Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-21 12:04 -0400 (Thu, 21 Aug 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" | 4819 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4597 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4539 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4536 |
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 1732/2318 | 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. |
Package: regutools |
Version: 1.21.0 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:regutools.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings regutools_1.21.0.tar.gz |
StartedAt: 2025-08-21 02:01:59 -0400 (Thu, 21 Aug 2025) |
EndedAt: 2025-08-21 02:10:21 -0400 (Thu, 21 Aug 2025) |
EllapsedTime: 502.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: regutools.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:regutools.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings regutools_1.21.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/regutools.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * 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 7.995 0.182 8.340 build_condition 5.912 0.224 6.366 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
regutools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL regutools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/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 4.5.1 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-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 70.801 2.521 75.759
regutools.Rcheck/regutools-Ex.timings
name | user | system | elapsed | |
build_condition | 5.912 | 0.224 | 6.366 | |
connect_database | 3.249 | 0.097 | 3.575 | |
convert_to_biostrings | 3.462 | 0.138 | 3.752 | |
convert_to_granges | 3.482 | 0.142 | 3.773 | |
existing_intervals | 0 | 0 | 0 | |
existing_partial_match | 0 | 0 | 0 | |
get_binding_sites | 3.405 | 0.095 | 3.694 | |
get_dataset | 3.496 | 0.097 | 3.750 | |
get_dna_objects | 3.435 | 0.100 | 3.585 | |
get_gene_regulators | 4.416 | 0.074 | 4.640 | |
get_gene_synonyms | 3.105 | 0.082 | 3.335 | |
get_regulatory_network | 3.085 | 0.081 | 3.316 | |
get_regulatory_summary | 3.236 | 0.083 | 3.467 | |
guess_id | 3.003 | 0.094 | 3.246 | |
list_attributes | 4.122 | 0.134 | 4.431 | |
list_datasets | 3.020 | 0.087 | 3.255 | |
non_existing_intervals | 0 | 0 | 0 | |
plot_dna_objects | 7.995 | 0.182 | 8.340 | |
regulondb | 3.078 | 0.256 | 3.535 | |