[pkg-bioc] what's up?

[Egon Willighagen]

On Tuesday 15 March 2005 03:04 pm, Egon Willighagen wrote:
> I'm back from vacation, and started up creating amd64 debs for CRAN
> packages again. You might have seen the commits to Alioth...
>
> After 276+ build debs, I found that most actually compile... 

Done. 448 debs build for CRAN with the script in CVS (v1.9).

The can't-build set is not that large:

my @cannotbuild = ("genetics",   ## depends on 'gdata' which is not on CRAN
                   "its",        ## fails with: Error in loadNamespace(name) : 
There is no package called 'its'
                   "LDheatmap",  ## depends on genetics which cannot be build
                   "mimR",
                   "r.matlab",   ## problems defining the dependency... it 
complains about the '.' in the name
                   "RmSQL", "ROracle",
                   "RSQLite",    ## has some Windows libs that trip lintian up
                   "RScaLAPACK", ## need to sort -dev packages out
                   "rsprng",     ## need to figure out why this fails
                   "RNetCDF",    ## doesn't find netcdf in /usr
                   "SciViews",   ## depends on tcltk but is not on CRAN
                   "seao",       ## fails with Lintian warning: W: seao 
source: maintainer-upload-has-incorrect-version-number 0.2.1-0.r2d.1; W: seao 
source: binary-nmu-debian-revision-in-source 0.2.1-0.r2d.1
                   "seao.gui",   ## depends on seao
                   "spdep",      ## fails with: Error in .DESC[["Package"]] : 
subscript out of bounds
                   "survey",     ## fails with: Error in open.connection(con, 
"rb") : unable to open connection
                   "udunits",    ## dep=udunits not in Debian
                   "uroot",      ## depends on tcltk but is not on CRAN
                   "IDPmisc",    ## fails with: Error in loadNamespace(name) : 
There is no package called 'IDPmisc'
                   ## BioC: can't do annaffy as we lack GO and KEGG data pkgs
                   "annaffy",
                   ## the next list of packages is mentioned in CRAN's 
Description subdir
                   ## but the tar.gz is not on CRAN. Dates for last test are 
behind package name
                   "gmp",        ## 2005-02-21
                   "boa",        ## 2005-02-21
);

my @cannotbuildamd64 = ("rpvm",        ## fails 
with: /usr/bin/ld: /usr/lib/gcc-lib/x86_64-linux/3.3.5/../../../../lib64/libgpvm3.a(pvmgsu_core.o): 
relocation R_X86_64_32 can not be used when making a shared object; recompile 
with -fPIC
                        "rgl",         ## fails with: 
usr/bin/ld: /usr/X11R6/lib/libGL.a(glapi.o): relocation R_X86_64_32 can not 
be used when making a shared object; recompile with -fPIC
);

I've not looked into these problems.

Ok, what remains to be done before actual setting up a repository?
- bugs db on Alioth?
- caching of the ChangeLog's

For the rest, it seems that the script is doing quite a good job!

Some minor issues:

1. the descriptions has too many '.'s... e.g.:

Description: GNU R package "R Based Genetic Algorithm"
 R based genetic algorithm for binary and floating pointchromosomes.
 .
 Author(s): Egon Willighagen <e.willighagen@science.ru.nl>
 Date: 2005-03-15
 .

2. Maintainer: Dirk Eddelbuettel <edd@debian.org>

Which should probably now say something like:

Maintainer: Alioth collborative packaging for CRAN and Bioconductor 
<pkg-bioc-devel@lists.alioth.debian.org>

Egon