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INSTALL report for scater on tokay2

This page was generated on 2018-10-17 08:41:42 -0400 (Wed, 17 Oct 2018).

Package 1320/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scater 1.8.4
Davis McCarthy
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/scater
Branch: RELEASE_3_7
Last Commit: d560a9a
Last Changed Date: 2018-08-13 06:13:02 -0400 (Mon, 13 Aug 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: scater
Version: 1.8.4
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/scater_1.8.4.tar.gz && rm -rf scater.buildbin-libdir && mkdir scater.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scater.buildbin-libdir scater_1.8.4.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL scater_1.8.4.zip && rm scater_1.8.4.tar.gz scater_1.8.4.zip
StartedAt: 2018-10-16 19:52:57 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 19:56:37 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 219.8 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/scater_1.8.4.tar.gz && rm -rf scater.buildbin-libdir && mkdir scater.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scater.buildbin-libdir scater_1.8.4.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL scater_1.8.4.zip && rm scater_1.8.4.tar.gz scater_1.8.4.zip
###
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2862k  100 2862k    0     0  31.7M      0 --:--:-- --:--:-- --:--:-- 34.0M

install for i386

* installing *source* package 'scater' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c calc_exprs.cpp -o calc_exprs.o
calc_exprs.cpp: In instantiation of 'Rcpp::RObject calc_exprs_internal(M, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject) [with T = int; V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>]':
calc_exprs.cpp:132:120:   required from here
calc_exprs.cpp:23:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (sfIt->size() != ncells) { 
                          ^
calc_exprs.cpp:30:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (sf_to_use.size()!=ngenes) { 
                         ^
calc_exprs.cpp:37:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (current < 1 || current > nsfsets) { 
                                    ^
calc_exprs.cpp: In instantiation of 'Rcpp::RObject calc_exprs_internal(M, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>]':
calc_exprs.cpp:135:123:   required from here
calc_exprs.cpp:23:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (sfIt->size() != ncells) { 
                          ^
calc_exprs.cpp:30:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (sf_to_use.size()!=ngenes) { 
                         ^
calc_exprs.cpp:37:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (current < 1 || current > nsfsets) { 
                                    ^
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:174:0,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from scater.h:5,
                 from calc_exprs.cpp:1:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<unsigned int, int*, double*>; typename V::iterator = double*; size_t = unsigned int; typename V::iterator = double*]':
calc_exprs.cpp:140:1:   required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<unsigned int, int*, int*>; typename V::iterator = int*; size_t = unsigned int; typename V::iterator = int*]':
calc_exprs.cpp:140:1:   required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c calc_top_features.cpp -o calc_top_features.o
calc_top_features.cpp: In instantiation of 'Rcpp::RObject calc_top_features_internal(M, Rcpp::RObject, Rcpp::RObject) [with T = int; V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
calc_top_features.cpp:83:91:   required from here
calc_top_features.cpp:27:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (ntop && (top[0] < 1 || top[ntop-1] > used_genes)) {
                                            ^
calc_top_features.cpp:61:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             while (x<=target_index && x<survivors.size()) {
                                        ^
calc_top_features.cpp: In instantiation of 'Rcpp::RObject calc_top_features_internal(M, Rcpp::RObject, Rcpp::RObject) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
calc_top_features.cpp:86:94:   required from here
calc_top_features.cpp:27:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (ntop && (top[0] < 1 || top[ntop-1] > used_genes)) {
                                            ^
calc_top_features.cpp:61:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             while (x<=target_index && x<survivors.size()) {
                                        ^
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:174:0,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from scater.h:5,
                 from calc_top_features.cpp:1:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<unsigned int, int*, double*>; typename V::iterator = double*; size_t = unsigned int; typename V::iterator = double*]':
calc_top_features.cpp:91:1:   required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<unsigned int, int*, int*>; typename V::iterator = int*; size_t = unsigned int; typename V::iterator = int*]':
calc_top_features.cpp:91:1:   required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c matrix_stats.cpp -o matrix_stats.o
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:174:0,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from scater.h:5,
                 from matrix_stats.cpp:1:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<unsigned int, int*, double*>; typename V::iterator = double*; size_t = unsigned int; typename V::iterator = double*]':
matrix_stats.cpp:340:1:   required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<unsigned int, int*, int*>; typename V::iterator = int*; size_t = unsigned int; typename V::iterator = int*]':
matrix_stats.cpp:340:1:   required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o scater.dll tmp.def calc_exprs.o calc_top_features.o init.o matrix_stats.o -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/library/beachmat/lib/i386 -lbeachmat -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/library/Rhdf5lib/lib/i386 -lhdf5_cpp -lhdf5 -lszip -lz -lpsapi -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/scater.buildbin-libdir/scater/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'mutate' in package 'scater'
Creating a new generic function for 'filter' in package 'scater'
** help
*** installing help indices
  converting help for package 'scater'
    finding HTML links ... done
    SCESet                                  html  
    accessors                               html  
    finding level-2 HTML links ... done

