Dear Simon, OK -- thanks for the further clarification.
If you can bear with me a bit longer, I've drafted an update to the Rcmdr installation notes, the relevant part of which now reads as follows -- [link] represents a hyperlink: -------------- snip --------------- . . . These instructions are for R version 3.0.0 or later; if you're using an earlier version of R, I suggest that you upgrade, or, failing that, consult the special Mac OS X installation notes [link] for the R Commander under older versions of R. Before installing R or the R Commander, make sure that your Mac OS X system is up-to-date by running Software Update from the "apple" menu at the top-left of the screen. This is important, because R assumes that the system is up-to-date and may not function properly if it is not. The procedure for installing the R Commander under Mac OS X is a bit complicated, so please read and follow these instructions carefully. These instructions and the associated files are intended for 10.6 (Snow Leopard), 10.7 (Lion), and 10.8 (Mountain Lion) systems. I assume that you've already installed R, version 3.0.0 or later. O Check to see if the X11 windowing system (X Windows) has already been installed on your computer. For OS X 10.6 and 10.7, the file X11.app should appear in the Utilities folder under Applications in the finder. This application should always be installed under OS X 10.7. For OS X 10.8, the file is named XQuartz.app and is no longer included with the operating system. O If X11.app is missing under OS X 10.6 or 10.7, you can (preferably) download and install XQuartz from http://xquartz.macosforge.org [link], following the directions for OS X 10.8 below, or you can install X11.app from your Mac OS X installation disc as follows: - Insert your Mac OS X install disc. (If you have two discs it will be on the"Install Disc 1"). - Double click on Optional Installs. - Double click on Optional Installs.mpkg, then click Continue and accept the license agreement. - Click the triangle next to Applications in order to expand the list of applications. - Check "X11", and then click Continue and Install. Click Close when the installation finishes. - If you install X11 from your Mac OS X discs rather than XQuartz, then run Software Update afterwards to make sure that your X11 system is up-to-date. Under OS X 10.8 (Mountain Lion), when you first try to use X11 -- for example, by installing and then loading the Rcmdr package in R (see the bullets below) -- OS X will offer to help you install X11, with a message like "To open 'R,' you need to install X11. Would you like to install X11 now?" O Click the continue button, which will take you to the Apple support website, and thence to http://xquartz.macosforge.org [link], where you can download the disk image (dmg) file for XQuartz. O When you open this file by double-clicking on it, you'll find XQuartz.pkg; double-click on it to run the installer, clicking through all the defaults. O After the installer runs, you'll have to log out and back on to your Mac OS X account. . . . -------------- snip --------------- Does that seem to cover the bases? Remember that many of the people using these instructions will be even more ignorant than I am about Mac OS X. Thanks for your help, John > -----Original Message----- > From: Simon Urbanek [mailto:[email protected]] > Sent: Thursday, September 19, 2013 11:16 AM > To: John Fox > Cc: 'David Winsemius'; 'Sarah Hardy'; 'r-sig-mac' > Subject: Re: [R-SIG-Mac] Problems loading Rcmdr on a Mac 10.7.2 and a > Mac 10.6.8 > > John, > > On Sep 19, 2013, at 10:29 AM, John Fox wrote: > > > Dear Simon, > > > > Thank you very much for these clarifications (and also for responding > to > > David and Sarah's posts in this thread). I think that I understand > what's > > going on now, and will add a note to the Rcmdr installation > instructions to > > run Software Update prior to installing R, the Rcmdr, and (if > necessary) > > XQuartz. > > > > (Sarah: You could try asking your student(s) to run Software Update, > and > > then reinstall R and the Rcmdr package. If you do this, can you > report to > > the list whether it works?) > > > > I do have one further question: I understand now that R will use an > older > > X-11 in preference to XQuartz if XQuartz doesn't install a symbolic > link to > > /usr/X11. Is there a reason for this? That is, why not have R use > XQuartz in > > preference to another X-11 if XQuartz is installed -- or to pick the > newest > > X-server, if it's possible to ascertain that? > > > > It's not. This is not about preferences - R has no choice, it has to > links against something and we picked something that's more likely to > exist. You cannot pick and choose at run time since the libraries (with > paths) are linked in. Note