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Bug 862252 - sci-biology/abyss-2.3.4 fails to compile (lto): museq.c:58:13: error: type of [-Werror=lto-type-mismatch]
Summary: sci-biology/abyss-2.3.4 fails to compile (lto): museq.c:58:13: error: type of...
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal
Assignee: Gentoo Science Biology related packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks: lto
  Show dependency tree
 
Reported: 2022-07-30 08:23 UTC by Agostino Sarubbo
Modified: 2024-03-08 11:09 UTC (History)
1 user (show)

See Also:
Package list:
Runtime testing required: ---


Attachments
build.log (build.log,77.73 KB, text/plain)
2022-07-30 08:23 UTC, Agostino Sarubbo
Details

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Description Agostino Sarubbo gentoo-dev 2022-07-30 08:23:24 UTC
https://blogs.gentoo.org/ago/2020/07/04/gentoo-tinderbox/

Issue: sci-biology/abyss-2.3.4 fails to compile (lto).
Discovered on: amd64 (internal ref: lto_tinderbox)

NOTE:
This machine uses lto with CFLAGS=-flto -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing

Here is a bit of explanation:

-Werror=lto-type-mismatch:
User to find possible runtime issues in packages. It likely means the package is unsafe to build & use with LTO.
For projects using the same identifier but with different types across different files, they must be fixed to be consistent across the codebase.

-Werror=odr:
Used to find possible runtime issues in packages. These bugs are a problem anyway but may be even worse when combined with LTO. C++ code must comply with the One Definition Rule (ODR) - see https://en.cppreference.com/w/cpp/language/definition#One_Definition_Rule.

-Werror=strict-aliasing:
Used to find possible runtime issues in packages. These bugs are a problem anyway but may be even worse when combined with LTO.

Workarounds:
- If upstream is friendly and still active, file a bug upstream. For emulators, codecs, games, or multimedia packages, it may be worth just applying a workaround instead, as upstreams sometimes aren't receptive to these bugs (VALID FOR ALL).
- Use the new 'filter-lto' from flag-o-matic.eclass as it's likely to be unsafe with LTO (VALID FOR lto-type-mismatch - odr).
- Fix it yourself if interested, of course (VALID FOR ALL).
- Append-flags -fno-strict-aliasing (VALID FOR strict-aliasing).
- Use memcpy() but a union is sometimes suitable too (VALID FOR strict-aliasing).
- -fstrict-aliasing is implied by -O2, so this must be addressed in some form (VALID FOR strict-aliasing).

See also: https://marc.info/?l=gentoo-dev&m=165639574126280&w=2
Comment 1 Agostino Sarubbo gentoo-dev 2022-07-30 08:23:26 UTC
Created attachment 795736 [details]
build.log

build log and emerge --info
Comment 2 Larry the Git Cow gentoo-dev 2024-03-08 11:09:44 UTC
The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=490ada295187ec9b28e867128b53f6bdf5f68f63

commit 490ada295187ec9b28e867128b53f6bdf5f68f63
Author:     Eli Schwartz <eschwartz93@gmail.com>
AuthorDate: 2024-03-08 01:20:48 +0000
Commit:     Sam James <sam@gentoo.org>
CommitDate: 2024-03-08 11:09:00 +0000

    sci-biology/abyss: mark as LTO-unsafe
    
    Closes: https://bugs.gentoo.org/862252
    Signed-off-by: Eli Schwartz <eschwartz93@gmail.com>
    Signed-off-by: Sam James <sam@gentoo.org>

 sci-biology/abyss/abyss-2.3.4.ebuild | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)