Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-06 12:08 -0400 (Sat, 06 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4618 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4565 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4544 |
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 1735/2322 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
regutools 1.21.0 (landing page) Joselyn Chavez
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 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 | OK | OK | ||||||||||
To the developers/maintainers of the regutools package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/regutools.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: regutools |
Version: 1.21.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:regutools.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings regutools_1.21.0.tar.gz |
StartedAt: 2025-09-05 11:16:42 -0000 (Fri, 05 Sep 2025) |
EndedAt: 2025-09-05 11:30:23 -0000 (Fri, 05 Sep 2025) |
EllapsedTime: 820.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: regutools.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:regutools.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings regutools_1.21.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/regutools.Rcheck’ * using R version 4.5.0 (2025-04-11) * 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 ‘regutools/DESCRIPTION’ ... OK * this is package ‘regutools’ version ‘1.21.0’ * 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 ‘regutools’ can be installed ... OK * 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 ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plot_dna_objects 9.678 0.321 15.271 build_condition 6.173 0.180 9.487 get_gene_synonyms 5.148 0.187 8.610 list_attributes 4.930 0.099 9.634 convert_to_biostrings 4.537 0.162 8.502 get_dna_objects 4.459 0.136 8.857 convert_to_granges 4.448 0.130 7.144 get_dataset 4.364 0.179 8.491 get_gene_regulators 4.374 0.086 7.664 connect_database 4.243 0.164 8.741 get_regulatory_summary 4.236 0.140 7.886 get_binding_sites 4.207 0.108 7.510 get_regulatory_network 4.046 0.214 8.724 regulondb 3.930 0.261 7.845 list_datasets 3.753 0.155 7.560 guess_id 3.822 0.084 6.372 * 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: OK
regutools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL regutools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘regutools’ ... ** this is package ‘regutools’ version ‘1.21.0’ ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (regutools)
regutools.Rcheck/tests/testthat.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six" Copyright (C) 2025 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. > library("testthat") > library("regutools") > > test_check("regutools") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 110 ] Warning message: call dbDisconnect() when finished working with a connection > > proc.time() user system elapsed 90.012 3.051 161.322
regutools.Rcheck/regutools-Ex.timings
name | user | system | elapsed | |
build_condition | 6.173 | 0.180 | 9.487 | |
connect_database | 4.243 | 0.164 | 8.741 | |
convert_to_biostrings | 4.537 | 0.162 | 8.502 | |
convert_to_granges | 4.448 | 0.130 | 7.144 | |
existing_intervals | 0.000 | 0.000 | 0.001 | |
existing_partial_match | 0.001 | 0.000 | 0.000 | |
get_binding_sites | 4.207 | 0.108 | 7.510 | |
get_dataset | 4.364 | 0.179 | 8.491 | |
get_dna_objects | 4.459 | 0.136 | 8.857 | |
get_gene_regulators | 4.374 | 0.086 | 7.664 | |
get_gene_synonyms | 5.148 | 0.187 | 8.610 | |
get_regulatory_network | 4.046 | 0.214 | 8.724 | |
get_regulatory_summary | 4.236 | 0.140 | 7.886 | |
guess_id | 3.822 | 0.084 | 6.372 | |
list_attributes | 4.930 | 0.099 | 9.634 | |
list_datasets | 3.753 | 0.155 | 7.560 | |
non_existing_intervals | 0.001 | 0.000 | 0.000 | |
plot_dna_objects | 9.678 | 0.321 | 15.271 | |
regulondb | 3.930 | 0.261 | 7.845 | |