Back to Multiple platform build/check report for BioC 3.11
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

INSTALL report for PureCN on tokay2

This page was generated on 2020-10-17 11:57:30 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE PureCN PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1379/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PureCN 1.18.1
Markus Riester
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/PureCN
Branch: RELEASE_3_11
Last Commit: 5ca3eb0
Last Changed Date: 2020-07-19 15:20:33 -0400 (Sun, 19 Jul 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: PureCN
Version: 1.18.1
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/PureCN_1.18.1.tar.gz && rm -rf PureCN.buildbin-libdir && mkdir PureCN.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PureCN.buildbin-libdir PureCN_1.18.1.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL PureCN_1.18.1.zip && rm PureCN_1.18.1.tar.gz PureCN_1.18.1.zip
StartedAt: 2020-10-16 19:20:24 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 19:22:37 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 133.3 seconds
RetCode: 0
Status:  OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/PureCN_1.18.1.tar.gz && rm -rf PureCN.buildbin-libdir && mkdir PureCN.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PureCN.buildbin-libdir PureCN_1.18.1.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL PureCN_1.18.1.zip && rm PureCN_1.18.1.tar.gz PureCN_1.18.1.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
100 2661k  100 2661k    0     0  15.8M      0 --:--:-- --:--:-- --:--:-- 16.4M

install for i386

* installing *source* package 'PureCN' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'PureCN'
    finding HTML links ... done
    PureCN-defunct                          html  
    PureCN-deprecated                       html  
    annotateTargets                         html  
    bootstrapResults                        html  
    calculateBamCoverageByInterval          html  
    calculateGCContentByInterval            html  
    calculateIntervalWeights                html  
    calculateLogRatio                       html  
    calculateMappingBiasVcf                 html  
    calculatePowerDetectSomatic             html  
    calculateTangentNormal                  html  
    callAlterations                         html  
    callAlterationsFromSegmentation         html  
    callAmplificationsInLowPurity           html  
    callCIN                                 html  
    callLOH                                 html  
    callMutationBurden                      html  
    centromeres                             html  
    correctCoverageBias                     html  
    createCurationFile                      html  
    createNormalDatabase                    html  
    createTargetWeights                     html  
    filterIntervals                         html  
    filterTargets                           html  
    filterVcfBasic                          html  
    filterVcfMuTect                         html  
    filterVcfMuTect2                        html  
    findFocal                               html  
    getSexFromCoverage                      html  
    getSexFromVcf                           html  
    plotAbs                                 html  
    poolCoverage                            html  
    predictSomatic                          html  
    preprocessIntervals                     html  
    processMultipleSamples                  html  
    purecn.DNAcopy.bdry                     html  
    purecn.example.output                   html  
    readCoverageFile                        html  
    readCurationFile                        html  
    readLogRatioFile                        html  
    readSegmentationFile                    html  
    runAbsoluteCN                           html  
    segmentationCBS                         html  
    segmentationHclust                      html  
    segmentationPSCBS                       html  
    setMappingBiasVcf                       html  
    setPriorVcf                             html  
** building package indices
** installing vignettes
** 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 'PureCN' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PureCN' as PureCN_1.18.1.zip
* DONE (PureCN)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'PureCN' successfully unpacked and MD5 sums checked