Running the "Software Update" and reinstalling R and Rcmdr worked for the student with the 10.7.2. We did not reinstall XQuartz. Now I will see if it works for the others. BTW - I have identified at least one student with a 10.6.8 who had no problems installing R and Rcmdr without installing XQuartz (per my instructions) - am going to check with other students tomorrow.
Best, Sarah On Thu, Sep 19, 2013 at 3:17 PM, John Fox <j...@mcmaster.ca> wrote: > Dear Simon, > > That's a good suggestion. In fact, I don't see a real function for the > technical details, so I've just eliminated them. I also think that adding > the step to run Software Update is harmless and a good idea, so I've added > that. The full set of instructions (including the parts that I omitted > earlier) now reads: > > ----------------- snip ------------- > > These instructions are for R version 3.0.1 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 for the R Commander under older > versions of R. R 3.0.1 only supports Mac OS X version 10.6.8 (Snow Leopard) > or greater. > > O Before installing R and 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. > > O Install R 3.0.1 or later from the Comprehensive R Archive Network (CRAN), > selecting a mirror site near you; a list of CRAN mirrors appears at the > upper left of the CRAN home page. > > O Install XQuartz from http://xquartz.macosforge.org. (The R Commander > uses > the tcltk package for R, which requires X-Windows. Your Mac may already > have > X-Windows installed, but it should not hurt in any event to install > XQuartz.) > > O Start R by running R.app. At the R > command prompt, type the following > command and press the return key (to avoid errors, you can copy the command > from this document and paste it at the R > command prompt): > > install.packages("Rcmdr") > > R will ask you to select a CRAN mirror; pick a mirror site near you. > > O Once it is installed, to load the Rcmdr package, simply issue the command > > library(Rcmdr) > > at the R > command prompt and press return. When you first load the Rcmdr > package, it will offer to download and install missing dependencies; allow > it to do so. > > ----------------- snip ------------- > > There's no need to respond again if you think these instructions are OK. > > Thanks again, > John > > > -----Original Message----- > > From: Simon Urbanek [mailto:simon.urba...@r-project.org] > > Sent: Thursday, September 19, 2013 11:49 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 > > > > Well, the I think it reads far more complicated that in needs to be. > > You should have a quickstart section that just says: > > > > * Install R 3.0.1 or later > > * Install XQuartz from http://xquartz.macosforge.org > > > > Done. Current R only supports 10.6.8+ and so does XQuartz so the above > > covers everything that is supported right now (I recall having that > > discussion earlier...). > > > > Then you can have troubleshooting section which says > > > > a) make sure you installed R with Tcl/Tk (it is the default) - if in > > doubt, re-install R from CRAN > > b) use Software Update > > > > Then you can have a technical section with the details you show below, > > but 99% of users should not need to read it. > > > > Cheers, > > Simon > > > > > > > > > > > > On Sep 19, 2013, at 11:36 AM, John Fox wrote: > > > > > 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:simon.urba...@r-project.org] > > >> 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:urba...@research.att.com] > > >>>> 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 <dwinsem...@comcast.net> 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 > > >>> > > > > > > > > -- Sarah Hardy, PhD Associate Professor of Mathematics University of Maine Farmington 207-778-7124 Office: Brinkman 100 [[alternative HTML version deleted]] _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
