Multiple platform build/check report for BioC 3.20 - INSTALL results for glmGamPoi on palomino6

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4677
palomino6	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4416
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4444
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4393
palomino8	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4373
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

INSTALL results for glmGamPoi on palomino6

To the developers/maintainers of the glmGamPoi package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/glmGamPoi.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: glmGamPoi

Version: 1.17.3

Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL glmGamPoi

StartedAt: 2024-07-15 15:29:38 -0400 (Mon, 15 Jul 2024)

EndedAt: 2024-07-15 15:31:11 -0400 (Mon, 15 Jul 2024)

EllapsedTime: 93.2 seconds

RetCode: 0

Status: OK

Command output

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### Running command:
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###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL glmGamPoi
###
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* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'glmGamPoi' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
using C++11
g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/beachmat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/beachmat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/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 Rcpp::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]
   32 |   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]
   44 |       if(n_matches > n){
      |          ~~~~~~~~~~^~~
beta_estimation.cpp: In function 'Rcpp::IntegerVector get_row_groups(const Rcpp::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]
   58 |   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:88:58:   required from here
../inst/include/deviance.h:76:20: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare]
   76 |   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:91:61:   required from here
../inst/include/deviance.h:76:20: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::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:81:16:   required from here
beta_estimation.cpp:15:20: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare]
   15 |   for(int i = 0; i < v.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 = int]':
beta_estimation.cpp:246:40:   required from 'Rcpp::List fitBeta_fisher_scoring_impl(Rcpp::RObject, const arma::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:301:70:   required from here
../inst/include/deviance.h:53:21: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare]
   53 |   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 arma::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:307:73:   required from here
../inst/include/deviance.h:53:21: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare]
g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/beachmat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/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:88:58:   required from here
../inst/include/deviance.h:76:20: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare]
   76 |   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:91:61:   required from here
../inst/include/deviance.h:76:20: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare]
g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/beachmat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c overdispersion.cpp -o overdispersion.o
overdispersion.cpp: In function 'Rcpp::List make_table_if_small(const Rcpp::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]
   26 |     if(counts.size() > stop_if_larger){
      |        ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
overdispersion.cpp: In function 'double conventional_loglikelihood_fast(Rcpp::NumericVector, Rcpp::NumericVector, double, const arma::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]
   93 |     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]
  101 |   for(size_t i = 0; i < y.size(); ++i){
      |                     ~~^~~~~~~~~~
overdispersion.cpp: In function 'double conventional_score_function_fast(Rcpp::NumericVector, Rcpp::NumericVector, double, const arma::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]
  137 |     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]
  160 |     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]
  178 |   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 arma::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]
  234 |     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]
  252 |   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:313:76:   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]
  275 |   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]
  275 |   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:315:76:   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]
  275 |   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]
  275 |   if(n_genes != mean_mat_bm->get_nrow() || n_samples != mean_mat_bm->get_ncol()){
      |                                            ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/beachmat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c utils.cpp -o utils.o
g++ -shared -s -static-libgcc -o glmGamPoi.dll tmp.def RcppExports.o beta_estimation.o deviance.o overdispersion.o utils.o -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lRlapack -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.20-bioc/R/library/00LOCK-glmGamPoi/00new/glmGamPoi/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** 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
* DONE (glmGamPoi)