Unit test for sci-libs/scipy-0.10.0 fails with a segmentation fault in /usr/lib64/libsuperlu.so.4. Reproducible: Always Steps to Reproduce: 1. start python console 2. import scipy as sp 3. sp.test(verbose=10) Actual Results: .... .... Solve: single precision ... SKIP: Skipping test: test_solve_without_umfpack UMFPACK appears not to be compiled test_non_square (test_linsolve.TestLinsolve) ... ok test_singular (test_linsolve.TestLinsolve) ... Segmentation fault The problem seems to be cause by libsuperlu: Program received signal SIGSEGV, Segmentation fault. 0x00007fffde08739e in dpivotL () from /usr/lib64/libsuperlu.so.4 (gdb) backtrace #0 0x00007fffde08739e in dpivotL () from /usr/lib64/libsuperlu.so.4 #1 0x00007fffde083386 in dgstrf () from /usr/lib64/libsuperlu.so.4 #2 0x00007fffde07e7cc in dgssv () from /usr/lib64/libsuperlu.so.4 #3 0x00007fffde2cc78d in ?? () from /usr/lib64/python2.7/site-packages/scipy/sparse/linalg/dsolve/_superlu.so Expected Results: Tests work According to this discussion http://projects.scipy.org/scipy/ticket/1513 it is recommended to link scipy against the bundled patched version of SuperLU. I am attaching a modified ebuild, which links against the bundled SuperLU. All tests pass with this version. While not "pretty", I propose that we link against the scipy version of SuperLU until the scipy specific changes get merged upstream.
Created attachment 302629 [details, diff] modified ebuild
Comment on attachment 302629 [details, diff] modified ebuild --- scipy-0.10.0.ebuild 2012-01-14 17:28:18.000000000 +0100 +++ - 2012-02-21 15:18:42.127881451 +0100 @@ -25,7 +25,6 @@ CDEPEND="dev-python/numpy media-libs/qhull sci-libs/arpack - >=sci-libs/superlu-4.3 virtual/cblas virtual/lapack umfpack? ( sci-libs/umfpack )" @@ -70,12 +69,9 @@ src_prepare() { # remove bundled libs - epatch \ - "${FILESDIR}"/${PN}-0.9.0-superlu.patch \ - "${FILESDIR}"/${PN}-0.9.0-superlu-4.3.patch \ - "${FILESDIR}"/${PN}-0.9.0-qhull.patch - rm -rf ./scipy/sparse/linalg/dsolve/SuperLU ./scipy/spatial/qhull - local libdir="${EPREFIX}"/usr/$(get_libdir) + epatch "${FILESDIR}"/${PN}-0.9.0-qhull.patch + rm -rf ./scipy/spatial/qhull + cat >> site.cfg <<-EOF [blas] include_dirs = $(pkg-config --cflags-only-I \
*** This bug has been marked as a duplicate of bug 364083 ***
