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

[Henrik Bengtsson]

On Tue, Feb 28, 2017 at 2:47 PM, Duncan Murdoch
<murdoch.duncan at gmail.com> wrote:
> 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...).

I like this idea.  It could be done such that R CMD build lists the
files omitted based solely on the content of .Rbuildignore, which I
assume is also what Hadley meant.  This way *.o files wouldn't be
listed since they're omitted by the built-in rules of R CMD build
itself.

/Henrik

>
> 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
>>
>>
>
> ______________________________________________
> R-package-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel