phylonet-hmm

LOW

maintainer malacology 0 votes scanned 2026-09-17 00:27:14.276658

View on AUR

Why flagged

The package downloads source files and a JAR from the project's official academic website; while the host is non-standard, the content is verifiable via checksums and consists of expected build/data files for a bioinformatics tool.

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 package downloads source files and a JAR from the project's official academic website; while the host is non-standard, the content is verifiable via checksums and consists of expected build/data files for a bioinformatics tool.

1 higher static finding superseded - not the current verdict (shown for transparency)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:19 source=("https://bioinfocs.rice.edu/sites/g/files/bxs266/f/phmm-0.1.tar_0.bz2" "https://bioinfocs.rice.edu/sites/g/files/bxs266/f/phmm_0.jar" "https://bioinfocs.rice.edu/sites/g/files/bxs266/f/simulated-datasets.tar.bz2" "https://bioinfocs.rice.edu/sites/g/files/bxs266/f/empirical-datasets.tar.bz2")

PKGBUILD

1 offending line(s) highlighted

      1# Maintainer: Malacology <guoyizhang at malacology dot com>
    
      2# Contributor: Malacology <guoyizhang at malacology dot com>
    
      3
    
      4pkgname=phylonet-hmm
    
      5_installname=PhyloNet
    
      6pkgver=0.1
    
      7pkgrel=1
    
      8depends=(
    
      9	'jre-openjdk-headless'
    
      10	'jre-openjdk'
    
      11	'jdk-openjdk'
    
      12	'openjdk-doc'
    
      13	'openjdk-src'
    
      14)
    
      15pkgdesc="An HMM-based comparative genomic framework for detecting introgression in eukaryotes"
    
      16arch=('x86_64')
    
      17url="https://bioinfocs.rice.edu/node/108"
    
      18license=('Apache (Software) License 2')
    
      19source=("https://bioinfocs.rice.edu/sites/g/files/bxs266/f/phmm-0.1.tar_0.bz2" "https://bioinfocs.rice.edu/sites/g/files/bxs266/f/phmm_0.jar" "https://bioinfocs.rice.edu/sites/g/files/bxs266/f/simulated-datasets.tar.bz2" "https://bioinfocs.rice.edu/sites/g/files/bxs266/f/empirical-datasets.tar.bz2")
    
      20sha256sums=('a05afde10e6cef5d3b2901c2258dbc11d93f02b2869c8373e678f0d0fdecd8f2'
    
      21            '3acd37b03c535864be0e8255c7035bf2620fa02141851aae61bb7e3552c6f3ed'
    
      22            '92812ad3ea26cb868addd4c2ac64c07037686df7f4e2d205d6144eeb4647cf68'
    
      23            '9cfc7db089d2a645375baf556084cfed74bf8e0f338a006e32651a6caa8d7ee9')
    
      24
    
      25package() {
    
      26    install -dm755 "$pkgdir"/usr/share/phylonet-hmm/{phmm-${pkgver},empirical-datasets,simulated-datasets}
    
      27    install -Dm644 ${srcdir}/phmm_0.jar ${pkgdir}/usr/share/phylonet-hmm/phmm.jar
    
      28    mv ${srcdir}/phmm-${pkgver}/* ${pkgdir}/usr/share/phylonet-hmm/phmm-${pkgver}
    
      29    mv ${srcdir}/data-MWN1287-DGA-C5-SEG1-RN5.REFERENCE.WGS ${pkgdir}/usr/share/phylonet-hmm/empirical-datasets
    
      30    mv ${srcdir}/data-Yu2097m-Yu2120f-C5-SEG1-RN5.REFERENCE.WGS ${pkgdir}/usr/share/phylonet-hmm/empirical-datasets
    
      31    mv ${srcdir}/MS-INTROGRESSION-SIMULATION ${pkgdir}/usr/share/phylonet-hmm/simulated-datasets
    
      32}
    
      33
    
      34

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