BioC 3.0: CHECK report for ChIPQC on moscato1

Package: ChIPQC

Version: 1.2.2

Command: rm -rf ChIPQC.buildbin-libdir ChIPQC.Rcheck && mkdir ChIPQC.buildbin-libdir ChIPQC.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPQC.buildbin-libdir ChIPQC_1.2.2.tar.gz >ChIPQC.Rcheck\00install.out 2>&1 && cp ChIPQC.Rcheck\00install.out ChIPQC-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=ChIPQC.buildbin-libdir --install="check:ChIPQC-install.out" --force-multiarch --no-vignettes --timings ChIPQC_1.2.2.tar.gz

StartedAt: 2015-04-09 23:34:32 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 23:45:48 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 675.7 seconds

RetCode: 0

Status:  OK

CheckDir: ChIPQC.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf ChIPQC.buildbin-libdir ChIPQC.Rcheck && mkdir ChIPQC.buildbin-libdir ChIPQC.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPQC.buildbin-libdir ChIPQC_1.2.2.tar.gz >ChIPQC.Rcheck\00install.out 2>&1 && cp ChIPQC.Rcheck\00install.out ChIPQC-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=ChIPQC.buildbin-libdir --install="check:ChIPQC-install.out" --force-multiarch --no-vignettes --timings ChIPQC_1.2.2.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/ChIPQC.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 'ChIPQC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChIPQC' version '1.2.2'
* 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 'ChIPQC' 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' calls in package code:
  'TxDb.Celegans.UCSC.ce6.ensGene'
  'TxDb.Dmelanogaster.UCSC.dm3.ensGene'
  'TxDb.Hsapiens.UCSC.hg18.knownGene'
  'TxDb.Hsapiens.UCSC.hg19.knownGene'
  'TxDb.Mmusculus.UCSC.mm10.knownGene'
  'TxDb.Mmusculus.UCSC.mm9.knownGene'
  'TxDb.Rnorvegicus.UCSC.rn4.ensGene'
  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 ... NOTE
Foreign function call to a different package:
  .Call("rle_sum_any", ..., PACKAGE = "chipseq")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... NOTE
GetGRanges: warning in read.delim(LoadFile, sep = sepr, header = TRUE,
  comment = "#"): partial argument match of 'comment' to 'comment.char'
GetGRanges: no visible global function definition for 'seqlevels<-'
findCovMaxPos: no visible global function definition for 'seqlengths'
findCovMaxPos: no visible global function definition for 'seqlengths<-'
getAnnotation: no visible binding for global variable
  'TxDb.Hsapiens.UCSC.hg19.knownGene'
getAnnotation: no visible binding for global variable
  'TxDb.Hsapiens.UCSC.hg18.knownGene'
getAnnotation: no visible binding for global variable
  'TxDb.Mmusculus.UCSC.mm10.knownGene'
getAnnotation: no visible binding for global variable
  'TxDb.Mmusculus.UCSC.mm9.knownGene'
getAnnotation: no visible binding for global variable
  'TxDb.Rnorvegicus.UCSC.rn4.ensGene'
getAnnotation: no visible binding for global variable
  'TxDb.Celegans.UCSC.ce6.ensGene'
getAnnotation: no visible binding for global variable
  'TxDb.Dmelanogaster.UCSC.dm3.ensGene'
getAnnotation: no visible global function definition for
  'fiveUTRsByTranscript'
getAnnotation: no visible global function definition for
  'threeUTRsByTranscript'
getAnnotation: no visible global function definition for 'cdsBy'
getAnnotation: no visible global function definition for
  'intronsByTranscript'
getAnnotation: no visible global function definition for 'transcripts'
getAnnotation: no visible global function definition for 'seqlengths'
makeCCplot: no visible binding for global variable 'Shift_Size'
makeCCplot: no visible binding for global variable 'CC_Score'
makeCoveragePlot: no visible binding for global variable 'Depth'
makeCoveragePlot: no visible binding for global variable 'log10_bp'
makeCoveragePlot: no visible binding for global variable 'Sample'
makeFriblPlot: no visible binding for global variable 'Sample'
makeFriblPlot: no visible binding for global variable 'FRIBL'
makeFriblPlot: no visible binding for global variable 'Reads'
makeFripPlot: no visible binding for global variable 'Sample'
makeFripPlot: no visible binding for global variable 'FRIP'
makeFripPlot: no visible binding for global variable 'Reads'
makePeakProfilePlot: no visible binding for global variable 'Distance'
makePeakProfilePlot: no visible binding for global variable 'Signal'
makeRapPlot: no visible binding for global variable 'Sample'
makeRapPlot: no visible binding for global variable 'CountsInPeaks'
makeRegiPlot: no visible binding for global variable 'Sample'
makeRegiPlot: no visible binding for global variable 'GenomicIntervals'
makeRegiPlot: no visible binding for global variable 'log2_Enrichment'
makeSSDPlot: no visible binding for global variable 'Sample'
makeSSDPlot: no visible global function definition for 'geom_point'
sampleQC: no visible global function definition for 'seqlevels<-'
plotCC,ChIPQCexperiment: no visible binding for global variable
  'Sample'
plotPeakProfile,ChIPQCexperiment: no visible binding for global
  variable 'Sample'
plotRap,ChIPQCexperiment: no visible global function definition for
  'coord_cartesian'
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [86s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
ChIPQCreport 35.87  14.77   52.32
** running examples for arch 'x64' ... [107s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
ChIPQCreport 46.8  15.54    63.6
* 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/ChIPQC.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'ChIPQC' ...
** R
** data
** 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 'ChIPQC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ChIPQC' as ChIPQC_1.2.2.zip
* DONE (ChIPQC)

