Re: [R-SIG-Mac] Libre SSL bug on MacOS Monterey => error in download.file()

2022-01-12 Thread Kasper Daniel Hansen
I am not an expert, but it seems to me that switching the backend is a runtime setting. Couldn't we detect which version of OS X we're running and then select the backend conditionally on that test? Best, Kasper On Wed, Jan 12, 2022 at 5:12 PM Jeroen Ooms wrote: > On Wed, Jan 12, 2022 at 10:05

Re: [R-SIG-Mac] https://mac.r-project.org/benchmarks/

2021-11-01 Thread Kasper Daniel Hansen
Out of curiosity, do we know if vecLib/Accelerate has been optimized for M1? On Sun, Oct 31, 2021 at 10:00 PM Kieran Healy wrote: > Thanks, Simon. > > With the vecLib/Accelerate BLAS, the results are indeed rather faster :) > > Kieran > > > 14” MacBook Pro / M1 Max > >R Benchmark 2.5 >

Re: [R-SIG-Mac] possible bug in R's make install

2021-05-18 Thread Kasper Daniel Hansen
fic issue that's where should go if > it is to be fixed. > > Cheers, > Simon > > > > On May 18, 2021, at 12:32 AM, Kasper Daniel Hansen < > kasperdanielhan...@gmail.com> wrote: > > > > This bug is still present in the R-4.1. > > > > Best, &

Re: [R-SIG-Mac] possible bug in R's make install

2021-05-17 Thread Kasper Daniel Hansen
beleive I have reported this some time ago > but no action was taken. Compiling R with R internal BLAS does not > results in the error. > > Peter > On Fri, Sep 28, 2018 at 10:52 AM Kasper Daniel Hansen > wrote: > > > > I am trying to compile and install R under High Sierr

Re: [R-SIG-Mac] [External] Re: [External] Behaviour or Quartz windows

2021-02-09 Thread Kasper Daniel Hansen
quartz is the graphics layer of OS X ( https://en.wikipedia.org/wiki/Quartz_(graphics_layer)). This is why the "native" Apple device is called quartz() in R. This is a super nice device IMO. Xquartz is a port of X11 to quartz. To use XQuartz on OS X you have to use the x11() device (or features

Re: [R-SIG-Mac] R for macOS Big Sur

2021-01-14 Thread Kasper Daniel Hansen
Greg, Perhaps you're confused by the wording? It says "R compiled for High Sierra OR HIGHER". This is a minimum OS version. It doesn't mean you need to run High Sierra to use this binary. Best, Kasper On Thu, Jan 14, 2021 at 8:32 PM Gregory Coats via R-SIG-Mac < r-sig-mac@r-project.org> wrote:

Re: [R-SIG-Mac] R for macOS Big Sur

2021-01-11 Thread Kasper Daniel Hansen
Jean: _guessing_ this may be about parallel processing in BLAS? Does your timing include linear algebra? On Mon, Jan 11, 2021 at 2:38 PM Jean Thioulouse < jean.thioulo...@univ-lyon1.fr> wrote: > Hi > > Both versions seem to run fine indeed, but on my Mac mini M1, the arm > version (homebrew R)

Re: [R-SIG-Mac] Rstan compilation hangs misterisouly

2020-11-09 Thread Kasper Daniel Hansen
This line will essentially overwrite what RStan does for compilation. So yes, this is potentially a bad thing. On Mon, Nov 9, 2020 at 4:57 AM Goncalo Ferraz via R-SIG-Mac < r-sig-mac@r-project.org> wrote: > ok, found it! Makevars is where you said it would be and it contains only > this line: >

Re: [R-SIG-Mac] Building R 4.0.2 from source via clang/xcode for MKL on macOS

2020-09-29 Thread Kasper Daniel Hansen
To use veclib you need --with-blas="-framework Accelerate" My full building script on OS X is currently ../${SRCDIR}/configure SHELL='/bin/bash' \ --prefix=/usr/local/R/${R_VERSION} --disable-R-framework\ CC="/usr/local/clang8/bin/clang" \ CXX="/usr/local/clang8/bin/clang++" \

Re: [R-SIG-Mac] Building R 4.0.2 from source via clang/xcode for MKL on macOS

2020-09-29 Thread Kasper Daniel Hansen
In my understanding, almost all of the speed up comes from using an optimized BLAS. Optimizing LAPACK tend to have negligible impact on performance. At least that is my impression, although I won't say I'm an expert. Best, Kasper On Tue, Sep 29, 2020 at 9:53 AM roy wrote: > Hi Simon, > Thanks

