| Back to First build/check report with an "external build node" |
This page was generated on 2023-06-01 18:17:19 -0400 (Thu, 01 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| xps15 | Linux (Ubuntu 23.04) | x86_64 | 4.3.0 Patched (2023-05-23 r84466) -- "Already Tomorrow" | 544 |
| 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 | ||||
|
To the developers/maintainers of the BiocStyle package: Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 18/91 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||||
| BiocStyle 2.29.0 (landing page) Bioconductor Package
| xps15 | Linux (Ubuntu 23.04) / x86_64 | OK | OK | OK | ||||||||
| Package: BiocStyle |
| Version: 2.29.0 |
| Command: /home/hpages/bbs-3.18-bioc/R/bin/R CMD check --install=check:BiocStyle.install-out.txt --library=/home/hpages/bbs-3.18-bioc-testing/Rlibs --timings BiocStyle_2.29.0.tar.gz |
| StartedAt: 2023-06-01 12:58:58 -0700 (Thu, 01 Jun 2023) |
| EndedAt: 2023-06-01 12:59:56 -0700 (Thu, 01 Jun 2023) |
| EllapsedTime: 58.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BiocStyle.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/hpages/bbs-3.18-bioc/R/bin/R CMD check --install=check:BiocStyle.install-out.txt --library=/home/hpages/bbs-3.18-bioc-testing/Rlibs --timings BiocStyle_2.29.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/hpages/bbs-3.18-bioc-testing/meat/BiocStyle.Rcheck’
* using R version 4.3.0 Patched (2023-05-23 r84466)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 12.2.0-17ubuntu1) 12.2.0
GNU Fortran (Ubuntu 12.2.0-17ubuntu1) 12.2.0
* running under: Ubuntu 23.04
* using session charset: UTF-8
* checking for file ‘BiocStyle/DESCRIPTION’ ... OK
* this is package ‘BiocStyle’ version ‘2.29.0’
* 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 R 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 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘AuthoringRmdVignettes.Rmd’ using ‘UTF-8’... OK
‘LatexStyle2.Rnw’ using ‘UTF-8’... OK
OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/hpages/bbs-3.18-bioc-testing/meat/BiocStyle.Rcheck/00check.log’
for details.
BiocStyle.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/hpages/bbs-3.18-bioc/R/bin/R CMD INSTALL BiocStyle ### ############################################################################## ############################################################################## * installing to library ‘/home/hpages/bbs-3.18-bioc-testing/Rlibs’ * 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 version 4.3.0 Patched (2023-05-23 r84466) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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 "/tmp/Rtmp8aOP40/file7b4ef1f08fc40_files/figure-html/plot-1.png" but not available.
The magick package is required to crop "/tmp/Rtmp8aOP40/file7b4ef1f08fc40_files/figure-html/small-1.png" but not available.
The magick package is required to crop "/tmp/Rtmp8aOP40/file7b4ef1f08fc40_files/figure-html/wide-1.png" but not available.
The magick package is required to crop "/tmp/Rtmp8aOP40/file7b4ef1f08fc40_files/figure-html/plot-1.png" but not available.
The magick package is required to crop "/tmp/Rtmp8aOP40/file7b4ef1f08fc40_files/figure-html/small-1.png" but not available.
The magick package is required to crop "/tmp/Rtmp8aOP40/file7b4ef1f08fc40_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: file7b4ef134e57cb.Rmd
output file: file7b4ef134e57cb.knit.md
/usr/bin/pandoc +RTS -K512m -RTS file7b4ef134e57cb.knit.md --to latex --from markdown+autolink_bare_uris+tex_math_single_backslash --output file7b4ef134e57cb.tex --lua-filter /home/hpages/bbs-3.18-bioc/R/site-library/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /home/hpages/bbs-3.18-bioc/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/hpages/bbs-3.18-bioc/R/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 /tmp/Rtmp8aOP40/7b4ef9e9bffe.tex --variable graphics --wrap preserve --variable subparagraph --template /tmp/Rtmp8aOP40/BiocStyle/template.tex --variable tables=yes --standalone --variable 'compact-title:yes'
Warning: LaTeX Warning: You have requested package `/home/hpages/bbs-3.18-bioc-testing/R
Warning: libs/BiocStyle/resources/tex/Bioconductor',
Warning: but the package provides `Bioconductor'.
Output created: file7b4ef134e57cb.pdf
RUNIT TEST PROTOCOL -- Thu Jun 1 12:59:41 2023
***********************************************
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
18.435 3.221 22.105
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 | 0.069 | 0.008 | 0.236 | |
| markdown | 0 | 0 | 0 | |
| md_document | 0 | 0 | 0 | |
| output | 0 | 0 | 0 | |
| pdf_document | 0.000 | 0.001 | 0.000 | |
| use_vignette | 0.001 | 0.002 | 0.003 | |