[Bioc-devel] Package submission with library requirement

avinash sahu avinash.sahu at gmail.com
Wed Jan 21 20:16:28 CET 2015 

Both the libraries are not thread safe. Although boost random genrator in
limited situation can be thread safe. I have tried them earlier they were
failing with multi-threading.
One way out might be, if I include the source code of ransampl with package
source code. There license allows this,  I can also mail ask the developer
of Ransampl about the permission.
Will this be acceptable to bioconductor folks?
thanks
avi
On Wed, Jan 21, 2015 at 7:57 PM, Steve Lianoglou <lianoglou.steve at gene.com>
wrote:

> Does the boost RNGs qualify?
>
> He's a vignette showing how to use them through R/Rcpp
>
>   http://gallery.rcpp.org/articles/timing-normal-rngs/
>
> Boost headers are provided via the BH library:
>
>   https://github.com/eddelbuettel/bh
>
> -steve
>
>
> On Wed, Jan 21, 2015 at 10:48 AM, avinash sahu <avinash.sahu at gmail.com>
> wrote:
> > 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/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
> >>>
> >>>         [[alternative HTML version deleted]]
> >>>
> >>> _______________________________________________
> >>> Bioc-devel at r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>
> >>>
> >>
> >> --
> >> Computational Biology / Fred Hutchinson Cancer Research Center
> >> 1100 Fairview Ave. N.
> >> PO Box 19024 Seattle, WA 98109
> >>
> >> Location: Arnold Building M1 B861
> >> Phone: (206) 667-2793
> >>
> >
> >         [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>
> --
> Steve Lianoglou
> Computational Biologist
> Genentech
>

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