[SciPy-User] pip install scipy: error adding symbols: bad value

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[SciPy-User] pip install scipy: error adding symbols: bad value

Daπid
I have upgraded to Fedora 23, that includes the new binary ABI, so I decided to recompile my modules. I created a new virtualenv, updated pip and setuptools, and installed numpy and scipy with pip. The second one failed spitting:

/bin/ld: build/temp.linux-x86_64-2.7/libdfftpack.a(zffti1.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC
    build/temp.linux-x86_64-2.7/libdfftpack.a: error adding symbols: Bad value
    collect2: error: ld returned 1 exit status

Find attached the full log. I am using GCC 5.1.1 and openBLAS 0.2.15.

For the record, Numpy's f2py tests are also failing.


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Re: pip install scipy: error adding symbols: bad value

David Cournapeau
You may have CFLAGS/CXXFLAGS defined, which override the distutils flags. Unset those (or append `-fPIC` to them)

David

On Wed, Dec 9, 2015 at 12:01 PM, Daπid <[hidden email]> wrote:
I have upgraded to Fedora 23, that includes the new binary ABI, so I decided to recompile my modules. I created a new virtualenv, updated pip and setuptools, and installed numpy and scipy with pip. The second one failed spitting:

/bin/ld: build/temp.linux-x86_64-2.7/libdfftpack.a(zffti1.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC
    build/temp.linux-x86_64-2.7/libdfftpack.a: error adding symbols: Bad value
    collect2: error: ld returned 1 exit status

Find attached the full log. I am using GCC 5.1.1 and openBLAS 0.2.15.

For the record, Numpy's f2py tests are also failing.


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Re: pip install scipy: error adding symbols: bad value

Daπid

On 9 December 2015 at 17:11, David Cournapeau <[hidden email]> wrote:
You may have CFLAGS/CXXFLAGS defined, which override the distutils flags. Unset those (or append `-fPIC` to them)

David

That is correct, I have them pointing at my architecture. But this was working before, ie, they were just being appended to the correct flags. Has there been any change lately?


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Re: pip install scipy: error adding symbols: bad value

David Cournapeau


On Wed, Dec 9, 2015 at 4:25 PM, Daπid <[hidden email]> wrote:

On 9 December 2015 at 17:11, David Cournapeau <[hidden email]> wrote:
You may have CFLAGS/CXXFLAGS defined, which override the distutils flags. Unset those (or append `-fPIC` to them)

David

That is correct, I have them pointing at my architecture. But this was working before, ie, they were just being appended to the correct flags. Has there been any change lately?

No, this "feature" has been in distutils forever as far as I can remember.

David


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Re: pip install scipy: error adding symbols: bad value

Daπid
In reply to this post by David Cournapeau

On 9 December 2015 at 17:11, David Cournapeau <[hidden email]> wrote:
You may have CFLAGS/CXXFLAGS defined, which override the distutils flags. Unset those (or append `-fPIC` to them)

I figured this one out. The culprit is actually FFLAGS. You can set CFLAGS and CXXFLAGS freely.

I noticed that Numpy compiled just fine, but produced errors with f2py; and the errors in Scipy's installation arise when gfortran is invoked. Also, last week I was building some FORTRAN, and I set the corresponding flags; hence the problem. Unsetting FFLAGS fixed the issue (but setting it to the empty string didn't!).

I confirm that distutils is just appending my CFLAGS to the preset ones, which seems to me a sane behaviour. I think f2py should do the same.

/David.


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Re: pip install scipy: error adding symbols: bad value

Charles R Harris


On Thu, Dec 10, 2015 at 2:41 AM, Daπid <[hidden email]> wrote:

On 9 December 2015 at 17:11, David Cournapeau <[hidden email]> wrote:
You may have CFLAGS/CXXFLAGS defined, which override the distutils flags. Unset those (or append `-fPIC` to them)

I figured this one out. The culprit is actually FFLAGS. You can set CFLAGS and CXXFLAGS freely.

I noticed that Numpy compiled just fine, but produced errors with f2py; and the errors in Scipy's installation arise when gfortran is invoked. Also, last week I was building some FORTRAN, and I set the corresponding flags; hence the problem. Unsetting FFLAGS fixed the issue (but setting it to the empty string didn't!).

I confirm that distutils is just appending my CFLAGS to the preset ones, which seems to me a sane behaviour. I think f2py should do the same.

Please open an numpy issue for this.

Chuck

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