Multiple platform build/check report for BioC 3.21 - INSTALL results for glmGamPoi on palomino7

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"	4777
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"	4545
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4576
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4528
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4458
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 palomino7

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: 1.19.5

Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL glmGamPoi

StartedAt: 2025-03-19 16:08:03 -0400 (Wed, 19 Mar 2025)

EndedAt: 2025-03-19 16:09:46 -0400 (Wed, 19 Mar 2025)

EllapsedTime: 103.7 seconds

RetCode: 0

Status: OK

Command output

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### Running command:
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###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL glmGamPoi
###
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'glmGamPoi' ...
** this is package 'glmGamPoi' version '1.19.5'
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
using C++17
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include/ -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppArmadillo/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include/ -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppArmadillo/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include'   -I"C:/rtools45/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:31:35: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   31 |   for(size_t row_idx = 0; row_idx < matrix.nrow(); row_idx++){
      |                           ~~~~~~~~^~~~~~~~~~~~~~~
beta_estimation.cpp:43:20: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   43 |       if(n_matches > n){
      |          ~~~~~~~~~~^~~
beta_estimation.cpp: In function 'Rcpp::IntegerVector get_row_groups(const Rcpp::NumericMatrix&, int, double)':
beta_estimation.cpp:57:35: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   57 |   for(size_t row_idx = 0; row_idx < matrix.nrow(); row_idx++){
      |                           ~~~~~~~~^~~~~~~~~~~~~~~
In file included from beta_estimation.cpp:5:
../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
   88 |     return compute_gp_deviance_residuals_matrix_impl<int>(Y, Mu, thetas);
      |            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
../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
   91 |     return compute_gp_deviance_residuals_matrix_impl<double>(Y, Mu, thetas);
      |            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
../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++){
      |                  ~~^~~~~~~~~~
beta_estimation.cpp: In instantiation of 'void clamp_inplace(arma::Mat<eT>&, double, double) [with NumericType = double]':
beta_estimation.cpp:80:16:   required from here
   80 |   clamp_inplace(mu_hat, 1e-50, 1e50);
      |   ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
beta_estimation.cpp:14:20: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare]
   14 |   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 = double]':
beta_estimation.cpp:256:40:   required from here
  256 |       dev_old = compute_gp_deviance_sum(counts, mu_hat, thetas(gene_idx)) + pen_sum;
      |                 ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../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++) {
      |                   ~~^~~~~~~~~~
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include/ -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppArmadillo/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include'   -I"C:/rtools45/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
   88 |     return compute_gp_deviance_residuals_matrix_impl<int>(Y, Mu, thetas);
      |            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
../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
   91 |     return compute_gp_deviance_residuals_matrix_impl<double>(Y, Mu, thetas);
      |            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
../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++){
      |                  ~~^~~~~~~~~~
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include/ -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppArmadillo/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include'   -I"C:/rtools45/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:25:22: 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]
   25 |     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:92:31: 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]
   92 |     for(size_t iter = 0; iter < count_frequencies.size(); ++iter){
      |                          ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
overdispersion.cpp:100:23: 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]
  100 |   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:136:31: 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]
  136 |     for(size_t iter = 0; iter < count_frequencies.size(); ++iter){
      |                          ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
overdispersion.cpp:159:31: 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]
  159 |     for(size_t iter = 0; iter < y.size(); ++iter){
      |                          ~~~~~^~~~~~~~~~
overdispersion.cpp:177:23: 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]
  177 |   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:233:31: 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]
  233 |     for(size_t iter = 0; iter < count_frequencies.size(); ++iter){
      |                          ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
overdispersion.cpp:251:23: 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]
  251 |   for(size_t i = 0; i < y.size(); ++i){
      |                     ~~^~~~~~~~~~
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include/ -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppArmadillo/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include'   -I"C:/rtools45/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 -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lRlapack -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lRblas -lgfortran -lquadmath -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-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)