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CHECK report for BiocStyle on merida1

This page was generated on 2021-05-06 12:34:26 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the BiocStyle package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 171/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocStyle 2.18.1  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/BiocStyle
Branch: RELEASE_3_12
Last Commit: 956f065
Last Changed Date: 2020-11-24 04:50:38 -0400 (Tue, 24 Nov 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: BiocStyle
Version: 2.18.1
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_2.18.1.tar.gz
StartedAt: 2021-05-05 23:40:46 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 23:42:03 -0400 (Wed, 05 May 2021)
EllapsedTime: 76.5 seconds
RetCode: 0
Status:   OK  
CheckDir: BiocStyle.Rcheck
Warnings: 0

Command output

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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_2.18.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/BiocStyle.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘2.18.1’
* 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 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
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/BiocStyle.Rcheck/00check.log’
for details.



Installation output

BiocStyle.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BiocStyle
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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)

Tests output

BiocStyle.Rcheck/tests/run_tests.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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: file15ab35ef2f844.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: file15ab35ef2f844.knit.md

/usr/local/bin/pandoc +RTS -K512m -RTS file15ab35ef2f844.utf8.md --to latex --from markdown+autolink_bare_uris+tex_math_single_backslash --output file15ab35ef2f844.tex --lua-filter /Library/Frameworks/R.framework/Versions/4.0/Resources/library/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.0/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.0/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/Rtmp85daXr/15ab32189690f.tex --variable graphics --wrap preserve --variable subparagraph --template /tmp/Rtmp85daXr/BiocStyle/template.tex --variable tables=yes --standalone --variable 'compact-title:yes' 

Output created: file15ab35ef2f844.pdf


RUNIT TEST PROTOCOL -- Wed May  5 23:41:56 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 
Warning message:
LaTeX Warning: You have requested package `/Library/Frameworks/R.framework/Vers
ions/4.0/Resources/library/BiocStyle/resources/tex/Bioconductor',
               but the package provides `Bioconductor'.
Package geometry Warning: Over-specification in `h'-direction.
    `width' (384.1122pt) is ignored.
Package Fancyhdr Warning: \fancyhead's `E' option without twoside option is use
less on input line 162.
LaTeX Warning: Font shape declaration has incorrect series value `mc'.
               It should not contain an `m'! Please correct it.
               Found on input line 20.
LaTeX Warning: Font shape declaration has incorrect series value `mc'.
               It should not contain an `m'! Please correct it.
               Found on input line 23.
LaTeX Warning: Font shape declaration has incorrect series value `mc'.
               It should not contain an `m'! Please correct it.
               Found on input line 26.
LaTeX Warning: Font shape declaration has incorrect series value `mc'.
  [... truncated] 
> 
> proc.time()
   user  system elapsed 
 28.462   6.992  41.748 

Example timings

BiocStyle.Rcheck/BiocStyle-Ex.timings

nameusersystemelapsed
helpers0.0080.0060.014
html_document0.0000.0010.001
latex000
macros0.0070.0020.009
markdown000
md_document0.0000.0000.001
output0.0000.0000.001
pdf_document0.0010.0000.000
use_vignette0.0070.0020.009