Multiple platform build/check report for BioC 3.6 - CHECK report for ChIPQC on tokay1

Package: ChIPQC

Version: 1.14.0

Command: rm -rf ChIPQC.buildbin-libdir ChIPQC.Rcheck && mkdir ChIPQC.buildbin-libdir ChIPQC.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPQC.buildbin-libdir ChIPQC_1.14.0.tar.gz >ChIPQC.Rcheck\00install.out 2>&1 && cp ChIPQC.Rcheck\00install.out ChIPQC-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ChIPQC.buildbin-libdir --install="check:ChIPQC-install.out" --force-multiarch --no-vignettes --timings ChIPQC_1.14.0.tar.gz

StartedAt: 2018-04-11 22:51:52 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 23:01:28 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 576.2 seconds

RetCode: 0

Status: OK

CheckDir: ChIPQC.Rcheck

Warnings: 0

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### Running command:
###
###   rm -rf ChIPQC.buildbin-libdir ChIPQC.Rcheck && mkdir ChIPQC.buildbin-libdir ChIPQC.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPQC.buildbin-libdir ChIPQC_1.14.0.tar.gz >ChIPQC.Rcheck\00install.out 2>&1 && cp ChIPQC.Rcheck\00install.out ChIPQC-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ChIPQC.buildbin-libdir --install="check:ChIPQC-install.out" --force-multiarch --no-vignettes --timings ChIPQC_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ChIPQC.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.14.0'
* 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 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
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.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 35.21   2.64    38.2
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
ChIPQCreport 32.86   2.12   35.46
* 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-3.6-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
  converting help for package 'ChIPQC'
    finding HTML links ... done
    ChIPQC-data                             html  
    finding level-2 HTML links ... done

    ChIPQC-package                          html  
    ChIPQC                                  html  
    ChIPQCexperiment-class                  html  
    ChIPQCreport                            html  
    ChIPQCsample-class                      html  
    FragmentLengthCrossCoverage-methods     html  
    Normalisedaveragepeaksignal-methods     html  
    QCannotation-methods                    html  
    QCcontrol-methods                       html  
    QCdba-methods                           html  
    QCmetadata-methods                      html  
    QCmetrics-methods                       html  
    QCsample-methods                        html  
    ReadLengthCrossCoverage-methods         html  
    RelativeCrossCoverage-methods           html  
    averagepeaksignal-methods               html  
    coveragehistogram-methods               html  
    crosscoverage-methods                   html  
    duplicateRate-methods                   html  
    duplicates-methods                      html  
    flagtagcounts-methods                   html  
    fragmentlength-methods                  html  
    frip-methods                            html  
    mapped-methods                          html  
    peaks-methods                           html  
    plotCC-methods                          html  
    plotCorHeatmap-methods                  html  
    plotCoverageHist-methods                html  
    plotFribl-methods                       html  
    plotFrip-methods                        html  
    plotPeakProfile-methods                 html  
    plotPrincomp-methods                    html  
    plotRap-methods                         html  
    plotRegi-methods                        html  
    plotSSD-methods                         html  
    readlength-methods                      html  
    reads-methods                           html  
    regi-methods                            html  
    ribl-methods                            html  
    rip-methods                             html  
    ssd-methods                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'ChIPQC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ChIPQC' as ChIPQC_1.14.0.zip
* DONE (ChIPQC)
In R CMD INSTALL
In R CMD INSTALL

