[Bioc-devel] Bioc releases and Bioconda

Hi Elena,

Could you tell me more about which package you are trying to wrap a recipe
for? And could you give me an example for what you mean by " determining
dependencies limits when one of the packages that you depend on changes its
public interface." ?

Best,

Nitesh

I am trying to ease Bioconda recipes writers for Bioconductor packages.
The issue at hand is determining dependencies limits when one of the
packages that you depend on changes its public interface.

Up to now I admit that I did not fix my packages deps (adding a pin to a >=
version of them) when this happened and I think that the same happens to
many other packages. I was thinking about how this could be managed
automagically: parsing/processing the svn logs could be an option?

Thanks,
E.
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Nitesh Turaga

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Could you tell me more about which package you are trying to wrap a recipe
for?

Right now my packages: the recipes are working, but the helper skeleton
script that create dependencies gets them from DESCRIPTION and if lower
limits for version are not there it cannot infer them.

And could you give me an example for what you mean by " determining
dependencies limits when one of the packages that you depend on changes
its public interface." ?

Package A depends on package B. Versions 1.0.0 of both packages work well
together. In version 1.2.0 package B changes something that A uses, so A
adapts to this change in 1.2.0, if this is not reflected in the DESCRIPTION
with
a pin on B version >=1.2.0 the corresponding bioconda packages could not
fit well together (imagine someone with B version 1.0.0 and A version
1.2.0).
Bioconda developers are reasoning on a way to annotate bioc version, this
should fix the issue without any work needed on single packages versions.

E.

Bioconda developers are reasoning on a way to annotate bioc version, this
should fix the issue without any work needed on single packages versions.

You need this; your current approach will not work.  You cannot assume that
package authors make this dependency information explicit, although they
sometimes do.

Best,
Kasper