Re: [Bioc-devel] R6 and Bioconductor

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

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

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] Question about BiocGeneric::order

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

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

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: [Rd] xrealloc namespace conflict

Thanks for the response. It looks like there is a dlopen flag that will fix the issue on Linux (RTLD_DEEPBIND); on Mac OS, symbols get resolved by searching in the library first, so the flag isn't needed. I don't know what the default behavior is on other platforms. See, e.g.

Re: [Bioc-devel] R6 and Bioconductor

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

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

Re: [Bioc-devel] R6 and Bioconductor

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

[Bioc-devel] R6 and Bioconductor

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: [Rd] R-3.3.3/R-3.4.0 change in sys.call(sys.parent())

On Thu, May 11, 2017 at 8:03 PM, William Dunlap wrote: > Here is a case where the current scheme fails: > > > with(datasets::mtcars, xyplot(mpg~wt|gear)$call) > xyplot(substitute(expr), data, enclos = parent.frame()) Right, thanks. So I guess I can't avoid setting $call