Hi Stefano,
So what are the implications of the external library changes for the
use of rgl? Will it now run so long as X11 is up? Is the new release
R 2.3 or R 2.2.1?
The potential plus to Jan's approach is that you could pre-load all
the needed binary packages, and kick the application launch off using
an applescript or shell script. Although, pre-loading the needed
binary packages may also be true for R.app, and I'm just not aware of
it.
As a related observation, what they have done on the Windows side to
allow someone to distribute a customized version of R is really
slick, it seems like creating a customized version of R is a somewhat
more daunting task on the Mac side, or at least, I perceive it to be.
Dan
On 19-Oct-05, at 10:08 AM, stefano iacus wrote:
>
> On 19/ott/05, at 18:23, Dan Putler wrote:
>
>
>> Hi Stefano,
>>
>> One problem that I ran into is that an R workspace (if it has been
>> saved after a prior session where R Commander was used) will load the
>> tcltk package at startup. This causes a fatal error in R, and the R
>> Console application will never come up if X11 isn't already running.
>> How I dealt with this problem was to write an applescript that
>> launched X11 followed by R. This worked under Panther, but my
>> applescript stopped working under Tiger, and I haven't taken the time
>> yet to diagnose the problem. However, I'm about to start working on R
>> Commander related things for class, and one of my goals is to look at
>> ways to make things easier for Mac users.
>>
>
> why you don't put X11.app in the startup app preferences? (if you
> have x11 running, you can even do this from the doc).
>
> Unfortunately X11.app must be installed by the end as it is not
> installed by the OS X Apple's installer by default (don't ask me
> why!!!)
>
> For several reasons we decided not to run the X11.app at R launch
> but, given that this is becoming a faq, I'm thinking about adding a
> Preference setting into R.app to launch X1.app at startup. At the
> moment R.app just sets the DISPLAY env var to :0 so that R can
> connect to the X11 server if present.
>
>
>>
>> As things stand now, it is far easier to get a novice Windows user up
>> and running with R Commander (they just need to double-click on a
>> customized installer, and after that when they launch R, R Commander
>> is automatically loaded along with all its support packages) than it
>> is for a Mac user (who may need to install X11, Xcode tools, and
>> download and compile libpng if they want access to rgl under R
>> Commander).
>>
>
> this is no longer true as libpng is statically linked to R. XCode
> tools and company are not needed as well, only if users want to
> build packages their own (but this is also true for Windog R I guess)
>
> btw next release (have a look on CRAN or wait for the official
> announcement ;) ) is now less dependent on external libraries
>
>
>
>> When you want to just run things under an application
>> GUI (like R Commander or James's limmaGUI and affylmGUI) it might be
>> the case that taking Jan's approach of running the console in an X11
>> terminal, using the X11 graphics devise (instead of Quartz), and
>> using aqua Tcl/Tk (to make the GUI feel more like a Mac app) works
>> best in terms of developing a simple configuration for novice users.
>>
>
> if you run R from the terminal and you assume you can use X11 for
> graphics instead of quartz, then I don't see why this is easier for
> the dummy user. He needs to run X11.app anyway before R. So why not
> telling him: please launch X11.app and then R (if you need Rcommander)
> In my opinion Jan's approach is probably the best approach if you
> need to run R from Emacs but not for dummy user
>
>
>> Over the next month I'll experiment with a few things, and post what
>> I find works best to the list.
>>
> thanks for this
> stefano
>
>
>>
>> Dan
>>
>> On 19-Oct-05, at 1:16 AM, stefano iacus wrote:
>>
>>
>>
>>>
>>> On 19/ott/05, at 09:21, James Wettenhall wrote:
>>>
>>>
>>>
>>>
>>>
>>>> Thanks Jan,
>>>>
>>>> That makes some sense to me. But I'm still not really clear on how
>>>> best
>>>> to advise a user of my R-Tcl/Tk package who says "I'm just a
>>>> dumb GUI
>>>> user. I don't want to use the R command-line, I only want to use
>>>> your
>>>> Tcl/Tk GUI. And I don't want to learn what an environment variable
>>>> is.
>>>> etc."