    areSizeFactorsCentred                   html  
    arrange                                 html  
    bootstraps                              html  
    calcAverage                             html  
    calcIsExprs                             html  
    calculateCPM                            html  
    calculateFPKM                           html  
    calculateQCMetrics                      html  
    calculateTPM                            html  
    centreSizeFactors                       html  
    downsampleCounts                        html  
    filter                                  html  
    findImportantPCs                        html  
    getBMFeatureAnnos                       html  
    isOutlier                               html  
    kallisto-wrapper                        html  
    librarySizeFactors                      html  
    multiplot                               html  
    mutate                                  html  
    nexprs                                  html  
    normalize                               html  
    normalizeExprs                          html  
    plotColData                             html  
    plotExplanatoryVariables                html  
    plotExpression                          html  
    plotExprsFreqVsMean                     html  
    plotExprsVsTxLength                     html  
    plotHeatmap                             html  
    plotHighestExprs                        html  
    plotPlatePosition                       html  
    plotQC                                  html  
    plotRLE                                 html  
    plotReducedDim                          html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpesBNfT/R.INSTALLd84528f6e9c/scater/man/plotReducedDim.Rd:21: file link 'plotPCA' in package 'scater' does not exist and so has been treated as a topic
    plotRowData                             html  
    plotScater                              html  
    plot_reddim                             html  
    read10xResults                          html  
    readTxResults                           html  
    rename                                  html  
    runDiffusionMap                         html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpesBNfT/R.INSTALLd84528f6e9c/scater/man/runDiffusionMap.Rd:25: file link 'DiffusionMap' in package 'destiny' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpesBNfT/R.INSTALLd84528f6e9c/scater/man/runDiffusionMap.Rd:33: file link 'DiffusionMap' in package 'destiny' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpesBNfT/R.INSTALLd84528f6e9c/scater/man/runDiffusionMap.Rd:43: file link 'DiffusionMap' in package 'destiny' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpesBNfT/R.INSTALLd84528f6e9c/scater/man/runDiffusionMap.Rd:67: file link 'plotDiffusionMap' in package 'scater' does not exist and so has been treated as a topic
    runMDS                                  html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpesBNfT/R.INSTALLd84528f6e9c/scater/man/runMDS.Rd:62: file link 'plotMDS' in package 'scater' does not exist and so has been treated as a topic
    runPCA                                  html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpesBNfT/R.INSTALLd84528f6e9c/scater/man/runPCA.Rd:84: file link 'plotPCA' in package 'scater' does not exist and so has been treated as a topic
    runTSNE                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpesBNfT/R.INSTALLd84528f6e9c/scater/man/runTSNE.Rd:81: file link 'plotTSNE' in package 'scater' does not exist and so has been treated as a topic
    salmon-wrapper                          html  
    sc_example_cell_info                    html  
    sc_example_counts                       html  
    scater-package                          html  
    scater-plot-args                        html  
    scater-vis-var                          html  
    scater_gui                              html  
    summariseExprsAcrossFeatures            html  
    toSingleCellExperiment                  html  
    uniquifyFeatureNames                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'scater' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c calc_exprs.cpp -o calc_exprs.o
calc_exprs.cpp: In instantiation of 'Rcpp::RObject calc_exprs_internal(M, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject) [with T = int; V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>]':
calc_exprs.cpp:132:120:   required from here
calc_exprs.cpp:23:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (sfIt->size() != ncells) { 
                          ^
