[Bioc-devel] package submission - problem with vignette

[Karim Mezhoud]

Hi,
I don't know why I have to use
%\VignetteEncoding{UTF-8}
instead
%\usepackage[UTF8]{inputenc}

it works.

On Tue, Apr 12, 2016 at 8:38 AM, Karim Mezhoud <kmezhoud at gmail.com> wrote:

> Dear Lara and Dan,
> In my case I am having this error.  Thanks
>
> * creating vignettes ... ERROR
> Error: Vignette 'bioCancer.Rmd' is non-ASCII but has no declared encoding
> Execution halted
> Error: Command failed (1)
> Execution halted
>
> Exited with status 1.
>
> I am setting vignette using knitr package.
>
> In DESCRIPTION file I added:
>
> Suggests:
>     BiocStyle,
>     AnnotationHub,
>     knitr,
>     rmarkdown,
>     testthat (>= 0.10.0),
>     rappdirs
> VignetteBuilder: knitr
>
> In Rmd file, I started by:
>
> ---
> title: "bioCancer: Interactive Multi-OMICS Cancers Data Visualization and
> Analysis"
> author: "\\
>     Karim Mezhoud (<kmezhoud at gmail.com>)\\
>         Nuclear Science Center of Tunisia, Nuclear Safety & Security
> Department"
> date: "`r Sys.Date()`"
> output:
>   BiocStyle::html_document:
>     toc: true
>   BiocStyle::pdf_document:
>     toc: true
> vignette: >
>   %\VignetteIndexEntry{bioCancer: Interactive Multi-OMICS Cancers Data
> Visualization and Analysis}
>   %\VignetteEngine{knitr::rmarkdown}
>   %\VignetteDepends{AnnotationHub}
>   %\usepackage[utf8]{inputenc}
> ---
>
>
> On Mon, Apr 11, 2016 at 9:52 PM, Lara Urban <lara.h.urban at ebi.ac.uk>
> wrote:
>
>> Dear Dan,
>>
>> Many thanks, apparently I just had to update one of the knitr-associated
>> components.
>>
>> I hope it will go through now.
>>
>> Many thanks again and enjoy your evening,
>> Lara
>>
>> 2016-04-11 17:39 GMT+01:00 Dan Tenenbaum <dtenenba at fredhutch.org>:
>>
>> >
>> >
>> > ----- Original Message -----
>> > > From: "Dan Tenenbaum" <dtenenba at fredhutch.org>
>> > > To: "Lara Urban" <lara.h.urban at ebi.ac.uk>
>> > > Cc: "bioc-devel" <bioc-devel at r-project.org>
>> > > Sent: Monday, April 11, 2016 9:29:30 AM
>> > > Subject: Re: [Bioc-devel] package submission - problem with vignette
>> >
>> > > It means that when you run R CMD build YourPackageName, the vignette
>> is
>> > not
>> > > built.
>> > >
>> > > It simply looks in the output of R CMD build for a line that starts:
>> > >
>> > >    * creating vignettes ...
>> > >
>> > > If this line is present, it means `R` has not detected that a vignette
>> > > needs to be built.
>> >
>> > Oops, that should say: "If this line is NOT present..."
>> >
>> > Dan
>> >
>> > >
>> > > It's `REQUIRED` that the vignette be built.
>> > >
>> > > If you have vignette sources yet still get this message, there could
>> > > be several causes:
>> > >
>> > > * Missing or invalid `VignetteBuilder` line in the `DESCRIPTION` file.
>> > > * Missing or invalid `VignetteEngine` line in the vignette source.
>> > >
>> > > See `knitr`'s [package vignette](
>> http://yihui.name/knitr/demo/vignette/)
>> > > page, or the
>> > > [Non-Sweave
>> > > vignettes](
>> >
>> https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Non_002dSweave-vignettes
>> > )
>> > > section of "Writing R Extensions" for more information.
>> > >
>> > > Dan
>> > >
>> > >
>> > > ----- Original Message -----
>> > >> From: "Lara Urban" <lara.h.urban at ebi.ac.uk>
>> > >> To: "bioc-devel" <bioc-devel at r-project.org>
>> > >> Sent: Monday, April 11, 2016 8:58:14 AM
>> > >> Subject: [Bioc-devel] package submission - problem with vignette
>> > >
>> > >> Dear BiocDevel,
>> > >>
>> > >> I have a question regarding the submission of my package; thank you
>> very
>> > >> much in advance.
>> > >>
>> > >> I have submitted my package to Bioconductor a few days ago and it
>> passed
>> > >> build, check and bioccheck. Now, that I had to change just one line
>> in
>> > my R
>> > >> code and submitted it again, I get an error on all three platforms,
>> > because
>> > >> it is required that my vignette is built by R CMD build; however, I
>> > still
>> > >> have my Rmd file in the order vignettes as before. Shouldn't it build
>> > >> automatically? Do you have any ideas what is going wrong here?
>> > >>
>> > >> Many thanks and kind regards,
>> > >> Lara
>> > >>
>> > >>
>> > >> --
>> > >> Lara Urban
>> > >>
>> > >> Predoctoral Fellow
>> > >> EMBL-European Bioinformatics Institute
>> > >> Wellcome Trust Genome Campus
>> > >> Hinxton, Cambridge
>> > >> CB10 1SD
>> > >> United Kingdom
>> > >>
>> > >> PhD Student
>> > >> Wolfson College
>> > >> University of Cambridge
>> > >>
>> > >> phone:  + 49 (0) 176 76 37 99 03
>> > <%2B%2044%20%280%29%201223%20494%20655>
>> > >> email: lara.h.urban at ebi.ac.uk <rfs32 at cam.ac.uk>
>> > >>
>> > >>      [[alternative HTML version deleted]]
>> > >>
>> > >> _______________________________________________
>> > >> Bioc-devel at r-project.org mailing list
>> > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> > >
>> > > _______________________________________________
>> > > Bioc-devel at r-project.org mailing list
>> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >
>>
>>
>>
>> --
>> Lara Urban
>>
>> Predoctoral Fellow
>> EMBL-European Bioinformatics Institute
>> Wellcome Trust Genome Campus
>> Hinxton, Cambridge
>> CB10 1SD
>> United Kingdom
>>
>> PhD Student
>> Wolfson College
>> University of Cambridge
>>
>> phone:  + 49 (0) 176 76 37 99 03 <%2B%2044%20%280%29%201223%20494%20655>
>> email: lara.h.urban at ebi.ac.uk <rfs32 at cam.ac.uk>
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>

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