[R-SIG-Mac] 64-bit build from source ... 64bit readline oddity solved; libiconv now solved
Jan de Leeuw
deleeuw at stat.ucla.edu
Sun Jul 26 02:19:59 CEST 2009
I am using
configure --with-aqua --with-blas='\''-framework vecLib'\'' --with-
lapack --prefix=/usr/local/R --disable-R-framework --with-readline --
with-cairo --enable-memory-profiling --enable-R-shlib --x-includes=/
usr/X11R6/include --x-libraries=/usr/X11R6/lib --build=x86_64-apple-
darwin10 --host=x86_64-apple-darwin10 --target=x86_64-apple-darwin10
with OS X 10.6 and a GNU svn build of gcc-4.2 and gfortran-4.2. The
resulting R has the quartz device as well, but cannot be used directly
with R.app. It also builds with the gcc-4.2 that comes with Xcode 3.2,
which I use for OBJC anyway, and maybe with Simon's gfortran (haven't
tried). Of course this is not a universal binary. I don't think 10.6
or Xcode 3.2 are essential.
My C, CXX, F, FC flags are
-m64 -O3 -fopenmp -mtune=native
and my LDFLAGS are
-m64 -fopenmp
For otool -L libR.dylib I get
libR.dylib:
libR.dylib (compatibility version 2.10.0, current version 2.10.0)
/System/Library/Frameworks/vecLib.framework/Versions/A/vecLib
(compatibility version 1.0.0, current version 268.0.0)
/usr/local/lib/libintl.8.dylib (compatibility version 9.0.0, current
version 9.2.0)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/
CoreFoundation (compatibility version 150.0.0, current version 549.0.0)
/usr/local/lib/libreadline.6.0.dylib (compatibility version 6.0.0,
current version 6.0.0)
/usr/lib/libicucore.A.dylib (compatibility version 1.0.0, current
version 40.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
version 123.0.0)
/usr/local/lib/libiconv.2.dylib (compatibility version 7.0.0, current
version 7.0.0)
Of course cairo, tcltk, jpeg, png, ... use additional stuff from /usr/
local.
Why am I using this instead of Simon's excellent work ? I have no
idea. It feels a bit embarrassing.
On Jul 25, 2009, at 16:32 , Vincent Carey wrote:
> i'm aware of the r.research.att.com site -- i am working with what i
> believe to be a relatively clean (out of the box
> only a couple of weeks, some fink extensions) macosx 10.5.7 with
> Xcode 3.1.2
>
> i won't deny that it is messed up but are there any ways of stating
> minimal conditions
> on the state of OSX needed to get a good 64 bit build? would xcode
> 3.1.3 make a big difference?
> looks like something much earlier is adequate at your place.
>
> thanks
>
> On Sat, Jul 25, 2009 at 6:06 PM, Simon
> Urbanek<simon.urbanek at r-project.org> wrote:
>> Vince,
>>
>> On Jul 25, 2009, at 5:04 PM, Vincent Carey wrote:
>>
>>> now it seems that by using gcc-4.2 to build libiconv in a non-
>>> central
>>> place and using
>>> DYLD_LIBRARY_PATH to find it, and using gcc-4.2 to compile R, all
>>> is well.
>>>
>>
>> FWIW suspect that your system is pretty badly messed up with all the
>> 3rd-party stuff you installed, because our 64-bit binaries don't
>> need any of
>> this... see
>> http://r.research.att.com/
>>
>> Also note that messing with DYLD_LIBRARY_PATH is really dangerous
>> and causes
>> a lot of problems since it overrides *all* system path searches
>> (unlike
>> LD_LIBRARY_PATH on Linux).
>>
>> Cheers,
>> Simon
>>
>>
>>
>>> On Sat, Jul 25, 2009 at 6:39 AM, Vincent
>>> Carey<stvjc at channing.harvard.edu> wrote:
>>>>
>>>> The solution to the readline problem was to remove all conflicting
>>>> libreadline.* on
>>>> the system. However, now similar problems are cropping up with
>>>> libiconv
>>>>
>>>> you should 'make docs' now ...
>>>> building/updating package metadata ...
>>>> dyld: lazy symbol binding failed: Symbol not found: _libiconv_open
>>>> Referenced from: /Users/stvjc/ExternalSoft/R-devel/lib/x86_64/
>>>> libR.dylib
>>>> Expected in: dynamic lookup
>>>>
>>>> installing a fresh 32/64-bit libiconv and removing all conflicting
>>>> versions has not helped.
>>>>
>>>> On Fri, Jul 24, 2009 at 3:54 PM, Vincent
>>>> Carey<stvjc at channing.harvard.edu> wrote:
>>>>>
>>>>> this build from a very recent svn checkout of devel is
>>>>> incomplete. it
>>>>> fails
>>>>> while trying to build base with the same error as occurs here
>>>>>
>>>>> bash-3.2$ bin/R
>>>>> dyld: Symbol not found: _rl_basic_word_break_characters
>>>>> Referenced from:
>>>>> /Users/stvjc/ExternalSoft/R-devel/lib/x86_64/libR.dylib
>>>>> Expected in: dynamic lookup
>>>>>
>>>>> Trace/BPT trap
>>>>>
>>>>> i built readline 6.0 from source with the -arch x86_64 switch on
>>>>> gcc
>>>>> and configure
>>>>> worked ok. i think the symbol exists
>>>>>
>>>>> nm /usr/local/lib/libreadline.6.0.dylib | grep break
>>>>> 000000000002b500 D _rl_basic_word_break_characters
>>>>> 000000000002b4f0 D _rl_completer_word_break_characters
>>>>> 000000000002b4e8 D _rl_completion_word_break_hook
>>>>>
>>>>> help! the past few days have been nothing but glitches and
>>>>> bugs...
>>>>>
>>>>> --
>>>>> Vincent Carey, PhD
>>>>> Biostatistics, Channing Lab
>>>>> 617 525 2265
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Vincent Carey, PhD
>>>> Biostatistics, Channing Lab
>>>> 617 525 2265
>>>>
>>>
>>>
>>>
>>> --
>>> Vincent Carey, PhD
>>> Biostatistics, Channing Lab
>>> 617 525 2265
>>>
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>
>>>
>>
>>
>
>
>
> --
> Vincent Carey, PhD
> Biostatistics, Channing Lab
> 617 525 2265
>
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
===
Jan de Leeuw; Distinguished Professor and Chair, UCLA Department of
Statistics;
Director: UCLA Center for Environmental Statistics (CES);
Editor: Journal of Multivariate Analysis, Journal of Statistical
Software;
US mail: 8125 Math Sciences Bldg, Box 951554, Los Angeles, CA 90095-1554
phone (310)-825-9550; fax (310)-206-5658; email: deleeuw at stat.ucla.edu
.mac: jdeleeuw ++++++ aim: deleeuwjan ++++++ skype: j_deleeuw
homepages: http://gifi.stat.ucla.edu ++++++ http://www.cuddyvalley.org
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