Multiple platform build/check report for BioC 3.8 - INSTALL report for scran on tokay1

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### Running command:
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###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/scran_1.10.2.tar.gz && rm -rf scran.buildbin-libdir && mkdir scran.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scran.buildbin-libdir scran_1.10.2.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL scran_1.10.2.zip && rm scran_1.10.2.tar.gz scran_1.10.2.zip
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install for i386

* installing *source* package 'scran' ...
** 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/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c build_snn.cpp -o build_snn.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/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c calc_log_count_stats.cpp -o calc_log_count_stats.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/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c combine_simes.cpp -o combine_simes.o
combine_simes.cpp: In function 'SEXPREC* combine_simes(SEXP, SEXP)':
combine_simes.cpp:15:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         } else if (ngenes!=current.size()) {
                          ^
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/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c compute_CV2.cpp -o compute_CV2.o
compute_CV2.cpp: In instantiation of 'SEXPREC* compute_CV2_internal(M, SEXP, SEXP, SEXP) [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*]':
compute_CV2.cpp:74:83:   required from here
compute_CV2.cpp:28:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (sizefacs.size()!=ncells) { 
                            ^
compute_CV2.cpp: In instantiation of 'SEXPREC* compute_CV2_internal(M, SEXP, SEXP, SEXP) [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*]':
compute_CV2.cpp:77:83:   required from here
compute_CV2.cpp:28:28: 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 scran.h:4,
                 from compute_CV2.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*]':
compute_CV2.cpp:80:1:   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*]':
compute_CV2.cpp:80:1:   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/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c compute_rho.cpp -o compute_rho.o
compute_rho.cpp: In member function 'std::vector<unsigned int> cache_manager::reorder(Rcpp::IntegerVector, Rcpp::IntegerVector)':
compute_rho.cpp:246:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (npairs!=g2.size()) {
                   ^
compute_rho.cpp:259:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (g1x < 0 || g1x >= Ngenes) {
                                ^
compute_rho.cpp:262:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (g2x < 0 || g2x >= Ngenes) {
                                ^
compute_rho.cpp: In function 'SEXPREC* combine_corP(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
compute_rho.cpp:338:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (Npairs!=second.size()) { 
               ^
compute_rho.cpp:343:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (Rho.size()!=Npairs) { 
                   ^
compute_rho.cpp:348:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (Pval.size()!=Npairs) {
                    ^
compute_rho.cpp:353:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (Limited.size()!=Npairs) { 
                       ^
compute_rho.cpp:358:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (Order.size()!=Npairs) { 
                     ^
compute_rho.cpp: In instantiation of 'SEXPREC* rank_subset_internal(M, SEXP, SEXP, SEXP, T) [with T = int; V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*]':
compute_rho.cpp:175:114:   required from here
compute_rho.cpp:159:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int cs=0; cs<cslen; ++cs, ++iIt){ 
                          ^
compute_rho.cpp: In instantiation of 'SEXPREC* rank_subset_internal(M, SEXP, SEXP, SEXP, T) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*]':
compute_rho.cpp:180:117:   required from here
compute_rho.cpp:159:26: 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 scran.h:4,
                 from compute_rho.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*]':
compute_rho.cpp:406:1:   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*]':
compute_rho.cpp:406:1:   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/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c find_mutual_nns.cpp -o find_mutual_nns.o
find_mutual_nns.cpp: In function 'SEXPREC* smooth_gaussian_kernel(SEXP, SEXP, SEXP, SEXP)':
find_mutual_nns.cpp:110:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (npairs!=_index.size()) { 
               ^
find_mutual_nns.cpp:125:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (i >= averages.size() || averages[i].size()==0) { 
                   ^
find_mutual_nns.cpp:126:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 if (i >= averages.size()) { 
                       ^
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 scran.h:4,
                 from find_mutual_nns.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*]':
find_mutual_nns.cpp:348:1:   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*]':
find_mutual_nns.cpp:348:1:   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/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c fit_linear_model.cpp -o fit_linear_model.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 scran.h:4,
                 from fit_linear_model.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*]':
fit_linear_model.cpp:139:1:   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*]':
fit_linear_model.cpp:139:1:   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/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c forge_system.cpp -o forge_system.o
