[R-pkg-devel] .bib file in vignette not found during R CMD check

[Duncan Murdoch]

On 28/02/2017 5:17 PM, Patrick Schratz wrote:
> Thanks Duncan, that was the problem! Although the Rbuildignore entry
> pointed to the main dir

No, it contains patterns, not paths, and is matched "case-insensitively 
against the file and directory names relative to the top-level package 
source directory".  Put ^ at the beginning if you want to refer to the 
main dir.

Hadley, reporting what gets omitted might be a good suggestion, but it 
might report too much in a package with compiled code (the .o files will 
generally be omitted; rgl has 51 of those in src...).

Duncan Murdoch

and my .bib file was lying under vignettes/...
> That Rbuildignore entry was a leftover when my .bib file was initially
> lying in the top directory and hence was throwing notes during R CMD check.
>
> Afterwards I used full paths in the vignette to specify the .bib
> location. This approach works fine until you submit to CRAN which of
> course cannot deal with full paths (and you forget about that you used a
> full path when releasing).
>
> @hadley
> Could be useful as most often you do not think of possible leftover
> entries in Rbuildignore...
>
> 2017-02-28 18:57 GMT+01:00 Duncan Murdoch <murdoch.duncan at gmail.com
> <mailto:murdoch.duncan at gmail.com>>:
>
>     On 28/02/2017 10:44 AM, Patrick Schratz wrote:
>
>         When building the vignette using R CMD Build or
>         `devtools::build_vignette()` everything works fine.
>
>         However, during R CMD check I get the following
>
>         ** checking running R code from vignettes ...*
>         *   ‘sperrorest-vignette.Rmd’ using ‘UTF-8’ ... OK*
>         * NONE*
>         ** checking re-building of vignette outputs ... WARNING*
>         *Error in re-building vignettes:*
>         *  ...*
>         *pandoc-citeproc: Could not find Biblio.bib*
>         *CallStack (from HasCallStack):*
>         *  error, called at src/Text/CSL/Pandoc.hs:224:39 in
>         pandoc-citeproc-0.10.4.1-EdjBizYp62fCPHef3CymGR:Text.CSL.Pandoc*
>         *pandoc: Error running filter /usr/local/bin/pandoc-citeproc*
>         *Filter returned error status 1*
>         *Error: processing vignette 'sperrorest-vignette.Rmd' failed with
>         diagnostics:*
>         *pandoc document conversion failed with error 83*
>         *Execution halted*
>
>         The .bib file is lying in `/vignettes`. There is a similar
>         question on SO
>         <http://stackoverflow.com/questions/41126556/any-way-of-attaching-csl-bib-files-by-using-knitcitations-package
>         <http://stackoverflow.com/questions/41126556/any-way-of-attaching-csl-bib-files-by-using-knitcitations-package>>
>         but
>         the answer does not address the problem.
>         When using full paths everything is fine. However, I cannot use
>         full paths
>         when submitting to CRAN.
>
>         If you want to check on your own, please use the `dev` branch;
>         https://github.com/pat-s/sperrorest/tree/dev
>         <https://github.com/pat-s/sperrorest/tree/dev>
>
>         pandoc-citeproc: stable 0.10.4.1 (bottled), HEAD
>         pandoc: stable 1.19.2.1 (bottled), HEAD
>
>
>     Your .Rbuildignore file says not to include Biblio.bib.  Don't do that.
>
>     Duncan Murdoch
>
>