Re: [R-SIG-Mac] R2.12 for Mac
Hi, On Mon, Nov 15, 2010 at 5:24 AM, Ivan Calandra ivan.calan...@uni-hamburg.de wrote: Dear users, I've seen a few problems on this list related to R2.12 on Mac. It looks to me that the Mac release is not really stable yet, or is it? Maybe it's just a few instances and most of you have no problems at all with it. I've been using R-2.12 since day 0 and don't have any issues to report. I've also stopped using R from the GUI for a long time now (I only run it via the terminal, or through emacs/terminal), so if there are problems with using that for an extended period of time, I wouldn't know (I'm guessing there aren't, though). Therefore, I've kept my R2.11 on my Mac. Would you advise to upgrade or to wait some time? And if I should/can upgrade, do you have any recommendations regarding how to do it correctly (that are not included in the FAQ)? Keep in mind that you can keep R-2.11 on your machine *and* install R-2.12. If for some reason you think R-2.12 isn't stable enough for you, you can switch back to R-2.11 with Rswitch, which you can find here: http://r.research.att.com/#other -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] How to revert back to R 2.11
Hi Steven, Are you still having problems? I'd be surprised if R-2.12 itself has anything to do with the problems you're seeing, but assuming 2.11 is still on your system, you can switch to it easily by using Rswitch, that you can find here: http://r.research.att.com/#other It assumes 2.11 was installed via the normal R installers, ie. it lives in: /Library/Frameworks/R.framework/Versions/2.11 A few Q's for you: (1) Did you reinstall your R libraries for 2.12 from scratch (good idea) , or did you copy them over from your 2.11 install (bad idea) (2) Are you using R from R.app or from the terminal? (2a) When you run are from the Terminal, does it still exhibit this behavior? (2b) How about if you start R with the --vanilla flag?, eg: $ R --vanilla If you want to completely uninstall R 2.12 and start from scratch, you can do that from the terminal, too: $ sudo rm -Rf /Library/Frameworks/R.framework/Versions/2.12 Hope that helps, -steve btw - I don't think MAC needs to be capitalized ... it's not an acronym ;-) On Fri, Nov 12, 2010 at 3:50 PM, steven mosher mosherste...@gmail.com wrote: I recently noticed that R was having memory race condition on my MAC. At start up it would race to 1.3GB of memory used. Just on start up. For no apparent reason. Then it would release memory and fall back down to 50-60MB. Upon opening any window to edit old files or start a new one, the race would come back. programs that used to execute in short periods would take forever. Often not completing after hours. So: 1. did did a MAC system update ( Leopard) 2. installed R 2.12 3. X11 gets clobbered so I had to reinstall that. 4. RGDAL had to be reinstalled but I was able to make that work after some time. Now raster programs that worked an hour ago are broken and I found out that ncdf is not available yet. What's the simplest way to revert to R 2.11 and diagnose the memory race I seem to be having. [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] memory race
Hi, On Sun, Nov 14, 2010 at 6:09 PM, steven mosher mosherste...@gmail.com wrote: I recently started getting what I can best describe as a memory race condition in my R snip Running R from the terminal R --vanilla did not exhibit these issues. Maybe you have some ghost data file that are being loaded on R startup? Look to see if there is a file named .RData in your home directory. What do you see when you run this command from the terminal? $ ls -ald ~/.R* If you see an .RData file there, either delete it, or rename it to something else since R will try to load this file if it finds it there (unless you start R with --vanilla, or --no-restore-data) -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] memory race
Hi, Don't forget to cc r-sig-mac to keep correspondence, you'll likely get quicker + more informed suggestions if the whole community can see what's going on. On Sun, Nov 14, 2010 at 9:30 PM, steven mosher mosherste...@gmail.com wrote: It sure looks like it is trying to access a file or something. The problem may have started when I was accessing some large files. is it possible there is a connection open I'm guessing not ... weird that `R --vanilla` worked for a bit, then stopped. Also, these errors from another email sent earlier: dyld: lazy symbol binding failed: Symbol not found: _iconv_open Referenced from: /Library/Frameworks/R.framework/Resources/lib/i386/libR.dylib Expected in: /sw/lib/libiconv.2.dylib dyld: Symbol not found: _iconv_open Referenced from: /Library/Frameworks/R.framework/Resources/lib/i386/libR.dylib Expected in: /sw/lib/libiconv.2.dylib It's weird that R is fishing into your fink install for something ... maybe someone else will be able to make some sense out of it. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] How to determine if a Mac is Nehalem-based
Hi, Although I should, I don't follow too closely in the places I should (I don't know where those places are) to know if Apple is aware of this vecLib breakdown issue ... are they? Where can we go to add our voices/votes for them to fix it? Apple still has their apple.com/science section, so I guess this should be (somehow) important to them ... maybe we can make an R-SIG-Mac 20-person-strong tidal wave to help force their hand? ;-) -steve On Thu, Oct 21, 2010 at 12:36 PM, Simon Urbanek simon.urba...@r-project.org wrote: On Oct 21, 2010, at 7:47 AM, Stefan Evert wrote: On 21 Oct 2010, at 03:28, Simon Urbanek wrote: It's not vague at all, it's MacPro4,1 and MacPro5,1 models (you can use use sysctl hw.model to find out what you have). If in doubt, check on Wikipedia ;) The latter uses the Nehalem architecture but I don't have a specimen of those so I can't confirm that the bug still holds true for those. Not just those ... I'm plagued by the same problem on my Penryn-based MacBookPro4,1. In 64-bit mode, BLAS performance breaks down to single core levels, whereas in 32-bit mode (i.e. R --arch=i386) it uses both cores. I posted some benchmark results to this list a few weeks ago. Well, given that it is only a two-thread CPU there is not much you can gain so I wouldn't lose my sleep over it. If you have 16-theads CPU it's a while different story ;). For illustration, those are the timings from your benchmarks (only those that use BLAS) for 64-bit R 2.1...@10.6.4 on a 2.66GHz MacPro4,1: test R BLAS vecLib ATLAS MKL inner M %*% t(M) D 19.961 3.470 0.519 0.662 inner tcrossprod D 0.658 1.867 0.243 0.235 inner crossprod t(M) D 9.574 1.849 0.242 0.256 cosine normalised D 0.798 2.009 0.385 0.411 cosine general D 0.770 1.993 0.380 0.352 euclid() D 2.072 3.271 1.637 1.635 euclid() small D 0.515 0.821 0.421 0.395 As you can see both MKL and ATLAS outperform vecLib and R BLAS by an order of magnitude. It's sad, because vecLib used to be fairly well optimized ... (in fact it is actually some version of ATLAS which is even more strange ...). My solution has also been to switch to the reference BLAS, which outperforms vecLib on most of the operations I benchmarked, except for crossprod(), which is terribly slow (more than 10x slower than tcrossprod()). I've just tested again with R 2.12.0, and the situation has become even worse: now an explicit matrix multiplication M %*% t(M) -- which used to be fast -- performs as poorly as crossprod(). Any ideas about this? The crossprod() slowdown isn't a Mac problem: I got similar results on a Pentium Dual Core laptop running Ubuntu. If this is a known problem of the reference BLAS, is there any way to work around it? Apart from the speed hiccups, in my benchmarks vecLib BLAS performed consistently slower than the reference BLAS. Is there evidence from other benchmarks / hardware architectures that vecLib can be faster? If not, perhaps the default should be _not_ to use vecLib on Mac? Or perhaps it would be possible to autodetect hardware in the R startup wrapper and select the BLAS that's known to run faster on this setup? I don't think we would want to do that since that would prevent the user from choosing the BLAS they want to use. We will probably abandon vecLib as the default for the next release (more due to its numerical instability issues) and maybe provide all three options (vecLib, R BLAS, ATLAS) for the user to choose from in case they have a machine that can take advantage of it. Cheers, Simon ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Unable to install StatET in Mac OS X 10.6.3
Hi, On Tue, Aug 24, 2010 at 9:53 PM, Ye Sun y...@utstat.utoronto.ca wrote: I have installed R.2.11.1 in My MAC pro (I have also installed rJava package). Now I am having trouble doing configuration for my Eclipse (version 3.5) /STATET. Perhaps you'll have better luck asking on the StatET mailing list: http://lists.r-forge.r-project.org/mailman/listinfo/statet-user -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] install two versions of R on a Mac
On Thu, Aug 5, 2010 at 8:38 AM, Mike Lawrence mike.lawre...@dal.ca wrote: Do you mean you want two different versions of R on the same machine (eg. R-2.11.1 R-2.10.1)? Or do you mean you simply want to run multiple sessions of the same version at once? If the latter, you simply install one version and open multiple terminal sessions. And if you (Irina) are after the former, the only way I know how to run two different versions of R *simultaneously* is to have one installed by source (ie. not via the R.pkg which installs into /Library/Frameworks/R.framework) due to the requirement of a valid Versions/Current symlink in that R.framework directory. -steve On Thu, Jul 29, 2010 at 2:47 PM, Irina Foss irina.f...@thurso.uhi.ac.uk wrote: Hello, I am trying to install two versions of R on a Mac OS laptop to run almost at the same time. I tried to use pkgutil--forget in the terminal but it did not seem to make any changes. Thank you, Irina [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Mike Lawrence Graduate Student Department of Psychology Dalhousie University Looking to arrange a meeting? Check my public calendar: http://tr.im/mikes_public_calendar ~ Certainty is folly... I think. ~ ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] general tips for R on Mac
Hi, On Mon, Aug 2, 2010 at 5:26 PM, Dwight Hines dwight.hi...@gmail.com wrote: Yes, I second the need for such a site or tiplist for Macs on R. A major problem is the slow downs in MacOs that appear to be related to just having R on the system. Uhm ... what slow downs are you talking about? You feel that your system has slowed down after simply installing R? Like ... when R isn't even running? The second problem is the absence of good error messages. Can you give an example of error messages that are poor on the mac, but different on other platforms? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] newbie macuser questions
Hi, On Tue, Jun 15, 2010 at 6:02 PM, David Winsemius dwinsem...@comcast.net wrote: On Jun 15, 2010, at 5:38 PM, Michael Friendly wrote: I have a shiny new MacBook Pro, but am a total Mac-newbie. I downloaded and installed R 2.11.1, Xtools, the R Mac developer tools (for building packages). I'd like to use eclipse/StatET/subclipse subversion to build my packages and sync with R-Forge as I do on Win. Don't know. Couldn't get them to play together nicely on my machine. FWIW, I've had this combo working just fine previously ... I'm guessing it should still be fine to have this working now. I'm not using Eclipse much these days, though. -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] R texteditor for mac OS
still i have the problem with the curly braces. if I hit alt+8 / alt+9 which
is supposed to create curly braces on a mac,
Hmm ... this is news to me.
I'm guessing this might be some international keyboard issue? Eg. on
my (US) keyboard, the curly brace is shift-[ and shift-].
I'm not really sure what to tell you if alt-8 is giving you { in
every program but emacs ... I'm sure there's some simple solution.
I am switched to the interface below the editor itself.
You mean the R console running inside emacs?
I am it surprised by these issues because I though aquamacs was supposed to
run on macs.
Yes, it only runs on macs, in fact.
You can find out where to get more aquamacs specific support here:
http://aquamacs.org/support.shtml
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| Memorial Sloan-Kettering Cancer Center
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Re: [R-SIG-Mac] R texteditor for mac OS
Hi,
I also tried to aquamacs / Emacs, but had some trouble because it was not
accepting my curly braces {} out of the box.
Sorry, I can't figure out what you mean by that. Could you please elaborate?
Plus, I just got the R console running inside emacs and not my script
submitted to R. Though, i´d like to give it another try - so you have any
suggestions how to get over the hump a little easier... go ahead :) .
If you have an R process running within emacs (M-x R) and are
currently working in an R source buffer, you can send the contents of
the buffer to your inferior R process by hitting:
ctrl-c ctrl-l
Is that what you meant?
To send just the current line where your point is:
ctrl-c ctrl-j
or
ctrl-c ctrl-n
Here's an ess cheatsheet you can peruse:
http://ess.r-project.org/refcard.pdf
Does anybody have some experience with that R console inside Eclipse...
