[R-SIG-Mac]Re: Jan's OS X Software
Jan de Leeuw
deleeuw@stat.ucla.edu
Mon, 18 Nov 2002 09:26:01 -0800
No, probably not.
installing fink on Jaguar
(http://fink.sourceforge.net/news/jag-bootstrap.php)
upgrading it to Jaguar (http://fink.sourceforge.net/news/jaguar.php).
On Monday, November 18, 2002, at 09:17 AM, David Firth wrote:
> I did a completely clean install of fink (deleted my
> existing /sw tree) after upgrading the
> OS to Jaguar. I'm assuming that would do it -- correct?
>
> D
>
> On 18 Nov 2002, Jan de Leeuw wrote:
>
>> Did you upgrade your fink distribution to Jaguar before starting all
>> this ?
>>
>> --- Jan
>>
>> On Monday, November 18, 2002, at 01:26 AM, David Firth wrote:
>>
>>> Jan, thanks. Unfortunately that didn't work either.
>>> I arranged things so that
>>>
>>> [nuff-pingo:/sw/lib] david% ls -l *ncurses*
>>> -rwxr-xr-x 1 root admin 492256 Nov 16 22:38 libncurses++.a
>>> lrwxr-xr-x 1 root admin 20 Nov 17 21:59 libncurses.5.dylib ->
>>> libncurses.dylib.5.2
>>> -rw-r--r-- 1 root admin 617424 Nov 16 22:37 libncurses.a
>>> lrwxr-xr-x 1 root admin 18 Nov 17 21:59 libncurses.dylib ->
>>> libncurses.dylib.5
>>> lrwxr-xr-x 1 root admin 20 Nov 17 21:59 libncurses.dylib.5 ->
>>> libncurses.dylib.5.2
>>> -rw-r--r-- 1 root admin 360092 Nov 16 22:37 libncurses.dylib.5.2
>>>
>>> but still I get that complaint when trying to run R:
>>>
>>> [nuff-pingo:/sw/lib] david% R
>>> dyld: /usr/local/lib/R/bin/R.bin version mismatch for library:
>>> /sw/lib/
>>> libncurses.5.dylib (compatibility version of user: 6.0.0 greater
>>> than library's version: 5.0.0)
>>> Trace/BPT trap
>>>
>>> I can only guess what's going on. Could it be that fink installs
>>> different
>>> versions of libncurses on G3 and G4 machines? And your R is built
>>> for G4
>>> not G3? Certainly the files in your /sw/lib look rather different
>>> from mine.
>>>
>>> As I say, I'm only guessing. Basically I'm clueless.
>>>
>>> I have failed also in building R for myself from the sources (my
>>> usual
>>> method on OS 10.1.*) on OS 10.2. I'll ask about that on R-SIG-Mac.
>>>
>>> Best wishes,
>>> David
>>>
>>> On Nov 17 2002, Jan de Leeuw wrote:
>>>
>>>> symlinks may solve the problem
>>>>
>>>> this is what I have in /sw/lib
>>>>
>>>> -rw-r--r-- 1 root admin 364320 Nov 12 22:30
>>>> libncurses.5.0.
>>>> 2.dylib
>>>> lrwxr-xr-x 1 root staff 22 Nov 16 20:23
>>>> libncurses.5.dylib -> libncurses.5.0.2.dylib
>>>> -rw-r--r-- 1 root admin 627628 Nov 12 22:30 libncurses.a
>>>> lrwxr-xr-x 1 root staff 22 Nov 16 20:23
>>>> libncurses.dylib -> libncurses.5.0.2.dylib
>>>> lrwxr-xr-x 1 root staff 30 Nov 16 20:23
>>>> libncurses.dylib.5 -> /sw/lib/libncurses.5.0.2.dylib
>>>> -rw-r--r-- 1 root admin 662 Nov 12 22:30
>>>> libncurses.la
>>>>
>>>> no, this is not frustrating -- I am sure all of the problems would
>>>> be
>>>> solved if we decided to install R directly from fink, but this means
>>>> giving up control 8-)
>>>>
>>>> -- jan
>>>>
>>>> On Sunday, November 17, 2002, at 01:14 AM, David Firth wrote:
>>>>
>>>>> Jan, many thanks for your further advice.
