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Re: build trouble on MacOS 10.5
From: |
Ben Abbott |
Subject: |
Re: build trouble on MacOS 10.5 |
Date: |
Mon, 21 Dec 2009 12:14:09 -0500 |
On Dec 21, 2009, at 7:26 AM, Ben Abbott wrote:
> On Dec 21, 2009, at 3:26 AM, Ben Abbott wrote:
>
>> On Dec 21, 2009, at 2:28 AM, Ben Abbott wrote:
>>
>>> On Dec 21, 2009, at 12:47 AM, Rob Mahurin wrote:
>>>
>>>> On Mon, Dec 21, 2009 at 12:36:55AM -0500, Rob Mahurin wrote:
>>>>> On Sun, Dec 20, 2009 at 02:52:28PM -0500, Ben Abbott wrote:
>>>>>> On Dec 20, 2009, at 2:34 PM, Rob Mahurin wrote:
>>>>>>> On the theory that it's a library conflict, I complied with
>>>>>>>
>>>>>>> ./configure CC=gcc-mp-4.3 CXX=g++-mp-4.3 F77=gfortran-mp-4.3
>>>>>>> LDFLAGS=-L/opt/local/lib --without-framework-carbon
>>>>>>> --without-qhull --without-z --without-hdf5 --without-fftw3
>>>>>>> --without-fftw3f --without-glpk --without-curl
>>>>>>> --without-framework-opengl --without-qrupdate --without-amd
>>>>>>> --without-camd --without-colamd --without-ccolamd
>>>>>>> --without-cholmod --without-cxsparse --without-umfpack
>>>>>>> --without-arpack --disable-readline
>>>>>>>
>>>>>>> That gives me a run-octave that runs without crashing.
>>>>> [...]
>>>>>>> Now the build succeeds.
>>>>>>>
>>>>>>> $ make check
>>>>>>> PASS 5321
>>>>>>> FAIL 5
>>>>>>
>>>>>> Maybe we should see if it is just one of the libraries that is
>>>>>> responsible. Perhaps multiple builds with just one of the
>>>>>> --without-foobar will tell us which one is the problem?
>>>>>
>>>>> I'm going the other way, removing --withouts one at a time. I started
>>>>> with qhull, since that was mentioned in the patch I submitted (thanks
>>>>> to Rik for applying it). I got extra failures when I removed
>>>>> cxsparse, so I left that one. About half the --withouts are gone,
>>>>> with three test failures.
>>>>>
>>>>>> BTW, you mention that run-octave didn't crash. I assume you mean you
>>>>>> can run and then quit without error?
>>>>>
>>>>> Right. With linking to external libraries restricted, I haven't yet
>>>>> reproduced the bus error on startup whose backtrace we compared
>>>>> earlier.
>>>>
>>>> Strike that: if I configure with
>>>>
>>>> ./configure CC=gcc-mp-4.3 CXX=g++-mp-4.3 F77=gfortran-mp-4.3
>>>> LDFLAGS=-L/opt/local/lib --without-framework-carbon
>>>> --without-z --without-hdf5 --without-fftw3 --without-fftw3f
>>>> --without-glpk --without-curl --without-cholmod
>>>> --without-cxsparse --without-umfpack
>>>>
>>>> then I get
>>>>
>>>> Making check in test
>>>> ../run-octave --norc --silent --no-history ./fntests.m .
>>>> make[2]: *** [check] Bus error
>>>>
>>>> The previous build included --without-framework-opengl, and that build
>>>> proceeded through "make check" with only three test failures. Do you
>>>> also have trouble with this library?
>>>>
>>>> Cheers,
>>>> Rob
>>>
>>> The first attempt I made, after reading your results, was a build with
>>> --without-framework-carbon and --without-framework-opengl.
>>>
>>> For me the bus error remained. I'm now trying to build including all the
>>> --without-xxx's.
>>>
>>> Ben
>>
>> I've run configure as shown below ...
>>
>> $ ./configure --prefix=/sw --infodir=${prefix}/share/info
>> --mandir=${prefix}/share/man --libexecdir=${prefix}/lib
>> --with-blas=-Wl,-framework -Wl,vecLib --without-framework-carbon
>> --without-framework-opengl --without-qhull --without-hdf5 --without-fftw3
>> --without-fftw3f --without-glpk --without-curl --without-qrupdate
>> --without-amd --without-camd --without-colamd --without-ccolamd
>> --without-cholmod --without-cxsparse --without-umfpack --without-arpack
>> --without-z --disable-readline
>>
>> "make" still fails with ...
>>
>> Making all in interpreter
>> /run-octave -f -q -H -p . --eval "geometryimages ('voronoi', 'txt');"
>> /bin/sh: /run-octave: No such file or directory
>> make[3]: *** [voronoi.txt] Error 127
>> make[2]: *** [all-recursive] Error 1
>> make[1]: *** [all-recursive] Error 1
>> make: *** [all] Error 2
>>
>> While Octave does run, it core-dumps when quit.
