Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 806/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GENIE3 1.29.0 (landing page) Van Anh Huynh-Thu
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
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: 1.29.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:GENIE3.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GENIE3_1.29.0.tar.gz |
StartedAt: 2024-12-24 07:00:42 -0000 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 07:01:27 -0000 (Tue, 24 Dec 2024) |
EllapsedTime: 45.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GENIE3.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:GENIE3.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GENIE3_1.29.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/GENIE3.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GENIE3/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GENIE3’ version ‘1.29.0’ * checking package namespace information ... NOTE Found export directive that requires package ‘methods’: ‘exportMethods’ Remove all such namespace directives (if obsolete) or ensure that the DESCRIPTION Depends or Imports field contains ‘methods’. * 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 ‘GENIE3’ can be installed ... OK * used C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’ * checking installed package size ... OK * 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 ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: VERSION 0.99.4 Removed argument "seed", use set.seed instead Minor improvemtents * 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 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 * 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: 3 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/GENIE3.Rcheck/00check.log’ for details.
GENIE3.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL GENIE3 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘GENIE3’ ... ** 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 -I"/home/biocbuild/R/R/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 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o GENIE3.so GENIE3.o -L/home/biocbuild/R/R/lib -lR installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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)
GENIE3.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu 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. > > testthat::test_check("GENIE3") Loading required package: GENIE3 [ FAIL 0 | WARN 0 | SKIP 0 | PASS 49 ] > > proc.time() user system elapsed 10.405 0.323 10.735
GENIE3.Rcheck/GENIE3-Ex.timings
name | user | system | elapsed | |
GENIE3 | 0.363 | 0.008 | 0.372 | |
getLinkList | 0.039 | 0.000 | 0.039 | |