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INSTALL report for CGHbase on tokay1

This page was generated on 2019-04-13 11:20:43 -0400 (Sat, 13 Apr 2019).

Package 228/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CGHbase 1.42.0
Mark van de Wiel
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/CGHbase
Branch: RELEASE_3_8
Last Commit: 56c1525
Last Changed Date: 2018-10-30 11:41:44 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK 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  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CGHbase
Version: 1.42.0
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/CGHbase_1.42.0.tar.gz && rm -rf CGHbase.buildbin-libdir && mkdir CGHbase.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CGHbase.buildbin-libdir CGHbase_1.42.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL CGHbase_1.42.0.zip && rm CGHbase_1.42.0.tar.gz CGHbase_1.42.0.zip
StartedAt: 2019-04-12 18:35:55 -0400 (Fri, 12 Apr 2019)
EndedAt: 2019-04-12 18:36:51 -0400 (Fri, 12 Apr 2019)
EllapsedTime: 56.2 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/CGHbase_1.42.0.tar.gz && rm -rf CGHbase.buildbin-libdir && mkdir CGHbase.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CGHbase.buildbin-libdir CGHbase_1.42.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL CGHbase_1.42.0.zip && rm CGHbase_1.42.0.tar.gz CGHbase_1.42.0.zip
###
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100  851k  100  851k    0     0  20.0M      0 --:--:-- --:--:-- --:--:-- 21.8M

install for i386

* installing *source* package 'CGHbase' ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CGHbase'
    finding HTML links ... done
    CGHbase-package                         html  
    Wilting                                 html  
    WiltingCalled                           html  
    WiltingNorm                             html  
    WiltingRaw                              html  
    WiltingRegions                          html  
    WiltingSeg                              html  
    avedist                                 html  
    chromosomes                             html  
    class.cghCall                           html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpMjWMSy/R.INSTALLfa42e8b2923/CGHbase/man/class.cghCall.Rd:42: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpMjWMSy/R.INSTALLfa42e8b2923/CGHbase/man/class.cghCall.Rd:56: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpMjWMSy/R.INSTALLfa42e8b2923/CGHbase/man/class.cghCall.Rd:95: file link 'AssayData-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpMjWMSy/R.INSTALLfa42e8b2923/CGHbase/man/class.cghCall.Rd:96: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpMjWMSy/R.INSTALLfa42e8b2923/CGHbase/man/class.cghCall.Rd:97: file link 'AnnotatedDataFrame' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpMjWMSy/R.INSTALLfa42e8b2923/CGHbase/man/class.cghCall.Rd:100: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpMjWMSy/R.INSTALLfa42e8b2923/CGHbase/man/class.cghCall.Rd:101: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpMjWMSy/R.INSTALLfa42e8b2923/CGHbase/man/class.cghCall.Rd:137: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpMjWMSy/R.INSTALLfa42e8b2923/CGHbase/man/class.cghCall.Rd:143: file link 'eSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    class.cghRaw                            html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpMjWMSy/R.INSTALLfa42e8b2923/CGHbase/man/class.cghRaw.Rd:25: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpMjWMSy/R.INSTALLfa42e8b2923/CGHbase/man/class.cghRaw.Rd:30: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpMjWMSy/R.INSTALLfa42e8b2923/CGHbase/man/class.cghRaw.Rd:62: file link 'AssayData-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpMjWMSy/R.INSTALLfa42e8b2923/CGHbase/man/class.cghRaw.Rd:63: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpMjWMSy/R.INSTALLfa42e8b2923/CGHbase/man/class.cghRaw.Rd:64: file link 'AnnotatedDataFrame' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpMjWMSy/R.INSTALLfa42e8b2923/CGHbase/man/class.cghRaw.Rd:67: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpMjWMSy/R.INSTALLfa42e8b2923/CGHbase/man/class.cghRaw.Rd:68: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpMjWMSy/R.INSTALLfa42e8b2923/CGHbase/man/class.cghRaw.Rd:82: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpMjWMSy/R.INSTALLfa42e8b2923/CGHbase/man/class.cghRaw.Rd:88: file link 'eSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    class.cghRegions                        html  
    class.cghSeg                            html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpMjWMSy/R.INSTALLfa42e8b2923/CGHbase/man/class.cghSeg.Rd:27: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpMjWMSy/R.INSTALLfa42e8b2923/CGHbase/man/class.cghSeg.Rd:33: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpMjWMSy/R.INSTALLfa42e8b2923/CGHbase/man/class.cghSeg.Rd:60: file link 'AssayData-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpMjWMSy/R.INSTALLfa42e8b2923/CGHbase/man/class.cghSeg.Rd:61: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpMjWMSy/R.INSTALLfa42e8b2923/CGHbase/man/class.cghSeg.Rd:62: file link 'AnnotatedDataFrame' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpMjWMSy/R.INSTALLfa42e8b2923/CGHbase/man/class.cghSeg.Rd:65: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpMjWMSy/R.INSTALLfa42e8b2923/CGHbase/man/class.cghSeg.Rd:66: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpMjWMSy/R.INSTALLfa42e8b2923/CGHbase/man/class.cghSeg.Rd:85: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpMjWMSy/R.INSTALLfa42e8b2923/CGHbase/man/class.cghSeg.Rd:91: file link 'eSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    copynumber                              html  
    frequencyPlot                           html  
    frequencyPlotCalls                      html  
    make_cghRaw                             html  
    plot                                    html  
    probloss                                html  
    regions                                 html  
    summaryPlot                             html  
** building package indices
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'CGHbase' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CGHbase' as CGHbase_1.42.0.zip
* DONE (CGHbase)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'CGHbase' successfully unpacked and MD5 sums checked
In R CMD INSTALL