[R-pkg-devel] URL syntax causes R CMD build failure - a fix

[J C Nash]

Thanks Uwe. I think you may have the reason, esp. if the url is output as LaTex
formatted text to the intermediate files.

 > Where is it in your package and what is the R CMD check output?

The issue was a failure to build the nlsr-devdoc.Rmd vignette. Unfortunately, the
messages were as below (indented). The package passed in May and earlier, and
failure occurred when pandoc updated recently on some platforms, so there is some
change in the toolchain that triggered this. While pandoc is a wonderful tool, its
message output can be very unhelpful. I've had difficulties outside of R converting
LaTex to epub for some of my historical novels. In those cases I've also seen apparent
success with "bits left out" which does upset the readers when the story has gaps.
I've never resolved the "why?", but have managed to work around, sometimes by simply
adding a vertical space (i.e., line ending), or otherwise rearranging text. It would
be nice to know the reason, but as with the present issue, the reward is not worth
the effort.

I've also seen awkwardness with currency symbols, though that may be my own lack of
detailed knowledge with LaTex. I need multiple currencies in some stories, and end
up editing with Sigil. I anticipate that some R users with vignettes that have
several currencies might want to check output.

Whether or not the url syntax that caused the present trouble is valid or not, the
percentage signs are likely worth avoiding if possible.

Thanks,

JN

On 2023-09-03 10:29, Uwe Ligges wrote:
> John can you point us to an example?
> Where is it in your package and what is the R CMD check output?
> 
> Guess: Within an Rd file you have to escape the %  characters otherwise they start a comment.
> 
> Best,
> Uwe Ligges
> 
> 
> 
> On 03.09.2023 00:30, Spencer Graves wrote:
>> I've encountered similar issues. However, it has been long enough ago that I don't remember enough details to say more 
>> without trying to update my CRAN packages to see what messages I get and maybe researching my notes from previous 
>> problems of this nature. Spencer Graves
>>
>>
>> On 9/2/23 4:23 PM, Greg Hunt wrote:
>>> The percent encoded characters appear to be valid in that URL, suggesting
>>> that rejecting them is an error. That kind of error could occur when the
>>> software processing them converts them back to a non-unicode character set.
>>>
>>> On Sun, 3 Sep 2023 at 4:34 am, J C Nash <profjcnash using gmail.com> wrote:
>>>
>>>> I'm posting this in case it helps some other developers getting build
>>>> failure.
>>>>
>>>> Recently package nlsr that I maintain got a message that it failed to
>>>> build on
>>>> some platforms. The exact source of the problem is still to be illuminated,
>>>> but seems to be in knitr::render and/or pandoc or an unfortunate
>>>> interaction.
>>>> An update to pandoc triggered a failure to process a vignette that had been
>>>> happily processed for several years. The error messages are unhelpful, at
>>>> least
>>>> to me,
>>>>
>>>>      Error at "nlsr-devdoc.knit.md" (line 5419, column 1):
>>>>      unexpected end of input
>>>>      Error: pandoc document conversion failed with error 64
>>>>      Execution halted
>>>>
>>>> Unfortunately, adding "keep_md: TRUE" (you need upper case TRUE to save it
>>>> when
>>>> there is no error of this type), did not save the intermediate file in this
>>>> case. However, searching for "pandoc error 64" presented one web page
>>>> where the author
>>>> used brute force search of his document by removing / replacing sections
>>>> to find
>>>> the line(s) that caused trouble. This is a little tedious, but effective.
>>>> In my
>>>> case, the offending line turned out to be a copied and pasted URL
>>>>
>>>> https://en.wikipedia.org/wiki/Levenberg%E2%80%93Marquardt_algorithm
>>>>
>>>> The coded characters can be replaced by a hyphen, to give,
>>>>
>>>> https://en.wikipedia.org/wiki/Levenberg-Marquardt_algorithm
>>>>
>>>> and this, when pasted in Mozilla Firefox at least, will go to the
>>>> appropriate
>>>> wikipedia page.
>>>>
>>>> I'd be interested in hearing from others who have had similar
>>>> difficulties. I
>>>> suspect this is relatively rare, and causing some sort of infelicity in the
>>>> output of knitr::render that then trips up some versions of pandoc, that
>>>> may,
>>>> for instance, be now applying stricter rules to URL syntax.
>>>>
>>>> Best,
>>>>
>>>> John Nash
>>>>
>>>> ______________________________________________
>>>> R-package-devel using r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>>
>>>
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