Re: [R-SIG-Mac] Installing Mac packages from a directory of .tgz files

2011-01-15 Thread Prof Brian Ripley
On Sat, 15 Jan 2011, Berend Hasselman wrote: On 15-01-2011, at 07:39, Murray Jorgensen wrote: Well, still no responses, but I'm further along the trail. I decided that I must need that 'PACKAGES' file so I went back to CRAN and got it, and placed it in my /Applications/tgz12.1/ folder.

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

2011-01-19 Thread Prof Brian Ripley
Missing labels has been reported several times, and AFAIK has always indicated a corrupt font cache (or other problems in the font book). There are various ways to repair that, so I'll leave you to Google for one. On Wed, 19 Jan 2011, Phillip Jardine wrote: Tena, I had the same problem

Re: [R-SIG-Mac] rgeos install

2011-03-02 Thread Prof Brian Ripley
On Wed, 2 Mar 2011, Andrew Bevan wrote: Dear list I am having problems installing rgeos from the R-forge site. It seems to install okay for the 64-bit version of R but not for the 32-bit version for some reason. For the latter, I get the following errors: --

Re: [R-SIG-Mac] system command in OS X failed when ampersand was added to command

2011-03-06 Thread Prof Brian Ripley
On Sun, 6 Mar 2011, Noah Lorang wrote: I'm not able to replicate using the same setup on several computers, either with R.app or R running in the terminal, so it's likely something highly specific to your setup. I'd suggest reinstalling or upgrading R and see if the problem goes away. The

Re: [R-SIG-Mac] would parallel computing help?

2011-03-08 Thread Prof Brian Ripley
This is an example of 'embarrassingly parallel' computation. Simply run each chain in a separate process in parallel. Packages such as snow or multicore can organize that for you. However, if you mean logistic regression (there are other binomial regressions such as probit), first check how

Re: [R-SIG-Mac] svg cairo support in 2.12.2 and higher?

2011-04-27 Thread Prof Brian Ripley
Try running 32-bit R on your platform: it does contain cairo support. (So does my own x86_64 build of 2.13.0: looks like there is/was a problem on the CRAN build machine. So you could also build R from the sources.) On Wed, 13 Apr 2011, Sarah Berke wrote: Hello, I'm not sure if this is the

Re: [R-SIG-Mac] install.packages without loading tcl tk interface for mirror selection

2011-04-27 Thread Prof Brian Ripley
On Wed, 20 Apr 2011, jmmi mijle wrote: Hi, Is it possible run install.packages() using the stock R Mac binary in the command line without it trying to load the tcl/tk interface to select a mirror? I'd rather just use the text-based numerical selection for the mirror and not have X11 start up

Re: [R-SIG-Mac] rgdal installation problems

2011-05-02 Thread Prof Brian Ripley
On Mon, 2 May 2011, António M. Rodrigues wrote: Hi, I'm trying to instal library rgdal in my macbook (os X 10.6.7). I have installed the latest R package (R-2.13.0.pkg). I have gdal 1.8 install. Also, I have loaded library sp which rgdal needs. I downloaded rdgal_0.6-33.tgz and using R

Re: [R-SIG-Mac] rgdal installation problems

2011-05-16 Thread Prof Brian Ripley
base other attached packages: [1] sp_0.9-81 loaded via a namespace (and not attached): [1] grid_2.13.0 lattice_0.19-23 tools_2.13.0 On May 2, 2011, at 1:03 PM, António M. Rodrigues wrote: No dia 2 de Maio de 2011 11:32, Prof Brian Ripley rip...@stats.ox.ac.ukescreveu: On Mon, 2 May

Re: [R-SIG-Mac] R plot and graphics fonts on Quartz

2011-05-21 Thread Prof Brian Ripley
On Sat, 21 May 2011, Simon Urbanek wrote: Carlo, On May 21, 2011, at 9:10 AM, Carlo Tambuatco wrote: This question has probably been asked to death already, I don't know yet...but when plotting using the Quartz framework on OS X, labels do not show up unless the sans font family is

Re: [R-SIG-Mac] packages failed to load - Now fixed

2011-05-25 Thread Prof Brian Ripley
It's really odd that people blog about their own inefficient scripts rather than read the R documentation. Because this scripts checks (very inefficiently) if a package is already installed, it would not solve the problem discussed in this thread. And install.packages() takes a vector of

Re: [R-SIG-Mac] building a package on a Mac: pdflatex

2011-07-05 Thread Prof Brian Ripley
And note too that this is looking first for a script texi2dvi. If you have that, *it* will look for pdflatex, possibly already knowing where to look. Also note that both the usual texi2dvi and tools::texi2dvi will consult environment variables such as PDFLATEX. If you have a standard Mac

Re: [R-SIG-Mac] building a package on a Mac: pdflatex

2011-07-05 Thread Prof Brian Ripley
On Tue, 5 Jul 2011, Federico Calboli wrote: On 5 Jul 2011, at 16:26, Kasper Daniel Hansen wrote: which texi2dvi /usr/bin/texi2dvi and $:/usr/local/texlive/2010/bin/x86_64-darwin$ ls texi* texindy but no texi2dvi. I did ask other mactex users and they also do not have texi2dvi Well, I

Re: [R-SIG-Mac] building a package on a Mac: pdflatex

2011-07-05 Thread Prof Brian Ripley
directly. And that this is all in the R-admin manual. On Wed, 6 Jul 2011, Berend Hasselman wrote: On 05-07-2011, at 17:39, Prof Brian Ripley wrote: On Tue, 5 Jul 2011, Federico Calboli wrote: On 5 Jul 2011, at 16:26, Kasper Daniel Hansen wrote: which texi2dvi /usr/bin/texi2dvi and $:/usr

Re: [R-SIG-Mac] Unicode characters in script?

