Re: [Rd] MKL Acceleration encouraging; need adjust package builds?

We said it before, but it bears repeating: BLAS is an interface. So unless you use on a static library build, these library can be switch after compilation and at essentially any point in time. My (unfinished) package gcbd shows how in its simple and vignette by comparing a number of BLAS

Re: [Bioc-devel] Behavior of select function in AnnotationDbi

On Mon, Nov 23, 2015 at 1:11 PM, Morgan, Martin < martin.mor...@roswellpark.org> wrote: > I would rather mapIds() continue to operate on a single column, return a > named character vector, and by default provide a 1:1 relationship between > input and output. multiVals=CharacterList does actually

Re: [Bioc-devel] Behavior of select function in AnnotationDbi

I would rather mapIds() continue to operate on a single column, return a named character vector, and by default provide a 1:1 relationship between input and output. multiVals=CharacterList does actually return a 1:many mapping in a way that retains parallel structure (I guess, maybe module

Re: [Rd] Best way to implement optional functions?

Yes, you do need at least a token about of documentation in both packages. I keep full documentation in the package where they originate, and minimal documentation in the rexporting package. The roxygen code in the reexporting package looks like this: #' Some function #' #' See

[Rd] capturing warnings using capture.output

>From the Details section of ?capture.output: Messages sent to stderr() (including those from message, warning and stop) are captured by type = "message". Note that this can be "unsafe" and should only be used with care. Capturing messages works as expected: capture.output(message("!!!"), type

Re: [Rd] compile question

Hi Michael, I experienced the same thing in the past. After you get the R-3.2.2.tar.gz and uncompress it, enter the R-3.2.2 directory and run the ./configure and make from there, rather than a different one. One other thing, you probably already did this, but just in case you might want to

[Rd] Custom C finalizers for .Call

WRE explains that R_alloc() can be used to allocate memory which automatically gets released by R at the end of a .C, .Call or .External, even in the case of an error or interruption. This is a really great feature to prevent memory leaks. I was wondering if there is a way to extend this mechanism

Re: [Rd] compile question

> On 23 Nov 2015, at 22:30 , aixtools wrote: > >> >> ./configure --enable-maintainer-mode ... Two things here - possibly irrelevant, but I'd avoid building in the source directory. (mkdir ../BUILD ; cd ../BUILD; ../R/configure) - don't turn on mantainer mode. You are

Re: [Rd] R-devel no longer supports Ubuntu 14.04 LTS (insufficient PCRE version)

Sebastian, Paul, Ubuntu 14.04 builds (for Linux 32 and 64 bit, ie i386 and amd64) of the (most current) pcre package (ie 8.35-7) for Ubuntu are now in my PPA at https://launchpad.net/~edd/+archive/ubuntu/misc/+packages These should work. You can add this PPA as I do in some Travis runs via

Re: [Bioc-devel] PANTHER.db GOSLIM_ID hosed?

Panther has been updated to the new 1.03, which should resolve this issue. Let us know if there are any further updates. On Fri, Nov 20, 2015 at 5:29 AM, Julius Müller wrote: > Dear Steve, > > thanks a lot for pointing out the error! The problem Martin described is > exactly

[Rd] compile question

Dear all, Starting all over again with R-devel of 22-11-2015. After getting the dependancies (minimal graphics initially) I have been able to come this far - with a 64-bit build on AIX. root@x072:[/data/prj/cran/64/R-devel]make make[1]: Entering directory '/data/prj/cran/64/R-devel/m4'

[Rd] MKL Acceleration encouraging; need adjust package builds?

Dear R-devel: The Cluster administrators at KU got enthusiastic about testing R-3.2.2 with Intel MKL when I asked for some BLAS integration. Below I forward a performance report, which is encouraging, and thought you would like to know the numbers. Appears to my untrained eye there are some

Re: [Rd] MKL Acceleration encouraging; need adjust package builds?

Hi Paul, We've been through this process ourselves for the Revolution R Open project. There are a number of pitfalls to avoid, but you can take a look at how we achieved it in the build scripts at: https://github.com/RevolutionAnalytics/RRO There are also some very useful notes in the R

Re: [Bioc-devel] Coverage test badge not updating

Thank you for fixing this Jim! I noticed it working now on devel. However, I believe that is still not working for the release branch. Cheers, Leo On Fri, Nov 20, 2015 at 3:37 PM, Jim Hester wrote: > The coverage tests were inadvertently not running, but they are now >

Re: [Rd] compile question

On 2015-11-23 18:52, aixtools wrote: Dear all, Starting all over again with R-devel of 22-11-2015. After getting the dependancies (minimal graphics initially) I have been able to come this far - with a 64-bit build on AIX. This is my configure call: #!/usr/bin/ksh # my_config_test .