Fail to compile julia on 10.8.3 with a error related with install_name_tool

[haphap]

I failed to compile julia on 10.8.3, it shows a error related with install_name_tool:

    brew install --HEAD julia
    ==> Cloning https://github.com/JuliaLang/julia.git
    Cloning into '/Library/Caches/Homebrew/julia--git'...
    remote: Counting objects: 579, done.
    remote: Compressing objects: 100% (525/525), done.
    remote: Total 579 (delta 23), reused 219 (delta 18)
    Receiving objects: 100% (579/579), 1.59 MiB | 666 KiB/s, done.
    Resolving deltas: 100% (23/23), done.
    Submodule 'deps/Rmath' (git://github.com/JuliaLang/Rmath.git) registered for path        'deps/Rmath'
    Submodule 'deps/libuv' (git://github.com/JuliaLang/libuv.git) registered for path 'deps/libuv'
    Submodule 'deps/openlibm' (git://github.com/JuliaLang/openlibm.git) registered for path 'deps/openlibm'
    Cloning into 'deps/Rmath'...
    remote: Counting objects: 291, done.
    remote: Compressing objects: 100% (110/110), done.
    remote: Total 291 (delta 179), reused 291 (delta 179)
    Receiving objects: 100% (291/291), 233.38 KiB | 148 KiB/s, done.
    Resolving deltas: 100% (179/179), done.
    Submodule path 'deps/Rmath': checked out '85dee98a799c193bedf6af35c839de08c2d233f6'
    Cloning into 'deps/libuv'...
    remote: Counting objects: 14840, done.
    remote: Compressing objects: 100% (3940/3940), done.
    remote: Total 14840 (delta 11675), reused 13851 (delta 10847)
    Receiving objects: 100% (14840/14840), 3.90 MiB | 803 KiB/s, done.
    Resolving deltas: 100% (11675/11675), done.
    Submodule path 'deps/libuv': checked out 'd469f03eda6c95f064be3c25b7a9e9a7547c7617'
    Cloning into 'deps/openlibm'...
    remote: Counting objects: 3456, done.
    remote: Compressing objects: 100% (1418/1418), done.
    remote: Total 3456 (delta 2213), reused 3267 (delta 2026)
    Receiving objects: 100% (3456/3456), 3.16 MiB | 331 KiB/s, done.
    Resolving deltas: 100% (2213/2213), done.
    Submodule path 'deps/openlibm': checked out'3c8738e6422bcd38320b2eb69fdbde0422fd6372'
    ==> Downloading patches
    ########################################################################                 100.0%
    ########################################################################         100.0%
    ==> Patching
    patching file deps/Makefile
    Hunk #1 succeeded at 1045 (offset 391 lines).
    patching file Make.inc
    Hunk #1 succeeded at 211 (offset 41 lines).
    Hunk #2 succeeded at 224 (offset 41 lines).
    ==> Using Homebrew-provided fortran compiler.
    This may be changed by setting the FC environment variable.
    ==> Downloading http://double-conversion.googlecode.com/files/double-conversion-1.1.1.tar.gz
    Already downloaded: /Library/Caches/Homebrew/double-conversion-1.1.1.tar.gz
    ==> Using double-conversion: /Library/Caches/Homebrew/double-conversion-1.1.1.tar.gz
    ==> Downloading http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/dSFMT-src-2.2.tar.gz
    Already downloaded: /Library/Caches/Homebrew/dSFMT-src-2.2.tar.gz
    ==> Using DSFMT: /Library/Caches/Homebrew/dSFMT-src-2.2.tar.gz
    ==> make -C contrib -f repackage_system_suitesparse4.make         PREFIX=/usr/local/Cellar/julia/HEAD
    ==> make release PREFIX=/usr/local/Cellar/julia/HEAD USE_LIB64=0         FC=/usr/local/bin/gfortran US
    ==> make PREFIX=/usr/local/Cellar/julia/HEAD USE_LIB64=0 FC=/usr/local/bin/gfortran USECLANG=1
    ==> install_name_tool -add_rpath /usr/local/opt/arpack-julia/lib /usr/local/Cellar/julia/HEAD/
    ==> install_name_tool -add_rpath /usr/local/opt/arpack-julia/lib /usr/local/Cellar/julia/HEAD/
    ==> install_name_tool -add_rpath /usr/local/opt/arpack-julia/lib /usr/local/Cellar/julia/HEAD/
    install_name_tool: can't open file: /usr/local/Cellar/julia/HEAD/bin/julia-release-webserver (No such file or directory)
    READ THIS: https://github.com/mxcl/homebrew/wiki/troubleshooting

And brew doctor:

    brew doctor                                                                               
    Your system is raring to brew.

