Re: [R-SIG-Mac] R for macOS Big Sur
> Le 11 janv. 2021 à 16:26, Kasper Daniel Hansen > a écrit : > > Jean: _guessing_ this may be about parallel processing in BLAS? Does your > timing include linear algebra? Yes it is mostly linear algebra, but the slowdown is the same in parallel processing and in single processor mode (4 times slower in both). > On Mon, Jan 11, 2021 at 2:38 PM Jean Thioulouse > wrote: > Hi > > Both versions seem to run fine indeed, but on my Mac mini M1, the arm version > (homebrew R) is much slower than the intel version (CRAN R), which is quite > disappointing. > > The speed ratio I get is about 4 times slower for the arm version compared to > the intel version, both in single processor and parallel computing mode. > > Any idea about why I get these results ? > > Thanks, > Jean > > —- > Jean THIOULOUSE - orcid.org/-0001-7664-0598 > http://lbbe.univ-lyon1.fr/-Thioulouse-Jean-.html > https://www.springer.com/fr/book/9781493988488 > > > > Le 11 janv. 2021 à 10:53, Denis-Alexander Engemann > > a écrit : > > > > I have been using both Rosetta emulation and the homebrew builds and > > everything looks very good so far. > > > > Here are two Twitter threads on M1 benchmarks. > > > > https://twitter.com/fxcoudert/status/1342598509418176514?s=20 > > > > https://twitter.com/dngman/status/1342580260815200257?s=20 > > > > Best, > > Denis > > > > On Mon, Jan 11, 2021 at 10:11 AM Dr Eberhard W Lisse wrote: > >> > >> I use the homebrew R for the Intel and then install.packages(), > >> update.package() from scripts and Rstudio’s Tools->. > >> > >> I don’t have an M1 (yet) but would be interested in seeing how that works > >> on the M1. Probably this will pull the sources and hence I would be > >> grateful to read about that. > >> > >> > >> greetings, el > >> > >> — > >> Sent from Dr Lisse’s iPhone > >> On 11 Jan 2021, 10:05 +0200, Patrick Schratz , > >> wrote: > >>> There is a [native arm64 big sur > >>> binary](https://github.com/Homebrew/homebrew-core/blob/8a6807be6abb44634e7d6d153348b6bba2a5ddc6/Formula/r.rb#L16) > >>> in homebrew since some days. > >>> > >>> On 10 Jan 2021, at 22:39, Gregory Coats via R-SIG-Mac wrote: > >>> > >>>> I purchased a new 13 inch Apple MacBook Pro with the M1 System on a > >>>> Chip. I understand that R is not yet available compiled for the M1 SoC > >>>> hardware, and so I am using Apple’s Rosetta 2. > >>>> However, this MacBook Pro requires Apple macOS Big Sur. From what I > >>>> see at https://mac.r-project.org/ R has not been compiled for macOS > >>>> Big Sur. Is there an executable of R for macOS Big Sur available to > >>>> download? > >>>> Greg Coats > >>>> > >>>> > >>>> [[alternative HTML version deleted]] > >>>> > >>>> ___ > >>>> R-SIG-Mac mailing list > >>>> R-SIG-Mac@r-project.org > >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > >>> > >>> [[alternative HTML version deleted]] > >>> > >>> ___ > >>> R-SIG-Mac mailing list > >>> R-SIG-Mac@r-project.org > >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > >> > >>[[alternative HTML version deleted]] > >> > >> ___ > >> R-SIG-Mac mailing list > >> R-SIG-Mac@r-project.org > >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > > > ___ > > R-SIG-Mac mailing list > > R-SIG-Mac@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > > -- > Best, > Kasper ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] problem with tkrplot package
I had this problem too. You can find messages in r-sig-mac about it. You must recompile the tkrplot package instead of using the binary from CRAN. Jean —- Jean THIOULOUSE - orcid.org/-0001-7664-0598 http://lbbe.univ-lyon1.fr/-Thioulouse-Jean-.html > Le 20 janv. 2016 à 14:01, ANA BELÉN NIETO LIBRERO <anani...@usal.es> a écrit : > > Hello, > I am trying to use the tkrplot in the last version of R in mac but the > program abort the session when I execute > library(tkrplot). > > My own package use this packages and I can't in this moment to use them due > to this problem. > What could be the problem of this library? > Thank you. > Ana B. Nieto > > [[alternative HTML version deleted]] > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac smime.p7s Description: S/MIME cryptographic signature ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] sort() under terminal
The difference is not between the Terminal and Rgui. Check your locale: in the
Terminal, I get
> sort(c("W", "e", "E"))
[1] "e" "E" "W"
> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)
locale:
[1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] adegraphics_1.0-4 RColorBrewer_1.1-2 sp_1.1-1 KernSmooth_2.23-14
[5] grid_3.2.1 ade4_1.7-2 lattice_0.20-31
Jean
> Le 12 oct. 2015 à 16:59, Adrian Dușa <dusa.adr...@unibuc.ro> a écrit :
>
> Dear All,
>
> I tried to search some information about this on Google, but didn't find
> anything yet.
