Check in svn for the sources. Sean On Aug 8, 2014 8:58 AM, "Kevin Rue-Albrecht" wrote: > 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 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]] > > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > [[alternative HTML version deleted]]