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INSTALL report for OUTRIDER on tokay1

This page was generated on 2019-04-13 11:29:30 -0400 (Sat, 13 Apr 2019).

Package 1108/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OUTRIDER 1.0.4
Christian Mertes
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/OUTRIDER
Branch: RELEASE_3_8
Last Commit: 18fcd8e
Last Changed Date: 2019-03-18 14:04:22 -0400 (Mon, 18 Mar 2019)
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: OUTRIDER
Version: 1.0.4
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/OUTRIDER_1.0.4.tar.gz && rm -rf OUTRIDER.buildbin-libdir && mkdir OUTRIDER.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=OUTRIDER.buildbin-libdir OUTRIDER_1.0.4.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL OUTRIDER_1.0.4.zip && rm OUTRIDER_1.0.4.tar.gz OUTRIDER_1.0.4.zip
StartedAt: 2019-04-12 20:11:48 -0400 (Fri, 12 Apr 2019)
EndedAt: 2019-04-12 20:13:42 -0400 (Fri, 12 Apr 2019)
EllapsedTime: 114.5 seconds
RetCode: 0
Status:  OK  

Command output

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### Running command:
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###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/OUTRIDER_1.0.4.tar.gz && rm -rf OUTRIDER.buildbin-libdir && mkdir OUTRIDER.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=OUTRIDER.buildbin-libdir OUTRIDER_1.0.4.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL OUTRIDER_1.0.4.zip && rm OUTRIDER_1.0.4.tar.gz OUTRIDER_1.0.4.zip
###
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install for i386

* installing *source* package 'OUTRIDER' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mtune=generic -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o
loss_n_gradient_functions.cpp: In function 'double truncLogLiklihoodD(arma::vec, arma::mat, arma::vec, arma::vec, arma::vec, double, arma::vec)':
loss_n_gradient_functions.cpp:41:19: warning: unused variable 'c' [-Wunused-variable]
     double b, ll, c;
                   ^
loss_n_gradient_functions.cpp: In function 'arma::vec gradientD(arma::vec, arma::mat, arma::vec, arma::vec, arma::vec, double, arma::vec)':
loss_n_gradient_functions.cpp:68:15: warning: unused variable 'c' [-Wunused-variable]
     double b, c;
               ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o OUTRIDER.dll tmp.def RcppExports.o loss_n_gradient_functions.o -fopenmp -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -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/OUTRIDER.buildbin-libdir/OUTRIDER/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'OUTRIDER'
    finding HTML links ... done
    OUTRIDER                                html  
    OutriderDataSet-class                   html  
    aberrant                                html  
    computeGeneLength                       html  
    computeLatentSpace                      html  
    computePvalues                          html  
    computeZscores                          html  
    controlForConfounders                   html  
    counts                                  html  
    estimateBestQ                           html  
    filterExpression                        html  
    findEncodingDim                         html  
    fit                                     html  
    fpkm                                    html  
    getter_setter_functions                 html  
    makeExampleOutriderDataSet              html  
    normalizationFactors                    html  
    plotFunctions                           html  
    results                                 html  
    sampleExclusionMask                     html  
    sizeFactors                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'OUTRIDER' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mtune=generic -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o
loss_n_gradient_functions.cpp: In function 'double truncLogLiklihoodD(arma::vec, arma::mat, arma::vec, arma::vec, arma::vec, double, arma::vec)':
loss_n_gradient_functions.cpp:41:19: warning: unused variable 'c' [-Wunused-variable]
     double b, ll, c;
                   ^
loss_n_gradient_functions.cpp: In function 'arma::vec gradientD(arma::vec, arma::mat, arma::vec, arma::vec, arma::vec, double, arma::vec)':
loss_n_gradient_functions.cpp:68:15: warning: unused variable 'c' [-Wunused-variable]
     double b, c;
               ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o OUTRIDER.dll tmp.def RcppExports.o loss_n_gradient_functions.o -fopenmp -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -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/OUTRIDER.buildbin-libdir/OUTRIDER/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OUTRIDER' as OUTRIDER_1.0.4.zip
* DONE (OUTRIDER)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'OUTRIDER' successfully unpacked and MD5 sums checked
In R CMD INSTALL