Date: Wed, 23 Jul 2014 11:33:44 -0700
From: Martin Morgan <mtmorgan at fhcrc.org>
To: Matthew McCall <mccallm at gmail.com>, Michael Lawrence
<lawrence.michael at gene.com>
Cc: "bioc-devel at r-project.org" <bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] Distinction between release and devel
package websites
Message-ID: <53D00008.1090100 at fhcrc.org>
Content-Type: text/plain; charset=windows-1252; format=flowed
Dan has implemented these changes. Go to the Bioconductor home page and in the
search box at the top right enter
supraHex
(winner of the ISMB 2014 Best Artwork Award! Check out the URL on the package
landing page). You'll see that the first link is to supraHex, and the second to
supraHex (development version).
On the supraHex (development version) page you'll see text indicating that
you're looking at the development version, and for the release you should go
somewhere else.
Further down the installation instructions are now in their own section, adding
a little more emphasis.
The Documentation section includes instructions -- browseVignettes("supraHex")
-- for getting your version of the vignettes.
The 'download' section is now called 'Package Archives'.
The Package Archives section starts with a sentence pointing to Installation
instructions.
Mousing over one of the links pops up a tool tip encouraging you once again to
use biocLite.
Relevant changes also apply to release landing pages.
As Vince mentioned, it is REALLY IMPORTANT that users do not mix release and
devel versions of packages in a single library. Even if it 'works for package
X', this invariably leads to incompatibilities and confusion. For those users
wanting new features, tell them to switch to using the development version,
e.g., as outlined at
http://bioconductor.org/packages/release/bioc/html/supraHex.html
Thanks for your input,
Martin
Hi, I just caught up to date with this conversation and I like the implemented changes. Great job! I hope that they will be effective. Just some minor details: * Maybe the tooltip over the zip and tarball links when on a devel page can show a link to http://bioconductor.org/developers/how-to/useDevel/ Alternatively, the link could be under the "Package Archives" section by modifying "Follow Installation instructions to use this package in your R session." to something like "Follow Installation instructions to use this package in your R session. Verify that you are using the devel version." * I was looking forward to the svn links (for devel pages), are you still going to add them? If not, I understand that they are not necessary. Also, about svn, well.... I guess that I'm from the more recent group that knows git/Mercurial but never learned svn (hence why I haven't followed up on Herv?'s suggestion in an earlier thread). I thought I wasn't going to need to (thanks to the Git-SVN bridge!), but well, seems like I'll at least need to learn some basic svn. Finally, regarding the issue of pushing new features to devel versions (and not release), I understand the reasons for doing so. In my case, what I have been trying to do to minimize major differences between the versions is to keep working on the package outside of BioC until we are more confident on its stability. Kind of pre-devel. Pre-devel users (just a handful) can then install it via devtools::install_github(). I understand that not every package workflow is like this, but well, it could be a suggestion worth mentioning at http://www.bioconductor.org/developers/package-guidelines/ Though of course, maybe it's better to have "pre-devel" packages be submitted to BioC-devel and drive all the traffic through BioC. Just some thoughts. Cheers, Leo