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
http://bioconductor.org/developers/new_packages/
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",
repos=BiocInstaller::biocinstallRepos())
Installing package into
'/home/mtmorgan/R/x86_64-pc-linux-gnu-library/3.3-Bioc-3.4'
(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.
Martin
Best wishes Wolfgang
On Jun 9, 2016, at 16:48 GMT+2, Maarten van Iterson
<mviter...@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 <jmac...@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.mor...@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
<mviter...@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
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Wolfgang
Wolfgang Huber Principal Investigator, EMBL Senior Scientist Genome
Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg,
Germany
wolfgang.hu...@embl.de http://www.huber.embl.de
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