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BioC 3.5: CHECK report for ChIPQC on tokay2

This page was generated on 2017-10-18 14:23:22 -0400 (Wed, 18 Oct 2017).

Package 209/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPQC 1.12.3
Tom Carroll , Rory Stark
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/ChIPQC
Branch: RELEASE_3_5
Last Commit: 4e432cd
Last Changed Date: 2017-08-08 13:33:45 -0400 (Tue, 08 Aug 2017)
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
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ChIPQC
Version: 1.12.3
Command: rm -rf ChIPQC.buildbin-libdir ChIPQC.Rcheck && mkdir ChIPQC.buildbin-libdir ChIPQC.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPQC.buildbin-libdir ChIPQC_1.12.3.tar.gz >ChIPQC.Rcheck\00install.out 2>&1 && cp ChIPQC.Rcheck\00install.out ChIPQC-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=ChIPQC.buildbin-libdir --install="check:ChIPQC-install.out" --force-multiarch --no-vignettes --timings ChIPQC_1.12.3.tar.gz
StartedAt: 2017-10-17 22:41:57 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 22:51:09 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 552.4 seconds
RetCode: 0
Status:  OK  
CheckDir: ChIPQC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ChIPQC.buildbin-libdir ChIPQC.Rcheck && mkdir ChIPQC.buildbin-libdir ChIPQC.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPQC.buildbin-libdir ChIPQC_1.12.3.tar.gz >ChIPQC.Rcheck\00install.out 2>&1 && cp ChIPQC.Rcheck\00install.out ChIPQC-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=ChIPQC.buildbin-libdir --install="check:ChIPQC-install.out" --force-multiarch --no-vignettes --timings ChIPQC_1.12.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/ChIPQC.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-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 '1.12.3'
* 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 ... NOTE
Namespace in Imports field not imported from: 'TxDb.Hsapiens.UCSC.hg38.knownGene'
  All declared Imports should be used.
Unexported object imported by a ':::' call: 'S4Vectors:::tabulate2'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'makeFripPlot' 'mergeMetadata'
* 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.hg38.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'
makeSSDPlot: no visible binding for global variable 'Sample'
makeSSDPlot: no visible binding for global variable 'SSD'
makeSSDPlot: no visible global function definition for 'geom_point'
sampleQC: no visible global function definition for 'seqlevels<-'
plotCC,ChIPQCexperiment: no visible binding for global variable
  'Sample'
plotCC,list: no visible binding for global variable 'Sample'
plotPeakProfile,ChIPQCexperiment: no visible binding for global
  variable 'Sample'
plotPeakProfile,list: no visible binding for global variable 'Sample'
Undefined global functions or variables:
  CC_Score CountsInPeaks Depth Distance FRIBL FRIP GenomicIntervals
  Reads SSD Sample Shift_Size Signal TxDb.Hsapiens.UCSC.hg38.knownGene
  geom_point log10_bp log2_Enrichment seqlengths seqlengths<-
  seqlevels<-
Consider adding
  importFrom("stats", "SSD")
to your NAMESPACE file.
* 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 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
ChIPQCreport 28.19   2.55   30.83
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
ChIPQCreport 29.36   2.23   31.79
* 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/ChIPQC.Rcheck/00check.log'
for details.


ChIPQC.Rcheck/00install.out:


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_1.12.3.zip
* DONE (ChIPQC)

ChIPQC.Rcheck/examples_i386/ChIPQC-Ex.timings:

nameusersystemelapsed
ChIPQC-data2.230.062.30
ChIPQC0.450.080.53
ChIPQCexperiment-class0.890.050.93
ChIPQCreport28.19 2.5530.83
ChIPQCsample-class1.750.001.75
FragmentLengthCrossCoverage-methods0.060.010.08
Normalisedaveragepeaksignal-methods0.040.000.03
QCannotation-methods0.010.020.03
QCcontrol-methods0.250.010.27
QCdba-methods0.160.000.15
QCmetadata-methods0.140.000.14
QCmetrics-methods0.370.030.41
QCsample-methods0.050.000.05
ReadLengthCrossCoverage-methods0.030.000.03
RelativeCrossCoverage-methods0.060.000.06
averagepeaksignal-methods0.030.000.03
coveragehistogram-methods0.040.020.05
crosscoverage-methods0.030.000.03
duplicateRate-methods0.010.020.03
duplicates-methods0.020.000.02
flagtagcounts-methods0.010.010.03
fragmentlength-methods0.050.020.06
frip-methods0.020.000.02
mapped-methods0.020.000.02
peaks-methods0.060.000.06
plotCC-methods1.480.001.49
plotCorHeatmap-methods0.250.010.26
plotCoverageHist-methods0.610.000.61
plotFribl-methods0.630.000.63
plotFrip-methods0.660.020.67
plotPeakProfile-methods1.680.001.68
plotPrincomp-methods0.250.010.27
plotRap-methods1.240.001.23
plotRegi-methods1.170.021.19
plotSSD-methods1.580.001.58
readlength-methods0.010.000.02
reads-methods0.010.000.02
regi-methods0.040.020.04
ribl-methods0.020.000.02
rip-methods0.030.000.03
ssd-methods0.010.000.01

ChIPQC.Rcheck/examples_x64/ChIPQC-Ex.timings:

nameusersystemelapsed
ChIPQC-data3.310.013.33
ChIPQC0.520.030.54
ChIPQCexperiment-class1.050.021.07
ChIPQCreport29.36 2.2331.79
ChIPQCsample-class2.140.022.16
FragmentLengthCrossCoverage-methods0.080.000.08
Normalisedaveragepeaksignal-methods0.060.020.08
QCannotation-methods0.030.000.03
QCcontrol-methods0.470.000.47
QCdba-methods0.160.010.17
QCmetadata-methods0.160.000.16
QCmetrics-methods0.420.030.45
QCsample-methods0.040.020.07
ReadLengthCrossCoverage-methods0.020.000.01
RelativeCrossCoverage-methods0.060.010.08
averagepeaksignal-methods0.020.020.03
coveragehistogram-methods0.030.020.05
crosscoverage-methods0.030.000.03
duplicateRate-methods0.020.000.01
duplicates-methods0.010.010.04
flagtagcounts-methods0.020.000.01
fragmentlength-methods0.060.020.08
frip-methods0.020.000.02
mapped-methods0.030.000.03
peaks-methods0.060.000.06
plotCC-methods1.530.001.53
plotCorHeatmap-methods0.390.000.39
plotCoverageHist-methods0.830.010.84
plotFribl-methods0.770.020.79
plotFrip-methods0.710.010.73
plotPeakProfile-methods2.600.022.61
plotPrincomp-methods0.250.010.27
plotRap-methods0.870.000.87
plotRegi-methods1.630.001.63
plotSSD-methods1.590.001.59
readlength-methods0.020.020.03
reads-methods0.010.000.02
regi-methods0.030.020.04
ribl-methods0.020.010.03
rip-methods0.020.000.02
ssd-methods0.010.000.02