calc_exprs.cpp:30:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (sf_to_use.size()!=ngenes) { 
                         ^
calc_exprs.cpp:37:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (current < 1 || current > nsfsets) { 
                                    ^
calc_exprs.cpp: In instantiation of 'Rcpp::RObject calc_exprs_internal(M, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>]':
calc_exprs.cpp:135:123:   required from here
calc_exprs.cpp:23:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (sfIt->size() != ncells) { 
                          ^
calc_exprs.cpp:30:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (sf_to_use.size()!=ngenes) { 
                         ^
calc_exprs.cpp:37:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (current < 1 || current > nsfsets) { 
                                    ^
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:174:0,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from scater.h:5,
                 from calc_exprs.cpp:1:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<long long unsigned int, int*, double*>; typename V::iterator = double*; size_t = long long unsigned int; typename V::iterator = double*]':
calc_exprs.cpp:140:1:   required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<long long unsigned int, int*, int*>; typename V::iterator = int*; size_t = long long unsigned int; typename V::iterator = int*]':
calc_exprs.cpp:140:1:   required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c calc_top_features.cpp -o calc_top_features.o
calc_top_features.cpp: In instantiation of 'Rcpp::RObject calc_top_features_internal(M, Rcpp::RObject, Rcpp::RObject) [with T = int; V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
calc_top_features.cpp:83:91:   required from here
calc_top_features.cpp:27:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (ntop && (top[0] < 1 || top[ntop-1] > used_genes)) {
                                            ^
calc_top_features.cpp:61:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             while (x<=target_index && x<survivors.size()) {
                                        ^
calc_top_features.cpp: In instantiation of 'Rcpp::RObject calc_top_features_internal(M, Rcpp::RObject, Rcpp::RObject) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
calc_top_features.cpp:86:94:   required from here
calc_top_features.cpp:27:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (ntop && (top[0] < 1 || top[ntop-1] > used_genes)) {
                                            ^
calc_top_features.cpp:61:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             while (x<=target_index && x<survivors.size()) {
                                        ^
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:174:0,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from scater.h:5,
                 from calc_top_features.cpp:1:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<long long unsigned int, int*, double*>; typename V::iterator = double*; size_t = long long unsigned int; typename V::iterator = double*]':
calc_top_features.cpp:91:1:   required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<long long unsigned int, int*, int*>; typename V::iterator = int*; size_t = long long unsigned int; typename V::iterator = int*]':
calc_top_features.cpp:91:1:   required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c matrix_stats.cpp -o matrix_stats.o
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:174:0,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from scater.h:5,
                 from matrix_stats.cpp:1:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<long long unsigned int, int*, double*>; typename V::iterator = double*; size_t = long long unsigned int; typename V::iterator = double*]':
matrix_stats.cpp:340:1:   required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<long long unsigned int, int*, int*>; typename V::iterator = int*; size_t = long long unsigned int; typename V::iterator = int*]':
matrix_stats.cpp:340:1:   required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o scater.dll tmp.def calc_exprs.o calc_top_features.o init.o matrix_stats.o -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/library/beachmat/lib/x64 -lbeachmat -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/library/Rhdf5lib/lib/x64 -lhdf5_cpp -lhdf5 -lszip -lz -lpsapi -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/scater.buildbin-libdir/scater/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scater' as scater_1.8.4.zip
* DONE (scater)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'scater' successfully unpacked and MD5 sums checked
In R CMD INSTALL