##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/glmGamPoi_1.6.0.tar.gz && rm -rf glmGamPoi.buildbin-libdir && mkdir glmGamPoi.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=glmGamPoi.buildbin-libdir glmGamPoi_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL glmGamPoi_1.6.0.zip && rm glmGamPoi_1.6.0.tar.gz glmGamPoi_1.6.0.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
5 343k 5 20039 0 0 166k 0 0:00:02 --:--:-- 0:00:02 167k
100 343k 100 343k 0 0 423k 0 --:--:-- --:--:-- --:--:-- 423k
install for i386
* installing *source* package 'glmGamPoi' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/beachmat/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/beachmat/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c beta_estimation.cpp -o beta_estimation.o
beta_estimation.cpp: In function 'bool lte_n_equal_rows(const NumericMatrix&, int, double)':
beta_estimation.cpp:32:35: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
for(size_t row_idx = 0; row_idx < matrix.nrow(); row_idx++){
~~~~~~~~^~~~~~~~~~~~~~~
beta_estimation.cpp:44:20: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
if(n_matches > n){
~~~~~~~~~~^~~
beta_estimation.cpp: In function 'Rcpp::IntegerVector get_row_groups(const NumericMatrix&, int, double)':
beta_estimation.cpp:58:35: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
for(size_t row_idx = 0; row_idx < matrix.nrow(); row_idx++){
~~~~~~~~^~~~~~~~~~~~~~~
In file included from beta_estimation.cpp:6:
../inst/include/deviance.h: In instantiation of 'arma::Mat<double> compute_gp_deviance_residuals_matrix_impl(arma::Mat<eT>, arma::Mat<double>, Rcpp::NumericVector) [with NumericType = int; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]':
../inst/include/deviance.h:88:72: required from here
../inst/include/deviance.h:76:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
for(int i = 0; i < Y.n_elem; i++){
~~^~~~~~~~~~
../inst/include/deviance.h: In instantiation of 'arma::Mat<double> compute_gp_deviance_residuals_matrix_impl(arma::Mat<eT>, arma::Mat<double>, Rcpp::NumericVector) [with NumericType = double; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]':
../inst/include/deviance.h:91:75: required from here
../inst/include/deviance.h:76:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
beta_estimation.cpp: In instantiation of 'void clamp_inplace(arma::Mat<eT>&, double, double) [with NumericType = double]':
beta_estimation.cpp:81:36: required from here
beta_estimation.cpp:15:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
for(int i = 0; i < v.n_elem; i++){
~~^~~~~~~~~~
In file included from beta_estimation.cpp:6:
../inst/include/deviance.h: In instantiation of 'double compute_gp_deviance_sum(const arma::Mat<eT>&, const arma::Mat<double>&, double) [with NumericType = int]':
beta_estimation.cpp:246:40: required from 'Rcpp::List fitBeta_fisher_scoring_impl(Rcpp::RObject, const mat&, Rcpp::RObject, Rcpp::NumericVector, SEXP, Rcpp::Nullable<Rcpp::Matrix<14> >, double, double, int, bool) [with NumericType = int; BMNumericType = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::List = Rcpp::Vector<19>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; arma::mat = arma::Mat<double>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; SEXP = SEXPREC*]'
beta_estimation.cpp:305:101: required from here
../inst/include/deviance.h:53:21: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
for (int i = 0; i < Y.n_elem; i++) {
~~^~~~~~~~~~
../inst/include/deviance.h: In instantiation of 'double compute_gp_deviance_sum(const arma::Mat<eT>&, const arma::Mat<double>&, double) [with NumericType = double]':
beta_estimation.cpp:246:40: required from 'Rcpp::List fitBeta_fisher_scoring_impl(Rcpp::RObject, const mat&, Rcpp::RObject, Rcpp::NumericVector, SEXP, Rcpp::Nullable<Rcpp::Matrix<14> >, double, double, int, bool) [with NumericType = double; BMNumericType = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::List = Rcpp::Vector<19>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; arma::mat = arma::Mat<double>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; SEXP = SEXPREC*]'
beta_estimation.cpp:311:104: required from here
../inst/include/deviance.h:53:21: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/beachmat/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c deviance.cpp -o deviance.o
In file included from deviance.cpp:3:
../inst/include/deviance.h: In instantiation of 'arma::Mat<double> compute_gp_deviance_residuals_matrix_impl(arma::Mat<eT>, arma::Mat<double>, Rcpp::NumericVector) [with NumericType = int; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]':
../inst/include/deviance.h:88:72: required from here
