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CHECK report for BiocStyle on veracruz1

This page was generated on 2018-04-12 13:37:03 -0400 (Thu, 12 Apr 2018).

Package 129/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocStyle 2.6.1
Bioconductor Package Maintainer
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/BiocStyle
Branch: RELEASE_3_6
Last Commit: 5ff52cb
Last Changed Date: 2017-11-29 06:02:17 -0400 (Wed, 29 Nov 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BiocStyle
Version: 2.6.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BiocStyle_2.6.1.tar.gz
StartedAt: 2018-04-12 00:57:26 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 00:58:02 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 36.5 seconds
RetCode: 0
Status:  OK 
CheckDir: BiocStyle.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BiocStyle_2.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/BiocStyle.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocStyle/DESCRIPTION’ ... OK
* this is package ‘BiocStyle’ version ‘2.6.1’
* 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:
  ‘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 sizes of PDF files under ‘inst/doc’ ... 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
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/BiocStyle.Rcheck/00check.log’
for details.



Installation output

BiocStyle.Rcheck/00install.out

* 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)

Tests output

BiocStyle.Rcheck/tests/run_tests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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'


RUNIT TEST PROTOCOL -- Thu Apr 12 00:57:58 2018 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
BiocStyle RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  7.906   2.665  10.525 

Example timings

BiocStyle.Rcheck/BiocStyle-Ex.timings

nameusersystemelapsed
helpers0.0030.0010.003
html_document0.0010.0000.001
latex0.0010.0000.001
macros0.0010.0000.001
markdown0.0000.0000.001
md_document0.0010.0000.001
output0.0000.0000.001
pdf_document0.0010.0000.001