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INSTALL report for CNVtools on tokay1

This page was generated on 2019-04-13 11:21:05 -0400 (Sat, 13 Apr 2019).

Package 297/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNVtools 1.76.0
Chris Barnes
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/CNVtools
Branch: RELEASE_3_8
Last Commit: ece5748
Last Changed Date: 2018-10-30 11:41:45 -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  OK  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: CNVtools
Version: 1.76.0
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/CNVtools_1.76.0.tar.gz && rm -rf CNVtools.buildbin-libdir && mkdir CNVtools.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CNVtools.buildbin-libdir CNVtools_1.76.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL CNVtools_1.76.0.zip && rm CNVtools_1.76.0.tar.gz CNVtools_1.76.0.zip
StartedAt: 2019-04-12 18:41:27 -0400 (Fri, 12 Apr 2019)
EndedAt: 2019-04-12 18:42:23 -0400 (Fri, 12 Apr 2019)
EllapsedTime: 56.0 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/CNVtools_1.76.0.tar.gz && rm -rf CNVtools.buildbin-libdir && mkdir CNVtools.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CNVtools.buildbin-libdir CNVtools_1.76.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL CNVtools_1.76.0.zip && rm CNVtools_1.76.0.tar.gz CNVtools_1.76.0.zip
###
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install for i386

* installing *source* package 'CNVtools' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c fitmodel.cpp -o fitmodel.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c glm_test.cpp -o glm_test.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c mla.cpp -o mla.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c routine.cpp -o routine.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c zeroin.c -o zeroin.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o CNVtools.dll tmp.def fitmodel.o glm_test.o mla.o routine.o zeroin.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/CNVtools.buildbin-libdir/CNVtools/libs/i386
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CNVtools'
    finding HTML links ... done
    A112                                    html  
    CNV.fitModel                            html  
    CNVtest.binary                          html  
    CNVtest.binary.T                        html  
    CNVtest.qt                              html  
    CNVtest.qt.T                            html  
    CNVtest.select.model                    html  
    CNVtools-package                        html  
    EM.starting.point                       html  
    ExpandData                              html  
    apply.ldf                               html  
    apply.pca                               html  
    cnv.plot                                html  
    compact.data.frame                      html  
    get.model.spec                          html  
    getQualityScore                         html  
    getparams                               html  
    qt.plot                                 html  
    test.posterior                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'CNVtools' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c fitmodel.cpp -o fitmodel.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c glm_test.cpp -o glm_test.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c mla.cpp -o mla.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c routine.cpp -o routine.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c zeroin.c -o zeroin.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o CNVtools.dll tmp.def fitmodel.o glm_test.o mla.o routine.o zeroin.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/CNVtools.buildbin-libdir/CNVtools/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CNVtools' as CNVtools_1.76.0.zip
* DONE (CNVtools)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'CNVtools' successfully unpacked and MD5 sums checked
In R CMD INSTALL