Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-14 13:06:09 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

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 303/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPQC 1.30.0  (landing page)
Tom Carroll , Rory Stark
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/ChIPQC
git_branch: RELEASE_3_14
git_last_commit: 566bb1a
git_last_commit_date: 2021-10-26 12:12:48 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: 1.30.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ChIPQC_1.30.0.tar.gz
StartedAt: 2022-01-13 16:59:44 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 17:08:27 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 523.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ChIPQC.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ChIPQC_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/ChIPQC.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.30.0'
* 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 23.16   1.84   25.01
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
ChIPQCreport 18.3    0.5   18.92
* 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-3.14-bioc/meat/ChIPQC.Rcheck/00check.log'
for details.



Installation output

ChIPQC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/ChIPQC_1.30.0.tar.gz && rm -rf ChIPQC.buildbin-libdir && mkdir ChIPQC.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChIPQC.buildbin-libdir ChIPQC_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL ChIPQC_1.30.0.zip && rm ChIPQC_1.30.0.tar.gz ChIPQC_1.30.0.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
 94 1073k   94 1012k    0     0  2472k      0 --:--:-- --:--:-- --:--:-- 2475k
100 1073k  100 1073k    0     0  2590k      0 --:--:-- --:--:-- --:--:-- 2593k

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_1.30.0.zip
* DONE (ChIPQC)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'ChIPQC' successfully unpacked and MD5 sums checked

Tests output


Example timings

ChIPQC.Rcheck/examples_i386/ChIPQC-Ex.timings

nameusersystemelapsed
ChIPQC-data1.190.111.29
ChIPQC0.500.090.59
ChIPQCexperiment-class1.360.001.36
ChIPQCreport23.16 1.8425.01
ChIPQCsample-class1.310.001.31
FragmentLengthCrossCoverage-methods0.060.000.07
Normalisedaveragepeaksignal-methods0.020.040.04
QCannotation-methods0.010.010.04
QCcontrol-methods0.270.020.28
QCdba-methods0.160.000.15
QCmetadata-methods0.160.000.15
QCmetrics-methods0.390.010.41
QCsample-methods0.060.020.08
ReadLengthCrossCoverage-methods0.020.010.03
RelativeCrossCoverage-methods0.060.000.06
averagepeaksignal-methods0.030.020.05
coveragehistogram-methods0.030.020.05
crosscoverage-methods0.030.010.04
duplicateRate-methods0.020.000.02
duplicates-methods0.030.000.03
flagtagcounts-methods0.030.000.03
fragmentlength-methods0.060.000.06
frip-methods0.030.000.03
mapped-methods0.020.020.03
peaks-methods0.230.010.25
plotCC-methods0.980.021.00
plotCorHeatmap-methods0.270.000.27
plotCoverageHist-methods0.390.030.42
plotFribl-methods0.450.000.45
plotFrip-methods0.450.000.45
plotPeakProfile-methods1.330.051.38
plotPrincomp-methods0.270.000.26
plotRap-methods0.720.010.74
plotRegi-methods1.060.021.07
plotSSD-methods1.260.011.29
readlength-methods0.030.000.03
reads-methods0.040.000.03
regi-methods0.060.000.06
ribl-methods0.010.020.03
rip-methods0.040.000.03
ssd-methods0.030.000.03

ChIPQC.Rcheck/examples_x64/ChIPQC-Ex.timings

nameusersystemelapsed
ChIPQC-data0.850.030.87
ChIPQC0.280.030.31
ChIPQCexperiment-class0.370.030.41
ChIPQCreport18.30 0.5018.92
ChIPQCsample-class1.010.021.03
FragmentLengthCrossCoverage-methods0.070.000.06
Normalisedaveragepeaksignal-methods0.030.000.03
QCannotation-methods0.010.000.02
QCcontrol-methods0.240.010.25
QCdba-methods0.090.000.11
QCmetadata-methods0.110.000.11
QCmetrics-methods0.310.030.34
QCsample-methods0.060.000.06
ReadLengthCrossCoverage-methods0.020.000.02
RelativeCrossCoverage-methods0.050.000.05
averagepeaksignal-methods0.030.000.03
coveragehistogram-methods0.030.000.03
crosscoverage-methods0.020.000.01
duplicateRate-methods0.000.020.02
duplicates-methods0.020.000.01
flagtagcounts-methods0.010.000.02
fragmentlength-methods0.050.000.04
frip-methods0.010.000.02
mapped-methods0.020.000.01
peaks-methods0.170.010.19
plotCC-methods0.890.000.89
plotCorHeatmap-methods0.150.020.17
plotCoverageHist-methods0.360.000.36
plotFribl-methods0.430.000.42
plotFrip-methods0.430.000.44
plotPeakProfile-methods1.080.031.11
plotPrincomp-methods0.200.000.21
plotRap-methods0.670.000.67
plotRegi-methods0.80.00.8
plotSSD-methods0.980.031.01
readlength-methods0.020.000.02
reads-methods0.010.000.01
regi-methods0.050.000.05
ribl-methods0.020.020.03
rip-methods0.010.000.02
ssd-methods0.020.000.01