[Bioc-devel] Error in Vignette of package

Hi,

the error seems to be related to some recent changes in the upstream
package rmarkdown v1.18. I will give you an update once I know more details.

Cheers,
Andrzej


On Sun, Dec 1, 2019 at 5:00 PM Benjamin Jean-Marie Tremblay <
b2tremblay at uwaterloo.ca> wrote:

Not using BiocStyle::pdf_document means you can?t use the helpers/macros.
Try this in a fresh interactive session:

  library(BiocStyle)
  rmarkdown::render("yourvignette.Rmd")

This should make the helpers/macros available. It won?t fix the issue
for passing R CMD check, but at least it?ll confirm what the issue is and
thus you?ll know to wait for BiocStyle to update.

BT

Le 1 d?c. 2019 ? 10:47, Ioannis Vardaxis <iova89 at hotmail.com> a ?crit :

Thanks for the answer. However replacing it resulted in another error

for me:

Quitting from lines 2-41 (MACPET.Rmd)
Error in doc_date() : could not find function "doc_date"
Calls: <Anonymous> ... inline_exec -> hook_eval -> withVisible -> eval

-> eval

Execution halted

Should I wait until BiocStyle is updated?

Best,
Ioannis

Fra: Martin Morgan <mtmorgan.bioc at gmail.com>
Sendt: s?ndag 1. desember 2019 11:51
Til: Benjamin Jean-Marie Tremblay <b2tremblay at uwaterloo.ca>; Ioannis

Vardaxis <iova89 at hotmail.com>

Kopi: bioc-devel at r-project.org <bioc-devel at r-project.org>
Emne: Re: [Bioc-devel] Error in Vignette of package

Thanks for that insight, we'll try to solve the issue with BiocStyle.

Martin

?On 12/1/19, 1:32 AM, "Bioc-devel on behalf of Benjamin Jean-Marie

Tremblay" <bioc-devel-bounces at r-project.org on behalf of
b2tremblay at uwaterloo.ca> wrote:

    I?ve been getting the exact same error for compiling the Rmarkdown
    vignettes in my own package. Some partial testing before the weekend
    revealed that in my case the error could be circumvented simply by

not

    using

        output: BiocStyle::pdf_document

    but instead

        output: pdf_document

    in the yaml header. I?m not quite sure why, but when BiocStyle is

used

    some of the latex code for code highlighting is repeated, leading

to the

    'already defined' error. I?ve not updated my package since before

this

    error started.

    BT

    > Le 30 nov. 2019 ? 10:25, Ioannis Vardaxis <iova89 at hotmail.com> a

?crit :

    >
    > Hey,
    >
    > I am trying to build my package Vegnette and I get the following

error:

    >
    > ! LaTeX Error: Command \VerbBar already defined.
    >               Or name \end... illegal, see p.192 of the manual.
    >
    > I tried to find what this means with no luck.
    >
    > Best,
    > Ioannis
    >
    >
    >    [[alternative HTML version deleted]]
    >
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