[Bioc-devel] developing R package for new release

[Nicholas Clark]

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 <jmacdon at uw.edu> wrote:
> 
> 
> 
> 
> On Fri, Mar 17, 2017 at 3:45 PM, Nicholas Clark <nicholas.clark00 at 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.
>  
> 
>> 
>> .
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>> 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.
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>> 
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>> 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/
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>>  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
> ).
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> 
>> 
>> 
>> 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
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>> 
>> 
>> )
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> 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.
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> 
> Jim
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> 
>> 
>> 
>> Best,
>> Nick Clark
>> 
>> 
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> 
> -- 
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
> 
> 

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