[Bioc-devel] ggbio: Support of object inheriting from 'GRanges'

2014-02-03 Thread Julian Gehring
Hi, while ggbio work well for 'GRanges' objects, it is not able to deal with objects inheriting from a 'GRanges', e.g. a 'VRanges' object: library(ggbio) library(GenomicRanges) library(VariantAnnotation) gr = GRanges(1, IRanges(1, 10)) vr = as(gr, VRanges) autoplot(gr) ## works autoplot(vr)

Re: [Bioc-devel] ggbio: Support of object inheriting from 'GRanges'

2014-02-03 Thread Tengfei Yin
Hi Julian, You are right, because autoplot() doesn't support VRanges object yet, it should not be a hard implementation, I will do this in devel branch this week. cheers Tengfei On Mon, Feb 3, 2014 at 11:54 AM, Julian Gehring julian.gehr...@embl.dewrote: Hi, while ggbio work well for

[Rd] String Vector Encoding

2014-02-03 Thread Saptarshi Guha
Hello, I was reading through serialize.c and i couldn't answer something. In readItem, case CHARSXP, rules exists to adjust the read string for string encoding. Q1. I couldn't find where the encoding of the elements of the string vector are written? Is it when writeItem writes out the

[Rd] LinkingTo self

2014-02-03 Thread Romain Francois
Hello, Shipping header files for a package in inst/include and let other packages use it with LinkingTo is popular. Unfortunately for the package itself, we still need to use something like : PKG_CPPFLAGS+=-I../inst/include/ in the Makevars and Makevars.win files. Could this become

Re: [Rd] String Vector Encoding

2014-02-03 Thread Duncan Murdoch
On 14-02-03 3:41 AM, Saptarshi Guha wrote: Hello, I was reading through serialize.c and i couldn't answer something. In readItem, case CHARSXP, rules exists to adjust the read string for string encoding. This is described in the R Internals manual. Duncan Murdoch Q1. I couldn't find

[Rd] Fwd: linker issue

2014-02-03 Thread Samuel Kemp
Hi, I am trying to compile C++ with R and I am coming up against - what I believe - is a linker configuration issue. For example, using has_develop() gives the following message... has_devel() C:/PROGRA~1/R/R-30~1.2/bin/i386/R --vanilla CMD SHLIB foo.c gcc -m32 -IC:/PROGRA~1/R/R-30~1.2/include

Re: [Rd] Fwd: linker issue

2014-02-03 Thread Duncan Murdoch
On 14-02-03 7:00 AM, Samuel Kemp wrote: Hi, I am trying to compile C++ with R and I am coming up against - what I believe - is a linker configuration issue. For example, using has_develop() gives the following message... has_devel() I assume you're using the function from devtools. It

[Rd] seq range argument

2014-02-03 Thread Berry Boessenkool
Hello dear developers, I find myself often having the result of range oder extendrange, which I want to create a sequence with. But seq needs two seperate arguments from and two. Could an argument range be added? Otherwise I will have to create an object with the range (may come from a longer

[Rd] Release plans for R versions 3.0.3 and 3.1.0

2014-02-03 Thread Peter Dalgaard
The upcoming wrap-up release 3.0.3 is scheduled for March 6. The start of the next series, 3.1.0 is scheduled for April 10. Detailed schedules will be published on developer.r-project.org. Package maintainers, especially of recommended packages, are asked to time potential modifications to

Re: [Rd] seq range argument

2014-02-03 Thread Lorenz, David
Berry, It sounds like you just need a little helper function like this: ser - function(x, len=100, f=0.1) { dr - extendrange(x, f=f) return(seq(dr[1L], dr[2L], length.out=len)) } I called it ser, short for sequence extended range. Use it thusly: Ijustneed - ser(D_orig) Hope this

Re: [Rd] String Vector Encoding

2014-02-03 Thread Saptarshi Guha
True but I was hoping someone could point me where in the source code this happens. Cheers Saptarshi On Feb 3, 2014 3:37 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 14-02-03 3:41 AM, Saptarshi Guha wrote: Hello, I was reading through serialize.c and i couldn't answer something.

Re: [Rd] seq range argument

2014-02-03 Thread Berry Boessenkool
Thanks Dave! I settled on something similar, but more general, for my function collection package. I just thought this could be wanted by more people and thus interesting for base::seq. In case anyone is interested in my solution, keep reading. Berry # Add a range argument to seq seqr -

Re: [Rd] seq range argument

2014-02-03 Thread Ista Zahn
This is slightly more verbose, but perhaps do.call(seq, as.list(c(extendrange(D_orig, f=0.1), len=100))) Best, Ista On Mon, Feb 3, 2014 at 9:00 AM, Lorenz, David lor...@usgs.gov wrote: Berry, It sounds like you just need a little helper function like this: ser - function(x, len=100,

Re: [Rd] String Vector Encoding

2014-02-03 Thread Simon Urbanek
On Feb 3, 2014, at 10:06 AM, Saptarshi Guha saptarshi.g...@gmail.com wrote: True but I was hoping someone could point me where in the source code this happens. src/main/serialize.c @1655 and @1663 Cheers Saptarshi On Feb 3, 2014 3:37 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote:

[Rd] capture.output(): Using a rawConnection() [linear] instead of textConnection() [exponential]?

2014-02-03 Thread Henrik Bengtsson
and attached PNG figure [also at http://xfer.aroma-project.org/tmp/20140203/capture.output_text-vs-raw.png]. I know little about text encoding, but I wouldn't be surprised I'm overseeing encoding issues when sinking to raw followed by rawToChar(). According to the below example, both approaches