Bug 862285 – sci-biology/qrna-2.0.3c-r3 fails to compile (lto): evolscorewithmodelscanfast.c:307:15: error: type of [-Werror=lto-type-mismatch]

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Agostino Sarubbo 2022-07-30 08:35:30 UTC]

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

Issue: sci-biology/qrna-2.0.3c-r3 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 2022-07-30 08:35:33 UTC]

Created attachment 795769 [details]
build.log

build log and emerge --info

[Comment 2 Larry the Git Cow 2024-03-21 05:58:43 UTC]

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

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c19c464def01a163fc04351c151a98d4048095e3

commit c19c464def01a163fc04351c151a98d4048095e3
Author:     Eli Schwartz <[e-mail]>
AuthorDate: 2024-03-21 00:25:02 +0000
Commit:     Sam James <[e-mail]>
CommitDate: 2024-03-21 05:57:37 +0000

    sci-biology/qrna: add 2.0.4
    
    This is the 2006 edition of the software. It has a bunch of useful
    fixes:
    - it fixes Modern C porting issues
    - it fixes LTO errors
    - it incorporates the glibc-2.10 patch
    
    just by upgrading! It's about time we upgrade, since it is 18 years
    later.
    
    Along the way we fix up the ebuild a bit:
    - bump to EAPI 8
    - acquire an actual SRC_URI, not just the gentoo mirror
    - update the homepage along with the SRC_URI. The original homepage is
      dead, and the domain redirects to a new domain (whence comes the new
      distfile).
    
    It has some shortcomings too:
    - the distfile comes with free .svn directories, which have to be
      pruned.
    - the distfile comes without the 80mb demos
    
    To solve this, we use the old distfile (which I think only exists on
    Gentoo's mirror network) and gate it behind a USE=examples flag, in case
    anyone needs them.
    
    Closes: https://bugs.gentoo.org/862285
    Closes: https://bugs.gentoo.org/884283
    Signed-off-by: Eli Schwartz <[e-mail]>
    Signed-off-by: Sam James <[e-mail]>

 sci-biology/qrna/Manifest                       |   1 +
 sci-biology/qrna/files/qrna-2.0.4-ldflags.patch | 381 ++++++++++++++++++++++++
 sci-biology/qrna/qrna-2.0.4.ebuild              |  61 ++++
 3 files changed, 443 insertions(+)

[Comment 3 Eli Schwartz 2024-03-21 19:44:56 UTC]

*** Bug 927387 has been marked as a duplicate of this bug. ***