Gentoo Websites Logo
Go to: Gentoo Home Documentation Forums Lists Bugs Planet Store Wiki Get Gentoo!

Bug 862717

Summary: sci-libs/h5part-1.6.6-r1 fails to compile (lto): H5Part.c:2095:11: error: too few arguments to function H5Oget_info_by_name3
Product: Gentoo Linux Reporter: Agostino Sarubbo <ago>
Component: Current packagesAssignee: Gentoo Science Related Packages <sci>
Severity: normal CC: gentoo, rossi.f, sci
Priority: Normal Keywords: PMASKED
Version: unspecified   
Hardware: All   
OS: Linux   
Package list:
Runtime testing required: ---
Bug Depends on: 933768    
Bug Blocks: 618550    
Attachments: build.log

Description Agostino Sarubbo gentoo-dev 2022-08-01 07:58:45 UTC

Issue: sci-libs/h5part-1.6.6 fails to compile (lto).
Discovered on: amd64 (internal ref: lto_tinderbox)

This machine uses lto with CFLAGS=-flto -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing

Here is a bit of explanation:

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.

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

Used to find possible runtime issues in packages. These bugs are a problem anyway but may be even worse when combined with LTO.

- 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:
Comment 1 Agostino Sarubbo gentoo-dev 2022-08-01 07:58:47 UTC
Created attachment 796459 [details]

build log and emerge --info
Comment 2 justXi 2022-09-17 15:49:03 UTC
Created attachment 807892 [details, diff]

A patch to overcome the compile errors. 
It compiles fine, but I didnĀ“t check the library if all works.
Comment 3 Fabio Rossi 2023-05-30 14:21:37 UTC
I have used the patch for compiling successfully the package. It fails during test but probably is not related to the patch (see also bug #831092)
Comment 4 Agostino Sarubbo gentoo-dev 2024-04-24 06:38:05 UTC
ci has reproduced this issue with version 1.6.6-r1 - Updating summary.
Comment 5 Larry the Git Cow gentoo-dev 2024-07-12 11:26:57 UTC
The bug has been referenced in the following commit(s):

commit fd84429f87be81d79c634bfa77d716abb34a7626
Author:     Arthur Zamarin <>
AuthorDate: 2024-07-12 11:24:50 +0000
Commit:     Arthur Zamarin <>
CommitDate: 2024-07-12 11:24:50 +0000

    sci-libs/h5part: treeclean
    Signed-off-by: Arthur Zamarin <>

 profiles/package.mask                         |  6 ------
 sci-libs/h5part/Manifest                      |  1 -
 sci-libs/h5part/files/h5part-1.6.6-mpio.patch | 26 -------------------------
 sci-libs/h5part/h5part-1.6.6-r1.ebuild        | 28 ---------------------------
 sci-libs/h5part/metadata.xml                  |  8 --------
 5 files changed, 69 deletions(-)