##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/scran_1.8.4.tar.gz && rm -rf scran.buildbin-libdir && mkdir scran.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scran.buildbin-libdir scran_1.8.4.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL scran_1.8.4.zip && rm scran_1.8.4.tar.gz scran_1.8.4.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 439k 100 439k 0 0 8817k 0 --:--:-- --:--:-- --:--:-- 9560k
install for i386
* installing *source* package 'scran' ...
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c build_snn.cpp -o build_snn.o
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:174:0,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
from scran.h:4,
from build_snn.cpp:1:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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*]':
build_snn.cpp:85:1: required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: 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˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-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˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c combine_simes.cpp -o combine_simes.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:174:0,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
from scran.h:4,
from compute_CV2.cpp:1:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (indices.size()!=this->get_nrow()) {
^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: 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˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:174:0,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
from scran.h:4,
from compute_rho.cpp:1:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (indices.size()!=this->get_nrow()) {
^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: 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˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:174:0,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
from scran.h:4,
from find_mutual_nns.cpp:1:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (indices.size()!=this->get_nrow()) {
^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: 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˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:174:0,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
from scran.h:4,
from fit_linear_model.cpp:1:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (indices.size()!=this->get_nrow()) {
^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: 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˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-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:103:30: 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:111:15: 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:115:22: 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:117:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (o < 0 || o > ncells) {
^
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:174:0,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
from scran.h:4,
from forge_system.cpp:1:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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:206:1: required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (indices.size()!=this->get_nrow()) {
^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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*]':
forge_system.cpp:206:1: required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: 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˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:174:0,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
from scran.h:4,
from get_residuals.cpp:1:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: 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˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:174:0,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
from scran.h:4,
from get_scaled_ranks.cpp:1:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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:90:1: required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (indices.size()!=this->get_nrow()) {
^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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:90:1: required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: 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˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-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˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c overlap_exprs.cpp -o overlap_exprs.o
overlap_exprs.cpp: In instantiation of 'SEXPREC* overlap_exprs_internal(M, const List&, SEXP, T) [with T = int; V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*; Rcpp::List = Rcpp::Vector<19>]':
overlap_exprs.cpp:135:96: required from here
overlap_exprs.cpp:63:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j=0; j<ngroups; ++j, ++counter) {
^
overlap_exprs.cpp:65:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (i!=j) {
^
overlap_exprs.cpp: In instantiation of 'SEXPREC* overlap_exprs_internal(M, const List&, SEXP, T) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*; Rcpp::List = Rcpp::Vector<19>]':
overlap_exprs.cpp:139:99: required from here
overlap_exprs.cpp:63:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j=0; j<ngroups; ++j, ++counter) {
^
overlap_exprs.cpp:65:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (i!=j) {
^
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:174:0,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
from scran.h:4,
from overlap_exprs.cpp:1:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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:142:1: required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (indices.size()!=this->get_nrow()) {
^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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:142:1: required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: 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˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-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˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:174:0,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
from scran.h:4,
from shuffle_matrix.cpp:1:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (indices.size()!=this->get_nrow()) {
^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: 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˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-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:93:130: required from here
shuffle_scores.cpp:28:15: 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:39:17: 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:41:17: 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:47:20: 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:96:130: required from here
shuffle_scores.cpp:28:15: 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:39:17: 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:41:17: 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:47:20: 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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:174:0,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
from scran.h:4,
from shuffle_scores.cpp:1:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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:131:1: required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (indices.size()!=this->get_nrow()) {
^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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:131:1: required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: 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˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-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 utils.o -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/library/beachmat/lib/i386 -lbeachmat -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/library/Rhdf5lib/lib/i386 -lhdf5_cpp -lhdf5 -lszip -lz -lpsapi -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-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
clusterModularity html
finding level-2 HTML links ... done
combineVar html
computeSpikeFactors html
