Re: [Rd] Detecting physical CPUs in detectCores() on Linux platforms

On 8 August 2023 at 13:17, Simon Urbanek wrote: | To be honest I think the motivation of this thread is dubious at best: it is a bad idea to use detectCore() blindly to specify parallelization and we explicitly say it's a bad idea - any sensible person will set it according to the demands,

Re: [Rd] Detecting physical CPUs in detectCores() on Linux platforms

> On 8/08/2023, at 12:07 PM, Dirk Eddelbuettel wrote: > > > On 8 August 2023 at 11:21, Simon Urbanek wrote: > | First, detecting HT vs cores is not necessarily possible in general, Linux > may assign core id to each HT depending on circumstances: > | > | $ grep 'cpu cores' /proc/cpuinfo |

Re: [Rd] Detecting physical CPUs in detectCores() on Linux platforms

On 8 August 2023 at 11:21, Simon Urbanek wrote: | First, detecting HT vs cores is not necessarily possible in general, Linux may assign core id to each HT depending on circumstances: | | $ grep 'cpu cores' /proc/cpuinfo | uniq | cpu cores : 32 | $ grep 'model name' /proc/cpuinfo | uniq |

Re: [Rd] Detecting physical CPUs in detectCores() on Linux platforms

First, detecting HT vs cores is not necessarily possible in general, Linux may assign core id to each HT depending on circumstances: $ grep 'cpu cores' /proc/cpuinfo | uniq cpu cores : 32 $ grep 'model name' /proc/cpuinfo | uniq model name : Intel(R) Xeon(R) Gold 6142 CPU @ 2.60GHz

[Rd] Vectorize library() to improve handling of versioned deps [sprint project proposal]

Hi All, This is a proposal for a project which could be worked on during the R development Sprint at the end of this month; it was requested that we start a discussion here to see what R-core's thoughts on it were before we officially add it to the docket. AFAIK, R officially supports both

Re: [R-pkg-devel] [External] Re: clang issue

В Mon, 7 Aug 2023 15:52:38 + "Grose, Daniel" пишет: > https://github.com/grosed/anomaly Ah, so this is why I couldn't find your package on CRAN. Now I can see the compiler log, together with the compiler command line: https://www.stats.ox.ac.uk/pub/bdr/clang17/anomaly.log It looks like

Re: [R-pkg-devel] [External] Re: clang issue

Hi Dirk My apologies. I thought you were asking for compiler output. You can find the code at https://github.com/grosed/anomaly [https://opengraph.githubassets.com/866d37f560339c5ee145d5cd7e40edf768223cf08b8e9f35ae97e14d1f2b47f5/grosed/anomaly] GitHub -

Re: [R-pkg-devel] [External] Re: clang issue

On 7 August 2023 at 13:55, Grose, Daniel wrote: | As I say - I cannot reproduce the error myself. I will try asking Uwe Ligges | for more information. Methinks you are doing it wrong. We created the r-package-devel list years ago to take load away from the overworked CRAN maintainers who are

Re: [Rd] A demonstrated shortcoming of the R package management system

Hi Ivan, I usually 'mentally applaud' when reading your replies on list but not here. On 7 August 2023 at 16:15, Ivan Krylov wrote: | SeuratObject 4.1.3. The breakage definitely exists, but not on the | source package level. You seem to overlook that a large part of the R Universe only works

Re: [R-pkg-devel] [External] Re: clang issue

Hi Ivan/Dirk As I say - I cannot reproduce the error myself. I will try asking Uwe Ligges for more information. Best wishes, Dan From: Dirk Eddelbuettel Sent: 07 August 2023 14:53 To: Grose, Daniel Cc: Ivan Krylov ; Dirk Eddelbuettel ;

Re: [R-pkg-devel] [External] Re: clang issue

On 7 August 2023 at 13:38, Grose, Daniel wrote: | No - unfortunately not. I cannot reproduce the error locally so I posted the | snippet that Uwe Ligges sent me regarding the failed CRAN submission. That is | all of the information I have. | | For now I will follow Dirk's advice and see if the