../inst/include/deviance.h:76:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
for(int i = 0; i < Y.n_elem; i++){
~~^~~~~~~~~~
../inst/include/deviance.h: In instantiation of 'arma::Mat<double> compute_gp_deviance_residuals_matrix_impl(arma::Mat<eT>, arma::Mat<double>, Rcpp::NumericVector) [with NumericType = double; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]':
../inst/include/deviance.h:91:75: required from here
../inst/include/deviance.h:76:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/beachmat/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c overdispersion.cpp -o overdispersion.o
overdispersion.cpp: In function 'Rcpp::List make_table_if_small(const NumericVector&, int)':
overdispersion.cpp:26:22: warning: comparison of integer expressions of different signedness: 'std::unordered_map<long int, unsigned int>::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
if(counts.size() > stop_if_larger){
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
overdispersion.cpp: In function 'double conventional_loglikelihood_fast(Rcpp::NumericVector, Rcpp::NumericVector, double, const mat&, bool, Rcpp::NumericVector, Rcpp::NumericVector)':
overdispersion.cpp:93:31: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for(size_t iter = 0; iter < count_frequencies.size(); ++iter){
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
overdispersion.cpp:101:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for(size_t i = 0; i < y.size(); ++i){
~~^~~~~~~~~~
overdispersion.cpp: In function 'double conventional_score_function_fast(Rcpp::NumericVector, Rcpp::NumericVector, double, const mat&, bool, Rcpp::NumericVector, Rcpp::NumericVector)':
overdispersion.cpp:137:31: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for(size_t iter = 0; iter < count_frequencies.size(); ++iter){
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
overdispersion.cpp:160:31: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for(size_t iter = 0; iter < y.size(); ++iter){
~~~~~^~~~~~~~~~
overdispersion.cpp:178:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for(size_t i = 0; i < y.size(); ++i){
~~^~~~~~~~~~
overdispersion.cpp: In function 'double conventional_deriv_score_function_fast(Rcpp::NumericVector, Rcpp::NumericVector, double, const mat&, bool, Rcpp::NumericVector, Rcpp::NumericVector)':
overdispersion.cpp:234:31: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for(size_t iter = 0; iter < count_frequencies.size(); ++iter){
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
overdispersion.cpp:252:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for(size_t i = 0; i < y.size(); ++i){
~~^~~~~~~~~~
overdispersion.cpp: In instantiation of 'Rcpp::List estimate_overdispersions_fast_internal(Rcpp::RObject, Rcpp::RObject, Rcpp::NumericMatrix, bool, double, int) [with NumericType = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::List = Rcpp::Vector<19>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::NumericMatrix = Rcpp::Matrix<14>]':
overdispersion.cpp:313:153: required from here
overdispersion.cpp:275:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
if(n_genes != mean_mat_bm->get_nrow() || n_samples != mean_mat_bm->get_ncol()){
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
overdispersion.cpp:275:54: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
if(n_genes != mean_mat_bm->get_nrow() || n_samples != mean_mat_bm->get_ncol()){
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
overdispersion.cpp: In instantiation of 'Rcpp::List estimate_overdispersions_fast_internal(Rcpp::RObject, Rcpp::RObject, Rcpp::NumericMatrix, bool, double, int) [with NumericType = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::List = Rcpp::Vector<19>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::NumericMatrix = Rcpp::Matrix<14>]':
overdispersion.cpp:315:153: required from here
overdispersion.cpp:275:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
if(n_genes != mean_mat_bm->get_nrow() || n_samples != mean_mat_bm->get_ncol()){
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
overdispersion.cpp:275:54: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
if(n_genes != mean_mat_bm->get_nrow() || n_samples != mean_mat_bm->get_ncol()){
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/beachmat/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utils.cpp -o utils.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o glmGamPoi.dll tmp.def RcppExports.o beta_estimation.o deviance.o overdispersion.o utils.o -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/glmGamPoi.buildbin-libdir/00LOCK-glmGamPoi/00new/glmGamPoi/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'glmGamPoi'
finding HTML links ... done
as.list.glmGamPoi html