forge_system.cpp: In function 'SEXPREC* forge_system(SEXP, SEXP, SEXP, SEXP)':
forge_system.cpp:20:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (SIZE < 1 || SIZE > ncells) { throw std::runtime_error("each element of sizes should be within [1, number of cells]"); }
                              ^
forge_system.cpp:28:15: 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"); }
               ^
forge_system.cpp:32:22: 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"); }
                      ^
forge_system.cpp:34:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (o < 0 || o > ncells) { 
                        ^
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 scran.h:4,
                 from forge_system.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*]':
forge_system.cpp:127:1:   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:/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/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c get_residuals.cpp -o get_residuals.o
get_residuals.cpp: In function 'SEXPREC* get_residuals(SEXP, SEXP, SEXP, SEXP, SEXP)':
get_residuals.cpp:39:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int c=0; c<ncells; ++c, ++tIt) {
                            ^
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 scran.h:4,
                 from get_residuals.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*]':
get_residuals.cpp:64:1:   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:/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/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c get_scaled_ranks.cpp -o get_scaled_ranks.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 scran.h:4,
                 from get_scaled_ranks.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*]':
get_scaled_ranks.cpp:113:1:   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*]':
get_scaled_ranks.cpp:113:1:   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/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/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/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c overlap_exprs.cpp -o overlap_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 scran.h:4,
                 from overlap_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*]':
overlap_exprs.cpp:152:1:   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*]':
overlap_exprs.cpp:152:1:   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/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c run_dormqr.cpp -o run_dormqr.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/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c shuffle_matrix.cpp -o shuffle_matrix.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 scran.h:4,
                 from shuffle_matrix.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*]':
shuffle_matrix.cpp:33:1:   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*]':
shuffle_matrix.cpp:33:1:   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/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c shuffle_scores.cpp -o shuffle_scores.o
shuffle_scores.cpp: In instantiation of 'SEXPREC* shuffle_scores_internal(M, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector) [with V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*; Rcpp::IntegerVector = Rcpp::Vector<13>]':
shuffle_scores.cpp:118:130:   required from here
shuffle_scores.cpp:53:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (npairs!=marker2.size()) { throw std::runtime_error("vectors of markers must be of the same length"); }
               ^
shuffle_scores.cpp:64:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (m1m >= nused || m1m < 0) { throw std::runtime_error("first marker indices are out of range"); }
                 ^
shuffle_scores.cpp:66:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (m2m >= nused || m2m < 0) { throw std::runtime_error("second marker indices are out of range"); }
                 ^
shuffle_scores.cpp:72:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (usedex >= ngenes || usedex < 0) { throw std::runtime_error("used gene indices are out of range"); }
                    ^
shuffle_scores.cpp: In instantiation of 'SEXPREC* shuffle_scores_internal(M, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*; Rcpp::IntegerVector = Rcpp::Vector<13>]':
shuffle_scores.cpp:121:130:   required from here
shuffle_scores.cpp:53:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (npairs!=marker2.size()) { throw std::runtime_error("vectors of markers must be of the same length"); }
               ^
shuffle_scores.cpp:64:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (m1m >= nused || m1m < 0) { throw std::runtime_error("first marker indices are out of range"); }
                 ^
shuffle_scores.cpp:66:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (m2m >= nused || m2m < 0) { throw std::runtime_error("second marker indices are out of range"); }
                 ^
shuffle_scores.cpp:72:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (usedex >= ngenes || usedex < 0) { throw std::runtime_error("used gene indices are out of range"); }
                    ^
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 scran.h:4,
                 from shuffle_scores.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*]':
shuffle_scores.cpp:156:1:   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*]':
shuffle_scores.cpp:156:1:   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/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c simple_sum_factors.cpp -o simple_sum_factors.o
simple_sum_factors.cpp: In instantiation of 'SEXPREC* simple_sum_factors_internal(M, Rcpp::IntegerMatrix, Rcpp::NumericMatrix, Rcpp::IntegerVector, SEXP, SEXP) [with V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*; Rcpp::IntegerMatrix = Rcpp::Matrix<13>; Rcpp::NumericMatrix = Rcpp::Matrix<14>; Rcpp::IntegerVector = Rcpp::Vector<13>]':
