[Bioc-devel] More than 1 citation in landing page

Dan Tenenbaum dtenenba at fredhutch.org
Sat Nov 1 18:57:00 CET 2014

----- Original Message -----
> From: "Leonardo Collado Torres" <lcollado at jhu.edu>
> To: bioc-devel at r-project.org
> Cc: "Jeff Leek" <jtleek at gmail.com>
> Sent: Friday, October 31, 2014 4:05:11 AM
> Subject: [Bioc-devel] More than 1 citation in landing page
> Hi,
> I'm wondering if it's possible to display more than 1 citation entry
> on the landing page.
> In my particular use case, the package I developed is based on a
> proposed statistical framework which is already published. So for
> now,
> we want the citation info to include the details for the software but
> also the original paper. You can see this at
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/derfinder/inst/CITATION
> However
> http://www.bioconductor.org/packages/devel/bioc/html/derfinder.html
> only shows the first citation entry.
> Otherwise, I can use bibentry(textVersion) and artificially include
> both citations. I would expect this workaround to work.

I see the problem. The CITATION file has:

        version = paste("R package version", packageVersion("derfinder"))

(even though this does not appear in the output of citation()). And this requires
derfinder to be installed. However, the citation file is generated using a different
R running as a different user than the build system. Even the build system R is not
guaranteed to have all packages installed. And this R that generates the citation 
output is almost guaranteed NOT to have most bioc packages installed.

So what happens is, since derfinder is not installed, the call to readCitationFile() fails
more or less silently. 

So what I would suggest is removing that version = ... line from your CITATION. And bumping the version number.

You would see the results of these changes after the next build cycle.


> Best,
> Leonardo
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