[R-SIG-Mac] 64-bit build from source ... 64bit readline oddity solved; libiconv now solved
Kasper Daniel Hansen
khansen at stat.berkeley.edu
Sun Jul 26 06:35:29 CEST 2009
Vince
I am building a 64bit version of R using only Xcode 3.1.2 as well as
the gfortran that Simon provides. This is on OS X 10.5.7. It is an old
installation, but I have only installed very few programs from source
(and have never used fink nor darwinports), like graphviz and similar
non-system-"like" programs. I have never had any problems with
readline or iconv.
I also have the i386 message on startup, but my sizeof.pointer is 8.
My otool output is
grue:~/Work/readbias/paper/> otool -L /Library/Frameworks/R.framework/
Versions/2.10/Resources/lib/libR.dylib
/Library/Frameworks/R.framework/Versions/2.10/Resources/lib/libR.dylib:
/Library/Frameworks/R.framework/Versions/2.10/Resources/lib/
libR.dylib (compatibility version 2.10.0, current version 2.10.0)
/Library/Frameworks/R.framework/Versions/2.10/Resources/lib/
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/local/lib/libreadline.5.2.dylib (compatibility version 5.0.0,
current version 5.2.0)
/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/lib/libiconv.2.dylib (compatibility version 7.0.0, current
version 7.0.0)
/usr/local/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current
version 1.0.0)
Hmm, I am wondering why it is linking to libgxx_s.1.dylib in /usr/
local/lib and not in /usr/lib, and similar with libreadline. Could
that be leftovers from an old GCC from Simon? Or an old(er) R install
from the CRAN binary? I certainly never compiled readline myself.
Kasper
On Jul 25, 2009, at 17:56 , Vincent Carey wrote:
> 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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