libamd.dylib malformed object when building on 10.9.1

[koshov]

Hi, I get the following error when installing the 64bit version of Julia on 10.9.1 using
brew install --64bit -v julia

install_name_tool: object: /private/tmp/julia-MRJP/usr/lib/libamd.dylib malformed object (unknown load command 4)

Full trace can be found here: https://gist.github.com/koshov/8803980

I have installed openblas64-julia manually using brew install --HEAD openblas64-julia due to CPUID issue with my version of MacBook.

The following packages are all installed correctly:

• gfortran
• arpack64-julia
• suite-sprase64-julia

[staticfloat]

Can you please brew rm suite-sparse64-julia and try again? libamd is actually from SuiteSparse.

Also, please post the output of brew --config and brew doctor

[koshov]

Julia fails to build with the same error after brew rm suite-sparse64-julia.
https://gist.github.com/koshov/8811370

Output of brew --config:

HOMEBREW_VERSION: 0.9.5
ORIGIN: https://github.com/Homebrew/homebrew.git
HEAD: 0434c3809aec7a7026691864e096b2c6e79e6edc
HOMEBREW_PREFIX: /usr/local
HOMEBREW_CELLAR: /usr/local/Cellar
CPU: 8-core 64-bit haswell
OS X: 10.9.1-x86_64
Xcode: 5.0.2
CLT: 5.0.1.0.1.1382131676
Clang: 5.0 build 500
X11: 2.7.5 => /opt/X11
System Ruby: 1.8.7-358
Perl: /usr/bin/perl
Python: /usr/local/bin/python => /usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/bin/python2.7
Ruby: /Users/goshe/.rvm/rubies/ruby-2.0.0-p247/bin/ruby

Output of brew doctor:

Warning: Some directories in /usr/local/share/man aren't writable.
This can happen if you "sudo make install" software that isn't managed
by Homebrew. If a brew tries to add locale information to one of these
directories, then the install will fail during the link step.
You should probably `chown` them:

    /usr/local/share/man/de
    /usr/local/share/man/de/man1

Warning: Unbrewed dylibs were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.

Unexpected dylibs:
    /usr/local/lib/libopencv_calib3d.2.4.7.dylib
    /usr/local/lib/libopencv_contrib.2.4.7.dylib
    /usr/local/lib/libopencv_core.2.4.7.dylib
    /usr/local/lib/libopencv_features2d.2.4.7.dylib
    /usr/local/lib/libopencv_flann.2.4.7.dylib
    /usr/local/lib/libopencv_gpu.2.4.7.dylib
    /usr/local/lib/libopencv_highgui.2.4.7.dylib
    /usr/local/lib/libopencv_imgproc.2.4.7.dylib
    /usr/local/lib/libopencv_legacy.2.4.7.dylib
    /usr/local/lib/libopencv_ml.2.4.7.dylib
    /usr/local/lib/libopencv_nonfree.2.4.7.dylib
    /usr/local/lib/libopencv_objdetect.2.4.7.dylib
    /usr/local/lib/libopencv_ocl.2.4.7.dylib
    /usr/local/lib/libopencv_photo.2.4.7.dylib
    /usr/local/lib/libopencv_stitching.2.4.7.dylib
    /usr/local/lib/libopencv_superres.2.4.7.dylib
    /usr/local/lib/libopencv_video.2.4.7.dylib
    /usr/local/lib/libopencv_videostab.2.4.7.dylib
    /usr/local/lib/libosxfuse_i32.2.dylib
    /usr/local/lib/libosxfuse_i64.2.dylib

Warning: Unbrewed .la files were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.

Unexpected .la files:
    /usr/local/lib/libosxfuse_i32.la
    /usr/local/lib/libosxfuse_i64.la

Warning: Unbrewed .pc files were found in /usr/local/lib/pkgconfig.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.

Unexpected .pc files:
    /usr/local/lib/pkgconfig/opencv.pc
    /usr/local/lib/pkgconfig/osxfuse.pc

Warning: Unbrewed static libraries were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.

Unexpected static libraries:
    /usr/local/lib/libopencv_ts.a

Warning: Homebrew's sbin was not found in your PATH but you have installed
formulae that put executables in /usr/local/sbin.
Consider setting the PATH for example like so
    echo export PATH='/usr/local/sbin:$PATH' >> ~/.bash_profile

Thanks!

[staticfloat]

Hmmm. This is weird. This SO answer recommends updating your xcode command line tools. Can you see if that helps things?

[koshov]

I just installed the latest Command Line Tools, tried both with Xcode installed and completely removed - the same error persists.

[staticfloat]

Please brew install -v -d --HEAD julia, and when it fails, opt to enter the shell so you can poke around the build directory.

Take the usr/lib/libamd.dylib file (relative to the build directory that the shell starts you in) and upload it somewhere so I can take a look at it. It's complaining about a certain load command, for reference here are the load commands in my libamd.dylib, found using otool -l libamd.dylib.

[koshov]

Here is my libamd.dylib.
It appears to be some memory dump rather than a list of load commands.
The file looks pretty much the same when compiling the 32bit version.

[staticfloat]

Hmm. The dylib definitely doesn't seem to be getting created properly. Can you send me the full log of brew install -v suite-sparse64-julia?

[koshov]

Here is the output.
I really appreciate your help! None of the solutions on SO seem to work.

[staticfloat]

Would you send me your libamd.a file from suite sparse's lib?

[koshov]

I managed to get the correct load commands from libamd.dylib.
Here is the libamd.a file.

[staticfloat]

What did you do differently to get otool to read the libamd.dylib file properly?

[koshov]

I simply repeated my previous attempts with both 32 and 64bit binaries - uninstalled all julia-related packages, installed openblas using brew install --HEAD openblas64-julia and had another go at brew install -v -d --HEAD --64bit julia, which yielded the same error as before:

install_name_tool: object: /private/tmp/julia-MRJP/usr/lib/libamd.dylib malformed object (unknown load command 4)

[staticfloat]

@koshov I can't find anything wrong with your libamd.a, so I don't understand why your .dylib would be corrupted.

Can you install julia manually? E.g. can you git clone https://github.com/JuliaLang/julia.git, cd julia, and make? This will take a while, so feel free to go make a sandwich or something while you're waiting. :)

[walski]

Any update on this one? Seeing the same over here :/

[staticfloat]

Are you able to build Julia from scratch as described in my message just
above yours

On Wed, Mar 12, 2014 at 3:38 PM, Thorben Schröder
notifications@github.comwrote:

Any update on this one? Seeing the same over here :/

Reply to this email directly or view it on GitHubhttps://github.com//issues/64#issuecomment-37478004
.