[pkg-bioc] State of BioC compilations

[Steffen Moeller]

On Saturday 10 February 2007 04:42:22 Dirk Eddelbuettel wrote:
> On 9 February 2007 at 16:09, Steffen Moeller wrote:

> Agreed. (But I see that your downloads set "Rversion=2.5" so maybe this
> opens the door to some changes we don't have in 2.4.1 ...

I got to that conclusion, too. I do not know why I thought we'd be running R 
2.5 in unstable :-/ 

> | Sorry, I meant the order at which the packages' .tar.gz files are
> | unpackage and dpkg-buildpackage is called. The detection of missing
> | installs by dpkg-buildpackage is perfectly fine ... but that is too late
> | and ends the build process.
>
> I'm still confused. When? Where? What?

With the --ignore option added such that the script does not die on errors, it 
is no longer too bad. However when I have B depend on A and C depend on A, 
then the build order should be A,B,C, or A,C,B, not anything else. I'd then 
go for a sudo dpkg -i for the fresh packages that have dependencies. Now I 
basically need to run the script multiple times. 

> | > Not bad!  54 down, 900 at CRAN to go :)
../bioc$ ls builds/r-bioc-*|cut -f1 -d_| sort|uniq|wc -l
88
../cran$ ls builds/r-cran-*|cut -f1 -d_| sort|uniq|wc -l
448

We go the more essential ones now as Debian packagse. The problem that I had 
reported on the graph library was due to my local R_LIBS env setting ... :-/

> | Some are already done. We'd now need a repository. We once had the OK to
> | use Alioth for that. Though I presume we should not go such public before
> | having improved on our automisation a bit.
>
> I want to see several weeks of sustained builds to the level that, say, Uwe
> Ligges does for Windoze before I go "public".
>
> I tried some builds following the recipe at
> http://wiki.debian.org/DebianBIOC but no luck. 'cran2deb bioc' dies trying
> to get the meta-information. It ends on
>
> [...]
> Patterns are determined for bioc
> Could not open description file at 'html/Biostrings.html'
> Could not open description file at 'sources/../html/Biostrings.html'
> print() on closed filehandle FILE at ./cran2deb.pl line 762, <PIPE> line
> 82. readline() on closed filehandle FILE at ./cran2deb.pl line 785.
> Undefined subroutine &main::lowerCase called at ./cran2deb.pl line 812.
This does not happen for me. The "Could not open" reports are much reduced 
once you have downloaded them once.

> and the code looks somewhat scary around lines 762 et al.
It _is_ scary. I took one "buh!" off the code, still frightening, though.

I'll look through the Wiki-based instructions another time.

The download script needs to be going for all packages rather than only the 
lite. For tilingArray I need r-cran-pixmap which does not work for me. The 
rcurl packages I found only with Omegahat. I played with something close to 
supporting them in the script, but not seriously.

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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