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

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