Re: MXE Octave: "... has no symbols" warning under Mac OS X

[Ben Abbott]

On Sep 20, 2013, at 9:09 AM, Anirudha Bose wrote:

> On Wed, Sep 4, 2013 at 12:18 AM, Ben Abbott <address@hidden> wrote:
> 
>> On Sep 3, 2013, at 1:40 PM, Anirudha Bose wrote:
>> 
>> > On Tue, Sep 3, 2013 at 9:56 PM, Benjamin Abbott <address@hidden> wrote:
>> >
>> >> On Sep 3, 2013, at 11:57 AM, Anirudha Bose <address@hidden> wrote:
>> >>
>> >>> On Tue, Sep 3, 2013 at 6:18 PM, Ben Abbott <address@hidden> wrote:
>> >>> On Sep 3, 2013, at 4:11 AM, Anirudha Bose wrote:
>> >>>
>> >>> >
>> >>> > On Tue, Aug 27, 2013 at 7:58 PM, Alexander Hansen <address@hidden> 
>> >>> > wrote:
>> >>> >> On 8/27/13 4:58 AM, Ben Abbott wrote:
>> >>> >>> On Aug 27, 2013, at 4:26 AM, Anirudha Bose wrote:
>> >>> >>>
>> >>> >>>> I have been working on reusing mxe-octave [1] to natively build 
>> >>> >>>> Octave for Mac OS X. I have been able to complete the build process 
>> >>> >>>> for the target i686-apple-darwin11, but the executable 
>> >>> >>>> usr/bin/octave doesn't launch Octave. Here is the error I see.
>> >>> >>>>
>> >>> >>>> dyld: Library not loaded: libcholmod.so
>> >>> >>>>    Referenced from: /Users/mac6-user1/./mxe-octave/usr/bin/octave
>> >>> >>>>    Reason: image not found
>> >>> >>>> Trace/BPT trap: 5
>> >>> >>>>
>> >>> >>>> I tried to trace back the error and saw that the library 
>> >>> >>>> libcholmod.so belongs to the package suitesparse. The following is 
>> >>> >>>> a part of the log of suitesparse,  which I think is responsible for 
>> >>> >>>> the above error.
>> >>> >>>>
>> >>> >>>> ar rv  libcholmod.a cholmod_aat.o cholmod_add.o cholmod_band.o 
>> >>> >>>> cholmod_change_factor.o cholmod_common.o cholmod_complex.o 
>> >>> >>>> cholmod_copy.o cholmod_dens$
>> >>> >>>> ar: creating archive libcholmod.a
>> >>> >>>> /opt/local/bin/ranlib: file: libcholmod.a(cholmod_ccolamd.o) has no 
>> >>> >>>> symbols
>> >>> >>>> /opt/local/bin/ranlib: file: libcholmod.a(cholmod_csymamd.o) has no 
>> >>> >>>> symbols
>> >>> >>>> /opt/local/bin/ranlib: file: libcholmod.a(cholmod_metis.o) has no 
>> >>> >>>> symbols
>> >>> >>>> /opt/local/bin/ranlib: file: libcholmod.a(cholmod_nesdis.o) has no 
>> >>> >>>> symbols
>> >>> >>>> /opt/local/bin/ranlib: file: libcholmod.a(cholmod_camd.o) has no 
>> >>> >>>> symbols
>> >>> >>>> /opt/local/bin/ranlib: file: libcholmod.a(cholmod_l_ccolamd.o) has 
>> >>> >>>> no symbols
>> >>> >>>> /opt/local/bin/ranlib: file: libcholmod.a(cholmod_l_csymamd.o) has 
>> >>> >>>> no symbols
>> >>> >>>> /opt/local/bin/ranlib: file: libcholmod.a(cholmod_l_metis.o) has no 
>> >>> >>>> symbols
>> >>> >>>> /opt/local/bin/ranlib: file: libcholmod.a(cholmod_l_nesdis.o) has 
>> >>> >>>> no symbols
>> >>> >>>> /opt/local/bin/ranlib: file: libcholmod.a(cholmod_l_camd.o) has no 
>> >>> >>>> symbols
>> >>> >>>>
>> >>> >>>> I suppose the problem is because Mac OS "ar" is not standard. I 
>> >>> >>>> have also noticed these warnings with other packages too. Can 
>> >>> >>>> anyone tell me how to get a proper build under Mac OS X?
>> >>> >>>>
>> >>> >>>> [1] http://hg.octave.org/mxe-octave
>> >>> >>>>
>> >>> >>>> - Anirudha
>> >>> >>>
>> >>> >>> MacOSX's toolchain avoids the use of static libraries (I assume to 
>> >>> >>> avoid violating GNU licenses).  That is likely at the root of the 
>> >>> >>> problem.
>> >>> >>>
>> >>> >>> In any event, I expect that both Fink and Macports include an "ar" 
>> >>> >>> with their basic installation.
>> >>> >>>
>> >>> >>> Ben
>> >>> >>
>> >>> >> You assume incorrectly in the case of Fink. :-)  We use the system's 
>> >>> >> "ar".
>> >>> >>
>> >>> >> It looks to me like the problem could be that 
>> >>> >> /Users/mac6-user1/./mxe-octave/usr/bin/octave wants to link 
>> >>> >> "libcholmod.so", which would be 
>> >>> >> /Users/mac6-user1/./mxe-octave/usr/bin/libcholmod.so .  You can check 
>> >>> >> this scenario using "otool -L 
>> >>> >> /Users/mac6-user1/./mxe-octave/usr/bin/octave" .
