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INSTALL report for scater on tokay2

This page was generated on 2019-10-16 12:35:00 -0400 (Wed, 16 Oct 2019).

Package 1461/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scater 1.12.2
Davis McCarthy
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/scater
Branch: RELEASE_3_9
Last Commit: 1518dc2
Last Changed Date: 2019-05-23 18:48:27 -0400 (Thu, 23 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: scater
Version: 1.12.2
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/scater_1.12.2.tar.gz && rm -rf scater.buildbin-libdir && mkdir scater.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scater.buildbin-libdir scater_1.12.2.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL scater_1.12.2.zip && rm scater_1.12.2.tar.gz scater_1.12.2.zip
StartedAt: 2019-10-15 21:02:12 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 21:05:34 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 202.3 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/scater_1.12.2.tar.gz && rm -rf scater.buildbin-libdir && mkdir scater.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scater.buildbin-libdir scater_1.12.2.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL scater_1.12.2.zip && rm scater_1.12.2.tar.gz scater_1.12.2.zip
###
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##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1145k  100 1145k    0     0   9.8M      0 --:--:-- --:--:-- --:--:-- 10.5M

install for i386

* installing *source* package 'scater' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-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::normalizer(M*, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject) [with M = beachmat::lin_matrix >; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl]':
calc_exprs.cpp:105:67:   required from 'Rcpp::RObject norm_exprs_internal(Rcpp::RObject, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject) [with M = beachmat::lin_matrix >; Rcpp::RObject = Rcpp::RObject_Impl; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>]'
calc_exprs.cpp:144:112:   required from here
calc_exprs.cpp:24:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (i < 0 || i >= nsets) {
                            ^
calc_exprs.cpp:39:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (current.size() != ncells) { 
                                ^
calc_exprs.cpp:51:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (set_id.size()!=ptr->get_nrow()) { 
                          ^
calc_exprs.cpp: In instantiation of 'normalizer::normalizer(M*, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject) [with M = beachmat::lin_matrix >; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl]':
calc_exprs.cpp:105:67:   required from 'Rcpp::RObject norm_exprs_internal(Rcpp::RObject, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject) [with M = beachmat::lin_matrix >; Rcpp::RObject = Rcpp::RObject_Impl; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>]'
calc_exprs.cpp:146:112:   required from here
calc_exprs.cpp:24:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (i < 0 || i >= nsets) {
                            ^
calc_exprs.cpp:39:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (current.size() != ncells) { 
                                ^
calc_exprs.cpp:51:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (set_id.size()!=ptr->get_nrow()) { 
                          ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-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:15:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t t=1; t; IT = double*; typename V::iterator = int*; size_t = unsigned int; Rcpp::IntegerVector = Rcpp::Vector<13>]':
combined_qc.cpp:274:109:   required from 'SEXPREC* top_cumprop_internal(Rcpp::RObject, Rcpp::IntegerVector) [with M = beachmat::lin_matrix >; SEXP = SEXPREC*; Rcpp::RObject = Rcpp::RObject_Impl; Rcpp::IntegerVector = Rcpp::Vector<13>]'
combined_qc.cpp:285:74:   required from here
combined_qc.cpp:35:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         while (x; IT = double*; typename V::iterator = double*; size_t = unsigned int; Rcpp::IntegerVector = Rcpp::Vector<13>]':
combined_qc.cpp:274:109:   required from 'SEXPREC* top_cumprop_internal(Rcpp::RObject, Rcpp::IntegerVector) [with M = beachmat::lin_matrix >; SEXP = SEXPREC*; Rcpp::RObject = Rcpp::RObject_Impl; Rcpp::IntegerVector = Rcpp::Vector<13>]'
combined_qc.cpp:287:74:   required from here
combined_qc.cpp:35:35: 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-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-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-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c num_exprs.cpp -o num_exprs.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c sum_counts.cpp -o sum_counts.o
sum_counts.cpp: In function 'SEXPREC* sum_row_counts(SEXP, SEXP, SEXP, SEXP)':
sum_counts.cpp:72:18: warning: unused variable 'ncells' [-Wunused-variable]
     const size_t ncells=end_index - start_index;
                  ^
sum_counts.cpp: In instantiation of 'Rcpp::RObject sum_col_counts_internal(Rcpp::RObject, const std::vector >&, size_t, size_t) [with M = beachmat::lin_matrix >; O = beachmat::lin_output >; Rcpp::RObject = Rcpp::RObject_Impl; size_t = unsigned int]':
sum_counts.cpp:150:83:   required from here
