Re: [Rd] parallel::detectCores(TRUE) gives: Error in system(cmd, TRUE) : error in running command

2014-08-22 Thread Prof Brian Ripley
But parallel::detectCores(TRUE) is a call of desparation: this ran code intended for FreeBSD. If all else fails read the help: It has methods to do so for Linux, OS X, FreeBSD, Solaris, Irix and Windows. ‘detectCores(TRUE)’ could be tried on other Unix-alike systems. On Fri, 2

Re: [Rd] parallel::detectCores(TRUE) gives: Error in system(cmd, TRUE) : error in running command

2014-08-22 Thread Marius Hofert
Thanks, Bill. The output is: > trace(system, quote(print(command))) parallel::detectCores(TRUE) Tracing function "system" in package "base" [1] "system" > Tracing system(cmd, TRUE) on entry [1] "/usr/sbin/sysctl -n hw.ncpu 2>/dev/null" Error in system(cmd, TRUE) : error in running command > On

Re: [Rd] parallel::detectCores(TRUE) gives: Error in system(cmd, TRUE) : error in running command

2014-08-22 Thread Mauricio Zambrano-Bigiarini
On 22/08/14 16:03, Marius Hofert wrote: Hi, Both under the current R-devel (r66456) and a version from about 3 months ago, I experience the following behavior: parallel::detectCores(TRUE) Error in system(cmd, TRUE) : error in running command traceback() 3: system(cmd, TRUE) 2: gsub("^ +",

Re: [Rd] parallel::detectCores(TRUE) gives: Error in system(cmd, TRUE) : error in running command

2014-08-22 Thread William Dunlap
There is no /usr/sbin/sysctl on my Ubuntu 12.04 machine. There is a /sbin/sysctl, but it does not accept the '-n hw.ncpu' arguments. Its /usr/bin/nproc [-all] will tell the number of available [installed] processing units and 'cat /proc/cpuinfo | grep processor | wc -l' will also give the number

Re: [Rd] parallel::detectCores(TRUE) gives: Error in system(cmd, TRUE) : error in running command

2014-08-22 Thread David Winsemius
On Aug 22, 2014, at 2:53 PM, Rui Barradas wrote: > Hello, > > Inline. > > Em 22-08-2014 22:18, Tobias Verbeke escreveu: >> - Original Message - >>> From: "Marius Hofert" >>> To: "R-devel" >>> Sent: Friday, August 22, 2014 10:03:13 PM >>> Subject: [Rd] parallel::detectCores(TRUE) gives

Re: [Rd] parallel::detectCores(TRUE) gives: Error in system(cmd, TRUE) : error in running command

2014-08-22 Thread William Dunlap
The same is true in R-2.14.1 on Ubuntu 12.04.4 LTS . Put a trace on system with trace(system, quote(print(command))) parallel::detectCores(TRUE) and you will see the offending shell command. Bill Dunlap TIBCO Software wdunlap tibco.com On Fri, Aug 22, 2014 at 1:03 PM, Marius Hofert wrote:

Re: [Rd] parallel::detectCores(TRUE) gives: Error in system(cmd, TRUE) : error in running command

2014-08-22 Thread Rui Barradas
Hello, Inline. Em 22-08-2014 22:18, Tobias Verbeke escreveu: - Original Message - From: "Marius Hofert" To: "R-devel" Sent: Friday, August 22, 2014 10:03:13 PM Subject: [Rd] parallel::detectCores(TRUE) gives: Error in system(cmd, TRUE) : error in running command Hi, Both under the

Re: [Rd] parallel::detectCores(TRUE) gives: Error in system(cmd, TRUE) : error in running command

2014-08-22 Thread Tobias Verbeke
- Original Message - > From: "Marius Hofert" > To: "R-devel" > Sent: Friday, August 22, 2014 10:03:13 PM > Subject: [Rd] parallel::detectCores(TRUE) gives: Error in system(cmd, TRUE) : > error in running command > > Hi, > > Both under the current R-devel (r66456) and a version from abo

[Rd] parallel::detectCores(TRUE) gives: Error in system(cmd, TRUE) : error in running command