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>> if this is the case, your user is probably an R.app user. Then this
>>> use will find on the R.app toolbar an icon with "X11" in it. Just
>>> click on it before launching your package (or any tcltk based
>>> package). That's all.
>>> One other option for your user is to read the OS X Faq, but I know
>>> this is rarely the case...
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>> It's very unlikely that the sort of user I'm talking about would be
>>>> using
>>>> emacs (and I don't use it either). I'm more interested in making
>>>> it as
>>>> easy as possible for a user to get started with an R-Tcl/Tk GUI who
>>>> doesn't know how to use the R command-line and who doesn't know
>>>> about
>>>> things like environment variables and .Rprofile files etc. So
>>>> that's why
>>>> I was wondering whether it would be possible for tcltk's .First.lib
>>>> () or
>>>> equivalent to test whether X11 is running, and if not, give a
>>>> friendly
>>>> error message.
>>>>
>>>> Best wishes,
>>>> James
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>> I run R from the terminal, from the Aqua GUI, from Carbon/Cocoa
>>>>> emacs, or from X11 emacs. In order to make sure that X11 is
>>>>> always available I start X11.app from the login items in system
>>>>> preferences. This is not enough, because running R from carbon/
>>>>> cocoa
>>>>> emacs cannot
>>>>> find $DISPLAY even if X11.app is running and it is defined
>>>>> in .tcshrc
>>>>> -- so in addition my Rprofile.site has
>>>>>
>>>>> local({
>>>>> options(device="x11")
>>>>> options(repos="http://cran.r-project.org";)
>>>>> options(pkgType="source")
>>>>> Sys.putenv(DISPLAY=":0.0")
>>>>> })
>>>>>
>>>>> .First <- function() {
>>>>> cat("\n Welcome to Jan's R-2.3.0 !\n\n")
>>>>> }
>>>>>
>>>>> This guarantees that library(tkrplot) or library(tcltk) always
>>>>> works in all my different GUI's.
>>>>>
>>>>> On Oct 18, 2005, at 19:24 , James Wettenhall wrote:
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> This problem of getting Tcl/Tk errors in R on MacOSX because X11
>>>>>> isn't
>>>>>> running seems to be quite common, and unfortunately R's tcltk
>>>>>> package is
>>>>>> currently unable to check whether X11 is running (if the
>>>>>> operating
>>>>>> system
>>>>>> is Darwin) and if not, give a friendly error message advising the
>>>>>> user to
>>>>>> run X11. My expertise on this is limited, but do people think it
>>>>>> would be
>>>>>> possible for the tcltk package to automatically check for X11?
>>>>>> Obviously
>>>>>> this is platform dependent - X11 is not required on Windows.
>>>>>>
>>>>>> A colleague of mine had Tcl/Tk errors and she found that she
>>>>>> could
>>>>>> only
>>>>>> start R-Tcl/Tk applications when her network cable was removed
>>>>>> from
>>>>>> her
>>>>>> laptop. When the network cable was plugged in, X11 appeared to
>>>>>> start OK,
>>>>>> but then it silently froze up due to some network problem. So
>>>>>> the
>>>>>> R-Tcl/Tk interface failed to initalize as a result.
>>>>>>
>>>>>> Hope this was of interest to some people.
>>>>>> Best wishes,
>>>>>> James
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>> Hi Cormac,
>>>>>>>
>>>>>>> The error you are getting is because X11 isn't launched prior to
>>>>>>> when
>>>>>>> you are launching the tcltk package in R. Try rebooting, and
>>>>>>> attempt
>>>>>>> to launch X11 before loading R. If X11 still doesn't launch,
>>>>>>> then
>>>>>>> your problem isn't with R, and you might reinstalling X11.
>>>>>>>
>>>>>>> You also probably want to look at the OS X installation
>>>>>>> instructions
>>>>>>> for R Commander (http://socserv.socsci.mcmaster.ca/jfox/Misc/
>>>>>>> Rcmdr/
>>>>>>> installation-notes.html).
