BioC 2.14: CHECK report for ChIPQC on morelia

Package: ChIPQC

Version: 1.0.9

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ChIPQC_1.0.9.tar.gz

StartedAt: 2014-10-07 21:50:41 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 21:56:24 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 343.4 seconds

RetCode: 0

Status:  OK

CheckDir: ChIPQC.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ChIPQC_1.0.9.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/ChIPQC.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (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 ... [26s/26s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [74s/74s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
ChIPQCreport 41.737  1.332  43.036
* 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
  ‘/Users/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	1.840	0.032	1.875
ChIPQC	0.958	0.014	0.974
ChIPQCexperiment-class	0.968	0.022	0.995
ChIPQCreport	41.737	1.332	43.036
ChIPQCsample-class	1.464	0.024	1.523
FragmentLengthCrossCoverage-methods	0.082	0.004	0.087
Normalisedaveragepeaksignal-methods	0.022	0.005	0.027
QCannotation-methods	0.014	0.004	0.019
QCcontrol-methods	0.273	0.009	0.282
QCdba-methods	0.107	0.005	0.112
QCmetadata-methods	0.113	0.007	0.120
QCmetrics-methods	0.718	0.013	0.733
QCsample-methods	0.094	0.006	0.101
ReadLengthCrossCoverage-methods	0.014	0.005	0.018
RelativeCrossCoverage-methods	0.107	0.005	0.112
averagepeaksignal-methods	0.022	0.005	0.028
coveragehistogram-methods	0.023	0.005	0.028
crosscoverage-methods	0.021	0.006	0.028
duplicateRate-methods	0.013	0.005	0.018
duplicates-methods	0.015	0.005	0.020
flagtagcounts-methods	0.013	0.004	0.019
fragmentlength-methods	0.095	0.005	0.102
frip-methods	0.014	0.005	0.018
mapped-methods	0.014	0.005	0.019
peaks-methods	0.150	0.005	0.155
plotCC-methods	0.870	0.013	0.884
plotCorHeatmap-methods	1.013	0.051	1.065
plotCoverageHist-methods	0.632	0.010	0.644
plotFribl-methods	0.649	0.009	0.671
plotFrip-methods	0.687	0.005	0.694
plotPeakProfile-methods	1.907	0.052	1.960
plotPrincomp-methods	1.360	0.061	1.423
plotRap-methods	1.038	0.008	1.048
plotRegi-methods	1.322	0.014	1.338
plotSSD-methods	1.441	0.016	1.466
readlength-methods	0.014	0.005	0.020
reads-methods	0.015	0.005	0.020
regi-methods	0.068	0.006	0.075
ribl-methods	0.015	0.006	0.021
rip-methods	0.015	0.005	0.020
ssd-methods	0.013	0.004	0.017