On Wed, Sep 25, 2019 at 2:28 PM Stuart Lee <[email protected]> wrote: > > Chiming in to say +1 to this. I also use pkgdown for the same purpose as > Laurent. With some kind of CI service you can automate the build of the > website after a successful R CMD CHECK. Not sure how tricky this would be to > integrate with Bioconductor's build system.
FYI, 'pkgdown' only supports vignettes that are written in the Rmarkdown format (https://github.com/r-lib/pkgdown/issues/781). /Henrik > ________________________________ > From: Bioc-devel <[email protected]> on behalf of Martin > Morgan <[email protected]> > Sent: Thursday, 26 September 2019 7:10 AM > To: Laurent Gatto <[email protected]>; Ludwig Geistlinger > <[email protected]>; [email protected] > <[email protected]> > Subject: Re: [Bioc-devel] Reference manual as HTML > > Our recollection is that there is no 'flag' in R CMD build to create HTML > rather than PDF vignettes; without that it would be non-trivial to create > html output, e.g., links across pages. (I *think* the installed package html > help pages are generated on the fly...) > > What is your experience with pkgdown? > > Martin > > On 9/25/19, 9:44 AM, "Bioc-devel on behalf of Laurent Gatto" > <[email protected] on behalf of [email protected]> > wrote: > > I think this would be very useful. This is one of the reasons I create > pkgdown sites for my packages: manual pages, news and html vignettes are > readily available for all (including me) to browse. > > Best wishes, > > Laurent > > ________________________________________ > From: Bioc-devel <[email protected]> on behalf of Ludwig > Geistlinger <[email protected]> > Sent: 25 September 2019 13:31 > To: [email protected] > Subject: [Bioc-devel] Reference manual as HTML > > Dear Bioc-Team, > > > I repeatedly wondered whether it would be possible to display the > reference manual > as HTML instead of PDF on a package's landing page. This is already > possible for vignettes. > > HTML reference manuals have at least two advantages: > > 1. links to functions of other package in the man pages of my package > would > actually work. Links to functions / classes of other packages of the form > > \code{\link{p.adjust}} > > or > > \code{\linkS4class{SummarizedExperiment}} > > within the pdf reference manual currently point nowhere (bring me back to > the > first page of the pdf). Within the html reference manual > > help(package="myPackage", help_type="html") > > these links work as expected, ie bring me to the help pages of functions > / classes > of other packages. > > 2. I could easily refer users to the documentation link of a specific > function > (without them having to search through the pdf) such as "check the > documentation of > the DESeq function here: https://rdrr.io/bioc/DESeq2/man/DESeq.html";. > > (where the link would be preferably: > bioconductor.org/packages/DESeq2/man/DESeq.html). > > > Thank you, > > Ludwig > > [[alternative HTML version deleted]] > > _______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > _______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > _______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > _______________________________________________ > > The information in this email is confidential and intended solely for the > addressee. > You must not disclose, forward, print or use it without the permission of the > sender. > > The Walter and Eliza Hall Institute acknowledges the Wurundjeri people of the > Kulin > Nation as the traditional owners of the land where our campuses are located > and > the continuing connection to country and community. > _______________________________________________ > > [[alternative HTML version deleted]] > > _______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
