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This page was generated on 2022-06-24 12:04:51 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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

CHECK results for glmGamPoi on nebbiolo1


To the developers/maintainers of the glmGamPoi package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 812/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
glmGamPoi 1.8.0  (landing page)
Constantin Ahlmann-Eltze
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/glmGamPoi
git_branch: RELEASE_3_15
git_last_commit: b723d61
git_last_commit_date: 2022-04-26 12:04:08 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: glmGamPoi
Version: 1.8.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:glmGamPoi.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings glmGamPoi_1.8.0.tar.gz
StartedAt: 2022-06-23 20:10:49 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 20:13:38 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 169.1 seconds
RetCode: 0
Status:   OK  
CheckDir: glmGamPoi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:glmGamPoi.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings glmGamPoi_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/glmGamPoi.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘glmGamPoi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘glmGamPoi’ version ‘1.8.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘glmGamPoi’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/glmGamPoi.Rcheck/00check.log’
for details.



Installation output

glmGamPoi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL glmGamPoi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘glmGamPoi’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.15-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-3.15-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.15-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 of integer expressions of different signedness: ‘size_t’ {aka ‘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 unsigned int’} and ‘int’ [-Wsign-compare]
   44 |       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 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:88:72:   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]
   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:91:75:   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]
   15 |   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]
   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 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]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.15-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:
../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]
   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:91:75:   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]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.15-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 of integer expressions of different signedness: ‘std::unordered_map<long int, long unsigned int>::size_type’ {aka ‘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 mat&, bool, Rcpp::NumericVector, Rcpp::NumericVector)’:
overdispersion.cpp:93:31: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘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 unsigned int’} and ‘R_xlen_t’ {aka ‘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 mat&, bool, Rcpp::NumericVector, Rcpp::NumericVector)’:
overdispersion.cpp:137:31: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘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 unsigned int’} and ‘R_xlen_t’ {aka ‘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 unsigned int’} and ‘R_xlen_t’ {aka ‘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 mat&, bool, Rcpp::NumericVector, Rcpp::NumericVector)’:
overdispersion.cpp:234:31: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘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 unsigned int’} and ‘R_xlen_t’ {aka ‘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:313:153:   required from here
overdispersion.cpp:275:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘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 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:315:153:   required from here
overdispersion.cpp:275:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘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 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"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/beachmat/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o glmGamPoi.so RcppExports.o beta_estimation.o deviance.o overdispersion.o utils.o -L/home/biocbuild/bbs-3.15-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.15-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-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)

Tests output

glmGamPoi.Rcheck/tests/testthat.Rout


R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(glmGamPoi)
> 
> test_check("glmGamPoi")
[ FAIL 0 | WARN 0 | SKIP 5 | PASS 394 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• Beta estimation is unprecise on Non-MacOS architectures (1)
• Printing tests should be run interactively (1)
• empty test (2)
• isNamespaceLoaded("devtools") is not TRUE (1)

[ FAIL 0 | WARN 0 | SKIP 5 | PASS 394 ]
> 
> proc.time()
   user  system elapsed 
 42.684  15.896  51.740 

Example timings

glmGamPoi.Rcheck/glmGamPoi-Ex.timings

nameusersystemelapsed
glm_gp1.2710.0361.307
loc_median_fit0.0570.0000.057
overdispersion_mle0.0120.0080.020
overdispersion_shrinkage0.080.000.08
predict.glmGamPoi0.0760.0000.075
test_de0.6260.0440.670