computeSumFactors html
convertTo html
correlatePairs html
cyclone html
decomposeVar html
denoisePCA html
exploreData html
findMarkers html
improvedCV2 html
makeTechTrend html
mnnCorrect html
multiBlockVar html
overlapExprs html
parallelPCA html
quickCluster html
sandbag html
selectorPlot 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˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c build_snn.cpp -o build_snn.o
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:174:0,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
from scran.h:4,
from build_snn.cpp:1:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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*]':
build_snn.cpp:85:1: required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: 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˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-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˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c combine_simes.cpp -o combine_simes.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:174:0,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
from scran.h:4,
from compute_CV2.cpp:1:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (indices.size()!=this->get_nrow()) {
^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: 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˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:174:0,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
from scran.h:4,
from compute_rho.cpp:1:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (indices.size()!=this->get_nrow()) {
^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: 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˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:174:0,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
from scran.h:4,
from find_mutual_nns.cpp:1:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (indices.size()!=this->get_nrow()) {
^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: 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˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:174:0,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
from scran.h:4,
from fit_linear_model.cpp:1:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (indices.size()!=this->get_nrow()) {
^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: 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˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-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:103:30: 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:111:15: 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:115:22: 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:117:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (o < 0 || o > ncells) {
^
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:174:0,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
from scran.h:4,
from forge_system.cpp:1:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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:206:1: required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (indices.size()!=this->get_nrow()) {
^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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*]':
forge_system.cpp:206:1: required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: 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˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:174:0,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
from scran.h:4,
from get_residuals.cpp:1:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: 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˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:174:0,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
from scran.h:4,
from get_scaled_ranks.cpp:1:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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:90:1: required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (indices.size()!=this->get_nrow()) {
^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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:90:1: required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: 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˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-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˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c overlap_exprs.cpp -o overlap_exprs.o
overlap_exprs.cpp: In instantiation of 'SEXPREC* overlap_exprs_internal(M, const List&, SEXP, T) [with T = int; V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*; Rcpp::List = Rcpp::Vector<19>]':
overlap_exprs.cpp:135:96: required from here
overlap_exprs.cpp:63:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j=0; j<ngroups; ++j, ++counter) {
^
overlap_exprs.cpp:65:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (i!=j) {
^
overlap_exprs.cpp: In instantiation of 'SEXPREC* overlap_exprs_internal(M, const List&, SEXP, T) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*; Rcpp::List = Rcpp::Vector<19>]':
overlap_exprs.cpp:139:99: required from here
overlap_exprs.cpp:63:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j=0; j<ngroups; ++j, ++counter) {
^
overlap_exprs.cpp:65:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (i!=j) {
^
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:174:0,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
from scran.h:4,
from overlap_exprs.cpp:1:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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:142:1: required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (indices.size()!=this->get_nrow()) {
^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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:142:1: required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: 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˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-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˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:174:0,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
from scran.h:4,
from shuffle_matrix.cpp:1:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (indices.size()!=this->get_nrow()) {
^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: 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˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-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:93:130: required from here
shuffle_scores.cpp:28:15: 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:39:17: 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:41:17: 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:47:20: 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:96:130: required from here
shuffle_scores.cpp:28:15: 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:39:17: 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:41:17: 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:47:20: 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-3.7-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:174:0,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
from scran.h:4,
from shuffle_scores.cpp:1:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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:131:1: required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (indices.size()!=this->get_nrow()) {
^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.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:131:1: required from here
C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include/beachmat/LIN_methods.h:58:23: 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˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-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 utils.o -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/library/beachmat/lib/x64 -lbeachmat -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/library/Rhdf5lib/lib/x64 -lhdf5_cpp -lhdf5 -lszip -lz -lpsapi -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/scran.buildbin-libdir/scran/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scran' as scran_1.8.4.zip
* DONE (scran)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'scran' successfully unpacked and MD5 sums checked
In R CMD INSTALL
