Re: [Rd] R with Array Hashes

2015-03-06 Thread Dirk Eddelbuettel
Jeff, Nice writeup and promising idea. From the gimme numbers department: - do you pass the R regression tests? - what sort of speedups do you see on which type of benchmarks? When you asked about benchmark code on Twitter, I shared the somewhat well-known (but no R ...)

[Rd] R with Array Hashes

2015-03-06 Thread Jeffrey Horner
Hi, I wanted to share with the mailing list members here details about the project I've been working on: https://github.com/jeffreyhorner/R-Array-Hash This is a re-implementation of R's hashed environments, the global variable cache, the global string cache and symbol table with cache-conscious

Re: [Bioc-devel] requirement for named assays in SummarizedExperiment

2015-03-06 Thread Valerie Obenchain
Hi Aaron, Thanks for catching this. I favor enforcing names in 'assays'. Combining by position alone is too dangerous. I'm thinking of the VCF class where the genome information is stored in 'assays' and the fields are rarely in the same order. Looks like we also need a more informative

Re: [Rd] R with Array Hashes

2015-03-06 Thread Jeffrey Horner
On Fri, Mar 6, 2015 at 9:36 AM, Dirk Eddelbuettel e...@debian.org wrote: Jeff, Nice writeup and promising idea. From the gimme numbers department: - do you pass the R regression tests? I made sure that the implementation passed 99% of the tests, however there were two that gave differing

[Rd] Hyper-dual numbers in R

2015-03-06 Thread Ravi Varadhan
Hi, Has anyone in R core thought about providing hyper-dual numbers in R? Hyper-dual (HD) numbers, invented by Jeffrey Fike at Stanford, are useful for computing exact second-order derivatives (e.g., Hessian). HD numbers are extensions of complex numbers. They are like quaternions and have 4

Re: [Bioc-devel] New(ish!) Seattle Bioconductor team member

2015-03-06 Thread Jim Hester
I realized I sent this response the first time from the wrong email, so I don't believe it made it to the mailing list. Apologies if you receive this twice. In regards to using covr with RUnit tests, covr is not dependent on using any particular testing framework it simply runs any commands