sum_counts.cpp:96:18: warning: unused variable 'ncells' [-Wunused-variable]
     const size_t ncells=mat->get_ncol();
                  ^
sum_counts.cpp: In instantiation of 'Rcpp::RObject sum_col_counts_internal(Rcpp::RObject, const std::vector >&, size_t, size_t) [with M = beachmat::lin_matrix >; O = beachmat::lin_output >; Rcpp::RObject = Rcpp::RObject_Impl; size_t = unsigned int]':
sum_counts.cpp:154:83:   required from here
sum_counts.cpp:96:18: warning: unused variable 'ncells' [-Wunused-variable]
In file included from sum_counts.cpp:5:0:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include/beachmat/utils/const_column.h: In instantiation of 'Rcpp::traits::storage_type<13>::type* beachmat::const_column::get_indices() [with M = beachmat::lin_matrix >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
sum_counts.cpp:120:49:   required from 'Rcpp::RObject sum_col_counts_internal(Rcpp::RObject, const std::vector >&, size_t, size_t) [with M = beachmat::lin_matrix >; O = beachmat::lin_output >; Rcpp::RObject = Rcpp::RObject_Impl; size_t = unsigned int]'
sum_counts.cpp:150:83:   required from here
C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include/beachmat/utils/const_column.h:66:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (ref->get_nrow() > indices.size()) {
                             ^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include/beachmat/utils/const_column.h: In instantiation of 'Rcpp::traits::storage_type<13>::type* beachmat::const_column::get_indices() [with M = beachmat::lin_matrix >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
sum_counts.cpp:120:49:   required from 'Rcpp::RObject sum_col_counts_internal(Rcpp::RObject, const std::vector >&, size_t, size_t) [with M = beachmat::lin_matrix >; O = beachmat::lin_output >; Rcpp::RObject = Rcpp::RObject_Impl; size_t = unsigned int]'
sum_counts.cpp:154:83:   required from here
C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include/beachmat/utils/const_column.h:66:29: 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-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-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:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/scater.buildbin-libdir/00LOCK-scater/00new/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 '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  
    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  
    plotRLE                                 html  
    plotReducedDim                          html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpO8jtKe/R.INSTALL243c4b581cae/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  
    rename                                  html  
    runDiffusionMap                         html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpO8jtKe/R.INSTALL243c4b581cae/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-3.9-bioc/tmpdir/RtmpO8jtKe/R.INSTALL243c4b581cae/scater/man/runDiffusionMap.Rd:31: file link 'DiffusionMap' in package 'destiny' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpO8jtKe/R.INSTALL243c4b581cae/scater/man/runDiffusionMap.Rd:41: file link 'DiffusionMap' in package 'destiny' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpO8jtKe/R.INSTALL243c4b581cae/scater/man/runDiffusionMap.Rd:46: file link 'DiffusionMap' in package 'destiny' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpO8jtKe/R.INSTALL243c4b581cae/scater/man/runDiffusionMap.Rd:68: 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-3.9-bioc/tmpdir/RtmpO8jtKe/R.INSTALL243c4b581cae/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-3.9-bioc/tmpdir/RtmpO8jtKe/R.INSTALL243c4b581cae/scater/man/runPCA.Rd:91: 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-3.9-bioc/tmpdir/RtmpO8jtKe/R.INSTALL243c4b581cae/scater/man/runTSNE.Rd:74: file link 'Rtsne_neighbors' in package 'Rtsne' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpO8jtKe/R.INSTALL243c4b581cae/scater/man/runTSNE.Rd:95: 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-3.9-bioc/tmpdir/RtmpO8jtKe/R.INSTALL243c4b581cae/scater/man/runUMAP.Rd:86: 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  
    sumCountsAcrossCells                    html  
    sumCountsAcrossFeatures                 html  
    toSingleCellExperiment                  html  
    uniquifyFeatureNames                    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 'scater' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-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::normalizer(M*, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject) [with M = beachmat::lin_matrix >; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl]':
calc_exprs.cpp:105:67:   required from 'Rcpp::RObject norm_exprs_internal(Rcpp::RObject, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject) [with M = beachmat::lin_matrix >; Rcpp::RObject = Rcpp::RObject_Impl; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>]'
calc_exprs.cpp:144:112:   required from here
calc_exprs.cpp:24:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (i < 0 || i >= nsets) {
                            ^
calc_exprs.cpp:39:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (current.size() != ncells) { 
                                ^
calc_exprs.cpp:51:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (set_id.size()!=ptr->get_nrow()) { 