2011-08-12 Thread Prof Brian Ripley
On Thu, 11 Aug 2011, Simon Urbanek wrote: On Aug 11, 2011, at 2:35 PM, Michael Hoban wrote: Hi all- I tried searching before posting, but this is one of those tricky questions to search for. My issue is this: within the R.app gui, I can use extended characters in plot labels without any

Re: [R-SIG-Mac] Old (versions of) packages

2011-09-06 Thread Prof Brian Ripley
You can transfer installed packages without compiled code from one platform to another. For packages with compiled code, you will need to get the old versions and compile from the sources. For CRAN old versions are available at http://cran.r-project.org/src/contrib/Archive Just what part of

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

2011-10-06 Thread Prof Brian Ripley
On Wed, 5 Oct 2011, Kasper Daniel Hansen wrote: This has everything to do with your configuration. I don't know why R does not do this out of the box when build with quartz support, but I It does for me, using either the CRAN build or my own build. See the code in

Re: [R-SIG-Mac] R_LIBS + .Rprofile: how to get a specific library in .libPaths()[1]

2011-10-10 Thread Prof Brian Ripley
You are taking the contents of a .Renviron file and putting it in .Rprofile. There is a whole section at the help page you quote about not confusing the two On Mon, 10 Oct 2011, Marius Hofert wrote: Dear all, I would like to use my own library for packages. It should go in

Re: [R-SIG-Mac] Difficulty installing package that works on Windows

2011-10-20 Thread Prof Brian Ripley
On Thu, 20 Oct 2011, Burgette, Lane wrote: Hi Everyone, I'm having problems installing a package locally from source on my Mac. It was developed on a Windows 7 machine (x86-64) and loads without incident under Windows (both x86-32 and x86-64) and Linux. When I try to install, it steps

Re: [R-SIG-Mac] problem installing geepack package

2011-10-25 Thread Prof Brian Ripley
This is something you need to take up with the geepack maintainer (who is also the doBy maintainer). I find his misuse of Depends ridiculous: we have Suggests and Enhances for such loose dependencies. You can easily get snow, as a source or a binary package. Did you update your packages?

Re: [R-SIG-Mac] Hmisc doesn't load

2011-11-19 Thread Prof Brian Ripley
See the list archives. Are you doing this in R.app, and have you updated R 2.14.0 recently? On Mon, 14 Nov 2011, Michael Kubovy wrote: After installing the Hmisc package in terminal: [mks-Mac-Pro:~/Downloads/14-11-11] mk% R CMD INSTALL Hmisc_3.9-0.tar .Rprofile: Setting US repository Loading

Re: [R-SIG-Mac] R 2.14.0 on MacBook Pro

2011-11-19 Thread Prof Brian Ripley
Please select a real CRAN mirror, not a broken one. On Wed, 16 Nov 2011, Christopher Giguere wrote: Hello everyone, I am working on a Mac OS X 10.6.8 (10K549). I need to install the package * fracdiff*. When I first ran into an issue I upgraded to R version 2.14 and tried to install again.

Re: [R-SIG-Mac] saving files using quartz engine

2011-11-19 Thread Prof Brian Ripley
On Wed, 2 Nov 2011, Denis Chabot wrote: Hi, is there a reason that the quartz device does not like the ~ in file names, whereas most functions handling files (including pdf() ) have no problem with it? Yes. [Hint: no one contributed a patch for this wishlist item. The authors of

Re: [R-SIG-Mac] manually load package

2011-11-23 Thread Prof Brian Ripley
Did you have a question? Your posting is two unconnected fragments. How to install source packages is described in the 'R Installation and Administration Manual'. You didn't tell us where you ran this, but very likely you need ~/Desktop/Design_2.3-0.tar.gz. But why not open a terminal and

Re: [R-SIG-Mac] Updating packages after updating R

2011-11-25 Thread Prof Brian Ripley
On 24/11/2011 16:17, christiaan pauw wrote: Hi Everybody I have updated to R 2.14 today from version 2.11 by installing the binary from http://cran.r-project.org/bin/macosx/. As the posting guide points out, there are no such versions of R. Have you read it? Is there an easy way to make

Re: [R-SIG-Mac] Cannot install RPostgreSQL from source but I have gcc

2011-11-25 Thread Prof Brian Ripley
On Fri, 25 Nov 2011, Simon Urbanek wrote: On Nov 25, 2011, at 2:52 AM, christiaan pauw wrote: Hi Everybody Im on Mac OS X 10.6.6 $ sw_vers ProductName: Mac OS X ProductVersion: 10.6.6 BuildVersion: 10J3210 I am trying to install the latest version of JavaGD from source using the GUI

Re: [R-SIG-Mac] Any script to package a built R binary to a Mac OS X installer?

