numpy fails to compile with SAGE_ATLAS_LIB

[vbraun]

If I'm building numpy with my own atlas install it fails. The cblas, atlas libraries are symlinked to SAGE_LOCAL/lib and the correct pkg-config output is present:

$ pkg-config --libs cblas
-L/mnt/disk/home/buildslave-sage/slave/sage_git/build/local/lib -lcblas -latlas 

Yet numpy fails with

$ ./sage -p numpy
This looks like the first time you are running Sage.
Updating various hardcoded paths...
(Please wait at most a few minutes.)
DO NOT INTERRUPT THIS.
Done updating paths.
Found local metadata for numpy-1.11.0
Using cached file /mnt/disk/home/buildslave-sage/slave/sage_git/build/upstream/numpy-1.11.0.tar.gz
numpy-1.11.0
====================================================
Setting up build directory for numpy-1.11.0
Finished set up
****************************************************
Host system:
Linux volker-desktop 4.4.7-300.fc23.x86_64 #1 SMP Wed Apr 13 02:52:52 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
****************************************************
C compiler: gcc
C compiler version:
Using built-in specs.
COLLECT_GCC=/usr/bin/gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/5.3.1/lto-wrapper
Target: x86_64-redhat-linux
Configured with: ../configure --enable-bootstrap --enable-languages=c,c++,objc,obj-c++,fortran,ada,go,lto --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-shared --enable-threads=posix --enable-checking=release --enable-multilib --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-plugin --enable-initfini-array --disable-libgcj --with-isl --enable-libmpx --enable-gnu-indirect-function --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
Thread model: posix
gcc version 5.3.1 20160406 (Red Hat 5.3.1-6) (GCC) 
****************************************************
Running from numpy source directory.

Note: if you need reliable uninstall behavior, then install
with pip instead of using `setup.py install`:

  - `pip install .`       (from a git repo or downloaded source
                           release)
  - `pip install numpy`   (last Numpy release on PyPi)


blas_opt_info:
blas_mkl_info:
Disabled blas_mkl_info: (MKL is None)
Disabled blas_mkl_info: (MKL is None)
  libraries mkl,vml,guide not found in []
  NOT AVAILABLE

openblas_info:
Disabled openblas_info: (OPENBLAS is None)
  libraries openblas not found in []
  NOT AVAILABLE

atlas_3_10_blas_threads_info:
Disabled atlas_3_10_blas_threads_info: (PTATLAS is None)
  libraries tatlas not found in []
  NOT AVAILABLE

atlas_3_10_blas_info:
Disabled atlas_3_10_blas_info: (ATLAS is None)
  libraries satlas not found in []
  NOT AVAILABLE

atlas_blas_threads_info:
Disabled atlas_blas_threads_info: (PTATLAS is None)
  libraries ptf77blas,ptcblas,atlas not found in []
  NOT AVAILABLE

atlas_blas_info:
Disabled atlas_blas_info: (ATLAS is None)
  libraries f77blas,cblas,atlas not found in []
  NOT AVAILABLE

/mnt/disk/home/buildslave-sage/slave/sage_git/build/local/var/tmp/sage/build/numpy-1.11.0/src/numpy/distutils/system_info.py:1640: UserWarning: 
    Atlas (http://math-atlas.sourceforge.net/) libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [atlas]) or by setting
    the ATLAS environment variable.
  warnings.warn(AtlasNotFoundError.__doc__)
blas_info:
C compiler: cc

creating /tmp/tmpKqg0LI/tmp
creating /tmp/tmpKqg0LI/tmp/tmpKqg0LI
compile options: '-I/usr/local/include -I/usr/include -I/mnt/disk/home/buildslave-sage/slave/sage_git/build/local/include -c'
cc: /tmp/tmpKqg0LI/source.c
cc /tmp/tmpKqg0LI/tmp/tmpKqg0LI/source.o -L/mnt/disk/home/buildslave-sage/slave/sage_git/build/local/lib -lcblas -o /tmp/tmpKqg0LI/a.out
/usr/bin/ld: warning: libatlas.so.3, needed by /mnt/disk/home/buildslave-sage/slave/sage_git/build/local/lib/libcblas.so, not found (try using -rpath or -rpath-link)
/mnt/disk/home/buildslave-sage/slave/sage_git/build/local/lib/libcblas.so: undefined reference to `ATL_sasum'
/mnt/disk/home/buildslave-sage/slave/sage_git/build/local/lib/libcblas.so: undefined reference to `ATL_dsyr2'
[...]

For some reason numpy forgot -latlas...

CC: @kiwifb

Component: packages: standard

Issue created by migration from https://trac.sagemath.org/ticket/20524

[kiwifb]

comment:1

What does the generated site.cfg look like?

[vbraun]

comment:2

[ALL]
library_dirs = /mnt/disk/home/buildslave-sage/slave/sage_git/build/local/lib
include_dirs = /mnt/disk/home/buildslave-sage/slave/sage_git/build/local/include
[blas]
library_dirs = /mnt/disk/home/buildslave-sage/slave/sage_git/build/local/lib
blas_libs    = atlas, f77blas, cblas
[lapack]
library_dirs = /mnt/disk/home/buildslave-sage/slave/sage_git/build/local/lib
lapack_libs  = lapack, f77blas, cblas, atlas

[vbraun]

comment:3

False alert, was due to #20487 not applying the numpy patches...