[pkg-bioc] My first steps with cran2deb.pl

[Frederic Lehobey]

Hi,

On Mon, Dec 12, 2005 at 09:19:54PM -0600, Dirk Eddelbuettel wrote:
> On 12 December 2005 at 15:23, Frederic Lehobey wrote:
> | > I can add you to pkg-bioc on alioth.
> | 
> | Thanks. My alioth id is `fdl-guest'.
> 
> You're now part of the group. Welcome aboard!

Thanks.

> | Well.  Actually, not.  At the time of writing cvsweb on alioth was not
> | working there:
> | http://cvs.alioth.debian.org/cgi-bin/cvsweb.cgi?cvsroot=pkg-bioc
> 
> It seems to be working now. Report back if it still fails for you, and check

Actually it seems it is a bug in the konqueror of sarge (works with
everything else I have tried after that.)

> the list archives for some rudimentary help / background on the script,
> and/or ask here.

I have read the archives.  Here are a few questions and some
feedback.

First cran2deb.pl is a pretty impressive script and I am still in the
process of understanding how it works in details.

I have successfully completed a complete run of it on the i386, sparc
and powerpc architectures (running sid).  kfreebsd-i386 is in progress
(on a slow machine).

I have updated http://wiki.debian.org/DebianCRAN accordingly (work
still in progress at the time of writing).

Here are my questions:

1/ I have noticed some of the packages in CRAN that are automagically
built by the script are actually already in the official Debian
archive.  What is the goal for them (ultimately)?  Having them built
by the script or being blacklisted from it one way or another.  In
other words, is it interesting to keep and track their status with
respect to automatic build?

2/ How am I supposed to deal with dependencies between newly built
CRAN packages?  More precisely, if the necessary dependencies stated
on http://wiki.debian.org/DebianCRAN are available in the build
environment (from the Debian archive), then a huge list of CRAN
packages can be built.  However, some of the failing ones (at first
pass) simply need that some of the newly built packages be added to
the build environment.  What it the proper way to do it?  Install them
`by hand' with dpkg -i?

3/ Some failures are architecture dependent (mostly endianness
problems for powerpc and sparc according to error messages).  How to
deal with that?  Setup some exclusion mechanism similar to
`cannotbuildamd64'?  (Then, there will be as many variables as
architectures.)

4/ No progress so far with BIOC.  I have failed to find anything in
the http://www.bioconductor.org/packages/bioc/devel/src/contrib/html/
directory stated by http://wiki.debian.org/DebianBIOC .  I have not
found any proper newer location.

5/ I have noticed the following warning when installing the built
packages (and some of the packages already in sid):

Ignoring deprecated option --htmllists called from postinst or postrm script.

I have not yet searched its origin.


Best regards,
Frederic
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