I briefly flirted with Eclipse + StatET a long time ago, but didn't
really get into it.
somehow I do not really trust it yet, but that´s just a gut feeling.
What about it seems so duplicitous to you?
--
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| Memorial Sloan-Kettering Cancer Center
| Weill Medical College of Cornell University
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Re: [R-SIG-Mac] Problems with Mac and X11.
Hi, On Wed, Apr 7, 2010 at 3:26 PM, steven mosher mosherste...@gmail.com wrote: I just downloaded the latest version of R for the MAC ( I have 10.5 ) and when I call pot routines I get errors on X11 libs. Any clue Not without any more details. Can you be more specific about the code you're trying, and the exact errors you're getting? For instance, this works fine for me: R X11() R plot(1:10) -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] feature request: paste and match style / open help files in external browser (R.app)
Hi Ben, On Wed, Mar 31, 2010 at 7:34 PM, Ben Madin li...@remoteinformation.com.au wrote: G'day Simon et al, On 31/03/2010, at 23:17 , Martin Batholdy wrote: I use the help-functions a lot to look up all the different arguments of a function. What I would love is if it would be possible to open help-files in a different program (like Safari). So that when I type ?par (or help(par)) my default web browser pops up and shows me the help-file. That would give me the opportunity to easily search the help-file via CMD+F and to quickly switch between a help-file and a script. An alternative feature option I often wished for when learning a new package would be the ability to select the text in the help window, and use the Command-Return key combination (as for the script window) to execute it (ie for the example text) instead of the copy - change window - paste - return combination... thus making stepping through example scripts much easier... but I suspect this to have hidden complexities! While this isn't exactly what you're asking for, I'm curious if you knew that typing, say: R example(lm) at the R prompt would run the code in the example section of the lm documentation? No copy-switch-paste necessary :-) -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Installation
Hi, On Sat, Feb 6, 2010 at 8:13 AM, Renzoandre De la Peña Lavander rzdelan...@gmail.com wrote: Hello My name is Renzo De la Peña, I change to R from SAS some time ago and I had never an inconvenient, until I changed to Snow Leopard couple weeks ago. I read all the FAQ's and instructions. I install Xcode from my retail DVD, downloaded gFortran even reinstalled X11 and every time I keep receiving this message when I statup During startup - Warning messages: 1: Setting LC_CTYPE failed, using C 2: Setting LC_COLLATE failed, using C 3: Setting LC_TIME failed, using C 4: Setting LC_MESSAGES failed, using C [R.app GUI 1.31 (5537) i386-apple-darwin9.8.0] WARNING: You're using a non-UTF8 locale, therefore only ASCII characters will work. Please read R for Mac OS X FAQ (see Help) section 9 and adjust your system preferences accordingly. I am running Java in 32-bits because I also use Berkeley Madonna for modeling which does not supports 64-bit for the chartflows, I really don't know what else to do here, if someone could help me I will be eternally grateful. It looks like the same error that popped up in this thread: https://stat.ethz.ch/pipermail/r-sig-mac/2009-December/006943.html Perhaps you can read through that to see what's up? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] R 2.10.0 instability (G5 iMac, Tiger 10.4.11)
Hi, On Nov 13, 2009, at 1:53 AM, Ken Knoblauch wrote: Lawrie Conole lconole at gmail.com writes: This looks similar to the problem that I reported where there seems to be some conflict about the GUI version indicated in the crash report for R 2.10 Tiger version. https://stat.ethz.ch/pipermail/r-sig-mac/2009-November/006750.html but to which there hasn't been a response yet. So far, I cleaned all old versions of R off my system and re-installed from scratch. Tried downloading the tar.gz version and installing that, but lately the link to the GUI.app only on the daily patch page seems to be dead. I haven't tried to compile the GUI by hand yet, next on my list, but maybe this independent report will attract more attention. So ... out of curiosity, do you folks get these crashes when running R from the terminal? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] R 2.10.0 instability (G5 iMac, Tiger 10.4.11)
Hi,
On Nov 13, 2009, at 5:20 PM, Lawrie Conole wrote:
Steve Lianoglou wrote:
So ... out of curiosity, do you folks get these crashes when
running R from the terminal?
Steve
I have no experience running R from the Terminal. My unix days are
a couple of decades behind me, so most (all?) of my familiarity with
that environment has disappeared. Do you expect it may behave
better there, without the GUI?
I'm not sure if it's going to fix your problems ... I only mentioned
it since Ken said something about a GUI version being different is all.
Perhaps running through the terminal can side-step your immediate
problem and let you keep working until someone can parse your error
log and come up with a better idea :-)
All you have to do is fire up Terminal.app and launch R from the prompt:
$ R
Try to source('/the/co.var/script.R') that's giving you problems and
see how it works.
HTH,
-steve
--
Steve Lianoglou
Graduate Student: Computational Systems Biology
| Memorial Sloan-Kettering Cancer Center
| Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact
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Re: [R-SIG-Mac] package installation issues
Heh ...
On Nov 12, 2009, at 12:45 PM, Michael Barnett wrote:
I apologize for not being more precise. I'm pasting the printout I
get below:
*
install.packages(igraph)
trying URL 'http://lib.stat.cmu.edu/R/CRAN/bin/macosx/leopard/
contrib/2.10/igraph_0.5.2-2.tgz'
Content type 'application/x-gzip' length 3312372 bytes (3.2 Mb)
opened URL
==
downloaded 3.2 Mb
The downloaded packages are in
/var/folders/7J/7JpbFNySGACoH3teAShOLE+++TM/-Tmp-//RtmpXG1NQC/
downloaded_packages
library(igraph)
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library '/Library/Frameworks/R.framework/
Resources/library/igraph/libs/x86_64/igraph.so':
dlopen(/Library/Frameworks/R.framework/Resources/library/igraph/
libs/x86_64/igraph.so, 10): Symbol not found: ___gmpz_clear
Referenced from: /Library/Frameworks/R.framework/Resources/library/
igraph/libs/x86_64/igraph.so
Expected in: dynamic lookup
Error : .onLoad failed in 'loadNamespace' for 'igraph'
Error: package/namespace load failed for 'igraph'
**
... that's really funny. I just tried to re-install igraph like you
did, and now I got the same error :-)
Do you have XCode installed? Installing the package from source seems
to do the trick:
install.packages('igraph', type='source')
... lots of compile info ...
Now loading igraph works (I had to restart R ... I guess having tried
to load the original compiled package hose the workspace, somehow).
I typically install most packages from source, anyway, so I guess this
is why I didn't see this before.
Does this work for you?
-steve
btw - I'm on a mac pro w/ snow leopard, not that I'm sure that matters
now ...
--
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| Memorial Sloan-Kettering Cancer Center
| Weill Medical College of Cornell University
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Re: [R-SIG-Mac] package installation issues
Hi Michael, On Nov 12, 2009, at 12:34 PM, Michael Barnett wrote: Hi R Mac list - I'm a newcomer to R and recently installed the new 2.10 version. I had to uninstall it and go back to 2.9 because I couldn't run the igraph package, it gave me an error. Also, I found that I couldn't load the rrgobi package into the new version either and there's an error message on the CRAN package site for the Mac version of rggobi as well. I just wanted to report this error, I'm happy with 2.9 for now. While I can't speak to using rrgobi, I definitely use igraph everyday, and I'm using R 2.10 Could you elaborate on the error you were getting when trying to run (load?) igraph? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] R package install (spp_1.7.tar.gz) problem
Hi, On Nov 4, 2009, at 11:34 AM, Yonwoo Jung wrote: I'm trying to install spp_1.7.tar.gz package. I always go this error message : bed2vector.C:13:31: boost/tokenizer.hpp: No such file or directory. If anyone could suggest it will be a great help. Below is more detail message. * installing to library Œ/Users/yonwoo/Library/R/2.10/library‚ * installing *source* package Œspp‚ ... ** libs ** arch - i386 g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/ Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/ include -D_FASTMAP -DMAQ_LONGREADS -fPIC -g -O2 -c bed2vector.C -o bed2vector.o In file included from /usr/include/c++/4.0.0/backward/strstream:51, from bed2vector.C:7: /usr/include/c++/4.0.0/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the X header for the X.h header for C++ includes, or iostream instead of the deprecated header iostream.h. To disable this warning use -Wno- deprecated. bed2vector.C:13:31: error: boost/tokenizer.hpp: No such file or directory I can't find the package in order to help and try this out, but it looks as if you just need to get the boost libraries: http://www.boost.org/ http://www.boost.org/doc/libs/1_40_0/more/getting_started/unix-variants.html Just make sure that the library is in your compiler's include path. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Building from source problems.
Hi, On Sun, Nov 1, 2009 at 2:46 PM, Rolf Turner r.tur...@auckland.ac.nz wrote: Checking on what I've got (following your instructions) I found that I have version 2.5 of Xcode. That appears to be the latest version of Xcode that runs on Tiger. The web page indicates that Xcode 2.5 dates from November 2007 which was about when I first installed Xcode. So re-installing Xcode 2.5 won't do any good. It might do some good, because it's possible that something got hosed ... (On Friday I mistakenly tried installing Xcode 3.1.3 or something like that, but of course that won't/doesn't/didn't work on Tiger.) So how do I get gcc-4.2 for my OS? (Mac OS X 10.4.11). Is this possible? The thing is, I'm not sure that you can. The best way to get the 'correct gcc compilers for your system is through the latest XCode available for your OS version. And, to be honest, I'm not sure that XCode 2.5 even has gcc 4.2, for some reason I think it only has 3.3 or 4.0.x ... of course I can be mistaken. Is it possible 4.2 came on your system from somewhere else? Did you try to install from the HPC compilers before? I have a Tiger machine sitting next to me at home, but it has XCode 2.0. I'm d/ling 2.5 to check and see if it comes with gcc-4.2 just in case ... I'll post back with those results when it's done d/ling and installing (I guess I should update it anyway ...). -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Building from source problems.
On Sun, Nov 1, 2009 at 4:00 PM, Rolf Turner r.tur...@auckland.ac.nz wrote: On 2/11/2009, at 9:48 AM, Steve Lianoglou wrote: Hi, On Sun, Nov 1, 2009 at 2:46 PM, Rolf Turner r.tur...@auckland.ac.nz wrote: Checking on what I've got (following your instructions) I found that I have version 2.5 of Xcode. That appears to be the latest version of Xcode that runs on Tiger. The web page indicates that Xcode 2.5 dates from November 2007 which was about when I first installed Xcode. So re-installing Xcode 2.5 won't do any good. It might do some good, because it's possible that something got hosed ... The way the Fates treat me, it will do no good with probability = 1!!! :-) After rereading the thread here (sorry if it feels like your talking to a wall), I'm guessing it won't, actually ... but it can't hurt. I don't ***have*** 4.2 at all, as far as I can tell. Simon Urbanek told me that I ***needed*** to use 4.2 in order to get things to build properly from source. He indicated that I should make the system ***use*** 4.2 by doing sudo gcc_select 4.2 but as I said, this just tells me that 4.2 ain't there. OH! I have a Tiger machine sitting next to me at home, but it has XCode 2.0. I'm d/ling 2.5 to check and see if it comes with gcc-4.2 just in case ... I'll post back with those results when it's done d/ling and installing (I guess I should update it anyway ...). Thanks. I look forward to your report with baited breath. (Like the cat that ate cheese and then sat by the mousehole ) :-) Well, XCode 2.5 is still downloading here ... I pay enough for this dang cable modem, but it's slower than slow. In the mean time, do you mind if we take one or two stabs in the dark? So, if I'm not mistaken, it seems your only problem now is compiling a package from source, and you're getting some mtune=core2 problem, right? THIS IS PROBABLY A BAD IDEA, BUT ... If we can't get your compiler to support these optimizations (maybe because we can't get gcc-4.2 on there), then how about we just don't use those optimizations when compiling? I'm not sure if that will cause problems, but perhaps we can try? Can you find where this is defined in your install? Doing: $ cd /Library/Frameworks/R.framework/Versions/2.10 $ grep -r mtune=core2 . for me brings up one file: ./Resources/bin/libtool:LTCFLAGS=-mtune=core2 -g -O2 Does it for you? I wonder what happens if you just comment that line out and insert below it: LTCFLAGS=-g -O2 Would all of your woes go away? As I said, it's probably a bad idea, but if you're brave, it might be worth a try. (I've been sitting on this email for a while now, because I don't want to make boneheaded suggestions in public, but my xcode d/l is @ 75% and I didn't want to leave you hanging for the rest of the day). -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Can't get help.start() to work.
