Back to "Blame Jeroen" build/check report for BioC 3.11

CHECK report for BiocStyle on tokay2

This page was generated on 2020-04-15 03:20:09 -0400 (Wed, 15 Apr 2020).

These builds are using Rtools40 and R-testing by Jeroen Ooms (available at https://cran.r-project.org/bin/windows/testing/rtools40.html)
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 18/89HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocStyle 2.15.6
Bioconductor Package Maintainer
Snapshot Date: 2020-04-14 17:00:05 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/BiocStyle
Branch: master
Last Commit: 502c11d
Last Changed Date: 2020-01-31 18:35:01 -0400 (Fri, 31 Jan 2020)
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK 

Summary

Package: BiocStyle
Version: 2.15.6
Command: C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD check --force-multiarch --install=check:BiocStyle.install-out.txt --library=C:\Users\bioctesting\bbs-3.11-bioc-testing\R\library --no-vignettes --timings BiocStyle_2.15.6.tar.gz
StartedAt: 2020-04-14 20:34:44 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 20:38:22 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 218.0 seconds
RetCode: 0
Status:  OK  
CheckDir: BiocStyle.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD check --force-multiarch --install=check:BiocStyle.install-out.txt --library=C:\Users\bioctesting\bbs-3.11-bioc-testing\R\library --no-vignettes --timings BiocStyle_2.15.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/BiocStyle.Rcheck'
* using R version 4.0.0 alpha (Rtools40) (2020-03-31 r78116)
* 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 '2.15.6'
* 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
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 ...
** 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/bioctesting/bbs-3.11-bioc-testing/meat/BiocStyle.Rcheck/00check.log'
for details.

Installation output

BiocStyle.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc-testing/src/contrib/BiocStyle_2.15.6.tar.gz && rm -rf BiocStyle.buildbin-libdir && mkdir BiocStyle.buildbin-libdir && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BiocStyle.buildbin-libdir BiocStyle_2.15.6.tar.gz && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL BiocStyle_2.15.6.zip && rm BiocStyle_2.15.6.tar.gz BiocStyle_2.15.6.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 61799  100 61799    0     0   667k      0 --:--:-- --:--:-- --:--:--  718k

install for i386

* installing *source* package 'BiocStyle' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BiocStyle'
    finding HTML links ... done
    BiocStyle-defunct                       html  
    helpers                                 html  
    html_document                           html  
    latex                                   html  
    macros                                  html  
    markdown                                html  
    md_document                             html  
    output                                  html  
    pdf_document                            html  
    finding level-2 HTML links ... done

    use_vignette                            html  
** 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

install for x64

* installing *source* package 'BiocStyle' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BiocStyle' as BiocStyle_2.15.6.zip
* DONE (BiocStyle)
* installing to library 'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library'
package 'BiocStyle' successfully unpacked and MD5 sums checked

Tests output

BiocStyle.Rcheck/tests_i386/run_tests.Rout


R version 4.0.0 alpha (Rtools40) (2020-03-31 r78116) -- "Blame Jeroen"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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: filed443ce645d9.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: filed443ce645d9.knit.md

"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS filed443ce645d9.utf8.md --to latex --from markdown+autolink_bare_uris+tex_math_single_backslash --output filed443ce645d9.tex --self-contained --table-of-contents --toc-depth 2 --number-sections --highlight-style tango --pdf-engine pdflatex --include-in-header "C:\Users\bioctesting\bbs-3.11-bioc-testing\tmpdir\Rtmpsj5aiz\d447aba2e62.tex" --variable graphics --lua-filter "C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/rmarkdown/rmd/lua/pagebreak.lua" --lua-filter "C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/rmarkdown/rmd/lua/latex-div.lua" --wrap preserve --variable subparagraph --template "C:\Users\bioctesting\bbs-3.11-bioc-testing\tmpdir\Rtmpsj5aiz/BiocStyle/template.tex" --variable tables=yes --standalone --variable "compact-title:yes" 

Output created: filed443ce645d9.pdf


RUNIT TEST PROTOCOL -- Tue Apr 14 20:36:50 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 `C:/Users/bioctesting/bbs-3.11-bioc-t
esting/R/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. 
> 
> proc.time()
   user  system elapsed 
   1.54    0.32   47.31

BiocStyle.Rcheck/tests_x64/run_tests.Rout


R version 4.0.0 alpha (Rtools40) (2020-03-31 r78116) -- "Blame Jeroen"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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: file137c3af81e5e.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

ERROR: Windows API error 5: Access is denied.


ERROR: Info: path="cprogramdatamiktex2.9miktexdatale1756f6ade37d5f870f23c05a7f81e257.fndb-5"
ERROR: Source: Libraries\MiKTeX\Core\MemoryMappedFile\win\winMemoryMappedFile.cpp
ERROR: Line: 111

Sorry, but pdfcrop.exe did not succeed.
  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

ERROR: Windows API error 5: Access is denied.


ERROR: Info: path="cprogramdatamiktex2.9miktexdatale1756f6ade37d5f870f23c05a7f81e257.fndb-5"
ERROR: Source: Libraries\MiKTeX\Core\MemoryMappedFile\win\winMemoryMappedFile.cpp
ERROR: Line: 111

Sorry, but pdfcrop.exe did not succeed.
  ordinary text without R code

label: sessionInfo (with options) 
List of 1
 $ echo: logi FALSE

output file: file137c3af81e5e.knit.md

"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS file137c3af81e5e.utf8.md --to latex --from markdown+autolink_bare_uris+tex_math_single_backslash --output file137c3af81e5e.tex --self-contained --table-of-contents --toc-depth 2 --number-sections --highlight-style tango --pdf-engine pdflatex --include-in-header "C:\Users\bioctesting\bbs-3.11-bioc-testing\tmpdir\Rtmp485T4s\137c858691a.tex" --variable graphics --lua-filter "C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/rmarkdown/rmd/lua/pagebreak.lua" --lua-filter "C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/rmarkdown/rmd/lua/latex-div.lua" --wrap preserve --variable subparagraph --template "C:\Users\bioctesting\bbs-3.11-bioc-testing\tmpdir\Rtmp485T4s/BiocStyle/template.tex" --variable tables=yes --standalone --variable "compact-title:yes" 

Output created: file137c3af81e5e.pdf


RUNIT TEST PROTOCOL -- Tue Apr 14 20:37:56 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 `C:/Users/bioctesting/bbs-3.11-bioc-t
esting/R/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. 
> 
> proc.time()
   user  system elapsed 
   1.67    0.32   63.59

Example timings

BiocStyle.Rcheck/examples_i386/BiocStyle-Ex.timings

nameusersystemelapsed
helpers0.000.000.05
html_document000
latex000
macros000
markdown000
md_document000
output000
pdf_document000
use_vignette000

BiocStyle.Rcheck/examples_x64/BiocStyle-Ex.timings

nameusersystemelapsed
helpers000
html_document000
latex000
macros0.010.000.01
markdown000
md_document000
output000
pdf_document000
use_vignette0.000.010.02