estimate_betas_fisher_scoring html
estimate_betas_group_wise html
estimate_betas_roughly html
estimate_betas_roughly_group_wise html
estimate_size_factors html
format_matrix html
glm_gp html
finding level-2 HTML links ... done
glm_gp_impl html
loc_median_fit html
overdispersion_mle html
overdispersion_shrinkage html
predict.glmGamPoi html
print.glmGamPoi html
residuals.glmGamPoi html
solve_lm_for_A html
test_de html
variance_prior html
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'glmGamPoi' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/beachmat/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/beachmat/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c beta_estimation.cpp -o beta_estimation.o
beta_estimation.cpp: In function 'bool lte_n_equal_rows(const NumericMatrix&, int, double)':
beta_estimation.cpp:32:35: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
for(size_t row_idx = 0; row_idx < matrix.nrow(); row_idx++){
~~~~~~~~^~~~~~~~~~~~~~~
beta_estimation.cpp:44:20: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(n_matches > n){
~~~~~~~~~~^~~
beta_estimation.cpp: In function 'Rcpp::IntegerVector get_row_groups(const NumericMatrix&, int, double)':
beta_estimation.cpp:58:35: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
for(size_t row_idx = 0; row_idx < matrix.nrow(); row_idx++){
~~~~~~~~^~~~~~~~~~~~~~~
In file included from beta_estimation.cpp:6:
../inst/include/deviance.h: In instantiation of 'arma::Mat<double> compute_gp_deviance_residuals_matrix_impl(arma::Mat<eT>, arma::Mat<double>, Rcpp::NumericVector) [with NumericType = int; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]':
../inst/include/deviance.h:88:72: required from here
../inst/include/deviance.h:76:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
for(int i = 0; i < Y.n_elem; i++){
~~^~~~~~~~~~
../inst/include/deviance.h: In instantiation of 'arma::Mat<double> compute_gp_deviance_residuals_matrix_impl(arma::Mat<eT>, arma::Mat<double>, Rcpp::NumericVector) [with NumericType = double; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]':
../inst/include/deviance.h:91:75: required from here
../inst/include/deviance.h:76:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
beta_estimation.cpp: In instantiation of 'void clamp_inplace(arma::Mat<eT>&, double, double) [with NumericType = double]':
beta_estimation.cpp:81:36: required from here
beta_estimation.cpp:15:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
for(int i = 0; i < v.n_elem; i++){
~~^~~~~~~~~~
In file included from beta_estimation.cpp:6:
../inst/include/deviance.h: In instantiation of 'double compute_gp_deviance_sum(const arma::Mat<eT>&, const arma::Mat<double>&, double) [with NumericType = int]':
beta_estimation.cpp:246:40: required from 'Rcpp::List fitBeta_fisher_scoring_impl(Rcpp::RObject, const mat&, Rcpp::RObject, Rcpp::NumericVector, SEXP, Rcpp::Nullable<Rcpp::Matrix<14> >, double, double, int, bool) [with NumericType = int; BMNumericType = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::List = Rcpp::Vector<19>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; arma::mat = arma::Mat<double>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; SEXP = SEXPREC*]'
beta_estimation.cpp:305:101: required from here
../inst/include/deviance.h:53:21: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
for (int i = 0; i < Y.n_elem; i++) {
~~^~~~~~~~~~
../inst/include/deviance.h: In instantiation of 'double compute_gp_deviance_sum(const arma::Mat<eT>&, const arma::Mat<double>&, double) [with NumericType = double]':
beta_estimation.cpp:246:40: required from 'Rcpp::List fitBeta_fisher_scoring_impl(Rcpp::RObject, const mat&, Rcpp::RObject, Rcpp::NumericVector, SEXP, Rcpp::Nullable<Rcpp::Matrix<14> >, double, double, int, bool) [with NumericType = double; BMNumericType = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::List = Rcpp::Vector<19>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; arma::mat = arma::Mat<double>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; SEXP = SEXPREC*]'
beta_estimation.cpp:311:104: required from here
../inst/include/deviance.h:53:21: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/beachmat/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c deviance.cpp -o deviance.o
In file included from deviance.cpp:3:
../inst/include/deviance.h: In instantiation of 'arma::Mat<double> compute_gp_deviance_residuals_matrix_impl(arma::Mat<eT>, arma::Mat<double>, Rcpp::NumericVector) [with NumericType = int; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]':
../inst/include/deviance.h:88:72: required from here
../inst/include/deviance.h:76:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
for(int i = 0; i < Y.n_elem; i++){
