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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL DropletUtils
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘DropletUtils’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c compute_multinom.cpp -o compute_multinom.o
compute_multinom.cpp: In instantiation of ‘Rcpp::NumericVector compute_multinom_internal(Rcpp::RObject, Rcpp::NumericVector, double) [with V = Rcpp::Vector<13>; MAT = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
compute_multinom.cpp:72:105:   required from here
compute_multinom.cpp:40:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (ambient.size()!=NR) {
         ~~~~~~~~~~~~~~^~~~
compute_multinom.cpp: In instantiation of ‘Rcpp::NumericVector compute_multinom_internal(Rcpp::RObject, Rcpp::NumericVector, double) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; MAT = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
compute_multinom.cpp:74:105:   required from here
compute_multinom.cpp:40:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from compute_multinom.cpp:5:0:
/home/biocbuild/bbs-3.11-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:53:18:   required from ‘Rcpp::NumericVector compute_multinom_internal(Rcpp::RObject, Rcpp::NumericVector, double) [with V = Rcpp::Vector<13>; MAT = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
compute_multinom.cpp:72:105:   required from here
/home/biocbuild/bbs-3.11-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()) {
/home/biocbuild/bbs-3.11-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:53:18:   required from ‘Rcpp::NumericVector compute_multinom_internal(Rcpp::RObject, Rcpp::NumericVector, double) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; MAT = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
compute_multinom.cpp:74:105:   required from here
/home/biocbuild/bbs-3.11-bioc/R/library/beachmat/include/beachmat/utils/const_column.h:66:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c downsample_counts.cpp -o downsample_counts.o
downsample_counts.cpp: In function ‘void check_downsampling_mode(size_t, Rcpp::NumericVector, bool)’:
downsample_counts.cpp:99:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (prop.size()!=ncells) {
             ~~~~~~~~~~~^~~~~~~~
downsample_counts.cpp: In function ‘Rcpp::IntegerVector downsample_runs(Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::NumericVector, bool)’:
downsample_counts.cpp:210:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (nmolecules!=reads.size()) {
         ~~~~~~~~~~^~~~~~~~~~~~~~
In file included from downsample_counts.cpp:5:0:
/home/biocbuild/bbs-3.11-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:174:17:   required from ‘Rcpp::RObject downsample_matrix_internal(Rcpp::RObject, Rcpp::NumericVector, bool) [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>]’
downsample_counts.cpp:192:55:   required from here
/home/biocbuild/bbs-3.11-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()) {
/home/biocbuild/bbs-3.11-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:174:17:   required from ‘Rcpp::RObject downsample_matrix_internal(Rcpp::RObject, Rcpp::NumericVector, bool) [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>]’
downsample_counts.cpp:196:55:   required from here
/home/biocbuild/bbs-3.11-bioc/R/library/beachmat/include/beachmat/utils/const_column.h:66:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c encode_sequences.cpp -o encode_sequences.o
encode_sequences.cpp: In function ‘Rcpp::IntegerVector encode_sequences(Rcpp::StringVector)’:
encode_sequences.cpp:8:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t i=0; i<output.size(); ++i) {
                      ~^~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c find_chimeric.cpp -o find_chimeric.o
find_chimeric.cpp: In function ‘Rcpp::List find_chimeric(Rcpp::StringVector, Rcpp::IntegerVector, Rcpp::IntegerVector, double, bool)’:
find_chimeric.cpp:28:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t i=0; i<nmolecules; ++i, ++uIt) {
                      ~^~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c find_swapped.cpp -o find_swapped.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c get_cell_barcodes.cpp -o get_cell_barcodes.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c group_cells.cpp -o group_cells.o
group_cells.cpp: In function ‘Rcpp::List group_cells(Rcpp::StringVector, Rcpp::IntegerVector)’:
group_cells.cpp:10:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (N!=gems.size()) {
         ~^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c hashed_deltas.cpp -o hashed_deltas.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c montecarlo_pval.cpp -o montecarlo_pval.o
montecarlo_pval.cpp: In function ‘Rcpp::IntegerVector montecarlo_pval(Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::NumericVector, Rcpp::NumericVector, int, double, Rcpp::List, Rcpp::IntegerVector)’:
montecarlo_pval.cpp:99:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (higher<curlen) {
                 ~~~~~~^~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I/usr/local/include   -fpic  -g -O2  -Wall -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) {
         ~~~~~~~~~~~~~~^~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o DropletUtils.so RcppExports.o compute_multinom.o downsample_counts.o encode_sequences.o find_chimeric.o find_swapped.o get_cell_barcodes.o group_cells.o hashed_deltas.o montecarlo_pval.o rand_custom.o utils.o /home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/lib/libhdf5.a /home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/lib/libsz.a -lz -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-DropletUtils/00new/DropletUtils/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DropletUtils)