octave-linear-algebra config error

[Mark Brethen]

Sorry, in such a rush I didn’t look at that closely. 

However, removing atlas and installing arpack @3.5.0_0+accelerate+gfortran fixed it.


Mark Brethen
mark.brethen at gmail.com



> On Apr 23, 2018, at 10:37 AM, Marius Schamschula <lists at schamschula.com> wrote:
> 
> Mark,
> 
> /path/to/liblapack.dylib was meant to be a placeholder for the library. In your case you have
> 
> /opt/local/lib/liblapack.a
> 
> So try 
> 
> nm  /opt/local/lib/liblapack.a  | grep dggsvd
> 
>> On Apr 23, 2018, at 10:29 AM, Mark Brethen <mark.brethen at gmail.com <mailto:mark.brethen at gmail.com>> wrote:
>> 
>> brethen-air:~ marbre$ port contents atlas | grep liblapack
>>   /opt/local/lib/liblapack.a
>> 
>> brethen-air:~ marbre$ nm /path/to/liblapack.dylib | grep dggsvd
>> /opt/local/libexec/llvm-5.0/bin/llvm-nm: /path/to/liblapack.dylib: No such file or directory.
>> 
>> There’s your answer.
>> 
>> Mark Brethen
>> mark.brethen at gmail.com <mailto:mark.brethen at gmail.com>
>> 
>> 
>> 
>>> On Apr 23, 2018, at 10:19 AM, Marius Schamschula <lists at schamschula.com <mailto:lists at schamschula.com>> wrote:
>>> 
>>> Mark,
>>> 
>>> I think it does, but for some reason there are missing symbols.
>>> 
>>> What does 
>>> 
>>> port contents atlas | grep liblapack
>>> 
>>> give you?
>>> 
>>> If you run
>>> 
>>> nm /path/to/liblapack.dylib | grep dggsvd
>>> 
>>> We can see if the symbol is there, but if we have a linking issue, or if it is missing altogether.
>>> 
>>>> On Apr 23, 2018, at 9:31 AM, Mark Brethen <mark.brethen at gmail.com <mailto:mark.brethen at gmail.com>> wrote:
>>>> 
>>>> I think atlas is providing liblapack, which in my case was built using gcc5.
>>>> 
>>>> Sent from my iPhone
>>>> 
>>>> On Apr 23, 2018, at 5:51 AM, Marius Schamschula <lists at schamschula.com <mailto:lists at schamschula.com>> wrote:
>>>> 
>>>>> Mark,
>>>>> 
>>>>> I get no such issue when building octave-linear-algebra against octave with the Accelerate Framework under High Sierra. The symbols seem to be missing from the liblapack.dylib you are linking against.
>>>>> 
>>>>>> On Apr 22, 2018, at 8:53 PM, Mark Brethen <mark.brethen at gmail.com <mailto:mark.brethen at gmail.com>> wrote:
>>>>>> 
>>>>>> I’m getting the following error for octave-linear-algebra during config:
>>>>>> 
>>>>>> :info:configure /usr/bin/arch -arch x86_64 /opt/local/bin/mkoctfile-4.2.2 --verbose -DHAVE_OCTAVE_42 -v -DHAVE_CONFIG_H -Wall gsvd.o dbleGSVD.o CmplxGSVD.o  -o gsvd.oct 
>>>>>> :info:configure /usr/bin/clang++ -std=gnu++11 -I/opt/local/include/octave-4.2.2/octave/.. -I/opt/local/include/octave-4.2.2/octave -I/opt/local/include  -D_THREAD_SAFE -pthread -pipe -Os -std=c++11 -stdlib=libc++ -arch x86_64 -bundle -bundle_loader /opt/local/bin/octave-4.2.2  -Wall -o gsvd.oct  gsvd.o dbleGSVD.o CmplxGSVD.o   -L/opt/local/lib/octave/4.2.2 -L/opt/local/lib  -L/opt/local/lib -lsatlas -loctinterp -loctave  
>>>>>> :info:configure clang: warning: argument unused during compilation: '-pthread'
>>>>>> :info:configure Undefined symbols for architecture x86_64:
>>>>>> :info:configure   "_dggsvd_", referenced from:
>>>>>> :info:configure       GSVD::init(Matrix const&, Matrix const&, GSVD::type) in dbleGSVD.o
>>>>>> :info:configure   "_zggsvd_", referenced from:
>>>>>> :info:configure       ComplexGSVD::init(ComplexMatrix const&, ComplexMatrix const&, GSVD::type) in CmplxGSVD.o
>>>>>> :info:configure ld: symbol(s) not found for architecture x86_64
>>>>>> :info:configure clang: error: linker command failed with exit code 1 (use -v to see invocation)
>>>>>> :info:configure make: *** [gsvd.oct] Error 1
>>>>>> 
>>>>>> My setup is:
>>>>>> OS 10.11.6
>>>>>> MacPorts  2.4.3
>>>>>> arpack -accelerate+atlas-gfortran+gcc5
>>>>>> atlas +gcc5
>>>>>> octave -accelerate+atlas
>>>>>> 
>>>>>> 
>>>>>> Mark Brethen
>>>>>> mark.brethen at gmail.com <mailto:mark.brethen at gmail.com>
>>>>>> 
>>>>>> 
>>>>>> 
>>>>> 
>>>>> Marius
>>>>> --
>>>>> Marius Schamschula
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>> 
>>> Marius
>>> --
>>> Marius Schamschula
>>> 
>>> 
>>> 
>> 
> 
> 
> 
> Marius
> --
> Marius Schamschula
> 
> 
> 

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