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BioC 3.5: CHECK report for ChIPQC on oaxaca

This page was generated on 2016-11-12 16:26:59 -0500 (Sat, 12 Nov 2016).

Package 193/1294HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPQC 1.11.0
Tom Carroll , Rory Stark
Snapshot Date: 2016-11-11 17:15:18 -0500 (Fri, 11 Nov 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChIPQC
Last Changed Rev: 122712 / Revision: 123911
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ChIPQC
Version: 1.11.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChIPQC_1.11.0.tar.gz
StartedAt: 2016-11-11 22:57:27 -0800 (Fri, 11 Nov 2016)
EndedAt: 2016-11-11 23:03:38 -0800 (Fri, 11 Nov 2016)
EllapsedTime: 370.4 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 ChIPQC_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ChIPQC.Rcheck’
* using R Under development (unstable) (2016-10-21 r71549)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.11.0’
* 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 ... 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 ... NOTE
Unexported object imported by a ':::' call: ‘S4Vectors:::tabulate2’
  See the note in ?`:::` about the use of this operator.
* 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: 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.hg20.knownGene’
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’
Undefined global functions or variables:
  CC_Score CountsInPeaks Depth Distance FRIBL FRIP GenomicIntervals
  Reads Sample Shift_Size Signal TxDb.Hsapiens.UCSC.hg20.knownGene
  log10_bp log2_Enrichment seqlengths seqlengths<- seqlevels<-
* 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 ... NOTE
  Error : .onLoad failed in loadNamespace() for 'TxDb.Hsapiens.UCSC.hg19.knownGene', details:
    call: initialize(value, ...)
    error: attempt to apply non-function
  Error in .requirePackage(package) : 
    unable to find required package 'ChIPQC'
  Calls: <Anonymous> ... getClass -> getClassDef -> .classEnv -> .requirePackage
  Execution halted
* 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 ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
ChIPQCreport 37.406  1.398  39.062
* 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
  ‘/Users/biocbuild/bbs-3.5-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-data2.1150.0692.263
ChIPQC0.6150.0190.634
ChIPQCexperiment-class0.5760.0210.596
ChIPQCreport37.406 1.39839.062
ChIPQCsample-class1.1420.0231.293
FragmentLengthCrossCoverage-methods0.0640.0040.068
Normalisedaveragepeaksignal-methods0.0240.0060.031
QCannotation-methods0.0160.0040.021
QCcontrol-methods0.2360.0130.249
QCdba-methods0.1360.0090.145
QCmetadata-methods0.1590.0100.170
QCmetrics-methods0.5980.0160.614
QCsample-methods0.0610.0080.069
ReadLengthCrossCoverage-methods0.0190.0080.026
RelativeCrossCoverage-methods0.0750.0070.082
averagepeaksignal-methods0.0270.0060.042
coveragehistogram-methods0.0290.0080.038
crosscoverage-methods0.0250.0080.033
duplicateRate-methods0.0200.0070.027
duplicates-methods0.0190.0060.026
flagtagcounts-methods0.0200.0070.026
fragmentlength-methods0.0880.0080.095
frip-methods0.0210.0070.028
mapped-methods0.0200.0080.028
peaks-methods0.0640.0070.071
plotCC-methods0.7730.0100.786
plotCorHeatmap-methods0.3050.0120.317
plotCoverageHist-methods0.7180.0090.728
plotFribl-methods0.8610.0110.873
plotFrip-methods0.7710.0100.798
plotPeakProfile-methods1.7870.0411.830
plotPrincomp-methods0.3320.0120.346
plotRap-methods1.5390.0181.558
plotRegi-methods1.5770.0251.604
readlength-methods0.0200.0070.028
reads-methods0.0190.0060.026
regi-methods0.0630.0070.070
ribl-methods0.0200.0070.027
rip-methods0.0200.0060.025
ssd-methods0.0210.0070.027