simple_sum_factors.cpp:122:123:   required from here
simple_sum_factors.cpp:50:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.ncol()!=ncells || distances.ncol()!=ncells) {
                                                   ^
simple_sum_factors.cpp:50:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.ncol()!=ncells || distances.ncol()!=ncells) {
                       ^
simple_sum_factors.cpp: In instantiation of 'SEXPREC* simple_sum_factors_internal(M, Rcpp::IntegerMatrix, Rcpp::NumericMatrix, Rcpp::IntegerVector, SEXP, SEXP) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*; Rcpp::IntegerMatrix = Rcpp::Matrix<13>; Rcpp::NumericMatrix = Rcpp::Matrix<14>; Rcpp::IntegerVector = Rcpp::Vector<13>]':
simple_sum_factors.cpp:125:124:   required from here
simple_sum_factors.cpp:50:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.ncol()!=ncells || distances.ncol()!=ncells) {
                                                   ^
simple_sum_factors.cpp:50:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.ncol()!=ncells || distances.ncol()!=ncells) {
                       ^
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 scran.h:4,
                 from simple_sum_factors.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*]':
simple_sum_factors.cpp:128:1:   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*]':
simple_sum_factors.cpp:128:1:   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/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c subset_and_divide.cpp -o subset_and_divide.o
subset_and_divide.cpp: In instantiation of 'SEXPREC* subset_and_divide_internal(M, SEXP, SEXP, SEXP) [with V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*]':
subset_and_divide.cpp:93:108:   required from here
subset_and_divide.cpp:28:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (scale_values.size()!=in->get_ncol()) {
                                ^
subset_and_divide.cpp: In instantiation of 'SEXPREC* subset_and_divide_internal(M, SEXP, SEXP, SEXP) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*]':
subset_and_divide.cpp:96:108:   required from here
subset_and_divide.cpp:28:32: 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 scran.h:4,
                 from subset_and_divide.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*]':
subset_and_divide.cpp:99:1:   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*]':
subset_and_divide.cpp:99:1:   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/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils.cpp -o utils.o
utils.cpp: In function 'Rcpp::IntegerVector check_subset_vector(SEXP, size_t)':
utils.cpp:6:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (isNA(s) || s < 0 || s >= len) {
                                   ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o scran.dll tmp.def build_snn.o calc_log_count_stats.o combine_simes.o compute_CV2.o compute_rho.o find_mutual_nns.o fit_linear_model.o forge_system.o get_residuals.o get_scaled_ranks.o init.o overlap_exprs.o run_dormqr.o shuffle_matrix.o shuffle_scores.o simple_sum_factors.o subset_and_divide.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:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -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/scran.buildbin-libdir/scran/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'scran'
    finding HTML links ... done
    DM                                      html  
    buildSNNGraph                           html  
    finding level-2 HTML links ... done

    cleanSizeFactors                        html  
    clusterModularity                       html  
    combineMarkers                          html  
    combinePValues                          html  
    combineVar                              html  
    computeSpikeFactors                     html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpENE6sX/R.INSTALL21b81d181eec/scran/man/computeSpikeFactors.Rd:87: file link 'isSpike' in package 'SingleCellExperiment' does not exist and so has been treated as a topic
    computeSumFactors                       html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpENE6sX/R.INSTALL21b81d181eec/scran/man/computeSumFactors.Rd:141: file link 'calcAverage' in package 'scater' does not exist and so has been treated as a topic
    convertTo                               html  
    correlatePairs                          html  
    cosineNorm                              html  
    cyclone                                 html  
    decomposeVar                            html  
    denoisePCA                              html  
    doubletCells                            html  
    doubletCluster                          html  
    fastMNN                                 html  
    findMarkers                             html  
    gene_selection                          html  
    improvedCV2                             html  
    makeTechTrend                           html  
    mnnCorrect                              html  
    multiBatchNorm                          html  
    multiBatchPCA                           html  
    multiBlockNorm                          html  
    multiBlockVar                           html  
    overlapExprs                            html  
    pairwiseTTests                          html  
    pairwiseWilcox                          html  
    parallelPCA                             html  
    quickCluster                            html  
    sandbag                                 html  
    scaledColRanks                          html  
    simpleSumFactors                        html  
    technicalCV2                            html  
    testVar                                 html  
    trendVar                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'scran' ...
