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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BiocStyle.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BiocStyle_2.20.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/BiocStyle.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocStyle/DESCRIPTION’ ... OK
* this is package ‘BiocStyle’ version ‘2.20.2’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 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 sizes of PDF files under ‘inst/doc’ ... 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/BiocStyle.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BiocStyle
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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")
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: file7ec47ed1bff.Rmd
   inline R code fragments

label: plot (with options) 
List of 2
 $ fig.cap: chr "Regular figure. The first sentence of the figure caption is automatically emphasized to serve as figure title."
 $ echo   : logi FALSE

  ordinary text without R code

label: small (with options) 
List of 3
 $ fig.cap  : chr "Small figure. A plot produced by a code chunk with option `fig.small = TRUE`."
 $ fig.small: logi TRUE
 $ echo     : logi FALSE

  ordinary text without R code

label: wide (with options) 
List of 3
 $ fig.cap : chr "Wide figure. A plot produced by a code chunk with option `fig.wide = TRUE`."
 $ fig.wide: logi TRUE
 $ echo    : logi FALSE

  ordinary text without R code

label: sessionInfo (with options) 
List of 1
 $ echo: logi FALSE

output file: file7ec47ed1bff.knit.md

/usr/local/bin/pandoc +RTS -K512m -RTS file7ec47ed1bff.knit.md --to latex --from markdown+autolink_bare_uris+tex_math_single_backslash --output file7ec47ed1bff.tex --lua-filter /Library/Frameworks/R.framework/Versions/4.1/Resources/library/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.1/Resources/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/RtmpltcXP5/7ec1fc9273d.tex --variable graphics --wrap preserve --variable subparagraph --template /tmp/RtmpltcXP5/BiocStyle/template.tex --variable tables=yes --standalone --variable 'compact-title:yes' 
Warning: LaTeX Warning: You have requested package `/Library/Frameworks/R.framework/Vers
Warning: ions/4.1/Resources/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: LaTeX Warning: Font shape declaration has incorrect series value `mc'.
Warning:                It should not contain an `m'! Please correct it.
Warning:                Found on input line 20.
Warning: LaTeX Warning: Font shape declaration has incorrect series value `mc'.
Warning:                It should not contain an `m'! Please correct it.
Warning:                Found on input line 23.
Warning: LaTeX Warning: Font shape declaration has incorrect series value `mc'.
Warning:                It should not contain an `m'! Please correct it.
Warning:                Found on input line 26.
Warning: LaTeX Warning: Font shape declaration has incorrect series value `mc'.
Warning:                It should not contain an `m'! Please correct it.
Warning:                Found on input line 46.

Output created: file7ec47ed1bff.pdf


RUNIT TEST PROTOCOL -- Thu Oct 14 16:47:29 2021 
*********************************************** 
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 
 28.131   7.257  35.836