Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 194/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BiocStyle 2.35.0 (landing page) Bioconductor Package Maintainer
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the BiocStyle package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiocStyle.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: BiocStyle |
Version: 2.35.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BiocStyle.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BiocStyle_2.35.0.tar.gz |
StartedAt: 2024-12-24 04:04:31 -0000 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 04:05:24 -0000 (Tue, 24 Dec 2024) |
EllapsedTime: 53.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BiocStyle.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:BiocStyle.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BiocStyle_2.35.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/BiocStyle.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BiocStyle/DESCRIPTION’ ... OK * this is package ‘BiocStyle’ version ‘2.35.0’ * 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 ‘BiocStyle’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: ‘rmarkdown:::partition_yaml_front_matter’ 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: pdf_document.Rd: includes Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘run_tests.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 ‘/home/biocbuild/bbs-3.21-bioc/meat/BiocStyle.Rcheck/00check.log’ for details.
BiocStyle.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL BiocStyle ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘BiocStyle’ ... ** 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 (BiocStyle)
BiocStyle.Rcheck/tests/run_tests.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-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. > BiocGenerics:::testPackage("BiocStyle") The magick package is required to crop "/home/biocbuild/tmp/RtmpNmGEoQ/file8e451a1d2833_files/figure-html/plot-1.png" but not available. The magick package is required to crop "/home/biocbuild/tmp/RtmpNmGEoQ/file8e451a1d2833_files/figure-html/small-1.png" but not available. The magick package is required to crop "/home/biocbuild/tmp/RtmpNmGEoQ/file8e451a1d2833_files/figure-html/wide-1.png" but not available. The magick package is required to crop "/home/biocbuild/tmp/RtmpNmGEoQ/file8e451a1d2833_files/figure-html/plot-1.png" but not available. The magick package is required to crop "/home/biocbuild/tmp/RtmpNmGEoQ/file8e451a1d2833_files/figure-html/small-1.png" but not available. The magick package is required to crop "/home/biocbuild/tmp/RtmpNmGEoQ/file8e451a1d2833_files/figure-html/wide-1.png" but not available. Writing to file maketitle_test_1.tex Processing code chunks with options ... 1 : keep.source term tex (label = style, maketitle_test_1.Rnw:5) You can now run (pdf)latex on 'maketitle_test_1.tex' Writing to file maketitle_test_2.tex Processing code chunks with options ... 1 : keep.source term tex (label = style, maketitle_test_2.Rnw:5) You can now run (pdf)latex on 'maketitle_test_2.tex' Writing to file maketitle_test_3.tex Processing code chunks with options ... 1 : keep.source term tex (label = style, maketitle_test_3.Rnw:5) You can now run (pdf)latex on 'maketitle_test_3.tex' Writing to file maketitle_test_4.tex Processing code chunks with options ... 1 : keep.source term tex (label = style, maketitle_test_4.Rnw:5) You can now run (pdf)latex on 'maketitle_test_4.tex' Writing to file maketitle_test_5.tex Processing code chunks with options ... 1 : keep.source term tex (label = style, maketitle_test_5.Rnw:5) You can now run (pdf)latex on 'maketitle_test_5.tex' processing file: file8e4577950abd.Rmd output file: file8e4577950abd.knit.md /home/biocbuild/bin/pandoc +RTS -K512m -RTS file8e4577950abd.knit.md --to latex --from markdown+autolink_bare_uris+tex_math_single_backslash --output file8e4577950abd.tex --lua-filter /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --table-of-contents --toc-depth 2 --number-sections --highlight-style tango --pdf-engine pdflatex --include-in-header /home/biocbuild/tmp/RtmpNmGEoQ/8e452abac3c3.tex --variable graphics --wrap preserve --variable subparagraph --template /home/biocbuild/tmp/RtmpNmGEoQ/BiocStyle/template.tex --variable tables=yes --standalone --variable 'compact-title:yes' Warning: LaTeX Warning: You have requested package `/home/biocbuild/R/R-4.5.0-devel_2024 Warning: -11-24/site-library/BiocStyle/resources/tex/Bioconductor', Warning: but the package provides `Bioconductor'. Output created: file8e4577950abd.pdf RUNIT TEST PROTOCOL -- Tue Dec 24 04:05:18 2024 *********************************************** Number of test functions: 3 Number of errors: 0 Number of failures: 0 1 Test Suite : BiocStyle RUnit Tests - 3 test functions, 0 errors, 0 failures Number of test functions: 3 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 15.359 2.544 25.943
BiocStyle.Rcheck/BiocStyle-Ex.timings
name | user | system | elapsed | |
helpers | 0.002 | 0.000 | 0.002 | |
html_document | 0 | 0 | 0 | |
latex | 0 | 0 | 0 | |
macros | 0.049 | 0.003 | 0.062 | |
markdown | 0 | 0 | 0 | |
md_document | 0 | 0 | 0 | |
output | 0 | 0 | 0 | |
pdf_document | 0 | 0 | 0 | |
use_vignette | 0.003 | 0.000 | 0.004 | |