>>>>>
>>>>> I am pretty sure it's the right R.bin.
>>>>>
>>>>> But I don't seem to have /sw/lib/libncurses.5.dylib, despite
>>>>> having done
>>>>> "fink rebuild ncurses" at 22:35 or so yesterday evening:
>>>>>
>>>>> [nuff-pingo:lib/R/bin] david% ls -l /sw/lib/libncurses*
>>>>> -rwxr-xr-x 1 root admin 492256 Nov 16 22:38
>>>>> /sw/lib/libncurses++.a
>>>>> -rw-r--r-- 1 root admin 617424 Nov 16 22:37 /sw/lib/libncurses.a
>>>>> lrwxr-xr-x 1 root admin 18 Nov 16 22:41
>>>>> /sw/lib/libncurses.dylib -> libncurses.dylib.5
>>>>> lrwxr-xr-x 1 root admin 20 Nov 16 22:41
>>>>> /sw/lib/libncurses.dylib.5 -> libncurses.dylib.5.2
>>>>> -rw-r--r-- 1 root admin 360092 Nov 16 22:37
>>>>> /sw/lib/libncurses.dylib.5.2
>>>>> [nuff-pingo:lib/R/bin] david%
>>>>>
>>>>> Is that why R is looking elsewhere for libncurses.5.dylib? Should
>>>>> I make
>>>>> some further symbolic links in /sw/lib? I guess it won't hurt to
>>>>> experiment.
>>>>>
>>>>> My fink.conf file is shown below. The only changes I have made
>>>>> are in the Trees: line. For the ncurses package should I perhaps
>>>>> be
>>>>> using "stable" rather than "unstable"?
>>>>>
>>>>> This must all be very frustrating for you (I'm extrapolating...)
>>>>> Maybe we (the "Darwin R" community) need to maintain our own
>>>>> set of "recommended" tools like Brian Ripley does for Windows?
>>>>> Or would that be more hassle still? Certainly we don't want to
>>>>> duplicate fink.
>>>>>
>>>>> Best wishes,
>>>>> David
>>>>>
>>>>> [nuff-pingo:lib/R/bin] david% cat /sw/etc/fink.conf
>>>>> # Fink configuration, initially created by bootstrap.pl
>>>>> Basepath: /sw
>>>>> RootMethod: sudo
>>>>> Trees: unstable/main unstable/crypto local/main stable/main
>>>>> stable/crypto
>>>>> local/bootstrap Mirror-cpan:
>>>>> ftp://ftp.cise.ufl.edu/pub/mirrors/CPAN/
>>>>> Mirror-ctan: ftp://ibiblio.org/pub/packages/TeX/
>>>>> Mirror-gimp: ftp://ftp.cs.umn.edu/pub/gimp/
>>>>> Mirror-gnome: ftp://ftp.cse.buffalo.edu/pub/Gnome
>>>>> Mirror-gnu: http://metalab.unc.edu/pub/gnu/
>>>>> Mirror-sourceforge: http://unc.dl.sourceforge.net/sourceforge/
>>>>> MirrorContinent: nam
>>>>> MirrorCountry: nam-us
>>>>> ProxyPassiveFTP: true
>>>>> Verbose: 3
>>>>>
>>>>>
>>>>>
>>>>> On Sunday, Nov 17, 2002, at 01:54 Europe/London, Jan de Leeuw
>>>>> wrote:
>>>>>
>>>>>> David
>>>>>>
>>>>>> If you look at your error message, you see that dyld is trying
>>>>>> to load /usr/lib/libncurses.5.dylib for R.bin. So it's strange
>>>>>> that
>>>>>> otool -L says that /sw/lib/ncurses.5.dylib (the fink version) is
>>>>>> needed. Are we talking about the same R.bin ? Do you have
>>>>>> two ? Maybe it didn't overwrite the old one ? Maybe rehash
>>>>>> or setenv DYLD_LIBRARY_PATH /sw/lib ?
