Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-08-04 11:43 -0400 (Mon, 04 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4565 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4603 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4544 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
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 195/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BiocPkgTools 1.26.2 (landing page) Sean Davis
| nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the BiocPkgTools package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiocPkgTools.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: BiocPkgTools |
Version: 1.26.2 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocPkgTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocPkgTools_1.26.2.tar.gz |
StartedAt: 2025-08-01 00:27:57 -0400 (Fri, 01 Aug 2025) |
EndedAt: 2025-08-01 00:41:14 -0400 (Fri, 01 Aug 2025) |
EllapsedTime: 796.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BiocPkgTools.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocPkgTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocPkgTools_1.26.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BiocPkgTools.Rcheck’ * using R version 4.5.1 RC (2025-06-05 r88288) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BiocPkgTools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BiocPkgTools’ version ‘1.26.2’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 25 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘BiocPkgTools’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘BiocManager:::.repositories’ ‘BiocManager:::.repositories_bioc’ ‘BiocManager:::.repository_container_version’ ‘BiocManager:::.version_bioc’ 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 ... 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 biocBuildReport 19.840 82.402 135.864 get_bioc_data 23.123 1.072 53.022 firstInBioc 22.986 0.777 48.093 pkgCombDependencyGain 21.965 1.349 45.247 biocDownloadStats 20.270 0.994 22.372 pkgDepMetrics 13.684 0.343 16.962 class-dependencies 12.578 0.468 18.327 inducedSubgraphByPkgs 7.716 0.726 18.716 biocMaintained 6.126 0.168 6.436 buildPkgDependencyDataFrame 5.262 0.091 5.528 pkgBiocRevDeps 4.390 0.637 10.079 githubDetails 3.329 0.599 7.891 getBiocVignette 2.628 0.148 5.635 * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/BiocPkgTools.Rcheck/00check.log’ for details.
BiocPkgTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BiocPkgTools ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘BiocPkgTools’ ... ** this is package ‘BiocPkgTools’ version ‘1.26.2’ ** 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 (BiocPkgTools)
BiocPkgTools.Rcheck/tests/testthat.Rout
R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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(BiocPkgTools) Loading required package: htmlwidgets > > test_check("BiocPkgTools") trying URL 'https://bioconductor.org/packages/3.21/bioc/vignettes/a4/inst/doc/a4vignette.pdf' Content type 'application/pdf' length 1397541 bytes (1.3 MB) ================================================== downloaded 1.3 MB [ FAIL 0 | WARN 2 | SKIP 0 | PASS 27 ] [ FAIL 0 | WARN 2 | SKIP 0 | PASS 27 ] > > proc.time() user system elapsed 65.091 55.488 142.142
BiocPkgTools.Rcheck/BiocPkgTools-Ex.timings
name | user | system | elapsed | |
activitySince | 0.001 | 0.001 | 0.003 | |
anacondaDownloadStats | 3.916 | 0.071 | 4.411 | |
biocBuildReport | 19.840 | 82.402 | 135.864 | |
biocDownloadStats | 20.270 | 0.994 | 22.372 | |
biocMaintained | 6.126 | 0.168 | 6.436 | |
biocPkgList | 2.513 | 0.040 | 2.810 | |
biocPkgRanges | 0.000 | 0.001 | 0.000 | |
biocRevDepEmail | 3.910 | 0.157 | 4.796 | |
buildPkgDependencyDataFrame | 5.262 | 0.091 | 5.528 | |
buildPkgDependencyIgraph | 2.507 | 0.041 | 2.591 | |
class-dependencies | 12.578 | 0.468 | 18.327 | |
firstInBioc | 22.986 | 0.777 | 48.093 | |
generateBiocPkgDOI | 0.000 | 0.001 | 0.001 | |
getBiocVignette | 2.628 | 0.148 | 5.635 | |
getPkgYearsInBioc | 0.001 | 0.001 | 0.003 | |
get_bioc_data | 23.123 | 1.072 | 53.022 | |
get_cre_orcids | 0.021 | 0.002 | 0.081 | |
githubDetails | 3.329 | 0.599 | 7.891 | |
githubURLParts | 1.825 | 0.058 | 3.497 | |
inducedSubgraphByPkgs | 7.716 | 0.726 | 18.716 | |
latestPkgStats | 0.001 | 0.001 | 0.001 | |
orcid_table | 0.000 | 0.001 | 0.001 | |
pkgBiocDeps | 1.998 | 0.067 | 3.173 | |
pkgBiocRevDeps | 4.390 | 0.637 | 10.079 | |
pkgCombDependencyGain | 21.965 | 1.349 | 45.247 | |
pkgDepImports | 0.601 | 0.018 | 0.670 | |
pkgDepMetrics | 13.684 | 0.343 | 16.962 | |
pkgDownloadRank | 3.521 | 0.252 | 3.982 | |
pkgDownloadStats | 0.065 | 0.005 | 0.337 | |
problemPage | 0.001 | 0.001 | 0.001 | |
repositoryStats | 0.119 | 0.010 | 0.133 | |
subgraphByDegree | 2.908 | 0.107 | 3.588 | |