[pkg-bioc] how to proceed?

[Egon Willighagen]

On Monday 21 February 2005 23:25, Dirk Eddelbuettel wrote:
> | 3. also added a section to can't build for package problems on CRAN
> |   e.g gmp is mentioned in Descriptions/ but the tar.gz is missing on CRAN
> |   others that seem to suffer from similar issues are: boa, mnp
>
> Way have been a temporary mirror glitch. I follow the page (in its
> time-sorted display):
>  http://cran.r-project.org/src/contrib/?M=D
> and all of these were recently updates.
>
> If they don't show up, maybe time to switch CRAN mirrors and tell
> cran@r-project.org?

Umm... yes, once one I know what exactly is going on, I'll report with CRAN...

> | The last should be reported to CRAN, but I don't have time today/tomorrow
> | to explore these things.
> |
> | Dirk, packages with src/ seems to be nicely detected as non all... and
> | compiling to binary code has not given problems on amd64 sofar...
>
> Awesome. And nice to detect my hardcoded i386 -- there will be more
> shortcuts like that. We just need to test, test, test.

Sofar, I basically only need to add the '--binarch' option... no real trouble 
with other hard coded stuff...

> | There are a few things that I think should be done:
> | - split build/no-build, dependency, etc info into separate files
>
> I'm lost. What do you mean?  The config into at the top? In that case Yes!!

I was actually thinking not at the top, but in a separate file... or database 
as you suggest..

> I was even thinking about a SQLite database (Perl and R can easily talk to
> SQLite).

I don't have experience with SQLite... how would we add information to that? 
Could we share the database in CVS?

> | - changelog should indeed be cached in some way... so that we can keep
> | track of what gets released
> | - there seems to be too many dots in the description in debian/control
> |
> | Again, haven't had time to explore these in much detail... take all this
> | as first experiences... btw, has anyone yet been able to run the
> | cran2deb.pl fully successfully?
>
> I'm lost again -- how much did you run it?  It sounds like you did a full
> load. Is that true?  

Yes, working on that.

> Did it all pass, i.e. the script finished? 

No. Since the deps were not all installed, and there were other problems, I 
have to restart the whole process now and then... we should adapt the .pl 
script to *not* stop when a build fails... and just report what failed...

Anyway, things are progressing. Not sure how far it went... 75 packages build 
sofar... including the genalg package I contributed to CRAN :) There seem to 
be 450 tar.gz...

> | PS. will be offline tomorrow.
>
> No problem.
>
> Thanks again for all this.

If we all contribute our bits, it should not be that difficult to have this 
going in a few months... It's a side/side/side thingy for me. Busy with last 
year of PhD, and working in spare time on open source projects, like Jmol, 
JChemPaint and CDK (http://[jmol|jchempaint|cdk].sf.net), so I might be quiet 
now and then... but I think that there is enough critical mass to get 
momentum...

There is something I 'worry' about at this moment:

people will start filing bugs at Alioth and we need to be able to close them 
and add this info to the ChangeLog... so, I think, we really need to find a 
way to preserve the changelogs... 

And a question: how is a new upstream release detected, versus a debian 
release, like -2, -3, etc I mean?

I've not looked at the debs yet. So no idea about the quality... More later.

Egon

-- 
e.willighagen@science.ru.nl
PhD student on Molecular Representation in Chemometrics
Radboud University Nijmegen
http://www.cac.science.ru.nl/people/egonw/
GPG: 1024D/D6336BA6