Bug 900551

Summary:	sci-biology/hmmer-2.3.2-r5 has implicit function declarations in configure logs (GCC-13-SYSTEM)
Product:	Gentoo Linux	Reporter:	Agostino Sarubbo <ago>
Component:	Current packages	Assignee:	Gentoo Science Biology related packages <sci-biology>
Status:	RESOLVED FIXED
Severity:	normal	Keywords:	PullRequest
Priority:	Normal
Version:	unspecified
Hardware:	All
OS:	Linux
See Also:	https://github.com/gentoo/gentoo/pull/36599
Whiteboard:	~arch only
Package list:		Runtime testing required:	---
Bug Depends on:
Bug Blocks:	906027
Attachments:	build.log

Description Agostino Sarubbo gentoo-dev

2023-03-09 14:09:45 UTC

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

Issue: sci-biology/hmmer-2.3.2-r5 has implicit function declarations in configure logs (GCC-13-SYSTEM).
Discovered on: amd64 (internal ref: gcc13_tinderbox)

NOTE:
(GCC-13-SYSTEM) in the summary means that the bug was found on a machine that runs gcc-13 but this bug MAY or MAY NOT BE related to the new compiler
See also: https://bugs.gentoo.org/898488#c4.

Comment 1 Agostino Sarubbo gentoo-dev

2023-03-09 14:09:48 UTC

Created attachment 856951 [details]
build.log

build log and emerge --info

Comment 2 Larry the Git Cow gentoo-dev

2024-05-09 01:13:41 UTC

The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4919e107f95d762348df57ca9a8e75307d9222bc

commit 4919e107f95d762348df57ca9a8e75307d9222bc
Author:     NHOrus <jy6x2b32pie9@yahoo.com>
AuthorDate: 2024-05-08 09:30:27 +0000
Commit:     Sam James <sam@gentoo.org>
CommitDate: 2024-05-09 01:09:05 +0000

    sci-biology/hmmer: Add missing include into configure
    
    There are no autotools source files, so we can't just autoreconf the problem out of existence
    
    [sam: Revbump.]
    
    Closes: https://bugs.gentoo.org/900551
    Signed-off-by: NHOrus <jy6x2b32pie9@yahoo.com>
    Closes: https://github.com/gentoo/gentoo/pull/36599
    Signed-off-by: Sam James <sam@gentoo.org>

 .../hmmer-2.3.2-fix-missing-include-in-configure.patch | 18 ++++++++++++++++++
 .../{hmmer-2.3.2-r5.ebuild => hmmer-2.3.2-r6.ebuild}   |  3 ++-
 2 files changed, 20 insertions(+), 1 deletion(-)