that this is *not* about the X11 that the > user will be running - this is just for internal libraries use by R - > these are two entirely separate things (server vs client). Also XQuartz > was really a development project, so it didn't seem like a good idea to > require it - in particular since we would ask people to install > parallel X11 implementation to an existing one - and have to answer the > "why?". In the meantime Apple has removed system X11 completely from > recent OS X so it may be worth re-visiting that option and just require > XQuartz. However, there is no guarantee that they will support the > targets we support (although so far they do). Finally, XQuartz will act > as system X11 but not vice-versa, so it's much safer to use the system > X11 location as it supports more setups. > > FWIW: I think this whole discussion is getting off the original topic: > if you don't keep your system up to date, nothing is guaranteed to work > - it has nothing to do with X11, it affects all system libraries and we > have seen that before. > > Cheers, > Simon > > > > Thanks again for your help, > > John > > > >> -----Original Message----- > >> From: Simon Urbanek [mailto:[email protected]] > >> Sent: Thursday, September 19, 2013 9:25 AM > >> To: John Fox > >> Cc: David Winsemius; Sarah Hardy; r-sig-mac > >> Subject: Re: [R-SIG-Mac] Problems loading Rcmdr on a Mac 10.7.2 and > a > >> Mac 10.6.8 > >> > >> On Sep 19, 2013, at 9:05 AM, John Fox wrote: > >> > >>> Dear David, > >>> > >>> On Thu, 19 Sep 2013 01:04:18 -0700 > >>> David Winsemius <[email protected]> wrote: > >>>> > >>>> On Sep 18, 2013, at 8:47 PM, John Fox wrote: > >>>> > >>> > >>> . . . > >>> > >>>>> It also seems apparent from the error message that there's a > >> mismatch between the version of Tcl/Tk, presumably the one supplied > >> with the R distribution, and the version of X-Windows. > >>>> > >>>> That is not what I am reading. libfreetype.6 version 13 is the > >> reported problem with a need to update to version 14. > >>>> > >>> > >>> Do you know where libfreetype.6 comes from? Is it installed > >> independently of Tcl/Tk and XQuartz? If so, do you know how to > update > >> it? > >>> > >>> . . . > >>> > >>>> I'm not really a student but maybe this will be useful anyway. > There > >> is a version of Tk at: > >>>> > >>>> http://r.research.att.com/src/tk8.6.0-src.tar.gz > >>>> > >>>> ... which appears to be the most up-to-date version. I'm actually > >> running version 8.5 with OSX 10.7.5 > >>>> > >>> > >>> Version 8.6-0 of Tcl/Tk for X-Windows is included in the R 3.0.1 > >> installer for Mac OS X. Is it possible that it doesn't get installed > if > >> there's already a Tcl/Tk for X-Windows installed? > >>> > >>> . . . > >>> > >>>> > >>>> The error message below says that libfreetype.6 is an old version > >> and that you need version 14.0 for libtk8.6 > >>>> > >>>> From Unix cmd line: > >>>> > >>>> otool -L /opt/local/lib/libfreetype.6.dylib > >>>> > >>>> # ---- reports ___________ > >>>> /opt/local/lib/libfreetype.6.dylib: > >>>> /opt/local/lib/libfreetype.6.dylib (compatibility version 16.0.0, > >> current version 16.0.0) > >>>> /opt/local/lib/libz.1.dylib (compatibility version 1.0.0, current > >> version 1.2.7) > >>>> /opt/local/lib/libbz2.1.0.dylib (compatibility version 1.0.0, > >> current version 1.0.6) > >>>> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current > >> version 125.2.11) > >>>> > >>> > >>> So tcltk and the Rcmdr 2.0-0 work on your system because you have a > >> sufficiently up-to-date libfreetype.6. It would be additionally > helpful > >> to be able to answer the following questions: > >>> > >>> (1) Why is it that some users have old versions of libfreetype.6. > >>> > >> > >> guess: they don't use Software Update and thus have outdated system > >> libraries > >> > >> > >>> (2) Why doesn't installing the newest versions of R (which includes > >> Tcl/Tk) and XQuartz, not solve this problem? > >>> > >> > >> guess: they are running an older version or didn't install R > properly > >> from the CRAN package > >> > >> > >>> (3) What can users experiencing this problem do to fix it? > >>> > >> > >> > >> Run Software Update for (1) , re-install R for (2)? > >> > >> We have only 3rd hand report here so we're reduced to guessing so > far. > >> As I said, one important thing is that we uses system X11 and not > >> XQuartz so installing XQuartz has no effect if there is a system X11 > >> installed. However, on an up-todate system there should be no > problems. > >> > >> Cheers, > >> S > >> > >> > >>> If I knew the answers to these questions, I could update the Rcmdr > >> installation notes to help users avoid the problem. > >>> > >>> Thank you for your help, > >>> John > > _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
