[Bioc-devel] Package submission with library requirement
Dan Tenenbaum
dtenenba at fredhutch.org
Fri Jan 23 19:58:33 CET 2015
----- Original Message -----
> From: "Martin Morgan" <mtmorgan at fredhutch.org>
> To: "avinash sahu" <avinash.sahu at gmail.com>, "Steve Lianoglou" <lianoglou.steve at gene.com>
> Cc: bioc-devel at r-project.org
> Sent: Friday, January 23, 2015 10:52:32 AM
> Subject: Re: [Bioc-devel] Package submission with library requirement
>
> On 01/21/2015 11:16 AM, avinash sahu wrote:
> > 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?
>
> yes, provided the license of the library allows for it, it is a good
> solution.
> There is guidance in RShowDoc("R-exts") on acknowledging this in the
> DESCRIPTION (and possibly LICENSE) file.
>
However, you should consider using Rlecuyer as it has no external dependencies (see Levi's post to this thread). Then your package should build on windows.
Dan
> Martin
>
> > thanks
> > avi
> > On Wed, Jan 21, 2015 at 7:57 PM, Steve Lianoglou
> > <lianoglou.steve at gene.com
> > <mailto: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
> > <mailto: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
> > <mailto: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
> > <mailto:dtenenba at fredhutch.org>>
> > >>> wrote:
> > >>>
> > >>> See my comments below.
> > >>>>
> > >>>> ----- Original Message -----
> > >>>>
> > >>>>> From: "avinash sahu" <avinash.sahu at gmail.com
> > <mailto:avinash.sahu at gmail.com>>
> > >>>>> To: "Karim Mezhoud" <kmezhoud at gmail.com
> > >>>>> <mailto:kmezhoud at gmail.com>>
> > >>>>> Cc: bioc-devel at r-project.org
> > >>>>> <mailto: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
> > <mailto: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
> > >>>>>> <mailto: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
> > >>>>>>> <mailto: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
> > >>>>> <mailto: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 <mailto: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 <tel:%28206%29%20667-2793>
> > >>
> > >
> > > [[alternative HTML version deleted]]
> > >
> > > _______________________________________________
> > > Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>
> > > mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> >
> >
> > --
> > Steve Lianoglou
> > Computational Biologist
> > Genentech
> >
> >
>
>
> --
> 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
>
> _______________________________________________
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