[pkg-bioc] Questions before breaking everything...

[Steffen Moeller]

On Wednesday 27 June 2007 00:02:20 Dirk Eddelbuettel wrote:
> On 26 June 2007 at 23:30, Steffen Moeller wrote:
> | On Tuesday 26 June 2007 03:41:36 Dirk Eddelbuettel wrote:
> | > Steffen,
> | >
> | > On 25 June 2007 at 10:06, Steffen Moeller wrote:
> | > | leaves the remainder intact. However, the untaring of a complete
> | > | system for every package, I think we can agree here, is not elegant
> | > | with respect to the utilisation of our resources. It may appear to be
> | > | required for complete security, but it is not elegant.
> | >
> | > Well but recall that basically every Debian package gets built that
> | > way. 10,000 source packages can't be wrong :)
> |
> | I better do not sign this email, but I really thought there was a mere
> | deinstallation by the buildds. Otherwise the deinstallation would be only
> | for extra security, but for that, only the just created deb would have to
> | be installed which it never is. This is how I interpreted the logs like
> | these:
> | http://experimental.ftbfs.de/fetch.php?&pkg=gammu&ver=1.05.00-4&arch=kfre
> |ebsd-i386&stamp=1143988918&file=log&as=raw
> |
> | So, in the end, is it a buildd that we really want?
> |
> | I do not know if I am kidding or not. Running cran2deb on all platforms
> | may be far easier than maintaining several buildds.
>
> pbuilder != buildd
>
> pbuilder allows you to (rather easily) build a package in a pristine
> environment that is newly created from the minimal system.
>
> AFAIK the buildd are similar, but different as they IIRC use something
> called sbuild. Doesn't matter.
>
> What appeals to David and me about the pbuilder is that it helps us to
> 'nail down' the Build-Depends. That is important for R with all the R
> Depends, LazyLoads etc pp.
>
> Now as you pointed out, there is cost in using pbuilder as the tarball
> needs to be built up, brought down, built up, ...  so I think a fair
> compromise would be to add a 'bulk' in which we will start from a fresh
> pbuilder but not bring it down after each package.
>
> How does that sound?

Great if the packages just installed are removed again. Maybe this helps:

$ dpkg --get-selections > a
$ sudo apt-get install kqemu-source
$ dpkg --get-selections > b
$ diff a b
457a458
> kqemu-source                                  install
1061a1063
> module-assistant                              install
$ sudo dpkg --purge `diff a b | grep install | awk '{print $2}'`
Reading database ... 188771 files and directories currently installed.)
Removing kqemu-source ...
Removing module-assistant ...
Purging configuration files for module-assistant ...
$ dpkg --get-selections > c
$ diff a c
$

The "a" list would be static or redone after every update of pbuilder. The "b" 
list is prepared after every build process. One could get "c" for a control 
or skip that.

Do you like that? It gets pbuilder pretty damn close to the buildds in my 
view.

Cheers,

Steffen


-- 

Dr. Steffen Möller
University of Lübeck
Institute for Neuro- and Bioinformatics
Ratzeburger Allee 160
23538 Lübeck
Germany
T: +49 451 500 5504
F: +49 451 500 5502
moeller at inb.uni-luebeck.de
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