# Mac El Capitan: problem with configure the MRtrix install

**URL:** https://community.mrtrix.org/t/mac-el-capitan-problem-with-configure-the-mrtrix-install/274
**Category:** Uncategorized
**Tags:** installation, macos
**Created:** [June 3, 2016, 1:32pm UTC](https://community.mrtrix.org/t/mac-el-capitan-problem-with-configure-the-mrtrix-install/274 "2016-06-03T13:32:45Z")
**Posts on this page:** 1
**Showing post:** 21

<div class="post-metadata">

### Author: ![jdtournier](https://community.mrtrix.org/user_avatar/community.mrtrix.org/jdtournier/32/2594_2.png) [@jdtournier](https://community.mrtrix.org/u/jdtournier)
#### Post date: [June 6, 2016, 11:13am UTC](https://community.mrtrix.org/t/mac-el-capitan-problem-with-configure-the-mrtrix-install/274/21 "2016-06-06T11:13:42Z")

</div>

Wow, you’re really not having much luck with this… You get full marks for tenacity though!

So the good news is that whatever was failing before seems to be working fine now. This last issue is different again from the previous ones: it looks like `./configure` falls over trying to clean up after itself…

Looking more closely at the log though, I think the issue occurs earlier, probably due to the output of `pkg-config` - I’ve certainly had issues with it on MacOSX in the past, whereby it would produce its output using a wide-character encoding. This is really difficult to detect, and I’ve no idea why it happens on some systems and not others. My best guess is it’ll depend on your system’s character encoding, and/or your filesystem’s character encoding…

So, two things to try. I’d really like you to at least try the first one, since if that works I’ll amend the `configure` script and hopefully avoid similar issues for others.

#### Option 1:

Open the `configure` script in a text editor, and change line 630 from:

```auto
    for entry in shlex.split (execute (['pkg-config', '--cflags', 'eigen3'], RuntimeError)[1]):
```

to:

```auto
    flags = ''
    for c in execute (['pkg-config', '--cflags', 'eigen3'], RuntimeError)[1]:
      if c is not 0: 
        flags += c
    for entry in shlex.split (flags):
```

Save the file, and try running it again…

#### Option 2:

Provide the path to Eigen3 manually, which bypasses the `pkg-config` automatic detection step - and so hopefully will avoid the issue:

```
$ export EIGEN_CFLAGS="-isystem /opt/local/include/eigen3"
$ ./configure

```

Not ideal, but at least it _might_ allow you to (finally) get MRtrix3 up and running…

And thanks for sticking through it, I appreciate this must be somewhat frustrating…

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