** 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/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c build_snn.cpp -o build_snn.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/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c calc_log_count_stats.cpp -o calc_log_count_stats.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/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c combine_simes.cpp -o combine_simes.o
combine_simes.cpp: In function 'SEXPREC* combine_simes(SEXP, SEXP)':
combine_simes.cpp:15:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         } else if (ngenes!=current.size()) {
                          ^
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/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c compute_CV2.cpp -o compute_CV2.o
compute_CV2.cpp: In instantiation of 'SEXPREC* compute_CV2_internal(M, SEXP, SEXP, SEXP) [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*]':
compute_CV2.cpp:74:83:   required from here
compute_CV2.cpp:28:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (sizefacs.size()!=ncells) { 
                            ^
compute_CV2.cpp: In instantiation of 'SEXPREC* compute_CV2_internal(M, SEXP, SEXP, SEXP) [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*]':
compute_CV2.cpp:77:83:   required from here
compute_CV2.cpp:28:28: 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 scran.h:4,
                 from compute_CV2.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*]':
compute_CV2.cpp:80:1:   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*]':
compute_CV2.cpp:80:1:   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/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c compute_rho.cpp -o compute_rho.o
compute_rho.cpp: In member function 'std::vector<long long unsigned int> cache_manager::reorder(Rcpp::IntegerVector, Rcpp::IntegerVector)':
compute_rho.cpp:246:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (npairs!=g2.size()) {
                   ^
compute_rho.cpp:259:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (g1x < 0 || g1x >= Ngenes) {
                                ^
compute_rho.cpp:262:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (g2x < 0 || g2x >= Ngenes) {
                                ^
compute_rho.cpp: In function 'SEXPREC* combine_corP(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
compute_rho.cpp:338:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (Npairs!=second.size()) { 
               ^
compute_rho.cpp:343:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (Rho.size()!=Npairs) { 
                   ^
compute_rho.cpp:348:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (Pval.size()!=Npairs) {
                    ^
compute_rho.cpp:353:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (Limited.size()!=Npairs) { 
                       ^
compute_rho.cpp:358:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (Order.size()!=Npairs) { 
                     ^
compute_rho.cpp: In instantiation of 'SEXPREC* rank_subset_internal(M, SEXP, SEXP, SEXP, T) [with T = int; V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*]':
compute_rho.cpp:175:114:   required from here
compute_rho.cpp:159:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int cs=0; cs<cslen; ++cs, ++iIt){ 
                          ^
compute_rho.cpp: In instantiation of 'SEXPREC* rank_subset_internal(M, SEXP, SEXP, SEXP, T) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*]':
compute_rho.cpp:180:117:   required from here
compute_rho.cpp:159:26: 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 scran.h:4,
                 from compute_rho.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*]':
compute_rho.cpp:406:1:   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*]':
compute_rho.cpp:406:1:   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/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c find_mutual_nns.cpp -o find_mutual_nns.o
find_mutual_nns.cpp: In function 'SEXPREC* smooth_gaussian_kernel(SEXP, SEXP, SEXP, SEXP)':
find_mutual_nns.cpp:110:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (npairs!=_index.size()) { 
               ^
find_mutual_nns.cpp:125:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (i >= averages.size() || averages[i].size()==0) { 
                   ^
find_mutual_nns.cpp:126:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 if (i >= averages.size()) { 
                       ^
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 scran.h:4,
                 from find_mutual_nns.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*]':
find_mutual_nns.cpp:348:1:   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*]':
find_mutual_nns.cpp:348:1:   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/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c fit_linear_model.cpp -o fit_linear_model.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 scran.h:4,
