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. > > > 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
