[Bioc-devel] Package submission with library requirement

[avinash sahu]

Hi Dan,

Thanks for the reply and quick support. I am sorry for so many issues, I am
somewhat novice in bioconductor.  I am replying to your comments inline.


On Wed, Jan 21, 2015 at 6:55 PM, Dan Tenenbaum <dtenenba at fredhutch.org>
wrote:

> 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?
>

Little bit of background first. GOAL is package, that will be a
accompanying software for the manuscript that we are submitting to nature
methods, so I would like to be as user friendly as possible. I spend couple
of days to compile the package in Windows, however it is getting stuck
because it uses Rcpp libraries along with third party libraries from other
packages. I tried to get help from Windows regular user but it need someone
expert in Windows OS to make it work. And I am no longer user of  Windows
so completely novice in it.

>
> > 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.
>
> I clarified in my dependencies that it requires ransampl and GSL.  In
addition I added details in README about installation instruction of those
libraries.

>
>
> > 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]]
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>

Regards
Avi

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