[Bioc-devel] Distinction between release and devel package websites

Leonardo Collado Torres lcollado at jhu.edu
Thu Jul 24 06:59:49 CEST 2014

On Thu, Jul 24, 2014 at 12:17 AM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> On 07/23/2014 06:41 PM, Leonardo Collado Torres wrote:
>> 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 athttp://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.
> Frankly, this doesn't sound like a good idea to me. It confuses the user
> (what, I'm supposed to be using github? I thought this was a Bioconductor
> package!), makes your life as a developer difficult (three versions to
> maintain), and introduces code (i.e., bugs!) where it isn't tested.
> I'd just go for broke, make wild changes to your devel code, let the build
> system do it's magic, get leading-edge users to knowingly try out your
> changes, shake out some bugs, and have a nice clean ride into release and a
> grateful audience of appreciative users. Sure work in git if that's your
> flavor, but merge frequently with master and sync with bioc; never expect
> your users to install 'the latest' from github.

I agree with what you said. I was just talking about the development
stage before you submit the package the first time to BioC. After it's
in BioC then yes, don't ask users to install from GitHub. And well, as
I understand it, the Git-SVN bridge makes it easy to push to
Bioc-devel and Bioc-release (following the suggestion posted here

Or what system do you suggest using for that first development cycle
before submitting to BioC?

Our way of hosting the pre-devel version on GitHub without any
publicity and iterating there until we feel the package is mature for
BioC seems to be working for us. But well, it might be slow and we
could be losing out a lot by not having it in Bioc-devel. On the other
hand, we wanted to avoid confusing users with major changes to the
package. In the end, I'm torn between the "you only make a first
impression once, so make it good" approach vs "get it out there, then
fix it" approach.

In the end, I'm a newbie at developing packages and I'm still learning ^^'

> Martin
> --
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
> Location: Arnold Building M1 B861
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