[Bioc-devel] package submission - problem with vignette

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]]

--
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]]

        [[alternative HTML version deleted]]