BioC 3.4: CHECK report for BiocStyle on malbec1

Package: BiocStyle

Version: 2.2.1

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings BiocStyle_2.2.1.tar.gz

StartedAt: 2017-04-14 21:15:04 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 21:15:26 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 21.9 seconds

RetCode: 0

Status:  OK

CheckDir: BiocStyle.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings BiocStyle_2.2.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/BiocStyle.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘2.2.1’
* 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
':::' call which should be '::': ‘rmarkdown:::from_rmarkdown’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘knitr:::comment_length’ ‘knitr:::new_defaults’
  ‘knitr:::theme_to_header_latex’ ‘rmarkdown:::latexmk’
  ‘rmarkdown:::normalize_path’ ‘rmarkdown:::pandoc’
  ‘rmarkdown:::pandoc_html_highlight_args’ ‘rmarkdown:::quoted’
  ‘rmarkdown:::rmarkdown_system_file’
  ‘rmarkdown:::with_pandoc_safe_environment’
  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 installed files from ‘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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/BiocStyle.Rcheck/00check.log’
for details.

* installing *source* package ‘BiocStyle’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BiocStyle)

name	user	system	elapsed
helpers	0.000	0.000	0.001
html_document	0	0	0
latex	0.000	0.000	0.001
latex2	0.004	0.000	0.001
macros	0.000	0.000	0.001
markdown	0	0	0
md_document	0	0	0
output	0	0	0
pdf_document	0	0	0