>>>>>>>
>>>>>>> Dan
>>>>>>>
>>>>>>> On 18-Oct-05, at 3:54 PM, Cormac Lawler wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>> (originally posted to R-Help - advised to post here)
>>>>>>>> Hi,
>>>>>>>> I'm using a Mac, I've downloaded R (base), and I'm trying to
>>>>>>>> download
>>>>>>>> the package R Commander. I thought I had already done this
>>>>>>>> (both
>>>>>>>> from
>>>>>>>> the web and from within R) but it doesn't seem to be working -
>>>>>>>> it's
>>>>>>>> not there as a "search()" reveals. However, there are plenty of
>>>>>>>> files
>>>>>>>> on my system linked with Rcmdr - located in
>>>>>>>> HD>Library>Frameworks>R.framework>Versions>2.1.1>Resources>Libr
>>>>>>>> ar
>>>>>>>> y
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>> R
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>> cm
>>>>>>>> dr.
>>>>>>>> Is it simply in the wrong location to use it? The other
>>>>>>>> possibility is
>>>>>>>> that I keep getting a tcltk error whenever I try to load up the
>>>>>>>> package from the Package Manager from within R - and when I
>>>>>>>> try to
>>>>>>>> upload the tcltk package, this also gives the same error [1]. I
>>>>>>>> also
>>>>>>>> get a "Couldn't launch application" error whenever I try to
>>>>>>>> launch the
>>>>>>>> X11.app.
>>>>>>>>
>>>>>>>> This is probably so basic it's staring me in the eyes, but I
>>>>>>>> need
>>>>>>>> your
>>>>>>>> help please. I'd be happy to give any extra info you need.
>>>>>>>>
>>>>>>>> Thanks
>>>>>>>> Cormac
>>>>>>>>
>>>>>>>> [1] Loading required package: tcltk
>>>>>>>> Loading Tcl/Tk interface ... Error in dyn.load(x, as.logical
>>>>>>>> (local),
>>>>>>>> as.logical(now)) :
>>>>>>>> unable to load shared library
>>>>>>>> '/Library/Frameworks/R.framework/Resources/library/tcltk/libs/
>>>>>>>> tcltk.so':
>>>>>>>> dlcompat: dyld: /Applications/R.app/Contents/MacOS/R can't
>>>>>>>> open
>>>>>>>> library: /usr/local/lib/libtk8.4.dylib (No such file or
>>>>>>>> directory,
>>>>>>>> errno = 2)
>>>>>>>> In addition: Warning messages:
>>>>>>>> 1: cannot create HTML package index in: make.packages.html()
>>>>>>>> 2: cannot create HTML package index in: make.packages.html()
>>>>>>>> Error: .onLoad failed in 'loadNamespace' for 'tcltk'
>>>>>>>> Error: package 'tcltk' could not be loaded
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> R-SIG-Mac mailing list
>>>>>>>> [email protected]
>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> R-SIG-Mac mailing list
>>>>>>> [email protected]
>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> R-SIG-Mac mailing list
>>>>>> [email protected]
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>> ===
>>>>> Jan de Leeuw; Distinguished Professor and Chair, UCLA
>>>>> Department of
>>>>> Statistics;
>>>>> Editor: Journal of Multivariate Analysis, Journal of Statistical
>>>>> Software
>>>>> US mail: 8130 Math Sciences Bldg, Box 951554, Los Angeles, CA
>>>>> 90095-1554
>>>>> phone (310)-825-9550; fax (310)-206-5658; email:
>>>>> [EMAIL PROTECTED]
>>>>> .mac: jdeleeuw ++++++ aim: deleeuwjan ++++++ skype: j_deleeuw
>>>>> homepages: http://gifi.stat.ucla.edu ++++++ http://
>>>>> www.cuddyvalley.org
>>>>>
>>>>> ------------------------------------------------------------------
>>>>> --
>>>>> -
>>>>> ---
>>>>> -------------------------
>>>>> No matter where you go, there you are. --- Buckaroo
>>>>> Banzai
>>>>> http://gifi.stat.ucla.edu/sounds/nomatter.au
>>>>>
>>>>> ------------------------------------------------------------------
>>>>> --
>>>>> -
>>>>> ---
>>>>> -------------------------
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>> _______________________________________________
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>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
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>>>
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>>
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