Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-09 12:09 -0400 (Sat, 09 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
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 194/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BiocPkgTools 1.27.9 (landing page) Sean Davis
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | 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 | ![]() | ||||||||
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: 1.27.9 |
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_1.27.9.tar.gz |
StartedAt: 2025-08-08 18:20:30 -0400 (Fri, 08 Aug 2025) |
EndedAt: 2025-08-08 18:22:54 -0400 (Fri, 08 Aug 2025) |
EllapsedTime: 143.9 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_1.27.9.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BiocPkgTools.Rcheck’ * using R version 4.5.1 Patched (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BiocPkgTools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BiocPkgTools’ version ‘1.27.9’ * 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 3.516 14.189 19.743 firstInBioc 5.316 0.129 5.852 get_bioc_data 5.046 0.188 5.834 biocDownloadStats 4.620 0.114 5.321 pkgCombDependencyGain 3.530 0.148 13.002 pkgDepMetrics 2.757 0.086 12.205 * 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-3.22-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-arm64/Resources/library’ * installing *source* package ‘BiocPkgTools’ ... ** this is package ‘BiocPkgTools’ version ‘1.27.9’ ** 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 Patched (2025-06-14 r88325) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-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/3.22/bioc/vignettes/a4/inst/doc/a4vignette.pdf' Content type 'application/pdf' length 1397518 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 10.822 9.216 22.252
BiocPkgTools.Rcheck/BiocPkgTools-Ex.timings
name | user | system | elapsed | |
activitySince | 0.001 | 0.000 | 0.000 | |
anacondaDownloadStats | 1.009 | 0.012 | 1.407 | |
biocBuildReport | 3.516 | 14.189 | 19.743 | |
biocDownloadStats | 4.620 | 0.114 | 5.321 | |
biocMaintained | 1.407 | 0.048 | 2.069 | |
biocPkgList | 0.504 | 0.011 | 0.657 | |
biocPkgRanges | 0.001 | 0.000 | 0.000 | |
biocRevDepEmail | 0.798 | 0.039 | 1.749 | |
buildPkgDependencyDataFrame | 1.074 | 0.020 | 1.232 | |
buildPkgDependencyIgraph | 0.557 | 0.011 | 0.691 | |
class-dependencies | 2.296 | 0.085 | 2.391 | |
firstInBioc | 5.316 | 0.129 | 5.852 | |
generateBiocPkgDOI | 0 | 0 | 0 | |
getBiocVignette | 0.497 | 0.024 | 0.877 | |
getPkgYearsInBioc | 0 | 0 | 0 | |
get_bioc_data | 5.046 | 0.188 | 5.834 | |
get_cre_orcids | 0.003 | 0.001 | 0.003 | |
githubDetails | 0.663 | 0.117 | 1.020 | |
githubURLParts | 0.482 | 0.008 | 0.514 | |
inducedSubgraphByPkgs | 1.753 | 0.051 | 2.126 | |
latestPkgStats | 0 | 0 | 0 | |
orcid_table | 0 | 0 | 0 | |
pkgBiocDeps | 0.523 | 0.014 | 0.538 | |
pkgBiocRevDeps | 0.678 | 0.015 | 0.693 | |
pkgCombDependencyGain | 3.530 | 0.148 | 13.002 | |
pkgDepImports | 0.054 | 0.000 | 0.055 | |
pkgDepMetrics | 2.757 | 0.086 | 12.205 | |
pkgDownloadRank | 0.678 | 0.043 | 0.967 | |
pkgDownloadStats | 0.011 | 0.001 | 0.038 | |
problemPage | 0 | 0 | 0 | |
repositoryStats | 0.026 | 0.000 | 0.026 | |
subgraphByDegree | 0.535 | 0.015 | 0.671 | |