[Bioc-devel] Package submission with library requirement

Martin Morgan mtmorgan at fredhutch.org
Fri Jan 23 19:52:32 CET 2015


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.

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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