fragrep

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

LOW

Why flagged The source is a tarball from the project's official academic domain, building the project's own code; the non-whitelisted host is plausibly legitimate, and no untrusted executable is 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 source is a tarball from the project's official academic domain, building the project's own code; the non-whitelisted host is plausibly legitimate, and no untrusted executable is 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1 higher static finding superseded - not the current verdict (shown for transparency)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:14 source=(http://www.bioinf.uni-leipzig.de/Software/fragrep/fragrep-${pkgver}.tar.gz

PKGBUILD

1 offending line(s) highlighted

      1# Maintainer: Ronny Lorenz <ronny at tbi dot univie dot ac dot at>
    
      2
    
      3pkgname=fragrep
    
      4pkgver=2
    
      5pkgrel=1
    
      6pkgdesc="Detect nucleotide pattern fragments in genomes that occur in a given order"
    
      7arch=('x86_64' 'i686')
    
      8license=('GPL2')
    
      9url="https://www.bioinf.uni-leipzig.de/Software/fragrep/"
    
      10depends=()
    
      11optdepends=()
    
      12makedepends=()
    
      13provides=()
    
      14source=(http://www.bioinf.uni-leipzig.de/Software/fragrep/fragrep-${pkgver}.tar.gz
    
      15        buildfix.patch)
    
      16md5sums=( '1b33fdeb039a65f98c26bc738c81c14e'
    
      17          '0c5606ea4b4a0b79b1df729ed5a32840')
    
      18
    
      19prepare() {
    
      20  cd "${srcdir}/${pkgname}-${pkgver}"
    
      21  patch -p1 < ../buildfix.patch
    
      22}
    
      23
    
      24build() {
    
      25  cd "${srcdir}/${pkgname}-${pkgver}"
    
      26  make release || return 1
    
      27}
    
      28
    
      29package() {
    
      30  cd "${srcdir}/${pkgname}-${pkgver}"
    
      31
    
      32  # install binaries
    
      33  install -Dm755 fragrep "${pkgdir}/usr/bin/fragrep"
    
      34  install -Dm755 pattern2eps "${pkgdir}/usr/bin/pattern2eps"
    
      35  install -Dm755 aln2pattern "${pkgdir}/usr/bin/aln2pattern"
    
      36  install -Dm755 alimatch "${pkgdir}/usr/bin/alimatch"
    
      37  install -Dm755 snglnaln "${pkgdir}/usr/bin/snglnaln"
    
      38  install -Dm755 fragexpand "${pkgdir}/usr/bin/fragexpand"
    
      39  install -Dm755 fasplit "${pkgdir}/usr/bin/fasplit"
    
      40  
    
      41
    
      42  # install manpages
    
      43  for man in man/*.1
    
      44  do
    
      45    file=`basename $man`
    
      46    install -Dm644 ${man} "${pkgdir}/usr/share/man/man1/${file}"
    
      47  done
    
      48
    
      49  # install documentation
    
      50  install -Dm644 doc/fragrep-tutorial.html "${pkgdir}/usr/share/doc/${pkgname}/fragrep-tutorial"
    
      51  install -Dm644 doc/fragrep.css "${pkgdir}/usr/share/doc/${pkgname}/fragrep.css"
    
      52  install -Dm644 doc/YRNA.aln "${pkgdir}/usr/share/doc/${pkgname}/YRNA.aln"
    
      53  install -Dm644 doc/X.fa "${pkgdir}/usr/share/doc/${pkgname}/X.fa"
    
      54
    
      55}
    
      56
    
      57

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