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CHECK report for BiocStyle on malbec1

This page was generated on 2020-08-11 11:19:21 -0400 (Tue, 11 Aug 2020).

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 162/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocStyle 2.17.0
Bioconductor Package Maintainer
Snapshot Date: 2020-08-10 14:50:56 -0400 (Mon, 10 Aug 2020)
URL: https://git.bioconductor.org/packages/BiocStyle
Branch: master
Last Commit: 7ca310e
Last Changed Date: 2020-04-27 14:35:13 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BiocStyle
Version: 2.17.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BiocStyle.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BiocStyle_2.17.0.tar.gz
StartedAt: 2020-08-11 00:16:53 -0400 (Tue, 11 Aug 2020)
EndedAt: 2020-08-11 00:17:28 -0400 (Tue, 11 Aug 2020)
EllapsedTime: 34.2 seconds
RetCode: 0
Status:  OK 
CheckDir: BiocStyle.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BiocStyle.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BiocStyle_2.17.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/BiocStyle.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocStyle/DESCRIPTION’ ... OK
* this is package ‘BiocStyle’ version ‘2.17.0’
* 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 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/BiocStyle.Rcheck/00check.log’
for details.



Installation output

BiocStyle.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL BiocStyle
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-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)

Tests output

BiocStyle.Rcheck/tests/run_tests.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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")
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: file3aef53bd8c13.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: file3aef53bd8c13.knit.md

/usr/bin/pandoc +RTS -K512m -RTS file3aef53bd8c13.utf8.md --to latex --from markdown+autolink_bare_uris+tex_math_single_backslash --output file3aef53bd8c13.tex --self-contained --table-of-contents --toc-depth 2 --number-sections --highlight-style tango --pdf-engine pdflatex --include-in-header /tmp/RtmpDLIUUb/3aef1aa3fca1.tex --variable graphics --lua-filter /home/biocbuild/bbs-3.12-bioc/R/library/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.12-bioc/R/library/rmarkdown/rmd/lua/latex-div.lua --wrap preserve --variable subparagraph --template /tmp/RtmpDLIUUb/BiocStyle/template.tex --include-in-header /home/biocbuild/bbs-3.12-bioc/R/library/rmarkdown/rmd/latex/subtitle.tex --variable tables=yes --variable 'compact-title:yes' 

Output created: file3aef53bd8c13.pdf


RUNIT TEST PROTOCOL -- Tue Aug 11 00:17:25 2020 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
BiocStyle RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
Warning message:
LaTeX Warning: You have requested package `/home/biocbuild/bbs-3.12-bioc/R/libr
ary/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. 
> 
> proc.time()
   user  system elapsed 
  8.672   0.792  12.585 

Example timings

BiocStyle.Rcheck/BiocStyle-Ex.timings

nameusersystemelapsed
helpers0.0040.0000.002
html_document000
latex000
macros0.0080.0000.006
markdown000
md_document0.0000.0000.001
output000
pdf_document0.0000.0000.001
use_vignette0.0040.0000.015