Hi, On Oct 29, 2009, at 7:08 PM, Rolf Turner wrote: On 30/10/2009, at 11:45 AM, Simon Urbanek wrote: snip Yes - at least when you don't tend to it properly. If you use a global library, you must make sure you delete it whenever you upgrade R, otherwise you'll end up with incompatible packages. (There are less radical approaches, but they require even more care on user's side to work). That's why we recommend versioned libraries. Are you saying that every time I upgrade R I should completely remove my private library of packages (``Rlib'') and then recreate Rlib and re-install everything that was in it? I guess I can automate this so that it's not too hard to do But is this the ``usual'' procedure? Does everybody but me do this? :-) Impossible to answer, but likely not everybody, though they should :-) Also, I have recently checked on freshly downloaded packages from CRAN and got warning messages about their having been built with older versions of R. So re-installing would seem not to completely solve the problem of incompatibility. ... not sure what to say about that, but it seems weird if that's really happening on freshly installed packages (ie. not picking up an older version of your libs somehow). What are ``versioned libraries''? Where can I read up on this concept? RSiteSearch(versioned libraries) turned up nothing useful. More info than you want/need to know (or may already know, but anyway): The Framework way that R is installed under OS X is an easy way to keep these versioned libraries. You see how R installs in: /Library/Frameworks/R/Versions/2.X/... There is no global R library, by default, but rather a global library for a particular *version* of R: /Library/Frameworks/R/Versions/2.X/Resources/library Then you get the fancy linking from /Library/Frameworks/R/Resources - Versions/2.X/Resources and what not so the running version of R thinks there is some global repo. Answering what you really asked more directly: I suspect Simon's recommendation for versioned libraries would be for you to do something along the same lines the system uses. For instance, if you want to install into ~/Rlib, perhaps you should rather have: ~/Rlib/2.9/ ~/Rlib/2.10/ etc with each having their own (appropriate) versions of the libraries that you use. Which is to say, to have versioned libraries. :-) If you decide to go that route, perhaps you can then have in your ~/.Rprofile some mechanism to pick which of these directories to add to your libPaths by checking R's major/minor version. There's probably a more clever way, but this way could work: r.version - paste(version['major'], as.integer(version['minor']), sep=.) Sys.setenv(R_LIBS=paste(/Users/rturner/Rlib/, r.version, sep=) Hope that's helpful, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] BBEdit Language Module Enhancements
Hi, On Oct 30, 2009, at 4:17 PM, Berend Hasselman wrote: Could be a difference between BBEdit 8.5 and TextWrangler 3.0, which is related to BBEdit 9.2 BTW. I use TextMate for R. Brilliant. OOC, have you made any mods to the R.tmbundle? I'd like to get it to recognize s4 function defs. It's not a huge thing for me, so haven't spent the time to figure out the lang definitions, but was thinking if lazyness could prevail and see if anyone else has done so :-) -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Small issue rendering on a Quartz device
Hi, On Oct 22, 2009, at 7:38 AM, Mark Daniel Ward wrote: Hi there A.R., I'll confirm that this happens in R 2.8.x and 2.9.x versions on OS X 10.5, but it surely must be a well known issue. My students ask me about it all the time, and I just encourage them to resize their windows when they notice the problem, and that is a temporary fix. Assuming I understand what the problem is that you two are explaining, I'm a bit puzzled. I can't recall this ever really happening to me and I practically use R 24/7 (since ~ R 2.8.x). I don't use R.app, though. I run R via the terminal and set my options (device=quartz) in ~/.Rprofile ... not sure if that would make a difference or not (I suspect not(?)). I've also been using R-devel (2.10) for some time too ... -steve Mark Quoting r-sig-mac-requ...@stat.math.ethz.ch: Send R-SIG-Mac mailing list submissions to r-sig-mac@stat.math.ethz.ch To subscribe or unsubscribe via the World Wide Web, visit https://stat.ethz.ch/mailman/listinfo/r-sig-mac or, via email, send a message with subject or body 'help' to r-sig-mac-requ...@stat.math.ethz.ch You can reach the person managing the list at r-sig-mac-ow...@stat.math.ethz.ch When replying, please edit your Subject line so it is more specific than Re: Contents of R-SIG-Mac digest... Date: Thu, 22 Oct 2009 11:00:59 +0200 From: Arcadio Rubio Garc?a arcadiorubiogar...@gmail.com Subject: [R-SIG-Mac] Small issue rendering on a Quartz device To: r-sig-mac@stat.math.ethz.ch Message-ID: 7e5df3fe0910220200h71e22530y17db97c8697f8...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi, I'm new to R and I've spotted what I think it might be a small issue when rendering on a Quartz device. All images are initially cut on their lower side. Once you resize the Quartz window, the image is correctly displayed, even if you resize it to the original size. E.g. I do: curve(dnorm, from = -10, to = 10), and the X axis of the plot is below the lower boundary of the window. This issue does not happen on a X11 device for instance. I'm running the latest stable version (2.9.2) on Snow Leopard 10.6.1. I think the issue happened as well on 10.5 but I'm not totally sure. Thanks in advance. Best regards, A.R. ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] R crash on startup in OS X
Hi Jordan, On Oct 21, 2009, at 3:05 PM, Jordan Thomson wrote: Hello, I'm having trouble running the latest version of R (2.9.2) in Mac OS X 10.4.11. Once installed, the program crashes on launch, with the crash log giving the following error: Library not loaded: /Library/Frameworks/R.framework/Versions/2.9/ Resources/lib/libR.dylib Referenced from: /Users/jordythomson/Desktop/All Things Academic/ Courses and TA Files/R Workshop/R.app/Contents/MacOS/R Reason: image not found The folder R is trying to access no longer exists. I had an older version of R there but uninstalled it and deleted the folder some time ago. Perhaps I'm misunderstanding you, but I'm not sure how this is possible? Your new version of R (2.9.2) is installed in precisely that folder ... the R.app file in your ../All Things Academic/../.. is simply referencing the R system installed in /Library/Frameworks/ R.framework/ So, in short, you need /Library/Frameworks/R.framework/Versions/2.9 and its contents to be there to have a working R on your system. Does that help? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] R crash on startup in OS X
On Oct 21, 2009, at 3:55 PM, Jordan Thomson wrote: Hi Steve, Thanks for the quick reply. The Framework folder and contents are all there at /Library/Frameworks/R.framework/Versions/2.9, including the library file (libR.dylib). For some reason, however, R still won't load that library and crashes on launch. I'm not sure why that would be. Do you have any other suggestions? Hmm ... so I'm not sure what just happened since it wasn't there before (did you reinstall just now or something?). I see Simon just responded to you, so definitely do what he suggests, but it seems something is wonky. To minimize the back and forths, you might consider trashing the R.app you have in your *Academic* folder and reinstalling the R version you like from the appropriate *.dmg/*.pkg (eg. the new 2.10 RC is up at r.research.att.com if you're interested in that). If I recall correctly, the installer should put a new R.app in your / Applications folder. You should be able to move that wherever you like if you really don't want it there and it should just work. -steve Thanks for your time, Jordy - Original Message - From: Steve Lianoglou mailinglist.honey...@gmail.com To: Jordan Thomson jatho...@sfu.ca Cc: r-sig-mac@stat.math.ethz.ch Sent: Wednesday, October 21, 2009 12:20:12 PM GMT -08:00 US/Canada Pacific Subject: Re: [R-SIG-Mac] R crash on startup in OS X Hi Jordan, On Oct 21, 2009, at 3:05 PM, Jordan Thomson wrote: Hello, I'm having trouble running the latest version of R (2.9.2) in Mac OS X 10.4.11. Once installed, the program crashes on launch, with the crash log giving the following error: Library not loaded: /Library/Frameworks/R.framework/Versions/2.9/ Resources/lib/libR.dylib Referenced from: /Users/jordythomson/Desktop/All Things Academic/ Courses and TA Files/R Workshop/R.app/Contents/MacOS/R Reason: image not found The folder R is trying to access no longer exists. I had an older version of R there but uninstalled it and deleted the folder some time ago. Perhaps I'm misunderstanding you, but I'm not sure how this is possible? Your new version of R (2.9.2) is installed in precisely that folder ... the R.app file in your ../All Things Academic/../.. is simply referencing the R system installed in /Library/Frameworks/ R.framework/ So, in short, you need /Library/Frameworks/R.framework/Versions/2.9 and its contents to be there to have a working R on your system. Does that help? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] compiling packages for 64 bit architecture
Hi, On Sep 22, 2009, at 1:36 AM, Christophe Dutang wrote: Thanks for the tips, it works now. Since randtoolbox depends on rngWELL, which also has a configure file, I need to the following to compile randtoolbox for both architectures: - for i386, - rm *.o in rngWELL/src - R --arch=i386 CMD INSTALL --libs-only rngWELL - rm *.o in randtoolbox/src - R --arch=i386 CMD INSTALL --libs-only randtoolbox - for x86_64, - rm *.o in rngWELL/src - R --arch=x86_64 CMD INSTALL --libs-only rngWELL - rm *.o in randtoolbox/src - R --arch= x86_64 CMD INSTALL --libs-only randtoolbox If I want to avoid to manually remove object files in src directory, can I use a makefile in this directory? Sure, why not? If it's not there, you can make one yourself, no? We can provide an example, if that's what you're after. I'm not sure how to get R to run a custom Makefile tho (R-gurus: can you?) Do you advise me to install packages in a different directory than R_HOME/library using -l option? I think this is a matter of personal taste. I just install all of my libs in the system directory, and don't specify a personal one, but then again: my os x box is just a single user machine. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] JGR on Mac OS X 10.6 (Snow Leopard)
Hi Micahel, On Sep 14, 2009, at 8:44 AM, Michael Kubovy wrote: Hi Simon, I'm sorry to say that I've tried and failed to set up 64-bit R 2.9.2 and JGR. (1) It's not clear to me where on http://r.research.att.com/ to download from. (I searched for snow, since all else assumed that I know what I'm doing.) Look at this section: Universal nightly builds for Mac OS X (10.4 Tiger and 10.5 Leopard) For R-2.9.2, you want to look at the third row of that table: R-2.9-branch R 2.9.2 Patched (2009-09-05) http://r.research.att.com/R-2.9-branch-leopard-universal.tar.gz Note that this is NOT an installer, you have to untar the file and have it inflate at the root of your file system. The way to do that is explained immediately after that download/table listing: Alternatively you can use the tar-ball (*.tar.gz) which must be unpacked in the root (e.g. tar fvxz R*.tar.gz -C /), but doesn't contain the GUI (see below for a separate download). (2) I don't understand why you say (below) to download 2.9.0 rather than 2.9.2. I don't know why he mentioned that, but if this is the case, look at the Leopard Build section, there is a *.pkg installer for 2.9.0 http://r.research.att.com/R-2.9.0.pkg So could you please give step by step fool-proof instructions? (Right now, after fiddling, I can't launch R or JGR.) Downloading and installing one of the two R versions above will at least get R back up and running on your system (from the terminal, at least -- perhaps the *.pkg has the R.app gui installed too, I'm not certain). If R is completely hosed, you might want to start by removing all current installs (/Library/Frameworks/R.framework) you have now to ensure everything is fresh and clean (but maybe not, up to you.). -steve Thanks, Michael On Sep 12, 2009, at 7:59 PM, Simon Urbanek wrote: To answer all those recent posts on both mailing lists regarding JGR on OS X 10.6 (Snow Leopard): You need 64-bit R to run JGR, because Apple has removed 32-bit Java from OS X 10.6. So follow those steps: 1) Install 64-bit R from http://r.research.att.com/ option a) install R 2.9.0 package (but choose to NOT install gfortran) option b) unpack the leopard tar ball for R 2.9.2 and get the GUI from http://r.research.att.com/R-GUI-5473-2.9-leopard-Leopard64.dmg (in fact you can do both if you wish... ;)) 2) install necessary packages as follows: install.packages(c(rJava,JavaGD,iplots)) install.packages(JGR,type=mac.binary) 3) download 64-bit JGR launcher from http://urbanek.info/JGR-1.6-SL.dmg Run the launcher and enjoy. --- If you want to use JGR 1.7 from RForge.net, you have to install the packages from sources (when building JGR you must set NOAWT=1). If you are using your own build of R, you must build everything from sources yourself. Cheers, Simon ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] [R] 64-bit OSX binary for 2.9.2