name	user	system	elapsed
ChIPQC-data	2.38	0.16	2.53
ChIPQC	0.36	0.05	0.41
ChIPQCexperiment-class	0.85	0.01	0.86
ChIPQCreport	35.21	2.64	38.20
ChIPQCsample-class	2.62	0.02	2.66
FragmentLengthCrossCoverage-methods	0.10	0.00	0.09
Normalisedaveragepeaksignal-methods	0.06	0.01	0.08
QCannotation-methods	0.03	0.00	0.03
QCcontrol-methods	0.47	0.00	0.47
QCdba-methods	0.17	0.02	0.19
QCmetadata-methods	0.16	0.01	0.17
QCmetrics-methods	0.42	0.00	0.42
QCsample-methods	0.05	0.00	0.05
ReadLengthCrossCoverage-methods	0.01	0.02	0.03
RelativeCrossCoverage-methods	0.07	0.00	0.06
averagepeaksignal-methods	0.03	0.00	0.03
coveragehistogram-methods	0.03	0.02	0.05
crosscoverage-methods	0.04	0.00	0.03
duplicateRate-methods	0.01	0.01	0.03
duplicates-methods	0.03	0.00	0.03
flagtagcounts-methods	0.02	0.00	0.02
fragmentlength-methods	0.06	0.00	0.06
frip-methods	0.02	0.02	0.03
mapped-methods	0.01	0.03	0.05
peaks-methods	0.08	0.00	0.08
plotCC-methods	2.41	0.01	2.42
plotCorHeatmap-methods	0.37	0.03	0.40
plotCoverageHist-methods	0.66	0.00	0.66
plotFribl-methods	0.7	0.0	0.7
plotFrip-methods	0.78	0.00	0.78
plotPeakProfile-methods	2.58	0.02	2.60
plotPrincomp-methods	0.37	0.02	0.39
plotRap-methods	0.88	0.00	0.87
plotRegi-methods	1.72	0.01	1.74
plotSSD-methods	3.22	0.03	3.25
readlength-methods	0.01	0.02	0.03
reads-methods	0.02	0.00	0.02
regi-methods	0.05	0.00	0.05
ribl-methods	0.02	0.01	0.03
rip-methods	0.04	0.00	0.05
ssd-methods	0.03	0.00	0.03

name	user	system	elapsed
ChIPQC-data	2.92	0.01	2.94
ChIPQC	0.45	0.00	0.45
ChIPQCexperiment-class	1.24	0.02	1.25
ChIPQCreport	32.86	2.12	35.46
ChIPQCsample-class	2.75	0.05	2.79
FragmentLengthCrossCoverage-methods	0.06	0.00	0.06
Normalisedaveragepeaksignal-methods	0.03	0.00	0.03
QCannotation-methods	0.02	0.02	0.03
QCcontrol-methods	0.3	0.0	0.3
QCdba-methods	0.12	0.00	0.12
QCmetadata-methods	0.13	0.00	0.13
QCmetrics-methods	0.46	0.01	0.48
QCsample-methods	0.05	0.00	0.05
ReadLengthCrossCoverage-methods	0.01	0.02	0.03
RelativeCrossCoverage-methods	0.07	0.00	0.06
averagepeaksignal-methods	0.03	0.01	0.05
coveragehistogram-methods	0.03	0.00	0.03
crosscoverage-methods	0.03	0.00	0.03
duplicateRate-methods	0.01	0.00	0.02
duplicates-methods	0.02	0.02	0.03
flagtagcounts-methods	0.02	0.00	0.01
fragmentlength-methods	0.06	0.01	0.08
frip-methods	0.01	0.00	0.02
mapped-methods	0.02	0.02	0.03
peaks-methods	0.06	0.00	0.06
plotCC-methods	1.71	0.02	1.72
plotCorHeatmap-methods	0.23	0.00	0.23
plotCoverageHist-methods	0.72	0.01	0.74
plotFribl-methods	0.78	0.00	0.78
plotFrip-methods	0.81	0.02	0.83
plotPeakProfile-methods	1.94	0.01	1.95
plotPrincomp-methods	0.34	0.00	0.34
plotRap-methods	1.08	0.00	1.08
plotRegi-methods	1.42	0.00	1.42
plotSSD-methods	1.78	0.02	1.80
readlength-methods	0.00	0.01	0.01
reads-methods	0.00	0.03	0.03
regi-methods	0.05	0.00	0.05
ribl-methods	0.01	0.02	0.03
rip-methods	0.02	0.00	0.02
ssd-methods	0.01	0.02	0.03

CHECK report for ChIPQC on tokay1

Summary

Command output

Installation output

Tests output

Example timings