Thanks for taking the time to reply, James.
I was confused by the fact that R 3.3.3 was released a few weeks ago and I was thinking that was previously the R-devel… meaning the R version you’re supposed to develop against would have just changed a few weeks ago. I re-read the sentence “R has a ‘.y’ release in x.y.z every year” and now it makes sense. The confusing was due to my misreading. Thanks for the clarification of how the git/subversion branches work as well. Best, Nick ————————————————————————————Nicholas Clark Graduate Research Assistant Laboratory for Statistical Genomics and Systems Biology University of Cincinnati > On Mar 20, 2017, at 10:58 AM, James W. MacDonald <jmac...@uw.edu> wrote: > > > > > On Fri, Mar 17, 2017 at 3:45 PM, Nicholas Clark <nicholas.clar...@gmail.com >>wrote: >> I’m planning on adding some new features to my package (GRmetrics) before >> this upcoming release and I have a few development questions. >> >> >> 1) Which version of R should I be using? I looked at this page >> (http://bioconductor.org/developers/how-to/useDevel/ >> >> >> ), but I was still confused as to whether I should use the recently released >> R 3.3.3 or the R-devel 3.4.0 at http://r.research.att.com/ >> > > For the spring release you should use R-devel. For the fall release you > should use the most current version of R. This is because we release twice a > year, but R is only released in spring. > > > Looking at the useDevel page I see that I am simply repeating (almost > verbatim) what is written there. Is there something unclear about this that > we should address? It seems clear enough to me, but I've been doing this a > long time. > > >> >> . >> >> >> 2) What is the best/easiest way to work with github? Should I fork the >> repository from the read-only Bioconductor repo and work on that or maintain >> a separate repo? Or does it not matter? >> > > I believe you should fork the repo from the Bioconductor mirror and use that. > There is some info here > (http://bioconductor.org/developers/how-to/git-mirrors/ > ). But there are some considerations to be made. Right now, we are using > subversion for version control, and anything you do in github has to be > 'subversionized' in order for your commits to be checked into the main > version control repository. It's far easier IMO to just use subversion to do > all your version control, because you don't have to worry about getting git > to talk to subversion. > > > That said, after the April release we are transitioning to git, so we will be > using git soon enough. But for now I am still using SVN because it's a direct > commit to the main repo. My advice is to use whatever the main repo is based > on, because mixing and matching adds an extra level of complexity that > doesn't appear to have much to offer in return. > > >> >> >> 3) Should I make a “release-3.5” branch and commit changes there, or should >> it be “devel”, or just the “master” branch? >> http://bioconductor.org/developers/how-to/git-mirrors/ >> >> >> >> talks about this, but again, it’s not clear to me. >> > > You never make your own branches. That's controlled by BioC core. Unless you > are fixing a bug in the release version of your package you should be using > the master branch (or if you use SVN, you should just be checking out of the > trunk, https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GRmetrics > ). > > >> >> >> 4) It looks like my package is failing the Windows build because it requires >> “SummarizedExperiment”, which is failing the Windows build. Is there >> anything I can do to fix this? Apologies if this has already been addressed. >> The error is: ERROR: dependency ‘SummarizedExperiment’ is not available for >> package ‘GRmetrics' >> (http://bioconductor.org/checkResults/release/bioc-LATEST/GRmetrics/tokay1-buildsrc.html >> >> >> >> >> ) >> >> > > If one of your dependencies is failing, and in particular if the dependency > is maintained by Bioc core, then the best thing to do is wait. If you are > relying on somebody else's package and they are consistently failing you > might contact them and find out if you can help. > > > Jim > > > > >> >> >> Best, >> Nick Clark >> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.org >> mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> >> > > > > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
