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add patch to fix integer overflow bug in scikit-bio v0.6.2#24233

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branfosj merged 1 commit intoeasybuilders:developfrom
gkaf89:20251014112959_new_pr_scikit-bio062
Oct 14, 2025
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add patch to fix integer overflow bug in scikit-bio v0.6.2#24233
branfosj merged 1 commit intoeasybuilders:developfrom
gkaf89:20251014112959_new_pr_scikit-bio062

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@gkaf89 gkaf89 commented Oct 14, 2025 •
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This PR back-ports a fix for an integer overflow bug in Cython that is caught during installation by the test suite.

The bug causes segmentation faults when creating large interval trees.

@gkaf89 gkaf89 changed the title Fix integer overflow bug Fix integer overflow bug in scikit-bio v0.6.2 Oct 14, 2025
@gkaf89 gkaf89 mentioned this pull request Oct 14, 2025
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branfosj commented Oct 14, 2025

@boegelbot please test @ jsc-zen3

@branfosj branfosj added this to the next release (5.2.0?) milestone Oct 14, 2025
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boegelbot commented Oct 14, 2025

@branfosj: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=24233 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_24233 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 8352

Test results coming soon (I hope)...

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Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

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boegelbot commented Oct 14, 2025

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/82fb1bebe55a68c38268e6ab686cdb00 for a full test report.

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branfosj commented Oct 14, 2025

Test report by @branfosj
SUCCESS
Build succeeded for 4 out of 4 (1 easyconfigs in total)
bear-pg0105u03a - Linux RHEL 8.10, x86_64, Intel(R) Xeon(R) Platinum 8360Y CPU @ 2.40GHz (icelake), Python 3.6.8
See https://gist.github.com/branfosj/f7cb0791962db49f6e54a59264cc12f9 for a full test report.

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branfosj commented Oct 14, 2025

Going in, thanks @gkaf89!

@branfosj branfosj merged commit 868fec6 into easybuilders:develop Oct 14, 2025
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@gkaf89 gkaf89 deleted the 20251014112959_new_pr_scikit-bio062 branch November 17, 2025 14:41
@boegel boegel changed the title Fix integer overflow bug in scikit-bio v0.6.2 add patch to fix integer overflow bug in scikit-bio v0.6.2 Nov 19, 2025
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