2014-08-22 Thread Marius Hofert
Hi, Both under the current R-devel (r66456) and a version from about 3 months ago, I experience the following behavior: > parallel::detectCores(TRUE) Error in system(cmd, TRUE) : error in running command > traceback() 3: system(cmd, TRUE) 2: gsub("^ +", "", system(cmd, TRUE)[1]) 1: parallel::dete

Re: [Rd] Inconsistent handling of data frames in min(), max(), and mean()

2014-08-22 Thread Gavin Simpson
Thanks Martin (sorry about the HTML - GMail and my incompetent use of it; hopefully I've beaten it into submission this time). I can see the point of view, however the inconsistency remains whether one patches the other summary stat functions to work as if given a matrix or squash all the Summary

Re: [Rd] How to (appropropriately) use require in a package?

2014-08-22 Thread Henrik Singmann
Dear Joshua, Sorry for resurrecting this thread, but I was on holidays earlier. I also had that problem and unfortunately using loadNamespace() as suggested by Prof. Ripley didn't work in my case (the reason is that the cluster is created by the user and the call executed on the cluster can co

Re: [Rd] markdown vignette with the vignette command

2014-08-22 Thread Leo Lahti
I followed the instructions in http://cran.r-project.org/web/packages/knitr/vignettes/knitr-markdown.html - add *.Rmd files under the vignettes directory - add VignetteBuilder: knitr to the DESCRIPTION file - specify the vignette engine \VignetteEngine{knitr::knitr} in the Rmd files (i

Re: [Rd] markdown vignette with the vignette command

2014-08-22 Thread Duncan Murdoch
On 22/08/2014 8:06 AM, Leo Lahti wrote: Solved, thanks! Could you post a short description of the solution, in case this problem arises for anyone else? These posts are archived, and can be a useful resource for others. Duncan Murdoch On Fri, Aug 22, 2014 at 1:04 PM, Duncan Murdoch mail

Re: [Rd] markdown vignette with the vignette command

2014-08-22 Thread Leo Lahti
Solved, thanks! Leo On Fri, Aug 22, 2014 at 1:04 PM, Duncan Murdoch wrote: > On 22/08/2014, 6:09 AM, Leo Lahti wrote: > > Dear list, > > > > we have a markdown vignette for our package in vignette/vignette.md > > > > This is not visible from within R with the vignette(package = > "mypackage")

Re: [Rd] markdown vignette with the vignette command

2014-08-22 Thread Duncan Murdoch
On 22/08/2014, 6:09 AM, Leo Lahti wrote: > Dear list, > > we have a markdown vignette for our package in vignette/vignette.md > > This is not visible from within R with the vignette(package = "mypackage") > command. > > I assume the reason is that the vignette function only shows PDF vignettes.

[Rd] markdown vignette with the vignette command

2014-08-22 Thread Leo Lahti
Dear list, we have a markdown vignette for our package in vignette/vignette.md This is not visible from within R with the vignette(package = "mypackage") command. I assume the reason is that the vignette function only shows PDF vignettes. Is there any way to circumvent this and display markdown

Re: [Rd] Inconsistent handling of data frames in min(), max(), and mean()

2014-08-22 Thread Martin Maechler
> Gavin Simpson > on Thu, 21 Aug 2014 12:32:31 -0600 writes: > This inconsistency recently came to my attention: >> df <- data.frame(A = 1:10, B = rnorm(10)) >> min(df) > [1] -1.768958 >> max(df) > [1] 10 >> mean(df) > [1] NA Warning message: In mean.d

Re: [Rd] [R-devel] what are labels in struct sxpinfo_struct from Rinternals.h mean?

2014-08-22 Thread Prof Brian Ripley
Once again[*], you really should study the posting guide. The documentation is the 'R Internals manual', and it does cover this. fortunes::fortune(14) applies. [*] After two postings on R-help which ignored it, one reply to which pointed out this manual. On 22/08/2014 07:32, PO SU wrote:

[Rd] [R-devel] what are labels in struct sxpinfo_struct from Rinternals.h mean?

2014-08-22 Thread PO SU
Dear Rdevelers,      The following struct is in the Rinternals.h. I want to know  the meanings of labels or names like "gp,mark,obj,named,trace." . TKS! struct sxpinfo_struct {     SEXPTYPE type      :  5;/* ==> (FUNSXP == 99) %% 2^5 == 3 == CLOSXP     * -> warning: