[Bioc-devel] package submission - problem with vignette

Tue Apr 12 15:21:13 CEST 2016

This directive
  %\VignetteEncoding{UTF-8}
is a message to R about the vignette encding.

This directive
%\usepackage[UTF8]{inputenc}
is a latex command.

Kasper

On Tue, Apr 12, 2016 at 7:17 AM, Karim Mezhoud <kmezhoud at gmail.com> wrote:

> 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
> >>
> >
> >
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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