>>
>> ...........................................................................................
>> done
>> GNU Octave, version 3.3.50+
>> Copyright (C) 2009 John W. Eaton and others.
>> This is free software; see the source code for copying conditions.
>> There is ABSOLUTELY NO WARRANTY; not even for MERCHANTABILITY or
>> FITNESS FOR A PARTICULAR PURPOSE. For details, type `warranty'.
>>
>> Octave was configured for "i386-apple-darwin10.2.0".
>>
>> Additional information about Octave is available at http://www.octave.org.
>>
>> Please contribute if you find this software useful.
>> For more information, visit http://www.octave.org/help-wanted.html
>>
>> Report bugs to <address@hidden> (but first, please read
>> http://www.octave.org/bugs.html to learn how to write a helpful report).
>>
>> For information about changes from previous versions, type `news'.
>>
>> Reading symbols for shared libraries . done
>> Reading symbols for shared libraries . done
>> Reading symbols for shared libraries . done
>> Reading symbols for shared libraries . done
>> Reading symbols for shared libraries . done
>> octave:1> quit
>>
>> Program received signal EXC_BAD_ACCESS, Could not access memory.
>> Reason: KERN_PROTECTION_FAILURE at address: 0x00000001
>> 0x00000001 in ?? ()
>> (gdb) bt
>> #0 0x00000001 in ?? ()
>> Cannot access memory at address 0x1
>> (gdb)
>>
>> I'm going to remove my FLTK libs and try again (is there a --without-fltk
>> option?).
>>
>> Ben
>
> With no FLTK libs, I'm back to the same result as before (i.e. no FLTK but
> with everything else).
>
> $ ./configure --prefix=/sw --infodir=${prefix}/share/info
> --mandir=${prefix}/share/man --libexecdir=${prefix}/lib
> --with-blas=-Wl,-framework -Wl,vecLib --without-framework-carbon
> --without-framework-opengl --without-qhull --without-hdf5 --without-fftw3
> --without-fftw3f --without-glpk --without-curl --without-qrupdate
> --without-amd --without-camd --without-colamd --without-ccolamd
> --without-cholmod --without-cxsparse --without-umfpack --without-arpack
> --without-z --disable-readline
>
> Program received signal EXC_BAD_ACCESS, Could not access memory.
> Reason: KERN_PROTECTION_FAILURE at address: 0x00000000
> 0x0280b02f in std::locale::operator= ()
> (gdb) bt
> #0 0x0280b02f in std::locale::operator= ()
> #1 0x02809c9e in std::ios_base::_M_init ()
> #2 0x0281f25a in std::basic_ios<char, std::char_traits<char> >::init ()
> #3 0x0014f8d3 in global constructors keyed to pager.cc () at ostream:362
> #4 0x8fe0ed6d in
> __dyld__ZN16ImageLoaderMachO18doModInitFunctionsERKN11ImageLoader11LinkContextE
> ()
> #5 0x8fe0d31e in
> __dyld__ZN11ImageLoader23recursiveInitializationERKNS_11LinkContextEj ()
> #6 0x8fe0d2c2 in
> __dyld__ZN11ImageLoader23recursiveInitializationERKNS_11LinkContextEj ()
> #7 0x8fe0d3d1 in
> __dyld__ZN11ImageLoader15runInitializersERKNS_11LinkContextE ()
> #8 0x8fe024a9 in __dyld__ZN4dyld24initializeMainExecutableEv ()
> #9 0x8fe07950 in __dyld__ZN4dyld5_mainEPK12macho_headermiPPKcS5_S5_ ()
> #10 0x8fe018b1 in __dyld__ZN13dyldbootstrap5startEPK12macho_headeriPPKcl ()
> #11 0x8fe01057 in __dyld__dyld_start ()
>
> Looking at the linked dylibs, I still have a conflict between Fink's freetype
> and X11's (Mac OS 10.6). I'll resolve that and try again.
>
> Ben
I tried Octave's freetype options, --with-ft-prefix=/usr/X11
--with-ft-exec-prefix=/usr/X11, but the resulting dynamic libraries still
included links to both Fink and Apple's dylibs.
I'm getting no where very slow. With no FLTK libs ...
$ ./configure --prefix=/sw --infodir=${prefix}/share/info
--mandir=${prefix}/share/man --libexecdir=${prefix}/lib
--with-blas=-Wl,-framework -Wl,vecLib --without-framework-carbon
--without-framework-opengl --without-qhull --without-hdf5 --without-fftw3
--without-fftw3f --without-glpk --without-curl --without-qrupdate --without-amd
--without-camd --without-colamd --without-ccolamd --without-cholmod
--without-cxsparse --without-umfpack --without-arpack --without-z
--disable-readline --without-x
The configure process ends with …
Octave is now configured for i386-apple-darwin10.2.0
Source directory: .
