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mtex-toolbox / mtex

MTEX is a free Matlab toolbox for quantitative texture analysis. Homepage:
http://mtex-toolbox.github.io/
GNU General Public License v2.0
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Problem MTEX on new iMac with Mac OS 10.11 El Capitan - solution that works #120

Closed DavidMainprice closed 6 years ago

DavidMainprice commented 9 years ago

The new “System Integrity Protection” (SIP) of Mac OS 10.11 El Capitan has been disabled and this has been checked twice via the terminal window using "csrutil status".

The error message is as follows ...

MTEX binary check failed!

The original error message was: Error using call_extern (line 158) Error running external program:

/MatLab Programs/mtex-4.1.4/c/bin/maci64/odf2pf /private/tmp/odf2pf591.txt 2>> /private/tmp/output_ManuelsiMaclocal_MThieme.log

We have now found a solution to this problem. Put your mtex-4.1.4 folder in MATLAB folder You should find this at Users/ User_Name/ Documents / MATLAB/ mtex-4.1.4

all the best David

ralfHielscher commented 9 years ago

Hi David,

is it with this configuration possible to run mtex with the System Integrity Protection enabled?

Ralf.

magnusho commented 8 years ago

Hi,

I have the above-mentioned problem when I try to run mtex 4.2.1 on El Capitan. The mtex-4.2.1 folder is located in Users/my_user/Documents/MATLAB/. I've disabled SIP, and the csrutil status returns

System Integrity Protection status: enabled (Custom Configuration).

Configuration: Apple Internal: disabled Kext Signing: disabled Filesystem Protections: disabled Debugging Restrictions: disabled DTrace Restrictions: disabled NVRAM Protections: disabled

Still I get the "binary check failed" message with reference to

/Users/magnush/Documents/MATLAB/mtex-4.2.1/c/bin/maci64/odf2pf

Is there anything I'm missing?

Thanks!

Magnus

DavidMainprice commented 8 years ago

Dear Magnus,

We have some times found it necessary to put MTEX folder in the MATLAB folder on iMacs.

The SIP has to disable of course, attached find a couple of PDFs covering both points.

all the best David

Le 11 févr. 2016 à 11:53, magnusho notifications@github.com a écrit :

Hi,

I have the above-mentioned problem when I try to run mtex 4.2.1 on El Capitan. The mtex-4.2.1 folder is located in Users/my_user/Documents/MATLAB/. I've disabled SIP, and the csrutil status returns

System Integrity Protection status: enabled (Custom Configuration).

Configuration: Apple Internal: disabled Kext Signing: disabled Filesystem Protections: disabled Debugging Restrictions: disabled DTrace Restrictions: disabled NVRAM Protections: disabled

Still I get the "binary check failed" message with reference to

/Users/magnush/Documents/MATLAB/mtex-4.2.1/c/bin/maci64/odf2pf

Is there anything I'm missing?

Thanks!Magnus

— Reply to this email directly or view it on GitHub https://github.com/mtex-toolbox/mtex/issues/120#issuecomment-182808301.

magnusho commented 8 years ago

Dear David,

This is actually my problem. I have disabled SIP and put the MTEX folder in the MATLAB folder (Users/my_user/Documents/MATLAB/) according to the instructions I found, but I still get the "binary check failed" issue.

Is there any other known issue that I could have missed?

Thanks again for your time!

//Magnus

DavidMainprice commented 8 years ago

I would try to make a new download of MTEX from the GitHub site

all the best David

Le 11 févr. 2016 à 13:42, magnusho notifications@github.com a écrit :

Dear David,

This is actually my problem. I have disabled SIP and put the MTEX folder in the MATLAB folder (Users/my_user/Documents/MATLAB/) according to the instructions I found, but I still get the "binary check failed" issue.

Is there any other known issue that I could have missed?

Thanks again for your time!

//Magnus

— Reply to this email directly or view it on GitHub https://github.com/mtex-toolbox/mtex/issues/120#issuecomment-182843970.

magnusho commented 8 years ago

Already on the 3rd version since yesterday... Regards, Magnus

DavidMainprice commented 8 years ago

What is the exact error message you get ?

all the best David

Le 11 févr. 2016 à 16:02, magnusho notifications@github.com a écrit :

Already on the 3rd version since yesterday... Regards, Magnus

— Reply to this email directly or view it on GitHub https://github.com/mtex-toolbox/mtex/issues/120#issuecomment-182899365.

magnusho commented 8 years ago

This is what I get on startup:

           MTEX binary check failed!

