Re: Does the bowtie2 2.3.5.1-1 package work for anyone else?
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
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