0	0
evalBinSize	0.71	0.00	0.72
exportGRanges	0	0	0
galp2gal	0.41	0.00	0.42
getAlignGal	0.16	0.00	0.15
logScoreWithControl	0	0	0
logScoreWithoutControl	0	0	0
mainSeek	11.65	0.02	11.67
mainSeekSingleChrom	2.91	0.00	2.90
nbh.GRanges	0	0	0
nbh	4	0	4
nbh.integer	0	0	0
nbh_chk	0	0	0
nbh_em	0.69	0.00	0.69
nbh_gen	0.01	0.00	0.02
nbh_init	3.04	0.00	3.04
nbh_vit	0.38	0.00	0.37
nbm_chk	0	0	0
nbm_em	0.46	0.00	0.45
plotCoverage	1.65	0.03	1.68
plotStrandedCoverage	2.86	0.06	3.03
randindx	0.18	0.01	0.20
ripSeek	0	0	0
rulebaseRIPSeek	0	0	0
scoreMergedBins	0.00	0.02	0.01
seekRIP	0	0	0
selectBinSize	5.26	0.25	5.51
statdis	0.35	0.01	0.37
viewRIP	0.02	0.00	0.02