           The original error message was:
           Error using call_extern (line 158)
           Error running external program:

           /Users/magnush/Documents/MATLAB/mtex-4.2.1/c/bin/maci64/odf2pf   
           /private/tmp/odf2pf1601.txt 2>> /private/tmp/output_MagnussMacBookAirlocal_magnush.log

Many functions still work. I can import EBSD data and plot scatterplots etc, trying to calculate the odf returns the same message followed by detailed error messages for functions

odf = calcODF(ebsd.orientations)

          Error using call_extern (line 158)
          Error running external program:

           /Users/magnush/Documents/MATLAB/mtex-4.2.1/c/bin/maci64/odf2fc
           /private/tmp/odf2fc6278.txt 2>>
           /private/tmp/output_MagnussMacBookAirlocal_magnush.log

          Error in unimodalComponent/calcFourier>gcA2fourier (line 67)
          f = call_extern('odf2fc','EXTERN',g,c,A);

          Error in unimodalComponent/calcFourier (line 29)
          f_hat = gcA2fourier(abg,c,A);

          Error in ODF/calcFourier (line 32)
          hat = calcFourier(odf.components{i},L,varargin{:});

          Error in ODF/FourierODF (line 8)
          f_hat = calcFourier(odf,varargin{:});

          Error in orientation/calcFourierODF (line 54)
          odf = FourierODF(odf,get_option(varargin,{'L','bandwidth','fourier'},L,'double'));

          Error in orientation/calcODF (line 64)
          odf = calcFourierODF(ori,varargin{:},'kernel',psi);
DavidMainprice commented 8 years ago

Now if I compare this with initial problem with our iMac

initialize MTEX 4.1.4 .... MTEX binary check failed!

The original error message was: Error using call_extern (line 158) Error running external program:

/MatLab Programs/mtex-4.1.4/c/bin/maci64/odf2pf /private/tmp/odf2pf591.txt 2>> /private/tmp/output_ManuelsiMaclocal_MThieme.log

Check the following options:

This looks very similar to your current message

I suspect if you have moved your MTEX folder MATLAB folder that your SIP is not disabled. When SIP is not disable you get an error associated with access to private folder (> /private/tmp/)

You can find the procedure and other things that need to be updated at:

https://www.dropbox.com/sh/n0lwhkxs4z7tgft/AAC9kf0kerY89-zJWBehjs4sa?dl=0

all the best David

Le 12 févr. 2016 à 09:53, magnusho notifications@github.com a écrit :

This is what I get on startup:

       MTEX binary check failed!

       The original error message was:
       Error using call_extern (line 158)
       Error running external program:

       /Users/magnush/Documents/MATLAB/mtex-4.2.1/c/bin/maci64/odf2pf   
       /private/tmp/odf2pf1601.txt 2>> /private/tmp/output_MagnussMacBookAirlocal_magnush.log

Many functions till works. I can import EBSD data and plot scatterplots etc, trying to calculate the odf returns the same message followed by detailed error messages for functions

odf = calcODF(ebsd.orientations)

      Error using call_extern (line 158)
      Error running external program:

       /Users/magnush/Documents/MATLAB/mtex-4.2.1/c/bin/maci64/odf2fc
       /private/tmp/odf2fc6278.txt 2>>
       /private/tmp/output_MagnussMacBookAirlocal_magnush.log

      Error in unimodalComponent/calcFourier>gcA2fourier (line 67)
      f = call_extern('odf2fc','EXTERN',g,c,A);

      Error in unimodalComponent/calcFourier (line 29)
      f_hat = gcA2fourier(abg,c,A);

      Error in ODF/calcFourier (line 32)
      hat = calcFourier(odf.components{i},L,varargin{:});

      Error in ODF/FourierODF (line 8)
      f_hat = calcFourier(odf,varargin{:});

      Error in orientation/calcFourierODF (line 54)
      odf = FourierODF(odf,get_option(varargin,{'L','bandwidth','fourier'},L,'double'));

      Error in orientation/calcODF (line 64)
      odf = calcFourierODF(ori,varargin{:},'kernel',psi);

— Reply to this email directly or view it on GitHub https://github.com/mtex-toolbox/mtex/issues/120#issuecomment-183237245.

magnusho commented 8 years ago

Hi,

As mentioned in my first post, SIP is disabled per the instructions (I included the confirmation from 'csrutil status' in the post) and I have placed the mtex folder in the MATLAB folder. I tried downloading and re-installing mtex several times. Still the same message unfortunately...

zmichels commented 8 years ago

Hi,

I can't quite tell from quickly perusing the earlier posts on this thread... But I had a similar problem when I was installing from folders I downloaded through the repository. It solved everything when I downloaded from the downloads page here:

http://mtex-toolbox.github.io/download

You have probably already done this. However, I just saw this thread and only have a a minute to reply, so I thought I'd throw it out there. I apologize if this is redundant from earlier advice.

Zach

On Feb 12, 2016, at 7:23 AM, magnusho notifications@github.com<mailto:notifications@github.com> wrote:

Hi,

As mentioned in my first post, SIP is disabled per the instructions (I included the confirmation from 'csrutil status' in the post) and I have placed the mtex folder in the MATLAB folder. I tried downloading and re-installing mtex several times. Still the same message unfortunately...

Reply to this email directly or view it on GitHubhttps://github.com/mtex-toolbox/mtex/issues/120#issuecomment-183326364.

magnusho commented 8 years ago

Zach,

Thanks a million, that worked perfectly!

David, thanks for your time.

Back to my odf's :-)

Rgards //Magnus