[Bioc-devel] package submission - problem with vignette

[Lara Urban]

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>

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