[Bioc-devel] Problems with vignette and makeovers file

Ioannis Vardaxis ioannis.vardaxis at ntnu.no
Sat Sep 16 00:13:23 CEST 2017


I am trying to build a package (called MACPET) and I am struggling to solve some problems.

First of all, I am using c++ code through the Rcpp package. I have read that there is no need of a makeovers file in the package anymore. Is that true? Or should I include a makevars file somewhere?

Furthermore, I have a vignette Rmd file. When I try to knit the file I get the following error:

/usr/local/bin/pandoc +RTS -K512m -RTS MACPET.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output /private/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T/RtmpGECAhX/preview-8e8131b72d.dir/MACPET.tex --table-of-contents --toc-depth 2 --template /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpsDFxOM/BiocStyle/template.tex --number-sections --highlight-style tango --latex-engine /Library/TeX/texbin/pdflatex --include-in-header /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpsDFxOM/90c2c32b20e.tex --variable tables=yes --standalone --filter /usr/local/bin/pandoc-citeproc
output file: MACPET.knit.md

Latexmk: This is Latexmk, John Collins, 19 Jan. 2017, version: 4.52c.

Latexmk: No file name specified, and I couldn't find any
   latexmk -help
to get usage information

Output created: /private/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T/RtmpGECAhX/preview-8e8131b72d.dir/MACPET.pdf
Error in tools::file_path_as_absolute(output_file) :
  file '/private/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T/RtmpGECAhX/preview-8e8131b72d.dir/MACPET.pdf' does not exist
Calls: <Anonymous> -> <Anonymous>
Execution halted

When I try system("R CMD Sweave --engine=knitr::rmarkdown --pdf vignettes/MACPET.Rmd") I get another error:

Latexmk: This is Latexmk, John Collins, 19 Jan. 2017, version: 4.52c.
Error in find_vignette_product(name, by = "weave", engine = engine) :
  Failed to locate the 'weave' output file (by engine 'knitr::rmarkdown') for vignette with name 'MACPET'. The following files exist in directory '.': 'DESCRIPTION', 'MACPET.Rproj', 'NAMESPACE'
Calls: <Anonymous> -> do.call -> <Anonymous> -> find_vignette_product
Execution halted

However, when I move the Rmd file outside the package, for example on my desktop, and knit it there, I don't get any error, it only happens when inside the package folders. My description file is as suggested in the Biostyle, and the yelm too.


Ioannis Vardaxis
Stipendiat IMF

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