Re: [R-pkg-devel] [External] Re: clang issue

Hi Ivan No - unfortunately not. I cannot reproduce the error locally so I posted the snippet that Uwe Ligges sent me regarding the failed CRAN submission. That is all of the information I have. For now I will follow Dirk's advice and see if the CRAN submission gets accepted. Thanks for your

Re: [Rd] Detecting physical CPUs in detectCores() on Linux platforms

On Mon, 2023-08-07 at 07:12 -0500, Dirk Eddelbuettel wrote: > > On 7 August 2023 at 08:48, Nils Kehrein wrote: > > I recently noticed that `detectCores()` ignores the `logical=FALSE` > > argument on Linux platforms. This means that the function will > > always > > return the number of logical

Re: [Rd] hist(..., log="y")

Log histograms are of particular interest when dealing with heavy tailed data/distributions. It is not just a matter of using a log scale on the y axis though because the base line of the histogram is at zero and the log of zero is minus infinity. I have implemented a version of a log

Re: [R-pkg-devel] [External] Re: clang issue

В Mon, 7 Aug 2023 13:16:33 + "Grose, Daniel" пишет: > I thought -DR_NO_REMAP in Makevars would set R_NO_REMAP across all > compilation units. Is this not the case ? It should have worked. Can we see the code? Is there a visible compiler command line in the check results that you quoted in

Re: [Rd] R-devel Digest, Vol 246, Issue 6

Two quite related and recent threads on R-devel: [1] proposal for WRE: clarify that use of S4 classes implies use of superclasses https://stat.ethz.ch/pipermail/r-devel/2023-July/082739.html [2] Should package version requirements assume installation from sources?

Re: [R-pkg-devel] [External] Re: clang issue

Hi Dirk Thanks for the quick response. I thought -DR_NO_REMAP in Makevars would set R_NO_REMAP across all compilation units. Is this not the case ? Thanks, Dan From: Dirk Eddelbuettel Sent: 07 August 2023 14:13 To: Grose, Daniel Cc:

Re: [Rd] A demonstrated shortcoming of the R package management system

В Sun, 6 Aug 2023 16:05:03 -0500 Dirk Eddelbuettel пишет: > One possibility may be to add a new (versioned) field 'Breaks:'. > Matrix could then have added 'Breaks: SeuratObject (<= 4.1.3)' > preventing an installation of Matrix 1.6.0 when SeuratObject 4.1.3 > (or earlier) is present, but

Re: [R-pkg-devel] clang issue

Daniel, This is not new, and not related to clang. On 7 August 2023 at 12:58, Grose, Daniel wrote: | Any ideas ? Add a line #define R_NO_REMAP 1 before _any_ inclusion of R headers. See Section 6 of Writing R Extensions. If you use eg Rcpp it is done for you when you include Rcpp

[R-pkg-devel] clang issue

Hi My package submission fails due to In file included from MeanAnomalyMV.cpp:7: In file included from ./Functions_mean.h:4: In file included from usr/local/clang-trunk/bin../include/c++/v1/vector:321: In file included from

Re: [Rd] Detecting physical CPUs in detectCores() on Linux platforms

On 7 August 2023 at 08:48, Nils Kehrein wrote: | I recently noticed that `detectCores()` ignores the `logical=FALSE` | argument on Linux platforms. This means that the function will always | return the number of logical CPUs, i.e. it will count the number of threads | that theoretically can run

[Rd] Detecting physical CPUs in detectCores() on Linux platforms

Dear all, I recently noticed that `detectCores()` ignores the `logical=FALSE` argument on Linux platforms. This means that the function will always return the number of logical CPUs, i.e. it will count the number of threads that theoretically can run in parallel due to e.g. hyper-threading.

Re: [Rd] hist(..., log="y")

> Ott Toomet > on Sat, 5 Aug 2023 23:49:38 -0700 writes: > Sorry if this topic has been discussed earlier. > Currently, hist(..., log="y") fails with >> hist(rexp(1000, 1), log="y") > Warning messages: 1: In plot.window(xlim, ylim, "", ...) : > nonfinite axis=2