[R-pkg-devel] R package manual failing only on R-devel-linux-x86_64-debian-gcc

[Zhian Kamvar]

For the curious, an update from Uwe Ligges:

Kurt Hornik found:
>
> <
> https://tex.stackexchange.com/questions/1522/pdfendlink-ended-up-in-different-nesting-level-than-pdfstartlink
> >
>
> and you shoudl be able to reproduce via
>
>    R_PAPERSIZE=a4 R CMD Rd2pdf /path/to/poppr
>
> Suggestion:
>
> Add a blank line before
>
>    Examples of analyses are available in a primer written by Niklaus
> J. Grünwald, Zhian N. Kamvar, and Sydney E.  Everhart at
> \url{http://grunwaldlab.github.io/Population_Genetics_in_R}.}
>


Zhian

On Tue, Jun 18, 2019 at 4:22 PM Zhian Kamvar <zkamvar using gmail.com> wrote:

> Thank you for the the insights, Gabor and Hugh! Line 186 happens to be a
> \begin{itemize} in the package documentation section (which is chock-full
> of links), I didn't change that, but I did expand the DESCRIPTION, so I
> guess it makes sense that one of those links have slid down and gotten
> stuck between the pages.
>
> Now if only I had a reliable way of reproducing the error -_-
>
> Thank you both for the quick responses!
> Zhian
>
> On Tue, Jun 18, 2019 at 4:00 PM Hugh Parsonage <hugh.parsonage using gmail.com>
> wrote:
>
>> Unfortunately this error is caused by a hyperlink straddling a page, so
>> it’s difficult to solve uniformly.
>>
>> The LaTeX error message provides a clue as to where the hyperlink might
>> be (near an \item near a \code) but no exact location.
>>
>> My advice would be to look where you have hyperlinks (including cross
>> references) in your documentation and either reword the documentation or
>> omit hyperlinks until you can produce a full pdf manual. Then, examine
>> where the hyperlink might have straddled two pages and more surgically
>> reword that paragraph/list to enable the original intent to be typeset.
>>
>> The hyperlink may also occur in a bibliography where you may have to make
>> more drastic omissions or additions in order for compilation to succeed.
>>
>> On Wed, 19 Jun 2019 at 12:37 am, Zhian Kamvar <zkamvar using gmail.com> wrote:
>>
>>> Hello,
>>>
>>> I'm having a really strange problem that I cannot reproduce locally
>>> (Ubuntu
>>> bionic) or on Rhub. I've run into an issue where the R package manual is
>>> failing only on this platform with ancient LaTeX runes that I struggle to
>>> decipher [0]
>>>
>>> > * checking PDF version of manual ... WARNING
>>> > LaTeX errors when creating PDF version.
>>> > This typically indicates Rd problems.
>>> > LaTeX errors found:
>>> > ! pdfTeX error (ext4): \pdfendlink ended up in different nesting level
>>> than \pd
>>> > fstartlink.
>>> > \AtBegShi using Output ...ipout \box \AtBeginShipoutBox
>>> >                                                   \fi \fi
>>> > l.186 \item \code
>>> > !  ==> Fatal error occurred, no output PDF file produced!
>>> > * checking PDF version of manual without hyperrefs or index ... OK
>>> > * checking for non-standard things in the check directory ... NOTE
>>> > Found the following files/directories:
>>> >   ‘poppr-manual.tex’
>>> >
>>> >
>>> The only information I could find on the error was a question with
>>> answers
>>> that were more questions: https://stackoverflow.com/q/2765229/2752888
>>>
>>> Uwe Ligges was kind enough to trigger a second build to see if this was
>>> an
>>> anomaly, but the same incantation appeared again. I've tried building
>>> this
>>> on Rhub debian-devel-gcc, but could not reproduce the error [1] and no
>>> other platform does this.
>>>
>>> Has anyone seen this before?
>>>
>>> Thanks,
>>> Zhian
>>>
>>> [0]:
>>>
>>> https://win-builder.r-project.org/incoming_pretest/poppr_2.8.3_20190618_151346/Debian/00check.log
>>> [1]:
>>>
>>> https://builder.r-hub.io/status/original/poppr_2.8.3.tar.gz-130d92cdeb2c4c46b94d8cc13b8921b9
>>>
>>>         [[alternative HTML version deleted]]
>>>
>>> ______________________________________________
>>> R-package-devel using r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>
>>

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