[Fedora-r-devel-list] Bioconductor in Fedora

[Pierre-Yves]

Pierre-Yves wrote:
> Alex Lancaster wrote:
>> This is just a heads-up about packaging of Bioconductor.  
> 
> This last email was some time ago and the situation evolved a bit.
<snip />
> * The list of packages to do in order to have the main packages of 
> Bioconductor is (I expect, I have not checked yet) around 60 to 70.
> I can maintain some but I don't want to do all myself, especially since 
> my situation might change quite a bit in January.
> Creating the specfile is not hard, here is a small python script that 
> helps to generate the specfile [1]
> Maintaining those packages is not really difficult, there is 1 release 
> every 6 month (for each major release of R).
> I developed a small python script [2] that handle most of the work, I 
> still have some ideas to improve it (I want to really personalize it for 
> Bioconductor packages).


I have been looking a bit at the dependencies question.
There is 20 main libraries of Bioconductor  (based on what the biocLite 
script install by default). The list is presented here
https://fedoraproject.org/wiki/Features/Bioconductor#Scope

With the help of Torbjorn on #R (irc.freenode.net) I modified a small 
perl script[1] that goes on the bioconductor SVN and for each packages 
retrieve both the depends and suggests dependencies.
The results is available here:
http://pingou.fedorapeople.org/Bioconductor/Dependencies2
To compare with
http://pingou.fedorapeople.org/Bioconductor/Dependencies
When there is only the Depends taken into account.

 From that list I used this script[2] to process the dependencies and 
sub-dependencies that we would need to package.
The results are presented here:
Depends+Suggests:
http://pingou.fedorapeople.org/Bioconductor/Dependencies-Depends_Suggests.txt
Depends only:
http://pingou.fedorapeople.org/Bioconductor/Depedencies-Depends.txt

The number of libraries to package jump from 36 to 75 if we take into 
account the Suggests dependencies.
This only takes into account the dependencies of the software part of 
Bioconductor, the libraries called 'metadata' or 'experiment data' which 
I believe can also have sub-dependencies are not presented here.

This can give us some insight on where to start.
However I would like to know what you, guys, think of the question 
dependencies "Depends" vs "Depends+Suggests".
"Suggests" add more work and leads to the problem of circular references 
quite often...

I have not heard from you about the global idea, do you 
like/appreciate/don't care about it ? (cross out the wrong option)

Regards,

Pierre


[1] http://pingou.fedorapeople.org/Bioconductor/bio.pl
[2] http://pingou.fedorapeople.org/Bioconductor/showDep_1.1.py