Back to the "Multiple platform build/check report" A  B [C] D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 2.14: CHECK report for ChIPQC on petty

This page was generated on 2014-10-08 09:01:49 -0700 (Wed, 08 Oct 2014).

Package 142/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPQC 1.0.9
Tom Carroll , Rory Stark
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/ChIPQC
Last Changed Rev: 92896 / Revision: 95116
Last Changed Date: 2014-07-27 11:50:41 -0700 (Sun, 27 Jul 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

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 21:12:57 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 21:23:43 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 646.3 seconds
RetCode: 0
Status:  OK 
CheckDir: ChIPQC.Rcheck
Warnings: 0

Command output

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


* 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-darwin10.8.0 (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 ... [46s/49s] 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 ... [144s/146s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
ChIPQCreport 88.858  2.621  93.047
* 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.

ChIPQC.Rcheck/00install.out:

* 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)

ChIPQC.Rcheck/ChIPQC-Ex.timings:

nameusersystemelapsed
ChIPQC-data3.9160.0874.019
ChIPQC1.6050.0271.644
ChIPQCexperiment-class1.5540.0371.601
ChIPQCreport88.858 2.62193.047
ChIPQCsample-class2.5860.0492.875
FragmentLengthCrossCoverage-methods0.1740.0070.196
Normalisedaveragepeaksignal-methods0.0330.0070.043
QCannotation-methods0.0190.0060.026
QCcontrol-methods0.5050.0160.536
QCdba-methods0.1730.0090.202
QCmetadata-methods0.1880.0110.209
QCmetrics-methods1.1800.0211.202
QCsample-methods0.1560.0090.165
ReadLengthCrossCoverage-methods0.0220.0080.030
RelativeCrossCoverage-methods0.1750.0090.184
averagepeaksignal-methods0.0380.0110.049
coveragehistogram-methods0.0340.0100.046
crosscoverage-methods0.0330.0100.042
duplicateRate-methods0.0220.0090.032
duplicates-methods0.0220.0090.030
flagtagcounts-methods0.0220.0090.031
fragmentlength-methods0.1710.0100.181
frip-methods0.0200.0090.030
mapped-methods0.0210.0080.029
peaks-methods0.2450.0100.255
plotCC-methods1.3920.0201.437
plotCorHeatmap-methods1.3560.1041.465
plotCoverageHist-methods1.0670.0151.098
plotFribl-methods1.1470.0081.168
plotFrip-methods1.2050.0091.229
plotPeakProfile-methods3.2860.0753.409
plotPrincomp-methods1.7450.1101.890
plotRap-methods1.7180.0191.743
plotRegi-methods2.3630.0292.395
plotSSD-methods2.3550.0302.462
readlength-methods0.0210.0130.036
reads-methods0.0210.0120.033
regi-methods0.1060.0140.125
ribl-methods0.0210.0110.034
rip-methods0.0210.0120.033
ssd-methods0.0210.0110.032