Octave gcc problem (Homebrew Mac)

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Octave gcc problem (Homebrew Mac)

vicnorton
Hi Sebastian,

I just did a brew upgrade and it killed octave. Here is the error message I get.
~$ octave
dyld: Library not loaded: /usr/local/opt/gcc/lib/gcc/6/libgfortran.3.dylib
  Referenced from: /usr/local/bin/octave-cli
  Reason: image not found
Abort trap: 6

Apparently the problem is that
  /usr/local/opt/gcc
has just become a symbolic link to
  /usr/local/Cellar/gcc/7.1.0
rather than the previous
  /usr/local/Cellar/gcc/6.3.0_1.
And a new libgfortran.4.dylib resides in the 7.1.0 version of gcc.

I hate to mess with Homebrew. I expect the problem might be fixed by forcing
  /usr/local/opt/gcc
to link to
  /usr/local/Cellar/gcc/6.3.0_1
as before, but it does seem that Homebrew’s octave-cli should be adjusted for the new gcc@7.

What is your advice? Right now I am dead in the water.

Regards,

Vic
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Re: Octave gcc problem (Homebrew Mac)

vicnorton

> On May 4, 2017, at 4:40 PM, Vic Norton <[hidden email]> wrote:
>
> Hi Sebastian,
>
> I just did a brew upgrade and it killed octave. Here is the error message I get.
> ~$ octave
> dyld: Library not loaded: /usr/local/opt/gcc/lib/gcc/6/libgfortran.3.dylib
>  Referenced from: /usr/local/bin/octave-cli
>  Reason: image not found
> Abort trap: 6
>
> Apparently the problem is that
>  /usr/local/opt/gcc
> has just become a symbolic link to
>  /usr/local/Cellar/gcc/7.1.0
> rather than the previous
>  /usr/local/Cellar/gcc/6.3.0_1.
> And a new libgfortran.4.dylib resides in the 7.1.0 version of gcc.
>
> I hate to mess with Homebrew. I expect the problem might be fixed by forcing
>  /usr/local/opt/gcc
> to link to
>  /usr/local/Cellar/gcc/6.3.0_1
> as before, but it does seem that Homebrew’s octave-cli should be adjusted for the new gcc@7.
>
> What is your advice? Right now I am dead in the water.
>
> Regards,
>
> Vic

Well, I hated to mess with Homebrew, but the above solution did work. I now have a working Octave. Here is what I did in Terminal.

1. I changed my directory to /usr/local/opt
2. I relabeled gcc as gcc-new
3. I ran
   $ ln -s /usr/local/Cellar/gcc/6.3.0_1 gcc

Now Octave 4.2.1 works as before, but I’ve messed up the latest Homebrew gcc in /usr/local/opt.

I don’t like this solution. I’d rather have an Octave that can use Homebrew’s gcc@7.

-
Vic


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Re: Octave gcc problem (Homebrew Mac)

Sebastian Schöps
Dear Vic,

you updated by purpose or accident your gcc. This may of course break dependencies like octave. The proper way is to recompile all dependencies, including octave

brew install --build-from-source octave

This is necessary as there is currently no octave binary for the new gcc. However, there will be a new one soon since this is a known issue:

https://github.com/Homebrew/homebrew-science/issues/4972#issuecomment-299394176

Sebastian

> Am 05.05.2017 um 14:18 schrieb Vic Norton <[hidden email]>:
>
>> On May 4, 2017, at 5:25 PM, Vic Norton <[hidden email]> wrote:
>>
>>
>>> On May 4, 2017, at 4:40 PM, Vic Norton <[hidden email]> wrote:
>>>
>>> Hi Sebastian,
>>>
>>> I just did a brew upgrade and it killed octave. Here is the error message I get.
>>> ~$ octave
>>> dyld: Library not loaded: /usr/local/opt/gcc/lib/gcc/6/libgfortran.3.dylib
>>> Referenced from: /usr/local/bin/octave-cli
>>> Reason: image not found
>>> Abort trap: 6
>>>
>>> Apparently the problem is that
>>> /usr/local/opt/gcc
>>> has just become a symbolic link to
>>> /usr/local/Cellar/gcc/7.1.0
>>> rather than the previous
>>> /usr/local/Cellar/gcc/6.3.0_1.
>>> And a new libgfortran.4.dylib resides in the 7.1.0 version of gcc.
>>>
>>> I hate to mess with Homebrew. I expect the problem might be fixed by forcing
>>> /usr/local/opt/gcc
>>> to link to
>>> /usr/local/Cellar/gcc/6.3.0_1
>>> as before, but it does seem that Homebrew’s octave-cli should be adjusted for the new gcc@7.
>>>
>>> What is your advice? Right now I am dead in the water.
>>>
>>> Regards,
>>>
>>> Vic
>>
>> Well, I hated to mess with Homebrew, but the above solution did work. I now have a working Octave. Here is what I did in Terminal.
>>
>> 1. I changed my directory to /usr/local/opt
>> 2. I relabeled gcc as gcc-new
>> 3. I ran
>>  $ ln -s /usr/local/Cellar/gcc/6.3.0_1 gcc
>>
>> Now Octave 4.2.1 works as before, but I’ve messed up the latest Homebrew gcc in /usr/local/opt.
>>
>> I don’t like this solution. I’d rather have an Octave that can use Homebrew’s gcc@7.
>>
>> -
>> Vic
>
> This morning the Homebrew Octave was upgraded to 4.2.1_2, which now links to gcc@7, so I undid the above kludge. Now the original error message
>>> ~$ octave
>>> dyld: Library not loaded: /usr/local/opt/gcc/lib/gcc/6/libgfortran.3.dylib
>>> Referenced from: /usr/local/bin/octave-cli
>>> Reason: image not found
>>> Abort trap: 6
> has gone away, but a new one has taken its place:
>  ~$ octave
>  dyld: Library not loaded: /usr/local/opt/gcc/lib/gcc/6/libgfortran.3.dylib
>    Referenced from: /usr/local/opt/qrupdate/lib/libqrupdate.1.dylib
>    Reason: image not found
>  Abort trap: 6
> Apparently qrupdate has not been upgraded to link to gcc@7.
>
> I am giving up my kludges. Is there any way I can get good Octave from Homebrew?
>
> -
> Vic
>
>


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Re: Octave gcc problem (Homebrew Mac)

vicnorton
Unfortunately your advice didn’t work for me, Sebastian. - Vic

~$ brew install --build-from-source octave
Updating Homebrew...
==> Auto-updated Homebrew!
Updated 3 taps (caskroom/cask, homebrew/core, homebrew/science).
==> Updated Formulae
certbot                                  homebrew/science/plink2
git-extras                               homebrew/science/poretools
homebrew/science/calculix-ccx            homebrew/science/qrupdate ✔
homebrew/science/gmsh                    kubernetes-helm
homebrew/science/p4est                   todoman
homebrew/science/pastix                  yadm
homebrew/science/plasma

Warning: homebrew/science/octave-4.2.1_2 already installed
~$ octave
dyld: Library not loaded: /usr/local/opt/gcc/lib/gcc/7/libgfortran.4.dylib
  Referenced from: /usr/local/bin/octave-cli
  Reason: image not found
Abort trap: 6