                 from fit_linear_model.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*]':
fit_linear_model.cpp:139:1:   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*]':
fit_linear_model.cpp:139:1:   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/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c forge_system.cpp -o forge_system.o
forge_system.cpp: In function 'SEXPREC* forge_system(SEXP, SEXP, SEXP, SEXP)':
forge_system.cpp:20:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (SIZE < 1 || SIZE > ncells) { throw std::runtime_error("each element of sizes should be within [1, number of cells]"); }
                              ^
forge_system.cpp:28:15: 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"); }
               ^
forge_system.cpp:32:22: 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"); }
                      ^
forge_system.cpp:34:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (o < 0 || o > ncells) { 
                        ^
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 scran.h:4,
                 from forge_system.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*]':
forge_system.cpp:127:1:   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:/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/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c get_residuals.cpp -o get_residuals.o
get_residuals.cpp: In function 'SEXPREC* get_residuals(SEXP, SEXP, SEXP, SEXP, SEXP)':
get_residuals.cpp:39:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int c=0; c<ncells; ++c, ++tIt) {
                            ^
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 scran.h:4,
                 from get_residuals.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*]':
get_residuals.cpp:64:1:   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:/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/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c get_scaled_ranks.cpp -o get_scaled_ranks.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 scran.h:4,
                 from get_scaled_ranks.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*]':
get_scaled_ranks.cpp:113:1:   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*]':
get_scaled_ranks.cpp:113:1:   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/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/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/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c overlap_exprs.cpp -o overlap_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 scran.h:4,
                 from overlap_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*]':
overlap_exprs.cpp:152:1:   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*]':
overlap_exprs.cpp:152:1:   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/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c run_dormqr.cpp -o run_dormqr.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/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c shuffle_matrix.cpp -o shuffle_matrix.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 scran.h:4,
                 from shuffle_matrix.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*]':
shuffle_matrix.cpp:33:1:   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*]':
shuffle_matrix.cpp:33:1:   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/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c shuffle_scores.cpp -o shuffle_scores.o
shuffle_scores.cpp: In instantiation of 'SEXPREC* shuffle_scores_internal(M, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector) [with V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*; Rcpp::IntegerVector = Rcpp::Vector<13>]':
shuffle_scores.cpp:118:130:   required from here
shuffle_scores.cpp:53:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (npairs!=marker2.size()) { throw std::runtime_error("vectors of markers must be of the same length"); }
               ^
shuffle_scores.cpp:64:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (m1m >= nused || m1m < 0) { throw std::runtime_error("first marker indices are out of range"); }
                 ^
shuffle_scores.cpp:66:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (m2m >= nused || m2m < 0) { throw std::runtime_error("second marker indices are out of range"); }
                 ^
shuffle_scores.cpp:72:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (usedex >= ngenes || usedex < 0) { throw std::runtime_error("used gene indices are out of range"); }
                    ^
shuffle_scores.cpp: In instantiation of 'SEXPREC* shuffle_scores_internal(M, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*; Rcpp::IntegerVector = Rcpp::Vector<13>]':
shuffle_scores.cpp:121:130:   required from here
shuffle_scores.cpp:53:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (npairs!=marker2.size()) { throw std::runtime_error("vectors of markers must be of the same length"); }
