[R-SIG-Mac] 64-bit build from source ... 64bit readline oddity solved; libiconv now solved
Vincent Carey
stvjc at channing.harvard.edu
Sun Jul 26 02:56:21 CEST 2009
Thanks, Jan. Here's the output of otool for my new libR
bash-3.2$ otool -L libR.dylib
libR.dylib:
libR.dylib (compatibility version 2.10.0, current version 2.10.0)
/usr/local/lib/libreadline.6.0.dylib (compatibility version
6.0.0, current version 6.0.0)
/usr/lib/libiconv.2.dylib (compatibility version 7.0.0,
current version 7.0.0)
libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
/usr/local/lib/libgfortran.2.dylib (compatibility version
3.0.0, current version 3.0.0)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
(compatibility version 150.0.0, current version 476.18.0)
/usr/lib/libicucore.A.dylib (compatibility version 1.0.0,
current version 36.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0,
current version 111.1.4)
/usr/local/lib/libgcc_s.1.dylib (compatibility version 1.0.0,
current version 1.0.0)
Any obvious problems?
Simon's binaries have been great; I am just trying the source build to
get more rapid access
to changes to devel.
One item that may be noteworthy -- for the new build,
> sessionInfo()
R version 2.10.0 Under development (unstable) (2009-07-24 r48993)
i386-apple-darwin9.7.0
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
> .Machine$sizeof.pointer
[1] 8
what must be done to get the i386- prefix corrected?
On Sat, Jul 25, 2009 at 8:19 PM, Jan de Leeuw<deleeuw at stat.ucla.edu> wrote:
> 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
> -------------------------------------------------------------------------------------------------
> No matter where you go, there you are. --- Buckaroo Banzai
> http://gifi.stat.ucla.edu/sounds/nomatter.au
> -------------------------------------------------------------------------------------------------
>
>
>
>
>
>
--
Vincent Carey, PhD
Biostatistics, Channing Lab
617 525 2265
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