Re: [R-SIG-Mac] making R.app and home-brew live happily together
On 5 Mar 2014, at 13:12, Prof Brian Ripley rip...@stats.ox.ac.uk wrote: On 05/03/2014 13:04, Federico Calboli wrote: On 4 Mar 2014, at 18:41, Davor Cubranic cubra...@stat.ubc.ca wrote: If you don’t care about Tcl/Tk, you could also install R without it. Just choose “Customize” in the installer and unselect it. isn’t there a different tcl/tk framework that one can use anyway? I’m referring to the active state one (http://www.activestate.com/activetcl/downloads) That Tcl/Tk is not a 'framework': there are frameworks you can use, but not with the CRAN distribution of R. See the R-admin manual. That’s it then — last time I used X11 on OSX was ~ 3 years ago (i.e. I am not a big tcl/tk user). I reinstalled R 3.0.3 RC from http://r.research.att.com/, customised the installation omitting tcl/tk, removed the tcl/tk related stuff I had installed before and now both R and HB are happy. BW F BW F Davor On Feb 28, 2014, at 9:51 AM, Federico Calboli f.calb...@imperial.ac.uk wrote: Simon, snip Unfortunately HB installs by default in /usr/local and requires full control so you cannot have native libraries and HB in the same place at the same time. So essentially you have to pick one or the other. There are two options: a) install HB in another place. This allows you to keep native libraries in /usr/local and parallel HB. HB is less tested that way, though, so that's why HB is shy of recommending it. b) ignore HB's moaning. It should be ok as long as you don't install tcl/tk via HB. It may get complicated if dependencies detect tcl/tk so for safety you could rename the .pc files and the t*Config.sh files if you don't expect to compile R packages that depend on tcl/tk. I am ignoring the moanings of brew doctor. I generally try and avoid compiling R packages if at all possible, and I never used stuff that uses tcl/tk (that I know of). My main concern is that I want to install SciPy and Python 3 (assuming this can be done in a way that will not get Mavericks throw a fit) and that might — or not — get some tcl/tk action in. If not, R.app and HB can live together for all I care. Best F Cheers, Simon BW F PS I also asked on apple stack, but I haven’t go any reasonable answer thus far and I’d rather get going. ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- 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 signature.asc Description: Message signed with OpenPGP using GPGMail ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] making R.app and home-brew live happily together
On Wed, Mar 5, 2014 at 9:21 AM, Simon Urbanek simon.urba...@r-project.orgwrote: On Mar 5, 2014, at 8:04 AM, Federico Calboli f.calb...@imperial.ac.uk wrote: On 4 Mar 2014, at 18:41, Davor Cubranic cubra...@stat.ubc.ca wrote: If you don't care about Tcl/Tk, you could also install R without it. Just choose Customize in the installer and unselect it. isn't there a different tcl/tk framework that one can use anyway? I'm referring to the active state one ( http://www.activestate.com/activetcl/downloads) No, because it doesn't work with R.app since that Tcl/Tk build assumes it's controlling the application and system event loop. Is this also true the other way? I mean, does the R Tcl/Tk work with other OSX apps that need Tcl/Tk? Gabor, another person annoyed by R and homebrew not playing well together. Cheers, S Davor On Feb 28, 2014, at 9:51 AM, Federico Calboli f.calb...@imperial.ac.uk wrote: Simon, snip Unfortunately HB installs by default in /usr/local and requires full control so you cannot have native libraries and HB in the same place at the same time. So essentially you have to pick one or the other. There are two options: a) install HB in another place. This allows you to keep native libraries in /usr/local and parallel HB. HB is less tested that way, though, so that's why HB is shy of recommending it. b) ignore HB's moaning. It should be ok as long as you don't install tcl/tk via HB. It may get complicated if dependencies detect tcl/tk so for safety you could rename the .pc files and the t*Config.sh files if you don't expect to compile R packages that depend on tcl/tk. I am ignoring the moanings of brew doctor. I generally try and avoid compiling R packages if at all possible, and I never used stuff that uses tcl/tk (that I know of). My main concern is that I want to install SciPy and Python 3 (assuming this can be done in a way that will not get Mavericks throw a fit) and that might -- or not -- get some tcl/tk action in. If not, R.app and HB can live together for all I care. Best F Cheers, Simon BW F PS I also asked on apple stack, but I haven't go any reasonable answer thus far and I'd rather get going. ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] making R.app and home-brew live happily together
