Bug 877887 – sci-biology/kallisto-0.46.2 fails to compile: main.cpp:2:10: fatal error: catch.hpp: No such file or directory

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Agostino Sarubbo 2022-10-22 07:41:29 UTC]

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

[Comment 1 Agostino Sarubbo 2022-10-22 07:41:32 UTC]

Created attachment 824997 [details]
build.log

build log and emerge --info

[Comment 2 Agostino Sarubbo 2022-10-22 07:41:33 UTC]

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

[Comment 3 Eli Schwartz 2024-04-05 00:36:06 UTC]

When the missing dep blocker was added it should have been evident that this is totally unrelated to LTO, and removed from the tracker.

[Comment 4 Larry the Git Cow 2024-04-07 06:17:35 UTC]

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 <[e-mail]>
AuthorDate: 2024-04-05 00:37:31 +0000
Commit:     Sam James <[e-mail]>
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 <[e-mail]>
    Signed-off-by: Sam James <[e-mail]>

 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(-)