Constantin Ahlmann-Eltze
| Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/glmGamPoi |
| git_branch: devel |
| git_last_commit: e8799cb |
| git_last_commit_date: 2024-12-09 18:01:38 -0500 (Mon, 09 Dec 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 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 | ||||
| Package 864/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| glmGamPoi 1.19.2 (landing page) Constantin Ahlmann-Eltze
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: glmGamPoi |
| Version: 1.19.2 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL glmGamPoi |
| StartedAt: 2024-12-23 19:40:01 -0000 (Mon, 23 Dec 2024) |
| EndedAt: 2024-12-23 19:41:28 -0000 (Mon, 23 Dec 2024) |
| EllapsedTime: 86.6 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD INSTALL glmGamPoi
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘glmGamPoi’ ...
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
using C++17
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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 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 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 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++) {
| ~~^~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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++){
| ~~^~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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 unsigned int>::size_type’ {aka ‘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 unsigned int’} and ‘R_xlen_t’ {aka ‘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 unsigned int’} and ‘R_xlen_t’ {aka ‘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 unsigned int’} and ‘R_xlen_t’ {aka ‘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 unsigned int’} and ‘R_xlen_t’ {aka ‘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 unsigned int’} and ‘R_xlen_t’ {aka ‘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 unsigned int’} and ‘R_xlen_t’ {aka ‘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 unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
251 | for(size_t i = 0; i < y.size(); ++i){
| ~~^~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c utils.cpp -o utils.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o glmGamPoi.so RcppExports.o beta_estimation.o deviance.o overdispersion.o utils.o -lopenblas -lgfortran -lm -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-glmGamPoi/00new/glmGamPoi/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (glmGamPoi)