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

<
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. Gr?nwald, Zhian N. Kamvar, and Sydney E.  Everhart at
\url{http://grunwaldlab.github.io/Population_Genetics_in_R}.}

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 at 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 at 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 at 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

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