2011-12-21 Thread Prof Brian Ripley
On 21/12/2011 19:49, Sang Chul Choi wrote: First, I apologize for sending this duplicate message to r-sig-gui. I thought that was the mailing list I should send questions about Mac GUI. I found that this r-sig-mac mailing list was the right place to ask the following question. Thank you.

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

2012-01-16 Thread Prof Brian Ripley
What precise OS and which architecture is this (see the posting guide)? AFAIK LogicReg will install on x86_64 on a Mac (nowadays the default for most people) but not the 32-bit architectures. It predefines some very large arrays: try reducing LGCn1MAX (twice) in slogic.f . It then works for

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

2012-01-25 Thread Prof Brian Ripley
On 25/01/2012 01:22, Steve Lianoglou wrote: Hi Peter, On Tue, Jan 24, 2012 at 8:06 PM, Peter Carrpc...@broadinstitute.org wrote: I, too, would like to run multiple versions of R, via command line, on Mac OS X. I have looked in vain for a clear explanation of why there can be one and only one

Re: [R-SIG-Mac] ERROR in R+Lion+X11: could not find any X11 fonts

2012-01-25 Thread Prof Brian Ripley
On 25/01/2012 12:22, Emilio Molinari wrote: Hi, after googling around I surrender and post to this list. Can you please follow the posting guide and tell us your sessionInfo() (and are you using R.app or R, the command-line version?). That your locale is not recognized by X11 may be

Re: [R-SIG-Mac] ERROR in R+Lion+X11: could not find any X11 fonts

2012-01-25 Thread Prof Brian Ripley
] kohonen_2.0.9 MASS_7.3-16 class_7.3-3 and, I am Running R in command line. thank you. emilio On 25 Jan , 2012, at 12:32, Prof Brian Ripley wrote: On 25/01/2012 12:22, Emilio Molinari wrote: Hi, after googling around I surrender and post to this list. Can you please follow the posting

Re: [R-SIG-Mac] OSX Binary Installation and testInstalledPackages()

2012-02-01 Thread Prof Brian Ripley
Yes, it was added on Windows at user request (including the ability to install the tests directory from sources). But as the Windows installers have much finer-grained granularity controlling what should be installed, people worried about space could skip it (and AFAIR it is not installed by

Re: [R-SIG-Mac] finding things in R manuals

2012-02-03 Thread Prof Brian Ripley
If you have multiple versions of R installed it is really convenient that they contain the appropriate manuals. I have an archive back to 2.0.0 (and a few before) that I consult surprisingly often. Our dept builds for Linux have always done 'make install install-pdf', and I think the

Re: [R-SIG-Mac] How to avoid this error: the following objects are masked from 'package: boot'

2012-02-27 Thread Prof Brian Ripley
On 27/02/2012 15:50, Jeffrey Ryan wrote: Not really a mac question at all. It isn't an error message either, it is a warning to alert you to the fact that two objects are now called the same thing and you may not be seeing the one you originally expected (now that the latter package is

Re: [R-SIG-Mac] ESC key and STOP button not working in R 2.14.1

2012-02-28 Thread Prof Brian Ripley
On 29/02/2012 00:02, R. Michael Weylandt michael.weyla...@gmail.com wrote: On Feb 28, 2012, at 4:41 PM, bugreport19621...@fastmail.fm wrote: The most recent email on this appears to be https://stat.ethz.ch/pipermail/r-sig-mac/2012-January/008967.html which says, the most recent GUI is

Re: [R-SIG-Mac] Installing packages from source for all installed sub-architectures

2012-03-05 Thread Prof Brian Ripley
On 06/03/2012 01:24, Simon Urbanek wrote: Dan, On Mar 5, 2012, at 7:09 PM, Dan Tenenbaum wrote: Hello, Are there plans to modify install.packages() on Mac so that if type=source, the package is installed for all installed sub-architectures? This works for Windows. Currently,

Re: [R-SIG-Mac] Installing packages from source for all installed sub-architectures

2012-03-05 Thread Prof Brian Ripley
Sorry, it appears that --merge-multiarch never got released except for Windows. We can certainly finish that off. On 06/03/2012 06:31, Dan Tenenbaum wrote: On Mon, Mar 5, 2012 at 10:22 PM, Prof Brian Ripley rip...@stats.ox.ac.uk wrote: On 06/03/2012 01:24, Simon Urbanek wrote: Dan

Re: [R-SIG-Mac] cannit get list of binary packages from the GUI

2012-03-16 Thread Prof Brian Ripley
On 16/03/2012 23:21, Simon Urbanek wrote: On Mar 16, 2012, at 8:55 AM, Prof Brian Ripley wrote: On 16/03/2012 12:31, Ken knoblauch wrote: Federico Calbolif.calboliat imperial.ac.uk writes: Apologies, I forgot to say, I have R 2.14.2, latest 64-bit GUI from http://r.research.att.com

