Package Details: plink1.9-git 1:1.9.b.7.11.r65.g0afaeb9f-1

Git Clone URL: https://aur.archlinux.org/plink1.9-git.git (read-only, click to copy)
Package Base: plink1.9-git
Description: whole-genome association analysis toolset, version 1.9
Upstream URL: https://www.cog-genomics.org/plink/1.9/
Keywords: genomics gwas plink
Licenses: GPL-3.0-only
Provides: plink1.9
Submitter: viralstitch
Maintainer: adityaruplaha
Last Packager: adityaruplaha
Votes: 2
Popularity: 0.000000
First Submitted: 2018-10-27 18:32 (UTC)
Last Updated: 2025-12-29 07:12 (UTC)

Latest Comments

adityaruplaha commented on 2025-12-26 17:39 (UTC) (edited on 2025-12-26 17:47 (UTC) by adityaruplaha)

Ah, my bad, missed the modification date on the Makefile. I'll push an update to the package so that AUR helpers know to update.

Also, thanks for pointing out the RFC, I was unaware of LTO-by-default.

chrchang523 commented on 2025-12-26 16:43 (UTC)

You are incorrect, -flto was nowhere to be found in the plink 1.9 compilation flags in the broken Aug 2025 build. It's added by default when compiling for Arch; see https://rfc.archlinux.page/0004-lto-by-default/ for when this was introduced.

-flto is present NOW because my Nov 2025 investigation was successful, and a very small code change was sufficient to address the LTO miscompilation; see https://github.com/chrchang/plink-ng/issues/313 for more details. So the simplest fix now is to recompile off the current GitHub source.

adityaruplaha commented on 2025-12-26 14:49 (UTC)

@chrchang523 Apologies for the delay. I believe you'd need to disable -flto upstream; the package itself doesn't modify core compilation flags beyond what is necessary for compilation on Arch.

chrchang523 commented on 2025-11-21 20:58 (UTC)

plink 1.9 and 2.0 are known to compile incorrectly with -flto. I will be investigating whether it is now practical to fix this, but in the meantime it is necessary to disable LTO for this (and the corresponding plink 2.0) package to work correctly.

adityaruplaha commented on 2025-08-27 13:54 (UTC)

I decided using --match is probably the way to go; better safe than sorry. Also, it looks like the convention is r#.g..., so I switched back to that.

adityaruplaha commented on 2025-08-25 07:10 (UTC) (edited on 2025-08-25 07:13 (UTC) by adityaruplaha)

I believe with how the upstream repo is structured, the 1.9/ folder should only ever yield tags matching v1.9*. Still, will check in detail.

Also, would it be more appropriate to have r#_g... or r#.g... in the pkgver()?

a821 commented on 2025-08-25 06:48 (UTC)

Thanks for updating!

Concerning the version, it really looks like upstream never heard of branches... I suggest to pass the --match option to git describe to match only the 1.9 tags in pkgver(), for example (the rest of the line is omitted).

git describe --long --tags --match='v1.9*' | sed ...

adityaruplaha commented on 2025-08-24 12:08 (UTC) (edited on 2025-08-24 14:13 (UTC) by adityaruplaha)

I'm still not sure if this is the correct way to version given what upstream does.

adityaruplaha commented on 2025-08-24 12:08 (UTC)

Should be fixed now, along with versioning updates from upstream.

a821 commented on 2025-08-22 10:59 (UTC)

Hi, this needs git in makedepends, otherwise I cannot compile it in a clean chroot.