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INSTALL report for isobar on tokay1

This page was generated on 2020-04-15 12:20:17 -0400 (Wed, 15 Apr 2020).

Package 866/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
isobar 1.32.0
Florian P Breitwieser
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/isobar
Branch: RELEASE_3_10
Last Commit: d229f6e
Last Changed Date: 2019-10-29 13:08:23 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: isobar
Version: 1.32.0
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/isobar_1.32.0.tar.gz && rm -rf isobar.buildbin-libdir && mkdir isobar.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=isobar.buildbin-libdir isobar_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL isobar_1.32.0.zip && rm isobar_1.32.0.tar.gz isobar_1.32.0.zip
StartedAt: 2020-04-14 19:22:36 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 19:23:32 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 55.9 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/isobar_1.32.0.tar.gz && rm -rf isobar.buildbin-libdir && mkdir isobar.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=isobar.buildbin-libdir isobar_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL isobar_1.32.0.zip && rm isobar_1.32.0.tar.gz isobar_1.32.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0 2190k    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2190k  100 2190k    0     0  8834k      0 --:--:-- --:--:-- --:--:-- 8941k

install for i386

* installing *source* package 'isobar' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for 'coerce' with signature '"MSnSet","IBSpectra"': no definition for class "MSnSet"
in method for 'coerce' with signature '"IBSpectra","MSnSet"': no definition for class "MSnSet"
Note: possible error in 'png(sprintf("pairwise_correlation_%s.png", ': unused argument (title = "Pairwise Correlation plot") 
** help
*** installing help indices
  converting help for package 'isobar'
    finding HTML links ... done
    IBSpectra-class                         html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmp2jjlMN/R.INSTALL9f06f26008/isobar/man/IBSpectra-class.Rd:175: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmp2jjlMN/R.INSTALL9f06f26008/isobar/man/IBSpectra-class.Rd:176: missing file link 'MSnbase'
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmp2jjlMN/R.INSTALL9f06f26008/isobar/man/IBSpectra-class.Rd:178: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmp2jjlMN/R.INSTALL9f06f26008/isobar/man/IBSpectra-class.Rd:232: file link 'ProteinGroup' in package 'isobar' does not exist and so has been treated as a topic
    NoiseModel-class                        html  
    ProteinGroup-class                      html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmp2jjlMN/R.INSTALL9f06f26008/isobar/man/ProteinGroup-class.Rd:177: file link 'IBSpectra' in package 'isobar' does not exist and so has been treated as a topic
    TlsParameter-class                      html  
    Tlsd-class                              html  
    calc.delta.score                        html  
    calc.startpos                           html  
    calculate-pvalues                       html  
    calculate.dNSAF                         html  
    calculate.emPAI                         html  
    correct.peptide.ratios                  html  
    distr-methods                           html  
    fit-distr                               html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmp2jjlMN/R.INSTALL9f06f26008/isobar/man/fit-distr.Rd:28: file link 'Cauchy' in package 'distr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmp2jjlMN/R.INSTALL9f06f26008/isobar/man/fit-distr.Rd:28: file link 'Norm' in package 'distr' does not exist and so has been treated as a topic
    getPeptideModifContext                  html  
    getPhosphoRSProbabilities               html  
    getPtmInfo                              html  
    groupMemberPeptides                     html  
    human.protein.names                     html  
    isobar-analysis                         html  
    isobar-data                             html  
    isobar-import                           html  
    isobar-log                              html  
    isobar-package                          html  
    isobar-plots                            html  
    isobar-preprocessing                    html  
    isobar-reports                          html  
    maplot.protein                          html  
    number.ranges                           html  
    observedKnownSites                      html  
    peptide.count                           html  
    proteinInfo-methods                     html  
    proteinNameAndDescription               html  
    ratio-summ                              html  
    ratiosReshapeWide                       html  
    reporter.protein-methods                html  
    sanitize                                html  
    shared.ratios                           html  
    shared.ratios.sign                      html  
    specificities                           html  
    spectra.count2                          html  
    subsetIBSpectra                         html  
    utils                                   html  
    writeHscoreData                         html  
    writeIBSpectra                          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 'isobar' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'isobar' as isobar_1.32.0.zip
* DONE (isobar)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'isobar' successfully unpacked and MD5 sums checked