• Bug#1105180: pique: depends on unavailable plink1.9 on arm64

    From =?utf-8?Q?=C3=89tienne?= Mollier@21:1/5 to All on Tue May 13 19:00:01 2025
    Hi Chris, Hi Release Team,

    Chris, thanks for watching us! I happen to have had a look at
    an eventual portability of plink1.9 to arm64 yesterday evening
    and my assessment is that it could only be a matter of adjusting
    detection of sse2 support by adding the missing macro at a few
    tactical points. However, it is also likely that I will run
    into the following autopkgtest error on arm64 if I don't get my
    patch right:

    PLINK v1.9.0-b.7.7 32-bit (22 Oct 2024) cog-genomics.org/plink/1.9/
    (C) 2005-2024 Shaun Purcell, Christopher Chang GNU General Public License v3
    Logging to plink.log.
    Options in effect:
    --file toy
    --freq

    128742 MB RAM detected; reserving 2047 MB for main workspace.
    .ped scan complete (for binary autoconversion).
    Performing single-pass .bed write (2 variants, 2 people).
    94%malloc(): invalid size (unsorted)
    qemu: uncaught target signal 6 (Aborted) - core dumped
    Aborted

    There are some comments in the code about misalignment issues
    around a malloc invocation. I can check tonight if I actually
    get somewhere with that strategy.

    Alternatively, if inclusion of plink1.9 in arm64 is not an
    option, then I suppose there is also the possibility to revert
    to pique 1.0 and inline the missing dataset necessary to resolve
    #1104275 into the debian/ directory instead of the upstream data
    introduced in 1.1; I think the dependency of plink1.9 came along
    with v1.1 while v1.0 worked fine with the older plain plink
    package.

    Have a nice day, :)
    --
    .''`. Étienne Mollier <emollier@debian.org>
    : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
    `. `' sent from /dev/pts/3, please excuse my verbosity
    `-

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