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

[John Fox]

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
> >>>
> >
> >