Steffi Grote
| Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/GOfuncR |
| git_branch: RELEASE_3_20 |
| git_last_commit: 6c07c88 |
| git_last_commit_date: 2024-10-29 10:24:24 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| 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 883/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GOfuncR 1.26.0 (landing page) Steffi Grote
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the GOfuncR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GOfuncR.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: GOfuncR |
| Version: 1.26.0 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL GOfuncR |
| StartedAt: 2024-11-19 20:41:47 -0000 (Tue, 19 Nov 2024) |
| EndedAt: 2024-11-19 20:44:34 -0000 (Tue, 19 Nov 2024) |
| EllapsedTime: 167.0 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD INSTALL GOfuncR
###
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* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘GOfuncR’ ...
** using staged installation
** libs
using C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’
using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c binom_categorytest.cc -o binom_categorytest.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c binom_randset.cc -o binom_randset.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c blocks.cpp -o blocks.o
blocks.cpp: In function 'std::set<int> rannum_blocks(std::vector<bed_str>, std::vector<bed_str>, const std::map<std::__cxx11::basic_string<char>, int>&, std::vector<gen_pos_str>)':
blocks.cpp:30:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<bed_str>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
30 | for (int j=0; j < candidate_bed.size(); j++){
| ~~^~~~~~~~~~~~~~~~~~~~~~
blocks.cpp:34:41: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<bed_str>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
34 | for (int k=0; k < background.size(); k++){
| ~~^~~~~~~~~~~~~~~~~~~
blocks.cpp:68:40: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<gen_pos_str>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
68 | for (int g=0; g<genes_pos.size(); g++){
| ~^~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c conti_categorytest.cc -o conti_categorytest.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c conti_randset.cc -o conti_randset.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c gene.cc -o gene.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c gene_binom.cc -o gene_binom.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c gene_conti.cc -o gene_conti.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c genes.cc -o genes.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c genes_binom.cc -o genes_binom.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c genes_conti.cc -o genes_conti.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c go.cc -o go.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c go_graph.cc -o go_graph.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c go_graph_binom.cc -o go_graph_binom.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c go_graph_conti.cc -o go_graph_conti.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c go_graph_hyper.cc -o go_graph_hyper.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c go_groups.cc -o go_groups.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c go_groups_binom.cc -o go_groups_binom.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c go_groups_conti.cc -o go_groups_conti.o
go_groups_conti.cc: In member function 'int* go_groups_conti::calculate_data(std::string&, std::ostream*)':
go_groups_conti.cc:71:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
71 | for ( int idx=0 ; idx < names.size() ; ++idx ) {
| ~~~~^~~~~~~~~~~~~~
go_groups_conti.cc: In member function 'int* go_groups_conti::calculate_rand(std::string&, std::ostream*)':
go_groups_conti.cc:172:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
172 | for ( int idx=0 ; idx < names.size() ; ++idx ) {
| ~~~~^~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c go_groups_hyper.cc -o go_groups_hyper.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c go_obj.cc -o go_obj.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c go_obj_binom.cc -o go_obj_binom.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c go_obj_conti.cc -o go_obj_conti.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c go_obj_hyper.cc -o go_obj_hyper.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c hyper_categorytest.cc -o hyper_categorytest.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c hyper_randset.cc -o hyper_randset.o
hyper_randset.cc: In function 'void hyper_randset(std::string, int, std::string, std::string, std::string, std::string, std::string, std::string, bool)':
hyper_randset.cc:217:54: warning: comparison of integer expressions of different signedness: 'std::set<int>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
217 | while (random_numbers.size() < n_candidate) {
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c idmap.cc -o idmap.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c init.c -o init.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ran_genelen.cpp -o ran_genelen.o
ran_genelen.cpp: In function 'std::set<int> rannum_genelen(int, const std::map<std::__cxx11::basic_string<char>, int>&, std::vector<gen_pos_str>, long int)':
ran_genelen.cpp:19:38: warning: comparison of integer expressions of different signedness: 'std::set<int>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
19 | while (random_numbers.size() < n_candidate) {
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c read_bed.cpp -o read_bed.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c roll.cpp -o roll.o
roll.cpp: In function 'std::set<int> rannum_roll(std::vector<bed_str>, std::vector<bed_str>, const std::map<std::__cxx11::basic_string<char>, int>&, std::vector<gen_pos_str>)':
roll.cpp:30:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<bed_str>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
30 | for (int j=0; j < candidate_bed.size(); j++){
| ~~^~~~~~~~~~~~~~~~~~~~~~
roll.cpp:36:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<bed_str>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
36 | for (int i=0; i < background_bed.size(); i++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~
roll.cpp:92:40: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<gen_pos_str>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
92 | for (int g=0; g<genes_pos.size(); g++){
| ~^~~~~~~~~~~~~~~~~
roll.cpp:106:32: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<bed_str>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
106 | if ((k == background_bed.size()) || (background_bed[k].chrom != ran_chrom)){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c transitions.cc -o transitions.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c unlock_environment.cc -o unlock_environment.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c wilcox_categorytest.cc -o wilcox_categorytest.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c wilcox_randset.cc -o wilcox_randset.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o GOfuncR.so RcppExports.o binom_categorytest.o binom_randset.o blocks.o conti_categorytest.o conti_randset.o gene.o gene_binom.o gene_conti.o genes.o genes_binom.o genes_conti.o go.o go_graph.o go_graph_binom.o go_graph_conti.o go_graph_hyper.o go_groups.o go_groups_binom.o go_groups_conti.o go_groups_hyper.o go_obj.o go_obj_binom.o go_obj_conti.o go_obj_hyper.o hyper_categorytest.o hyper_randset.o idmap.o init.o ran_genelen.o read_bed.o roll.o transitions.o unlock_environment.o wilcox_categorytest.o wilcox_randset.o -L/home/biocbuild/R/R-4.4.1/lib -lR
installing to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-GOfuncR/00new/GOfuncR/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (GOfuncR)