On 5 Mar 2014, at 14:53, Simon Urbanek simon.urba...@r-project.org wrote: On Mar 5, 2014, at 9:24 AM, Gábor Csárdi csardi.ga...@gmail.com wrote: On Wed, Mar 5, 2014 at 9:21 AM, Simon Urbanek simon.urba...@r-project.org wrote: On Mar 5, 2014, at 8:04 AM, Federico Calboli f.calb...@imperial.ac.uk wrote: On 4 Mar 2014, at 18:41, Davor Cubranic cubra...@stat.ubc.ca wrote: If you don’t care about Tcl/Tk, you could also install R without it. Just choose “Customize” in the installer and unselect it. isn’t there a different tcl/tk framework that one can use anyway? I’m referring to the active state one (http://www.activestate.com/activetcl/downloads) No, because it doesn't work with R.app since that Tcl/Tk build assumes it's controlling the application and system event loop. Is this also true the other way? I mean, does the R Tcl/Tk work with other OSX apps that need Tcl/Tk? AFAIK, yes. It's the native Tcl/Tk port that causes issues. However, for pure Tcl/Tk apps users may prefer the native look to X11. Gabor, another person annoyed by R and homebrew not playing well together. I just checked, and homebrew proper doesn't even provide Tcl/Tk so it seems like this is not really an issue at all. Even the dupes version installs in a hidden location so it doesn't clash. Homebrew typically tries not to mess up the system so it was historically working along with R very well. So do you have some evidence for them not playing well together? I know MacPorts and Fink were disasters, but Homebrew has so far tried to learn from their mistakes. My original comment comes from ‘brew doctor’ throwing warnings up. Having said that, because I do not use Tcl/Tk ever, whether in R or elsewhere, my question was proactive — 'how can I avoid problems given I’m getting warnings' — rather than ‘something broke’. Many people I know use HB to get R and have never had any problems, but I like the R.app GUI. Best F Cheers, Simon Cheers, S Davor On Feb 28, 2014, at 9:51 AM, Federico Calboli f.calb...@imperial.ac.uk wrote: Simon, snip Unfortunately HB installs by default in /usr/local and requires full control so you cannot have native libraries and HB in the same place at the same time. So essentially you have to pick one or the other. There are two options: a) install HB in another place. This allows you to keep native libraries in /usr/local and parallel HB. HB is less tested that way, though, so that's why HB is shy of recommending it. b) ignore HB's moaning. It should be ok as long as you don't install tcl/tk via HB. It may get complicated if dependencies detect tcl/tk so for safety you could rename the .pc files and the t*Config.sh files if you don't expect to compile R packages that depend on tcl/tk. I am ignoring the moanings of brew doctor. I generally try and avoid compiling R packages if at all possible, and I never used stuff that uses tcl/tk (that I know of). My main concern is that I want to install SciPy and Python 3 (assuming this can be done in a way that will not get Mavericks throw a fit) and that might — or not — get some tcl/tk action in. If not, R.app and HB can live together for all I care. Best F Cheers, Simon BW F PS I also asked on apple stack, but I haven’t go any reasonable answer thus far and I’d rather get going. ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac signature.asc Description: Message signed with OpenPGP using GPGMail ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] making R.app and home-brew live happily together
On Wed, Mar 5, 2014 at 9:53 AM, Simon Urbanek simon.urba...@r-project.orgwrote: [...] I just checked, and homebrew proper doesn't even provide Tcl/Tk so it seems like this is not really an issue at all. Even the dupes version installs in a hidden location so it doesn't clash. Homebrew typically tries not to mess up the system so it was historically working along with R very well. So do you have some evidence for them not playing well together? I know MacPorts and Fink were disasters, but Homebrew has so far tried to learn from their mistakes. Hmmm. It seems that brew tcl-tk does not put anything in /usr/, so it all seems to be fine, actually. Quite possibly, my problems come up because I am compiling R from source, which is a much less serious case. Will try. Anyway, sorry for the noise. Gabor Cheers, Simon Cheers, S Davor On Feb 28, 2014, at 9:51 AM, Federico Calboli f.calb...