[R-SIG-Mac] Problems loading Rcmdr on a Mac 10.7.2 and a Mac 10.6.8
Prof Brian Ripley
ripley at stats.ox.ac.uk
Fri Sep 20 08:49:05 CEST 2013
On 20/09/2013 01:52, John Fox wrote:
> Dear Sarah,
>
>> -----Original Message-----
>> From: Sarah Hardy [mailto:sarah.hardy at maine.edu]
>> Sent: Thursday, September 19, 2013 8:08 PM
>> To: John Fox
>> Cc: Simon Urbanek; David Winsemius; r-sig-mac
>> Subject: Re: [R-SIG-Mac] Problems loading Rcmdr on a Mac 10.7.2 and a
>> Mac 10.6.8
>>
>> 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
>
> I'm glad that this worked. Apparently, the student had an old version of
> X-Windows that was updated by Software Update. As Simon explained, in this
> situation installing XQuartz is irrelevant because the other version of
> X-Windows is invoked by R.
>
>> 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.
>
> If the student installed a sufficiently up-to-date X-Windows, that should
> work, and apparently did. The X-Windows used needn't be XQuartz. My new
> instructions suggest that everyone install XQuartz because that will give
> them an up-to-date X-Windows if they don't already have X-windows installed,
> and will do no harm if they do have another X-Windows.
I am not so sure about that. It will do no harm running CRAN binary R.
But it does mean that there are multiple versions of X11 things about
and that will cause problems for other things (including possibly
installing packages from source).
>
> Best,
> John
>
>>
>>
>> Best,
>>
>> Sarah
>>
>>
>>
>> On Thu, Sep 19, 2013 at 3:17 PM, John Fox <jfox at 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 at 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 at 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 at 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 at 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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--
Brian D. Ripley, ripley at 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, UK Fax: +44 1865 272595
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