Re: [Bioc-devel] new download stats

Hi Weijun, Mmmh... we never promised that the link to the download stats for a given package was going to be a permanent URL. The only permanent URLs we promised are the short URLs to the package landing page which is https://bioconductor.org/packages/pathview in the case of the pathview

Re: [Bioc-devel] new download stats

- Original Message - > From: "bioc-devel" > To: "bioc-devel" , "Hervé Pagès" > > Sent: Thursday, May 12, 2016 5:27:17 PM > Subject: Re: [Bioc-devel] new download stats > Hervé, > Thanks for the update, it looks

[Rd] objects intermittently shared between vignettes

Hello: Is it widely known that objects not explicitly deleted from one vignette in a package can be available to a second in "R CMD build" and "R CMD check" but not when the second vignette is built manually, at least under RStudio on Mac OS X 10.11.4 using R 3.3.0? For an

Re: [Bioc-devel] new download stats

Hervé, Thanks for the update, it looks great! Here is one problem though. I noticed that the original download stats link has change too. For my pathview package, it was: http://bioconductor.org/packages/stats/bioc/pathview.html now changed to:

Re: [Rd] where to send patches to R source code

Hi Peter, Martin, and others, Thanks for your replies. - The bugs apply to all systems that use GNU Readline, not just Linux or Arch Linux. - Readline version 6.3 changed the signal handling so that SIGWINCH is no longer handled automatically by the library. This means it's not currently

Re: [Bioc-devel] new download stats

Awesome, thanks Hervé! Cheers, Leo On Thu, May 12, 2016 at 1:55 PM, Hervé Pagès wrote: > Hi, > > We've refactored the download stats a little: > > https://bioconductor.org/packages/stats/ > > 2 new visible features are (1) yearly stats since 2009 to present > and (2)

[Bioc-devel] new download stats

Hi, We've refactored the download stats a little: https://bioconductor.org/packages/stats/ 2 new visible features are (1) yearly stats since 2009 to present and (2) downloadable stats in tabulated format (.tab extension, import in R with 'read.table(, header=TRUE)'). Feedback welcome.

Re: [R-pkg-devel] develop package with lots of tcltk in it

Thanks, Dirk. Sorry for my lack of clarity. I do want to create a package and have created one and it works, but the structure is awkward. I'm hoping someone can help me straighten out the organization. In package/R folder, I have several files that define standalone functions that crunch data.

Re: [Rd] Single-threaded aspect

On 12 May 2016 at 09:18, Dirk Eddelbuettel wrote: | | On 12 May 2016 at 13:11, Mark van der Loo wrote: | | Charles, | | | | 1. Perhaps this question is better directed at the R-help or | | R-pacakge-devel mailinglist. | | | | 2. It basically means that R itself can only evaluate one R

Re: [Rd] Single-threaded aspect

Thank you Simon for the detailed reply. That explains much more of what I was looking for from the R side. Dirk, I'm sorry if I seem hung up on anything here but I am trying to understand the details. My reply about XPtr or XPtr on arma/Eigen was to confirm my understanding was correct, which

Re: [Rd] Single-threaded aspect

On 12 May 2016 at 13:11, Mark van der Loo wrote: | Charles, | | 1. Perhaps this question is better directed at the R-help or | R-pacakge-devel mailinglist. | | 2. It basically means that R itself can only evaluate one R expression at | the time. | | The parallel package circumvents this by

Re: [Rd] Single-threaded aspect

The R language itself has features that limit how much mulitthreading/parallel processing can be done. There are functions with side effects, such as library(), plot(), runif(), <-, and <<- and there are no mechanisms to isolate them. Bill Dunlap TIBCO Software wdunlap tibco.com On Thu, May 12,

Re: [Rd] Single-threaded aspect

As others said XPtr is not something in R so Rcpp mailing list would be the right place for that aspect. However, it you forget Rcpp and phrase it as an R question, you also get much closer to the reason and answer. SEXP type is the internal representation of all objects in R. I assume your

Re: [Rd] where to send patches to R source code

> On 12 May 2016, at 10:03 , Martin Maechler wrote: > >> >>on Wed, 11 May 2016 23:00:20 -0700 writes: > >> Dear R Developers, >> I wrote to this list a week ago with some patches that fix bugs in R's >> GNU Readline interface, but I