Re: [R-SIG-Mac] Error when fitting a brms model, maybe associated with Catalina MacOS

2019-12-16 Thread Kasper Daniel Hansen
Just a comment on the macos-rtools. It seems wrong to me to set the user level ~/.R/Makevars. On Sat, Dec 14, 2019 at 9:29 PM Manuel Spínola wrote: > Thank you very much John. > > I restarted my computer, and everything looks fine now, I fitted a brms > model without the error message. > >

Re: [R-SIG-Mac] Apparent interaction between XQuartz and the Catalina (10.15) macOS upgrade

2019-10-09 Thread Kasper Daniel Hansen
Bob, You ran the betas. On issues like this, that could be a big difference. So Im not sure it is yet an issue that could be user dependent. Best, Kasper On Tue, Oct 8, 2019 at 10:00 PM Bob Rudis wrote: > I've been running Catalina since the first beta and upgraded to GM the day > of release.

Re: [R-SIG-Mac] Warning on XCode / Command Line Tools 11

2019-06-04 Thread Kasper Daniel Hansen
Thanks a lot for checking this so quickly. I was alarmed by the label "beta 1", and frankly surprised that this got pushed to my machine. I believe it is the first time system updated has suggested a beta version for something on my laptop. I am wondering if this could have been a mistake; it is

Re: [R-SIG-Mac] Xcode 10.2.1

2019-04-24 Thread Kasper Daniel Hansen
/Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg > \ > > -target / > > -Roy > > > On Apr 24, 2019, at 8:36 AM, Kasper Daniel Hansen < > kasperdanielhan...@gmail.com> wrote: > > > > I am on Mojave. I recently updated to Xcode 10.2.1 and I did t

[R-SIG-Mac] Xcode 10.2.1

2019-04-24 Thread Kasper Daniel Hansen
I am on Mojave. I recently updated to Xcode 10.2.1 and I did the associated update of the command line tools. Following this, I reinstalled clang6 and gfortran 6 from CRAN. When I use the clang6 compiler from CRAN, it is unable to find stdio.h. When I compare the include path from clang6 to the

[R-SIG-Mac] possible bug in R's make install

2018-09-28 Thread Kasper Daniel Hansen
I am trying to compile and install R under High Sierra with Accelerate BLAS but with R lapack. My relevant configure call is --with-blas="-framework Accelerate" but omitting --with-lapack. Full call is pasted at the end of this email I can do make make check but make install fails with

Re: [R-SIG-Mac] disabling threads when using Accelerate BLAS

2018-09-09 Thread Kasper Daniel Hansen
Thanks for the extremely helpful pointers on this. Clearly I need to remove --with-lapack in my configure step. On Sun, Sep 9, 2018 at 4:12 AM Prof Brian Ripley wrote: > On 08/09/2018 22:01, Kasper Daniel Hansen wrote: > > For timing purposes, is it possible to control the number o

[R-SIG-Mac] disabling threads when using Accelerate BLAS

2018-09-08 Thread Kasper Daniel Hansen
For timing purposes, is it possible to control the number of threads / cores when I have compiled R to use the BLAS in the Accelerate framework (by building R using ./configure --with-blas="-framework Accelerate" --with-lapack ) ? (The alternative is of course to build R using the supplied

Re: [R-SIG-Mac] Xcode 9

2017-09-27 Thread Kasper Daniel Hansen
Thanks. Nice to know it got fixed despite the somewhat pessimistic original post. Best, Kasper On Wed, Sep 27, 2017 at 4:32 AM, peter dalgaard <pda...@gmail.com> wrote: > > > On 27 Sep 2017, at 08:43 , Prof Brian Ripley <rip...@stats.ox.ac.uk> > wrote: > > > >

Re: [R-SIG-Mac] Xcode 9

2017-09-26 Thread Kasper Daniel Hansen
I don't see this with Xcode 9 OS X Sierra (10.12.6) and either R Under development (unstable) (2017-09-26 r73351) -- "Unsuffered Consequences" Copyright (C) 2017 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin16.7.0 (64-bit) or R version 3.4.2 RC (2017-09-26

Re: [R-SIG-Mac] Experiences with macOS Sierra

2016-09-22 Thread Kasper Daniel Hansen
Thanks for the work on this, especially the comment on xml2. I had noticed problems with xml2 while compiling Emacs 25.1 using the new Xcode on El Capitan, but I have not had time to track it down. Best, Kasper On Thu, Sep 22, 2016 at 2:39 AM, Prof Brian Ripley wrote: >

Re: [R-SIG-Mac] How to get a Fortran compiler compatible to Xcode?

