Bioconductor Package
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/BiocStyle |
| git_branch: devel |
| git_last_commit: 18ce82e |
| git_last_commit_date: 2023-10-24 09:54:46 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:40:22 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 193/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BiocStyle 2.31.0 (landing page) Bioconductor Package
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | 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: 2.31.0 |
| Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:BiocStyle.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings BiocStyle_2.31.0.tar.gz |
| StartedAt: 2024-03-28 03:14:25 -0000 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 03:15:16 -0000 (Thu, 28 Mar 2024) |
| EllapsedTime: 50.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BiocStyle.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:BiocStyle.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings BiocStyle_2.31.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/BiocStyle.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocStyle/DESCRIPTION’ ... OK
* this is package ‘BiocStyle’ version ‘2.31.0’
* 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 ... 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
* 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: 1 NOTE
See
‘/home/biocbuild/bbs-3.19-bioc/meat/BiocStyle.Rcheck/00check.log’
for details.
BiocStyle.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL BiocStyle ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/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) (2024-03-19 r86153) -- "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/Rtmp4Lrehx/file34476416000ce0_files/figure-html/plot-1.png" but not available.
The magick package is required to crop "/home/biocbuild/tmp/Rtmp4Lrehx/file34476416000ce0_files/figure-html/small-1.png" but not available.
The magick package is required to crop "/home/biocbuild/tmp/Rtmp4Lrehx/file34476416000ce0_files/figure-html/wide-1.png" but not available.
The magick package is required to crop "/home/biocbuild/tmp/Rtmp4Lrehx/file34476416000ce0_files/figure-html/plot-1.png" but not available.
The magick package is required to crop "/home/biocbuild/tmp/Rtmp4Lrehx/file34476416000ce0_files/figure-html/small-1.png" but not available.
The magick package is required to crop "/home/biocbuild/tmp/Rtmp4Lrehx/file34476416000ce0_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: file344764918f986.Rmd
output file: file344764918f986.knit.md
/home/biocbuild/bin/pandoc +RTS -K512m -RTS file344764918f986.knit.md --to latex --from markdown+autolink_bare_uris+tex_math_single_backslash --output file344764918f986.tex --lua-filter /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/R/R-4.4-devel-2024.03.20/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/Rtmp4Lrehx/3447647cdbe547.tex --variable graphics --wrap preserve --variable subparagraph --template /home/biocbuild/tmp/Rtmp4Lrehx/BiocStyle/template.tex --variable tables=yes --standalone --variable 'compact-title:yes'
Warning: LaTeX Warning: You have requested package `/home/biocbuild/R/R-4.4-devel-2024.0
Warning: 3.20/site-library/BiocStyle/resources/tex/Bioconductor',
Warning: but the package provides `Bioconductor'.
Output created: file344764918f986.pdf
RUNIT TEST PROTOCOL -- Thu Mar 28 03:15:13 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
9.897 1.603 11.514
BiocStyle.Rcheck/BiocStyle-Ex.timings
| name | user | system | elapsed | |
| helpers | 0.001 | 0.000 | 0.002 | |
| html_document | 0 | 0 | 0 | |
| latex | 0 | 0 | 0 | |
| macros | 0.036 | 0.003 | 3.483 | |
| markdown | 0 | 0 | 0 | |
| md_document | 0 | 0 | 0 | |
| output | 0 | 0 | 0 | |
| pdf_document | 0 | 0 | 0 | |
| use_vignette | 0.003 | 0.000 | 0.005 | |