Back to Mac ARM64 build report for BioC 3.20 |
|
This page was generated on 2024-05-20 11:32:08 -0400 (Mon, 20 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4381 |
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 186/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BiocPkgTools 1.23.0 (landing page) Sean Davis
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | |||||||
To the developers/maintainers of the BiocPkgTools package: - 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: 1.23.0 |
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_1.23.0.tar.gz |
StartedAt: 2024-05-19 06:34:43 -0400 (Sun, 19 May 2024) |
EndedAt: 2024-05-19 06:39:44 -0400 (Sun, 19 May 2024) |
EllapsedTime: 301.4 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_1.23.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/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 ‘1.23.0’ * 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 8.200 25.900 37.505 get_bioc_data 13.848 0.361 14.875 firstInBioc 13.674 0.342 14.635 biocDownloadStats 12.822 0.338 14.022 pkgDepMetrics 7.365 0.152 7.612 pkgCombDependencyGain 7.099 0.148 7.728 class-dependencies 6.844 0.204 7.072 inducedSubgraphByPkgs 4.594 0.163 5.325 biocRevDepEmail 2.380 0.129 5.056 * 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-mac-arm64/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 27.455 26.107 58.347
BiocPkgTools.Rcheck/BiocPkgTools-Ex.timings
name | user | system | elapsed | |
activitySince | 0.000 | 0.001 | 0.001 | |
anacondaDownloadStats | 1.767 | 0.036 | 2.969 | |
biocBuildReport | 8.200 | 25.900 | 37.505 | |
biocDownloadStats | 12.822 | 0.338 | 14.022 | |
biocMaintained | 3.155 | 0.095 | 3.940 | |
biocPkgList | 1.146 | 0.025 | 1.221 | |
biocPkgRanges | 0 | 0 | 0 | |
biocRevDepEmail | 2.380 | 0.129 | 5.056 | |
buildPkgDependencyDataFrame | 2.715 | 0.065 | 2.974 | |
buildPkgDependencyIgraph | 1.116 | 0.028 | 1.160 | |
class-dependencies | 6.844 | 0.204 | 7.072 | |
firstInBioc | 13.674 | 0.342 | 14.635 | |
generateBiocPkgDOI | 0.001 | 0.000 | 0.000 | |
getBiocVignette | 0.891 | 0.046 | 1.181 | |
get_bioc_data | 13.848 | 0.361 | 14.875 | |
get_cre_orcids | 0.011 | 0.001 | 0.011 | |
githubDetails | 1.537 | 0.316 | 2.692 | |
githubURLParts | 0.964 | 0.018 | 1.002 | |
inducedSubgraphByPkgs | 4.594 | 0.163 | 5.325 | |
latestPkgStats | 0 | 0 | 0 | |
orcid_table | 0 | 0 | 0 | |
pkgBiocDeps | 1.555 | 0.047 | 1.601 | |
pkgBiocRevDeps | 1.964 | 0.052 | 2.017 | |
pkgCombDependencyGain | 7.099 | 0.148 | 7.728 | |
pkgDepImports | 0.287 | 0.015 | 0.303 | |
pkgDepMetrics | 7.365 | 0.152 | 7.612 | |
pkgDownloadRank | 1.635 | 0.116 | 2.888 | |
pkgDownloadStats | 0.035 | 0.004 | 0.252 | |
problemPage | 0 | 0 | 0 | |
repositoryStats | 0.081 | 0.004 | 0.085 | |
subgraphByDegree | 0.983 | 0.029 | 1.054 | |