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

[Leonardo Collado Torres]

Hi Dan,

Thank you for the info!

I'm now using the following short function in the CITATION file to get
the correct version.

pkgVer <- function(pkg, default) {
    x <- packageDescription(pkg, fields = 'Version')
    ver <- ifelse(is.na(x), default, x)
}

Basically, it'll get the correct version numbers for any user who has
installed the package while also allowing me to specify a default
value to use in the R version that generates the citation info for the
Bioc website.

It's correctly deploying on both BioC 3.0 and 3.1 ^_^

Cheers,
Leo


On Sat, Nov 1, 2014 at 1:57 PM, Dan Tenenbaum <dtenenba at fredhutch.org> wrote:
>
>
> ----- 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.
>
> Dan
>
>
>
>
>> Best,
>> Leonardo
>>
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>>