https://blogs.gentoo.org/ago/2020/07/04/gentoo-tinderbox/ Issue: sci-chemistry/pymol-2.5.0-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 795967 [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: fatal: not a git repository (or any parent up to mount point /var/tmp) contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:62:16: error: type ‘struct parm’ violates the C++ One Definition Rule [-Werror=odr]
lto_tinderbox has reproduced this issue with version 2.5.0-r4 - Updating summary.
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=dfe0f62750dadf6273bd4146db194c7165181781 commit dfe0f62750dadf6273bd4146db194c7165181781 Author: Alexey Shvetsov <alexxy@gentoo.org> AuthorDate: 2024-05-17 19:20:35 +0000 Commit: Alexey Shvetsov <alexxy@gentoo.org> CommitDate: 2024-05-17 19:20:35 +0000 sci-chemistry/pymol: Update to 3.0.0 and drop old Closes: https://bugs.gentoo.org/862441 Closes: https://bugs.gentoo.org/910511 Closes: https://bugs.gentoo.org/929762 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org> sci-chemistry/pymol/Manifest | 2 +- sci-chemistry/pymol/pymol-2.5.0-r3.ebuild | 100 --------------------- .../{pymol-2.5.0-r5.ebuild => pymol-3.0.0.ebuild} | 9 +- 3 files changed, 6 insertions(+), 105 deletions(-)
Alexey, did you check and reproduce the problem with the old version using the described CFLAGS / CXXFLAGS / LDFLAGS before assuming this was fixed?
Now that I actually reported it upstream, it has been fixed quite fast. :) https://github.com/schrodinger/pymol-open-source/commit/9d3061ca58d8b69d7dad74a68fc13fe81af0ff8e
