BioC 3.5: CHECK report for BiocStyle on tokay2

Package: BiocStyle

Version: 2.4.1

Command: rm -rf BiocStyle.buildbin-libdir BiocStyle.Rcheck && mkdir BiocStyle.buildbin-libdir BiocStyle.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocStyle.buildbin-libdir BiocStyle_2.4.1.tar.gz >BiocStyle.Rcheck\00install.out 2>&1 && cp BiocStyle.Rcheck\00install.out BiocStyle-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=BiocStyle.buildbin-libdir --install="check:BiocStyle-install.out" --force-multiarch --no-vignettes --timings BiocStyle_2.4.1.tar.gz

StartedAt: 2017-08-15 22:18:02 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 22:19:09 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 67.2 seconds

RetCode: 0

Status:  OK

CheckDir: BiocStyle.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf BiocStyle.buildbin-libdir BiocStyle.Rcheck && mkdir BiocStyle.buildbin-libdir BiocStyle.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocStyle.buildbin-libdir BiocStyle_2.4.1.tar.gz >BiocStyle.Rcheck\00install.out 2>&1 && cp BiocStyle.Rcheck\00install.out BiocStyle-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=BiocStyle.buildbin-libdir --install="check:BiocStyle-install.out" --force-multiarch --no-vignettes --timings BiocStyle_2.4.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/BiocStyle.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BiocStyle/DESCRIPTION' ... OK
* this is package 'BiocStyle' version '2.4.1'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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:
  'rmarkdown:::normalize_path' 'rmarkdown:::pandoc_html_highlight_args'
  'rmarkdown:::partition_yaml_front_matter'
  'rmarkdown:::rmarkdown_system_file'
  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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'run_tests.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/BiocStyle.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'BiocStyle' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BiocStyle' as BiocStyle_2.4.1.zip
* DONE (BiocStyle)

name	user	system	elapsed
helpers	0.01	0.00	0.02
html_document	0	0	0
latex	0	0	0
latex2	0	0	0
macros	0	0	0
markdown	0	0	0
md_document	0	0	0
output	0	0	0
pdf_document	0	0	0

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