[Bioc-devel] Error in Vignette of package

Hi all,
I've been following this conversation as I was having the same issue for
the swfdr package. Happy to see that it's now fixed on malbec and merida,
though I now see a different error on tokay, also referring to the
vignettes. I looked around a bit, and a bunch of other packages now have
the tokay error, which is:

* creating vignettes ... ERROR
--- re-building 'swfdrQ.Rmd' using rmarkdown
Error: processing vignette 'swfdrQ.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building 'swfdrQ.Rmd'


https://master.bioconductor.org/checkResults/3.10/bioc-LATEST/swfdr/tokay1-buildsrc.html


Thanks!
Cheers,
Simina



On Fri, Dec 6, 2019 at 3:18 PM Pages, Herve <hpages at fredhutch.org> wrote:

Great news Andrzej! We'll keep a close eye on the build reports in the
next few days. Fingers crossed. Thanks!

H.


On 12/6/19 03:46, Andrzej Ole? wrote:

Dear Package Developers,

An updated version of BiocStyle has been deployed to both the

development

and the release branch. The fix addresses vignette build errors

occurring

with rmarkdown v1.18, these should clear up within the next build cycle.

Cheers,
Andrzej

On Wed, Dec 4, 2019 at 2:31 PM Andrzej Ole? <andrzej.oles at gmail.com>

wrote:

Dear Package Developers,

BiocStyle will be patched within the next couple of days to address the
observed errors. Until then please refrain from making any changes to

your

package, the issue should resolve itself once BiocStyle is updated.

Cheers,
Andrzej

On Mon, Dec 2, 2019 at 11:20 AM Andrzej Ole? <andrzej.oles at gmail.com>
wrote:

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]]
     >
     > _______________________________________________
     > Bioc-devel at r-project.org mailing list
     >

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--
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
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E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

--
Simina M. Boca
Assistant Professor
Innovation Center for Biomedical Informatics  (ICBI)
Departments of Oncology and Biostatistics, Bioinformatics and
Biomathematics | Georgetown University Medical Center
Cancer Prevention and Control Program | Lombardi Comprehensive Cancer
Center

2115 Wisconsin Ave NW, Suite 110, Washington, DC 20007
Phone: (202) 687-1545, Fax: (202) 687-5011
http://icbi.georgetown.edu/boca
https://sites.google.com/georgetown.edu/siminaboca/