[Bioc-devel] Vignette Latex error

[Pages, Herve]

Excellent. Thanks for taking good care of your package :-)

H.

On 4/8/19 10:26, Karl Stamm wrote:
Thank you so much. That fixed the issue. My package is now building correctly on all services.  We switched from biblatex to natbib. I did have to update the citation commands in the text to go with the natbib standard, and meanwhile did some reformatting of the vignette overall.

On Thu, Apr 4, 2019 at 7:47 PM Pages, Herve <hpages using fredhutch.org<mailto:hpages using fredhutch.org>> wrote:
Hi Karl,

On 4/2/19 15:03, Karl Stamm wrote:
> I'm having a build error on only the OSX servers.
>
> * creating vignettes ... ERROR
> --- re-building ‘rgsepd.Rnw’ using knitr
> Error: processing vignette 'rgsepd.Rnw' failed with diagnostics:
> Running 'texi2dvi' on 'rgsepd.tex' failed.
> LaTeX errors:
> ! Use of \blx using bbl@verbadd using i doesn't match its definition.
> l.142     \verb
>
>
> The tex file is written by the Rnw with knitr, so maybe it's a knitr
> problem, or an incompatibility to the OSX side??   I tried removing
> all references to \verb and that doesnt seem to have done anything.

A little bit of detective work indicates that the vignette was building
fine on all platforms until commit 7ed2a00e This commit added 2 things
to the rgsepd.Rnw vignette: (1) a new biblio entry and (2) a \verb
paragraph with reference to the new biblio entry.

Apparently, the new biblio entry is causing problems. It seems to
trigger some bad interaction between knitr and biblatex that seems to be
specific to the MacTeX version (mactex-20161009) that we use on our Mac
builders. Remember that we're stuck with El Capitan on these builders so
updating things there can be tricky.

Anyway, the problem goes away if you use natbib (used by hundreds of
Bioconductor packages) instead of biblatex (only used by a handful of
Bioconductor packages). That is, if you replace:

   \usepackage[backend=bibtex]{biblatex}

with

   \usepackage{natbib}

and move

   \bibliography{references}

to the line where you currently have

   \printbibliography

(get rid of the \printbibliography directive)

With this change, I can successfully 'R CMD build rgsepd' on merida2
(didn't try on celaya2 though).

Hope this helps,

H.


>
>
> I want to get the package building without errors before the brach
> lockdown in a few weeks.
>
> Since it builds on my end just fine, and also on the Windows and Linux
> servers, surely it's a build server platform specific problem.   Maybe
> Knitr is not supported anyone and I need to change everything over to
> another RMD format ?
>
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>
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--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages using fredhutch.org<mailto:hpages using fredhutch.org>
Phone:  (206) 667-5791
Fax:    (206) 667-1319


--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages using fredhutch.org<mailto:hpages using fredhutch.org>
Phone:  (206) 667-5791
Fax:    (206) 667-1319


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