[Bioc-devel] Package submission with library requirement

Yes. I tried R internal libraries for random number generator also those
provided by Rcpp but they are were not thread safe so it with
multi-threading. I can try using other libraries, if anyone know random
generator that are thread safe and not slow.

thanks
avi

On Wed, Jan 21, 2015 at 7:38 PM, Martin Morgan <mtmorgan at fredhutch.org>
wrote:

On 01/21/2015 10:17 AM, avinash sahu wrote:

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.

have you thought carefully about the need for third-party libraries? For
instance, R has extensive random number facilities, and these are available
at the C level. This is documented in section 6 of RShowDoc("R-exts")

Martin

 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/package?guidelines/

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/how?to/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

   ?__
  c/ /'_;~~~~kmezhoud
(*) \(*)   ?????  ??????
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

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Regards
Avi

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