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INSTALL report for BASiCS on tokay1

This page was generated on 2018-04-12 13:30:33 -0400 (Thu, 12 Apr 2018).

Package 93/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BASiCS 1.0.1
Catalina A. Vallejos
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/BASiCS
Branch: RELEASE_3_6
Last Commit: dba7914
Last Changed Date: 2018-03-18 15:01:01 -0400 (Sun, 18 Mar 2018)
malbec1 Linux (Ubuntu 16.04.1 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
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BASiCS
Version: 1.0.1
Command: rm -rf BASiCS.buildbin-libdir && mkdir BASiCS.buildbin-libdir && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/BASiCS_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=BASiCS.buildbin-libdir --merge-multiarch BASiCS_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL BASiCS_1.0.1.zip && rm BASiCS_1.0.1.tar.gz BASiCS_1.0.1.zip
StartedAt: 2018-04-11 18:53:30 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 18:55:15 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 105.5 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   rm -rf BASiCS.buildbin-libdir && mkdir BASiCS.buildbin-libdir  && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/BASiCS_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=BASiCS.buildbin-libdir --merge-multiarch BASiCS_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL BASiCS_1.0.1.zip  && rm BASiCS_1.0.1.tar.gz BASiCS_1.0.1.zip
###
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100 1998k  100 1998k    0     0  23.2M      0 --:--:-- --:--:-- --:--:-- 24.0M

install for i386

* installing *source* package 'BASiCS' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c BASiCS_CPPcode.cpp -o BASiCS_CPPcode.o
BASiCS_CPPcode.cpp: In function 'arma::mat muUpdateNoSpikes(const vec&, const vec&, const double&, const mat&, const vec&, const vec&, const vec&, const double&, const int&, const int&, arma::vec&, arma::vec&, const int&, const uvec&, const uvec&, const int&)':
BASiCS_CPPcode.cpp:1226:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i < ConstrainGene.size(); i++)
                   ^
BASiCS_CPPcode.cpp:1251:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0; i < NotConstrainGene.size(); i++)
                     ^
BASiCS_CPPcode.cpp: In function 'Rcpp::List HiddenBASiCS_MCMCcppNoSpikes(int, int, int, Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, double, double, double, double, double, double, double, double, double, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, double, Rcpp::NumericVector, Rcpp::NumericVector, int, int, int, double, double, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, double, Rcpp::NumericVector, int, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, int)':
BASiCS_CPPcode.cpp:1648:14: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
     if(i%Thin==0 & i>=Burn)
              ^
BASiCS_CPPcode.cpp:1666:19: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
     if(i%(2*Thin) == 0 & PrintProgress == 1)
                   ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o BASiCS.dll tmp.def BASiCS_CPPcode.o RcppExports.o -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/BASiCS.buildbin-libdir/BASiCS/libs/i386
** R
** data
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'BASiCS'
    finding HTML links ... done
    BASiCS_Chain-methods                    html  
    BASiCS_Chain                            html  
    BASiCS_D_TestDE                         html  
    BASiCS_DenoisedCounts                   html  
    finding level-2 HTML links ... done

    BASiCS_DenoisedRates                    html  
    BASiCS_DetectHVG_LVG                    html  
    BASiCS_Filter                           html  
    BASiCS_LoadChain                        html  
    BASiCS_MCMC                             html  
    BASiCS_Sim                              html  
    BASiCS_Summary-methods                  html  
    BASiCS_Summary                          html  
    BASiCS_TestDE                           html  
    BASiCS_VarThresholdSearchHVG_LVG        html  
    BASiCS_VarianceDecomp                   html  
    ChainRNA                                html  
    ChainSC                                 html  
    Summary-BASiCS_Chain-method             html  
    displayChainBASiCS-BASiCS_Chain-method
                                            html  
    displaySummaryBASiCS-BASiCS_Summary-method
                                            html  
    makeExampleBASiCS_Data                  html  
    newBASiCS_Chain                         html  
    newBASiCS_Data                          html  
    plot-BASiCS_Chain-method                html  
    plot-BASiCS_Summary-method              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'BASiCS' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c BASiCS_CPPcode.cpp -o BASiCS_CPPcode.o
BASiCS_CPPcode.cpp: In function 'arma::mat muUpdateNoSpikes(const vec&, const vec&, const double&, const mat&, const vec&, const vec&, const vec&, const double&, const int&, const int&, arma::vec&, arma::vec&, const int&, const uvec&, const uvec&, const int&)':
BASiCS_CPPcode.cpp:1226:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i < ConstrainGene.size(); i++)
                   ^
BASiCS_CPPcode.cpp:1251:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0; i < NotConstrainGene.size(); i++)
                     ^
BASiCS_CPPcode.cpp: In function 'Rcpp::List HiddenBASiCS_MCMCcppNoSpikes(int, int, int, Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, double, double, double, double, double, double, double, double, double, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, double, Rcpp::NumericVector, Rcpp::NumericVector, int, int, int, double, double, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, double, Rcpp::NumericVector, int, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, int)':
BASiCS_CPPcode.cpp:1648:14: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
     if(i%Thin==0 & i>=Burn)
              ^
BASiCS_CPPcode.cpp:1666:19: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
     if(i%(2*Thin) == 0 & PrintProgress == 1)
                   ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o BASiCS.dll tmp.def BASiCS_CPPcode.o RcppExports.o -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/BASiCS.buildbin-libdir/BASiCS/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BASiCS' as BASiCS_1.0.1.zip
* DONE (BASiCS)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.6-bioc/R/library'
package 'BASiCS' successfully unpacked and MD5 sums checked
In R CMD INSTALL