Steffi Grote
| Snapshot Date: 2024-04-28 14:00:16 -0400 (Sun, 28 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/GOfuncR |
| git_branch: devel |
| git_last_commit: fe22b6c |
| git_last_commit_date: 2024-02-03 06:52:40 -0400 (Sat, 03 Feb 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-04-29 11:40:53 -0400 (Mon, 29 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4752 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4518 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4475 |
| 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 891/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GOfuncR 1.23.2 (landing page) Steffi Grote
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | 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 | ||||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.23.2 |
| Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:GOfuncR.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings GOfuncR_1.23.2.tar.gz |
| StartedAt: 2024-04-29 06:41:03 -0000 (Mon, 29 Apr 2024) |
| EndedAt: 2024-04-29 06:46:42 -0000 (Mon, 29 Apr 2024) |
| EllapsedTime: 338.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GOfuncR.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:GOfuncR.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings GOfuncR_1.23.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/GOfuncR.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GOfuncR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GOfuncR’ version ‘1.23.2’
* 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 ‘GOfuncR’ can be installed ... OK
* used C compiler: ‘gcc (GCC) 10.3.1’
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking installed package size ... NOTE
installed size is 14.5Mb
sub-directories of 1Mb or more:
R 1.9Mb
libs 12.5Mb
* 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 code 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 loading without being on the library search path ... 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 R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
refine 39.046 0.686 39.832
get_anno_categories 14.154 1.029 15.223
plot_anno_scores 13.932 0.491 14.497
go_enrich 5.320 0.200 5.530
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.19-bioc/meat/GOfuncR.Rcheck/00check.log’
for details.
GOfuncR.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL GOfuncR
###
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* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘GOfuncR’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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:30:19: 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:34:20: 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:68:19: 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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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:71:24: 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:172:24: 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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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:217:33: 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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c idmap.cc -o idmap.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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:19:31: 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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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:30:18: 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:36:19: 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:92:19: 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:106:11: 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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/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)
GOfuncR.Rcheck/tests/testthat.Rout
R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
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Platform: aarch64-unknown-linux-gnu
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> library(testthat)
> library(GOfuncR)
Loading required package: vioplot
Loading required package: sm
Package 'sm', version 2.2-6.0: type help(sm) for summary information
Loading required package: zoo
Attaching package: 'zoo'
The following objects are masked from 'package:base':
as.Date, as.Date.numeric
>
> test_check("GOfuncR")
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 73 ]
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 73 ]
>
> proc.time()
user system elapsed
121.701 3.063 125.002
GOfuncR.Rcheck/GOfuncR-Ex.timings
| name | user | system | elapsed | |
| get_anno_categories | 14.154 | 1.029 | 15.223 | |
| get_anno_genes | 2.737 | 0.104 | 2.893 | |
| get_child_nodes | 0.116 | 0.004 | 0.120 | |
| get_ids | 0.239 | 0.000 | 0.239 | |
| get_names | 0.02 | 0.00 | 0.02 | |
| get_parent_nodes | 0.127 | 0.000 | 0.127 | |
| go_enrich | 5.32 | 0.20 | 5.53 | |
| plot_anno_scores | 13.932 | 0.491 | 14.497 | |
| refine | 39.046 | 0.686 | 39.832 | |