> There seems to be a difference between sorting in the Terminal app and
> sorting in the Rgui:
>
> In the Terminal:
>
>> sort(c("W", "e", "E"))
> [1] "E" "W" "e"
>> R.version
> _
> platform x86_64-apple-darwin13.4.0
> arch x86_64
> os darwin13.4.0
> system x86_64, darwin13.4.0
> status
> major 3
> minor 2.2
> year 2015
> month 08
> day14
> svn rev69053
> language R
> version.string R version 3.2.2 (2015-08-14)
> nickname Fire Safety
>
>
>
> In the Rgui:
>
>> sort(c("W", "e", "E"))
> [1] "e" "E" "W"
>> R.version
> _
> platform x86_64-apple-darwin13.4.0
> arch x86_64
> os darwin13.4.0
> system x86_64, darwin13.4.0
> status
> major 3
> minor 2.2
> year 2015
> month 08
> day14
> svn rev69053
> language R
> version.string R version 3.2.2 (2015-08-14)
> nickname Fire Safety
>
>
> Could anyone point me to some information, please?
> Best wishes,
> Adrian
>
>
> --
> Adrian Dusa
> University of Bucharest
> Romanian Social Data Archive
> Soseaua Panduri nr.90
> 050663 Bucharest sector 5
> Romania
>
> [[alternative HTML version deleted]]
>
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—-
Jean THIOULOUSE
http://lbbe.univ-lyon1.fr/-Thioulouse-Jean-.html
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Re: [R-SIG-Mac] loading tkrplot causes a segfault
Re-install X11 XQuartz (I think that this is in the FAQ).
Jean
Le 11 juil. 2015 à 00:54, Dan Tenenbaum dtene...@fredhutch.org a écrit :
Hi,
loading the tkrplot package (version 0.0-23) causes a segfault. This only
seems to happen on Mavericks, not Snow Leopard, Linux, or Windows.
library(tkrplot)
Loading required package: tcltk
*** caught segfault ***
address 0x998, cause 'memory not mapped'
Traceback:
1: structure(.External(.C_dotTclObjv, objv), class = tclObj)
2: .Tcl.objv(.Tcl.args.objv(...))
3: tcl(load, file, Rplot)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(tcl(load, file, Rplot), error = function(e) warning(loading
Rplot failed, call. = FALSE))
8: fun(libname, pkgname)
9: doTryCatch(return(expr), name, parentenv, handler)
10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
11: tryCatchList(expr, classes, parentenv, handlers)
12: tryCatch(fun(libname, pkgname), error = identity)
13: runHook(.onLoad, env, package.lib, package)
14: loadNamespace(package, c(which.lib.loc, lib.loc))
15: doTryCatch(return(expr), name, parentenv, handler)
16: tryCatchOne(expr, names, parentenv, handlers[[1L]])
17: tryCatchList(expr, classes, parentenv, handlers)
18: tryCatch(expr, error = function(e) {call - conditionCall(e)if
(!is.null(call)) {if (identical(call[[1L]], quote(doTryCatch)))
call - sys.call(-4L)dcall - deparse(call)[1L]prefix
- paste(Error in, dcall, : )LONG - 75Lmsg -
conditionMessage(e)sm - strsplit(msg, \n)[[1L]]w - 14L +
nchar(dcall, type = w) + nchar(sm[1L], type = w)if (is.na(w))
w - 14L + nchar(dcall, type = b) + nchar(sm[1L],
type = b)if (w LONG) prefix - paste0(prefix, \n )
}else prefix - Error : msg - paste0(prefix,
conditionMessage(e), \n).Internal(seterrmessage(msg[1L]))if
(!silent identical(getOption(show.error.messages), TRUE)) {
cat(msg, file = stderr()).Internal(printDeferredWarnings())}
invisible(structure(msg, class = try-error, condition = e))})
19: try({ns - loadNamespace(package, c(which.lib.loc, lib.loc))env
- attachNamespace(ns, pos = pos, deps)})
20: library(tkrplot)
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
My sessionInfo() is:
sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.9.5 (Mavericks)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
Any ideas?
Thanks,
Dan
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[R-SIG-Mac] error compiling package - ld: library not found for -lSystemStubs
Hi, Sorry to bother you about what is probably a bad configuration of my system. I have the following error when checking a package on my Mac (Mac Pro mid-2010 with Mac OS X Lion 10.7.3 (11D50), running R-2.14.2 from CRAN). I have Xcode 4.3.2 and the GNU Fortran compiler from http://r.research.att.com/. The package is prepRISA and it compiles without problem on R-Forge. Here is the install.out file of R CMD check prepRISA: * installing *source* package ‘prepRISA’ ... ** libs *** arch - i386 gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/mysql/include -I/usr/local/include-fPIC -g -O2 -c repClass.c -o repClass.o gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o prepRISA.so repClass.o -L/usr/local/mysql/lib -lmysqlclient -lSystemStubs -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: library not found for -lSystemStubs collect2: ld returned 1 exit status make: *** [prepRISA.so] Error 1 ERROR: compilation failed for package ‘prepRISA’ * removing ‘/Volumes/Macintosh-HD/Users/jthioulo/Desktop/prepRISA.Rcheck/prepRISA’ I tried to search about this SystemStubs library, but could only find that it is deprecated in MacOS X 10.7. Here is my sessionInfo: sessionInfo() R version 2.14.2 (2012-02-29) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets tcltk methods [8] base other attached packages: [1] ade4TkGUI_0.2-5 ade4_1.4-17 What can I do to get rid of this problem ? Thank you, Jean -- Jean Thioulouse - Labo Biometrie et Biologie Evolutive, UMR CNRS 5558 Universite Lyon 1, Batiment Mendel, 69622 Villeurbanne Cedex - France Tel : (33)(0)472432756 Fax : (33)(0)472431388 Cel : (33)(0)675122302 http://pbil.univ-lyon1.fr/JTHome/Biblio/ ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
