##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BiocStyle.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings BiocStyle_2.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/BiocStyle.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BiocStyle/DESCRIPTION' ... OK
* this is package 'BiocStyle' version '2.27.0'
* 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 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: 1 NOTE
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/BiocStyle.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL BiocStyle
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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'
texify: major issue: So far, you have not checked for updates as a MiKTeX user.
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'
texify: major issue: So far, you have not checked for updates as a MiKTeX user.
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'
texify: major issue: So far, you have not checked for updates as a MiKTeX user.
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'
texify: major issue: So far, you have not checked for updates as a MiKTeX user.
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'
texify: major issue: So far, you have not checked for updates as a MiKTeX user.


processing file: file43505aa523ea.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

!!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
  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

!!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
  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

!!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
  ordinary text without R code

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

output file: file43505aa523ea.knit.md

"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS file43505aa523ea.knit.md --to latex --from markdown+autolink_bare_uris+tex_math_single_backslash --output file43505aa523ea.tex --lua-filter "F:\biocbuild\bbs-3.17-bioc\R\library\bookdown\rmarkdown\lua\custom-environment.lua" --lua-filter "F:\biocbuild\bbs-3.17-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.17-bioc\R\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 "F:\biocbuild\bbs-3.17-bioc-rtools43\tmpdir\Rtmp4y0Nn9\4350532014ac.tex" --variable graphics --wrap preserve --variable subparagraph --template "F:\biocbuild\bbs-3.17-bioc-rtools43\tmpdir\Rtmp4y0Nn9/BiocStyle/template.tex" --variable tables=yes --standalone --variable "compact-title:yes" 
Warning: LaTeX Warning: You have requested package `F:/biocbuild/bbs-3.17-bioc/R/library
Warning: /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.
Warning: (fancyhdr)                Please consider using the `twoside' option on input l
Warning: ine 162.
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: file43505aa523ea.pdf


RUNIT TEST PROTOCOL -- Wed Dec 28 21:58:31 2022 
*********************************************** 
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 
   2.78    0.54   51.81