https://blogs.gentoo.org/ago/2020/07/04/gentoo-tinderbox/ Issue: sci-biology/kallisto-0.46.2 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 824997 [details] build.log build log and emerge --info
Error(s) that match a know pattern in addition to what has been reported in the summary: /var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/unit_tests/main.cpp:2:10: fatal error: catch2/catch.hpp: No such file or directory /var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/unit_tests/test_index.cpp:1:10: fatal error: catch2/catch.hpp: No such file or directory /var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/unit_tests/test_kmerhashtable.cpp:1:10: fatal error: catch2/catch.hpp: No such file or directory FAILED: unit_tests/CMakeFiles/tests.dir/main.cpp.o FAILED: unit_tests/CMakeFiles/tests.dir/test_index.cpp.o FAILED: unit_tests/CMakeFiles/tests.dir/test_kmerhashtable.cpp.o /var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/unit_tests/main.cpp:2:10: fatal error: catch2/catch.hpp: No such file or directory
When the missing dep blocker was added it should have been evident that this is totally unrelated to LTO, and removed from the tracker.
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=14bc51e9759c448132391901ff1eb528fe0f5a0c commit 14bc51e9759c448132391901ff1eb528fe0f5a0c Author: Eli Schwartz <eschwartz93@gmail.com> AuthorDate: 2024-04-05 00:37:31 +0000 Commit: Sam James <sam@gentoo.org> CommitDate: 2024-04-07 06:16:09 +0000 sci-biology/kallisto: port to catch2 version 3 Which is the current default distributed version. Nicer than requiring people to downgrade to an old version. Closes: https://bugs.gentoo.org/877887 Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org> sci-biology/kallisto/files/kallisto-0.46.2-catch2.patch | 10 +++++----- sci-biology/kallisto/files/kallisto-0.46.2-cmake.patch | 2 +- sci-biology/kallisto/kallisto-0.46.2.ebuild | 10 +++++++--- 3 files changed, 13 insertions(+), 9 deletions(-)