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INSTALL report for BiocSingular on tokay1

This page was generated on 2020-04-15 12:31:51 -0400 (Wed, 15 Apr 2020).

Package 159/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocSingular 1.2.2
Aaron Lun
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/BiocSingular
Branch: RELEASE_3_10
Last Commit: 1dd1697
Last Changed Date: 2020-02-14 03:19:44 -0400 (Fri, 14 Feb 2020)
malbec1 Linux (Ubuntu 18.04.4 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: BiocSingular
Version: 1.2.2
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/BiocSingular_1.2.2.tar.gz && rm -rf BiocSingular.buildbin-libdir && mkdir BiocSingular.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BiocSingular.buildbin-libdir BiocSingular_1.2.2.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL BiocSingular_1.2.2.zip && rm BiocSingular_1.2.2.tar.gz BiocSingular_1.2.2.zip
StartedAt: 2020-04-14 19:10:22 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 19:11:36 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 74.2 seconds
RetCode: 0
Status:  OK  

Command output

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### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/BiocSingular_1.2.2.tar.gz && rm -rf BiocSingular.buildbin-libdir && mkdir BiocSingular.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BiocSingular.buildbin-libdir BiocSingular_1.2.2.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL BiocSingular_1.2.2.zip && rm BiocSingular_1.2.2.tar.gz BiocSingular_1.2.2.zip
###
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install for i386

* installing *source* package 'BiocSingular' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c compute_scale.cpp -o compute_scale.o
compute_scale.cpp: In instantiation of 'Rcpp::NumericVector compute_scale_internal(Rcpp::RObject, Rcpp::RObject) [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
compute_scale.cpp:60:79:   required from here
compute_scale.cpp:21:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (numeric_centers.size()!=ncols) {
                                   ^
compute_scale.cpp: In instantiation of 'Rcpp::NumericVector compute_scale_internal(Rcpp::RObject, Rcpp::RObject) [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
compute_scale.cpp:62:79:   required from here
compute_scale.cpp:21:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o BiocSingular.dll tmp.def RcppExports.o compute_scale.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/BiocSingular.buildbin-libdir/00LOCK-BiocSingular/00new/BiocSingular/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BiocSingular'
    finding HTML links ... done
    BiocSingularParam                       html  
    finding level-2 HTML links ... done

    DeferredMatrix                          html  
    LowRankMatrix                           html  
    ResidualMatrix                          html  
    options                                 html  
    runExactSVD                             html  
    runIrlbaSVD                             html  
    runPCA                                  html  
    runRandomSVD                            html  
    runSVD                                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'BiocSingular' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c compute_scale.cpp -o compute_scale.o
compute_scale.cpp: In instantiation of 'Rcpp::NumericVector compute_scale_internal(Rcpp::RObject, Rcpp::RObject) [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
compute_scale.cpp:60:79:   required from here
compute_scale.cpp:21:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (numeric_centers.size()!=ncols) {
                                   ^
compute_scale.cpp: In instantiation of 'Rcpp::NumericVector compute_scale_internal(Rcpp::RObject, Rcpp::RObject) [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
compute_scale.cpp:62:79:   required from here
compute_scale.cpp:21:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o BiocSingular.dll tmp.def RcppExports.o compute_scale.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/BiocSingular.buildbin-libdir/BiocSingular/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BiocSingular' as BiocSingular_1.2.2.zip
* DONE (BiocSingular)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'BiocSingular' successfully unpacked and MD5 sums checked