hisat2-bin

maintainer Chocobo1 · 0 votes · scanned 2026-08-03 00:08:14.047287

LOW

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1 higher static finding superseded - not the current verdict (shown for transparency)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