BioC 2.14: CHECK report for ChIPQC on moscato2

Package: ChIPQC

Version: 1.0.9

Command: rm -rf ChIPQC.buildbin-libdir && mkdir ChIPQC.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPQC.buildbin-libdir ChIPQC_1.0.9.tar.gz >ChIPQC-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=ChIPQC.buildbin-libdir --install="check:ChIPQC-install.out" --force-multiarch --no-vignettes --timings ChIPQC_1.0.9.tar.gz

StartedAt: 2014-10-07 23:39:41 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:47:34 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 473.4 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 && mkdir ChIPQC.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPQC.buildbin-libdir ChIPQC_1.0.9.tar.gz >ChIPQC-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=ChIPQC.buildbin-libdir --install="check:ChIPQC-install.out" --force-multiarch --no-vignettes --timings ChIPQC_1.0.9.tar.gz
###
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* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/ChIPQC.Rcheck'
* using R version 3.1.1 (2014-07-10)
* 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 '1.0.9'
* 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 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 ... 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 ...
** running examples for arch 'i386' ... [72s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
ChIPQCreport 30.17  14.74   45.14
** running examples for arch 'x64' ... [83s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
ChIPQCreport 35.09  14.71   49.95
* 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
  'E:/biocbld/bbs-2.14-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_1.0.9.zip
* DONE (ChIPQC)

name	user	system	elapsed
ChIPQC-data	1.76	0.01	1.82
ChIPQC	0.78	0.00	0.78
ChIPQCexperiment-class	0.76	0.00	0.76
ChIPQCreport	30.17	14.74	45.14
ChIPQCsample-class	1.23	0.05	1.43
FragmentLengthCrossCoverage-methods	0.13	0.00	0.13
Normalisedaveragepeaksignal-methods	0.03	0.00	0.03
QCannotation-methods	0.02	0.00	0.01
QCcontrol-methods	0.28	0.00	0.28
QCdba-methods	0.12	0.00	0.13
QCmetadata-methods	0.14	0.00	0.14
QCmetrics-methods	0.63	0.02	0.64
QCsample-methods	0.09	0.00	0.09
ReadLengthCrossCoverage-methods	0.01	0.00	0.02
RelativeCrossCoverage-methods	0.10	0.00	0.09
averagepeaksignal-methods	0.03	0.00	0.03
coveragehistogram-methods	0.03	0.00	0.03
crosscoverage-methods	0.03	0.00	0.03
duplicateRate-methods	0.02	0.00	0.02
duplicates-methods	0.01	0.00	0.02
flagtagcounts-methods	0.02	0.00	0.01
fragmentlength-methods	0.09	0.00	0.10
frip-methods	0.02	0.00	0.01
mapped-methods	0.01	0.00	0.02
peaks-methods	0.13	0.00	0.12
plotCC-methods	0.92	0.00	0.92
plotCorHeatmap-methods	0.93	0.01	0.95
plotCoverageHist-methods	0.57	0.00	0.56
plotFribl-methods	0.60	0.00	0.61
plotFrip-methods	0.61	0.00	0.61
plotPeakProfile-methods	1.53	0.00	1.53
plotPrincomp-methods	1.16	0.00	1.15
plotRap-methods	0.89	0.03	0.93
plotRegi-methods	1.37	0.02	1.39
plotSSD-methods	1.33	0.01	1.34
readlength-methods	0.02	0.00	0.02
reads-methods	0.01	0.02	0.03
regi-methods	0.05	0.00	0.04
ribl-methods	0.03	0.00	0.04
rip-methods	0.01	0.00	0.01
ssd-methods	0.02	0.00	0.02

name	user	system	elapsed
ChIPQC-data	2.22	0.04	2.26
ChIPQC	0.99	0.00	1.00
ChIPQCexperiment-class	1.03	0.02	1.04
ChIPQCreport	35.09	14.71	49.95
ChIPQCsample-class	1.48	0.02	1.50
FragmentLengthCrossCoverage-methods	0.11	0.00	0.11
Normalisedaveragepeaksignal-methods	0.03	0.00	0.03
QCannotation-methods	0.02	0.00	0.02
QCcontrol-methods	0.28	0.01	0.29
QCdba-methods	0.11	0.00	0.11
QCmetadata-methods	0.12	0.00	0.13
QCmetrics-methods	0.72	0.02	0.73
QCsample-methods	0.45	0.00	0.45
ReadLengthCrossCoverage-methods	0.02	0.00	0.02
RelativeCrossCoverage-methods	0.11	0.00	0.11
averagepeaksignal-methods	0.03	0.00	0.12
coveragehistogram-methods	0.03	0.00	0.04
crosscoverage-methods	0.03	0.00	0.03
duplicateRate-methods	0.02	0.00	0.01
duplicates-methods	0.01	0.00	0.02
flagtagcounts-methods	0.02	0.00	0.01
fragmentlength-methods	0.11	0.00	0.11
frip-methods	0.01	0.00	0.02
mapped-methods	0.02	0.00	0.01
peaks-methods	0.14	0.00	0.14
plotCC-methods	0.98	0.00	0.99
plotCorHeatmap-methods	0.86	0.04	0.95
plotCoverageHist-methods	0.64	0.00	0.64
plotFribl-methods	0.72	0.00	0.72
plotFrip-methods	0.71	0.00	0.71
plotPeakProfile-methods	2.04	0.02	2.06
plotPrincomp-methods	1.61	0.01	1.62
plotRap-methods	1.00	0.02	1.01
plotRegi-methods	1.40	0.00	1.52
plotSSD-methods	1.69	0.00	1.68
readlength-methods	0.01	0.00	0.02
reads-methods	0.02	0.00	0.01
regi-methods	0.06	0.00	0.07
ribl-methods	0.02	0.00	0.01
rip-methods	0.01	0.00	0.02
ssd-methods	0.00	0.02	0.01