Hi, On Sep 14, 2009, at 6:34 PM, Loren Engrav wrote: I too would vote for a 1 2 3 set of install instructions David's post should have all-but-nailed it ... some comments in line: , maybe for 32bit and 64bit if they differ They don't. The R that you install following the instructions below is a universal build, so 32bit and 64 bit (ppc + intel) are all installed. R is then launched in 32 bit or 64 bit mode by the command line args sent to it on launch. The various GUI's (if you go that route) take care of this for you. The 64 bit gui are the ones w/ 64 at the end of their download link, eg: * http://r.research.att.com/R-GUI-5426-2.1-leopard-Leopard.dmg (32 bit); vs * http://r.research.att.com/R-GUI-5426-2.1-leopard-Leopard64.dmg (64 bit) If you launch R from the terminal, it defaults to 32bit. If you want to launch R form the terminal in 64bit, you would do: For intel: $ R --arch x86_64 For ppc: $ R --arch ppc64 I did the 123 below and 1-the were many messages during install like x Library/Frameworks/R.framework/Versions/2.9/Resources/share/texmf/: Can't update time for Library/Frameworks/R.framework/Versions/2.9/Resources/share/texmf: Operation not permitted, but 2-2.9.2 seems to function OK after simple testing; is that warning insignificant Long version: This is because you need to run the tar command as a user who has privileges to write to the directory that the files are being uncompressed to. Short version: 2c of David's commands should be: 2. c) click on the Terminal window and (i) Type (without quotes): sudo (ii) Paste in the tar command: cmd-V to paste-in that command. So, the command to execute at 2c in your terminal is: $ sudo tar fvxz R*.tar.gz -C / I would do this again to ensure you have all of the 2.9.2 parts in there (ie, don't assume that everything was OK when you did it and got all those permission denied warnings/errors). 3-R.app available at http://r.research.att.com/ is 5426 but 5455 32 and 64 bit available at http://r.research.att.com/R-GUI-5455-2.9-leopard-Leopard.dmg as per 8/6/09 r-sig-mac discussion so I put in 5455; but why 5426 here and 5455 there? I don't have an answer for that, 5455 is a later build of the .app, so if it's working for you, I guess just go ahead and keep using that one. Otherwise, fall back to the one on the site. Hope that helps some, -steve Thank you Loren Engrav, MD U Washington From: David Winsemius dwinsem...@comcast.net Date: Mon, 14 Sep 2009 13:00:52 -0400 To: Steve Lianoglou mailinglist.honey...@gmail.com Cc: r-help r-h...@stat.math.ethz.ch, ivo welch ivo_we...@brown.edu, r-sig-mac@stat.math.ethz.ch r-sig-mac@stat.math.ethz.ch Subject: Re: [R-SIG-Mac] [R] 64-bit OSX binary for 2.9.2 On Sep 14, 2009, at 11:59 AM, Steve Lianoglou wrote: Hi, On Sep 14, 2009, at 11:44 AM, ivo welch wrote: dear R wizards: I am looking for a binary package distribution of R 2.9.2 for OSX . Looking at http://r.research.att.com/ , there seems to be only a binary for 2.9.0 . is the 2.9.2 version binary package available somewhere? (at this point, would it make sense to elevate the 64- bit version to a standard recommended rather than just a boutique version?) There isn't a *.pkg / *.dmg install for it, but it's there. In this section: Universal nightly builds for Mac OS X (10.4 Tiger and 10.5 Leopard) Third row in the table: http://r.research.att.com/R-2.9-branch-leopard-universal.tar.gz You have to inflate it at the root of your HD. The text right below the d/l table tells you how to do that: Alternatively you can use the tar-ball (*.tar.gz) which must be unpacked in the root (e.g. tar fvxz R*.tar.gz -C /), but doesn't contain the GUI (see below for a separate download). The problem may arise for *NIX-newbies ( a group in which I still claim membership) that they are unable to operationalize that message. For one thing they may not even know how to open a Terminal window. For another they may not know that the / at the end of that command will take care of unpacking at the root, so they will not need to navigate away from the place that they find themselves when Terminal opens up a bash session. The steps broken down would be something along these lines: First : Download the nightly build, and select Save to file rather than opening with Stuffit, and then it by default should end up in the user/Downloads/ folder. 1. a-c) Go to the Utilities folder of the Applications folder and double-click on Terminal.app 2. a) Go back to the browser and select the string: tar fvxz R*.tar.gz -C / (I would solicit some input here from more competent UNIXers regarding whether one would ever need to prefix this command with sudo.) 2. b) cmd-C to put it in the clipboard 2. c) click on the Terminal window and cmd-V to paste-in that command. 2 d) use the arrow and backspace keys (since mouse-clicking does not change the cursor position in Terminal sessions) to delete
Re: [R-SIG-Mac] rnorm.halton
Hi, On Mon, Sep 14, 2009 at 8:28 PM, Anirban Mukherjee anirb...@smu.edu.sg wrote: To add: If I try to install using the mac.binary, it tells me (on opening the 64 bit app) that the package is not installed for x64. And does not let me load the library when using 64 bit mode. However, if I install the package from source, then it installs for x64, but gives me weird results. Again: would appreciate if some one could confirm so that I can contact the authors and let them know. I do need Halton normals for some thing I am working on, and I am sitting right on that borderline point where the memory constraints of the 32 bit app are making me lose sleep ... I wouldn't know what to look for to tell you if it's going wrong or not. I have no idea about anything related to financial modeling and don't have the fOptions package installed anyway. Perhaps if you post the two images you get: i. what you expect to see/what you get from 32bit ii. the wrong image that you're getting from the 64bit version One of us can confirm/deny that we get the same thing. Otherwise, I really can't give you an educated answer w/o having to looking into what this 'halton' stuff is anyway ... So .. help us help you :-) I'm not sitting at a 64 bit machine atm, so hopefully someone else can help you before I get back to school tomorrow ... -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] JGR on Mac OS X 10.6 (Snow Leopard)
Hi Prof Kubovy, On Mon, Sep 14, 2009 at 9:10 PM, Michael Kubovy kub...@virginia.edu wrote: You've helped me get R up and running again, with R 2.9.0 GUI Leopard build 64-bit and R version 2.9.2 Patched (2009-09-05 r49613) x86_64-apple-darwin9.8.0 I again ran install.packages(c(rJava,JavaGD,iplots)) and install.packages(JGR,type=mac.binary). Then I downloaded http://urbanek.info/JGR-1.6-SL.dmg and installed it. It, however, failed to run. The splash creen starts, and the familiar JGR window appears, but then it fails. The console says: 9/14/09 9:01:40 PM com.apple.launchd.peruser.501[219] ([0x0-0x16ea6e9].org.rosuda.JGR[10908]) Exited with exit code: 2 I've never installed JGR, so I'm not sure what's going on and that message isn't really telling me much. Is there any other messages (above or below) that can help diagnose this? Perhaps it's something trivial w/ R+JGR, but I'm just not familiar with it. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] lme4 under 64 bit (Snow Leopard)
Hi,
On Mon, Sep 14, 2009 at 11:30 PM, Michael Kubovy kub...@virginia.edu wrote:
Error in library.dynam(lib, package, package.lib) :
shared library 'lme4' not found
[Workspace restored from /.RData]
Assuming you mean to autoload the .Rdata file ...
trying URL
'http://lib.stat.cmu.edu/R/CRAN/src/contrib/lme4_0.999375-31.tar.gz'
Content type 'application/x-gzip' length 839548 bytes (819 Kb)
opened URL
==
downloaded 819 Kb
* Installing *source* package ‘lme4’ ...
** libs
** arch - i386
sh: make: command not found
ERROR: compilation failed for package ‘lme4’
Did you install XCode after upgrading to Snow Leopard? It looks like
it can't find the make tool.
...
Error: package 'lme4' is not installed for 'arch=x86_64'
Being that you just installed 64 bit version of R, this makes sense.
Just install the new XCode and install a source package:
R install.packages('lme4', type='source')
It should work out fine.
-steve
--
Steve Lianoglou
Graduate Student: Computational Systems Biology
| Memorial Sloan-Kettering Cancer Center
| Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact
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Re: [R-SIG-Mac] Multiple threads on MacPro
Hi, On Aug 31, 2009, at 12:10 PM, Matthew Fero wrote: I'm wondering what is the best way is to take advantage of the multiple CPUs on a MacPro? For example, does someone have suggestions on how to setup and use parApply functions, in the snow package, on a multi-core Mac? I don't know if it's the best, but lately I like using the foreach package with the multicore backend * http://cran.r-project.org/web/packages/foreach/index.html * http://cran.r-project.org/web/packages/doMC/index.html * http://cran.r-project.org/web/packages/multicore/ -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] OT: Snow Leopard and Application Compatibility
Hi, On Aug 27, 2009, at 11:43 AM, Jan de Leeuw wrote: I have been using SL for over a year. Compiling and running a x86-84 bit R can be done without problems. There are about 600 packages in my R install, all build and run without problems. I don't know about R.app, though. I do find that R on SL, with suitable optimization flags, feels quite a bit faster. Would you mind sharing what optimization flags those might be? :-) In one of your previous posts you mention that you configure R for source compilation via this command: configure --with-aqua --with-blas='\''-framework vecLib'\'' --with- lapack --prefix=/usr/local/R --disable-R-framework --with-readline -- with-cairo --enable-memory-profiling --enable-R-shlib --x-includes=/ usr/X11R6/include --x-libraries=/usr/X11R6/lib --build=x86_64-apple- darwin10 --host=x86_64-apple-darwin10 --target=x86_64-apple-darwin10 I'm not sure I see any optimization flags there (aside from specifying darwin10 (for snow leopard, I reckon?)), but is all that you mean? Thanks, -steve On Aug 27, 2009, at 05:20 , Prof Brian Ripley wrote: There are list members with access to the developer pre-release 'seeds', and I have seen 'Mac OS X 10.6' in one report (with a corresponding sessionInfo() output). So it seems very likely there is no problem with R, and most likely none with with R.app. (We are deferring upgrading until our sysadmins are back from holiday absences.) On Thu, 27 Aug 2009, Marc Schwartz wrote: http://snowleopard.wikidot.com/ All, Above is the link to a web site that is being updated with information on potential application compatibility issues with Snow Leopard (SL). Curiously, R is listed there...with an Unknown Status. Our copy of SL should arrive tomorrow. Before updating, you should review this list to see if there are any potential issues with programs that you are using and SL. If there are, you may have to wait to upgrade the OS until an application is updated to be compatible. I have to wait until PGP (my whole disk encryption program) is updated, which supposedly will be soon according to their tech support folks. Regards, Marc Schwartz ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac === Jan de Leeuw; Distinguished Professor and Chair, UCLA Department of Statistics; Director: UCLA Center for Environmental Statistics (CES); Editor: Journal of Multivariate Analysis, Journal of Statistical Software; US mail: 8125 Math Sciences Bldg, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: dele...@stat.ucla.edu .mac: jdeleeuw ++ aim: deleeuwjan ++ skype: j_deleeuw homepages: http://gifi.stat.ucla.edu ++ http://www.cuddyvalley.org - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Problem with multicore/doMC/foreach combo on Leopard
Hi,
I just wanted to post a follow up on this issue. It seems that someone
notified Steve Weston of my problems shortly after I sent this email
to the list and he was kind enough to exchange a few words with me off
list (thanks to both of you!).
It looks as if this problem w/ the doMC backend was coming from my
having been sourcing the /Applications/R.app/Contents/Resources/GUI-
tools.R file in my ~/.Rprofile in order to get some functionality
like quartz.save(..) when running from terminal (I don't really use
R.app all that often).
