py-numpy: Build failure with +atlas and version 1.11.0_0

[mf2k (Frank Schima)]

I'm trying to update both py35-numpy and py27-numpy to the latest version 1.11.0_0 but neither build for me. I'm attaching the log for py35-numpy.

Here are the variants I am using:

$ port installed py35-numpy
The following ports are currently installed:
  py35-numpy @1.10.4_0+atlas+gcc5 (active)

[mf2k (Frank Schima)]

It looks like the error could be:

:info:build ld: unknown option: -rpath=/opt/local/lib

[michaelld (Michael Dickens)]

Well that's just ducky. I tested for default variants as well as +openblas (I don't have atlas installed, and use OpenBLAS instead); let me test for +gcc5 & see what comes of it.

[mf2k (Frank Schima)]

It appears that the atlas variant is the problem. It built fine for me without it.

$ port installed py35-numpy
The following ports are currently installed:
  py35-numpy @1.11.0_0+gcc5 (active)

[michaelld (Michael Dickens)]

Agreed. I just tested with +gcc5 +gfortran and +gcc5 +gfortran +openblas, and both worked. I don't have atlas installed. Maybe you can figure out the issue? Maybe it's some commit since the prior release that added in the rpath stuff?

[mf2k (Frank Schima)]

This stuff is way over my head. All I know is that +atlas worked with the previous version of numpy.

[michaelld (Michael Dickens)]

OK. I'll get atlas installed & try to figure out what's going on. No promises on timing.

[stromnov (Andrey Stromnov)]

Cc Me!

[michaelld (Michael Dickens)]

The issue seems to be that when +atlas is specified, the linker use is MacPorts' "ld" ($preifx/bin/ld), which supports the rpath syntax "-rpath PATH" whereas GNU linkers support the syntax "-rpath=PATH". Thus, I'm guessing when using +atlas on 10.9 and newer (libc++), GCC will use MacPorts "ld" whereas on 10.8 and prior (libstdc++), it will use GCC's linker -- just a guess, since I can't easily test. I think just patching the specific files to use " " instead of "=" will work for most folks. But, who knows? I've no idea why 1.10.4 worked by 1.11.0 does not. This "rpath" stuff didn't change, so it's the consequence of an indirect change. I'll attach a patch here for folks to try, when I get a chance.

[petrrr]

Cc Me!

[skymoo (Adam Mercer)]

Cc Me!

[bkappes@…]

Apologies ahead for not knowing the proper way to do this, but I moved into the build directory for py27-numpy and ran:

grep -R "rpath=" * | grep -v "Binary file" | awk -F':' '{print $1}' | xargs sed -i.bkp -E 's/rpath=/rpath /g'

as Michael suggests, replacing "rpath=" with "rpath ". Subsequent upgrade of py27-numpy was successful.

I'm sorry I'm unable to put together a more robust fix.

[shapovalow@…]

Cc Me!

[dliessi (Davide Liessi)]

Cc Me!

[dliessi (Davide Liessi)]

Same error on 10.6.8.

[josephsacco]

The same rpath issue exists when building py[27|34]-numpy on a G4-based PPC running OSX 10.5.8 using +atlas and +gcc49.

The two errant files are

./numpy/distutils/fcompiler/gnu.py

and

./numpy/distutils/fcompiler/intel.py [not relevant for PPC's, but the same issue]

Replacing "rpath=" with "rpath " in these files allows numpy to build.

Constructing a patch is simple. Knowing what to add to the Portfile is another issue that I will defer to people like Michael who actually understand this stuff.

-Joseph

[EJFielding (Eric Fielding)]

Cc Me!

[EJFielding (Eric Fielding)]

I have been using the +atlas variant with py27-numpy for a long time, but got the same error after upgrading to 1.11.0. I forget now why I was using +atlas, so I switched to +openblas and it now builds OK.

[mark.chilenski@…]

Cc Me!

[astrofitz (Michael Fitzgerald)]

Cc Me!

[mf2k (Frank Schima)]

Cc'ing atlas maintainer for possible comment.

[larryv (Lawrence Velázquez)]

Cc Me!

[posita (Matt Bogosian)]

Cc Me!

[stromnov (Andrey Stromnov)]

Related NumPy issue: ​https://github.com/numpy/numpy/issues/7750

[captainproton1971 (Captain Proton)]

Cc Me!

[astroboylrx (Rixin Li)]

Cc Me!

[michaelld (Michael Dickens)]

This issue is related to #1419.

I just attached a patch for NumPy that should fix this build error. It should work on at least 10.9 and newer (libc++). I don't have a 10.[6-8] box around for testing (libstdc++ via GCC 4.2.1). I did verify that the rpath setting works on a modern Linux box running GCC 4.9 ("-Wl,-rpath -Wl,"/R/P/A/T/H", where "/R/P/A/T/H" is the actual desired rpath, in ""s to allow for spaces in directory names).

Could others please test & verify? You'll need to do roughly the following (assuming the patch is in ~/Downloads/patch-numpy_rpath.diff):

pushd $(port dir py27-numpy)
sudo patch -p0 < ~/Downloads/patch-numpy_rpath.diff
sudo port upgrade py27-numpy

assuming that works, then do:

sudo patch -R -p0 < ~/Downloads/patch-numpy_rpath.diff

[seanfarley (Sean Farley)]

Yep, this patch fixes it for me. I would say go ahead and push it.

[michaelld (Michael Dickens)]

OK. done in r153885.