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.st...@gene.com <mailto:lianoglou.st...@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.s...@gmail.com <mailto:avinash.s...@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 <mtmor...@fredhutch.org <mailto:mtmor...@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 <dtene...@fredhutch.org <mailto:dtene...@fredhutch.org>> >>> wrote: >>> >>> See my comments below. >>>> >>>> ----- Original Message ----- >>>> >>>>> From: "avinash sahu" <avinash.s...@gmail.com <mailto:avinash.s...@gmail.com>> >>>>> To: "Karim Mezhoud" <kmezh...@gmail.com <mailto:kmezh...@gmail.com>> >>>>> Cc: bioc-devel@r-project.org <mailto:bioc-devel@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 <kmezh...@gmail.com <mailto:kmezh...@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.s...@gmail.com <mailto:avinash.s...@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@r-project.org <mailto:Bioc-devel@r-project.org> mailing list >>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>> [[alternative HTML version deleted]] >>>>> >>>>> _______________________________________________ >>>>> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list >>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>>>> >>>>> >>>> >>> Regards >>> Avi >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioc-devel@r-project.org <mailto:Bioc-devel@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@r-project.org <mailto:Bioc-devel@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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