[staticfloat]

This looks to be because Julia is not auto-compiling the web interface. Can you try removing line 189 from the juila formula? That is, edit:

    rpaths.each do |rpath|
      system "install_name_tool", "-add_rpath", rpath, "#{bin}/julia-#{target}-basic"
      system "install_name_tool", "-add_rpath", rpath, "#{bin}/julia-#{target}-readline"
      system "install_name_tool", "-add_rpath", rpath, "#{bin}/julia-#{target}-webserver"      
    end

to read as:

    rpaths.each do |rpath|
      system "install_name_tool", "-add_rpath", rpath, "#{bin}/julia-#{target}-basic"
      system "install_name_tool", "-add_rpath", rpath, "#{bin}/julia-#{target}-readline"
    end

[haphap]

Hi,I have tried to modify the formula of julia, but it doesn't work,

brew install --HEAD julia
==> Cloning https://github.com/JuliaLang/julia.git
Cloning into '/Library/Caches/Homebrew/julia--git'...
remote: Counting objects: 651, done.
remote: Compressing objects: 100% (576/576), done.
remote: Total 651 (delta 91), reused 252 (delta 38)
Receiving objects: 100% (651/651), 1.62 MiB | 73 KiB/s, done.
Resolving deltas: 100% (91/91), done.
Submodule 'deps/Rmath' (git://github.com/JuliaLang/Rmath.git) registered for path 'deps/Rmath'
Submodule 'deps/libuv' (git://github.com/JuliaLang/libuv.git) registered for path 'deps/libuv'
Submodule 'deps/openlibm' (git://github.com/JuliaLang/openlibm.git) registered for path 'deps/openlibm'
Cloning into 'deps/Rmath'...
remote: Counting objects: 291, done.
remote: Compressing objects: 100% (110/110), done.
remote: Total 291 (delta 179), reused 291 (delta 179)
Receiving objects: 100% (291/291), 233.38 KiB, done.
Resolving deltas: 100% (179/179), done.
Submodule path 'deps/Rmath': checked out '85dee98a799c193bedf6af35c839de08c2d233f6'
Cloning into 'deps/libuv'...
remote: Counting objects: 14840, done.
remote: Compressing objects: 100% (3940/3940), done.
remote: Total 14840 (delta 11675), reused 13851 (delta 10847)
Receiving objects: 100% (14840/14840), 3.90 MiB | 1.28 MiB/s, done.
Resolving deltas: 100% (11675/11675), done.
Submodule path 'deps/libuv': checked out 'd469f03eda6c95f064be3c25b7a9e9a7547c7617'
Cloning into 'deps/openlibm'...
remote: Counting objects: 3456, done.
remote: Compressing objects: 100% (1418/1418), done.
remote: Total 3456 (delta 2213), reused 3267 (delta 2026)
Receiving objects: 100% (3456/3456), 3.16 MiB | 1.25 MiB/s, done.
Resolving deltas: 100% (2213/2213), done.
Submodule path 'deps/openlibm': checked out '3c8738e6422bcd38320b2eb69fdbde0422fd6372'
==> Downloading patches
######################################################################## 100.0%
######################################################################## 100.0%
==> Patching
patching file deps/Makefile
Hunk #1 succeeded at 1045 (offset 391 lines).
patching file Make.inc
Hunk #1 succeeded at 211 (offset 41 lines).
Hunk #2 succeeded at 224 (offset 41 lines).
==> Using Homebrew-provided fortran compiler.
This may be changed by setting the FC environment variable.
==> Downloading http://double-conversion.googlecode.com/files/double-conversion-
Already downloaded: /Library/Caches/Homebrew/double-conversion-1.1.1.tar.gz
==> Using double-conversion: /Library/Caches/Homebrew/double-conversion-1.1.1.ta
==> Downloading http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/dSFMT-src-2
Already downloaded: /Library/Caches/Homebrew/dSFMT-src-2.2.tar.gz
==> Using DSFMT: /Library/Caches/Homebrew/dSFMT-src-2.2.tar.gz
==> make -C contrib -f repackage_system_suitesparse4.make PREFIX=/usr/local/Cell
_cholmod_metis in libcholmod.a(cholmod_metis.o)
_cholmod_l_metis in libcholmod.a(cholmod_l_metis.o)
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [default] Error 1

READ THIS: https://github.com/mxcl/homebrew/wiki/troubleshooting

[kadrach]

With homebrew "standard" suite-sparse installed, I get exactly the same error as haphap.

Unlinking homebrew suite-sparse, I get a different error:

See http://pastebin.com/xmCFrcKB for full log.

It seems using standard "env", this formula picks up the wrong suite-sparse.

Using the 64bit option, I get an additional homebrew error:
==> Using Homebrew-provided fortran compiler.
This may be changed by setting the FC environment variable.
Warning: Cannot compile 64-bit on a 32-bit architecture!

