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INSTALL report for LINC on tokay2

This page was generated on 2018-10-17 08:42:50 -0400 (Wed, 17 Oct 2018).

Package 788/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LINC 1.8.0
Manuel Goepferich
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/LINC
Branch: RELEASE_3_7
Last Commit: fb436a1
Last Changed Date: 2018-04-30 10:35:43 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: LINC
Version: 1.8.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/LINC_1.8.0.tar.gz && rm -rf LINC.buildbin-libdir && mkdir LINC.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=LINC.buildbin-libdir LINC_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL LINC_1.8.0.zip && rm LINC_1.8.0.tar.gz LINC_1.8.0.zip
StartedAt: 2018-10-16 20:16:23 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 20:18:14 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 111.1 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/LINC_1.8.0.tar.gz && rm -rf LINC.buildbin-libdir && mkdir LINC.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=LINC.buildbin-libdir LINC_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL LINC_1.8.0.zip && rm LINC_1.8.0.tar.gz LINC_1.8.0.zip
###
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install for i386

* installing *source* package 'LINC' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Cppspear.cpp -o Cppspear.o
Cppspear.cpp: In function 'Rcpp::NumericMatrix Cppspear(Rcpp::NumericMatrix, Rcpp::NumericMatrix)':
Cppspear.cpp:78:14: warning: unused variable 'qspear' [-Wunused-variable]
       double qspear;double nfraction;
              ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c LINC_init.c -o LINC_init.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c docdd.cpp -o docdd.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c doesd.cpp -o doesd.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o LINC.dll tmp.def Cppspear.o LINC_init.o RcppExports.o docdd.o doesd.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/LINC.buildbin-libdir/LINC/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'history' in package 'LINC'
** help
*** installing help indices
  converting help for package 'LINC'
    finding HTML links ... done
    Arith-methods                           html  
    BRAIN_EXPR                              html  
    LINCbio-class                           html  
    LINCcluster-class                       html  
    LINCfeature-class                       html  
    LINCmatrix-class                        html  
    LINCsingle-class                        html  
    assignment-methods                      html  
    changeOrgDb                             html  
    clusterlinc-methods                     html  
    correlation-methods                     html  
    express-methods                         html  
    feature                                 html  
    getbio-methods                          html  
    getcoexpr                               html  
    getlinc-methods                         html  
    history-methods                         html  
    justlinc-methods                        html  
    linCenvir-methods                       html  
    linc-methods                            html  
    linctable-methods                       html  
    plotlinc-methods                        html  
    querycluster                            html  
    results-methods                         html  
    singlelinc-methods                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'LINC' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Cppspear.cpp -o Cppspear.o
Cppspear.cpp: In function 'Rcpp::NumericMatrix Cppspear(Rcpp::NumericMatrix, Rcpp::NumericMatrix)':
Cppspear.cpp:78:14: warning: unused variable 'qspear' [-Wunused-variable]
       double qspear;double nfraction;
              ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c LINC_init.c -o LINC_init.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c docdd.cpp -o docdd.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c doesd.cpp -o doesd.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o LINC.dll tmp.def Cppspear.o LINC_init.o RcppExports.o docdd.o doesd.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/LINC.buildbin-libdir/LINC/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'LINC' as LINC_1.8.0.zip
* DONE (LINC)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'LINC' successfully unpacked and MD5 sums checked
In R CMD INSTALL