[R-SIG-Mac] Problems loading Rcmdr on a Mac 10.7.2 and a Mac 10.6.8

Thu Sep 19 17:36:39 CEST 2013

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
> >