~~^~~~~~~~~~
../inst/include/deviance.h: In instantiation of 'arma::Mat<double> compute_gp_deviance_residuals_matrix_impl(arma::Mat<eT>, arma::Mat<double>, Rcpp::NumericVector) [with NumericType = double; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]':
../inst/include/deviance.h:91:75: required from here
../inst/include/deviance.h:76:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/beachmat/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c overdispersion.cpp -o overdispersion.o
overdispersion.cpp: In function 'Rcpp::List make_table_if_small(const NumericVector&, int)':
overdispersion.cpp:26:22: warning: comparison of integer expressions of different signedness: 'std::unordered_map<long int, long long unsigned int>::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(counts.size() > stop_if_larger){
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
overdispersion.cpp: In function 'double conventional_loglikelihood_fast(Rcpp::NumericVector, Rcpp::NumericVector, double, const mat&, bool, Rcpp::NumericVector, Rcpp::NumericVector)':
overdispersion.cpp:93:31: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
for(size_t iter = 0; iter < count_frequencies.size(); ++iter){
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
overdispersion.cpp:101:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
for(size_t i = 0; i < y.size(); ++i){
~~^~~~~~~~~~
overdispersion.cpp: In function 'double conventional_score_function_fast(Rcpp::NumericVector, Rcpp::NumericVector, double, const mat&, bool, Rcpp::NumericVector, Rcpp::NumericVector)':
overdispersion.cpp:137:31: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
for(size_t iter = 0; iter < count_frequencies.size(); ++iter){
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
overdispersion.cpp:160:31: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
for(size_t iter = 0; iter < y.size(); ++iter){
~~~~~^~~~~~~~~~
overdispersion.cpp:178:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
for(size_t i = 0; i < y.size(); ++i){
~~^~~~~~~~~~
overdispersion.cpp: In function 'double conventional_deriv_score_function_fast(Rcpp::NumericVector, Rcpp::NumericVector, double, const mat&, bool, Rcpp::NumericVector, Rcpp::NumericVector)':
overdispersion.cpp:234:31: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
for(size_t iter = 0; iter < count_frequencies.size(); ++iter){
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
overdispersion.cpp:252:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
for(size_t i = 0; i < y.size(); ++i){
~~^~~~~~~~~~
overdispersion.cpp: In instantiation of 'Rcpp::List estimate_overdispersions_fast_internal(Rcpp::RObject, Rcpp::RObject, Rcpp::NumericMatrix, bool, double, int) [with NumericType = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::List = Rcpp::Vector<19>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::NumericMatrix = Rcpp::Matrix<14>]':
overdispersion.cpp:313:153: required from here
overdispersion.cpp:275:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
if(n_genes != mean_mat_bm->get_nrow() || n_samples != mean_mat_bm->get_ncol()){
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
overdispersion.cpp:275:54: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
if(n_genes != mean_mat_bm->get_nrow() || n_samples != mean_mat_bm->get_ncol()){
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
overdispersion.cpp: In instantiation of 'Rcpp::List estimate_overdispersions_fast_internal(Rcpp::RObject, Rcpp::RObject, Rcpp::NumericMatrix, bool, double, int) [with NumericType = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::List = Rcpp::Vector<19>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::NumericMatrix = Rcpp::Matrix<14>]':
overdispersion.cpp:315:153: required from here
overdispersion.cpp:275:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
if(n_genes != mean_mat_bm->get_nrow() || n_samples != mean_mat_bm->get_ncol()){
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
overdispersion.cpp:275:54: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
if(n_genes != mean_mat_bm->get_nrow() || n_samples != mean_mat_bm->get_ncol()){
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/beachmat/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utils.cpp -o utils.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o glmGamPoi.dll tmp.def RcppExports.o beta_estimation.o deviance.o overdispersion.o utils.o -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/glmGamPoi.buildbin-libdir/glmGamPoi/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'glmGamPoi' as glmGamPoi_1.6.0.zip
* DONE (glmGamPoi)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'glmGamPoi' successfully unpacked and MD5 sums checked
