Package: DropletUtils

Version: 1.3.13

Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/DropletUtils_1.3.13.tar.gz && rm -rf DropletUtils.buildbin-libdir && mkdir DropletUtils.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DropletUtils.buildbin-libdir DropletUtils_1.3.13.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL DropletUtils_1.3.13.zip && rm DropletUtils_1.3.13.tar.gz DropletUtils_1.3.13.zip

StartedAt: 2019-04-08 19:55:54 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-08 19:59:47 -0400 (Mon, 08 Apr 2019)

EllapsedTime: 233.1 seconds

RetCode: 0

Status:  OK

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### Running command:
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###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/DropletUtils_1.3.13.tar.gz && rm -rf DropletUtils.buildbin-libdir && mkdir DropletUtils.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DropletUtils.buildbin-libdir DropletUtils_1.3.13.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL DropletUtils_1.3.13.zip && rm DropletUtils_1.3.13.tar.gz DropletUtils_1.3.13.zip
###
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install for i386

* installing *source* package 'DropletUtils' ...
** 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:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c compute_multinom.cpp -o compute_multinom.o
compute_multinom.cpp: In instantiation of 'SEXPREC* compute_multinom_internal(SEXP, SEXP, SEXP) [with V = Rcpp::Vector<13>; MAT = beachmat::lin_matrix<int, Rcpp::Vector<13> >; SEXP = SEXPREC*]':
compute_multinom.cpp:73:105:   required from here
compute_multinom.cpp:41:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (ambient.size()!=NR) {
                       ^
compute_multinom.cpp: In instantiation of 'SEXPREC* compute_multinom_internal(SEXP, SEXP, SEXP) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; MAT = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; SEXP = SEXPREC*]':
compute_multinom.cpp:75:105:   required from here
compute_multinom.cpp:41:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from compute_multinom.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<M>::get_indices() [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
compute_multinom.cpp:54:45:   required from 'SEXPREC* compute_multinom_internal(SEXP, SEXP, SEXP) [with V = Rcpp::Vector<13>; MAT = beachmat::lin_matrix<int, Rcpp::Vector<13> >; SEXP = SEXPREC*]'
compute_multinom.cpp:73:105:   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<M>::get_indices() [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
compute_multinom.cpp:54:45:   required from 'SEXPREC* compute_multinom_internal(SEXP, SEXP, SEXP) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; MAT = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; SEXP = SEXPREC*]'
compute_multinom.cpp:75:105:   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:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c downsample_counts.cpp -o downsample_counts.o
downsample_counts.cpp: In function 'bool check_downsampling_mode(size_t, Rcpp::NumericVector, Rcpp::LogicalVector)':
downsample_counts.cpp:99:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (prop.size()!=ncells) {
                        ^
downsample_counts.cpp: In function 'SEXPREC* downsample_runs(SEXP, SEXP, SEXP, SEXP)':
downsample_counts.cpp:209:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (nmolecules!=read_vec.size()) {
                   ^
In file included from downsample_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<M>::get_indices() [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
downsample_counts.cpp:171:17:   required from 'Rcpp::RObject downsample_matrix_internal(Rcpp::RObject, Rcpp::NumericVector, Rcpp::LogicalVector) [with V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; O = beachmat::lin_output<int, Rcpp::Vector<13> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::LogicalVector = Rcpp::Vector<10, Rcpp::PreserveStorage>]'
downsample_counts.cpp:189:55:   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<M>::get_indices() [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
downsample_counts.cpp:171:17:   required from 'Rcpp::RObject downsample_matrix_internal(Rcpp::RObject, Rcpp::NumericVector, Rcpp::LogicalVector) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; O = beachmat::lin_output<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::LogicalVector = Rcpp::Vector<10, Rcpp::PreserveStorage>]'
downsample_counts.cpp:193:55:   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:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c encode_sequences.cpp -o encode_sequences.o
encode_sequences.cpp: In function 'SEXPREC* encode_sequences(SEXP)':
encode_sequences.cpp:11:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t i=0; i<output.size(); ++i) {
                       ^
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:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c find_swapped.cpp -o find_swapped.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:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c get_cell_barcodes.cpp -o get_cell_barcodes.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:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c group_cells.cpp -o group_cells.o
group_cells.cpp: In function 'SEXPREC* group_cells(SEXP, SEXP)':
group_cells.cpp:38:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t i=1; i<output.size(); ++i) {
                           ^
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:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/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:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c montecarlo_pval.cpp -o montecarlo_pval.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/linear_congruential.hpp:30,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/additive_combine.hpp:27,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random.hpp:36,
                 from montecarlo_pval.cpp:3:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/pending/integer_log2.hpp:7:89: note: #pragma message: This header is deprecated. Use <boost/integer/integer_log2.hpp> instead.
 BOOST_HEADER_DEPRECATED("<boost/integer/integer_log2.hpp>");
                                                                                         ^
montecarlo_pval.cpp: In function 'SEXPREC* montecarlo_pval(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
montecarlo_pval.cpp:95:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 if (chosen >= ngenes) {
                            ^
montecarlo_pval.cpp:111:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (higher<curlen) {
                       ^
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:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c rand_custom.cpp -o rand_custom.o
rand_custom.cpp: In function 'void check_pcg_vectors(Rcpp::List, Rcpp::IntegerVector, size_t, const char*)':
rand_custom.cpp:8:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (seeds.size()!=N) {
                     ^
rand_custom.cpp:14:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (streams.size()!=N) {
                       ^
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:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/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 DropletUtils.dll tmp.def compute_multinom.o downsample_counts.o encode_sequences.o find_swapped.o get_cell_barcodes.o group_cells.o init.o montecarlo_pval.o rand_custom.o utils.o -LC:/Users/BIOCBU˜1/BBS-3˜1.9-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˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/DropletUtils.buildbin-libdir/00LOCK-DropletUtils/00new/DropletUtils/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DropletUtils'
    finding HTML links ... done
    barcodeRanks                            html  
    finding level-2 HTML links ... done

