dev-python/pybedtools: version bump 0.11.0 and enable docs

[mschubert]

No description provided.

[Nowa-Ammerlaan]

dependency on cython is not required when DISTUTILS_EXT=1 is set

[mschubert]

I've removed this and am now getting a QA Notice:

• QA Notice: Package seems to be missing a BDEPEND on dev-python/cython.

[Nowa-Ammerlaan]

Then please check if you are using the most recent version of the eclass.

[mschubert]

I have the main tree synced at 2025-01-27 11:18:44 UTC, so this should include the latest distutils-r1 eclass. I still get the QA notice

[Nowa-Ammerlaan]

0x55c30ed92fbf internal_error(char const*, ...)
???:0
0x55c30d335cf8 read_cgraph_and_symbols(unsigned int, char const**)
???:0
0x55c30d2f9807 lto_main()
???:0
Please submit a full bug report, with preprocessed source (by using -freport-bug).
Please include the complete backtrace with any bug report.
See <https://bugs.gentoo.org/> for instructions.
lto-wrapper: fatal error: /usr/bin/x86_64-pc-linux-gnu-g++ returned 1 exit status
compilation terminated.

It fails to build on my end

[mschubert]

Was this with USE=doc?

I realized I misunderstood how I still have to set this flag for sphinx, so that is likely broken (looking into it)

[Nowa-Ammerlaan]

Was this with USE=doc?

I realized I misunderstood how I still have to set this flag for sphinx, so that is likely broken (looking into it)

It was, but not sure if the error originates from sphinx.

[mschubert]

I've disabled the docs again, making this a simple version bump.

I don't know where the compile error comes from, does the current ebuild compile fine? And/or does reinstalling sci-biology/bedtools solve the problem? In this case, I'd think I'd have to add sci-biology/bedtools:0= to RDEPEND

[Nowa-Ammerlaan]

It's still failing, looks like an lto issue, please try to build it with lto enabled on your end.

[mschubert]

I can confirm this is broken with -flto, but this already happens with the previous version 0.10.0.

I've got no idea how to debug this.

[Nowa-Ammerlaan]

I can confirm this is broken with -flto, but this already happens with the previous version 0.10.0.

I've got no idea how to debug this.

Don't bother, just add filter-lto to the ebuild to ensure the lto flags are removed if they are present.

[mschubert]

Added in the current commit

[Nowa-Ammerlaan]

Thanks 👍