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 <jfox@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.urbanek@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.urbanek@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:urbanek@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 <dwinsemius@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

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