https://blogs.gentoo.org/ago/2020/07/04/gentoo-tinderbox/ Issue: sci-biology/samtools-0.1.20-r4 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 795772 [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: <artificial>:(.text+0x747a): undefined reference to `update_posmap' collect2: error: ld returned 1 exit status
The bug has been referenced in the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=633606351dc15e89b2392510a297928f45c724a0 commit 633606351dc15e89b2392510a297928f45c724a0 Author: David Seifert <soap@gentoo.org> AuthorDate: 2023-04-06 19:29:10 +0000 Commit: David Seifert <soap@gentoo.org> CommitDate: 2023-04-06 19:29:10 +0000 package.mask: Last rite dev-perl/Bio-SamTools, sci-biology/samtools:0.1-legacy Closes: https://github.com/gentoo/gentoo/pull/30502 Bug: https://bugs.gentoo.org/862288 Signed-off-by: David Seifert <soap@gentoo.org> profiles/package.mask | 7 +++++++ 1 file changed, 7 insertions(+)
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f8ed4029d610b62eb95b85692efd9396ab8fd933 commit f8ed4029d610b62eb95b85692efd9396ab8fd933 Author: David Seifert <soap@gentoo.org> AuthorDate: 2023-05-05 09:19:58 +0000 Commit: David Seifert <soap@gentoo.org> CommitDate: 2023-05-05 09:19:58 +0000 sci-biology/samtools: drop 0.1.20-r4 Closes: https://bugs.gentoo.org/862288 Signed-off-by: David Seifert <soap@gentoo.org> profiles/package.mask | 6 - sci-biology/samtools/Manifest | 1 - .../files/samtools-0.1.20-buildsystem.patch | 206 --------------------- sci-biology/samtools/samtools-0.1.20-r4.ebuild | 73 -------- 4 files changed, 286 deletions(-)
