Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-26 12:03 -0400 (Tue, 26 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" | 4821 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4610 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4553 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4539 |
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 195/2319 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BiocPkgTools 1.27.10 (landing page) Sean Davis
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
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 | TIMEOUT | ||||||||||
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: 1.27.10 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BiocPkgTools.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BiocPkgTools_1.27.10.tar.gz |
StartedAt: 2025-08-25 20:34:18 -0400 (Mon, 25 Aug 2025) |
EndedAt: 2025-08-25 20:39:43 -0400 (Mon, 25 Aug 2025) |
EllapsedTime: 324.4 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: BiocPkgTools.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BiocPkgTools.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BiocPkgTools_1.27.10.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BiocPkgTools.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 ‘BiocPkgTools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BiocPkgTools’ version ‘1.27.10’ * 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 loading without being on the library search path ... 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 ... ERROR Running examples in ‘BiocPkgTools-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: pkgDepMetrics > ### Title: Report package dependency burden > ### Aliases: pkgDepMetrics > > ### ** Examples > > depdf <- buildPkgDependencyDataFrame( + dependencies=c("Depends", "Imports"), + repo=c("BioCsoft", "CRAN") + ) > pkgDepMetrics('BiocPkgTools', depdf) Error in loadNamespace(name) : there is no package called ‘rorcid’ Calls: pkgDepMetrics ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed biocBuildReport 10.314 5.565 12.813 firstInBioc 13.481 0.719 15.061 get_bioc_data 12.688 0.388 13.822 class-dependencies 11.190 1.066 15.786 pkgCombDependencyGain 10.149 0.982 19.644 biocDownloadStats 10.491 0.343 11.564 inducedSubgraphByPkgs 4.941 0.222 6.923 buildPkgDependencyDataFrame 4.635 0.127 7.363 biocMaintained 4.007 0.073 5.240 * 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 ... ERROR Error(s) in re-building vignettes: --- re-building ‘BiocPkgTools.Rmd’ using rmarkdown Quitting from BiocPkgTools.Rmd:315-317 [unnamed-chunk-18] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `loadNamespace()`: ! there is no package called 'rorcid' --- Backtrace: ▆ 1. └─BiocPkgTools::pkgDepMetrics("BiocPkgTools", depdf) 2. └─base::getNamespaceExports(p) 3. └─base::asNamespace(ns) 4. └─base::getNamespace(ns) 5. ├─.Internal(getRegisteredNamespace(name)) %||% ... 6. └─base::loadNamespace(name) 7. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 8. └─base (local) withOneRestart(expr, restarts[[1L]]) 9. └─base (local) doWithOneRestart(return(expr), restart) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'BiocPkgTools.Rmd' failed with diagnostics: there is no package called 'rorcid' --- failed re-building ‘BiocPkgTools.Rmd’ SUMMARY: processing the following file failed: ‘BiocPkgTools.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 2 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/BiocPkgTools.Rcheck/00check.log’ for details.
BiocPkgTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BiocPkgTools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘BiocPkgTools’ ... ** this is package ‘BiocPkgTools’ version ‘1.27.10’ ** 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 (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(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 28.506 5.125 32.991
BiocPkgTools.Rcheck/BiocPkgTools-Ex.timings
name | user | system | elapsed | |
activitySince | 0.001 | 0.000 | 0.000 | |
anacondaDownloadStats | 2.560 | 0.170 | 3.338 | |
biocBuildReport | 10.314 | 5.565 | 12.813 | |
biocDownloadStats | 10.491 | 0.343 | 11.564 | |
biocMaintained | 4.007 | 0.073 | 5.240 | |
biocPkgList | 1.241 | 0.004 | 1.402 | |
biocPkgRanges | 0 | 0 | 0 | |
biocRevDepEmail | 2.288 | 0.086 | 3.147 | |
buildPkgDependencyDataFrame | 4.635 | 0.127 | 7.363 | |
buildPkgDependencyIgraph | 2.525 | 0.051 | 4.467 | |
class-dependencies | 11.190 | 1.066 | 15.786 | |
firstInBioc | 13.481 | 0.719 | 15.061 | |
generateBiocPkgDOI | 0 | 0 | 0 | |
getBiocVignette | 1.241 | 0.037 | 1.535 | |
getPkgYearsInBioc | 0 | 0 | 0 | |
get_bioc_data | 12.688 | 0.388 | 13.822 | |
get_cre_orcids | 0.009 | 0.000 | 0.009 | |
githubDetails | 1.419 | 0.042 | 1.677 | |
githubURLParts | 1.191 | 0.051 | 1.389 | |
inducedSubgraphByPkgs | 4.941 | 0.222 | 6.923 | |
latestPkgStats | 0 | 0 | 0 | |
orcid_table | 0.001 | 0.000 | 0.000 | |
pkgBiocDeps | 1.204 | 0.009 | 1.215 | |
pkgBiocRevDeps | 2.273 | 0.003 | 2.277 | |
pkgCombDependencyGain | 10.149 | 0.982 | 19.644 | |
pkgDepImports | 0.213 | 0.012 | 0.225 | |