>> >>> >
>> >>> > This is exactly the reason why I am seeing the above errors. I am 
>> >>> > using install_name_tool for changing the paths, but is there any way 
>> >>> > to automate this job? The errors exist in too many executables and 
>> >>> > shared libraries to be done manually one by one. I also recompiled 
>> >>> > Octave with a new LDFLAG -headerpad_max_install_names to reserve 
>> >>> > enough space for changing all dynamic shared library paths.
>> >>>
>> >>> Maybe there is a better way ... but I wrote scripts to handle this task
>> >>>
>> >>>         
>> >>> http://wiki.octave.org/Create_a_MacOS_X_App_Bundle_Using_MacPorts#Fixing_.22dyld:_Library_not_loaded.22_Errors
>> >>>
>> >>> I got the following error when I executed your scripts.
>> >>>
>> >>> octave:1> dylibs_fix ("bin/octave", "lib", false)
>> >>> Working in directory -> "lib" ...error: 'dylibs_isdylib' undefined near 
>> >>> line 74 column 21
>> >>> error: evaluating argument list element number 1
>> >>> error: called from:
>> >>> error:   
>> >>> /Users/mac6-user1/mxe/mxe-octave-anirudha/usr/x86_64-apple-darwin12.2.1/dylibs_find.m
>> >>>  at line 74, column 13
>> >>> error:   
>> >>> /Users/mac6-user1/mxe/mxe-octave-anirudha/usr/x86_64-apple-darwin12.2.1/dylibs_fix.m
>> >>>  at line 160, column 12
>> >>>
>> >>> I have saved all the m-scripts at one place, and my working directory 
>> >>> contained the bin and lib folders. Am I doing something wrong?
>> >>>
>> >>> - Anirudha
>> >>
>> >> Please add the directory containing the scripts to your path.
>> >
>> > This doesn't seem to solve my problem. After adding the directory to my 
>> > path, this is what "echo $PATH" returns --
>> >
>> > /opt/local/bin:/opt/local/sbin:/opt/local/bin:/opt/local/sbin:/usr/local/upgraded/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/Users/mac6-user1/mxe/mxe-octave-anirudha/usr/x86_64-apple-darwin12.2.1/
>> >
>> > The last path contains all the 4 scripts. I opened Octave and executed 
>> > dylibs_fix ("bin/octave", "lib", false), but got the same errors.
>> 
>> The directory to the scripts needs to be added to Octave's path (not your 
>> shell's path).
>> 
>> Ben
> 
> Hi Ben.
> 
> I am in the process of creating Octave.app which will contain all the 
> compiled binaries. I have been able to create an app bundle containing the 
> "bin" and "lib" folders built with MXE. However the present problem is that 
> the dynamic libraries refer to the libraries contained in the original path 
> (in mxe directory), and not the libraries inside the app bundle (as reported 
> by otool). I applied your scripts, but they did not work for me. Please see 
> the log of your scripts [1] and the otool output [2].
> 
> [1] http://pastebin.ca/2455382
> [2] http://pastebin.ca/2455389
> 
> Ideally, all the library path names should point to the relative paths inside 
> the application bundle. Are your scripts capable of fixing  this, or I am 
> doing something wrong? I am aware of some Python modules like py2app which 
> solve such problems.
> 
> -Anirudha

You need to point dylibs_fix to the actual Octave binary (not the directory 
containing the binary). Notice the first problem reported is ...

        otool: can't map file: 
/Users/mac6-user1/Documents/Octave-3.7.5.app/Contents/Resources/bin (Invalid 
argument)

If the binary's file name is "octave-3.6.4", then I expect the command you need 
is ...

        dylibs_fix("bin/octave-3.6.4","lib",true)

Also the warnings below need to be resolved.

        warning: dylibs_fix: Missing dynamic library "libgfortran.3.dylib" 
needed by "libarpack.so"
        warning: dylibs_fix: Missing dynamic library "libgcc_s.1.dylib" needed 
by "libarpack.so"
        warning: dylibs_fix: Missing dynamic library "libquadmath.0.dylib" 
needed by "libarpack.so"

Where are these missing libraries located?  Did dylibs_fix miss them or are 
they not yet in your bundle?

Ben