Re: [Rd] Single-threaded aspect

Thanks for the replies. Regarding the answer by Dirk, I didn't feel like I still understood the reasoning why mclapply or foreach cannot handle XPtr objects. Instead of cluttering the SO question with comments I was getting the impression that this was a limitation inherited with R objects

Re: [Rd] Single-threaded aspect

Charles, 1. Perhaps this question is better directed at the R-help or R-pacakge-devel mailinglist. 2. It basically means that R itself can only evaluate one R expression at the time. The parallel package circumvents this by starting multiple R-sessions and dividing workload. Compiled code

Re: [Rd] Single-threaded aspect

On 12/05/2016 8:45 AM, Charles Determan wrote: R Developers, Could someone help explain what it means that R is single threaded? I am trying to understand what is actually going on inside R when users want to parallelize code. For example, using mclapply or foreach (with some backend) somehow

[Rd] Single-threaded aspect

R Developers, Could someone help explain what it means that R is single threaded? I am trying to understand what is actually going on inside R when users want to parallelize code. For example, using mclapply or foreach (with some backend) somehow allows users to benefit from multiple CPUs.

[Rd] Suggestion: mkString(NULL) should be NA

I would like to propose that Rf_mkString(NULL) and Rf_mkChar(NULL) return NA rather than segfault. Case: the mkString() and mkChar() functions are convenient to wrap strings returned by e.g. external C libraries into an R vector. However sometimes a library returns NULL instead of a string when

Re: [Rd] R process killed when allocating too large matrix (Mac OS X)

On Thu, 12 May 2016 12:07:29 +0200 Jeroen Ooms wrote: > On Thu, May 12, 2016 at 9:51 AM, Martin Maechler > wrote: > > My conclusion was I could not use the RAppArmor package. > > > > (But that's wrong: For the rlimit*() functions below,

Re: [Rd] R process killed when allocating too large matrix (Mac OS X)

On Thu, May 12, 2016 at 9:51 AM, Martin Maechler wrote: > My conclusion was I could not use the RAppArmor package. > > (But that's wrong: For the rlimit*() functions below, one do > *NOT* need an AppArmor-enabled version of Linux !) Yes, it is a relatively recent

Re: [R-pkg-devel] What to do when you can't reproduce CRAN R CMD check unit test failures?

On Thu, 2016-05-12 at 01:09 -0500, Kevin Ushey wrote: > Is it possible that `getwd()` is reporting something on the CRAN > build > servers that your `decompose_path()` doesn't handle? For example, > your > tests fail for me if I run them while in the root directory (on OS > X). It does not work

Re: [Rd] Too many spaces in deparsed complex numbers with digits17 control option

> Richard Cotton > on Thu, 5 May 2016 09:37:42 +0300 writes: > If you set the "digits17" control option in deparse, you get a lot of > unnecessary space in the representation of complex numbers. > > deparse(0 + 0i) > [1] "0+0i" > > deparse(0 + 0i, control =

Re: [Rd] where to send patches to R source code

> > on Wed, 11 May 2016 23:00:20 -0700 writes: > Dear R Developers, > I wrote to this list a week ago with some patches that fix bugs in R's > GNU Readline interface, but I haven't had a reply. I'm not in a hurry > but I'd like to make sure that my

Re: [Rd] R process killed when allocating too large matrix (Mac OS X)

> Kirill Müller > on Wed, 11 May 2016 10:42:56 +0200 writes: > My ulimit package exposes this API ([1], should finally submit it to > CRAN); unfortunately this very API seems to be unsupported on OS X > [2,3]. Last time I looked into it,

Re: [R-pkg-devel] What to do when you can't reproduce CRAN R CMD check unit test failures?

Is it possible that `getwd()` is reporting something on the CRAN build servers that your `decompose_path()` doesn't handle? For example, your tests fail for me if I run them while in the root directory (on OS X). Kevin On Thu, May 12, 2016 at 12:37 AM, Richard Cotton

[Rd] where to send patches to R source code

Dear R Developers, I wrote to this list a week ago with some patches that fix bugs in R's GNU Readline interface, but I haven't had a reply. I'm not in a hurry but I'd like to make sure that my message is getting read by the right people. Should I be sending my patches somewhere else? Thank you,