Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-11-02 11:40:27 -0400 (Thu, 02 Nov 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
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 191/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
biocthis 1.12.0 (landing page) Leonardo Collado-Torres
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the biocthis package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biocthis.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: biocthis |
Version: 1.12.0 |
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:biocthis.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings biocthis_1.12.0.tar.gz |
StartedAt: 2023-11-02 08:42:57 -0000 (Thu, 02 Nov 2023) |
EndedAt: 2023-11-02 08:43:29 -0000 (Thu, 02 Nov 2023) |
EllapsedTime: 32.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: biocthis.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:biocthis.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings biocthis_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/biocthis.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * 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 ‘biocthis/DESCRIPTION’ ... OK * this is package ‘biocthis’ version ‘1.12.0’ * 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 ‘biocthis’ 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 R 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 ... NOTE Missing object imported by a ':::' call: ‘usethis:::get_active_r_file’ Unexported objects imported by ':::' calls: ‘BiocManager:::.version_map_get_online’ ‘BiocManager:::isDevel’ ‘usethis:::asciify’ ‘usethis:::check_is_package’ ‘usethis:::check_vignette_name’ ‘usethis:::create_directory’ ‘usethis:::is_package’ ‘usethis:::proj_desc_field_update’ ‘usethis:::proj_version’ ‘usethis:::project_name’ ‘usethis:::render_template’ ‘usethis:::target_repo_spec’ ‘usethis:::use_dot_github’ ‘usethis:::uses_git’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE use_bioc_github_action: no visible global function definition for ‘browseURL’ Undefined global functions or variables: browseURL Consider adding importFrom("utils", "browseURL") to your NAMESPACE file. * 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 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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-3.18-bioc/meat/biocthis.Rcheck/00check.log’ for details.
biocthis.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL biocthis ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’ * installing *source* package ‘biocthis’ ... ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biocthis)
biocthis.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (64-bit) 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(biocthis) > > test_check("biocthis") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ] > > proc.time() user system elapsed 1.271 0.099 1.555
biocthis.Rcheck/biocthis-Ex.timings
name | user | system | elapsed | |
bioc_badges | 0 | 0 | 0 | |
bioc_style | 0.521 | 0.056 | 0.607 | |
biocthis_example_pkg | 0.059 | 0.020 | 0.079 | |
use_bioc_citation | 0.185 | 0.058 | 0.284 | |
use_bioc_coc | 0.162 | 0.040 | 0.204 | |
use_bioc_description | 0.176 | 0.020 | 0.199 | |
use_bioc_feature_request_template | 0.122 | 0.008 | 0.131 | |
use_bioc_github_action | 0 | 0 | 0 | |
use_bioc_issue_template | 0.106 | 0.024 | 0.132 | |
use_bioc_news_md | 0.104 | 0.027 | 0.201 | |
use_bioc_pkg_templates | 0.218 | 0.043 | 0.270 | |
use_bioc_pkgdown_css | 0.116 | 0.012 | 0.130 | |
use_bioc_readme_rmd | 0.207 | 0.043 | 0.267 | |
use_bioc_support | 0.124 | 0.016 | 0.140 | |
use_bioc_vignette | 1.084 | 0.084 | 1.263 | |