Hi,

Thank you for your replying.

Thanks Kasper, I had looked at other vignettes, but in the packages I
looked at so far I only found the PDF end-result. (e.g. edgeR), or the
sources. On the other hand, Biobase, for instance, gives its sources, but
does not have a "references" section. Anyway, your minfi provides me with
both, thank you!
I see you used natbib. I might try that one, or maybe bibtex, whichever
feels easier to me. I suppose if I manage to make it compile on my server,
it is likely to work on the Bioconductor build servers too, as it did so
far for the rest of my package.

Thanks Vincent as well, you were right as I initially want to make it work
in my R studio environment (I only submit a new version to Bioconductor
after I checked that it compiles properly on my server where I use "RStudio
server"), but in the end, what really matters is that it builds on the
Bioconductor servers if I want it to be accepted there. From your answers,
it seems to me that my issue resides more in the LaTeX side than the R
Studio one.
I will try to put the references in a .bib file as you suggested, and take
example on Kasper's source vignette to cite them in my vignette using an
appropriate package. LaTeX manuals, here I come!

Thanks a lot (any further advice welcome though)
Kévin




On 7 August 2014 19:56, Vincent Carey <stvjc@channing.harvard.edu> wrote:

> It seemed to me that this question concerned how to do this in Rstudio
> specifically,
> if you are using it as the sole development environment, so I do not
> really have an example
> but I think uploading the relevant .bib file to the vignettes directory
> would be appropriate
> and it may well be that the builder will automatically run bibtex.
>
>
> On Thu, Aug 7, 2014 at 1:36 PM, Kasper Daniel Hansen <
> kasperdanielhansen@gmail.com> wrote:
>
>> I would recommend looking at existing vignettes, for example minfi, but
>> there are tons of them.
>>
>>
>> On Thu, Aug 7, 2014 at 12:38 PM, Kevin Rue-Albrecht <
>> kevin.rue@ucdconnect.ie
>> > wrote:
>>
>> > Dear all,
>> >
>> > My name is Kevin Rue-Albrecht and I am working to improve a package
>> > currently in review by Bioconductor. I am blocked while trying to add
>> the
>> > final touch to the package.
>> >
>> > I was wondering about the recommended way of inserting bibliographic
>> > references in the body of the package vignette using R Studio to build
>> > the source package.
>> >
>> > I am developing the package using R Studio on a standard Linux Ubuntu
>> 12.04
>> > distribution. The package contains a Sweave vignette (.Rnw file) which
>> > succesfully compiles on the Bioconductor package tracker with bits of R
>> > code and bits of LaTeX.
>> >
>> > So far, I have only found this page which confuses me for different
>> reasons
>> > (
>> >
>> >
>> http://texblog.org/2013/08/20/rknitr-automatic-bibliography-generation-with-biblatex-in-rstudio/
>> > ):
>> >
>> >    - It refers to the knitr type of vignette, not the Sweave that I have
>> >    used so far
>> >    - At some point the person writes "tell RStudio where to find the
>> .tex,
>> >    .bib and .bst files"
>> >       - In the minimal example, he seems to include the .bib file into
>> the
>> >       source of the vignette file. I probably should not do that with
>> many
>> >       references.
>> >
>> > I haven't found the information in the "Writing R Extensions" page, the
>> > Bioconductor pacakge guidelines or the archives of this mailing list.
>> >
>> >
>> >    - Can anyone point me to a place where my question might be already
>> >    answered that I haven't found yet?
>> >    - Or can anyone tell me how to store the references (probably in a
>> >    separate file), and how to refer to them in the .Rnw vignette file so
>> > that
>> >    it compiles properly on the Bioconductor servers?
>> >
>> >
>> > Many thanks in advance !
>> >
>> > Best regards,
>> > Kevin
>> >
>> >
>> > --
>> > Kévin RUE-ALBRECHT
>> > Wellcome Trust Computational Infection Biology PhD Programme
>> > University College Dublin
>> > Ireland
>> > http://fr.linkedin.com/pub/k%C3%A9vin-rue/28/a45/149/en
>> >
>> >         [[alternative HTML version deleted]]
>> >
>> >
>> > _______________________________________________
>> > Bioc-devel@r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >
>> >
>>
>>         [[alternative HTML version deleted]]
>>
>>
>> _______________________________________________
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>


-- 
Kévin RUE-ALBRECHT
Wellcome Trust Computational Infection Biology PhD Programme
University College Dublin
Ireland
http://fr.linkedin.com/pub/k%C3%A9vin-rue/28/a45/149/en

	[[alternative HTML version deleted]]