               ^
shuffle_scores.cpp:64:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (m1m >= nused || m1m < 0) { throw std::runtime_error("first marker indices are out of range"); }
                 ^
shuffle_scores.cpp:66:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (m2m >= nused || m2m < 0) { throw std::runtime_error("second marker indices are out of range"); }
                 ^
shuffle_scores.cpp:72:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (usedex >= ngenes || usedex < 0) { throw std::runtime_error("used gene indices are out of range"); }
                    ^
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 scran.h:4,
                 from shuffle_scores.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*]':
shuffle_scores.cpp:156:1:   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*]':
shuffle_scores.cpp:156:1:   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/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c simple_sum_factors.cpp -o simple_sum_factors.o
simple_sum_factors.cpp: In instantiation of 'SEXPREC* simple_sum_factors_internal(M, Rcpp::IntegerMatrix, Rcpp::NumericMatrix, Rcpp::IntegerVector, SEXP, SEXP) [with V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*; Rcpp::IntegerMatrix = Rcpp::Matrix<13>; Rcpp::NumericMatrix = Rcpp::Matrix<14>; Rcpp::IntegerVector = Rcpp::Vector<13>]':
simple_sum_factors.cpp:122:123:   required from here
simple_sum_factors.cpp:50:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.ncol()!=ncells || distances.ncol()!=ncells) {
                                                   ^
simple_sum_factors.cpp:50:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.ncol()!=ncells || distances.ncol()!=ncells) {
                       ^
simple_sum_factors.cpp: In instantiation of 'SEXPREC* simple_sum_factors_internal(M, Rcpp::IntegerMatrix, Rcpp::NumericMatrix, Rcpp::IntegerVector, SEXP, SEXP) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*; Rcpp::IntegerMatrix = Rcpp::Matrix<13>; Rcpp::NumericMatrix = Rcpp::Matrix<14>; Rcpp::IntegerVector = Rcpp::Vector<13>]':
simple_sum_factors.cpp:125:124:   required from here
simple_sum_factors.cpp:50:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.ncol()!=ncells || distances.ncol()!=ncells) {
                                                   ^
simple_sum_factors.cpp:50:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.ncol()!=ncells || distances.ncol()!=ncells) {
                       ^
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 scran.h:4,
                 from simple_sum_factors.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*]':
simple_sum_factors.cpp:128:1:   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*]':
simple_sum_factors.cpp:128:1:   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/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c subset_and_divide.cpp -o subset_and_divide.o
subset_and_divide.cpp: In instantiation of 'SEXPREC* subset_and_divide_internal(M, SEXP, SEXP, SEXP) [with V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*]':
subset_and_divide.cpp:93:108:   required from here
subset_and_divide.cpp:28:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (scale_values.size()!=in->get_ncol()) {
                                ^
subset_and_divide.cpp: In instantiation of 'SEXPREC* subset_and_divide_internal(M, SEXP, SEXP, SEXP) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*]':
subset_and_divide.cpp:96:108:   required from here
subset_and_divide.cpp:28:32: 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 scran.h:4,
                 from subset_and_divide.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*]':
subset_and_divide.cpp:99:1:   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*]':
subset_and_divide.cpp:99:1:   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/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils.cpp -o utils.o
utils.cpp: In function 'Rcpp::IntegerVector check_subset_vector(SEXP, size_t)':
utils.cpp:6:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (isNA(s) || s < 0 || s >= len) {
                                   ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o scran.dll tmp.def build_snn.o calc_log_count_stats.o combine_simes.o compute_CV2.o compute_rho.o find_mutual_nns.o fit_linear_model.o forge_system.o get_residuals.o get_scaled_ranks.o init.o overlap_exprs.o run_dormqr.o shuffle_matrix.o shuffle_scores.o simple_sum_factors.o subset_and_divide.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:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -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/scran.buildbin-libdir/scran/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scran' as scran_1.10.2.zip
* DONE (scran)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'scran' successfully unpacked and MD5 sums checked
In R CMD INSTALL
INSTALL report for scran on tokay1

Summary

Command output
