BioC 3.2: CHECK report for ChIPQC on moscato1

Package: ChIPQC

Version: 1.6.1

Command: rm -rf ChIPQC.buildbin-libdir ChIPQC.Rcheck && mkdir ChIPQC.buildbin-libdir ChIPQC.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPQC.buildbin-libdir ChIPQC_1.6.1.tar.gz >ChIPQC.Rcheck\00install.out 2>&1 && cp ChIPQC.Rcheck\00install.out ChIPQC-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=ChIPQC.buildbin-libdir --install="check:ChIPQC-install.out" --force-multiarch --no-vignettes --timings ChIPQC_1.6.1.tar.gz

StartedAt: 2016-04-23 00:33:40 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 00:47:46 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 845.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: ChIPQC.Rcheck

Warnings: 2

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### Running command:
###
###   rm -rf ChIPQC.buildbin-libdir ChIPQC.Rcheck && mkdir ChIPQC.buildbin-libdir ChIPQC.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPQC.buildbin-libdir ChIPQC_1.6.1.tar.gz >ChIPQC.Rcheck\00install.out 2>&1 && cp ChIPQC.Rcheck\00install.out ChIPQC-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=ChIPQC.buildbin-libdir --install="check:ChIPQC-install.out" --force-multiarch --no-vignettes --timings ChIPQC_1.6.1.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/ChIPQC.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 'ChIPQC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChIPQC' version '1.6.1'
* 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 ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... WARNING
'library' or 'require' call not declared from: 'TxDb.Hsapiens.UCSC.hg38.knownGene'
'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.Hsapiens.UCSC.hg38.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.Hsapiens.UCSC.hg38.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 'index'
sampleQC: no visible global function definition for 'BamFile'
sampleQC: no visible global function definition for 'indexBam'
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 ... WARNING
Missing link or links in documentation object 'plotCC-methods.Rd':
  'ggplot2'

Missing link or links in documentation object 'plotCoverageHist-methods.Rd':
  'ggplot2'

Missing link or links in documentation object 'plotFribl-methods.Rd':
  'ggplot2'

Missing link or links in documentation object 'plotFrip-methods.Rd':
  'ggplot2'

Missing link or links in documentation object 'plotPeakProfile-methods.Rd':
  'ggplot2'

Missing link or links in documentation object 'plotRap-methods.Rd':
  'ggplot2'

Missing link or links in documentation object 'plotRegi-methods.Rd':
  'ggplot2'

Missing link or links in documentation object 'plotSSD-methods.Rd':
  'ggplot2'

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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' ... [110s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
ChIPQCreport 48.98  18.27   69.99
** running examples for arch 'x64' ... [134s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
ChIPQCreport 60.39   20.5   81.66
* 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: 2 WARNINGs, 3 NOTEs
See
  'D:/biocbld/bbs-3.2-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_1.6.1.zip
* DONE (ChIPQC)

name	user	system	elapsed
ChIPQC-data	2.01	0.02	2.22
ChIPQC	0.57	0.00	0.56
ChIPQCexperiment-class	0.53	0.01	0.55
ChIPQCreport	48.98	18.27	69.99
ChIPQCsample-class	0.83	0.00	0.83
FragmentLengthCrossCoverage-methods	0.09	0.00	0.10
Normalisedaveragepeaksignal-methods	0.03	0.00	0.03
QCannotation-methods	0.02	0.01	0.03
QCcontrol-methods	0.23	0.00	0.23
QCdba-methods	0.13	0.00	0.13
QCmetadata-methods	0.14	0.00	0.14
QCmetrics-methods	0.51	0.07	0.58
QCsample-methods	0.06	0.00	0.06
ReadLengthCrossCoverage-methods	0.02	0.01	0.03
RelativeCrossCoverage-methods	0.09	0.00	0.09
averagepeaksignal-methods	0.04	0.00	0.03
coveragehistogram-methods	0.01	0.02	0.04
crosscoverage-methods	0.02	0.01	0.03
duplicateRate-methods	0.01	0.02	0.03
duplicates-methods	0.03	0.00	0.03
flagtagcounts-methods	0.01	0.00	0.01
fragmentlength-methods	0.11	0.02	0.13
frip-methods	0.03	0.00	0.03
mapped-methods	0.04	0.00	0.03
peaks-methods	0.11	0.01	0.12
plotCC-methods	1.27	0.03	1.31
plotCorHeatmap-methods	2.70	0.03	2.73
plotCoverageHist-methods	0.86	0.02	0.88
plotFribl-methods	1.08	0.00	1.07
plotFrip-methods	0.98	0.00	0.99
plotPeakProfile-methods	2.39	0.01	2.40
plotPrincomp-methods	2.82	0.04	2.85
plotRap-methods	1.3	0.0	1.3
plotRegi-methods	2.15	0.01	2.56
plotSSD-methods	1.90	0.02	1.92
readlength-methods	0.01	0.01	0.03
reads-methods	0.02	0.02	0.03
regi-methods	0.08	0.01	0.10
ribl-methods	0.00	0.02	0.01
rip-methods	0.03	0.00	0.03
ssd-methods	0.01	0.00	0.02

name	user	system	elapsed
ChIPQC-data	2.59	0.05	3.14
ChIPQC	1.87	0.00	1.87
ChIPQCexperiment-class	0.81	0.05	0.86
ChIPQCreport	60.39	20.50	81.66
ChIPQCsample-class	1.22	0.00	1.22
FragmentLengthCrossCoverage-methods	0.12	0.00	0.13
Normalisedaveragepeaksignal-methods	0.02	0.01	0.03
QCannotation-methods	0.02	0.02	0.03
QCcontrol-methods	0.21	0.00	0.22
QCdba-methods	0.10	0.01	0.11
QCmetadata-methods	0.12	0.00	0.12
QCmetrics-methods	0.84	0.03	0.87
QCsample-methods	0.08	0.00	0.08
ReadLengthCrossCoverage-methods	0.03	0.00	0.03
RelativeCrossCoverage-methods	0.08	0.02	0.09
averagepeaksignal-methods	0.03	0.00	0.03
coveragehistogram-methods	0.05	0.00	0.05
crosscoverage-methods	0.01	0.02	0.03
duplicateRate-methods	0.02	0.01	0.03
duplicates-methods	0.01	0.02	0.03
flagtagcounts-methods	0.02	0.01	0.04
fragmentlength-methods	0.09	0.02	0.10
frip-methods	0.02	0.01	0.04
mapped-methods	0.01	0.00	0.01
peaks-methods	0.1	0.0	0.1
plotCC-methods	1.29	0.00	1.29
plotCorHeatmap-methods	3.17	0.02	3.18
plotCoverageHist-methods	0.81	0.00	0.81
plotFribl-methods	1.19	0.00	1.18
plotFrip-methods	1.26	0.00	1.27
plotPeakProfile-methods	2.23	0.00	2.43
plotPrincomp-methods	4.14	0.06	4.20
plotRap-methods	1.46	0.02	1.48
plotRegi-methods	2.50	0.03	2.52
plotSSD-methods	1.7	0.0	1.7
readlength-methods	0.02	0.02	0.03
reads-methods	0.01	0.02	0.04
regi-methods	0.10	0.01	0.11
ribl-methods	0.00	0.02	0.01
rip-methods	0.01	0.01	0.03
ssd-methods	0.02	0.00	0.02