[Bioc-devel] package submission - problem with vignette

[Karim Mezhoud]

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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