> On May 5, 2017, at 8:29 AM, Sebastian Schöps <[hidden email]> wrote:
>
> Dear Vic,
>
> you updated by purpose or accident your gcc. This may of course break dependencies like octave. The proper way is to recompile all dependencies, including octave
>
> brew install --build-from-source octave
>
> This is necessary as there is currently no octave binary for the new gcc. However, there will be a new one soon since this is a known issue:
>
> https://github.com/Homebrew/homebrew-science/issues/4972#issuecomment-299394176
>
> Sebastian
>
>> Am 05.05.2017 um 14:18 schrieb Vic Norton <[hidden email]>:
>>
>>> On May 4, 2017, at 5:25 PM, Vic Norton <[hidden email]> wrote:
>>>
>>>
>>>> On May 4, 2017, at 4:40 PM, Vic Norton <[hidden email]> wrote:
>>>>
>>>> Hi Sebastian,
>>>>
>>>> I just did a brew upgrade and it killed octave. Here is the error message I get.
>>>> ~$ octave
>>>> dyld: Library not loaded: /usr/local/opt/gcc/lib/gcc/6/libgfortran.3.dylib
>>>> Referenced from: /usr/local/bin/octave-cli
>>>> Reason: image not found
>>>> Abort trap: 6
>>>>
>>>> Apparently the problem is that
>>>> /usr/local/opt/gcc
>>>> has just become a symbolic link to
>>>> /usr/local/Cellar/gcc/7.1.0
>>>> rather than the previous
>>>> /usr/local/Cellar/gcc/6.3.0_1.
>>>> And a new libgfortran.4.dylib resides in the 7.1.0 version of gcc.
>>>>
>>>> I hate to mess with Homebrew. I expect the problem might be fixed by forcing
>>>> /usr/local/opt/gcc
>>>> to link to
>>>> /usr/local/Cellar/gcc/6.3.0_1
>>>> as before, but it does seem that Homebrew’s octave-cli should be adjusted for the new gcc@7.
>>>>
>>>> What is your advice? Right now I am dead in the water.
>>>>
>>>> Regards,
>>>>
>>>> Vic
>>>
>>> Well, I hated to mess with Homebrew, but the above solution did work. I now have a working Octave. Here is what I did in Terminal.
>>>
>>> 1. I changed my directory to /usr/local/opt
>>> 2. I relabeled gcc as gcc-new
>>> 3. I ran
>>> $ ln -s /usr/local/Cellar/gcc/6.3.0_1 gcc
>>>
>>> Now Octave 4.2.1 works as before, but I’ve messed up the latest Homebrew gcc in /usr/local/opt.
>>>
>>> I don’t like this solution. I’d rather have an Octave that can use Homebrew’s gcc@7.
>>>
>>> -
>>> Vic
>>
>> This morning the Homebrew Octave was upgraded to 4.2.1_2, which now links to gcc@7, so I undid the above kludge. Now the original error message
>>>> ~$ octave
>>>> dyld: Library not loaded: /usr/local/opt/gcc/lib/gcc/6/libgfortran.3.dylib
>>>> Referenced from: /usr/local/bin/octave-cli
>>>> Reason: image not found
>>>> Abort trap: 6
>> has gone away, but a new one has taken its place:
>> ~$ octave
>> dyld: Library not loaded: /usr/local/opt/gcc/lib/gcc/6/libgfortran.3.dylib
>>   Referenced from: /usr/local/opt/qrupdate/lib/libqrupdate.1.dylib
>>   Reason: image not found
>> Abort trap: 6
>> Apparently qrupdate has not been upgraded to link to gcc@7.
>>
>> I am giving up my kludges. Is there any way I can get good Octave from Homebrew?
>>
>> -
>> Vic
>>
>>
>


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Re: Octave gcc problem (Homebrew Mac)

Sebastian Schöps
Ok, what about this?

