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

[Ben Abbott]

On Sep 20, 2013, at 1:05 PM, Anirudha Bose wrote:

> On Fri, Sep 20, 2013 at 10:14 PM, Ben Abbott <address@hidden> wrote:
> 
> On Sep 20, 2013, at 12:21 PM, Anirudha Bose wrote:
> 
> > On Fri, Sep 20, 2013 at 9:03 PM, Ben Abbott <address@hidden> wrote:
> >
> > 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)
> >
> >> After doing the above change, I am getting this result [1]. Note that aven 
> >> after applying your scripts, I am getting the following results, which 
> >> indicates that the MXE library paths are still there.
> >>
> >>     IIITs-iMac-7:Resources mac6-user1$ otool -L ./lib/libreadline.6.2.dylib
> >> ./lib/libreadline.6.2.dylib:
> >>     @executable_path/..//libreadline.6.2.dylib (compatibility version 
> >> 6.0.0, current version 6.2.0)
> >>     
> >> /Users/mac6-user1/mxe/mxe-octave-anirudha/usr/x86_64-apple-darwin12.2.1/lib/libncurses.5.dylib
> >>  (compatibility version 5.0.0, current version 5.0.0)
> >>     /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current 
> >> version 169.3.0)
> 
> The current versions all look to be above the compatible versions, so I think 
> you are ok there.  However, I'm not sure why they are not the same ... maybe 
> this is normal, but it looks unexpected to me.  For now, I'd just assume this 
> is normal behavior.
> 
> >> IIITs-iMac-7:Resources mac6-user1$ otool -L 
> >> ./lib/octave/3.7.5/liboctinterp.1.dylib
> >> ./lib/octave/3.7.5/liboctinterp.1.dylib:
> >>     @executable_path/..//liboctinterp.1.dylib (compatibility version 
> >> 2.0.0, current version 2.1.0)
> >>     /System/Library/Frameworks/JavaVM.framework/Versions/A/JavaVM 
> >> (compatibility version 1.0.0, current version 1.0.0)
> >>     
> >> /Users/mac6-user1/mxe/mxe-octave-anirudha/usr/x86_64-apple-darwin12.2.1/lib/octave/3.7.5/liboctave.1.dylib
> >>  (compatibility version 2.0.0, current version 2.1.0)
> 
> Don't you think the above path should be relative? It points to the library 
> inside MXE directory.

ah ... ok. From the last Macports bundle I attempted I see ...

$ otool -L liboctinterp.dylib
liboctinterp.dylib:
        @executable_path/../lib/octave/3.7.0+/liboctinterp.1.dylib 
(compatibility version 2.0.0, current version 2.1.0)
        @executable_path/../lib/octave/3.7.0+/liboctave.1.dylib (compatibility 
version 2.0.0, current version 2.1.0)
        @executable_path/../lib/octave/3.7.0+/libcruft.1.dylib (compatibility 
version 2.0.0, current version 2.0.0)
        @executable_path/../lib/libarpack.2.dylib (compatibility version 3.0.0, 
current version 3.0.0)
        @executable_path/../lib/libtatlas.dylib (compatibility version 3.10.0, 
current version 3.10.0)
        @executable_path/../lib/libqrupdate.1.dylib (compatibility version 
0.0.0, current version 0.0.0)
        @executable_path/../lib/libreadline.6.2.dylib (compatibility version 
6.0.0, current version 6.2.0)
        @executable_path/../lib/libncurses.5.dylib (compatibility version 
5.0.0, current version 5.0.0)
        /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current 
version 159.1.0)
        @executable_path/../lib/gcc45/libgfortran.3.dylib (compatibility 
version 4.0.0, current version 4.0.0)
        @executable_path/../lib/libfltk_gl.1.3.dylib (compatibility version 
1.3.0, current version 1.3.0)
        /System/Library/Frameworks/AGL.framework/Versions/A/AGL (compatibility 
version 1.0.0, current version 1.0.0)
        /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL 
(compatibility version 1.0.0, current version 1.0.0)
        
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices
 (compatibility version 1.0.0, current version 41.0.0)
        @executable_path/../lib/libfltk.1.3.dylib (compatibility version 1.3.0, 
current version 1.3.0)
        /System/Library/Frameworks/Cocoa.framework/Versions/A/Cocoa 
(compatibility version 1.0.0, current version 17.0.0)
        @executable_path/../lib/libhdf5.7.dylib (compatibility version 8.0.0, 
current version 8.3.0)
        @executable_path/../lib/libfftw3.3.dylib (compatibility version 7.0.0, 
current version 7.2.0)
        @executable_path/../lib/libfftw3f.3.dylib (compatibility version 7.0.0, 
current version 7.2.0)
        @executable_path/../lib/libpcre.1.dylib (compatibility version 2.0.0, 
current version 2.0.0)
        @executable_path/../lib/libfontconfig.1.dylib (compatibility version 
7.0.0, current version 7.0.0)
        @executable_path/../lib/libiconv.2.dylib (compatibility version 8.0.0, 
current version 8.1.0)
        @executable_path/../lib/libfreetype.6.dylib (compatibility version 
15.0.0, current version 15.1.0)
        @executable_path/../lib/libz.1.dylib (compatibility version 1.0.0, 
current version 1.2.7)
        @executable_path/../lib/libbz2.1.0.dylib (compatibility version 1.0.0, 
current version 1.0.6)
        @executable_path/../lib/libexpat.1.dylib (compatibility version 8.0.0, 
current version 8.0.0)
        /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon 
(compatibility version 2.0.0, current version 153.0.0)
        @executable_path/../lib/gcc45/libstdc++.6.dylib (compatibility version 
7.0.0, current version 7.14.0)
        /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 
1105.0.0)
        @executable_path/../lib/gcc45/libgcc_s.1.dylib (compatibility version 
1.0.0, current version 1.0.0)
        
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation 
(compatibility version 150.0.0, current version 635.21.0)

When you ran fix_dylibs() was you pwd() equal to 
"/Users/mac6-user1/Documents/Octave-3.7.5.app/Contents/Resources"?  If not, 
perhaps you applied install_name_tool to the MXE libraries?

Ben