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BUILD BIN report for scater on tokay1

This page was generated on 2019-04-13 11:26:20 -0400 (Sat, 13 Apr 2019).

Package 1391/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scater 1.10.1
Davis McCarthy
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/scater
Branch: RELEASE_3_8
Last Commit: 2e6694a
Last Changed Date: 2019-01-04 13:48:22 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS 
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: scater
Version: 1.10.1
Command: rm -rf scater.buildbin-libdir && mkdir scater.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scater.buildbin-libdir scater_1.10.1.tar.gz
StartedAt: 2019-04-13 07:55:16 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 07:57:08 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 112.6 seconds
RetCode: 0
Status:  OK  
PackageFile: scater_1.10.1.zip
PackageFileSize: 5.712 MiB

Command output

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###
### Running command:
###
###   rm -rf scater.buildbin-libdir && mkdir scater.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scater.buildbin-libdir scater_1.10.1.tar.gz
###
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install for i386

* installing *source* package 'scater' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-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 'normalizer<V, M>::normalizer(M, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject) [with V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
calc_exprs.cpp:86:64:   required from 'Rcpp::RObject norm_exprs_internal(M, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject) [with 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:126:110:   required from here
calc_exprs.cpp:14:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (i < 0 || i >= nsets) {
                            ^
calc_exprs.cpp:29:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (current.size() != ncells) { 
                                ^
calc_exprs.cpp:41:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (set_id.size()!=ptr->get_nrow()) { 
                          ^
calc_exprs.cpp: In instantiation of 'normalizer<V, M>::normalizer(M, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
calc_exprs.cpp:86:64:   required from 'Rcpp::RObject norm_exprs_internal(M, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject) [with 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:129:110:   required from here
calc_exprs.cpp:14:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (i < 0 || i >= nsets) {
                            ^
calc_exprs.cpp:29:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (current.size() != ncells) { 
                                ^
calc_exprs.cpp:41:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (set_id.size()!=ptr->get_nrow()) { 
                          ^
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from scater.h:5,
                 from calc_exprs.cpp:1:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.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:172:1:   required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.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:172:1:   required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: 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˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c combined_qc.cpp -o combined_qc.o
combined_qc.cpp: In function 'void check_topset(const IntegerVector&)':
combined_qc.cpp:6:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t t=1; t<top.size(); ++t) {
                       ^
combined_qc.cpp: In instantiation of 'void compute_cumsum(typename V::iterator, size_t, const IntegerVector&, IT) [with T = int; V = Rcpp::Vector<13>; IT = double*; typename V::iterator = int*; size_t = unsigned int; Rcpp::IntegerVector = Rcpp::Vector<13>]':
combined_qc.cpp:257:77:   required from 'SEXPREC* top_cumprop_internal(M, Rcpp::IntegerVector) [with T = int; V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*; Rcpp::IntegerVector = Rcpp::Vector<13>]'
combined_qc.cpp:269:77:   required from here
combined_qc.cpp:26:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         while (x<target_index && x<ngenes) { // '<' as top contains 1-based indices.
                                   ^
combined_qc.cpp: In instantiation of 'void compute_cumsum(typename V::iterator, size_t, const IntegerVector&, IT) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; IT = double*; typename V::iterator = double*; size_t = unsigned int; Rcpp::IntegerVector = Rcpp::Vector<13>]':
combined_qc.cpp:257:77:   required from 'SEXPREC* top_cumprop_internal(M, Rcpp::IntegerVector) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*; Rcpp::IntegerVector = Rcpp::Vector<13>]'
combined_qc.cpp:272:80:   required from here
combined_qc.cpp:26:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from scater.h:5,
                 from combined_qc.cpp:1:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.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*]':
combined_qc.cpp:277:1:   required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.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*]':
combined_qc.cpp:277:1:   required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: 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˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c num_exprs.cpp -o num_exprs.o
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from scater.h:5,
                 from num_exprs.cpp:1:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.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*]':
num_exprs.cpp:137:1:   required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.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*]':
num_exprs.cpp:137:1:   required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: 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˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c sum_counts.cpp -o sum_counts.o
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from scater.h:5,
                 from sum_counts.cpp:1:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.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*]':
sum_counts.cpp:61:1:   required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.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*]':
sum_counts.cpp:61:1:   required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: 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˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o scater.dll tmp.def calc_exprs.o combined_qc.o init.o num_exprs.o sum_counts.o utils.o -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/library/beachmat/lib/i386 -lbeachmat -LC:/Users/BIOCBU˜1/BBS-3˜1.8-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˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-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

