BioC 3.3: CHECK report for ChIPQC on linux2.bioconductor.org

Package: ChIPQC

Version: 1.7.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings ChIPQC_1.7.0.tar.gz

StartedAt: 2015-10-27 02:28:31 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 02:33:53 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 321.5 seconds

RetCode: 0

Status:  OK

CheckDir: ChIPQC.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings ChIPQC_1.7.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/ChIPQC.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPQC’ version ‘1.7.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ChIPQC’ can be installed ... [25s/25s] 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
* 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’
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’
plotSSD,ChIPQCexperiment: no visible binding for global variable
  ‘shiftlength’
plotSSD,ChIPQCexperiment: no visible binding for global variable
  ‘ccvector’
plotSSD,ChIPQCexperiment: no visible binding for global variable
  ‘readlen’
Undefined global functions or variables:
  CC_Score CountsInPeaks Depth Distance FRIBL FRIP GenomicIntervals
  Reads Sample Shift_Size Signal 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
  ccvector cdsBy coord_cartesian fiveUTRsByTranscript
  intronsByTranscript log10_bp log2_Enrichment readlen seqlengths
  seqlengths<- seqlevels<- shiftlength threeUTRsByTranscript
  transcripts
* 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 ... [66s/66s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
ChIPQCreport 38.187  0.414   38.66
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/ChIPQC.Rcheck/00check.log’
for details.

* 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
* DONE (ChIPQC)

name	user	system	elapsed
ChIPQC-data	0.896	0.016	0.913
ChIPQC	0.804	0.000	0.805
ChIPQCexperiment-class	0.337	0.008	0.345
ChIPQCreport	38.187	0.414	38.660
ChIPQCsample-class	0.55	0.04	0.59
FragmentLengthCrossCoverage-methods	0.061	0.000	0.061
Normalisedaveragepeaksignal-methods	0.019	0.000	0.019
QCannotation-methods	0.011	0.000	0.011
QCcontrol-methods	0.191	0.000	0.191
QCdba-methods	0.077	0.004	0.081
QCmetadata-methods	0.126	0.000	0.126
QCmetrics-methods	0.576	0.012	0.588
QCsample-methods	0.049	0.000	0.050
ReadLengthCrossCoverage-methods	0.013	0.000	0.012
RelativeCrossCoverage-methods	0.061	0.000	0.060
averagepeaksignal-methods	0.019	0.000	0.020
coveragehistogram-methods	0.018	0.000	0.018
crosscoverage-methods	0.017	0.000	0.017
duplicateRate-methods	0.013	0.000	0.012
duplicates-methods	0.009	0.004	0.013
flagtagcounts-methods	0.012	0.000	0.012
fragmentlength-methods	0.048	0.000	0.047
frip-methods	0.012	0.000	0.012
mapped-methods	0.011	0.000	0.011
peaks-methods	0.051	0.000	0.051
plotCC-methods	0.523	0.000	0.524
plotCorHeatmap-methods	2.556	0.048	2.613
plotCoverageHist-methods	0.349	0.000	0.348
plotFribl-methods	0.416	0.000	0.416
plotFrip-methods	0.4	0.0	0.4
plotPeakProfile-methods	1.660	0.000	1.662
plotPrincomp-methods	2.127	0.008	2.137
plotRap-methods	0.519	0.008	0.528
plotRegi-methods	0.828	0.000	0.829
readlength-methods	0.012	0.000	0.012
reads-methods	0.011	0.000	0.011
regi-methods	0.035	0.004	0.039
ribl-methods	0.012	0.000	0.011
rip-methods	0.011	0.000	0.012
ssd-methods	0.007	0.004	0.011