sci-biology/allpaths:3 has never compiled for me under gcc 4.4. This turns out to be due to the optimizer in recent gcc's removing code that isn't dead. I have reported the bug upstream. The latest upstream version is 3.2. The ebuild doesn't respect CXXFLAGS and always uses "-O3", but -O2 breaks it as well. In addition, the ebuild puts executable code in /usr/share. I'm attaching an ebuild that addresses the issues above. I don't have a fix for the optimizer problem, so my ebuild doesn't respect CXXFLAGS, nor does it respect LDFLAGS (http://bugs.gentoo.org/show_bug.cgi?id=335374). However, it does work for me. Reproducible: Always Steps to Reproduce: 1. emerge allpaths:3 Actual Results: ./.libs/libAllPaths3.a(MuxWalkGraph.o): In function `MuxWalkGraph_to_HyperKmerPath::AssociateClosers(HyperKmerPath&) const': /root/allpaths/allpaths3-3.2/src/paths/MuxWalkGraph.cc:740: undefined reference to `digraphE<KmerPath>::TransferEdges(int, int, unsigned char)'
Created attachment 245645 [details] allpaths-3.2.ebuild
Created attachment 250477 [details, diff] allpaths-3.34911.ebuild.patch Version numbering and URL have changed; ebuild still does not respect CFLAGS, nor does it use --as-needed. Patch against allpaths-3.1.ebuild.
sci-biology/allpaths moved to sci-biology/allpathslg, all old ebuilds will be dropped. Please check if the problem persists with the latest sci-biology/allpathslg and reopen the bug if appropriate.
