[gentoo-science] lapack 3.6.0 harmful for scipy

[François Bissey]

So lapack 3.6.0 landed while I wasn't looking.
scipy (0.16.1) doesn't like it:
ldd -r /usr/lib64/python2.7/site-packages/scipy/linalg/_flapack.so
linux-vdso.so.1 (0x00007fff84da2000)
libopenblas_threads.so.0 => /usr/lib64/libopenblas_threads.so.0
(0x00007f5ac2513000)
libreflapack.so.3 => /usr/lib64/libreflapack.so.3
(0x00007f5ac1d4d000)
libpython2.7.so.1.0 => /usr/lib64/libpython2.7.so.1.0
(0x00007f5ac198e000)
libc.so.6 => /lib64/libc.so.6 (0x00007f5ac15f3000)
libm.so.6 => /lib64/libm.so.6 (0x00007f5ac12ee000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f5ac10d2000)
libgfortran.so.3 =>
/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.3/libgfortran.so.3 (0x00007f5ac0daa000)
libgcc_s.so.1 =>
/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.3/libgcc_s.so.1 (0x00007f5ac0b92000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007f5ac098e000)
libutil.so.1 => /lib64/libutil.so.1 (0x00007f5ac078b000)
/lib64/ld-linux-x86-64.so.2 (0x00007f5ac2da9000)
libquadmath.so.0 =>
/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.3/libquadmath.so.0 (0x00007f5ac054c000)
undefined symbol: sgegv_
(/usr/lib64/python2.7/site-packages/scipy/linalg/_flapack.so)
undefined symbol: dgegv_
(/usr/lib64/python2.7/site-packages/scipy/linalg/_flapack.so)
undefined symbol: cgegv_
(/usr/lib64/python2.7/site-packages/scipy/linalg/_flapack.so)
undefined symbol: zgegv_
(/usr/lib64/python2.7/site-packages/scipy/linalg/_flapack.so)

There may be other. Those functions have been deprecated for a while
apparently and now they have been removed.
My first thought was it should mean a soname change for lapack but
I am not sure how long it's been deprecated. I haven't found an upstream
bug in scipy yet, but we will need a patch quickly unless lapack is masked.

Francois

[François Bissey]

upstream scipy PR for 0.17:
https://github.com/scipy/scipy/pull/5518

Post by François Bissey
So lapack 3.6.0 landed while I wasn't looking.
ldd -r /usr/lib64/python2.7/site-packages/scipy/linalg/_flapack.so
linux-vdso.so.1 (0x00007fff84da2000)
libopenblas_threads.so.0 => /usr/lib64/libopenblas_threads.so.0
(0x00007f5ac2513000)
libreflapack.so.3 => /usr/lib64/libreflapack.so.3
(0x00007f5ac1d4d000)
libpython2.7.so.1.0 => /usr/lib64/libpython2.7.so.1.0
(0x00007f5ac198e000)
libc.so.6 => /lib64/libc.so.6 (0x00007f5ac15f3000)
libm.so.6 => /lib64/libm.so.6 (0x00007f5ac12ee000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f5ac10d2000)
libgfortran.so.3 =>
/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.3/libgfortran.so.3
(0x00007f5ac0daa000)
libgcc_s.so.1 =>
/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.3/libgcc_s.so.1 (0x00007f5ac0b92000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007f5ac098e000)
libutil.so.1 => /lib64/libutil.so.1 (0x00007f5ac078b000)
/lib64/ld-linux-x86-64.so.2 (0x00007f5ac2da9000)
libquadmath.so.0 =>
/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.3/libquadmath.so.0
(0x00007f5ac054c000)
undefined symbol: sgegv_
(/usr/lib64/python2.7/site-packages/scipy/linalg/_flapack.so)
undefined symbol: dgegv_
(/usr/lib64/python2.7/site-packages/scipy/linalg/_flapack.so)
undefined symbol: cgegv_
(/usr/lib64/python2.7/site-packages/scipy/linalg/_flapack.so)
undefined symbol: zgegv_
(/usr/lib64/python2.7/site-packages/scipy/linalg/_flapack.so)
There may be other. Those functions have been deprecated for a while
apparently and now they have been removed.
My first thought was it should mean a soname change for lapack but
I am not sure how long it's been deprecated. I haven't found an upstream
bug in scipy yet, but we will need a patch quickly unless lapack is masked.
Francois

[Justin Lecher (jlec)]

Post by François Bissey
https://github.com/scipy/scipy/pull/5518

Hi,

thanks for digging all that out. I saw the configure switch for those
routines, but I assumed given the long release cycles, they were
removed in most programs. There is now a configure switch to build
those symbols in again.

Justin

commit 5cc6855b8f846521f1c354e79c943fa3120bea34
Author: Justin Lecher <***@gentoo.org>
Date: Tue Dec 1 07:51:57 2015 +0100

sci-libs/lapack-reference: Add USE to build deprecated routines

Package-Manager: portage-2.2.25
Signed-off-by: Justin Lecher <***@gentoo.org>