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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BiocStyle.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings BiocStyle_2.27.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/BiocStyle.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘BiocStyle/DESCRIPTION’ ... OK
* this is package ‘BiocStyle’ version ‘2.27.1’
* 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/biocbuild/bbs-3.17-bioc/meat/BiocStyle.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL BiocStyle
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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)

R version 4.3.0 alpha (2023-04-03 r84154)
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/RtmpN8DoC9/filec6f9c7de6af19_files/figure-html/plot-1.png" but not available.
The magick package is required to crop "/tmp/RtmpN8DoC9/filec6f9c7de6af19_files/figure-html/small-1.png" but not available.
The magick package is required to crop "/tmp/RtmpN8DoC9/filec6f9c7de6af19_files/figure-html/wide-1.png" but not available.
The magick package is required to crop "/tmp/RtmpN8DoC9/filec6f9c7de6af19_files/figure-html/plot-1.png" but not available.
The magick package is required to crop "/tmp/RtmpN8DoC9/filec6f9c7de6af19_files/figure-html/small-1.png" but not available.
The magick package is required to crop "/tmp/RtmpN8DoC9/filec6f9c7de6af19_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: filec6f9c6f54a20b.Rmd
output file: filec6f9c6f54a20b.knit.md

/usr/bin/pandoc +RTS -K512m -RTS filec6f9c6f54a20b.knit.md --to latex --from markdown+autolink_bare_uris+tex_math_single_backslash --output filec6f9c6f54a20b.tex --lua-filter /home/biocbuild/bbs-3.17-bioc/R/site-library/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /home/biocbuild/bbs-3.17-bioc/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.17-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/RtmpN8DoC9/c6f9c282e75cb.tex --variable graphics --wrap preserve --variable subparagraph --template /tmp/RtmpN8DoC9/BiocStyle/template.tex --variable tables=yes --standalone --variable 'compact-title:yes' 
Warning: LaTeX Warning: You have requested package `/home/biocbuild/bbs-3.17-bioc/R/site
Warning: -library/BiocStyle/resources/tex/Bioconductor',
Warning:                but the package provides `Bioconductor'.
Warning: Package geometry Warning: Over-specification in `h'-direction.
Warning:     `width' (384.1122pt) is ignored.
Warning: Package fancyhdr Warning: \fancyhead's `E' option without twoside option is use
Warning: less on input line 162.
Warning: Package microtype Warning: Unable to apply patch `eqnum' on input line 140.
Warning: Package fancyhdr Warning: \headheight is too small (42.67912pt): 
Warning: (fancyhdr)                Make it at least 46.27916pt, for example:
Warning: (fancyhdr)                \setlength{\headheight}{46.27916pt}.
Warning: (fancyhdr)                You might also make \topmargin smaller to compensate:
Warning: Package fancyhdr Warning: \headheight is too small (42.67912pt): 
Warning: (fancyhdr)                Make it at least 46.27916pt, for example:
Warning: (fancyhdr)                \setlength{\headheight}{46.27916pt}.
Warning: (fancyhdr)                You might also make \topmargin smaller to compensate:
Warning: Package fancyhdr Warning: \headheight is too small (42.67912pt): 
Warning: (fancyhdr)                Make it at least 46.27916pt, for example:
Warning: (fancyhdr)                \setlength{\headheight}{46.27916pt}.
Warning: (fancyhdr)                You might also make \topmargin smaller to compensate:
Warning: Package fancyhdr Warning: \headheight is too small (42.67912pt): 
Warning: (fancyhdr)                Make it at least 46.27916pt, for example:
Warning: (fancyhdr)                \setlength{\headheight}{46.27916pt}.
Warning: (fancyhdr)                You might also make \topmargin smaller to compensate:

Output created: filec6f9c6f54a20b.pdf


RUNIT TEST PROTOCOL -- Tue Apr 11 18:52:11 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 
 11.683   3.514  15.242