name	user	system	elapsed
ChIPQC-data	1.62	0.03	1.67
ChIPQC	1.06	0.00	1.06
ChIPQCexperiment-class	0.81	0.02	0.82
ChIPQCreport	35.87	14.77	52.32
ChIPQCsample-class	0.86	0.00	0.86
FragmentLengthCrossCoverage-methods	0.09	0.00	0.09
Normalisedaveragepeaksignal-methods	0.03	0.00	0.04
QCannotation-methods	0.02	0.00	0.01
QCcontrol-methods	0.23	0.02	0.25
QCdba-methods	0.13	0.00	0.13
QCmetadata-methods	0.11	0.01	0.12
QCmetrics-methods	0.63	0.02	0.66
QCsample-methods	0.07	0.02	0.07
ReadLengthCrossCoverage-methods	0.00	0.01	0.02
RelativeCrossCoverage-methods	0.08	0.00	0.08
averagepeaksignal-methods	0.03	0.00	0.03
coveragehistogram-methods	0.03	0.00	0.03
crosscoverage-methods	0.02	0.02	0.04
duplicateRate-methods	0.01	0.00	0.01
duplicates-methods	0.02	0.00	0.02
flagtagcounts-methods	0.03	0.00	0.03
fragmentlength-methods	0.08	0.00	0.08
frip-methods	0.02	0.00	0.02
mapped-methods	0.02	0.00	0.01
peaks-methods	0.09	0.00	0.10
plotCC-methods	0.89	0.00	0.89
plotCorHeatmap-methods	1.53	0.06	1.59
plotCoverageHist-methods	0.6	0.0	0.6
plotFribl-methods	0.64	0.00	1.65
plotFrip-methods	0.67	0.00	0.67
plotPeakProfile-methods	1.60	0.00	1.61
plotPrincomp-methods	1.74	0.00	1.73
plotRap-methods	0.84	0.00	0.84
plotRegi-methods	1.25	0.01	1.26
plotSSD-methods	1.3	0.0	1.3
readlength-methods	0.01	0.00	0.01
reads-methods	0.02	0.00	0.02
regi-methods	0.08	0.00	0.07
ribl-methods	0.01	0.00	0.02
rip-methods	0.02	0.00	0.02
ssd-methods	0.01	0.00	0.01

name	user	system	elapsed
ChIPQC-data	3.30	0.01	3.32
ChIPQC	1.61	0.00	1.61
ChIPQCexperiment-class	1.12	0.02	1.14
ChIPQCreport	46.80	15.54	63.60
ChIPQCsample-class	1	0	1
FragmentLengthCrossCoverage-methods	0.11	0.00	0.11
Normalisedaveragepeaksignal-methods	0.02	0.00	0.01
QCannotation-methods	0.00	0.01	0.02
QCcontrol-methods	0.26	0.00	0.26
QCdba-methods	0.11	0.00	0.11
QCmetadata-methods	0.10	0.02	0.11
QCmetrics-methods	0.77	0.00	0.76
QCsample-methods	0.09	0.00	0.10
ReadLengthCrossCoverage-methods	0.01	0.00	0.01
RelativeCrossCoverage-methods	0.11	0.00	0.11
averagepeaksignal-methods	0.05	0.00	0.05
coveragehistogram-methods	0.03	0.00	0.06
crosscoverage-methods	0.03	0.00	0.03
duplicateRate-methods	0.03	0.00	0.03
duplicates-methods	0.02	0.00	0.02
flagtagcounts-methods	0.02	0.01	0.03
fragmentlength-methods	0.18	0.00	0.19
frip-methods	0.03	0.00	0.03
mapped-methods	0.02	0.00	0.01
peaks-methods	0.14	0.02	0.16
plotCC-methods	1.25	0.03	1.28
plotCorHeatmap-methods	2.09	0.02	2.10
plotCoverageHist-methods	0.64	0.01	0.66
plotFribl-methods	0.72	0.00	0.72
plotFrip-methods	0.68	0.00	0.68
plotPeakProfile-methods	2.13	0.00	2.54
plotPrincomp-methods	2.27	0.05	2.31
plotRap-methods	1.09	0.03	1.12
plotRegi-methods	1.37	0.00	1.38
plotSSD-methods	1.35	0.01	1.37
readlength-methods	0.02	0.00	0.02
reads-methods	0.02	0.00	0.02
regi-methods	0.07	0.00	0.07
ribl-methods	0	0	0
rip-methods	0.00	0.02	0.01
ssd-methods	0.02	0.00	0.02