[Bioc-devel] Citation not updating

Pages, Herve hp@ge@ @end|ng |rom |redhutch@org
Fri Oct 18 01:50:59 CEST 2019

Hi David,

It took me a while to figure this out but at the root of the problem is 
the non-conformance of your CITATION file. The problem is that it 
contains a call to packageVersion() which is not allowed in CITATION files.

Here is what the "CITATION files" section of the "Writing R Extensions" 
manual says about this:

   It is desirable (and essential for CRAN) that the CITATION file does
   not contain calls to functions such as packageDescription which
   assume the package is installed in a library tree on the package
   search path.

As explained in the manual, the correct way to inject things like the 
package Version or Date in the citation is to pick them from the object 
'meta' e.g. to use 'meta$Version' or 'meta$Date' in the CITATION file.

onlineFDR is not the only package to have this problem. Unfortunately 
there are currently about 40 Bioconductor software packages that have 
calls to things like `packageDescription()`, `packageVersion()`, or 
`packageDate()` in their CITATION file. They'll all need to be fixed 
(for all them the citation that ends up being displayed on the landing 
page is wrong).

I'll send a separate communication about this.


On 10/16/19 22:10, Pages, Herve wrote:
> Hi David,
> Thanks for bringing this to our attention. We'll be looking into it.
> H.
> On 10/16/19 08:21, Robertson, David wrote:
>> Dear Bioc-devel,
>> I updated the development version of the onlineFDR package almost a month ago, but have noticed that the citation information displayed on the relevant Bioconductor webpage still has not updated: https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_packages_devel_bioc_html_onlineFDR.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=50zupoiw-U2tN2NZbpj2yMLDW6MPtV5K2RX3RpjBSWk&s=egZvMzYM0gDWORZAQftwInYGkwlO_H4f0QQHAJzktWY&e=
>> One change made during the update was adding a citation file (within the inst folder) - I'm not sure if that's causing the problem?
>> Thanks for your help,
>> David
>> 	[[alternative HTML version deleted]]
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages using fredhutch.org
Phone:  (206) 667-5791
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