[Bioc-devel] rtracklayer Export BED itemRgb Annotation

The documentation says that itemRgb must be a character vector of hex color codes, as returned by col2rgb. However, the return value of col2rgb is An integer matrix with three or four rows. -- Dario Strbenac PhD Student University of Sydney Camperdown NSW

Re: [Bioc-devel] VcfFile and VcfFileList

I think there are fairly clear use cases for a VcfFile class. It's nice to be able to dispatch on the file/path, for example in visualization tools. Please add this when you have a chance. Thanks, Michael On Wed, Jul 17, 2013 at 9:56 AM, Valerie Obenchain voben...@fhcrc.orgwrote: Hi Robert,

Re: [Bioc-devel] rtracklayer Export BED itemRgb Annotation

Thanks, I've clarified the docs, and an integer matrix of color codes is now supported. On Thu, Jul 18, 2013 at 1:00 AM, Dario Strbenac dstr7...@uni.sydney.edu.auwrote: The documentation says that itemRgb must be a character vector of hex color codes, as returned by col2rgb. However, the

[Rd] question about Makeconf and nvcc/CUDA

Dear R development: I'm not sure if this is the appropriate list, but it's a start. I would like to put together a package which contains a CUDA program on Windows 7. I believe that it has to do with the Makeconf file in the etc directory. But when I just use the nvcc with the shared

Re: [Rd] question about Makeconf and nvcc/CUDA

On 18/07/2013 07:45, Hodgess, Erin wrote: Dear R development: I'm not sure if this is the appropriate list, but it's a start. I would like to put together a package which contains a CUDA program on Windows 7. I believe that it has to do with the Makeconf file in the etc directory. That

Re: [Rd] Problem following an R bug fix to integrate()

Thanks for the help. What bothers me is that it works on most systems and does not work on some more 'exotic' systems -- though it should work everywhere however small the user chooses the tolerance (with some warnings, maybe). I decided I will apply my own integration routines in this example

Re: [Rd] Problem following an R bug fix to integrate()

On 2013-07-16 07:55, Hans W Borchers wrote: I have been told by the CRAN administrators that the following code generated an error on 64-bit Fedora Linux (gcc, clang) and on Solaris machines (sparc, x86), but runs well on all other systems): fn- function(x, y) ifelse(x^2 + y^2= 1, 1 -

Re: [Rd] question about Makeconf and nvcc/CUDA

Now let's try again. I set up the CYGWIN environment command as kindly suggested by Prof. Ripley. Here are my next steps: R CMD build cudasize * checking for file 'cudasize/DESCRIPTION' ... OK * preparing 'cudasize': * checking DESCRIPTION meta-information ... OK * cleaning src Warning:

Re: [Rd] question about Makeconf and nvcc/CUDA

You will need a src/Makevars.win to get a .cu file to compile. It is not a known extension: see §1.1.4 of 'Writing R Extensions' Most likely you need something like cudasize.dll: nvcc -m32 --shared -o $@ cuda4.cu in Makevars.win. Also, heed the advice about trying R CMD INSTALL

Re: [Rd] question about Makeconf and nvcc/CUDA

Hi Erin Glad you are making progress on this with Brian's help. I thought I would mention a different approach that might save you some programming time and actually make the code more flexible at the same time. Basically, in a high-level language like R, it is nice to keep the code calling a

[Rd] parLapplyLB: Load balancing?

[cross-posted on R-devel and Bioc-devel, since the functions from the parallel package discussed here are mirrored in the BiocGenerics package] Hi, I am currently running a lengthy simulation study (no details necessary) on a large multi-core system. The simulated data sets are stored in a

Re: [Rd] question about Makeconf and nvcc/CUDA

Hi again: Here is another problem that I am having. Hope this will be the last one. I really want to see if I can put it together. Sorry for belaboring the issue. Well, here is my story: c:\Program Files\R\R-3.0.1\bin\i386R CMD build cudasize R CMD build cudasize * checking for file

Re: [Rd] question about Makeconf and nvcc/CUDA

Hi Erin It appears that there is only one file in src that is compile, i.e. cuda4.cu. That does not contain a routine named cuda4, which is what you are trying to invoke via the .Call(cuda4) expression. Instead, it contains two routines - one kernel square_array which runs on the GPU, and the

Re: [Rd] question about Makeconf and nvcc/CUDA

Hi again. I put in the extern statement. However, I'm not sure what you mean by changing the signature, please. I changed out the routine name from stuff to cuda4 in the cuda4.cu program. Still getting: library(cudasize) library(cudasize) .C(cuda4,as.character(5))

Re: [Rd] question about Makeconf and nvcc/CUDA

Hi Erin See the code below. Basically, I have created a new routine that you will call from R as .C(cuda4, 1L, 5) where 1L is the number of arguments you are passing and 5 is the character vector of arguments. We are using .C() here for simplicity. For other cases involving data, .Call()

Re: [Rd] question about Makeconf and nvcc/CUDA

Wow! This is just amazing! Thanks so much. I didn't realize how intense this is. From: Duncan Temple Lang [dtemplel...@ucdavis.edu] Sent: Thursday, July 18, 2013 3:08 PM To: Hodgess, Erin Cc: r-devel@r-project.org Subject: Re: [Rd] question about

Re: [Rd] question about Makeconf and nvcc/CUDA

All right. I'm still stuck even with all of the help. Here is the first part: R CMD INSTALL --no-multiarch cudasize_1.0.tar.gz R CMD INSTALL --no-multiarch cudasize_1.0.tar.gz * installing to library 'c:/myRlib' * installing *source* package 'cudasize' ... ** libs nvcc -m32 --shared -o