# get new versions
brew update

# install new versions
brew upgrade

# uninstall broken octave
brew uninstall octave

# reinstall octave from source
brew install --build-from-source octave

Bye
Sebastian

> Am 05.05.2017 um 14:55 schrieb Vic Norton <[hidden email]>:
>
> Unfortunately your advice didn’t work for me, Sebastian. - Vic
>
> ~$ brew install --build-from-source octave
> Updating Homebrew...
> ==> Auto-updated Homebrew!
> Updated 3 taps (caskroom/cask, homebrew/core, homebrew/science).
> ==> Updated Formulae
> certbot                                  homebrew/science/plink2
> git-extras                               homebrew/science/poretools
> homebrew/science/calculix-ccx            homebrew/science/qrupdate ✔
> homebrew/science/gmsh                    kubernetes-helm
> homebrew/science/p4est                   todoman
> homebrew/science/pastix                  yadm
> homebrew/science/plasma
>
> Warning: homebrew/science/octave-4.2.1_2 already installed
> ~$ octave
> dyld: Library not loaded: /usr/local/opt/gcc/lib/gcc/7/libgfortran.4.dylib
>  Referenced from: /usr/local/bin/octave-cli
>  Reason: image not found
> Abort trap: 6
>
>> On May 5, 2017, at 8:29 AM, Sebastian Schöps <[hidden email]> wrote:
>>
>> Dear Vic,
>>
>> you updated by purpose or accident your gcc. This may of course break dependencies like octave. The proper way is to recompile all dependencies, including octave
>>
>> brew install --build-from-source octave
>>
>> This is necessary as there is currently no octave binary for the new gcc. However, there will be a new one soon since this is a known issue:
>>
>> https://github.com/Homebrew/homebrew-science/issues/4972#issuecomment-299394176
>>
>> Sebastian
>>
>>> Am 05.05.2017 um 14:18 schrieb Vic Norton <[hidden email]>:
>>>
>>>> On May 4, 2017, at 5:25 PM, Vic Norton <[hidden email]> wrote:
>>>>
>>>>
>>>>> On May 4, 2017, at 4:40 PM, Vic Norton <[hidden email]> wrote:
>>>>>
>>>>> Hi Sebastian,
>>>>>
>>>>> I just did a brew upgrade and it killed octave. Here is the error message I get.
>>>>> ~$ octave
>>>>> dyld: Library not loaded: /usr/local/opt/gcc/lib/gcc/6/libgfortran.3.dylib
>>>>> Referenced from: /usr/local/bin/octave-cli
>>>>> Reason: image not found
>>>>> Abort trap: 6
>>>>>
>>>>> Apparently the problem is that
>>>>> /usr/local/opt/gcc
>>>>> has just become a symbolic link to
>>>>> /usr/local/Cellar/gcc/7.1.0
>>>>> rather than the previous
>>>>> /usr/local/Cellar/gcc/6.3.0_1.
>>>>> And a new libgfortran.4.dylib resides in the 7.1.0 version of gcc.
>>>>>
>>>>> I hate to mess with Homebrew. I expect the problem might be fixed by forcing
>>>>> /usr/local/opt/gcc
>>>>> to link to
>>>>> /usr/local/Cellar/gcc/6.3.0_1
>>>>> as before, but it does seem that Homebrew’s octave-cli should be adjusted for the new gcc@7.
>>>>>
>>>>> What is your advice? Right now I am dead in the water.
>>>>>
>>>>> Regards,
>>>>>
>>>>> Vic
>>>>
>>>> Well, I hated to mess with Homebrew, but the above solution did work. I now have a working Octave. Here is what I did in Terminal.
>>>>
>>>> 1. I changed my directory to /usr/local/opt
>>>> 2. I relabeled gcc as gcc-new
>>>> 3. I ran
>>>> $ ln -s /usr/local/Cellar/gcc/6.3.0_1 gcc
>>>>
>>>> Now Octave 4.2.1 works as before, but I’ve messed up the latest Homebrew gcc in /usr/local/opt.
>>>>
>>>> I don’t like this solution. I’d rather have an Octave that can use Homebrew’s gcc@7.
>>>>
>>>> -
>>>> Vic
>>>
>>> This morning the Homebrew Octave was upgraded to 4.2.1_2, which now links to gcc@7, so I undid the above kludge. Now the original error message
>>>>> ~$ octave
>>>>> dyld: Library not loaded: /usr/local/opt/gcc/lib/gcc/6/libgfortran.3.dylib
>>>>> Referenced from: /usr/local/bin/octave-cli
>>>>> Reason: image not found
>>>>> Abort trap: 6
>>> has gone away, but a new one has taken its place:
>>> ~$ octave
>>> dyld: Library not loaded: /usr/local/opt/gcc/lib/gcc/6/libgfortran.3.dylib
>>>  Referenced from: /usr/local/opt/qrupdate/lib/libqrupdate.1.dylib
>>>  Reason: image not found
>>> Abort trap: 6
>>> Apparently qrupdate has not been upgraded to link to gcc@7.
>>>
>>> I am giving up my kludges. Is there any way I can get good Octave from Homebrew?
>>>
>>> -
>>> Vic
>>>
>>>
>>
>


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Re: Octave gcc problem (Homebrew Mac)