[R-SIG-Mac] Building binary packages for distribution

2012-04-13 Thread Prof Brian Ripley
I have hitherto used a Leopard system to build Mac binary packages for distribution, but that system has died and we only have Lion systems left (and the replacement hardware only runs Lion). I'm only concerned with building i386/x86_64 packages. We saw problems with packages built on Snow

Re: [R-SIG-Mac] packages, R-patched and RC [Was: Importing Excel files]

2012-06-20 Thread Prof Brian Ripley
On 20/06/2012 11:20, peter dalgaard wrote: On Jun 19, 2012, at 23:29 , Prof Brian Ripley wrote: On 19/06/2012 17:35, Simon Urbanek wrote: On Jun 19, 2012, at 5:36 AM, peter dalgaard wrote: On Jun 19, 2012, at 01:16 , Colstat wrote: I think the error says it package Œgdata‚ was built

Re: [R-SIG-Mac] packages, R-patched and RC [Was: Importing Excel files]

2012-06-23 Thread Prof Brian Ripley
On 23/06/2012 07:28, David Winsemius wrote: On Jun 23, 2012, at 12:50 AM, Prof Brian Ripley wrote: Other messages say this is a temporary snafu on the Mac builder, which will be resolved once it percolates through CRAN: the master is OK already. Then I must be confused. I thought

Re: [R-SIG-Mac] installXLSXsupport() error

2012-07-16 Thread Prof Brian Ripley
On 16/07/2012 17:17, Davor Cubranic wrote: You didn't have to go through the command line. In the R GUI's package installer, if you switched package repository to CRAN (sources), you would have found XLConnect there too. You don't mention the version of OS X you're running, but for me with Lion

Re: [R-SIG-Mac] Question on warnings like wchar_t is Unicode on this platform

2012-07-19 Thread Prof Brian Ripley
On 19/07/2012 17:14, Hans-Jörg Bibiko wrote: Hi, [Since I have not a Windows machine at hand - I cannot say if it's a general R issue.] It's nothing to do with Windows, and everything to do with Apple's contempt for standards conformance (which these days vies with Microsoft's). I'm

Re: [R-SIG-Mac] R and Valgrind hangs on Snow Leopard

2012-08-13 Thread Prof Brian Ripley
On Mon, 13 Aug 2012, Cule, Erika wrote: (Reposted in plain text, with apologies) I am having the problem described in this post: https://stat.ethz.ch/pipermail/r-sig-mac/2011-November/008848.html In summary, running Valgrind with R hangs. As in the linked case above, if a file test.R

Re: [R-SIG-Mac] R and Valgrind hangs on Snow Leopard

2012-08-15 Thread Prof Brian Ripley
it would also work from the R session. This circumvents the system call used to remove the session temporary directory at the end of the session. On 13/08/2012 13:14, Prof Brian Ripley wrote: On Mon, 13 Aug 2012, Cule, Erika wrote: (Reposted in plain text, with apologies) I am having

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

2012-09-02 Thread Prof Brian Ripley
Do you need R.app? If not, I would recommend using ActiveTcl Tcl/Tk by e.g. ./configure ... --with-tcl-config=/Library/Frameworks/Tcl.framework/tclConfig.sh --with-tk-config=/Library/Frameworks/Tk.framework/tkConfig.sh I've been using it for some time, and it has much nicer ttk widgets.

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

2012-09-03 Thread Prof Brian Ripley
On 03/09/2012 01:11, Kasper Daniel Hansen wrote: On Sun, Sep 2, 2012 at 3:54 PM, Prof Brian Ripley rip...@stats.ox.ac.uk wrote: Do you need R.app? If not, I would recommend using ActiveTcl Tcl/Tk by e.g. ./configure ... --with-tcl-config=/Library/Frameworks/Tcl.framework/tclConfig.sh

Re: [R-SIG-Mac] ‘package ‘XML’ is not installed for 'arch=x86_64'’

2012-09-28 Thread Prof Brian Ripley
With a package such as XML available from multiple repositories, you have to be very precise what you are talking about. On CRAN, there is a source package for version 3.9-4. That can be compiled for multiple architectures on a Mac, and there are such binaries on CRAN. It only works in a

Re: [R-SIG-Mac] ‘package ‘XML’ is not installed for 'arch=x86_64'’

2012-09-29 Thread Prof Brian Ripley
On 29/09/2012 11:11, R. Michael Weylandt wrote: On Sat, Sep 29, 2012 at 10:58 AM, ricardo.julio.rodriguez.fernan...@sergas.es wrote: Please, allow me to hijack this thread to put in another, for me, related question I'm trying to work out on the list. To the best of my understanding and by

Re: [R-SIG-Mac] R Update - FAILED- HELP!!!

2012-10-06 Thread Prof Brian Ripley
On 06/10/2012 22:12, Jean Jang wrote: Apologies, I forgot to include the message from the Terminal: jeans-macbook-104:~ jean$ R R version 2.13.1 (2011-07-08) Please try installing a current version of R from CRAN: that is several versions old and 2.15.1 is current (and 2.15.2 imminent).