>>>>>>
>>>>>> --- Jan
>>>>>>
>>>>>> On Saturday, November 16, 2002, at 02:53 PM, David Firth wrote:
>>>>>>
>>>>>>> Jan, many thanks for your reply.
>>>>>>>
>>>>>>> From "otool -L R.bin" I got the same as you.
>>>>>>>
>>>>>>> I did "fink rebuild ncurses" as you suggested -- but the
>>>>>>> problem persists.
>>>>>>>
>>>>>>> (The ncurses I got from "fink rebuild ncurses" is version 5.2-7)
>>>>>>>
>>>>>>> Oh well, never mind. I guess I'll delay upgrading to 10.2
>>>>>>> on my main work machine.
>>>>>>>
>>>>>>> Cheers,
>>>>>>> David
>>>>>>>
>>>>>>> On Saturday, Nov 16, 2002, Jan de Leeuw wrote:
>>>>>>>
>>>>>>>> David
>>>>>>>>
>>>>>>>> You probably need to "fink rebuild ncurses".
>>>>>>>> See what you get from " otool -L R.bin", compare
>>>>>>>> with what I get below.
>>>>>>>>
>>>>>>>> -- Jan
>>>>>>>>
>>>>>>>> [cabledoc68:lib/R/bin] deleeuw% otool -L R.bin
>>>>>>>> R.bin:
>>>>>>>>
>>>>>>>> /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon
>>>>>>>> (compatibility version 2.0.0, current version 122.0.0)
>>>>>>>> /usr/lib/libSystem.B.dylib (compatibility version
>>>>>>>> 1.0.0, current version 61.0.0)
>>>>>>>> /sw/lib/libpcre.0.dylib (compatibility version 1.0.0,
>>>>>>>> current version 1.1.0)
>>>>>>>> /sw/lib/libbz2.1.dylib (compatibility version 1.0.1,
>>>>>>>> current version 1.0.2)
>>>>>>>> /usr/lib/libz.1.1.3.dylib (compatibility version 1.0.0,
>>>>>>>> current version 1.1.3)
>>>>>>>> /sw/lib/libreadline.4.dylib (compatibility version
>>>>>>>> 4.2.0, current version 4.3.0)
>>>>>>>> /sw/lib/libdl.0.dylib (compatibility version 0.0.0,
>>>>>>>> current version 0.0.0)
>>>>>>>> /sw/lib/libncurses.5.dylib (compatibility version
>>>>>>>> 6.0.0, current version 6.2.0)
>>>>>>>>
>>>>>>>>
>>>>>>>> On Saturday, November 16, 2002, at 01:07 PM, David Firth wrote:
>>>>>>>>
>>>>>>>>> Hello Jan,
>>>>>>>>>
>>>>>>>>> I am trying to get R going on Mac OS 10.2.2. No success yet.
>>>>>>>>>
>>>>>>>>> I downloaded your R-1.6.1.tar.gz today, and unpacked in /.
>>>>>>>>>
>>>>>>>>> When I try to run R I get:
>>>>>>>>>
>>>>>>>>> [nuff-pingo:~] david% R
>>>>>>>>> dyld: /usr/local/lib/R/bin/R.bin version mismatch for library:
>>>>>>>>> /usr/lib/libncurses.5.dylib (compatibility version of user:
>>>>>>>>> 6.0.0 greater than library's version: 5.0.0)
>>>>>>>>> Trace/BPT trap
>>>>>>>>> [nuff-pingo:~] david%
>>>>>>>>>
>>>>>>>>> -- any idea what I can do about this? The message doesn't
>>>>>>>>> mean much to me.
>>>>>>>>>
>>>>>>>>> I have a G3 iBook.
