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INSTALL report for SingleR on tokay1

This page was generated on 2020-04-15 12:33:02 -0400 (Wed, 15 Apr 2020).

Package 1606/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SingleR 1.0.6
Aaron Lun
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/SingleR
Branch: RELEASE_3_10
Last Commit: 5803a1f
Last Changed Date: 2020-04-08 12:05:48 -0400 (Wed, 08 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: SingleR
Version: 1.0.6
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/SingleR_1.0.6.tar.gz && rm -rf SingleR.buildbin-libdir && mkdir SingleR.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SingleR.buildbin-libdir SingleR_1.0.6.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL SingleR_1.0.6.zip && rm SingleR_1.0.6.tar.gz SingleR_1.0.6.zip
StartedAt: 2020-04-14 19:38:47 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 19:40:26 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 99.8 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/3.10/bioc/src/contrib/SingleR_1.0.6.tar.gz && rm -rf SingleR.buildbin-libdir && mkdir SingleR.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SingleR.buildbin-libdir SingleR_1.0.6.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL SingleR_1.0.6.zip && rm SingleR_1.0.6.tar.gz SingleR_1.0.6.zip
###
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install for i386

* installing *source* package 'SingleR' ...
** 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 fine_tune_de.cpp -o fine_tune_de.o
fine_tune_de.cpp: In constructor 'de_markers::de_markers(Rcpp::List)':
fine_tune_de.cpp:6:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t i=0; i<marker_genes.size(); ++i) {
                           ^
fine_tune_de.cpp:9:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (size_t j=0; j<internals.size(); ++j) {
                               ^
fine_tune_de.cpp: In function 'Rcpp::List fine_tune_label_de(SEXP, Rcpp::NumericMatrix, Rcpp::List, double, double, Rcpp::List)':
fine_tune_de.cpp:38:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t i=0; i<References.size(); ++i) {
                       ^
In file included from fine_tune_de.cpp:2:0:
fine_tuner.h: In instantiation of 'tuned_stats fine_tuner::assign(int, beachmat::numeric_matrix*, Rcpp::NumericMatrix, const matrix_list&, double, double, const PICKER&) [with PICKER = de_markers; tuned_stats = std::tuple<int, double, double>; beachmat::numeric_matrix = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::NumericMatrix = Rcpp::Matrix<14>; matrix_list = std::vector<std::unique_ptr<beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> > > >]':
fine_tune_de.cpp:51:95:   required from here
fine_tuner.h:42:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t i=0; i<cur_scores.size(); ++i) {
                           ^
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 fine_tune_sd.cpp -o fine_tune_sd.o
fine_tune_sd.cpp: In function 'Rcpp::List fine_tune_label_sd(SEXP, Rcpp::NumericMatrix, Rcpp::List, double, double, Rcpp::NumericMatrix, double)':
fine_tune_sd.cpp:46:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t i=0; i<References.size(); ++i) {
                       ^
In file included from fine_tune_sd.cpp:2:0:
fine_tuner.h: In instantiation of 'tuned_stats fine_tuner::assign(int, beachmat::numeric_matrix*, Rcpp::NumericMatrix, const matrix_list&, double, double, const PICKER&) [with PICKER = sd_markers; tuned_stats = std::tuple<int, double, double>; beachmat::numeric_matrix = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::NumericMatrix = Rcpp::Matrix<14>; matrix_list = std::vector<std::unique_ptr<beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> > > >]':
fine_tune_sd.cpp:59:95:   required from here
fine_tuner.h:42:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t i=0; i<cur_scores.size(); ++i) {
                           ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o SingleR.dll tmp.def RcppExports.o fine_tune_de.o fine_tune_sd.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/SingleR.buildbin-libdir/00LOCK-SingleR/00new/SingleR/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SingleR'
    finding HTML links ... done
    BlueprintEncodeData                     html  
    finding level-2 HTML links ... done

    DatabaseImmuneCellExpressionData        html  
    HumanPrimaryCellAtlasData               html  
    ImmGenData                              html  
    MonacoImmuneData                        html  
    MouseRNAseqData                         html  
    NovershternHematopoieticData            html  
    SingleR                                 html  
    aggregateReference                      html  
    classifySingleR                         html  
    combineResults                          html  
    getDeltaFromMedian                      html  
    matchReferences                         html  
    plotScoreDistribution                   html  
    plotScoreHeatmap                        html  
    pruneScores                             html  
    trainSingleR                            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 'SingleR' ...
** 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 fine_tune_de.cpp -o fine_tune_de.o
fine_tune_de.cpp: In constructor 'de_markers::de_markers(Rcpp::List)':
fine_tune_de.cpp:6:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t i=0; i<marker_genes.size(); ++i) {
                           ^
fine_tune_de.cpp:9:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (size_t j=0; j<internals.size(); ++j) {
                               ^
fine_tune_de.cpp: In function 'Rcpp::List fine_tune_label_de(SEXP, Rcpp::NumericMatrix, Rcpp::List, double, double, Rcpp::List)':
fine_tune_de.cpp:38:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t i=0; i<References.size(); ++i) {
                       ^
In file included from fine_tune_de.cpp:2:0:
fine_tuner.h: In instantiation of 'tuned_stats fine_tuner::assign(int, beachmat::numeric_matrix*, Rcpp::NumericMatrix, const matrix_list&, double, double, const PICKER&) [with PICKER = de_markers; tuned_stats = std::tuple<int, double, double>; beachmat::numeric_matrix = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::NumericMatrix = Rcpp::Matrix<14>; matrix_list = std::vector<std::unique_ptr<beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> > > >]':
fine_tune_de.cpp:51:95:   required from here
fine_tuner.h:42:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t i=0; i<cur_scores.size(); ++i) {
                           ^
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 fine_tune_sd.cpp -o fine_tune_sd.o
fine_tune_sd.cpp: In function 'Rcpp::List fine_tune_label_sd(SEXP, Rcpp::NumericMatrix, Rcpp::List, double, double, Rcpp::NumericMatrix, double)':
fine_tune_sd.cpp:46:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t i=0; i<References.size(); ++i) {
                       ^
In file included from fine_tune_sd.cpp:2:0:
fine_tuner.h: In instantiation of 'tuned_stats fine_tuner::assign(int, beachmat::numeric_matrix*, Rcpp::NumericMatrix, const matrix_list&, double, double, const PICKER&) [with PICKER = sd_markers; tuned_stats = std::tuple<int, double, double>; beachmat::numeric_matrix = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::NumericMatrix = Rcpp::Matrix<14>; matrix_list = std::vector<std::unique_ptr<beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> > > >]':
fine_tune_sd.cpp:59:95:   required from here
fine_tuner.h:42:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t i=0; i<cur_scores.size(); ++i) {
                           ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o SingleR.dll tmp.def RcppExports.o fine_tune_de.o fine_tune_sd.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/SingleR.buildbin-libdir/SingleR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SingleR' as SingleR_1.0.6.zip
* DONE (SingleR)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'SingleR' successfully unpacked and MD5 sums checked