vicnorton
That seemed to work fine, Sebastian. Thanks so much!!!  - Vic

> On May 5, 2017, at 8:59 AM, Sebastian Schöps <[hidden email]> wrote:
>
> Ok, what about this?
>
> # get new versions
> brew update
>
> # install new versions
> brew upgrade
>
> # uninstall broken octave
> brew uninstall octave
>
> # reinstall octave from source
> brew install --build-from-source octave
>
> Bye
> Sebastian
>
>> Am 05.05.2017 um 14:55 schrieb Vic Norton <[hidden email]>:
>>
>> Unfortunately your advice didn’t work for me, Sebastian. - Vic
>>
>> ~$ brew install --build-from-source octave
>> Updating Homebrew...
>> ==> Auto-updated Homebrew!
>> Updated 3 taps (caskroom/cask, homebrew/core, homebrew/science).
>> ==> Updated Formulae
>> certbot                                  homebrew/science/plink2
>> git-extras                               homebrew/science/poretools
>> homebrew/science/calculix-ccx            homebrew/science/qrupdate ✔
>> homebrew/science/gmsh                    kubernetes-helm
>> homebrew/science/p4est                   todoman
>> homebrew/science/pastix                  yadm
>> homebrew/science/plasma
>>
>> Warning: homebrew/science/octave-4.2.1_2 already installed
>> ~$ octave
>> dyld: Library not loaded: /usr/local/opt/gcc/lib/gcc/7/libgfortran.4.dylib
>> Referenced from: /usr/local/bin/octave-cli
>> Reason: image not found
>> Abort trap: 6
>>
>>> On May 5, 2017, at 8:29 AM, Sebastian Schöps <[hidden email]> wrote:
>>>
>>> Dear Vic,
>>>
>>> you updated by purpose or accident your gcc. This may of course break dependencies like octave. The proper way is to recompile all dependencies, including octave
>>>
>>> brew install --build-from-source octave
>>>
>>> This is necessary as there is currently no octave binary for the new gcc. However, there will be a new one soon since this is a known issue:
>>>
>>> https://github.com/Homebrew/homebrew-science/issues/4972#issuecomment-299394176
>>>
>>> Sebastian
>>>
>>>> Am 05.05.2017 um 14:18 schrieb Vic Norton <[hidden email]>:
>>>>
>>>>> On May 4, 2017, at 5:25 PM, Vic Norton <[hidden email]> wrote:
>>>>>
>>>>>
>>>>>> On May 4, 2017, at 4:40 PM, Vic Norton <[hidden email]> wrote:
>>>>>>
>>>>>> Hi Sebastian,
>>>>>>
>>>>>> I just did a brew upgrade and it killed octave. Here is the error message I get.
>>>>>> ~$ octave
>>>>>> dyld: Library not loaded: /usr/local/opt/gcc/lib/gcc/6/libgfortran.3.dylib
>>>>>> Referenced from: /usr/local/bin/octave-cli
>>>>>> Reason: image not found
>>>>>> Abort trap: 6
>>>>>>
>>>>>> Apparently the problem is that
>>>>>> /usr/local/opt/gcc
>>>>>> has just become a symbolic link to
>>>>>> /usr/local/Cellar/gcc/7.1.0
>>>>>> rather than the previous
>>>>>> /usr/local/Cellar/gcc/6.3.0_1.
>>>>>> And a new libgfortran.4.dylib resides in the 7.1.0 version of gcc.
>>>>>>
>>>>>> I hate to mess with Homebrew. I expect the problem might be fixed by forcing
>>>>>> /usr/local/opt/gcc
>>>>>> to link to
>>>>>> /usr/local/Cellar/gcc/6.3.0_1
>>>>>> as before, but it does seem that Homebrew’s octave-cli should be adjusted for the new gcc@7.
>>>>>>
>>>>>> What is your advice? Right now I am dead in the water.
>>>>>>
>>>>>> Regards,
>>>>>>
>>>>>> Vic
>>>>>
>>>>> Well, I hated to mess with Homebrew, but the above solution did work. I now have a working Octave. Here is what I did in Terminal.
>>>>>
>>>>> 1. I changed my directory to /usr/local/opt
>>>>> 2. I relabeled gcc as gcc-new
>>>>> 3. I ran
>>>>> $ ln -s /usr/local/Cellar/gcc/6.3.0_1 gcc
>>>>>
>>>>> Now Octave 4.2.1 works as before, but I’ve messed up the latest Homebrew gcc in /usr/local/opt.
>>>>>
>>>>> I don’t like this solution. I’d rather have an Octave that can use Homebrew’s gcc@7.
>>>>>
>>>>> -
>>>>> Vic
>>>>
>>>> This morning the Homebrew Octave was upgraded to 4.2.1_2, which now links to gcc@7, so I undid the above kludge. Now the original error message
>>>>>> ~$ octave
>>>>>> dyld: Library not loaded: /usr/local/opt/gcc/lib/gcc/6/libgfortran.3.dylib
>>>>>> Referenced from: /usr/local/bin/octave-cli
>>>>>> Reason: image not found
>>>>>> Abort trap: 6
>>>> has gone away, but a new one has taken its place:
>>>> ~$ octave
>>>> dyld: Library not loaded: /usr/local/opt/gcc/lib/gcc/6/libgfortran.3.dylib
>>>> Referenced from: /usr/local/opt/qrupdate/lib/libqrupdate.1.dylib
>>>> Reason: image not found
>>>> Abort trap: 6
>>>> Apparently qrupdate has not been upgraded to link to gcc@7.
>>>>
>>>> I am giving up my kludges. Is there any way I can get good Octave from Homebrew?
>>>>
>>>> -
>>>> Vic
>>>>
>>>>
>>>
>>
>


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