Dear Bioconductor team :

I aware that deadline for new package submission is approaching, and I have few doubt with it. I am new with bioinformatics field and I did my very first step to develop bioconductor packages according to my project requirement. So far, development of all custom function is fairly done, checking whole R script and testing function is ongoing. I've followed package guideline on bioconductor site. However, Now I am following package submission part which provided on the site, and stick with this steps. 

These are my doubt need to find answer :

firstly, I have difficulty to do peer review because no one familiar with bioconductor software development in our lab. I have deployed all source code on github and really need to find experienced programmer to review my code and give comment on that.In this way, I can facilitate package submission process. Please help

secondly, this is my very first time to develop bioconductor packages, I am bit of confused how to generate documentation in desired way, writing trial package manual for this new package submission. I aware that knitr packages can automatically generate documentation, but I am not familiar with it. How can I make writing package documentation easier?  Any recourse that I can refer to or learn? 

thirdly, what if my package has building error, or unexpected bug (assume few failed R CMD check happens), is that possible to submit my packages ? what's the efficient solution to fix this ? How can I facilitate package submission process ? I can't say my package will build successfully in my first attempt, so there must be a lot of things to do and learn. Package submission is the only way that I can finalize my projects and work on future version of this packages. Any advise is appreciated.

Because of the deadline of package submission is ahead, I don't know what should I do now. I don't want to miss this deadline and give to try for my very first package submission. Please help me out. Thanks your effort and contribution.

All the best :

Jurat

Questions about package development should be on the 'bioc-devel' mailing list.

It is good to find someone to look at your package. At the very least get colleagues to 'use' it; they will surely have trouble (experienced package authors will tell you the value of having people use the software).

There are two popular ways of writing R 'help' pages. The original approach is described in the reference document 'Writing R Extensions' chapter 2. The other common way to write documentation is using the rmarkdown2 package, typically in conjunction with the devtools package; a good introduction is the chapter in Hadley Wickham's "R Packages" book. Both Writing R Extensions and R Packages are worth reading carefully and completely.

If you submit your package and it fails to pass R CMD build / R CMD check R CMD BiocCheck, then the reviewer will wait until you fix the issues and it does pass R CMD build, etc. So you might as well fix things up first, and then submit. Remember, you can run these functions on your own package, so there is no reason to be 'surprised' when Bioconductor runs the tests (well, a common problem is that people use the release or old version of Bioconductor, rather than the devel version).

Please also consider carefully whether your package is ready for Bioconductor. It does not do you or the project any favors to make available a package that in a too preliminary form.