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.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> > 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> > > 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 > > > >>> wrote: > >>> > >>> See my comments below. > >>>> > >>>> ----- Original Message ----- > >>>> > >>>>> From: "avinash sahu" <avinash.s...@gmail.com> > >>>>> To: "Karim Mezhoud" <kmezh...@gmail.com> > >>>>> Cc: 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> > >>>>> 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> > >>>>>> 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 mailing list > >>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel > >>>>>>> > >>>>>>> > >>>>>> > >>>>>> > >>>>> [[alternative HTML version deleted]] > >>>>> > >>>>> _______________________________________________ > >>>>> 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 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@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > -- > Steve Lianoglou > Computational Biologist > Genentech > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
