phast

LOW

maintainer vejnar 1 votes scanned 2026-09-17 00:27:14.276658

View on AUR

Why flagged

The non-standard host (netlib.org) hosts CLAPACK, a legitimate scientific computing library, used as a build dependency; the main code is from the project's official GitHub, and no untrusted executables are run.

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 non-standard host (netlib.org) hosts CLAPACK, a legitimate scientific computing library, used as a build dependency; the main code is from the project's official GitHub, and no untrusted executables are run.

1 higher static finding superseded - not the current verdict (shown for transparency)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:10 source=("http://www.netlib.org/clapack/clapack.tgz"

PKGBUILD

1 offending line(s) highlighted

      1# Maintainer: Charles Vejnar <first name [dot] last name [at] gmail [dot] com>
    
      2
    
      3pkgname=phast
    
      4pkgver=1.7
    
      5pkgrel=1
    
      6pkgdesc="Phylogenetic analysis with space/time models"
    
      7arch=("x86_64")
    
      8url="http://compgen.bscb.cornell.edu/phast"
    
      9license=("BSD")
    
      10source=("http://www.netlib.org/clapack/clapack.tgz"
    
      11        "$pkgname-$pkgver.tar.gz::https://github.com/CshlSiepelLab/phast/archive/refs/tags/v${pkgver}.tar.gz"
    
      12        "stdio.patch"
    
      13        "stdio_blas.patch"
    
      14        "tstiee.patch")
    
      15sha256sums=('6dc4c382164beec8aaed8fd2acc36ad24232c406eda6db462bd4c41d5e455fac'
    
      16            '710e71f201cfb6c263ccb9ab38f4e63bc50f2fe16405c1e4562f6d737c7ca9eb'
    
      17            'cd9817d19b6d4824ba1e72c55ada20a43c677a22d086b7ab0f014968a17eb758'
    
      18            'ff6d3e320044079426d323589ce36feb1c52213a011e4fb0ecf72daf68c115a9'
    
      19            'daeb183a38b15e8428ec5007718c867fbbaa7731f9b5dbe12025d299298d017f')
    
      20
    
      21prepare() {
    
      22    # Apply patches
    
      23    cd "${srcdir}/CLAPACK-3.2.1"
    
      24    patch -p1 -i "${srcdir}/stdio.patch"
    
      25    patch -p1 -i "${srcdir}/stdio_blas.patch"
    
      26    patch -p1 -i "${srcdir}/tstiee.patch"
    
      27}
    
      28
    
      29build() {
    
      30    # Build CLAPACK
    
      31    cd "$srcdir/CLAPACK-3.2.1"
    
      32    cp make.inc.example make.inc
    
      33    make f2clib
    
      34    make blaslib
    
      35    make lib
    
      36
    
      37    # Build Phast
    
      38    cd "$srcdir/phast-${pkgver}/src"
    
      39    make CLAPACKPATH="$srcdir/CLAPACK-3.2.1"
    
      40}
    
      41
    
      42package() {
    
      43    cd "$srcdir/phast-${pkgver}/bin"
    
      44    for fname in $(ls -1); do
    
      45        install -Dm755 $fname "$pkgdir/usr/bin/$fname"
    
      46    done
    
      47    cd "$srcdir/phast-${pkgver}/doc/man"
    
      48    for fname in $(ls -1); do
    
      49        install -Dm644 $fname "$pkgdir/usr/share/man/man1/$fname"
    
      50    done
    
      51}
    
      52

Scan history

Scanned at (UTC)	Severity	Rules
2026-09-17 00:27:14	Low	2
2026-09-16 00:03:17	Low	2
2026-09-15 00:25:31	Low	2
2026-09-14 00:27:57	Low	2
2026-09-13 00:19:54	Low	2
2026-09-12 00:25:17	Low	2
2026-09-11 00:19:22	Low	2
2026-09-10 00:22:44	Low	2
2026-09-09 00:04:09	Low	2
2026-09-08 00:18:08	Low	2
2026-09-07 00:30:15	Low	2
2026-09-06 00:17:06	Low	2
2026-09-05 00:16:27	Low	2
2026-09-04 00:03:13	Low	2
2026-09-03 00:15:47	Low	2
2026-09-02 00:02:31	Low	2
2026-09-01 00:11:19	Low	2
2026-08-31 00:19:57	Low	2
2026-08-30 00:04:14	Low	2
2026-08-29 00:29:17	Low	2