Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:42 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 186/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BiocPkgTools 1.23.1 (landing page) Sean Davis
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 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: 1.23.1 |
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_1.23.1.tar.gz |
StartedAt: 2024-06-10 13:01:57 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 13:07:08 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 311.1 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_1.23.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BiocPkgTools.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: aarch64-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 Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BiocPkgTools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BiocPkgTools’ version ‘1.23.1’ * 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 9.545 34.293 47.074 firstInBioc 15.386 0.384 16.417 biocDownloadStats 13.824 0.313 15.015 get_bioc_data 13.204 0.395 14.233 pkgCombDependencyGain 7.350 0.183 7.861 class-dependencies 6.973 0.194 7.213 pkgDepMetrics 6.081 0.089 6.508 * 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-arm64/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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 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/3.20/bioc/vignettes/a4/inst/doc/a4vignette.pdf' Content type 'application/pdf' length 1305410 bytes (1.2 MB) ================================================== downloaded 1.2 MB [ FAIL 0 | WARN 2 | SKIP 0 | PASS 27 ] [ FAIL 0 | WARN 2 | SKIP 0 | PASS 27 ] > > proc.time() user system elapsed 28.163 25.384 58.497
BiocPkgTools.Rcheck/BiocPkgTools-Ex.timings
name | user | system | elapsed | |
activitySince | 0 | 0 | 0 | |
anacondaDownloadStats | 1.901 | 0.033 | 3.082 | |
biocBuildReport | 9.545 | 34.293 | 47.074 | |
biocDownloadStats | 13.824 | 0.313 | 15.015 | |
biocMaintained | 2.759 | 0.097 | 3.170 | |
biocPkgList | 1.496 | 0.024 | 1.559 | |
biocPkgRanges | 0 | 0 | 0 | |
biocRevDepEmail | 2.215 | 0.108 | 4.933 | |
buildPkgDependencyDataFrame | 2.344 | 0.060 | 2.464 | |
buildPkgDependencyIgraph | 0.991 | 0.040 | 1.080 | |
class-dependencies | 6.973 | 0.194 | 7.213 | |
firstInBioc | 15.386 | 0.384 | 16.417 | |
generateBiocPkgDOI | 0 | 0 | 0 | |
getBiocVignette | 0.917 | 0.049 | 1.566 | |
get_bioc_data | 13.204 | 0.395 | 14.233 | |
get_cre_orcids | 0.012 | 0.001 | 0.012 | |
githubDetails | 1.461 | 0.299 | 2.893 | |
githubURLParts | 1.078 | 0.021 | 1.133 | |
inducedSubgraphByPkgs | 4.664 | 0.136 | 4.862 | |
latestPkgStats | 0 | 0 | 0 | |
orcid_table | 0.000 | 0.001 | 0.001 | |
pkgBiocDeps | 1.540 | 0.047 | 1.587 | |
pkgBiocRevDeps | 1.957 | 0.049 | 2.007 | |
pkgCombDependencyGain | 7.350 | 0.183 | 7.861 | |
pkgDepImports | 0.164 | 0.002 | 0.166 | |
pkgDepMetrics | 6.081 | 0.089 | 6.508 | |
pkgDownloadRank | 1.526 | 0.081 | 2.575 | |
pkgDownloadStats | 0.032 | 0.002 | 0.448 | |
problemPage | 0.001 | 0.000 | 0.000 | |
repositoryStats | 0.076 | 0.002 | 0.079 | |
subgraphByDegree | 1.502 | 0.027 | 1.567 | |