Installation prefix: /sw
C compiler: gcc-4 -mieee-fp -Wall -W -Wshadow -Wformat
-I/sw/include -O1 -g -D_THREAD_SAFE
C++ compiler: g++-4 -mieee-fp -I/sw/include/freetype2
-I/sw/include -I/usr/X11/include -Wall -W -Wshadow -Wold-style-cast -Wformat
-I/sw/include -O1 -g
Fortran compiler: /sw/bin/gfortran -O1 -ff2c -g -mieee-fp
Fortran libraries: /sw/lib/gcc4.4/lib/libgfortran.dylib
Lex libraries:
LIBS: -lm
AMD CPPFLAGS:
AMD LDFLAGS:
AMD libraries:
ARPACK libraries:
BLAS libraries: -Wl,-framework -Wl,vecLib
CAMD CPPFLAGS:
CAMD LDFLAGS:
CAMD libraries:
CARBON libraries:
CCOLAMD CPPFLAGS:
CCOLAMD LDFLAGS:
CCOLAMD libraries:
CHOLMOD CPPFLAGS:
CHOLMOD LDFLAGS:
CHOLMOD libraries:
COLAMD CPPFLAGS:
COLAMD LDFLAGS:
COLAMD libraries:
CURL CPPFLAGS:
CURL LDFLAGS:
CURL libraries:
CXSPARSE CPPFLAGS:
CXSPARSE LDFLAGS:
CXSPARSE libraries:
DL libraries: -ldl
FFTW3 CPPFLAGS:
FFTW3 LDFLAGS:
FFTW3 libraries:
FFTW3F CPPFLAGS:
FFTW3F LDFLAGS:
FFTW3F libraries:
fontconfig CFLAGS: -I/usr/X11/include
fontconfig LIBS: -L/usr/X11/lib -lfontconfig
FT2_CFLAGS: -I/sw/include/freetype2 -I/sw/include
FT2_LIBS: -L/sw/lib -lfreetype -lz
-Wl,-framework,CoreServices -Wl,-framework,ApplicationServices
GLPK CPPFLAGS:
GLPK LDFLAGS:
GLPK libraries:
graphics CFLAGS:
graphics LIBS:
GraphicsMagick++ CPPFLAGS: -I/sw/include/GraphicsMagick
GraphicsMagick++ LDFLAGS: -L/sw/lib
GraphicsMagick++ libraries: -lGraphicsMagick++ -lGraphicsMagick
HDF5 CPPFLAGS:
HDF5 LDFLAGS:
HDF5 libraries:
LAPACK libraries:
OPENGL libraries: -L/usr/X11/lib -lfontconfig -L/usr/X11R6/lib
-lGL -lGLU
PTHREAD flags: -D_THREAD_SAFE
PTHREAD libraries:
QHULL CPPFLAGS:
QHULL LDFLAGS:
QHULL libraries:
QRUPDATE libraries:
READLINE libraries:
REGEX libraries: -L/sw/lib -lpcre
TERM libraries: -lncurses
UMFPACK libraries:
X11 include flags:
X11 libraries:
Z CPPFLAGS:
Z LDFLAGS:
Z libraries:
Default pager: less
gnuplot: gnuplot
Do internal array bounds checking: false
Build static libraries: false
Build shared libraries: true
Dynamic Linking: true (dlopen)
Include support for GNU readline: false
64-bit array dims and indexing: false
configure:43565: WARNING: command editing and history features require GNU
Readline
configure:43601: WARNING: UMFPACK not found. This will result in some lack of
functionality for sparse matrices.
configure:43607: WARNING: qrupdate not found. The QR & Cholesky updating
functions will be slow.
configure:43613: WARNING: AMD library not found. This will result in some lack
of functionality for sparse matrices.
configure:43619: WARNING: COLAMD library not found. This will result in some
lack of functionality for sparse matrices.
configure:43625: WARNING: CCOLAMD library not found. This will result in some
lack of functionality for sparse matrices.
configure:43631: WARNING: CHOLMOD library not found. This will result in some
lack of functionality for sparse matrices.
configure:43637: WARNING: CXSparse library not found. This will result in some
lack of functionality for sparse matrices.
configure:43643: WARNING: arpack not found. The eigs function will be disabled.
configure:43649: WARNING: cURL library not found. The ftp objects, urlread and
urlwrite functions will be disabled.
configure:43661: WARNING: GLPK library not found. The glpk function for
solving linear programs will be disabled.
configure:43673: WARNING: HDF5 library not found. Octave will not be able to
save or load HDF5 data files.
configure:43691: WARNING: Qhull library not found -- this will result in loss
of functionality of some geometry functions.
configure:43808: WARNING: FLTK config script not found. Native graphics will
be disabled.
configure:43824: WARNING:
configure:43826: WARNING: I didn't find the necessary libraries to compile
native
configure:43828: WARNING: graphics. It isn't necessary to have native graphics
configure:43830: WARNING: but you will have to use gnuplot or you won't be able
configure:43832: WARNING: to use any of Octave's plotting commands
configure:43834: WARNING:
configure:43840:
configure:43842: NOTE: libraries may be skipped if a library is not found OR
configure:43844: NOTE: if the library on your system is missing required
features.