                          ^
calc_exprs.cpp: In instantiation of 'normalizer::normalizer(M*, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject) [with M = beachmat::lin_matrix >; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl]':
calc_exprs.cpp:105:67:   required from 'Rcpp::RObject norm_exprs_internal(Rcpp::RObject, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject) [with M = beachmat::lin_matrix >; Rcpp::RObject = Rcpp::RObject_Impl; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>]'
calc_exprs.cpp:146:112:   required from here
calc_exprs.cpp:24:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (i < 0 || i >= nsets) {
                            ^
calc_exprs.cpp:39:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (current.size() != ncells) { 
                                ^
calc_exprs.cpp:51:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (set_id.size()!=ptr->get_nrow()) { 
                          ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-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:15:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t t=1; t; IT = double*; typename V::iterator = int*; size_t = long long unsigned int; Rcpp::IntegerVector = Rcpp::Vector<13>]':
combined_qc.cpp:274:109:   required from 'SEXPREC* top_cumprop_internal(Rcpp::RObject, Rcpp::IntegerVector) [with M = beachmat::lin_matrix >; SEXP = SEXPREC*; Rcpp::RObject = Rcpp::RObject_Impl; Rcpp::IntegerVector = Rcpp::Vector<13>]'
combined_qc.cpp:285:74:   required from here
combined_qc.cpp:35:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         while (x; IT = double*; typename V::iterator = double*; size_t = long long unsigned int; Rcpp::IntegerVector = Rcpp::Vector<13>]':
combined_qc.cpp:274:109:   required from 'SEXPREC* top_cumprop_internal(Rcpp::RObject, Rcpp::IntegerVector) [with M = beachmat::lin_matrix >; SEXP = SEXPREC*; Rcpp::RObject = Rcpp::RObject_Impl; Rcpp::IntegerVector = Rcpp::Vector<13>]'
combined_qc.cpp:287:74:   required from here
combined_qc.cpp:35:35: 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-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-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-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c num_exprs.cpp -o num_exprs.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c sum_counts.cpp -o sum_counts.o
sum_counts.cpp: In function 'SEXPREC* sum_row_counts(SEXP, SEXP, SEXP, SEXP)':
sum_counts.cpp:72:18: warning: unused variable 'ncells' [-Wunused-variable]
     const size_t ncells=end_index - start_index;
                  ^
sum_counts.cpp: In instantiation of 'Rcpp::RObject sum_col_counts_internal(Rcpp::RObject, const std::vector >&, size_t, size_t) [with M = beachmat::lin_matrix >; O = beachmat::lin_output >; Rcpp::RObject = Rcpp::RObject_Impl; size_t = long long unsigned int]':
sum_counts.cpp:150:83:   required from here
sum_counts.cpp:96:18: warning: unused variable 'ncells' [-Wunused-variable]
     const size_t ncells=mat->get_ncol();
                  ^
sum_counts.cpp: In instantiation of 'Rcpp::RObject sum_col_counts_internal(Rcpp::RObject, const std::vector >&, size_t, size_t) [with M = beachmat::lin_matrix >; O = beachmat::lin_output >; Rcpp::RObject = Rcpp::RObject_Impl; size_t = long long unsigned int]':
sum_counts.cpp:154:83:   required from here
sum_counts.cpp:96:18: warning: unused variable 'ncells' [-Wunused-variable]
In file included from sum_counts.cpp:5:0:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include/beachmat/utils/const_column.h: In instantiation of 'Rcpp::traits::storage_type<13>::type* beachmat::const_column::get_indices() [with M = beachmat::lin_matrix >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
sum_counts.cpp:120:49:   required from 'Rcpp::RObject sum_col_counts_internal(Rcpp::RObject, const std::vector >&, size_t, size_t) [with M = beachmat::lin_matrix >; O = beachmat::lin_output >; Rcpp::RObject = Rcpp::RObject_Impl; size_t = long long unsigned int]'
sum_counts.cpp:150:83:   required from here
C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include/beachmat/utils/const_column.h:66:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (ref->get_nrow() > indices.size()) {
                             ^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include/beachmat/utils/const_column.h: In instantiation of 'Rcpp::traits::storage_type<13>::type* beachmat::const_column::get_indices() [with M = beachmat::lin_matrix >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
sum_counts.cpp:120:49:   required from 'Rcpp::RObject sum_col_counts_internal(Rcpp::RObject, const std::vector >&, size_t, size_t) [with M = beachmat::lin_matrix >; O = beachmat::lin_output >; Rcpp::RObject = Rcpp::RObject_Impl; size_t = long long unsigned int]'
sum_counts.cpp:154:83:   required from here
C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include/beachmat/utils/const_column.h:66:29: 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-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-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:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/scater.buildbin-libdir/scater/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scater' as scater_1.12.2.zip
* DONE (scater)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'scater' successfully unpacked and MD5 sums checked