[pkg-bioc] State of BioC compilations

[Dirk Eddelbuettel]

On 9 February 2007 at 16:09, Steffen Moeller wrote:
| If you check out the patches directory then you will see that this is all I 
| patched:
| 
| --- biobase-1.13.36/R/strings.R 2007-02-02 10:28:39.000000000 +0100
| +++ biobase-1.13.36/R/strings.R 2007-02-08 11:12:04.000000000 +0100
| @@ -37,7 +37,7 @@
|          ## The +1 and +2 are because substr is funny
|         ss = substr(x, nc - i + 1, nc)
|         if( any(ss != ss[1] )) {
| -           if (i == 1L)                 # trailing char mismatch
| +           if (i == 1)                 # trailing char mismatch
|               return("")
|             return(substr(x[1], nc - i + 2, nc))
|         }
| 
| It is supposed to be plain R code.

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 ...

| 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?

| > Both CRAN and BioC also get too big, so we should have 'Debian task views'
| > (better term suggestions welcomes) that cover subareas.
| 
| BioC procides groups already. We could adapt them for debtags.

Yup, that's what I thought. Same with CRAN task views which could suit as well.
 
| > Not bad!  54 down, 900 at CRAN to go :)
| 
| 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.

and the code looks somewhat scary around lines 762 et al.

Dirk

-- 
Hell, there are no rules here - we're trying to accomplish something. 
                                                  -- Thomas A. Edison