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###
### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL scran
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘scran’ ...
** 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/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/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c build_snn.cpp -o build_snn.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/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c combine_rho.cpp -o combine_rho.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/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c combine_simes.cpp -o combine_simes.o
combine_simes.cpp: In instantiation of ‘size_t instantiate_list(Rcpp::List, std::vector<T>&, std::__cxx11::string) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; size_t = long unsigned int; Rcpp::List = Rcpp::Vector<19>; std::__cxx11::string = std::__cxx11::basic_string<char>]’:
combine_simes.cpp:28:70:   required from here
combine_simes.cpp:13:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t c=0; c<input.size(); ++c) {
                      ~^~~~~~~~~~~~~
combine_simes.cpp: In instantiation of ‘size_t instantiate_list(Rcpp::List, std::vector<T>&, std::__cxx11::string) [with V = Rcpp::Vector<13>; size_t = long unsigned int; Rcpp::List = Rcpp::Vector<19>; std::__cxx11::string = std::__cxx11::basic_string<char>]’:
combine_simes.cpp:145:67:   required from here
combine_simes.cpp:13:23: 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/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c compute_blocked_stats.cpp -o compute_blocked_stats.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/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c compute_residual_stats.cpp -o compute_residual_stats.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/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c compute_rho_null.cpp -o compute_rho_null.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/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c compute_rho_pairs.cpp -o compute_rho_pairs.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/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c cyclone_scores.cpp -o cyclone_scores.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/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c fit_linear_model.cpp -o fit_linear_model.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/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c get_residuals.cpp -o get_residuals.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/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c get_scaled_ranks.cpp -o get_scaled_ranks.o
get_scaled_ranks.cpp: In instantiation of ‘SEXPREC* average_ranks_internal(SEXP, SEXP, SEXP, SEXP) [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; SEXP = SEXPREC*]’:
get_scaled_ranks.cpp:137:100:   required from here
get_scaled_ranks.cpp:67:16: warning: unused variable ‘accumulated_rank’ [-Wunused-variable]
         double accumulated_rank=0;
                ^~~~~~~~~~~~~~~~
get_scaled_ranks.cpp: In instantiation of ‘SEXPREC* average_ranks_internal(SEXP, SEXP, SEXP, SEXP) [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; SEXP = SEXPREC*]’:
get_scaled_ranks.cpp:139:100:   required from here
get_scaled_ranks.cpp:67:16: warning: unused variable ‘accumulated_rank’ [-Wunused-variable]
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/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c overlap_exprs.cpp -o overlap_exprs.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/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pool_size_factors.cpp -o pool_size_factors.o
pool_size_factors.cpp: In function ‘Rcpp::List pool_size_factors(Rcpp::RObject, Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::IntegerVector)’:
pool_size_factors.cpp:36:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (ngenes!=pseudo_cell.size()) { throw std::runtime_error("length of pseudo-cell vector is not the same as the number of cells"); }
         ~~~~~~^~~~~~~~~~~~~~~~~~~~
pool_size_factors.cpp:39:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (order.size() < ncells*2-1)  { throw std::runtime_error("ordering vector is too short for number of cells"); }
         ~~~~~~~~~~~~~^~~~~~~~~~~~
pool_size_factors.cpp:101:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     for (auto i=0; i<n; ++i, ++val, ++idx) {
                                    ~^~
In file included from pool_size_factors.cpp:4:0:
/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<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]’:
pool_size_factors.cpp:52:34:   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()) {
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/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
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/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c run_dormqr.cpp -o run_dormqr.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/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/dqrng/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c subset_and_divide.cpp -o subset_and_divide.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/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 scran.so RcppExports.o build_snn.o combine_rho.o combine_simes.o compute_blocked_stats.o compute_residual_stats.o compute_rho_null.o compute_rho_pairs.o cyclone_scores.o fit_linear_model.o get_residuals.o get_scaled_ranks.o overlap_exprs.o pool_size_factors.o rand_custom.o run_dormqr.o subset_and_divide.o utils.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.11-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-scran/00new/scran/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 (scran)