[kadrach]

Here's some more info. The command that fails is the actual make, i.e.

make debug PREFIX=/usr/local/Cellar/julia/HEAD USE_LIB64=1 FC=/usr/local/bin/gfortran USECLANG=1
USE_SYSTEM_ZLIB=1 USE_SYSTEM_FFTW=1 USE_SYSTEM_READLINE=1 USE_SYSTEM_GLPK=1
USE_SYSTEM_GMP=1 USE_SYSTEM_LLVM=1 USE_SYSTEM_PCRE=1 USE_SYSTEM_BLAS=1
USE_SYSTEM_LAPACK=1 USE_SYSTEM_SUITESPARSE=1 USE_SYSTEM_ARPACK=1
USE_SYSTEM_NGINX=1

Using homebrews debug features, rerunning that command at the point where it fails:

gfortran: error: core2: No such file or directory
gfortran: error: core2: No such file or directory
make[3]: *** [amos/d1mach.f.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: *** [amos/zabs.f.o] Error 1
gfortran: error: core2: No such file or directory
make[3]: *** [amos/zasyi.f.o] Error 1
gfortran: error: core2: No such file or directory
make[3]: *** [amos/zbesk.f.o] Error 1
make[2]: *** [openlibm/libopenlibm-extras.dylib] Error 2
make[1]: *** [julia-debug] Error 2
make: *** [debug] Error 2

I can't make sense of the above, as it's not very descriptive (for me).

env |grep FC
FCFLAGS=-Os -w -pipe -mmacosx-version-min=10.8 core2 -msse4
FC=/usr/local/bin/gfortran

[kadrach]

Compiling without the core2 fortran flag works, but I'm not sure what that really does ;)

[staticfloat]

@haphap can you try this again? I have updated the suite-sparse formula

[haphap]

hi @staticfloat , I have tried to update suite-sparse for julia, and recompiled julia, but it still failed

 ○  brew install --HEAD julia                                                  ⏎

==> Cloning https://github.com/JuliaLang/julia.git
Updating /Library/Caches/Homebrew/julia--git
==> Downloading patches
######################################################################## 100.0%
######################################################################## 100.0%
==> Patching
patching file deps/Makefile
Hunk #1 succeeded at 1076 (offset 422 lines).
patching file Make.inc
Hunk #1 succeeded at 217 (offset 47 lines).
Hunk #2 succeeded at 230 (offset 47 lines).
==> Using Homebrew-provided fortran compiler.
This may be changed by setting the FC environment variable.
==> Downloading http://double-conversion.googlecode.com/files/double-conversion-
Already downloaded: /Library/Caches/Homebrew/double-conversion-1.1.1.tar.gz
==> Using double-conversion: /Library/Caches/Homebrew/double-conversion-1.1.1.ta
==> Downloading http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/dSFMT-src-2
Already downloaded: /Library/Caches/Homebrew/dSFMT-src-2.2.tar.gz
==> Using DSFMT: /Library/Caches/Homebrew/dSFMT-src-2.2.tar.gz
==> make -C contrib -f repackage_system_suitesparse4.make PREFIX=/usr/local/Cell
typeinfo for spqr_zippystd::complex in libspqr.a(spqr_parallel.o)
typeinfo for spqr_zippy in libspqr.a(spqr_parallel.o)
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [default] Error 1

READ THIS: https://github.com/mxcl/homebrew/wiki/troubleshooting

[staticfloat]

Please use brew install -v --HEAD julia so I can see the whole log. Also, please try removing suite-sparse-julia and reinstalling. (You may have to brew rm suite-sparse-julia multiple times to remove older versions. Keep doing it until it says suite-sparse-julia is not installed)

[haphap]

hi @staticfloat ,here it is the log of compilation

https://gist.github.com/haphap/ce67450013a88196b9a9

[staticfloat]

@haphap please run brew update, you should get suite-sparse-julia version 4.2.1, then remove suite-sparse-julia and try again.

[haphap]

Hi @staticfloat , i updated the suite-sparse-julia to 4.2.1, but the result is the same,
here it is the gist:https://gist.github.com/haphap/d851b4a0fea1e0537c17
Thank you very much

    ○ brew info suite-sparse-julia                                                                          ⏎
    suite-sparse-julia: stable 4.2.1
    http://www.cise.ufl.edu/research/sparse/SuiteSparse

    This formula is keg-only.
    Conflicts with suite-sparse

    Depends on: openblas-julia
    /usr/local/Cellar/suite-sparse-julia/4.2.1 (76 files, 3.6M)
      Built from source
    https://github.com/staticfloat/homebrew-julia/commits/master/suite-sparse-julia.rb
    ==> Options
    --with-accelerate
        Compile against Accelerate/vecLib instead of OpenBLAS
    --with-metis
        Compile in metis libraries

[staticfloat]

@haphap Do you have suite-sparse installed? I realize now that you may be finding the libraries from Homebrew's other suite-sparse formula which has libraries that depend on TBB and are thus not 100% compatible with julia. If you have suite-sparse installed, can you try removing (or unlinking) it and installing Julia again?

[haphap]

@staticfloat you are right, that is the problem, I have removed the suite-sparse and now it is ok for compilation of julia, thanks very much!!

[staticfloat]

If everything is working now, (please be sure to run brew test -v julia to double check!) I will leave it up to you to close this issue!

[haphap]

thanks @staticfloat ,it passed the relative tests, but the version of julia is "0.0.0-prerelease", is it right?