I just wanted to let folks (and google) know that this problem hasn't
popped up for me since I've stopped sourcing that file. I actually got
the idea to source that file off some message in this list a while
ago, so perhaps putting this message out there will help anyone who
might find themselves in a similar situation I landed in.
Thanks for the help,
-steve
On Jul 28, 2009, at 5:50 PM, Steve Lianoglou wrote:
Hi all,
I'm posting this here first because (i) this might be a problem
specific to macs, and (ii) Simon is the maintainer of the multicore
package.
I'm using the doMC package to use the multicore library as a backend
for the foreach library.
Every now and again I'm getting mess-load of these errors when I
run a new multicore task via:
foreach ( ... ) %dopar% {
...
}
That look like so:
=== Error ===
*** caught segfault ***
address 0x1c86b7d80, cause 'memory not mapped'
The process has forked and you cannot use this CoreFoundation
functionality safely. You MUST exec().
Break on
__THE_PROCESS_HAS_FORKED_AND_YOU_CANNOT_USE_THIS_COREFOUNDATION_FUNCTIONALITY___YOU_MUST_EXEC__
() to debug.
The process has forked and you cannot use this CoreFoundation
functionality safely. You MUST exec().
Break on
__THE_PROCESS_HAS_FORKED_AND_YOU_CANNOT_USE_THIS_COREFOUNDATION_FUNCTIONALITY___YOU_MUST_EXEC__
() to debug.
==
I'm guessing it might be mac specific due to (i) reference to
CoreFoundation, and (ii) this answer given by Scott Lahteine in this
thread:
http://discussions.apple.com/thread.jspa?threadID=1209537tstart=0
Which I'm pasting here:
==
This is caused by programs that use the fork() or daemon() function
in combination with higher-level APIs. In Leopard you cannot use the
CoreFoundation (CF...) APIs on the child side of a fork() without
following it with an exec*() function. This has always been true,
but Leopard is much more stingy about this kind of thing.
To solve this issue, uninstall all third-party drivers and system
customizers, then reinstall them with the latest versions, and make
sure those versions have been updated for Leopard. Any drivers and
background software that use CF but haven't been updated for Leopard
will continue to output these messages, even though they may
function fine.
==
Does this suggest that the multicore package needs some updating for
leapord, or am I barking up the wrong tree? I don't see (nor would
have expected to see) any calls to CoreFoundation specific API's in
the multicore::fork.c file, so I'm not sure what's up since neither
doMC or foreach have any C code in them.
I'm running OS X.5.7 and 64-bit R 2.9.1. sessionInfo() is pasted below
I'll ask again in the main R-help if that's more appropriate.
Thanks,
-steve
sessionInfo()
R version 2.9.1 Patched (2009-06-28 r48863)
x86_64-apple-darwin9.7.0
locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] doMC_1.1.1 multicore_0.1-3 foreach_1.2.1 codetools_0.2-2
[5] iterators_1.0.1
--
Steve Lianoglou
Graduate Student: Computational Systems Biology
| Memorial Sloan-Kettering Cancer Center
| Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact
--
Steve Lianoglou
Graduate Student: Computational Systems Biology
| Memorial Sloan-Kettering Cancer Center
| Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact
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Re: [R-SIG-Mac] Nightly dmg builds
Hi Peter, On Aug 14, 2009, at 8:44 PM, Peter Cowan wrote: The night build page http://R.research.att.com/, conveniently include a dmg build of R-devel (2.10). However, I notice that the current dmg, is from a revision 48594, which is May I believe. Would it be possible have a more recent revision package as a dmg? Also, what is the preferred method of installing the tar.gz files? I was unclear how to use them in a fashion that would allow me to use Rswitch to switch versions. Just follow the instructions listed below that downloads table: Alternatively you can use the tar-ball (*.tar.gz) which must be unpacked in the root (e.g. tar fvxz R*.tar.gz -C /) So. assuming you d/l this: http://r.research.att.com/R-devel-leopard-universal.tar.gz Open up your terminal and cd into your ~/Downloads folder (assuming that's where it was d/l'd). Then call this: tar fvxz R-devel-leopard-universal.tar.gz -C / R will be installed in the correct place (ie: /Library/Frameworks/ R.framework/Versions/2.10). Unpacking like this at first switches the symlink to point to the 2.10 install (I'm pretty sure). You can then use RSwitch as normal to jump back and forth between 2.9 and 2.10. Hope that helps, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] Problem with multicore/doMC/foreach combo on Leopard
Hi all,
I'm posting this here first because (i) this might be a problem
specific to macs, and (ii) Simon is the maintainer of the multicore
package.
I'm using the doMC package to use the multicore library as a backend
for the foreach library.
Every now and again I'm getting mess-load of these errors when I run
a new multicore task via:
foreach ( ... ) %dopar% {
...
}
That look like so:
=== Error ===
*** caught segfault ***
address 0x1c86b7d80, cause 'memory not mapped'
The process has forked and you cannot use this CoreFoundation
functionality safely. You MUST exec().
Break on
__THE_PROCESS_HAS_FORKED_AND_YOU_CANNOT_USE_THIS_COREFOUNDATION_FUNCTIONALITY___YOU_MUST_EXEC__
() to debug.
The process has forked and you cannot use this CoreFoundation
functionality safely. You MUST exec().
Break on
__THE_PROCESS_HAS_FORKED_AND_YOU_CANNOT_USE_THIS_COREFOUNDATION_FUNCTIONALITY___YOU_MUST_EXEC__
() to debug.
==
I'm guessing it might be mac specific due to (i) reference to
CoreFoundation, and (ii) this answer given by Scott Lahteine in this
thread:
http://discussions.apple.com/thread.jspa?threadID=1209537tstart=0
Which I'm pasting here:
==
This is caused by programs that use the fork() or daemon() function in
combination with higher-level APIs. In Leopard you cannot use the
CoreFoundation (CF...) APIs on the child side of a fork() without
following it with an exec*() function. This has always been true, but
Leopard is much more stingy about this kind of thing.
To solve this issue, uninstall all third-party drivers and system
customizers, then reinstall them with the latest versions, and make
sure those versions have been updated for Leopard. Any drivers and
background software that use CF but haven't been updated for Leopard
will continue to output these messages, even though they may function
fine.
==
Does this suggest that the multicore package needs some updating for
leapord, or am I barking up the wrong tree? I don't see (nor would
have expected to see) any calls to CoreFoundation specific API's in
the multicore::fork.c file, so I'm not sure what's up since neither
doMC or foreach have any C code in them.
I'm running OS X.5.7 and 64-bit R 2.9.1. sessionInfo() is pasted below
I'll ask again in the main R-help if that's more appropriate.
Thanks,
-steve
sessionInfo()
R version 2.9.1 Patched (2009-06-28 r48863)
x86_64-apple-darwin9.7.0
locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] doMC_1.1.1 multicore_0.1-3 foreach_1.2.1 codetools_0.2-2
[5] iterators_1.0.1
--
Steve Lianoglou
Graduate Student: Computational Systems Biology
| Memorial Sloan-Kettering Cancer Center
| Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact
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Re: [R-SIG-Mac] R/qtl installation on Leopard 10.5.7
Out of curiosity: In addition: Warning message: package 'qtl' was built under R version 2.10.0 Are you running the devel version of R (2.10.0)? Or is something fishy going on? -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Debugging package code in Xcode?
Hi, This is also above my paygrade so was waiting for Simon or Prof. Ripley to chime in, but until then, I do have one suggestion: Was rgl.so compiled with debug symbols turned on? I don't know: it was compiled by R CMD INSTALL rgl. I was told a couple of years ago that symbols were included by default, but I don't know if that's still true. I think so (based on my success with C functions). I think you need to compile with the -g flag, and you'll probably want to turn off optimization (I think R CMD BUILD/INSTALL defaults to -O2) I think you can probably change these inline when you do R CMD INSTALL ... , but I just tweak my Makevars whenever I want to compile with different settings. I do this be creating the file ~/.R/ Makevars. Compiling with debug flags and no optimization, that file would look like this: CC=/usr/bin/gcc -arch x86_64 -std=gnu99 CPP=/usr/bin/gcc -arch x86_64 -std=gnu99 -E CXX=/usr/bin/g++ -arch x86_64 CXXCPP=/usr/bin/g++ -arch x86_64 -E OBJC=/usr/bin/gcc -arch x86_64 -std=gnu99 CFLAGS=-g CXXFLAGS=-g When I want R to use its default settings, I just comment out the lines in that file. Maybe when you compile with these args, it might get you closer to getting your debugger working as you take the rest of the steps that you've described. By the looks of it, you're way more of a C/gdb jedi than I, but perhaps this might help. -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] mac OS X 10.5.7 rgdal installation problems
:// www.cuddyvalley.org - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au - -- Stephen Sefick Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] mac OS X 10.5.7 rgdal installation problems
here is everything so far, and I still don't know what is going on. thanks, Well, it seems like it can't find the right include files it needs from your proj install, see: checking proj_api.h usability... no checking proj_api.h presence... no checking for proj_api.h... no Error: proj_api.h not found. If the PROJ.4 library is installed in a non-standard location, use --configure-args='--with-proj-include=/opt/local/include' for example, replacing /opt/local/* with appropriate values for your installation. If PROJ.4 is not installed, install it. ERROR: configuration failed for package ‘rgdal’ * Removing ‘/Library/Frameworks/R.framework/Resources/library/rgdal’ Can you find proj_api.h? Try `locate proj_api.h` ... is it there? You're using: R CMD install --configure-args='--with-proj-include=/sw/include/ proj' rgdal Depending on what the locate command tells you about where proj_api.h is, perhaps you'll need to change that. Would '--with-proj-include=/sw/ include/proj' suffice? Not sure what you'll have to set it to precisely, but that's why the compile is bombing on you right now. -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] mac OS X 10.5.7 rgdal installation problems
Sorry: R CMD install --configure-args='--with-proj-include=/sw/include/ proj' rgdal Depending on what the locate command tells you about where proj_api.h is, perhaps you'll need to change that. Would '--with- proj-include=/sw/include/proj' suffice? I rather meant '--with-proj-include=/sw/include' -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] mac OS X 10.5.7 rgdal installation problems
On Jul 2, 2009, at 3:29 PM, stephen sefick wrote: locate proj_api.h /Applications/GrassGIS.app/Contents/Resources/app/grass-6.3.0/ include/gproj_api.h /Applications/GrassGIS.app/Contents/Resources/app/grass-6.3.0/ include/grass/gproj_api.h /Applications/GrassGIS.app/Contents/Resources/app/x11/grass-6.3.0/ include/grass/gproj_api.h /Applications/GrassGIS.app/Contents/Resources/grasslib/include/ proj_api.h /Library/Frameworks/PROJ.framework/Versions/4.6/Headers/proj_api.h /sw/include/proj_api.h Right, so as suggested, instead of: R CMD install --configure-args='--with-proj-include=/sw/include/proj' rgdal do R CMD install --configure-args='--with-proj-include=/sw/include' rgdal -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] mac OS X 10.5.7 rgdal installation problems
Same problem as before -- you're not telling the build system where to find your proj install. You told it where the 'includes' are, now you have to tell it where the library is -- just *read* the error message: Error: libproj.a not found. If the PROJ.4 library is installed in a non-standard location, use --configure-args='--with-proj-lib=/opt/local/lib' for example, replacing /opt/local/* with appropriate values for your installation. If PROJ.4 is not installed, install it. It's telling you what you need to do, perhaps something like: R CMD install --configure-args='--with-proj-include=/sw/include --with- proj-lib=/sw/lib' rgdal Does that work? -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] RSwitch
Hi, On Jul 1, 2009, at 5:26 PM, cstrato wrote: Dear Simon, On my Mac (10.4.11) I have installed different versions of R and thus like RSwitch very much. However, in my case it works only when I am logged in as administrator. Since I am usually logged in as normal user I have to: logout - login as admin - run RSwitch - logout - login as user I know this tool is unsupported but do you think there is a possibility for an update? You can *probably* get this behavior by changing the permissions on your R.framework directory. By default, I think it's set to: drwxrwxr-x 9 root admin 306 Jun 29 10:39 /Library/Frameworks/ R.framework/ Since the RSwitch program monkeys around with which symlinks point to what in that folder, you'll need admin rights to use it. I'm guessing that if you chown or chgrp that directory such that your logged in user has the rights to change stuff in there, you can then use the app as a non admin .. w/o an app update :-) HTH, -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] R 2.9.1
Hi, On Jun 30, 2009, at 8:41 AM, Federico Calboli wrote: It's on CRAN now; perhaps the mirror you're using is a little slow to update? Probably quite a bit slow: 2009-06-26 13:29 R-2.9.1.dmg so the Mac binary was actually out very early this time ... you could install it while having your afternoon tea on the R release date :). In the bottomless pit of my stupidity I always wanted to ask the following, but I've always been too ashamed (or lazy) to ask. I always download the full dmg, but I never install any of the supplementary packages. Should I? only in case of a fresh installation (I'm upgrading now)? I have Xcode and X11 installed already anyway. I would use the full installer at least once :-) It provides a tcl/tk library that R can use, as well as a gfortran compiler that can target the different Mac architectures (ppc/x86 32 and 64 bit). While XCode will compile source package that only rely on C source, you'd be marooned w/o the gfortran compiler if a package has fortran source. That said, if you're just installing the binary package, then you probably wouldn't even notice. I used the mini installer this time to upgrade from 2.9.0 to 2.9.1. -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Too many dependencies with BioConductor packages?