    arrange                                 html  
    bootstraps                              html  
    calcIsExprs                             html  
    calculateAverage                        html  
    calculateCPM                            html  
    calculateFPKM                           html  
    calculateQCMetrics                      html  
    calculateTPM                            html  
    centreSizeFactors                       html  
    filter                                  html  
    getBMFeatureAnnos                       html  
    getExplanatoryPCs                       html  
    getVarianceExplained                    html  
    isOutlier                               html  
    librarySizeFactors                      html  
    multiplot                               html  
    mutate                                  html  
    nexprs                                  html  
    normalize                               html  
    normalizeCounts                         html  
    plotColData                             html  
    plotExplanatoryPCs                      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-3.8-bioc/tmpdir/RtmpEXgkMi/R.INSTALL30a44feb460a/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  
    readSparseCounts                        html  
    readTxResults                           html  
    rename                                  html  
    runDiffusionMap                         html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpEXgkMi/R.INSTALL30a44feb460a/scater/man/runDiffusionMap.Rd:26: file link 'DiffusionMap' in package 'destiny' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpEXgkMi/R.INSTALL30a44feb460a/scater/man/runDiffusionMap.Rd:34: file link 'DiffusionMap' in package 'destiny' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpEXgkMi/R.INSTALL30a44feb460a/scater/man/runDiffusionMap.Rd:44: file link 'DiffusionMap' in package 'destiny' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpEXgkMi/R.INSTALL30a44feb460a/scater/man/runDiffusionMap.Rd:49: file link 'DiffusionMap' in package 'destiny' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpEXgkMi/R.INSTALL30a44feb460a/scater/man/runDiffusionMap.Rd:71: 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-3.8-bioc/tmpdir/RtmpEXgkMi/R.INSTALL30a44feb460a/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-3.8-bioc/tmpdir/RtmpEXgkMi/R.INSTALL30a44feb460a/scater/man/runPCA.Rd:90: 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-3.8-bioc/tmpdir/RtmpEXgkMi/R.INSTALL30a44feb460a/scater/man/runTSNE.Rd:82: file link 'plotTSNE' in package 'scater' does not exist and so has been treated as a topic
    runUMAP                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpEXgkMi/R.INSTALL30a44feb460a/scater/man/runUMAP.Rd:69: file link 'plotUMAP' in package 'scater' does not exist and so has been treated as a topic
    sc_example_cell_info                    html  
    sc_example_counts                       html  
    scater-package                          html  
    scater-plot-args                        html  
    scater-vis-var                          html  
    sumCountsAcrossFeatures                 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˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-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 'normalizer<V, M>::normalizer(M, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject) [with V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
calc_exprs.cpp:86:64:   required from 'Rcpp::RObject norm_exprs_internal(M, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject) [with 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:126:110:   required from here
calc_exprs.cpp:14:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (i < 0 || i >= nsets) {
                            ^
calc_exprs.cpp:29:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (current.size() != ncells) { 
                                ^
calc_exprs.cpp:41:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (set_id.size()!=ptr->get_nrow()) { 
                          ^
calc_exprs.cpp: In instantiation of 'normalizer<V, M>::normalizer(M, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
calc_exprs.cpp:86:64:   required from 'Rcpp::RObject norm_exprs_internal(M, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject) [with 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:129:110:   required from here
calc_exprs.cpp:14:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (i < 0 || i >= nsets) {
                            ^
calc_exprs.cpp:29:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (current.size() != ncells) { 
                                ^
calc_exprs.cpp:41:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (set_id.size()!=ptr->get_nrow()) { 
                          ^
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from scater.h:5,
                 from calc_exprs.cpp:1:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.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:172:1:   required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.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:172:1:   required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: 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˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c combined_qc.cpp -o combined_qc.o
combined_qc.cpp: In function 'void check_topset(const IntegerVector&)':
combined_qc.cpp:6:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t t=1; t<top.size(); ++t) {
                       ^
combined_qc.cpp: In instantiation of 'void compute_cumsum(typename V::iterator, size_t, const IntegerVector&, IT) [with T = int; V = Rcpp::Vector<13>; IT = double*; typename V::iterator = int*; size_t = long long unsigned int; Rcpp::IntegerVector = Rcpp::Vector<13>]':
combined_qc.cpp:257:77:   required from 'SEXPREC* top_cumprop_internal(M, Rcpp::IntegerVector) [with T = int; V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*; Rcpp::IntegerVector = Rcpp::Vector<13>]'
combined_qc.cpp:269:77:   required from here
combined_qc.cpp:26:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         while (x<target_index && x<ngenes) { // '<' as top contains 1-based indices.
                                   ^
combined_qc.cpp: In instantiation of 'void compute_cumsum(typename V::iterator, size_t, const IntegerVector&, IT) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; IT = double*; typename V::iterator = double*; size_t = long long unsigned int; Rcpp::IntegerVector = Rcpp::Vector<13>]':
combined_qc.cpp:257:77:   required from 'SEXPREC* top_cumprop_internal(M, Rcpp::IntegerVector) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*; Rcpp::IntegerVector = Rcpp::Vector<13>]'
combined_qc.cpp:272:80:   required from here
combined_qc.cpp:26:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from scater.h:5,
                 from combined_qc.cpp:1:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.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*]':
combined_qc.cpp:277:1:   required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.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*]':
combined_qc.cpp:277:1:   required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: 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˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c num_exprs.cpp -o num_exprs.o
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from scater.h:5,
                 from num_exprs.cpp:1:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.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*]':
num_exprs.cpp:137:1:   required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.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*]':
num_exprs.cpp:137:1:   required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: 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˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c sum_counts.cpp -o sum_counts.o
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from scater.h:5,
                 from sum_counts.cpp:1:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.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*]':
sum_counts.cpp:61:1:   required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.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*]':
sum_counts.cpp:61:1:   required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: 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˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o scater.dll tmp.def calc_exprs.o combined_qc.o init.o num_exprs.o sum_counts.o utils.o -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/library/beachmat/lib/x64 -lbeachmat -LC:/Users/BIOCBU˜1/BBS-3˜1.8-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˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/scater.buildbin-libdir/scater/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scater' as scater_1.10.1.zip
* DONE (scater)
In R CMD INSTALL
In R CMD INSTALL