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

[Simon Urbanek]

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
>>> 
> 
>