Re: [R-SIG-Mac] [R] missing gcc-42-5666.3-darwin11.pkg

2012-10-12 Thread Prof Brian Ripley
On 12/10/2012 17:50, Torben Griebe wrote: Hi there, I just wanted to install gfortran via homebrew on mac os x mountain lion. It uses the package gcc-42-5666.3-darwin11.pkg for installation. Unfortunately I recognized that this package is not available anymore. But the google cache told me that

Re: [R-SIG-Mac] warning on macintosh 2.16 that is not on 2.15.2 or on windows

2012-10-20 Thread Prof Brian Ripley
This is about lattice not using rep() correctly. There is no '2.16' and never will be (see the posting guide). From the NEWS for R-devel: \item The undocumented use \code{rep(NULL, length.out = n)} for \code{n 0} (which returns \code{NULL}) now gives a warning. Deepayan is aware

Re: [R-SIG-Mac] accessing SQL Server 10.00.1600

2012-10-24 Thread Prof Brian Ripley
On Wed, 24 Oct 2012, ricardo.julio.rodriguez.fernan...@sergas.es wrote: Hi! I'm happy using RMySQL to access a number of MySQL databases and RJDBC to PostgreSQL ones here, but now I do need to integrate data from SQL Server 10.00.1600. To the best of my knowledge and after googling for a

Re: [R-SIG-Mac] R 2.15.2

2012-10-27 Thread Prof Brian Ripley
On 27/10/2012 17:10, Roy Mendelssohn wrote: Hi: I see that R 2.15.2 is now available for the Mac. In some of the other R mail-lists people have mentioned having to reinstall packages when they upgraded to 2.15.2. Is this likely to be the case or should most packages that worked worked with

Re: [R-SIG-Mac] R 2.15.2

2012-10-27 Thread Prof Brian Ripley
On 27/10/2012 17:25, Prof Brian Ripley wrote: On 27/10/2012 17:10, Roy Mendelssohn wrote: Hi: I see that R 2.15.2 is now available for the Mac. In some of the other R mail-lists people have mentioned having to reinstall packages when they upgraded to 2.15.2. Is this likely to be the case

Re: [R-SIG-Mac] drag drop on R icon not changing directory

2012-11-06 Thread Prof Brian Ripley
On 06/11/2012 17:30, David Winsemius wrote: On Nov 6, 2012, at 6:05 AM, Ken Knoblauch wrote: Hi, just noticed this in R version 2.15.2 Patched (2012-11-04 r61084), that dragging a file onto the R icon when starting a session is not changing to the directory of the file. sessionInfo() R

Re: [R-SIG-Mac] R.app and launchpad and 32 bit

2012-11-08 Thread Prof Brian Ripley
On 08/11/12 12:24, Andrew Yee wrote: Hi, I'm new to Mac and when i installed the R.app, I noticed that it put the 32 bit version of R onto the Launchpad instead of the 64 bit version. Is this by design? The R installer put both R,app and R64.app there for me. What exactly did you do (you

Re: [R-SIG-Mac] R 32-bit suddenly the default on Mountain Lion 10.8.2?

2012-11-13 Thread Prof Brian Ripley
Marc, Start with 'which R', or run /usr/bin/R explicitly. That should be a symlink to /Library/Frameworks/R.framework/Resources/bin/R and that should be a symlink, If it is not like lrwxr-xr-x 1 root admin 3 28 Oct 08:03 /Library/Frameworks/R.framework/Resources/bin/R@ - R64 or is

Re: [R-SIG-Mac] switching between 2 versions of R in the GUI

2012-11-14 Thread Prof Brian Ripley
On 14/11/2012 20:26, Richard Friedman wrote: Dear R-Sig-mac, I have both the development version of R 2.16 and R2.15.2 on my Mac (OS 10.7.5). I only have one GUI (for R2.16). I can start R windows for the 2 versions from the command lines. I used to be able to switch with Rswitch but i

Re: [R-SIG-Mac] What's up with RSwitch

2012-11-16 Thread Prof Brian Ripley
On 16/11/2012 12:40, Duncan Murdoch wrote: On 12-11-15 11:57 PM, Paul Puglia wrote: As anybody successfully downloaded the RSwitch gui at r.research.att.com recently? I've tried to download both the .dmg and source files for the last week, and I all I get is a Not Found message. Does

Re: [R-SIG-Mac] library not found for -lX11

2012-11-29 Thread Prof Brian Ripley
But those paths should not be used unconditionally (as you have). They are not right for most x86_64 Linux, Solaris, ... and they might not even be right on Mac OS X (depending on the X installation). And PKG_CPPFLAGS was correct: that means flags for cpp, the C pre-processor, not for C++

Re: [R-SIG-Mac] library not found for -lX11

2012-11-29 Thread Prof Brian Ripley
On 29/11/2012 17:37, Federico Calboli wrote: On 29 Nov 2012, at 17:29, Jochen jochen.laubr...@gmail.com wrote: Just a guess, but maybe XCode and its command line tools need to be installed? I don't know for third parties, but I do have the latest XCode + command line tools installed (and I

Re: [R-SIG-Mac] R and R-Studio in new MacBook Pro retina with flash storage

2012-12-15 Thread Prof Brian Ripley
On 15/12/2012 02:36, Ray DiGiacomo, Jr. wrote: Hi Victor, I have a MacBook Pro with Retina display and use R everyday. I have not seen any issues related to the flash storage. I have not used RStudio very frequently so I cannot say if that software works well on a Retina model - but I am

