[R-pkg-devel] R_useDynamicSymbols and R_forceSymbols

I am trying to get a handle on what R_useDynamicSymbols and R_forceSymbols are used for in the C init functions for R packages. From the documentation, they appear to have something to do with controlling visibility of functions within the compiled package library, but there is no description

Re: [Bioc-devel] Feedback wanted on design of fixed-width Ranges class

Gabe - very cool! I'll be following this with interest. Ryan - conceptually I haven't been thinking of fixed-width ranges as different from general ranges, hence why I think it'd be neat if the user just got the benefits of space-efficient representation without having to know/care about the

Re: [Bioc-devel] Feedback wanted on design of fixed-width Ranges class

Hi all, In addition to the technical concerns, I suppose we should consider whether fixed-width ranges are conceptually different enough from general ranges to warrant a separate class, or whether this is just being considered for purely technical reasons. My feeling is that fixed-width

Re: [Bioc-devel] Feedback wanted on design of fixed-width Ranges class

Hey all, I just wanted to chime in on this as it relates to some work I'm doing with Luke Tierney and Tomas Kalibera. There's another approach to this that will be available in the near future (we hope). Alternative internal representations of atomic vectors, including compact representations,

Re: [Bioc-devel] Feedback wanted on design of fixed-width Ranges class

Is it possible to allow the width slot of IRanges to be either a normal vector or an Rle? On 11/23/16 6:18 PM, Peter Hickey wrote: I've been toying with the idea of a fixed/constant width Ranges subclass. The motivation comes from storing DNA methylation data at CH loci (non-CpG methylation):

Re: [Bioc-devel] Feedback wanted on design of fixed-width Ranges class

Vince - From my understanding GPos mostly gains its efficiencies when positions are adjacent, which is generally not the case for the types of positions I'm considering. In fact, the @ranges slot of the @pos_runs slot in a GPos object is just a IRanges object where n adjacent positions are

Re: [Bioc-devel] Feedback wanted on design of fixed-width Ranges class

pace Wolfgang Huber ... Peter I don't mean to be rude. Your comments deserve more study. But it was fun to remember GPos, which I had forgotten. On Wed, Nov 23, 2016 at 6:34 PM, Vincent Carey wrote: > library(GenomicRanges) > class?GPos > > On Wed, Nov 23, 2016 at

[Bioc-devel] Feedback wanted on design of fixed-width Ranges class

I've been toying with the idea of a fixed/constant width Ranges subclass. The motivation comes from storing DNA methylation data at CH loci (non-CpG methylation): there are 1.1 billion CH loci in the human genome, so to store these as a GRanges object requires 2 x 1.1 billion integer vectors, one

Re: [Bioc-devel] Rgraphviz on ppc64le needs updated config.{sub, guess}

This is a good place to report a bug; technically bugs should always be reported to the package maintainer; some packages have a BugReport URL or email in the packageDescription. I'll fix this soon and I would appreciate a test run from you. Best, Kasper On Wed, Nov 23, 2016 at 2:04 AM, Daniel

[Bioc-devel] Issue with biovizBase::parseArgsForAes(), likely just a namespace issue

Hi, The latest build report for derfinderPlot (1.9.2) shows the following error: Quitting from lines 188-190 (derfinderPlot.Rmd) Error: processing vignette 'derfinderPlot.Rmd' failed with diagnostics: could not find function "aes" I traced it down to biovizBase::parseArgsForAes() as shown

Re: [Rd] shared libraries: missing soname

On 22 November 2016 at 22:21, Joseph Mingrone wrote: | Is this a more appropriate example? | | # ldd /usr/local/lib/R/library/tseries/libs/tseries.so | grep libR | libRblas.so => /usr/local/lib/R/lib/libRblas.so (0x80120c000) | libR.so => /usr/local/lib/R/lib/libR.so (0x801c0) No it is not.

Re: [Bioc-devel] BiocStyle issue

Dear all, the compatibility issue with rmarkdown 1.2 have been resolved in https://github.com/Bioconductor-mirror/BiocStyle/commit/307ad19 Guangchuang, thank you for the heads up on the problem. Even though I was aware of the incompatibility with rmarkdown release candidate, I couldn't address

Re: [Rd] shared libraries: missing soname

Martin Maechler writes: > To the issue: I also don't see what your point is. > R works with these so libraries as intended in all cases as > far as we know, and so I don't understand why anything needs to > be changed. > All these libraries "belong to R" and are

Re: [Rd] shared libraries: missing soname

> Joseph Mingrone > on Tue, 22 Nov 2016 22:21:49 -0400 writes: > Dirk Eddelbuettel writes: >> On 22 November 2016 at 00:02, Joseph Mingrone wrote: >> | These are also not fatal errors on FreeBSD, where everything, for now, also just >>

Re: [Bioc-devel] still issues with ggplot2/ggproto in Mac OS X, stable

Hi Hervé, Thanks for the detailed analysis. On Wed, 23-11-2016, at 00:41, Hervé Pagès wrote: > Hi Ramon, > > All packages (including ggrepel) were re-installed from scratch after we > updated R on the release build machines one week ago. However it seems > that