phylonet-hmm

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

LOW

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1 higher static finding superseded - not the current verdict (shown for transparency)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
2026-08-03 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