BioC 2.14: CHECK report for ChIPQC on zin2

Package: ChIPQC

Version: 1.0.9

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings ChIPQC_1.0.9.tar.gz

StartedAt: 2014-10-07 22:31:47 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:36:29 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 282.2 seconds

RetCode: 0

Status:  OK

CheckDir: ChIPQC.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings ChIPQC_1.0.9.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/ChIPQC.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-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 ‘1.0.9’
* 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 ... [21s/21s] 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
* 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 ... OK
* 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 the chapter ‘System and foreign language interfaces’ of 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'
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’
plotCC,ChIPQCexperiment: no visible binding for global variable
  ‘Sample’
plotPeakProfile,ChIPQCexperiment: no visible binding for global
  variable ‘Sample’
* 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 ... [60s/61s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
ChIPQCreport 33.15  0.216  33.515
* 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.14-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	1.568	0.024	1.596
ChIPQC	0.800	0.004	0.808
ChIPQCexperiment-class	0.824	0.004	0.829
ChIPQCreport	33.150	0.216	33.515
ChIPQCsample-class	1.312	0.012	1.328
FragmentLengthCrossCoverage-methods	0.084	0.000	0.081
Normalisedaveragepeaksignal-methods	0.024	0.000	0.022
QCannotation-methods	0.012	0.000	0.012
QCcontrol-methods	0.237	0.004	0.243
QCdba-methods	0.088	0.008	0.097
QCmetadata-methods	0.104	0.000	0.105
QCmetrics-methods	0.572	0.004	0.576
QCsample-methods	0.088	0.000	0.087
ReadLengthCrossCoverage-methods	0.016	0.000	0.015
RelativeCrossCoverage-methods	0.092	0.000	0.093
averagepeaksignal-methods	0.024	0.000	0.026
coveragehistogram-methods	0.016	0.008	0.024
crosscoverage-methods	0.024	0.000	0.022
duplicateRate-methods	0.016	0.000	0.015
duplicates-methods	0.016	0.000	0.014
flagtagcounts-methods	0.016	0.000	0.014
fragmentlength-methods	0.088	0.000	0.088
frip-methods	0.016	0.000	0.015
mapped-methods	0.016	0.000	0.014
peaks-methods	0.120	0.000	0.118
plotCC-methods	0.692	0.004	0.695
plotCorHeatmap-methods	0.944	0.020	0.969
plotCoverageHist-methods	0.580	0.000	0.609
plotFribl-methods	0.576	0.000	0.577
plotFrip-methods	0.604	0.000	0.605
plotPeakProfile-methods	1.552	0.000	1.564
plotPrincomp-methods	1.496	0.004	1.504
plotRap-methods	0.888	0.000	0.928
plotRegi-methods	1.2	0.0	1.2
plotSSD-methods	1.356	0.004	1.361
readlength-methods	0.012	0.000	0.013
reads-methods	0.012	0.000	0.013
regi-methods	0.056	0.000	0.055
ribl-methods	0.012	0.000	0.013
rip-methods	0.012	0.000	0.012
ssd-methods	0.012	0.000	0.012