Re: [Bioc-devel] R6 and Bioconductor

2017-05-12 Thread Gabe Becker
On May 12, 2017 4:23 PM, "Garth Ilsley" wrote: Thank you. > One place where one might think of using R6 is in the implementation of a mutable data model underlying a GUI like a Shiny app. > If mutable semantics are required, consider using S4 reference classes, as they

Re: [Bioc-devel] R6 and Bioconductor

2017-05-12 Thread Michael Lawrence
Just to add to what Gabe already said, defer your performance concerns until you've actually got something that works and is well written. If you hit up against a performance barrier, come back and we can help. On Fri, May 12, 2017 at 4:22 PM, Garth Ilsley wrote: > Thank

Re: [Bioc-devel] R6 and Bioconductor

2017-05-12 Thread Garth Ilsley
Thank you. > One place where one might think of using R6 is in the implementation of a > mutable data model underlying a GUI like a Shiny app. > If mutable semantics > are required, consider using S4 reference classes, as they offer more > features than R6 and will integrate > directly with

Re: [Bioc-devel] R6 and Bioconductor

2017-05-12 Thread Martin Morgan
On 05/12/2017 07:11 AM, Martin Morgan wrote: On 05/12/2017 02:05 AM, Garth Ilsley wrote: Hello, I am thinking of creating package for Bioconductor, and I am wondering about the use of R6 classes (from the R6 package). I do indeed intend to use existing Bioconductor classes such as

[Bioc-devel] R6 and Bioconductor

2017-05-12 Thread Garth Ilsley
Hello, I am thinking of creating package for Bioconductor, and I am wondering about the use of R6 classes (from the R6 package). I do indeed intend to use existing Bioconductor classes such as SummarizedExperiment and interact and make use of other Bioconductor packages, such as scater and

Re: [Bioc-devel] R6 and Bioconductor

2017-05-12 Thread Michael Lawrence
One place where one might think of using R6 is in the implementation of a mutable data model underlying a GUI like a Shiny app. If mutable semantics are required, consider using S4 reference classes, as they offer more features than R6 and will integrate directly with Bioconductor S4 classes.

Re: [Bioc-devel] R6 and Bioconductor

2017-05-12 Thread Martin Morgan
On 05/12/2017 02:05 AM, Garth Ilsley wrote: Hello, I am thinking of creating package for Bioconductor, and I am wondering about the use of R6 classes (from the R6 package). I do indeed intend to use existing Bioconductor classes such as SummarizedExperiment and interact and make use of other

Re: [Bioc-devel] unable to push local changes to bioconductor svn repository

2017-05-12 Thread Martin Morgan
On 05/11/2017 10:02 AM, Xu, Zongli (NIH/NIEHS) [E] wrote: Hi, I got a new Linux computer, cloned my package from github, made some changes. I am able to update the changes to github, but can not push it to Bioconductor svn repository. Can someone help me to solve the problem. The following

Re: [Bioc-devel] Question about BiocGeneric::order

2017-05-12 Thread Michael Lawrence
Thanks for noticing that. I'll fix that in R soon. I'm going through and generalizing many of the stats default methods so that they work automatically with Rle. For order,Rle(), I fixed the method argument default and added a fast path for the single arg case. I guess we'll keep it around. On