2015-05-10 Thread Kasper Daniel Hansen
On Sun, May 10, 2015 at 6:06 PM, Kasper Daniel Hansen kasperdanielhan...@gmail.com wrote: This is where you look for add-ons http://r.research.att.com/libs for OS X. For texi2any I would install a new version of MacTex. Finally, see the R-admin manual. Best, Kasper

Re: [R-SIG-Mac] Command Line Quartz Device in Yosemite

2014-10-31 Thread Kasper Daniel Hansen
I am self-compiling on Yosemite using the libraries provided by Simon. I get quartz. Best, Kasper On Fri, Oct 31, 2014 at 6:23 AM, peter dalgaard pda...@gmail.com wrote: On 31 Oct 2014, at 10:24 , Colin A. Smith co...@colinsmith.org wrote: This thread got a bit off the topics I was

Re: [R-SIG-Mac] Mac OS X tcltk/X11 issues

2014-07-18 Thread Kasper Daniel Hansen
On Thu, Jul 17, 2014 at 2:05 AM, Simon Urbanek simon.urba...@r-project.org wrote: On Jul 15, 2014, at 3:01 PM, Kasper Daniel Hansen kasperdanielhan...@gmail.com wrote: Prof Ripley and other people involved with tcltk, You could have the tcltk building routine leave some evidence behind

Re: [R-SIG-Mac] Mac OS X tcltk/X11 issues

2014-07-15 Thread Kasper Daniel Hansen
Prof Ripley and other people involved with tcltk, You could have the tcltk building routine leave some evidence behind re. how it was build. For example, in Rgraphviz we used to grapple with something similar at the abstract level - was the Graphviz version used to build a binary distributed

Re: [R-SIG-Mac] ESS on Mavericks

2014-04-08 Thread Kasper Daniel Hansen
Do you use the same .emacs as before? This sounds like having to do with fortification and the R buffer, and might be solvable by using (setq comint-scroll-to-bottom-on-output 'others) in your .emacs. It would be strange if this is the source of your problem unless you're using a new .emacs.

Re: [R-SIG-Mac] trouble running invoking R from the terminal in a new install

2014-02-12 Thread Kasper Daniel Hansen
Have you set an alias or soft link somewhere? Try which -a R and look in your .bashrc / .profile. Kasper On Wed, Feb 12, 2014 at 7:39 AM, Catherine A. Lozupone catherine.lozup...@colorado.edu wrote: Hello, I am on Mac OS X Version 10.8.5. I recently installed R-3.0.2.pkg on my machine

Re: [R-SIG-Mac] Inaccurate inaccuracies on Mac only?

2013-12-02 Thread Kasper Daniel Hansen
I don't think your assumption that different systems will return the same (accurate or inaccurate) answers is correct. I don't even think you can assume that running the same code twice on the same system will give you the same answers, although in practice it often will. Kasper On Sat, Nov

Re: [R-SIG-Mac] Automatically detecting and setting CXX compiler using configure/Makevars

2013-10-09 Thread Kasper Daniel Hansen
binary distribution? Thank you again for all your help! Cheers, -Rob On Oct 8, 2013, at 5:57 PM, Kasper Daniel Hansen kasperdanielhan...@gmail.com wrote: Rob, What you should do, is _always_ inherit the compiler which was used to build R. That is the 'Right' way to go and it is what

Re: [R-SIG-Mac] Automatically detecting and setting CXX compiler using configure/Makevars

2013-10-08 Thread Kasper Daniel Hansen
Rob, What you should do, is _always_ inherit the compiler which was used to build R. That is the 'Right' way to go and it is what will happen per default if you are using Makevars to compile you package. If you need to use configure, there are hints in R-exts and we can help more specifically,

Re: [R-SIG-Mac] Installing packages with type=source instead of the default binary?

2013-09-09 Thread Kasper Daniel Hansen
The advantages are very minor (although I do source compilation myself). To Prof Ripley's list I will add that I personally like to know I can compile from source for packages that I depend on in package development, so I can trace down bugs and run R CMD check - but this is a very, very minor

Re: [R-SIG-Mac] Trouble with tcltk

2013-09-03 Thread Kasper Daniel Hansen
For those of us who compile from source, I assume this tcl8.6.0-darwin10-x86_64.tar.gz from http://r.research.att.com/libs/ is the recommend version? Indeed, I always assume I should just grab the newest version of everything I need from this location. Best, Kasper On Tue, Sep 3, 2013 at

