Errors in suitesparse when compiling

[spott]

When I attempt to compile, I get the error shown here.

Any ideas?

[staticfloat]

Looks like SuiteSparse has been updated and Homebrew is lagging behind. I've modified the julia formula to use a custom SuiteSparse formula, and in the meantime submitted a pull request to Homebrew main to accept the new, updated SuiteSparse version.

Additionally, there's a small patch that I needed to get Julia to compile, so I've submitted a pull request to Julia as well, and I'm using my personal fork of Julia in the formula until it is accepted.

[spott]

Hey, thanks for updating so quickly, I'll try again.

[spott]

So, after trying again, I'm getting another error:

https://gist.github.com/3107461

It seems to be complaining about something to do with readline, but I don't know what...

[staticfloat]

There's a lot of confusion that arises from Julia's parallel building when
something doesn't go right. I've disabled the parallel build process so
that things are a little easier to read. Can you re-run it now? (I also
submitted a patch for a linker problem that doesn't seem to be your
problem)

Oh, and of course, you will need to brew update in order to make use of
any changes I make in the formula

[spott]

Hopefully this helps:

https://gist.github.com/3107999

Thanks for the help.

[staticfloat]

Interesting. This appears to be a segfault while Julia is bootstrapping
the sys0.ji file. This is a julia problem, not a compilation problem. I'd
go ask over at the Julia issues (https://github.com/JuliaLang/julia/issues)
page instead, and see if they can help you.

On Fri, Jul 13, 2012 at 3:36 PM, Andrew Spott <
[email protected]

wrote:

Hopefully this helps:

https://gist.github.com/3107999

Thanks for the help.

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[samueljohn]

@spott would you mind to try to brew https://github.com/samueljohn/homebrew-julia/blob/master/julia.rb? I had some issues like you (but cannot remember exactly if that one with the segfault was among them). My patch is an attempt (successful so far) to build julia on 10.7.4 with Xcode 4.3.3 (with_out_ the command line tools).

[spott]

@samueljohn I tried to do that... both by using the command you gave (with the install), and by untaping staticfloats homebrew-julia and retapping yours.

It is complaining about a lack of arpack-ng:

Error: No available formula for arpack-ng (dependency of julia)
Please tap it and then try again: brew tap staticfloat/julia

Thanks for the help.

[samueljohn]

oh I see the problem. You need arpack-ng and suite_sparse from staticfloat/julia first. The two dependencies are not automatically installed with the direct web link.

[samueljohn]

So don't untapped staticfloat/julia. Install these two deps and then my julia formula.

[spott]

Ok, I got it to attempt to install, but run into this error:

==> Installing julia
==> Cloning https://github.com/JuliaLang/julia.git
Cloning into '/Library/Caches/Homebrew/julia--git'...
remote: Counting objects: 2276, done.
remote: Compressing objects: 100% (1665/1665), done.
remote: Total 2276 (delta 1212), reused 1162 (delta 534)
Receiving objects: 100% (2276/2276), 2.50 MiB | 162 KiB/s, done.
Resolving deltas: 100% (1212/1212), done.
Submodule 'deps/libuv' (http://github.com/JuliaLang/libuv.git) registered for path 'deps/libuv'
Cloning into 'deps/libuv'...
remote: Counting objects: 11101, done.
remote: Compressing objects: 100% (2776/2776), done.
remote: Total 11101 (delta 8704), reused 10548 (delta 8272)
Receiving objects: 100% (11101/11101), 3.14 MiB | 134 KiB/s, done.
Resolving deltas: 100% (8704/8704), done.
Submodule path 'deps/libuv': checked out 'd48c5bd0adcb08fc8793529aed8a19530efde9ee'
==> Patching
patching file Make.inc
Hunk #1 FAILED at 61.
1 out of 1 hunk FAILED -- saving rejects to file Make.inc.rej
patching file base/Makefile
patching file deps/Makefile
patching file deps/Rmath/src/Makefile
patching file extras/Makefile
Error: Failure while executing: /usr/bin/patch -f -p1 -i 000-homebrew.diff

[samueljohn]

==> Patching
patching file Make.inc
Hunk #1 FAILED at 61.

Well, probably something in Julia's Make.inc was changed upstream in
the meantime. Julia develops quite fast and I think patches are the
wrong way here. I should better try to use homebrew's inreplace
function.

[samueljohn]

Yep, the Make.inc in julia has changed. I adapted to that now.

@spott I updated my formula https://github.com/samueljohn/homebrew-julia/blob/master/julia.rb to use inreplace instead of patches to avoid future breakage.

If you like, please try again.

[spott]

Well, it attempted to compile, but I still get the segfault in the same place:

JULIA usr/lib/julia/sys0.ji
/bin/sh: line 1: 21510 Segmentation fault: 11  /private/tmp/homebrew-julia-HEAD-4Ebo/usr/bin/julia-release-readline -b stage0.jl
make[1]: *** [/private/tmp/homebrew-julia-HEAD-4Ebo/usr/lib/julia/sys0.ji] Error 139

[samueljohn]

Okay, was worth a try.

What does brew --config and brew doctor say? Can you gist that?

[spott]

brew config: https://gist.github.com/3123677

brew doctor: is clean, except for an unlinked keg (which wasn't installed by homebrew, and isn't required by anything).

[samueljohn]

@spott the only difference to my system is:

• You have installed the command line tools. That should not be a problem. Most often the opposite is true.
• Your cpu is not detected correctly: CPU: 8-core 64-bit dunno. Mine is CPU: 8-core 64-bit sandybridge.

Any idea what that could be? Do you have one of these ivybridge Retina MBPs?

[spott]

I do have one of the ivy bridge MacBook pros. I don't think that is the
problem though.
On Jul 16, 2012 11:17 AM, "Samuel John" <
[email protected]>
wrote:

@spott the only difference to my system is:

• You have installed the command line tools. That should not be a problem.
  Most often the opposite is true.
• Your cpu is not detected correctly: CPU: 8-core 64-bit dunno. Mine is
  CPU: 8-core 64-bit sandybridge.

Any idea what that could be? Do you have one of these ivybridge Retina
MBPs?

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[samueljohn]

You don't happen to have an older Mac to test on, right?

[spott]

No, I don't... but I did have a very similar problem before when I tried to
install on the old one.
On Jul 16, 2012 11:49 AM, "Samuel John" <
[email protected]>
wrote:

You don't happen to have an older Mac to test on, right?

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[samueljohn]

As you can guess, I am running out of options. Perhaps post this issue to the julia tracker, they might have a guess or at least know how to debug.

[spott]

I have, thank you for all the help. I'll post the julia issue link when I
am at a computer.
On Jul 16, 2012 11:54 AM, "Samuel John" <
[email protected]>
wrote:

As you can guess, I am running out of options. Perhaps post this issue to
the julia tracker, they might have a guess or at least know how to debug.

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[staticfloat]

I've got your back, @spott.

I'm going to close this issue, marking it as an upstream problem. If the Julia gurus say it's a Homebrew problem, come back here and I'll reopen it.