Hi,
On Jun 23, 2009, at 9:29 AM, Gad Abraham wrote:
[Some clipping]
OK, so it installs all the Depends, Imports, Suggests, and Enhances.
Maybe this should be mentioned somehow in the GUI (rename install
dependencies?). It's not too much of an issue for CRAN, but in
BioConductor there are large packages (10s of MB at least) which can
get downloaded needlessly but are only Suggested.
While this might not be here nor there, it's certainly somewhere
in between:
If you stick with the recommended way of installing bioconductor
libraries, ie:
R source('http://bioconductor.org/biocLite.R')
R biocLite('GOstats')
You'd likely circumvent this problem. GOstats is installed in my
system, but most all of the extra packages you were pulling down are
not.
-steve
--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Medical College of Cornell University
http://cbio.mskcc.org/~lianos
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Re: [R-SIG-Mac] problem installing lme4 package with R 2.9.0
Hi Robert, On May 26, 2009, at 1:13 PM, Robert Seyfarth wrote: When attempting to install the lme4 package I get the following error message: Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/Library/Frameworks/R.framework/ Versions/2.9/Resources/library/lme4/libs/i386/lme4.so': dlopen(/Library/Frameworks/R.framework/Versions/2.9/Resources/ library/lme4/libs/i386/lme4.so, 6): Library not loaded: /usr/local/ lib/libgfortran.2.dylib Referenced from: /Library/Frameworks/R.framework/Versions/2.9/ Resources/library/lme4/libs/i386/lme4.so Reason: image not found Error: package/namespace load failed for 'lme4' But when I look in the library folder lme4.so is there. Thanks for any help... I think this error message is saying that it can't load the libgfortran.2.dylib library in: /usr/local/lib/libgfortran.2.dylib Do you have this file? If not, I believe this library should be installed by the full (not the mini) R installer (since it also installs gfortran by default), so if you don't have it, try to install gfortran from there. Hope that helps, -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University http://cbio.mskcc.org/~lianos ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Linux user asks: What about that Editor you have built-in. Can we compile it too?
Hi, I'm not sure either, but I don't think it'd be all that trivial to port over the editor if it's cocoa based. If for some reason your emacs/ess issues don't get solved and you're looking for an editor/R combo, perhaps taking a look at Eclipse with the StatET[1] plugin might be a better option than trying to compile your own editor together :-) HTH, -steve [1] StatET: http://www.walware.de/goto/statet On May 15, 2009, at 4:50 PM, Rob Goedman wrote: Paul, Hopefully someone with knowledge of Emacs ESS R on Linux will help you first! I would guess recompiling just the Editor is virtually impossible. R.app, in which the Editor is embedded, is Cocoa based. It would be a major undertaking to port R.app or at least major parts of it (and subsequent maintenance). E.g. http://www.gnu.org/software/gnustep/resources/BookClarifications.html talks about some of the issues. And there is a 3rd edition of the Hillegass book. If the Emacs/ESS issues absolutely cannot be resolved, maybe a more feasible/easier route would be to use tcl/tk, like John Fox has done in Rcmdr. Maybe start-off with something like MetPad? Not simple either, but doable. Rob On May 15, 2009, at 12:59 PM, Paul Johnson wrote: I use Linux only and have been teaching students with Emacs ESS. Lately, we've had some troubles with that combination that are not solved, and it has caused me to look about for alternatives. One of my students has a Macintosh and he showed me that the R that he installed came with an editor that does what we need. The command-shift sends lines over. So I started to wonder: why can't we compile that Editor in Linux? If a Mac is really BSD Unix with a layer of libraries, it should be possible. There are GNUstep libraries to duplicate much of the NextStep framework, but I have not studied enough on current Mac systems to know how close we might be to building the Mac R editor along with R itself. I've been Googling and searching in this lists archive and don't find much discussion on this. If anybody has ideas about whether this is possible, please advise. pj -- Paul E. Johnson Professor, Political Science 1541 Lilac Lane, Room 504 University of Kansas ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University http://cbio.mskcc.org/~lianos ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Compiling packages with specific gcc
Hi Simon, R uses the Apple compiler, but I'm not hard-coding the full path. In your case apparently your PATH has /usr/local/bin before the system paths, so it overrides the default. Another (simpler?) way to solve this is to simply move /usr/local/bin at the end of your PATH (recommended) and all should be well without changing any config files. I actually wanted to avoid doing this because I tend to install newer versions of standard things into /usr/local/* that I'd like to use instead of the default ones in /usr/bin/* so I was looking for a back door ... As for the rest of your comments (which I'll keep below for posterity), they're spot on. Thanks for the thorough and informative feedback. I've nuked all traces of the HPC compilers and will now just explicitly compile w/ /usr/bin/g++-4.2 when necessary ... that's a simple-enough sol'n for me until Apple decides to set some gcc = 4.2 as the default compiler. Thanks again, -steve This kind of leads me into another related question, then. So, I actually d/l'd the HPC compiler so I can compile w/ -fopenmp (to use OpenMP for some easy parallelization). You can use -fopenmp with Apple's compilers as well, just make sure you make the gcc-4.2 compilers the default (sudo gcc_select 4.2 if you have gcc_spect on your system, otherwise change the symlinks like ln -sf gcc-4.2 /usr/bin/gcc etc. - or specify them directly as you did). Apple's gcc-4.2 compilers are supported by the CRAN binary. Does this mean that I shouldn't do that w/ a vanilla R install and perhaps recompile R from source w/ the HPC compiler? And if Simon doesn't like using the HPC compiler, then should we stay away from this in general? In general, yes. As you have seen yourself the HPC compilers are not complete, so they cannot build universal binaries. Also they don't use Apple's driver, so all Apple-specific flags will fail. I didn't check the last HPC release, but before they were partially broken causing miscompilations, included wrong binaries (i.e. even the compiler for Tiger would include symbols for Leopard so the binary would not work), etc. I was trying to contact the maintainer a few times, but without avail, so I don't think it's well supported, either. Cheers, Simon -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University http://cbio.mskcc.org/~lianos ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] Compiling packages with specific gcc
Hi all, I'm wondering if/where I can go to tell R to use a specific version of my gcc compiler when installing packages from source, via `install.packages(..., type='source')` or when running `R CMD INSTALL some_source_packge.tar.gz` from the command line. The reason I ask is because I've downloaded gcc-4.4 from HPC/OSX[1], and it unfortunately puts the compilers in /usr/local/bin/gcc, w/o version info (it would be nice if it were /usr/local/bin/gcc-4.4). R tries to use this when compiling, but these compilers do not support the -arch=... flags, so it bombs. I've been hunting around in the tools:::.install_packges code and also the R Installation and Adminstration[2] document, but can't find what I'm looking for. I have a feeling that perhaps I can put something into my ~/.R/Makevars, or ~/.R/Makevars-i386-apple- darwin8.11.1 file, but I'm just taking stabs at the dark, so not having much luck. I can work around this by temporarily removing /usr/local/bin from my path when trying to `R CMD INSTALL` packages by source, but I was hoping there might be a more elegant solution. The fact that installing by source gets the `make` command from the system environment makes me a bit hopeful, but I'm not really sure. Thanks for any help, -steve [1] HPC/OSX: http://hpc.sourceforge.net/ [2] R Install/admin: http://cran.r-project.org/doc/manuals/R-admin.html#Linear-algebra -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University http://cbio.mskcc.org/~lianos ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Compiling packages with specific gcc
Thanks Duncan Kasper, I've been able to squeeze out of my problem ... Duncan: You can pass configure args with the configure.args parameter to install.packages. I'm not sure how many you need to set, but you'll likely need to set CC, CPP, CXX, F77, FC, OBJC, and maybe some of the associated flags. You can see the list using R CMD config in the console. The R CMD config was the trick. I actually put set those flags in my ~/.R/Makevars-PLATFORM file, as it seems the build step is picking these up so I don't have to pass them into the configure.args param. For the record, since I'm on a first generation MBP, the name of that file is Makevars-i386-apple-darwin8.11.1, and it looks like: CC=/usr/bin/gcc CPP=/usr/bin/cpp CXX=/usr/bin/g++ CXXCPP=/usr/bin/cpp OBJC=/usr/bin/gcc Kasper: You will want to recompile R with the new compiler. Then, whenever you compile a package, it will use the same compiler as R was compiled with. Thanks for the preemptive warning. On the computer where I'm having this problem, R is actually installed from the official cran installer, so I just needed to set it to use the apple gcc by default. I have to assume that this R was also built w/ Apple's gcc, so perhaps R doesn't use the same compiler by default, as you suggest? I'm not sure. Mixing compilers might be possible using the hints from Duncan, but I am pretty sure it is discouraged. In the past Simon has discouraged use of the HPC compilers. I don't remember the reasons, but I respect the source of the information :) He knows way more about mac compilers than I do. Of course, this was a while back and things might have changed. Yeah, I'd trust that source of information as well :-) This kind of leads me into another related question, then. So, I actually d/l'd the HPC compiler so I can compile w/ -fopenmp (to use OpenMP for some easy parallelization). Does this mean that I shouldn't do that w/ a vanilla R install and perhaps recompile R from source w/ the HPC compiler? And if Simon doesn't like using the HPC compiler, then should we stay away from this in general? Thanks, -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University http://cbio.mskcc.org/~lianos ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Compiling packages with specific gcc
Sorry to spam, but I just wanted to post this follow up just in case someone asks google about this later. I found that I can get the R's default settings for the ones I needed to override (CC, CPP, etc.) by typing `R CMD config SETTING` at the command line. So, for instance, to find out what R had config'd for CPP: $ R CMD config CPP gcc -arch i386 -std=gnu99 -E So I used that to redefine my Makevars, only now I have an absolute to gcc/g++ so that I can get the ones from Apple, and not the one in my / usr/local/bin. So, the contents of my Makevars file is now: CC=/usr/bin/gcc -arch i386 -std=gnu99 CPP=/usr/bin/gcc -arch i386 -std=gnu99 -E CXX=/usr/bin/g++ -arch i386 CXXCPP=/usr/bin/g++ -arch i386 -E OBJC=/usr/bin/gcc -arch i386 -std=gnu99 -steve On May 5, 2009, at 3:03 PM, Steve Lianoglou wrote: Thanks Duncan Kasper, I've been able to squeeze out of my problem ... Duncan: You can pass configure args with the configure.args parameter to install.packages. I'm not sure how many you need to set, but you'll likely need to set CC, CPP, CXX, F77, FC, OBJC, and maybe some of the associated flags. You can see the list using R CMD config in the console. The R CMD config was the trick. I actually put set those flags in my ~/.R/Makevars-PLATFORM file, as it seems the build step is picking these up so I don't have to pass them into the configure.args param. For the record, since I'm on a first generation MBP, the name of that file is Makevars-i386-apple- darwin8.11.1, and it looks like: CC=/usr/bin/gcc CPP=/usr/bin/cpp CXX=/usr/bin/g++ CXXCPP=/usr/bin/cpp OBJC=/usr/bin/gcc Kasper: You will want to recompile R with the new compiler. Then, whenever you compile a package, it will use the same compiler as R was compiled with. Thanks for the preemptive warning. On the computer where I'm having this problem, R is actually installed from the official cran installer, so I just needed to set it to use the apple gcc by default. I have to assume that this R was also built w/ Apple's gcc, so perhaps R doesn't use the same compiler by default, as you suggest? I'm not sure. Mixing compilers might be possible using the hints from Duncan, but I am pretty sure it is discouraged. In the past Simon has discouraged use of the HPC compilers. I don't remember the reasons, but I respect the source of the information :) He knows way more about mac compilers than I do. Of course, this was a while back and things might have changed. Yeah, I'd trust that source of information as well :-) This kind of leads me into another related question, then. So, I actually d/l'd the HPC compiler so I can compile w/ -fopenmp (to use OpenMP for some easy parallelization). Does this mean that I shouldn't do that w/ a vanilla R install and perhaps recompile R from source w/ the HPC compiler? And if Simon doesn't like using the HPC compiler, then should we stay away from this in general? Thanks, -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University http://cbio.mskcc.org/~lianos -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University http://cbio.mskcc.org/~lianos ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Reminder: Please test the 2.9.0 beta/rc binaries!
