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This page was generated on 2021-07-23 15:05:59 -0400 (Fri, 23 Jul 2021).

CHECK results for ChIPQC on tokay2

To the developers/maintainers of the ChIPQC package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChIPQC.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 295/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPQC 1.28.0  (landing page)
Tom Carroll , Rory Stark
Snapshot Date: 2021-07-22 04:50:13 -0400 (Thu, 22 Jul 2021)
URL: https://git.bioconductor.org/packages/ChIPQC
Branch: RELEASE_3_13
Last Commit: 047a9a4
Last Changed Date: 2021-05-19 12:04:03 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: ChIPQC
Version: 1.28.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ChIPQC_1.28.0.tar.gz
StartedAt: 2021-07-22 21:09:57 -0400 (Thu, 22 Jul 2021)
EndedAt: 2021-07-22 21:20:23 -0400 (Thu, 22 Jul 2021)
EllapsedTime: 625.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ChIPQC.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ChIPQC_1.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ChIPQC.Rcheck'
* using R version 4.1.0 (2021-05-18)
* 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 '1.28.0'
* 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
* 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 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 ... WARNING
  Error loading dataset 'exampleExp':
   Error in .requirePackage(package) : 
    unable to find required package 'ChIPQC'
  
  Error loading dataset 'tamoxifen':
   Error in .requirePackage(package) : 
    unable to find required package 'ChIPQC'
  
  The dataset(s) may use package(s) not declared in the DESCRIPTION file.
* 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 (user + system) or elapsed time > 5s
              user system elapsed
ChIPQCreport 23.67   1.97   25.72
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
ChIPQCreport 23.11   0.28   23.48
* 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: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/ChIPQC.Rcheck/00check.log'
for details.



Installation output

ChIPQC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/ChIPQC_1.28.0.tar.gz && rm -rf ChIPQC.buildbin-libdir && mkdir ChIPQC.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChIPQC.buildbin-libdir ChIPQC_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ChIPQC_1.28.0.zip && rm ChIPQC_1.28.0.tar.gz ChIPQC_1.28.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  9 1074k    9  101k    0     0   812k      0  0:00:01 --:--:--  0:00:01  812k
100 1074k  100 1074k    0     0  4325k      0 --:--:-- --:--:-- --:--:-- 4333k

install for i386

* installing *source* package 'ChIPQC' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare 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
   'ChIPQC.Rnw' 
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'ChIPQC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ChIPQC' as ChIPQC_1.28.0.zip
* DONE (ChIPQC)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'ChIPQC' successfully unpacked and MD5 sums checked

Tests output


Example timings

ChIPQC.Rcheck/examples_i386/ChIPQC-Ex.timings

nameusersystemelapsed
ChIPQC-data1.070.291.36
ChIPQC0.430.040.49
ChIPQCexperiment-class0.410.050.46
ChIPQCreport23.67 1.9725.72
ChIPQCsample-class1.140.001.14
FragmentLengthCrossCoverage-methods0.060.000.06
Normalisedaveragepeaksignal-methods0.030.000.03
QCannotation-methods0.020.020.03
QCcontrol-methods0.260.000.27
QCdba-methods0.160.000.15
QCmetadata-methods0.160.000.16
QCmetrics-methods0.420.010.44
QCsample-methods0.060.020.07
ReadLengthCrossCoverage-methods0.020.010.04
RelativeCrossCoverage-methods0.060.000.06
averagepeaksignal-methods0.030.020.05
coveragehistogram-methods0.030.000.03
crosscoverage-methods0.030.010.04
duplicateRate-methods0.030.000.03
duplicates-methods0.030.000.04
flagtagcounts-methods0.040.000.03
fragmentlength-methods0.040.020.06
frip-methods0.030.000.03
mapped-methods0.040.000.03
peaks-methods0.180.000.19
plotCC-methods0.890.020.91
plotCorHeatmap-methods0.220.010.23
plotCoverageHist-methods0.420.050.47
plotFribl-methods0.440.010.45
plotFrip-methods0.420.020.44
plotPeakProfile-methods1.210.091.30
plotPrincomp-methods0.230.000.23
plotRap-methods0.670.030.70
plotRegi-methods1.020.051.07
plotSSD-methods1.140.021.15
readlength-methods0.010.010.03
reads-methods0.020.020.04
regi-methods0.050.000.04
ribl-methods0.010.010.03
rip-methods0.020.020.03
ssd-methods0.010.010.04

ChIPQC.Rcheck/examples_x64/ChIPQC-Ex.timings

nameusersystemelapsed
ChIPQC-data1.030.081.11
ChIPQC0.450.000.45
ChIPQCexperiment-class0.370.010.39
ChIPQCreport23.11 0.2823.48
ChIPQCsample-class1.20.01.2
FragmentLengthCrossCoverage-methods0.050.000.05
Normalisedaveragepeaksignal-methods0.020.020.03
QCannotation-methods0.030.000.03
QCcontrol-methods0.230.000.23
QCdba-methods0.140.000.14
QCmetadata-methods0.170.000.17
QCmetrics-methods0.410.020.42
QCsample-methods0.080.000.08
ReadLengthCrossCoverage-methods0.010.000.01
RelativeCrossCoverage-methods0.050.010.07
averagepeaksignal-methods0.020.020.03
coveragehistogram-methods0.030.000.03
crosscoverage-methods0.030.000.03
duplicateRate-methods0.020.000.02
duplicates-methods0.010.010.03
flagtagcounts-methods0.020.000.01
fragmentlength-methods0.060.000.06
frip-methods0.010.000.02
mapped-methods0.020.020.03
peaks-methods0.250.000.25
plotCC-methods1.060.001.06
plotCorHeatmap-methods0.210.000.21
plotCoverageHist-methods0.480.010.50
plotFribl-methods0.480.000.48
plotFrip-methods0.520.000.52
plotPeakProfile-methods1.660.001.65
plotPrincomp-methods0.250.000.25
plotRap-methods0.980.000.99
plotRegi-methods0.840.020.86
plotSSD-methods1.110.011.12
readlength-methods0.040.020.05
reads-methods0.030.000.03
regi-methods0.070.020.09
ribl-methods0.020.010.04
rip-methods0.050.000.04
ssd-methods0.030.020.05