[Bioc-devel] Announcement of a new package called bacon

Martin Morgan martin.morgan at roswellpark.org
Sat Jun 11 20:24:20 CEST 2016

On 06/11/2016 07:02 AM, Wolfgang Huber wrote:
> There exist people that use Bioconductor devel branch packages even
> though they are not developers and don’t subscribe to bioc-devel, so
> I think announcing on the support site can be appropriate.

yes, probably, provided each announcement indicates that the package is 
available to users of bioc-devel. It's funny how complicated this is; 
the message to the support  site will persist after the next release, 
where mention of bioc-devel would no longer be appropriate.

FWIW, packages added to the devel repository are posted to our twitter
account and are summarized on the new packages log


so there are already several opportunities for the enthusiast to stay up 
to date.

> I understand that problems might arise with & for users who do not
> easily handle versioning, but IMHO they are more than offset by
> highlightung a potentially useful package to as many people as
> possible as early as possible. (I haven’t checked this for a while -
> does ‘biocLite’ give a useful error message when asked to install a
> ‘devel only’ package on a system that is set up for release?)

It says that it is not available for your version of R, forwarding the
warning from install.packages

> install.packages("I_AM_NOT_A_PACKAGE",
Installing package into
(as 'lib' is unspecified)
Warning message:
package 'I_AM_NOT_A_PACKAGE' is not available (for R version 3.3.0 Patched)

An alternative would requiring checking packages that fail to install
against release (in case the person is using an olde version of
Bioconductor) and devel (in case they're using a current version of Bioc
but not devel) and then presenting some kind of sensible message (the
message above may not be accurate, in the current release cycle a new
package is available for users of R 3.3.0 who are also using 
bioc-devel). This seems to be quite complicated, and likely to 
frequently cause more harm than good.


> Best wishes Wolfgang
>> On Jun 9, 2016, at 16:48 GMT+2, Maarten van Iterson
>> <mviterson at gmail.com> wrote:
>> So the policy could be: before release to bioc-devel and after
>> release to the support-site. Maybe it is more useful to post only
>> on the support-site on release? I assume most bioc-devel
>> subscribers follow the support-site.
>> Maarten
>> On Thu, Jun 9, 2016 at 3:29 PM, James W. MacDonald <jmacdon at uw.edu>
>> wrote:
>>> I agree, but bacon is part of release. As Maarten said " *I would
>>> like to introduce the package bacon that has been added
>>> tobioconductor just before the release of version 3.3." ��*
>>> On Thu, Jun 9, 2016 at 10:09 AM, Martin Morgan <
>>> martin.morgan at roswellpark.org> wrote:
>>>> On 06/09/2016 10:06 AM, James W. MacDonald wrote:
>>>>> You should post this on the support site (
>>>>> https://support.bioconductor.org), using the 'News' item
>>>>> description. This bioc-devel is intended for discussion of
>>>>> issues with development of packages, not really for
>>>>> announcing new packages.
>>>> actually the email to developers on package acceptance
>>>> encourages them to post to bioc-devel.
>>>> I think the rationale was that the package is only available in
>>>> devel, so advertising on the support site would just lead to
>>>> disappointment.
>>>> Open to revised policies / suggestions, though.
>>>> Martin
>>>>> Jim
>>>>> On Thu, Jun 9, 2016 at 9:37 AM, Maarten van Iterson
>>>>> <mviterson at gmail.com
>>>>> wrote:
>>>>> Dear list,
>>>>>> I would like to introduce the package bacon that has been
>>>>>> added to bioconductor just before the release of version
>>>>>> 3.3.
>>>>>> bacon can be used to estimate and control for bias and
>>>>>> inflation often present in epigenome- and
>>>>>> transcriptome-wide association studies(EWAS/TWAS). The idea
>>>>>> behind bacon is to estimate the empirical null distribution
>>>>>> from the data (using Bayesian statistics) and use the
>>>>>> empirical null i.s.o. a theoretical null for inference.
>>>>>> Bacon supports bias- and inflation-controlled fixed-effect
>>>>>> meta-analysis that can be executed in parallel. A
>>>>>> manuscript is available from biorxiv (
>>>>>> http://biorxiv.org/content/early/2016/05/27/055772).
>>>>>> Kind regards,
>>>>>> Maarten van Iterson
>>>>>> [[alternative HTML version deleted]]
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>>> -- James W. MacDonald, M.S. Biostatistician University of
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>> [[alternative HTML version deleted]]
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
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> Wolfgang
> Wolfgang Huber Principal Investigator, EMBL Senior Scientist Genome
> Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg,
> Germany
> wolfgang.huber at embl.de http://www.huber.embl.de
> _______________________________________________
> Bioc-devel at r-project.org mailing list
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