Hi, On Apr 10, 2009, at 2:22 AM, Prof Brian Ripley wrote: This is not a bug (and nothing to do with the subject line). I felt it did have to do w/ the subject line since it seemed like bug- like behavior to me and one I thought might be simple to correct before 2.9 if that was the case. Sorry if that caused any confusion. As it turns out, it was just a rather silly oversight on my part and indeed a boneheaded one at that because the behavior would have been clear if I took a quick peak at the implementation of the plot.default function. Thanks for taking the time to clear it up for me. -steve You need to set 'ylab', e.g. p2 - list(x=rnorm(500), main='bug?', col='orange', type='l', ylab=) Why? Because the default is the deparse of 'x', and that is a long string. On Thu, 9 Apr 2009, Steve Lianoglou wrote: Hi, On Apr 8, 2009, at 3:52 PM, Simon Urbanek wrote: I would like to remind everyone that we are in the final week of the beta testing of R 2.9.0, so please test the binaries now! There are installers for both the Tiger (32-bit) and Leopard (32- bit and 64-bit) binaries at http://R.research.att.com/ Reporting bugs right *after* the release is pointless - that's why we are providing beta and rc builds, so please test them well before 4/17! Post any issues you have with it here. Sorry I can't test this directly since I'm in the middle of doing some analysis and don't want to install 2.9 and have something explode. But it seems like I've hit a bug in R in general (I'm primarily on a mac, but just tested on one of your linux servers (also R 2.8.1), and the same is happening). R p2 - list(x=rnorm(500), main='bug?', col='orange', type='l') R do.call(plot, p2) You see that all of the data points are *written* on the graphics device. Hmm, you mean their numeric values are written as the y label, if x are ints, I don't get this problem: R p3 - list(x=1:500, main='bug?', col='orange', type='l') R do.call(plot, p3) They are still written as the y label, in a compact form. Nothing to do with being 'ints', rather a colon sequence. If you have all ints + 1 double, the problem appears: R p4 - list(x=c(1:500, .5), main='bug?', col='orange', type='l') R do.call(plot,p4) Is this a known bug, or am I doing something boneheaded? R sessionInfo() R version 2.8.1 Patched (2009-01-07 r47515) i386-apple-darwin9.6.0 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base Thanks, -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University http://cbio.mskcc.org/~lianos ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University http://cbio.mskcc.org/~lianos ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Reminder: Please test the 2.9.0 beta/rc binaries!
Hi, On Apr 8, 2009, at 3:52 PM, Simon Urbanek wrote: I would like to remind everyone that we are in the final week of the beta testing of R 2.9.0, so please test the binaries now! There are installers for both the Tiger (32-bit) and Leopard (32-bit and 64- bit) binaries at http://R.research.att.com/ Reporting bugs right *after* the release is pointless - that's why we are providing beta and rc builds, so please test them well before 4/17! Post any issues you have with it here. Sorry I can't test this directly since I'm in the middle of doing some analysis and don't want to install 2.9 and have something explode. But it seems like I've hit a bug in R in general (I'm primarily on a mac, but just tested on one of your linux servers (also R 2.8.1), and the same is happening). R p2 - list(x=rnorm(500), main='bug?', col='orange', type='l') R do.call(plot, p2) You see that all of the data points are *written* on the graphics device. if x are ints, I don't get this problem: R p3 - list(x=1:500, main='bug?', col='orange', type='l') R do.call(plot, p3) If you have all ints + 1 double, the problem appears: R p4 - list(x=c(1:500, .5), main='bug?', col='orange', type='l') R do.call(plot,p4) Is this a known bug, or am I doing something boneheaded? R sessionInfo() R version 2.8.1 Patched (2009-01-07 r47515) i386-apple-darwin9.6.0 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base Thanks, -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University http://cbio.mskcc.org/~lianos ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] R does not start on my MacBook Pro3,1
Hi Mary, On Mar 2, 2009, at 11:11 AM, Mary Meyer wrote: Help! I was running R code and started getting error messages that would not stop repeating. I force-quit R, but when I attempted to run it again, it would not start (Icon kept bouncing until I force- quit again). I restarted the computer, then I reinstalled R, but that did not fix the problem. I deleted everything I could find related to R, and installed again. Each time I install I get a successful message, but it does not start. I don't know what to try next. I have the latest versions of the operating system. Can you be a bit more specific about the error messages you were getting? (I guess if you can't even start R, it's not likely, but maybe you remember something about what the error was saying that kept repeating?) Also, I'm not sure what version 3,1 means in your MBP description, which MBP are you runnning? (Though, I doubt it's a problem with the type of computer) In the meantime: * I think the only thing you need to delete in order to clean R out of your system is: * the /Library/Frameworks/R.framework directory * /Applications/R.app Is that what you cleaned? * After cleaning and re-install (or now, even), can you run R from the terminal? Just open up Terminal.app and type R (no quotes). -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University http://cbio.mskcc.org/~lianos ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] R does not start on my MacBook Pro3,1
Hi Osee, I think your email will get lost in the mix because you: (a) replied to an ongoing thread with a new/different question. Please just start a new thread by sending a fresh email to the group; and (b) you're asking your question on the wrong group. Since you're having problems with a bioconductor package, repost your question there if you still can't figure out what's going on: http://www.bioconductor.org/docs/mailList.html -steve On Mar 2, 2009, at 12:53 PM, Osee Sanogo wrote: Hello, I am a beginner in R and I am having the error message: maqc - read.xysfiles(xys.files) Error in geometry(get(pkgname)) : no slot of name geometry for this object of class platformDesign Could someone tell me what this means and how to correct it? Here is my session history with the error message at the end. Thanks a lot Osee library(oligo) Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation(Biobase)' and for packages 'citation(pkgname)'. Loading required package: splines Loading required package: RSQLite Loading required package: DBI Loading required package: preprocessCore Loading required package: AnnotationDbi Loading required package: affxparser Loading required package: oligoClasses oligo Package - Series 1.5.x Warning message: package 'affxparser' was built under R version 2.8.1 library(maqcExpression4plex) /---\ | SAMPLE EXPRESSION DATA - MAQC/ HG18 - NGS | |---| | Data provided by NimbleGen Systems (NGS). | | This package is meant to be used only for | | demonstration of BioConductor packages. | |---| | The contents of this package are provided | | in good faith and the maintainer does not | | warrant their accuracy. | \---/ library(genefilter) Loading required package: survival library(geneplotter) Loading required package: lattice Loading required package: annotate Loading required package: xtable KernSmooth 2.22 installed Copyright M. P. Wand 1997 library(limma) library(RColorBrewer) Warning message: package 'RColorBrewer' was built under R version 2.8.1 palette(brewer.pal(8, Dark2)) library(splines) library(RSQLite) library(DBI) library(preprocessCore) library(AnnotationDbi) library(affxparser) library(oligoClasses) library(survival) library(lattice) library(annotate) library(xtablekkl) Error in library(xtablekkl) : there is no package called 'xtablekkl' library(xtable) extdata - system.file(., + package=maqcExpression4plex) xys.files - list.xysfiles(., + full.names=TRUE) basename(xys.files) [1] 15515902_532.xys 15517302_532.xys 15521702_532.xys 15524302_532.xys [5] 15524402_532.xys 15524802_532.xys 15524902_532.xys 15525102_532.xys [9] 15526302_532.xys 15661702_532.xys maqc - read.xysfiles(xys.files) Loading required package: pd.2007.07.05.g.aculeatus.expr Error in geometry(get(pkgname)) : no slot of name geometry for this object of class platformDesign library(pd.2007.07.05.g.aculeatus.expr) maqc - read.xysfiles(xys.files) Error in geometry(get(pkgname)) : no slot of name geometry for this object of class platformDesign On 3/2/09 11:22 AM, David Winsemius dwinsem...@comcast.net wrote: In order to do that, the OP may need to open a Terminal window, determine where the .Rhistory file resides, and issue the command 'rm .Rhistory'. The Mac GUI hides a lot of the system innards including all the . files. ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University http://cbio.mskcc.org/~lianos ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Execute code to the GUI R.app from Smultron or BBEdit
Hi, On Dec 28, 2008, at 7:46 PM, Guillaume Chapron wrote: Hello, I would like to know how (if) I can, with Smultron or BBEdit as external editors, execute a line or the whole document into the GUI R.app. Ideally, I would type Apple+R and this would go. There is a bundle to do this with Textmate, but I have not found anything for Smultron or BBEdit. Has anyone been able to do this? Thanks! Check out these recent threads: TextWrangler: https://stat.ethz.ch/pipermail/r-sig-mac/2008-November/005534.html Smultron: https://stat.ethz.ch/pipermail/r-sig-mac/2008-December/005691.html -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University http://cbio.mskcc.org/~lianos ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Running older versions to test package
Hi Stephen,
On Dec 1, 2008, at 10:53 AM, stephen sefick wrote:
Version are installed in || ? I know where the versions are located
but I can not firgure out how to get them to crank up:
/Library/Frameworks/R.Framework/Versions/2.7/Resources/library
My problem is that I am having problems with the StreamMetabolism -
essentially relying on chron to work, and chron is not working as it
has in the past. This issue has cropped up in the upgrade to 2.8. It
is taking a much longer time to do things compared to 2.7.2. 2.3-25
chron under R 2.8 and 2.3-24 chron under 2.7.2. I would like to be
able to run both of these versions side by side to try and find out
what has happened.
thanks for your help,
I think there's some setting of env vars that are necessary to run R
that are (somehow) automatically taken care of when the /Library/
Frameworks/R.framewor/{Headers,Libraries,etc.} link to the appropriate
Versions/* directory.
If you want to run from the terminal, I think you might be able to
(easily) do what you're after by using the RSwitch application that
you can d/l from here:
http://r.research.att.com/
I'd try to launch R (I guess 2.8 will come up first). Once it's up and
running, use RSwitch to pick version 2.7, then open another terminal
and launch R again (should be 2.7 now).
Alternatively, if you want to run using R.app (the GUI), I *believe*
you can download the 2.7 and 2.8 GUIs (from the same r.research page),
and rename them from R.app, to R27.app/R28.app and launch them that way.
