https://blogs.gentoo.org/ago/2020/07/04/gentoo-tinderbox/ Issue: sci-biology/mothur-1.27.0-r1 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
Created attachment 795757 [details] build.log build log and emerge --info
It's pretty out of date.
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4aa71fb389486acee786f07025f7e24cfa07360a commit 4aa71fb389486acee786f07025f7e24cfa07360a Author: Sam James <sam@gentoo.org> AuthorDate: 2024-03-22 08:11:38 +0000 Commit: Sam James <sam@gentoo.org> CommitDate: 2024-03-22 08:43:28 +0000 sci-biology/mothur: add 1.48.0 Filter LTO too, and no-SA. Not reported upstream as it has a lot of open bugs already and seems low activity. Closes: https://bugs.gentoo.org/862273 Signed-off-by: Sam James <sam@gentoo.org> sci-biology/mothur/Manifest | 1 + sci-biology/mothur/files/mothur-1.48.0-build.patch | 79 ++++++++++++++++++++++ sci-biology/mothur/metadata.xml | 5 ++ sci-biology/mothur/mothur-1.48.0.ebuild | 54 +++++++++++++++ 4 files changed, 139 insertions(+)
