On 10/14/19 7:26 PM, Michael Crusoe wrote: > I can't get it to build from source in a cowbuilder "sid" chroot on my > laptop, which is currently running Ubuntu Bionic with the 5.0.0-20-generic > #21~18.04.1-Ubuntu kernel. > > running bowtie2-build --usage (or anything) results in a segfault > > [34760.926015] bowtie2-align-s[19983]: segfault at 7fff11b4bff8 ip > 00007f14b12a393d sp 00007fff11b4c000 error 6 in libdl-2.29.so > [7f14b12a3000+1000] > [34760.926022] Code: e8 28 f7 ff ff e9 42 ff ff ff e8 3e f7 ff ff 66 66 2e > 0f 1f 84 00 00 00 00 00 0f 1f 00 48 83 3d 90 26 00 00 00 41 54 49 89 fc > <55> 48 89 f5 53 74 7c 48 8d 35 05 fc ff ff 48 8d 3d 76 27 00 00 e8
Just managed to build git cloned bowtie2 on Buster and Bionic, both work. The one in LXC with Sid is working too. As a wild guess, what is ulimit -s for the shell? May be disabling apparmor helps? > > But maybe it is just my system and someone else could confirm on a real > Debian sid/unstable system without virtualization/chroot/containerization. There is no point in excluding any kind of virtualization/chroot/containerization IMHO. Best, Alex
