The configure step fails, as it can't find blas. My system only contains intel's blas implementation. I used scipy 0.13.0, however, 0.12.* also has the problem. Reproducible: Always Steps to Reproduce: 1. emerge mkl, I used the latest version from science overlay, but that shouldn't matter 2. eselect cblas, blas and lapack to mkl. I used "mkl64-int64-dynamic" in every case. 3. emerge scipy The error occurs due to a "failure" in site.cfg. The runtime library, libmkl_rt is included twice in the library section. The following patch generates a correct configuration file and thus, the package compiles fine.
Created attachment 364592 [details, diff] fix for the ebuild This fixes the generated scite.cfg for me. It simply removes double library names.
Created attachment 364598 [details, diff] a better, more general, fix for the ebuild
+*scipy-0.13.2-r1 (26 Dec 2013) + + 26 Dec 2013; Justin Lecher <jlec@gentoo.org> +scipy-0.13.2-r1.ebuild: + Fix for linking with mkl, #493318 +
I'm sorry, this doesn't fix the problem for me. The issue is the same, the sed command in the ebuild doesn't remove the double library entries. I'll attach a patch for the ebuild. My version gives: pkg-config --libs-only-l cblas blas | sed -e 's/[ ]-l*\(pthread\|m\)[ ]*//g' -e 's/^-l//' -e 's/[ ]*-l/\n/g' -e 's/[ ]*$//' mkl_rt mkl_rt The current ebuild gives: pkg-config --libs-only-l cblas blas | sed -e 's/[ ]-l*\(pthread\|m\)\([ ]\|$\)//g' -e 's/^-l//' -e 's/[ ]*-l/,/g' -e 's/[ ]*$//' mkl_rt,mkl_rt And thus uniq doesn't do it's magic.
Created attachment 368866 [details, diff] fix for current version of ebuild Patch for scipy-0.13.2-r1.ebuild to resolve above issue
