Bug 898112

Summary:	sci-biology/abyss-2.3.4 calls commands that do not exist (MUSL-CLANG-SYSTEM): :
Product:	Gentoo Linux	Reporter:	Agostino Sarubbo <ago>
Component:	Current packages	Assignee:	Gentoo Science Biology related packages <sci-biology>
Status:	CONFIRMED ---
Severity:	normal	CC:	eschwartz93
Priority:	Normal
Version:	unspecified
Hardware:	All
OS:	Linux
See Also:	https://github.com/bcgsc/abyss/pull/475
Whiteboard:
Package list:		Runtime testing required:	---
Attachments:	build.log

Description Agostino Sarubbo gentoo-dev

2023-02-27 10:11:34 UTC

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

Issue: sci-biology/abyss-2.3.4 calls commands that do not exist (MUSL-CLANG-SYSTEM).
Discovered on: amd64 (internal ref: tinderbox_musl)

NOTE:
(MUSL-CLANG-SYSTEM) in the summary means that bug was found on a machine that runs MUSL libc + clang16 but this bug MAY or MAY NOT BE related to musl/clang16.
Please look for 'command not found' and/or 'no such file or directory'.

Comment 1 Agostino Sarubbo gentoo-dev

2023-02-27 10:11:36 UTC

Created attachment 854970 [details]
build.log

build log and emerge --info

Comment 2 Agostino Sarubbo gentoo-dev

2023-02-27 10:11:37 UTC

Error(s) that match a know pattern in addition to what has been reported in the summary:


./configure: line 7028: : command not found
./Timer.h:17:3: error: unknown type name 'clock_t'