[Bioc-devel] DMRcate: TIMEOUT

2017-05-30 Thread Tim Peters
Hi bioc, Recently, under R/3.4.0, the newest version of DMRcate is taking 47mins to build on my local machine and I am getting TIMEOUTs on the build on the checkResults page http://master.bioconductor.org/checkResults/3.5/bioc-LATEST/DMRcate/malbec2-buildsrc.html. I have not made any changes

[Bioc-devel] Survey results: How and why CRAN and Bioconductor developers handle breaking changes differently

2017-05-30 Thread Chris Bogart
As promised,here are the results: of the survey about breaking changes we ran last fall: http://breakingapis.org/survey/ The R ecosystem stood out in some interesting ways; for example package authors in CRAN and Bioconductor are more likely than other ecosystemsto get personally contacted

Re: [Bioc-devel] Git Transition Plan

2017-05-30 Thread Nathan Sheffield
Hi Nitesh and all, Can you give any status update on the SVN-to-git transition? I haven't seen any news since this exchange in March -- is the announced public beta in progress or ongoing? Are new package submissions going straight into git at this point? Or did I miss something? Thanks,

Re: [Bioc-devel] DataFrame errors with a Surv class column

2017-05-30 Thread Michael Lawrence
tail() is broken for Surv objects, because despite Surv objects exposing their implementation as matrices (probably a bad decision), they do not inherit from class "matrix". One option is to make length.Surv return the number of elements (rows in the matrix) instead of the number of cells, but who