Bug 882355

Summary:	sci-biology/hmmer-3.1_beta2-r1 leaves trace of segfault in dmesg
Product:	Gentoo Linux	Reporter:	Agostino Sarubbo <ago>
Component:	Current packages	Assignee:	Gentoo Science Biology related packages <sci-biology>
Status:	CONFIRMED ---
Severity:	normal
Priority:	Normal
Version:	unspecified
Hardware:	All
OS:	Linux
Whiteboard:
Package list:		Runtime testing required:	---

Description Agostino Sarubbo gentoo-dev

2022-11-21 08:42:06 UTC

https://blogs.gentoo.org/ago/2020/07/04/gentoo-tinderbox/

Issue: sci-biology/hmmer-3.1_beta2-r1 leaves trace of segfault in dmesg.
Discovered on: amd64 (internal ref: ci)

NOTE:
To reproduce this issue:
1) Install the package with FEATURES=test
2) Check dmesg output with: dmesg -T | grep -E '( segfault | traps:| audit:)'

This type of report comes from a check that is a bit outside of the tinderbox, that's the reason because build.log was not provided (however in cases like these the build.log doesn't help much) but if you need further help to diagnose this issue feel free to ask.

In any case I'm providing what I can see via dmesg.

Comment 1 Agostino Sarubbo gentoo-dev

2022-11-21 08:42:30 UTC

[Sun Nov 20 22:25:19 2022] hmmpgmd[47804]: segfault at 8 ip 000055fa54e2c84e sp 00007ffcb096e350 error 4 in hmmpgmd[55fa54dc4000+b1000]