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Update lima: set binary_relocation: False to fix EL8 segfault #44388

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merged 1 commit into from
Nov 22, 2023

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nathanweeks
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lima consistently segfaults on EL8 (RHEL 8, Rocky Linux 8, etc.) due to an interaction with patchelf --set-rpath (possibly for certain versions of patchelf?) and the kernel version used by EL8. This PR disables such binary relocation ordinarily performed by conda-build, resulting in the packaging of unmodified PacBio-built lima executables.

Tested locally (bioconda-utils build --packages lima) on Rocky 8.

Reference: PacificBiosciences/pbbioconda#557 (comment)

@nathanweeks
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@BiocondaBot please fetch artifacts

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Package(s) built on Azure are ready for inspection:

Arch Package Zip File
linux-64 lima-2.9.0-h9ee0642_1.tar.bz2 LinuxArtifacts

You may also use conda to install these after downloading and extracting the appropriate zip file. From the LinuxArtifacts or OSXArtifacts directories:

conda install -c ./packages <package name>

Docker image(s) built (images are in the LinuxArtifacts zip file above):

Package Tag Install with docker
lima 2.9.0--h9ee0642_1
showgzip -dc LinuxArtifacts/images/lima:2.9.0--h9ee0642_1.tar.gz | docker load

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@BiocondaBot please add label

@BiocondaBot BiocondaBot added the please review & merge set to ask for merge label Nov 21, 2023
@nathanweeks
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lima-2.9.0-h9ee0642_1.tar.bz2 works for me on EL8:

(lima) $ lima --version
lima 2.9.0

Using:
  lima      : 2.9.0 (commit v2.9.0)
  pbbam     : 2.5.0 (commit v2.5.0)
  pbcopper  : 2.4.0 (commit v2.4.0)
  boost     : 1.81
  htslib    : 1.17
  zlib      : 1.2.13

@mencian mencian merged commit 9daf843 into bioconda:master Nov 22, 2023
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@nathanweeks nathanweeks deleted the lima branch November 22, 2023 01:54
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4 participants