Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 191/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BiocPkgTools 1.24.0 (landing page) Sean Davis
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | 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 | |||||||||
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: 1.24.0 |
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_1.24.0.tar.gz |
StartedAt: 2024-12-20 00:15:58 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 00:28:17 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 738.7 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_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BiocPkgTools.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * 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 ‘1.24.0’ * 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 ‘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_base’ ‘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 17.073 68.992 106.602 pkgCombDependencyGain 22.160 1.484 47.267 get_bioc_data 21.729 1.029 43.814 firstInBioc 21.571 0.634 44.633 biocDownloadStats 17.326 0.566 18.365 pkgDepMetrics 13.273 0.435 15.134 class-dependencies 12.158 0.361 17.981 inducedSubgraphByPkgs 6.686 0.269 15.920 biocMaintained 5.992 0.182 7.011 pkgBiocRevDeps 4.517 1.186 15.972 buildPkgDependencyDataFrame 5.241 0.088 6.047 biocRevDepEmail 3.985 0.141 5.783 githubDetails 3.080 0.619 8.401 pkgBiocDeps 2.618 0.303 5.953 getBiocVignette 2.506 0.179 5.347 * 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-3.20-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/4.4-x86_64/Resources/library’ * installing *source* package ‘BiocPkgTools’ ... ** 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 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 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/3.20/bioc/vignettes/a4/inst/doc/a4vignette.pdf' Content type 'application/pdf' length 1398374 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 64.509 53.923 140.671
BiocPkgTools.Rcheck/BiocPkgTools-Ex.timings
name | user | system | elapsed | |
activitySince | 0.000 | 0.001 | 0.001 | |
anacondaDownloadStats | 3.055 | 0.066 | 3.448 | |
biocBuildReport | 17.073 | 68.992 | 106.602 | |
biocDownloadStats | 17.326 | 0.566 | 18.365 | |
biocMaintained | 5.992 | 0.182 | 7.011 | |
biocPkgList | 2.567 | 0.039 | 2.779 | |
biocPkgRanges | 0.000 | 0.000 | 0.001 | |
biocRevDepEmail | 3.985 | 0.141 | 5.783 | |
buildPkgDependencyDataFrame | 5.241 | 0.088 | 6.047 | |
buildPkgDependencyIgraph | 2.646 | 0.051 | 3.168 | |
class-dependencies | 12.158 | 0.361 | 17.981 | |
firstInBioc | 21.571 | 0.634 | 44.633 | |
generateBiocPkgDOI | 0.000 | 0.001 | 0.001 | |
getBiocVignette | 2.506 | 0.179 | 5.347 | |
get_bioc_data | 21.729 | 1.029 | 43.814 | |
get_cre_orcids | 0.018 | 0.004 | 0.260 | |
githubDetails | 3.080 | 0.619 | 8.401 | |
githubURLParts | 2.401 | 0.081 | 4.868 | |
inducedSubgraphByPkgs | 6.686 | 0.269 | 15.920 | |
latestPkgStats | 0.000 | 0.001 | 0.001 | |
orcid_table | 0.001 | 0.001 | 0.001 | |
pkgBiocDeps | 2.618 | 0.303 | 5.953 | |
pkgBiocRevDeps | 4.517 | 1.186 | 15.972 | |
pkgCombDependencyGain | 22.160 | 1.484 | 47.267 | |
pkgDepImports | 0.442 | 0.030 | 0.550 | |
pkgDepMetrics | 13.273 | 0.435 | 15.134 | |
pkgDownloadRank | 2.816 | 0.322 | 3.742 | |
pkgDownloadStats | 0.064 | 0.009 | 0.339 | |
problemPage | 0.001 | 0.001 | 0.001 | |
repositoryStats | 0.116 | 0.009 | 0.126 | |
subgraphByDegree | 2.565 | 0.062 | 2.907 | |