"make" ended with …
Making all in interpreter
../../run-octave -f -q -H -p . --eval "geometryimages ('voronoi', 'txt');"
make[3]: *** [voronoi.txt] Bus error
make[2]: *** [all-recursive] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
Running from the debugger ...
Program received signal EXC_BAD_ACCESS, Could not access memory.
Reason: KERN_PROTECTION_FAILURE at address: 0x00000000
0x0255e02f in std::locale::operator= ()
(gdb) bt
#0 0x0255e02f in std::locale::operator= ()
#1 0x0255cc9e in std::ios_base::_M_init ()
#2 0x0257225a in std::basic_ios<char, std::char_traits<char> >::init ()
#3 0x0256b049 in std::basic_ofstream<char, std::char_traits<char>
>::basic_ofstream ()
#4 0x0014e76d in global constructors keyed to pager.cc () at pager.cc:59
#5 0x8fe0ed6d in
__dyld__ZN16ImageLoaderMachO18doModInitFunctionsERKN11ImageLoader11LinkContextE
()
#6 0x8fe0d31e in
__dyld__ZN11ImageLoader23recursiveInitializationERKNS_11LinkContextEj ()
#7 0x8fe0d2c2 in
__dyld__ZN11ImageLoader23recursiveInitializationERKNS_11LinkContextEj ()
#8 0x8fe0d3d1 in __dyld__ZN11ImageLoader15runInitializersERKNS_11LinkContextE
()
#9 0x8fe024a9 in __dyld__ZN4dyld24initializeMainExecutableEv ()
#10 0x8fe07950 in __dyld__ZN4dyld5_mainEPK12macho_headermiPPKcS5_S5_ ()
#11 0x8fe018b1 in __dyld__ZN13dyldbootstrap5startEPK12macho_headeriPPKcl ()
#12 0x8fe01057 in __dyld__dyld_start ()
Looking at pager.cc
55 // The name of the current diary file.
56 static std::string diary_file;
57
58 // The diary file.
59 static std::ofstream external_diary_file;
60
61 static std::string
62 default_pager (void)
std::ofstream is from /sw/lib/gcc4.4/lib/libstdc++.6.dylib or from
/usr/lib/libstdc++.6.dylib. The latter is linked to via
/usr/X11/lib/libGLU.1.dylib, and was built using gcc 4.2.1.
I'm out of ideas.
Rob, I'll be tracking your progress. If I have the time and motivation, I may
dig up an old Mac running 10.5 and try to duplicate your success.
Ben
- Re: build trouble on MacOS 10.5, (continued)
- Re: build trouble on MacOS 10.5, Rob Mahurin, 2009/12/20
- Re: build trouble on MacOS 10.5, Ben Abbott, 2009/12/20
- Re: build trouble on MacOS 10.5, Rob Mahurin, 2009/12/21
- Re: build trouble on MacOS 10.5, Rob Mahurin, 2009/12/21
- Re: build trouble on MacOS 10.5, Ben Abbott, 2009/12/21
- Re: build trouble on MacOS 10.5, Ben Abbott, 2009/12/21
- Re: build trouble on MacOS 10.5, Ben Abbott, 2009/12/21
- Re: build trouble on MacOS 10.5,
Ben Abbott <=
- Re: build trouble on MacOS 10.5, Ben Abbott, 2009/12/21
- Re: build trouble on MacOS 10.5, Ben Abbott, 2009/12/22
- Re: build trouble on MacOS 10.5 [patch], Rob Mahurin, 2009/12/22
- Re: build trouble on MacOS 10.5 [patch], Ben Abbott, 2009/12/22
- Re: build trouble on MacOS 10.5 [changeset], Thomas Treichl, 2009/12/22
- Re: build trouble on MacOS 10.5 [changeset], Ben Abbott, 2009/12/22
- Re: build trouble on MacOS 10.5 [changeset], Ben Abbott, 2009/12/28
- Re: build trouble on MacOS 10.5 [changeset], John W. Eaton, 2009/12/28
- Re: build trouble on MacOS 10.5 [changeset], Ben Abbott, 2009/12/28
- Re: build trouble on MacOS 10.5 [patch], John W. Eaton, 2009/12/22