>>>>>>>>>
>>>>>>>>> Best wishes,
>>>>>>>>> David
>>>>>>>>>
>>>>>>>>>
>>>>>>>> ===
>>>>>>>> Jan de Leeuw; Professor and Chair, UCLA Department of
>>>>>>>> Statistics;
>>>>>>>> Editor: Journal of Multivariate Analysis, Journal of
>>>>>>>> Statistical Software
>>>>>>>> US mail: 9432 Boelter Hall, Box 951554, Los Angeles, CA
>>>>>>>> 90095-1554
>>>>>>>> phone (310)-825-9550; fax (310)-206-5658; email:
>>>>>>>> deleeuw@stat.ucla.edu
>>>>>>>> homepage: http://gifi.stat.ucla.edu
>>>>>>>>
>>>>>>>> ----------------------------------------------------------------
>>>>>>>> -- -------------------------------
>>>>>>>> No matter where you go, there you are. --- Buckaroo
>>>>>>>> Banzai
>>>>>>>> http://gifi.stat.ucla.edu/sounds/nomatter.au
>>>>>>>>
>>>>>>>> ----------------------------------------------------------------
>>>>>>>> -- -------------------------------
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>> ===
>>>>>> Jan de Leeuw; Professor and Chair, UCLA Department of Statistics;
>>>>>> Editor: Journal of Multivariate Analysis, Journal of Statistical
>>>>>> Software
>>>>>> US mail: 9432 Boelter Hall, Box 951554, Los Angeles, CA 90095-1554
>>>>>> phone (310)-825-9550; fax (310)-206-5658; email:
>>>>>> deleeuw@stat.ucla.edu
>>>>>> homepage: http://gifi.stat.ucla.edu
>>>>>>
>>>>>> ------------------------------------------------------------------
>>>>>> -- -----------------------------
>>>>>> No matter where you go, there you are. --- Buckaroo
>>>>>> Banzai
>>>>>> http://gifi.stat.ucla.edu/sounds/nomatter.au
>>>>>>
>>>>>> ------------------------------------------------------------------
>>>>>> -- -----------------------------
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>> ===
>>>> Jan de Leeuw; Professor and Chair, UCLA Department of Statistics;
>>>> Editor: Journal of Multivariate Analysis, Journal of Statistical
>>>> Software
>>>> US mail: 9432 Boelter Hall, Box 951554, Los Angeles, CA 90095-1554
>>>> phone (310)-825-9550; fax (310)-206-5658; email:
>>>> deleeuw@stat.ucla.edu
>>>> homepage: http://gifi.stat.ucla.edu
>>>>
>>>> --------------------------------------------------------------------
>>>> -- ---------------------------
>>>> No matter where you go, there you are. --- Buckaroo Banzai
>>>> http://gifi.stat.ucla.edu/sounds/nomatter.au
>>>>
>>>> --------------------------------------------------------------------
>>>> -- ---------------------------
>>>>
>>>>
>>>
>>>
>> ===
>> Jan de Leeuw; Professor and Chair, UCLA Department of Statistics;
>> Editor: Journal of Multivariate Analysis, Journal of Statistical
>> Software
>> US mail: 9432 Boelter Hall, Box 951554, Los Angeles, CA 90095-1554
>> phone (310)-825-9550; fax (310)-206-5658; email:
>> deleeuw@stat.ucla.edu
>> homepage: http://gifi.stat.ucla.edu
>>
>> ----------------------------------------------------------------------
>> -- -------------------------
>> No matter where you go, there you are. --- Buckaroo Banzai
>> http://gifi.stat.ucla.edu/sounds/nomatter.au
>>
>> ----------------------------------------------------------------------
>> -- -------------------------
>>
>>
>
>
===
Jan de Leeuw; Professor and Chair, UCLA Department of Statistics;
Editor: Journal of Multivariate Analysis, Journal of Statistical
Software
US mail: 9432 Boelter Hall, Box 951554, Los Angeles, CA 90095-1554
phone (310)-825-9550; fax (310)-206-5658; email: deleeuw@stat.ucla.edu
homepage: http://gifi.stat.ucla.edu
------------------------------------------------------------------------
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No matter where you go, there you are. --- Buckaroo Banzai
http://gifi.stat.ucla.edu/sounds/nomatter.au
------------------------------------------------------------------------
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