HTH,
-steve
--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Medical College of Cornell University
http://cbio.mskcc.org/~lianos
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Re: [R-SIG-Mac] installing multiple versions of R
Hi Stephen, On Dec 1, 2008, at 11:29 AM, stephen sefick wrote: I would like to install R 2.7.2 in || with R 2.8 to test what is wrong with a package I am maintaining. It worked fine with R 2.7.2 chron 2.3-24 and doesn't work with R 2.8 chron 2.3-24 or chron 2.3-25. thanks You can easily do so. Just download the appropriate installers for each version and install them: 2.8.x : http://cran.r-project.org/bin/macosx/R-2.8.0.dmg 2.7.x : http://cran.r-project.org/bin/macosx/old/R-2.7.2.dmg FYI, they'll install in: /Library/Frameworks/R.framework/Versions/2.* You can switch between which version to run at go time as I described in my previous email: (i) either by using the RSwitch application; or (ii) by renaming the R.app that's installed to R28.app, and R27.app as appropriate. Both RSwitch and the R guis can be downloaded from: http://r.research.att.com/ HTH, -steve ps - I'm not sure of (ii), since I haven't tested it for R27 vs R28 (only R in 68bit vs R 32bit, which works), though I believe it works. I have tested and previously used (i). -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University http://cbio.mskcc.org/~lianos ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] installing multiple versions of R
I downloaded the Rswitch application, but the current version and that is the only version that is available even if I push the rediscover button. Weird ... and you have both versions installed? ie. you have full install trees under: /Library/Frameworks/R.framework/Versions/2.7 ; and /Library/Frameworks/R.framework/Versions/2.8 ? The second approach I outlined (using different versions of R.app) won't work either w/o successfully using RSwitch, either (just tried it). Weird ... not sure what to say if both versions of R are installed correctly. I'm just guessing, but if you change the /Library/Framework/ R.framework/Versions/Current link to point to 2.7 instead of 2.8, that might work as well (I feel like that's the only thing that RSwitch app does, but I'm not certain). If all of the above isn't working, I guess we'll have to wait for an R/ mac guru to pop in. What version of OS X are you using and are you using the appropriate leopard/tiger builds? -steve On Mon, Dec 1, 2008 at 11:46 AM, Steve Lianoglou [EMAIL PROTECTED] wrote: Hi Stephen, On Dec 1, 2008, at 11:29 AM, stephen sefick wrote: I would like to install R 2.7.2 in || with R 2.8 to test what is wrong with a package I am maintaining. It worked fine with R 2.7.2 chron 2.3-24 and doesn't work with R 2.8 chron 2.3-24 or chron 2.3-25. thanks You can easily do so. Just download the appropriate installers for each version and install them: 2.8.x : http://cran.r-project.org/bin/macosx/R-2.8.0.dmg 2.7.x : http://cran.r-project.org/bin/macosx/old/R-2.7.2.dmg FYI, they'll install in: /Library/Frameworks/R.framework/Versions/2.* You can switch between which version to run at go time as I described in my previous email: (i) either by using the RSwitch application; or (ii) by renaming the R.app that's installed to R28.app, and R27.app as appropriate. Both RSwitch and the R guis can be downloaded from: http://r.research.att.com/ HTH, -steve ps - I'm not sure of (ii), since I haven't tested it for R27 vs R28 (only R in 68bit vs R 32bit, which works), though I believe it works. I have tested and previously used (i). -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University http://cbio.mskcc.org/~lianos -- Stephen Sefick Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University http://cbio.mskcc.org/~lianos ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] installing R-2.8 from source - segmentation faults at make check
Hi Mike, Just gonna CC the list back so that more people can chime in if necessary: Thanks. I have been trying to access the r.research.att.com site all weekend, to no avail. When I run your command below, all I get is jibberish in the terminal window. Are you experiencing the same problems (i.e., is the jibberish normal?). I'm not getting jibberish ... I'm also not having any problems accessing the r.research.att.com site, so ... is that still happening for you? Anyway, an alternative you can try is to just d/l the binary directly using your browser, and run the necessary commands (the tar stuff) from the terminal. That would look something like this. 1) Download the 2.8 binary using your browser by just dropping its URL your address field: http://r.research.att.com/R-2.8-branch-leopard-universal.tar.gz I will assume that you're using Leopard + Safari, which is important for two things (i) It should d/l that binary into your ~/Downloads folder (ii) it will automagically unzip the gz and leave you with the R-2.8- *.tar file (I think, mine does this automatically) 2) You'll have to unpack the tar archive *into* the correct location, which is the root of your system. That's why you need to use `sudo` and that's what the -C / is doing at the end of the tar command. So, now that you've d/led the archive w/ your browser, from the terminal, type: $ sudo tar xvf ~/Downloads/R-2.8-branch-leopard-universal.tar -C / Note that it's not tar xvfz since it's unzipped ... if your binary ends in *.tar.gz then you'd add the z Anyway, that should do the trick, too, so let us know if that works. -steve On Nov 24, 2008, at 12:33 PM, Steve Lianoglou wrote: Hi Michael, On Nov 24, 2008, at 12:03 PM, Michael Braun wrote: I should note that the only reason I am compiling from source is that, as far as I can tell, there are no 64-bit binaries available for Leopard yet. If someone could point me to such binaries, that might solve my problem. Check out this page here: http://r.research.att.com/ Primarily that blue box about 1/2-way down the page, that says: Leopard builds can be installed as follows - paste in Terminal (for R 2.8.x): curl -s http://r.research.att.com/R-2.8-branch-leopard-universal.tar.gz | sudo tar fvxz - -C / That should do the trick and save you the hassle of compiling yourself. ;-) -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University http://cbio.mskcc.org/~lianos --- Michael Braun Homer A. Burnell Career Development Professor, and Assistant Professor of Management Science (Marketing Group) MIT Sloan School of Management One Amherst St., E40-169 Cambridge, MA 02142 [EMAIL PROTECTED] 617-253-3436 -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University http://cbio.mskcc.org/~lianos ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] help() start page - how to set
Howdy, On Nov 17, 2008, at 8:27 PM, Bill Northcott wrote: On 18/11/2008, at 10:11 AM, Sean Davis wrote: Does help.start() do what you want? I don't use Eclipse, so I wouldn't know for sure. That works running R in a Terminal window, but in the Eclipse console I get: snip Any suggestions would be welcome. I'm curious to see if using StatET is useful, too ... as this is quite eclipse/plugin specific, perhaps you'd get better feedback from the StatET mailing list? https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/statet-user It doesn't seem like it has too much traffic, but there seems to be someone there answering questions. Good luck! -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University http://cbio.mskcc.org/~lianos ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] upgradeable R layout
Hi David, The installation of the Tools is the sticking point: I am attemptng to follow the directions at http://r.research.att.com/tools/ Checked Xcode and finding that it was 3.0 and seeing that 3.1.1 was available, download and installed a 1GB file. Checked to see that Xcode.app had been updated. Downloaded and installed the gfortran package from the ATT website. copied export PATH=$PATH:/usr/local/bin to Terminal line. Followed Tools on CRAN link: devpack4-darwin8-bin4.tar.gz was download via Firefox to /Users/ Downloads/ and automatically expanded to a folder with Library and usr descendants within /Downloads/ which I think is not the correct location. The contents of Library were apparently destined for / Applications/Frameworks/R.framework/Resources/ so I dragged the fontconfig file there. That looks wrong to me. After having d/l'd the devpack to see what was going on, it looks like the archive is destined to be expanded at the root level of your system, meaning the Library folder in there should really expand into: /Library/Frameworks/R.framework ... Same goes for the usr/local/blah/blah stuffs: this should be in /usr/ local/blah/blah. I'm not sure if there's any undoing that needs to be done on your side (doesn't seem so(?)). So, assuming we're starting from scratch: in order to properly install the devpack that is d/l'd in your downloads folder, you can type this in the terminal and all files will expand into their correct place: $ sudo tar fvxz /Users/davidwinsemius/Downloads/devpack4-darwin8- bin4.tar.gz -C / Viewing the world through the Mac Finder it is unclear where the / usr/local folder contents are supposed to go. You can't see that folder, by default, via the Finder as its hidden. You can force the Finder to open it in a window a few different ways, though. One way is to open a new finder window, hit Cmd-Shift-G to drop down the Go to folder dialog (Also available via the Go menu), and then type /usr/local. Another way would be to fire up Terminal.app and type: $ open /usr/local There is probably a Unix command that will safely copy the contents of the /usr/ folder currently residing in /Downlaods to where the true /usr/ folder resides. So I opened a Terminal window and typed: cp /usr/local/ This isn't really a valid command, as cp takes two arguments. Maybe you meant `cd`? Can I now just type: cp /Users/davidwinsemius/Downloads/devpack4-darwin8-bin4/usr/local/* . If you meant `cd` above, this command wouldn't successfully copy all of the stuff over to your directory, since you'll need the -R command to copy the directories over ... So, to re-iterate, all you have to do to get the devpack items installed in the right place is to fire off the `tar xvfz ... ` command I listed above, don't do any more cp'ing or whatever else you tried after that. Honestly, though, I'm tempted to provide a word of caution since it seems you might not be very comfortable using the command line (sorry if I'm making an incorrect assumption). You'll have to use `sudo` to get this to work, and may unintentionally blow out something in the process that could your system (the command I gave you is safe, tho (I just ran it on my system and I'm doing OK :-)). Anyway, hope this helps. -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University http://cbio.mskcc.org/~lianos ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] 64 bit R tcltk library problem: Symbol not found: _Tk_Init
Hi, I then installed R.app from R-GUI-5256-2.8-leopard-Deployment64.dmg and installed a number of bioconductor libraries from source. I advanced farther in getting 64-bit R and libraries up and running than at any previous attempt, and thought I finally had functional 64 bit R available on my Mac. But I keep hitting a tcltk problem that I can't seem to solve. Whenever I'm trying to install a package that requires tcltk the installation fails with this message: Loading required package: tcltk Loading Tcl/Tk interface ... Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/Library/Frameworks/R.framework/ Resources/library/tcltk/libs/ppc64/tcltk.so': dlopen(/Library/Frameworks/R.framework/Resources/library/tcltk/libs/ ppc64/tcltk.so, 10): Symbol not found: _Tk_Init Referenced from: /Library/Frameworks/R.framework/Resources/library/ tcltk/libs/ppc64/tcltk.so Expected in: dynamic lookup I know this doesn't really help you at all, but it seems that tcltk installed smoothly on my machine (Mac Pro) and I was able to compile a 4-way fat binary. In trying to be a little helpful, though ... Initially I installed several Bioconductor packages, using biocLite() e.g. biocLite(beadarray, type = source) You don't actually need to install bioconductor packages from source -- they're already compiled as a 4-way fat binary for Leopard as of bioconductor 2.3 ... while it doesn't help you much here, perhaps it's good to know to save you install/compile time in the future. -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University http://cbio.mskcc.org/~lianos ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] 64 bit - Installing packages from source
You don't actually need to install bioconductor packages from source Can Simon Urbanek weigh in on this? I've been keeping an eye on R-SIG-Mac and have been seeing repeated references in the last few weeks about installing from source for 64-bit R. ... For some tangential weight, see this posting where Patrick Aboyoun answered my question regarding using 64bit bioconductor on os x: http://thread.gmane.org/gmane.science.biology.informatics.conductor/20273/focus=20404 As a point of reference, although he doesn't list ppc64 there, looking through my d/l'd bioconductor I see most all of the packages have ppc64 builds in their libs folders. The only one that doesn't have ppc64 is `affy`, which is curious. Given that limma and affy both d/l when you do a default BioC install with `biocLite()`, I'm not sure why that's the case. -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University http://cbio.mskcc.org/~lianos ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] File creation date
Hi, On Oct 28, 2008, at 6:00 PM, Loren Engrav wrote: Ok, I give up I am exploring some workspace files created long long ago And need the creation date of some of the files I try ls() but cannot see the parameters to show creation date I try file.info and get NA How do I get creation date to show One way is to navigate to the file via the Finder, select it, and hit Cmd-I (File Get Info) You'll find what you're looking for in the General section. HTH, -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University http://cbio.mskcc.org/~lianos ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] [BioC] affy won't load
Are you? Did you actually test it? I'm pretty sure that you're wrong, because the commands below compile libintl.8.dylib(!) and thus won't help (that one is fine and part of your Gtk binary). Ouch, well I stand corrected then. Sorry for sending out misinformation ... I'm still puzzled at where the BioC team gets libintl.3 ... Yeah. Even more puzzling (to me) is where mine came from ... as someone else mentioned before, I also have a fairly clean install of leopard (having just replaced my hard drive a few weeks ago) and libnitl.3.dylib is magically there. My apologies once again. -steve ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
