pamlx

maintainer malacology · 0 votes · scanned 2026-08-03 00:08:14.047287

LOW

Why flagged The source is a tarball from the project's official host (abacus.gene.ucl.ac.uk), which is not on the whitelist but is plausibly legitimate; building from official project source is normal AUR packaging behavior and poses low risk.

Triggered rules

LOW AI review downgraded a static finding llm_review

The static rules flagged this MEDIUM, but an AI model (qwen/qwen3-235b-a22b-07-25) reviewed the full PKGBUILD and judged it LOW (confidence 95%): The source is a tarball from the project's official host (abacus.gene.ucl.ac.uk), which is not on the whitelist but is plausibly legitimate; building from official project source is normal AUR packaging behavior and poses low risk.

1 higher static finding superseded - not the current verdict (shown for transparency)

MEDIUM source=() URL on a non-standard host source_untrusted_domain

One or more source=() URLs point to a host outside the trusted allowlist (github.com, gitlab.com, codeberg.org, pypi.org, …).

PKGBUILD:13 source=("http://abacus.gene.ucl.ac.uk/software/pamlX${pkgver}-src.tgz" "pamlX.desktop" "qt4to5.patch")

PKGBUILD

1 offending line(s) highlighted

      1# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
    
      2pkgname=pamlx
    
      3_pkgname=pamlX
    
      4pkgver=1.3.1
    
      5pkgrel=4
    
      6pkgdesc="A Graphical User Interface for PAML https://doi.org/10.1093/molbev/mst179"
    
      7arch=('x86_64')
    
      8url="http://abacus.gene.ucl.ac.uk/software/"
    
      9license=('custom')
    
      10depends=('qt5-base' 'paml')
    
      11makedepends=('make')
    
      12provides=('pamlx')
    
      13source=("http://abacus.gene.ucl.ac.uk/software/pamlX${pkgver}-src.tgz" "pamlX.desktop" "qt4to5.patch")
    
      14sha256sums=('e6abbbc715aff1d9ebcb6d9b7c2fb494f916bee53f9cf807bf38cebc7bd625bf'
    
      15            'e70746b45dfdde9baa1f38db29474296fbd3cb0a8b1fb685260d6c01f373938b'
    
      16            'f1ae154e78d95f1c6656c9d4d838de825e8ef92b9002803ceed9b2f1445b95e3')
    
      17
    
      18prepare(){
    
      19	cd $_pkgname$pkgver-src
    
      20	patch -p1 < $srcdir/qt4to5.patch
    
      21}
    
      22
    
      23build() {
    
      24	cd $_pkgname$pkgver-src
    
      25	qmake
    
      26	make
    
      27}
    
      28
    
      29package() {
    
      30	mkdir -p $pkgdir/usr/{bin,share/{icons,applications}}
    
      31	install -Dm 755 $_pkgname.desktop $pkgdir/usr/share/applications/$_pkgname.desktop
    
      32	cd $_pkgname$pkgver-src
    
      33	install -Dm 755 $_pkgname $pkgdir/usr/bin/$_pkgname
    
      34	install -Dm755 pamlxlogo.png $pkgdir/usr/share/icons/$_pkgname.png
    
      35}
    
      36
    
      37

Scan history

Scanned at (UTC)	Severity	Rules
2026-08-03 00:08:14	LOW	2
2026-08-02 00:16:08	LOW	2
2026-08-01 00:11:18	LOW	2
2026-07-31 00:14:10	LOW	2
2026-07-30 00:17:23	LOW	2
2026-07-29 00:25:53	LOW	2
2026-07-28 00:07:28	LOW	2
2026-07-27 00:24:32	LOW	2
2026-07-26 00:07:32	LOW	2
2026-07-25 00:13:44	LOW	2
2026-07-24 00:02:28	LOW	2
2026-07-23 00:14:47	LOW	2
2026-07-22 00:29:32	LOW	2
2026-07-21 00:24:15	LOW	2
2026-07-20 00:19:49	LOW	2
2026-07-19 00:17:08	LOW	2
2026-07-18 00:14:48	LOW	2
2026-07-17 00:06:16	LOW	2
2026-07-16 00:05:41	LOW	2
2026-07-15 00:09:25	LOW	2