Van Anh Huynh-Thu
| Snapshot Date: 2025-10-24 13:45 -0400 (Fri, 24 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/GENIE3 |
| git_branch: devel |
| git_last_commit: 05a2b25 |
| git_last_commit_date: 2025-04-15 11:12:53 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-25 12:07 -0400 (Sat, 25 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 836/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GENIE3 1.31.0 (landing page) Van Anh Huynh-Thu
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | NA | NA | ||||||||||
|
To the developers/maintainers of the GENIE3 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GENIE3.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: GENIE3 |
| Version: 1.31.0 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL GENIE3 |
| StartedAt: 2025-10-23 20:25:58 -0000 (Thu, 23 Oct 2025) |
| EndedAt: 2025-10-23 20:26:17 -0000 (Thu, 23 Oct 2025) |
| EllapsedTime: 19.5 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
###
### /home/biocbuild/R/R/bin/R CMD INSTALL GENIE3
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘GENIE3’ ...
** this is package ‘GENIE3’ version ‘1.31.0’
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c GENIE3.c -o GENIE3.o
GENIE3.c: In function ‘find_the_best_threshold_multiregr’:
GENIE3.c:1370:27: warning: ‘best_info’ may be used uninitialized [-Wmaybe-uninitialized]
1370 | current_threshold_info=best_info;
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
GENIE3.c:1328:31: note: ‘best_info’ was declared here
1328 | SCORE_TYPE best_score=-1.0, best_info, current_score, w;
| ^~~~~~~~~
GENIE3.c:1368:24: warning: ‘best_threshold’ may be used uninitialized [-Wmaybe-uninitialized]
1368 | current_threshold.f=best_threshold;
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
GENIE3.c:1329:9: note: ‘best_threshold’ was declared here
1329 | float best_threshold;
| ^~~~~~~~~~~~~~
GENIE3.c: In function ‘build_one_tree_ensemble’:
GENIE3.c:1052:7: warning: ‘fp’ may be used uninitialized [-Wmaybe-uninitialized]
1052 | write_one_tree(current_tree, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GENIE3.c:987:9: note: ‘fp’ was declared here
987 | FILE *fp;
| ^~
GENIE3.c: In function ‘find_the_best_threshold_symb_multiregr’:
GENIE3.c:1466:27: warning: ‘best_info’ may be used uninitialized [-Wmaybe-uninitialized]
1466 | current_threshold_info=best_info;
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
GENIE3.c:1412:31: note: ‘best_info’ was declared here
1412 | SCORE_TYPE best_score=-1.0, best_info, current_score;
| ^~~~~~~~~
GENIE3.c: In function ‘compute_ltrees_variable_importance_multiregr_separate’:
GENIE3.c:1753:6: warning: ‘flag_continue’ may be used uninitialized [-Wmaybe-uninitialized]
1753 | if (flag_continue == 1) {
| ^
GENIE3.c:1725:7: note: ‘flag_continue’ was declared here
1725 | int flag_continue;
| ^~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o GENIE3.so GENIE3.o -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/site-library/00LOCK-GENIE3/00new/GENIE3/libs
** R
** inst
** byte-compile and prepare package for lazy loading
in method for ‘GENIE3’ with signature ‘"SummarizedExperiment"’: no definition for class “SummarizedExperiment”
in method for ‘GENIE3’ with signature ‘"ExpressionSet"’: no definition for class “ExpressionSet”
** 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 (GENIE3)