[Bioc-devel] Vignette Latex error

[Pages, Herve]

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 ?
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=3Hn9oJd7m-EISYIjrDfM2rGF3UqKvg3mgHYf4PnNqOQ&s=H6d4L0vfGz_cNaO4ENIq5QU-NpIcucw9hPfbzD6j6aY&e=

-- 
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
Phone:  (206) 667-5791
Fax:    (206) 667-1319