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INSTALL report for glmGamPoi on malbec1

This page was generated on 2021-05-06 12:27:46 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the glmGamPoi package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 748/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
glmGamPoi 1.2.0  (landing page)
Constantin Ahlmann-Eltze
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/glmGamPoi
Branch: RELEASE_3_12
Last Commit: a11d461
Last Changed Date: 2020-10-27 11:55:36 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: glmGamPoi
Version: 1.2.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL glmGamPoi
StartedAt: 2021-05-05 16:25:32 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 16:26:47 -0400 (Wed, 05 May 2021)
EllapsedTime: 74.3 seconds
RetCode: 0
Status:   OK  

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL glmGamPoi
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘glmGamPoi’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include' -I/usr/local/include   -fpic  -g -O2  -Wall -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 between signed and unsigned integer expressions [-Wsign-compare]
   for(size_t row_idx = 0; row_idx < matrix.nrow(); row_idx++){
                           ~~~~~~~~^~~~~~~~~~~~~~~
beta_estimation.cpp:44:20: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
   for(size_t row_idx = 0; row_idx < matrix.nrow(); row_idx++){
                           ~~~~~~~~^~~~~~~~~~~~~~~
In file included from beta_estimation.cpp:6:0:
../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:76:72:   required from here
../inst/include/deviance.h:64:20: warning: comparison between signed and unsigned integer expressions [-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:79:75:   required from here
../inst/include/deviance.h:64:20: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 0; i < v.n_elem; i++){
                  ~~^~~~~~~~~~
In file included from beta_estimation.cpp:6:0:
../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:174:45:   required from ‘Rcpp::List fitBeta_fisher_scoring_impl(Rcpp::RObject, const mat&, Rcpp::RObject, Rcpp::NumericVector, SEXP, 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:224:101:   required from here
../inst/include/deviance.h:53:21: warning: comparison between signed and unsigned integer expressions [-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:174:45:   required from ‘Rcpp::List fitBeta_fisher_scoring_impl(Rcpp::RObject, const mat&, Rcpp::RObject, Rcpp::NumericVector, SEXP, 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:230:104:   required from here
../inst/include/deviance.h:53:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c deviance.cpp -o deviance.o
In file included from deviance.cpp:3:0:
../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:76:72:   required from here
../inst/include/deviance.h:64:20: warning: comparison between signed and unsigned integer expressions [-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:79:75:   required from here
../inst/include/deviance.h:64:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include' -I/usr/local/include   -fpic  -g -O2  -Wall -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 between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
     for(size_t iter = 0; iter < count_frequencies.size(); ++iter){
                          ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
overdispersion.cpp:101:23: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
     for(size_t iter = 0; iter < count_frequencies.size(); ++iter){
                          ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
overdispersion.cpp:160:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(size_t iter = 0; iter < y.size(); ++iter){
                          ~~~~~^~~~~~~~~~
overdispersion.cpp:178:23: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
     for(size_t iter = 0; iter < count_frequencies.size(); ++iter){
                          ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
overdispersion.cpp:252:23: warning: comparison between signed and unsigned integer expressions [-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:305:153:   required from here
overdispersion.cpp:275:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(n_genes != mean_mat_bm->get_nrow() || n_samples != mean_mat_bm->get_ncol()){
      ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
overdispersion.cpp:275:54: warning: comparison between signed and unsigned integer expressions [-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:307:153:   required from here
overdispersion.cpp:275:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(n_genes != mean_mat_bm->get_nrow() || n_samples != mean_mat_bm->get_ncol()){
      ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
overdispersion.cpp:275:54: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(n_genes != mean_mat_bm->get_nrow() || n_samples != mean_mat_bm->get_ncol()){
                                            ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o glmGamPoi.so RcppExports.o beta_estimation.o deviance.o overdispersion.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.12-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/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)