[pkg-bioc] how to proceed?

[Egon Willighagen]

On Wednesday 23 February 2005 03:09 am, Dirk Eddelbuettel wrote:
> On 22 February 2005 at 10:29, Egon Willighagen wrote:
> | > | 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..
>
> Agreed, but let's start with a simple config file first. The db will make a
> nice entry on the TODO list.

Agreed.

> | > 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?
>
> A textfile, yes, I suppose.

Sure. Let's set that up.

> | > | - 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...
>
> I think I reported and abort on purpose as there is some implicit sorting
> going on. I.e. it first builds packages with no depends, then packages with
> simple depends and so on.  So whenever it fails, fix the cause, restart and
> it pretty whizzes up to the point where it failed and continues.

Yes, you explained about the sorting.

> That way, with a few re-starts (but many, many build depends inflating my
> system) I got to build the 400-some packages.

When was that?

> | 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...
>
> Yes, it always grows.
>
> | > | 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...
>
> I guess we all have real jobs and other projects going.

Indeed.

> | 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...
>
> Just a new stateful directory "changelogs", preserved in CVS?  This may
> also leads to patches.

Sounds good.

> | And a question: how is a new upstream release detected, versus a debian
> | release, like -2, -3, etc I mean?
>
> See the Debian Policy and/or Developer Reference manuals. It's all in
> there.

I think I was not clear enough... I meant, what tools (perl scripts, etc) do 
we have available and maybe already used in the cran2deb.pl to detect wether
it should make a new upstream release, or a debian subrelease...

> | I've not looked at the debs yet. So no idea about the quality... More
> | later.
>
> Do "$ apt-get install lintian" and call lintian at the end of each built.
> Lintian *is* your friend.

Anyone tried linda already for this?

> Keep up the excellent work, Dirk

Egon