Re: [R-SIG-Mac] packages impute

2013-01-02 Thread Prof Brian Ripley
On 02/01/2013 10:23, Guillaume Meurice wrote: Dear all, I recently got problem using impute package, which raise the following error message : Error in ximp[junk$imiss == 2] - NA : invalid type (bytecode) for 'dimnames' (must be a vector) And from time-to-time, it also cause some

Re: [R-SIG-Mac] x11/plot issue on Mac OSX

2013-01-22 Thread Prof Brian Ripley
On 23/01/2013 02:40, m p wrote: Hello, I have R running on my Mac OSX 10.7.5 under X11 and when I interactively in R issue x11() and plot(..) it exits with messages below. I can display multiple image formats including xwd. Is that fixable under X11, how? What do you think seq(1:10) does? Add

Re: [R-SIG-Mac] R packages on Mac

2013-01-23 Thread Prof Brian Ripley
On 23/01/13 10:27, Ross Tinsley wrote: Originally posted this on the standard mailing list and it was suggested that I post here on SIG Mac list. Have also included Beren's response who emphasised using the R.app GUI, however I am doing this as my first step. The below error message turns up

Re: [R-SIG-Mac] Encoding issue with text output from R

2013-02-01 Thread Prof Brian Ripley
On 31/01/2013 21:15, MacQueen, Don wrote: Something like this might help: Sys.setlocale(category = LC_ALL, locale = C) check Sys.getlocale() beforehand. -Don As others have said, use options(fancyQuotes=FALSE). Please don't change all the locale settings just because of

Re: [R-SIG-Mac] installing rgl with the 3.0 RC

2013-02-05 Thread Prof Brian Ripley
On 05/02/2013 13:25, Duncan Murdoch wrote: On 13-02-05 8:07 AM, Bryan Hanson wrote: Thanks for taking the time to look at this carefully Duncan. I don't see the warning you mention, and I don't see the string R_pretty0 in the log either. I'm appending right here in case there is something

Re: [R-SIG-Mac] installing rgl with the 3.0 RC

2013-02-05 Thread Prof Brian Ripley
i386 and x86_64. If you only want 64-bit packages, use R CMD INSTALL --no-multiarch. On Feb 5, 2013, at 11:01 AM, Prof Brian Ripley rip...@stats.ox.ac.uk wrote: On 05/02/2013 15:56, Bryan Hanson wrote: Is that something I can control? I've never had to worry about that before, never run

Re: [R-SIG-Mac] Block indent/un-indent crashes R 3.0 RC

2013-02-06 Thread Prof Brian Ripley
On 06/02/2013 01:22, Bryan Hanson wrote: Using the GUI indent/un-indent with more than one line of code selected crashes R for the version below. Modifying only one line does not. There is no '3.0 RC' (and never will be: the version will be 3.0.0. See the posting guide). Why do you think

Re: [R-SIG-Mac] Installing biOps fails with Symbol not found: _TIFFClose

2013-02-16 Thread Prof Brian Ripley
On 16/02/2013 16:37, Dominic Steinitz wrote: I have searched the archives and while I can find reports of this problem, I was unable to find any information on what to do to fix it. Apologies if this is already documented somewhere (and if so please point me at it). Let me know if should post

Re: [R-SIG-Mac] Installing biOps fails with Symbol not found: _TIFFClose

2013-02-19 Thread Prof Brian Ripley
On 19/02/2013 11:07, Dominic Steinitz wrote: Hi Brian, Thanks very much for this. You should have contacted the package maintainer as per the R posting guide. But Ok I shall do this. checking for TIFFOpen in -ltiff... no is the clue. See what config.log has to say …. I've

Re: [R-SIG-Mac] Change Rscript to 64-bit

2013-02-22 Thread Prof Brian Ripley
On 23/02/2013 04:32, Alton Ing wrote: How can we change Rscript to execute in 64-bit? The following script prints i386-apple-darwin9.8.0/i386 (32-bit) : #!/usr/bin/env Rscript sessionInfo()$platform I want to run RHadoop (rmr2) locally on Mac OS X 10.8.2 (Mountain Lion) but it only works with

Re: [R-SIG-Mac] library(rgl) hangs in all enviroments but R.app

2013-02-24 Thread Prof Brian Ripley
On 25/02/2013 04:56, Andrew Christianson wrote: So this is a strange one. Is it? Do you have X11 installed (from Xquartz on your OS)? The standard rgl (like the standard Tk) is an X11 application. If you do have Xquartz installed, try launching manually first, in case launchd is somehow

Re: [R-SIG-Mac] Buffering console output in R.app

2013-02-25 Thread Prof Brian Ripley
On 25/02/2013 20:00, Davor Cubranic wrote: R.app GUI 1.53 (6335 Leopard build 64-bit) and R 2.15.2 GUI 1.53 Leopard build 64-bit (6335) When I have a long-running call into C or C++, any output I try to print to the console with Rprintf or REprintf appears only after control returns to R,