    defaultDrops                            html  
    downsampleMatrix                        html  
    downsampleReads                         html  
    emptyDrops                              html  
    encodeSequences                         html  
    get10xMolInfoStats                      html  
    makeCountMatrix                         html  
    read10xCounts                           html  
    read10xMolInfo                          html  
    swappedDrops                            html  
    write10xCounts                          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 'DropletUtils' ...
** 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:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c compute_multinom.cpp -o compute_multinom.o
compute_multinom.cpp: In instantiation of 'SEXPREC* compute_multinom_internal(SEXP, SEXP, SEXP) [with V = Rcpp::Vector<13>; MAT = beachmat::lin_matrix<int, Rcpp::Vector<13> >; SEXP = SEXPREC*]':
compute_multinom.cpp:73:105:   required from here
compute_multinom.cpp:41:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (ambient.size()!=NR) {
                       ^
compute_multinom.cpp: In instantiation of 'SEXPREC* compute_multinom_internal(SEXP, SEXP, SEXP) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; MAT = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; SEXP = SEXPREC*]':
compute_multinom.cpp:75:105:   required from here
compute_multinom.cpp:41:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from compute_multinom.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<M>::get_indices() [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
compute_multinom.cpp:54:45:   required from 'SEXPREC* compute_multinom_internal(SEXP, SEXP, SEXP) [with V = Rcpp::Vector<13>; MAT = beachmat::lin_matrix<int, Rcpp::Vector<13> >; SEXP = SEXPREC*]'
compute_multinom.cpp:73:105:   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<M>::get_indices() [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
compute_multinom.cpp:54:45:   required from 'SEXPREC* compute_multinom_internal(SEXP, SEXP, SEXP) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; MAT = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; SEXP = SEXPREC*]'
compute_multinom.cpp:75:105:   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:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c downsample_counts.cpp -o downsample_counts.o
downsample_counts.cpp: In function 'bool check_downsampling_mode(size_t, Rcpp::NumericVector, Rcpp::LogicalVector)':
downsample_counts.cpp:99:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (prop.size()!=ncells) {
                        ^
downsample_counts.cpp: In function 'SEXPREC* downsample_runs(SEXP, SEXP, SEXP, SEXP)':
downsample_counts.cpp:209:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (nmolecules!=read_vec.size()) {
                   ^
In file included from downsample_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<M>::get_indices() [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
downsample_counts.cpp:171:17:   required from 'Rcpp::RObject downsample_matrix_internal(Rcpp::RObject, Rcpp::NumericVector, Rcpp::LogicalVector) [with V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; O = beachmat::lin_output<int, Rcpp::Vector<13> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::LogicalVector = Rcpp::Vector<10, Rcpp::PreserveStorage>]'
downsample_counts.cpp:189:55:   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<M>::get_indices() [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
downsample_counts.cpp:171:17:   required from 'Rcpp::RObject downsample_matrix_internal(Rcpp::RObject, Rcpp::NumericVector, Rcpp::LogicalVector) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; O = beachmat::lin_output<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::LogicalVector = Rcpp::Vector<10, Rcpp::PreserveStorage>]'
downsample_counts.cpp:193:55:   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:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c encode_sequences.cpp -o encode_sequences.o
encode_sequences.cpp: In function 'SEXPREC* encode_sequences(SEXP)':
encode_sequences.cpp:11:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t i=0; i<output.size(); ++i) {
                       ^
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:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c find_swapped.cpp -o find_swapped.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:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c get_cell_barcodes.cpp -o get_cell_barcodes.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:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c group_cells.cpp -o group_cells.o
group_cells.cpp: In function 'SEXPREC* group_cells(SEXP, SEXP)':
group_cells.cpp:38:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t i=1; i<output.size(); ++i) {
                           ^
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:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/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:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c montecarlo_pval.cpp -o montecarlo_pval.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/linear_congruential.hpp:30,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/additive_combine.hpp:27,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random.hpp:36,
                 from montecarlo_pval.cpp:3:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/pending/integer_log2.hpp:7:89: note: #pragma message: This header is deprecated. Use <boost/integer/integer_log2.hpp> instead.
 BOOST_HEADER_DEPRECATED("<boost/integer/integer_log2.hpp>");
                                                                                         ^
montecarlo_pval.cpp: In function 'SEXPREC* montecarlo_pval(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
montecarlo_pval.cpp:95:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 if (chosen >= ngenes) {
                            ^
montecarlo_pval.cpp:111:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (higher<curlen) {
                       ^
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:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c rand_custom.cpp -o rand_custom.o
rand_custom.cpp: In function 'void check_pcg_vectors(Rcpp::List, Rcpp::IntegerVector, size_t, const char*)':
rand_custom.cpp:8:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (seeds.size()!=N) {
                     ^
rand_custom.cpp:14:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (streams.size()!=N) {
                       ^
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:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/dqrng/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 DropletUtils.dll tmp.def compute_multinom.o downsample_counts.o encode_sequences.o find_swapped.o get_cell_barcodes.o group_cells.o init.o montecarlo_pval.o rand_custom.o utils.o -LC:/Users/BIOCBU˜1/BBS-3˜1.9-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˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/DropletUtils.buildbin-libdir/DropletUtils/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DropletUtils' as DropletUtils_1.3.13.zip
* DONE (DropletUtils)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'DropletUtils' successfully unpacked and MD5 sums checked