[Bioc-devel] Package submission with library requirement

[Dan Tenenbaum]

See my comments below.

----- Original Message -----
> From: "avinash sahu" <avinash.sahu at gmail.com>
> To: "Karim Mezhoud" <kmezhoud at gmail.com>
> Cc: bioc-devel at r-project.org
> Sent: Wednesday, January 21, 2015 7:50:38 AM
> Subject: Re: [Bioc-devel] Package submission with library requirement
> 
> Thanks for mail Karim.
> 
> I have GOAL staisfies all guidelines.
> However, GOAL is not compiling in windows and because of its heavy
> computational  requirement its cannot be used with Windows.

Can you please be very specific about why the package cannot be used with windows? Wherever possible we want packages to run on all the platforms we support. Have you attempted to compile it under windows and if so, what is the problem you ran into?


> Regarding third party code, bioconductor website mentions (i.e.
> ransampl):
> "In cases where the external library is complex the author may need
> to
> supply pre-built binary versions for some platforms." How to provide
> such
> binaries for linux and Mac to bioconductor.
> 

I'm not sure you need to provide binaries for ransampl. However, can you clarify the type of dependency that your package has on ransampl and GSL?
Is the dependency build-time only? If that is the case, then users on Mac and Windows will not need to have ransampl and GSL installed, but they will if they need them at runtime.



> thanks
> avi
> 
> On Wed, Jan 21, 2015 at 2:39 PM, Karim Mezhoud <kmezhoud at gmail.com>
> wrote:
> 
> > Hi,
> >
> > Before you submit your package, please make sure that it satisfies
> > all our
> >
> > guidelines here.
> >
> > http://www.bioconductor.org/developers/package­guidelines/
> >


In the sense that Bioconductor is open source and belongs to everyone, these are 'our' guidelines, but just to be clear, Karim is not affiliated with the core team.


> > Be sure that you tested it with the appropriate version of R. To
> > work
> >
> > out which version that is, please have a look at this site here:
> >
> > http://www.bioconductor.org/developers/how­to/useDevel/
> >
> > Then use our tracking system for package submission (which can be
> >
> > found here):
> >
> > https://tracker.bioconductor.org/
> >
> > recommended video:
> > https://www.youtube.com/watch?v=QfqaK_BHebU
> >
> > Karim
> >
> >   Ô__
> >  c/ /'_;~~~~kmezhoud
> > (*) \(*)   ⴽⴰⵔⵉⵎ  ⵎⴻⵣⵀⵓⴷ
> > http://bioinformatics.tn/
> >
> >
> >
> > On Wed, Jan 21, 2015 at 2:24 PM, avinash sahu
> > <avinash.sahu at gmail.com>
> > wrote:
> >
> >> Hi all,
> >>
> >> I am trying to submit a package (https://github.com/vinash85/GOAL)
> >> in
> >> bioconductor. It requires a ransampl (
> >> http://sourceforge.net/projects/ransampl/) and gsl libraries
> >> already
> >> installed in system.
> >> The package is failing to install at automated package installer
> >> of
> >> bioconductor (
> >>
> >> http://bioconductor.org/spb_reports/GOAL_0.99.0_buildreport_20150121045701.html
> >> ).
> >> How to take care of additional Libraries?
> >>
> >> Further, the package is meant for Linux and Mac ( it is NOT
> >> currently
> >> compiling in windows). Is it possible to submit the package in
> >> pre-compiled
> >> binaries form for Mac and Linux.
> >>

I will install ransampl on our build machines (GSL is already installed).

Dan


> >> This is the first package that I am submitting to BioConductor, so
> >> I am
> >> not
> >> aware of these issues.
> >>
> >> thanks in advance
> >> avi
> >>
> >>         [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
> >> Bioc-devel at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >
> >
> 
> 	[[alternative HTML version deleted]]
> 
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