Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-28 11:35:28 -0400 (Tue, 28 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4752 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4517 |
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 189/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BiocPkgTools 1.22.0 (landing page) Sean Davis
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
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: 1.22.0 |
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_1.22.0.tar.gz |
StartedAt: 2024-05-27 19:23:21 -0400 (Mon, 27 May 2024) |
EndedAt: 2024-05-27 19:31:48 -0400 (Mon, 27 May 2024) |
EllapsedTime: 507.4 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_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/BiocPkgTools.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BiocPkgTools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BiocPkgTools’ version ‘1.22.0’ * 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 7.599 34.640 46.215 get_bioc_data 12.827 0.623 14.016 firstInBioc 12.422 0.627 13.584 biocDownloadStats 11.580 0.581 12.900 class-dependencies 6.717 0.283 7.128 pkgCombDependencyGain 6.417 0.357 17.000 pkgDepMetrics 6.184 0.264 9.602 inducedSubgraphByPkgs 6.094 0.240 9.905 biocMaintained 4.304 0.216 5.122 pkgBiocRevDeps 3.920 0.238 6.877 biocRevDepEmail 2.576 0.155 10.017 * 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-3.19-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 4.4.0 (2024-04-24) -- "Puppy Cup" 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/3.19/bioc/vignettes/a4/inst/doc/a4vignette.pdf' Content type 'application/pdf' length 1305508 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 32.943 42.732 124.896
BiocPkgTools.Rcheck/BiocPkgTools-Ex.timings
name | user | system | elapsed | |
activitySince | 0.000 | 0.001 | 0.001 | |
anacondaDownloadStats | 1.787 | 0.058 | 2.433 | |
biocBuildReport | 7.599 | 34.640 | 46.215 | |
biocDownloadStats | 11.580 | 0.581 | 12.900 | |
biocMaintained | 4.304 | 0.216 | 5.122 | |
biocPkgList | 1.523 | 0.046 | 1.596 | |
biocPkgRanges | 0 | 0 | 0 | |
biocRevDepEmail | 2.576 | 0.155 | 10.017 | |
buildPkgDependencyDataFrame | 3.003 | 0.101 | 3.311 | |
buildPkgDependencyIgraph | 1.615 | 0.061 | 1.747 | |
class-dependencies | 6.717 | 0.283 | 7.128 | |
firstInBioc | 12.422 | 0.627 | 13.584 | |
generateBiocPkgDOI | 0.000 | 0.000 | 0.001 | |
getBiocVignette | 1.414 | 0.128 | 1.806 | |
get_bioc_data | 12.827 | 0.623 | 14.016 | |
get_cre_orcids | 0.011 | 0.002 | 0.013 | |
githubDetails | 1.708 | 0.349 | 2.630 | |
githubURLParts | 1.344 | 0.059 | 1.431 | |
inducedSubgraphByPkgs | 6.094 | 0.240 | 9.905 | |
latestPkgStats | 0.001 | 0.000 | 0.001 | |
orcid_table | 0.001 | 0.000 | 0.000 | |
pkgBiocDeps | 1.813 | 0.076 | 3.207 | |
pkgBiocRevDeps | 3.920 | 0.238 | 6.877 | |
pkgCombDependencyGain | 6.417 | 0.357 | 17.000 | |
pkgDepImports | 0.283 | 0.109 | 0.549 | |
pkgDepMetrics | 6.184 | 0.264 | 9.602 | |
pkgDownloadRank | 1.569 | 0.111 | 4.089 | |
pkgDownloadStats | 0.030 | 0.002 | 0.077 | |
problemPage | 0.000 | 0.001 | 0.001 | |
repositoryStats | 0.067 | 0.006 | 0.352 | |
subgraphByDegree | 1.173 | 0.045 | 2.324 | |