@imperial.ac.uk wrote: Simon, snip Unfortunately HB installs by default in /usr/local and requires full control so you cannot have native libraries and HB in the same place at the same time. So essentially you have to pick one or the other. There are two options: a) install HB in another place. This allows you to keep native libraries in /usr/local and parallel HB. HB is less tested that way, though, so that's why HB is shy of recommending it. b) ignore HB's moaning. It should be ok as long as you don't install tcl/tk via HB. It may get complicated if dependencies detect tcl/tk so for safety you could rename the .pc files and the t*Config.sh files if you don't expect to compile R packages that depend on tcl/tk. I am ignoring the moanings of brew doctor. I generally try and avoid compiling R packages if at all possible, and I never used stuff that uses tcl/tk (that I know of). My main concern is that I want to install SciPy and Python 3 (assuming this can be done in a way that will not get Mavericks throw a fit) and that might -- or not -- get some tcl/tk action in. If not, R.app and HB can live together for all I care. Best F Cheers, Simon BW F PS I also asked on apple stack, but I haven't go any reasonable answer thus far and I'd rather get going. ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] making R.app and home-brew live happily together
Federico, On Feb 28, 2014, at 7:59, Federico Calboli f.calb...@imperial.ac.uk wrote: Hi All, I recently moved from OS 10.8.5 to 10.9.2. So far so good. After years of using Macports (without any issues) I decided on a whim to give Homebrew a try. Before installing Homebrew I had installed R-3.0-branch-snowleopard-signed.pkg from http://r.research.att.com. Using brew doctor tell me that: brew doctor Warning: Unbrewed dylibs were found in /usr/local/lib. If you didn't put them there on purpose they could cause problems when building Homebrew formulae, and may need to be deleted. Unexpected dylibs: /usr/local/lib/libtcl8.6.dylib /usr/local/lib/libtk8.6.dylib Warning: Unbrewed .pc files were found in /usr/local/lib/pkgconfig. If you didn't put them there on purpose they could cause problems when building Homebrew formulae, and may need to be deleted. Unexpected .pc files: /usr/local/lib/pkgconfig/tcl.pc /usr/local/lib/pkgconfig/tk.pc Warning: Unbrewed static libraries were found in /usr/local/lib. If you didn't put them there on purpose they could cause problems when building Homebrew formulae, and may need to be deleted. Unexpected static libraries: /usr/local/lib/libtclstub8.6.a /usr/local/lib/libtkstub8.6.a pkgutil identifies these files as coming from the R pkg. Can I safely ignore the whining of brew doctor or not (I like R.app and I’d rather keep it)? I plan to use home-brew to install gcc, gsl, ffmpeg, and scipy (for python 3). I would say I do not envision conflicts and bugs but I’d rather ask first. Unfortunately HB installs by default in /usr/local and requires full control so you cannot have native libraries and HB in the same place at the same time. So essentially you have to pick one or the other. There are two options: a) install HB in another place. This allows you to keep native libraries in /usr/local and parallel HB. HB is less tested that way, though, so that's why HB is shy of recommending it. b) ignore HB's moaning. It should be ok as long as you don't install tcl/tk via HB. It may get complicated if dependencies detect tcl/tk so for safety you could rename the .pc files and the t*Config.sh files if you don't expect to compile R packages that depend on tcl/tk. Cheers, Simon BW F PS I also asked on apple stack, but I haven’t go any reasonable answer thus far and I’d rather get going. ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] making R.app and home-brew live happily together
Simon, snip Unfortunately HB installs by default in /usr/local and requires full control so you cannot have native libraries and HB in the same place at the same time. So essentially you have to pick one or the other. There are two options: a) install HB in another place. This allows you to keep native libraries in /usr/local and parallel HB. HB is less tested that way, though, so that's why HB is shy of recommending it. b) ignore HB's moaning. It should be ok as long as you don't install tcl/tk via HB. It may get complicated if dependencies detect tcl/tk so for safety you could rename the .pc files and the t*Config.sh files if you don't expect to compile R packages that depend on tcl/tk. I am ignoring the moanings of brew doctor. I generally try and avoid compiling R packages if at all possible, and I never used stuff that uses tcl/tk (that I know of). My main concern is that I want to install SciPy and Python 3 (assuming this can be done in a way that will not get Mavericks throw a fit) and that might — or not — get some tcl/tk action in. If not, R.app and HB can live together for all I care. Best F Cheers, Simon BW F PS I also asked on apple stack, but I haven’t go any reasonable answer thus far and I’d rather get going. ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac signature.asc Description: Message signed with OpenPGP using GPGMail ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