Re: [R-SIG-Mac] Darwin open and '--vanilla' for R.app

2013-02-27 Thread Prof Brian Ripley
You are attributing documentation for R to R.app, a separate project not part of the R sources. R.app calls R with arguments --no-save --no-restore --gui=aqua, and does not pass its own arguments on. A fluent speaker of Objective C could change this easily enough. On 26/02/2013 14:02, Ben

Re: [R-SIG-Mac] issues with browseEnv, drag drop

2013-03-04 Thread Prof Brian Ripley
On 05/03/2013 03:41, Peter Dixon wrote: Hi - I'm not sure that this is precisely a Mac issue, but in a fresh install of R 2.15.2, I get the error: Error in browseEnv(html = F) : could not find function invsible whenever I open the workspace browser from the menu bar. This seems to be a typo

Re: [R-SIG-Mac] .../x86_64/ldpaths: No such file or directory after installing R-devel build

2013-03-16 Thread Prof Brian Ripley
On 16/03/2013 12:25, Richard D. Morey wrote: I installed the OSX R-devel 3.0 build, in pkg format, today from here: http://r.research.att.com/#nightly The postflight installation script breaks it. This has been reported: you need either to install from the sources or wait for tomorrow.

[R-SIG-Mac] R 3.0.0 beta

2013-03-20 Thread Prof Brian Ripley
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 http://r.research.att.com/snowleopard/R-3.0-branch/R-3.0-branch-snowleopard-signed.pkg . A high proportion of CRAN is available as binary packages, and we will

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

2013-03-20 Thread Prof Brian Ripley
beloved of g++'s lack of C++ standards conformance, and quite a high proportion of C++-using packages do not compile with clang++ (nor the Solaris CC). 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

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

2013-03-20 Thread Prof Brian Ripley
On 20/03/2013 14:38, R. Michael Weylandt wrote: On Wed, Mar 20, 2013 at 2:29 PM, Prof Brian Ripley rip...@stats.ox.ac.uk wrote: On 20/03/2013 14:14, Kasper Daniel Hansen wrote: I have heard rumors of GCC 4.7.2, has this been abandoned? At least for 3.0.0. It did not work well enough

Re: [R-SIG-Mac] Compiling R-packages on Mac

2013-03-30 Thread Prof Brian Ripley
On 30/03/2013 11:29, Petar Milin wrote: Hello ALL! I am a newbie on Mac, with long Linux experience (Ubuntu, than Debian, finally Fedora, for many years). R on Mac is very pleasant and works nicely. However, I noticed something strange, while I was trying to compile a package on which my

Re: [R-SIG-Mac] Installing R-3.0.0 RC (2013/03/30, r62448) installs tcl/tk in /local

2013-03-31 Thread Prof Brian Ripley
On 31/03/2013 09:18, Berend Hasselman wrote: I've just installed R-3.0.0 RC. I noticed that tcl/tk 8.6 was installed in /local. Shouldn't this be /usr/local? Yes, and has been reported. Can I just remove /local? Not if you want to use package tcltk. Copy it over /usr/local. Berend

Re: [R-SIG-Mac] R.app crashing

2013-04-16 Thread Prof Brian Ripley
That log says Library not loaded: /Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libR.dylib '3.1' means R-devel, not 3.0.0 and not R-patched. I can confirm this from today's R-patched: it looks like the wrong version of R.app got bundled: tystie% otool -L

Re: [R-SIG-Mac] Which command line tools for XCode 4.2.1

2013-04-18 Thread Prof Brian Ripley
Since I have heard that R and Bioconductor packages should in the future be built with clang since Apple will be discontinuing support of gcc, my question is: I've not heard that, and you give no reference. It's a pretty safe prediction except for timing: it could be a year away. So your

Re: [R-SIG-Mac] how to compile R for use with binary CRAN packages

2013-04-29 Thread Prof Brian Ripley
On 28/04/2013 18:43, Tobias Verbeke wrote: Dear list, The build page at http://r.research.att.com/building.html explicitly mentions quote Note that your binary will require you to install all packages from sources. /quote Is there any documentation on how to compile R from source in such a

Re: [R-SIG-Mac] R-3.0.0: choice of gfortran compiler in install.packages()

2013-05-09 Thread Prof Brian Ripley
Note that the recommended CRAN gfortran *does* go into /usr/local. This one: http://cran.r-project.org/bin/macosx/tools/gfortran-4.2.3.pkg as described at http://cran.r-project.org/doc/manuals/r-release/R-admin.html#OS-X . That's for R 3.0.0: other versions were recommended for earlier

Re: [R-SIG-Mac] R-3.0.0: choice of gfortran compiler in install.packages()

2013-05-10 Thread Prof Brian Ripley
, although I didn't know that the path would be different. You don't see any mention that they are recommended Davor On 2013-05-08, at 11:40 PM, Prof Brian Ripley wrote: Note that the recommended CRAN gfortran *does* go into /usr/local. This one: http://cran.r-project.org/bin/macosx/tools

Re: [R-SIG-Mac] R quits on update.packages()