Re: [R-SIG-Mac] R.app doesn't respect DYLD_FALLBACK_LIBRARY_PATH

2013-08-08 Thread Kasper Daniel Hansen
Setting DYLD_FALLBACK_LIBRARY_PATH is super dangerous and I would be highly suspicious of whoever told you to do that (in the sense that they don't really know how this works) It has the potential to really wreck your system. Especially if you set it in such a way that all GUI apps inherit

Re: [R-SIG-Mac] hidden files and directories

2013-08-06 Thread Kasper Daniel Hansen
Rohmatul, Check by doing R CMD build pkgName R CMD check pkgName_X_Y_Z.tar.gz The building step excludes many common files, and is recommended. Kasper On Tue, Aug 6, 2013 at 3:43 AM, Prof Brian Ripley rip...@stats.ox.ac.ukwrote: On 06/08/2013 08:41, Rohmatul Fajriyah wrote: Dear Prof.

Re: [R-SIG-Mac] R 3.0.0 beta

2013-03-20 Thread Kasper Daniel Hansen
I have heard rumors of GCC 4.7.2, has this been abandoned? Kasper On Wed, Mar 20, 2013 at 5:23 AM, Prof Brian Ripley rip...@stats.ox.ac.uk wrote: R 3.0.0 is due to be released on Apr 3, and is now in beta. Simon is travelling but before he left put up a binary distribution at

Re: [R-SIG-Mac] R 3.0.0 beta

2013-03-20 Thread Kasper Daniel Hansen
Prof Ripley, I highly appreciated the clarifications in this thread. I am sure I am not the only one. Good luck with finding a new compiler; I am happy to provide whatever help I can. Best, Kasper On Wed, Mar 20, 2013 at 1:08 PM, Marc Schwartz marc_schwa...@me.com wrote: Prof Ripley, A

Re: [R-SIG-Mac] error: unrecognized option ‘-arch’ -- suggestion!

2012-09-28 Thread Kasper Daniel Hansen
On Fri, Sep 28, 2012 at 10:58 AM, Prof Brian Ripley rip...@stats.ox.ac.uk wrote: On 28/09/2012 15:29, Kasper Daniel Hansen wrote: So I had a few emails with Peder, and I think he gets it now. However, one point came up which I have been wondering about as well. In Makeconf R only stores

Re: [R-SIG-Mac] error: unrecognized option ‘-arch’ -- suggestion!

2012-09-27 Thread Kasper Daniel Hansen
On Thu, Sep 27, 2012 at 10:07 AM, Peder Axensten peder.axens...@slu.se wrote: On 27 sep 2012, at 14:27, Simon Urbanek simon.urba...@r-project.org wrote: On Sep 27, 2012, at 5:02 AM, Peder Axensten wrote: The compiler (clang) and linker that Apple includes (with Xcode) uses the argument

Re: [R-SIG-Mac] compiling from source on ML, tcltk

2012-09-02 Thread Kasper Daniel Hansen
, and it has much nicer ttk widgets. On 02/09/2012 19:21, Kasper Daniel Hansen wrote: I now want to get tcltk support working under ML (because I need to test a few packages). I have installed Xquartz and I have just install the new tcltk 8.5.5 from CRAN (which is not signed btw). Running

[R-SIG-Mac] building R under Lion

2012-08-28 Thread Kasper Daniel Hansen
I am running Lion, with the newest version of Xcode, and the 5666 build of gcc+gfortran from Simon's page. This is on Macbook pro last generation, with a quad core i7. I have installed the latest stable release of Xquartz. I am building R, not as a framework (--disable-framework), but I am

Re: [R-SIG-Mac] texi2dvi error Sweave and exams

2012-08-19 Thread Kasper Daniel Hansen
Paul, The standard way to install Tex on the Mac is to use MacTex (a port of Texlive to the Mac), see http://tug.org/mactex/ You should probably install the big 2.1GB package on the front page. That should also place the tex utilities on your path (as far as I recall). Kasper On Sun, Aug 19,

Re: [R-SIG-Mac] graphics device with record=TRUE

2012-07-05 Thread Kasper Daniel Hansen
On Thu, Jul 5, 2012 at 9:42 AM, David Winsemius dwinsem...@comcast.net wrote: On Jul 4, 2012, at 11:47 PM, Richard M. Heiberger wrote: David, thank you. it works. Where is it documented? The first place I find written documentation of the cmd-arrow functions is in the R MacOSX FAQ:

Re: [R-SIG-Mac] Lion and X11

2012-01-28 Thread Kasper Daniel Hansen
For what it is worth I don't see this problem on Snow Leopard, self-compiled. You can make quartz the default device by putting Sys.setenv(R_INTERACTIVE_DEVICE = quartz) in your .Rprofile. Kasper On Fri, Jan 27, 2012 at 7:17 PM, Martin Renner greatauk...@gmail.com wrote: Hi All, Is anybody

Re: [R-SIG-Mac] LogicReg package problems

2012-01-16 Thread Kasper Daniel Hansen
On Mon, Jan 16, 2012 at 2:57 AM, BEES INC bees@gmail.com wrote: Hey there I am having a bit of trouble getting this working, I had to do a bit of fiddling with makefiles to get it to find the right gfortran, but it builds links without error, however the install gives the following

Re: [R-SIG-Mac] LogicReg package problems

2012-01-16 Thread Kasper Daniel Hansen
the same error. Can you build the package OK? Thanks On Tue, Jan 17, 2012 at 1:16 AM, Kasper Daniel Hansen kasperdanielhan...@gmail.com wrote: On Mon, Jan 16, 2012 at 2:57 AM, BEES INC bees@gmail.com wrote: Hey there I am having a bit of trouble getting this working, I had to do a bit

Re: [R-SIG-Mac] L after a number returns that number, what does it mean?

2011-11-22 Thread Kasper Daniel Hansen
This is not the appropriate email list for this question, but I can tell you that L means integer. Kasper On Tue, Nov 22, 2011 at 9:16 PM, Colstat cols...@gmail.com wrote: Hi, all When you enter 3L or 10L in R console, it still returns the number 3, 10, respectively.  It's amazing that

Re: [R-SIG-Mac] Multiple R versions: set Current via symbolic link: permissions?

2011-10-11 Thread Kasper Daniel Hansen
Marius, Note that this will _not_ make it possible to run the different R versions simultaneously. Kasper On Tue, Oct 11, 2011 at 10:19 AM, Simon Urbanek simon.urba...@r-project.org wrote: On Oct 11, 2011, at 6:24 AM, Marius Hofert wrote: Hi, I have multiple R versions installed and would

Re: [R-SIG-Mac] Screen device under macOS X

2011-10-06 Thread Kasper Daniel Hansen
I am on Snow Leopard. As Brian mentions, my DISPLAY variable is set (to echo $DISPLAY /tmp/launch-SN2m7Z/org.x:0 ), but this is not something I do myself. I have always thought that on (newer) OS X, DISPLAY got set automatically. Not too infrequently do I use X11 on a remote server and I always

Re: [R-SIG-Mac] Minor bug in Quartz sizing

2011-09-03 Thread Kasper Daniel Hansen
On Sat, Sep 3, 2011 at 12:47 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: With a current R-patched (2.13.1 Patched (2011-09-02 r56906)), the following code generates plots missing the bottom labels: par(mfrow = c(4, 5), mar = c(2.1, 2.1, 4.1, 1.1)) for (i in 1:20) plot(1) If I resize

Re: [R-SIG-Mac] install.packages: location of system-wide library tree

2011-05-25 Thread Kasper Daniel Hansen
.Library.site becomes not empty when you create a site library, for example by mkdir {PATH to R}/R/lib64/site-library (of course lib64 assumes a 64 bit architecture) Kasper On Wed, May 25, 2011 at 6:51 AM, Sean Davis sdav...@mail.nih.gov wrote: See help(.Library). Sean On Wed, May 25,

Re: [R-SIG-Mac] Where are my packages?

2011-05-19 Thread Kasper Daniel Hansen
You can have packages two places (1) system wide (2) user specific The packages that ship with R always install system wide which is why - when you look in your user specific packages - you don't see any. You need to reinstall the packages for 2.13. You cannot just copy the directories. You

Re: [R-SIG-Mac] problem checking packages with R 2.13.0

2011-04-17 Thread Kasper Daniel Hansen
On Sun, Apr 17, 2011 at 7:16 PM, John Fox j...@mcmaster.ca wrote: Dear Kaspar, -Original Message- From: Kasper Daniel Hansen [mailto:kasperdanielhan...@gmail.com] Sent: April-17-11 5:59 PM To: John Fox Cc: Prof Brian Ripley; r-sig-mac@r-project.org Subject: Re: [R-SIG-Mac] problem

Re: [R-SIG-Mac] plot() does not give labels under quartz

2011-01-19 Thread Kasper Daniel Hansen
This _may_ be unrelated to a corrupt font cache. Note that the OP says the issue is fixed by resizing the quartz screen. To see this in action (explanation below) I have posted http://www.biostat.jhsph.edu/~khansen/screen1.png (the initial look of the quartz window)