[pkg-bioc] what's up?

[Dirk Eddelbuettel]

Howdy,

Quick/short reply as I'm about to go running ...

On 17 March 2005 at 10:47, Egon Willighagen wrote:
| I've added a section for packages in Debian. Should we skip creating *all* 
| packages in Debian, or still try to get them to build with the new script?

In theory it should be "all" ...

| Anyway, I've now set up a section in the script for those which fail and which 
| are already in Debian:
| 
| ## packages which are already in Debian, and which fails with the current 
| script.
| my @alreadyindebian = (
|   "its",        ## in Debian as r-cran-its
|   "rsprng",     ##              r-cran-rsprng
| );

... so this is the Right Thing as it minimized the exception list.  Mind you,
with building all the Debian r-cran-* packages too, we may have to work
harder again on initial Build-Depends (e.g. recommended packages,
Design/Hmisc, ...) 

| > | The can't-build set is not that large:
| > |
| > | my @cannotbuild = ("genetics",   ## depends on 'gdata' which is not on
| > | CRAN
| >
| > Maybe it is in BioC?
| 
| Have to check. What's the status of the bioc2deb.pl script?

Needs work :)

[...]
 
| > | - caching of the ChangeLog's
| >
| > As flat files?  More funky?  Do you want to prototype something?
| 
| Flat files... What I need to figure out is:
| 
| - where in cran2deb.pl the ChangeLog is created

It is in the corresponding CRAN2DEB.pm, I believe, and it is real simple ...

| - add detection of a cached ChangeLog there
| - detect wether it's a debian -(n+1) release or a new upstream release

... as this is treated as always Debian --- ie. -1  for now.

| - have his append to the cache

[...]

| > That is the best I could do in a quick job with Perl. Better Perl wizardry
| > welcome.  It;s difficult, though, as the DESCRIPTION format it not enforced
| > by CRAN.  What is done here is done via a smart Perl formatting heuristic.
| > I think we'd waste out time trying to better that.
| 
| I'll see if I have make a simple patch to at least remove the spurious periods 
| on empty lines. (Should not be that difficult...)

[...]

| What's DSC2005? A google showed a conference on transport simulation... ??

Distributed Scientific Computing -- that was the main R conference in Vienna
in 1999, 2001, 2003 based on some funding the Vienna people have. Now same
name and R, BioC, Omegahat... focus but in Vienna.  There is one short
announcement by Thomas Lumley on r-devel. For the older conference, google
for "DSC $year Hornik".

Cheers, Dirk

-- 
Better to have an approximate answer to the right question than a precise 
answer to the wrong question.  --  John Tukey as quoted by John Chambers