2013-05-29 Thread Prof Brian Ripley
On 29/05/2013 02:28, Michael Herron wrote: Hello. I have installed 3.0.1 on an iMac. I just logged in remotely, tried to update.packages(), and R quit. For example: [brahms:~] herron% R R version 3.0.1 (2013-05-16) -- Good Sport Copyright (C) 2013 The R Foundation for Statistical Computing

Re: [R-SIG-Mac] Same code, working with R.app Mac GUI 1.61 (R 3.0.1), not with R 3.0.1 from terminal

2013-05-29 Thread Prof Brian Ripley
On 29/05/2013 14:12, Nathan Uyttendaele wrote: Hello, I have a very peculiar problem to share. I wrote a (rather) large R function that also includes some C code. When I run it with R.app Mac GUI 1.61 (R 3.0.1), no problem at all. When I run it from R 3.0.1 from terminal (on the same Mac), I

Re: [R-SIG-Mac] rgl crashes after one successful draw on R.app

2013-05-30 Thread Prof Brian Ripley
On 30/05/2013 02:27, Bryan Hanson wrote: Unfortunately, I already have XQuartz 2.7.4 and it gives the problem I reported. :-( Bryan But as I said way back in this thread, there are two different rgl devices and this trhead has conflated two problems, on in each. Roger was using the

Re: [R-SIG-Mac] Installing igraph

2013-06-27 Thread Prof Brian Ripley
On 27/06/2013 14:32, Thomas wrote: I've been given an old Mac to run some R programs on and I'm having trouble setting up. I just need to get igraph working It's OS X 10.5.6 and I have installed R 2.15.3 plus the copy of XCode that came on the DVD. For some reason I can't use the package

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

2013-08-06 Thread Prof Brian Ripley
On 06/08/2013 01:16, David Winsemius wrote: On Aug 5, 2013, at 5:00 PM, Rohmatul Fajriyah wrote: Dear All, I tried to build an R package (from the terminal) and everything was ok until R CMD check PackageName and I got this message: .. * checking for hidden files and directories ...

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

2013-08-06 Thread Prof Brian Ripley
*From:* Prof Brian Ripley rip...@stats.ox.ac.uk *To:* David Winsemius dwinsem...@comcast.net *Cc:* Rohmatul Fajriyah rfajri...@yahoo.com; r-sig-mac@r-project.org r-sig-mac@r-project.org *Sent:* Tuesday, August 6, 2013 8:06 AM *Subject:* Re: [R-SIG-Mac] hidden files and directories On 06

Re: [R-SIG-Mac] Rglpk package

2013-08-19 Thread Prof Brian Ripley
On 19/08/2013 05:02, Simon Urbanek wrote: On Aug 18, 2013, at 6:50 PM, Michael Weylandt wrote: On Aug 18, 2013, at 15:47, David Winsemius dwinsem...@comcast.net wrote: On Aug 18, 2013, at 11:45 AM, Horst R. Wolf wrote: Is there any reason why the OS X binary is still not available?

Re: [R-SIG-Mac] Rglpk package

2013-08-19 Thread Prof Brian Ripley
On 19/08/2013 05:02, Simon Urbanek wrote: On Aug 18, 2013, at 6:50 PM, Michael Weylandt wrote: On Aug 18, 2013, at 15:47, David Winsemius dwinsem...@comcast.net wrote: On Aug 18, 2013, at 11:45 AM, Horst R. Wolf wrote: Is there any reason why the OS X binary is still not available?

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

2013-09-03 Thread Prof Brian Ripley
On 03/09/2013 11:21, Michael Kubovy wrote: Many packages require tcltk. I have installed http://cran.r-project.org/bin/macosx/tools/tcltk-8.5.5-x11.pkg and yet, when I try That is the wrong version for R 3.0.1, so please remove it. You may need to re-install R, as that ships with the

Re: [R-SIG-Mac] R on Mac: framework or homebrew?

2013-09-12 Thread Prof Brian Ripley
On 12/09/2013 17:15, MacQueen, Don wrote: I've been using R on OS X probably ever since there was an R on OS X, and like you I use it from the command line. In the early days I installed R from sources, but quite a few years ago I switched to using the framework version. I can't think of any

Re: [R-SIG-Mac] [Caution: Message contains Suspicious URL content] R 3.0.1 build from sources: Wrong library paths

2013-09-13 Thread Prof Brian Ripley
On 13/09/2013 07:52, Anirban MUKHERJEE wrote: Hi Simon, On a related note, there has been progress on openmp in llvm/clang: http://www.phoronix.com/scan.php?page=news_itempx=MTQ0NjQ http://lists.cs.uiuc.edu/pipermail/llvmdev/2013-August/065169.html http://clang-omp.github.io/ That might be

Re: [R-SIG-Mac] [Caution: Message contains Suspicious URL content] R 3.0.1 build from sources: Wrong library paths

2013-09-13 Thread Prof Brian Ripley
CRAN package checks: CRAN does it daily so it must be possible. Best Simon On Sep 13, 2013, at 10:52 AM, Prof Brian Ripley rip...@stats.ox.ac.uk wrote: On 13/09/2013 07:52, Anirban MUKHERJEE wrote: Hi Simon, On a related note, there has been progress on openmp in llvm/clang: http

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