hisat2-bin

LOW

maintainer Chocobo1 0 votes scanned 2026-09-17 00:27:14.276658

View on AUR

Why flagged

The package downloads a prebuilt binary from a university-hosted cloud service, which is not on standard whitelists but is plausibly affiliated with the project; the worst case of a swapped source is limited to code execution from an unofficial binary, but the context suggests it is intended to be the official release.

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 a prebuilt binary from a university-hosted cloud service, which is not on standard whitelists but is plausibly affiliated with the project; the worst case of a swapped source is limited to code execution from an unofficial binary, but the context suggests it is intended to be the official release.

1 higher static finding superseded - not the current verdict (shown for transparency)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:14 source_x86_64=("https://cloud.biohpc.swmed.edu/index.php/s/oTtGWbWjaxsQ2Ho/download")

PKGBUILD

1 offending line(s) highlighted

      1# Maintainer: Chocobo1 <chocobo1 AT archlinux DOT net>
    
      2
    
      3pkgname=hisat2-bin
    
      4pkgver=2.2.2
    
      5pkgrel=2
    
      6pkgdesc="A fast and sensitive alignment program for mapping sequencing reads"
    
      7arch=('x86_64')
    
      8url="https://daehwankimlab.github.io/hisat2/"
    
      9license=('GPL-3.0-or-later')
    
      10depends=('libgcc' 'libstdc++' 'glibc')
    
      11optdepends=('perl' 'python')
    
      12provides=("hisat2=$pkgver")
    
      13conflicts=('hisat2')
    
      14source_x86_64=("https://cloud.biohpc.swmed.edu/index.php/s/oTtGWbWjaxsQ2Ho/download")
    
      15sha256sums_x86_64=('ae53af930729787a126944f7db34d4065c06f589c4fb05f4cfa9a348cacd5cb4')
    
      16
    
      17
    
      18package() {
    
      19  cd "hisat2-2.2.1"
    
      20
    
      21  install -Dm755 hisat2{,-*} -t "$pkgdir/usr/bin"
    
      22  rm "$pkgdir/usr/bin"/*-debug
    
      23
    
      24  install -Dm644 {MANUAL.markdown,TUTORIAL} -t "$pkgdir/usr/share/doc/hisat2"
    
      25}
    
      26

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