tmtools

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

LOW

Why flagged The source is a tarball from the project's official academic host for a legitimate bioinformatics tool, building from source; the host is non-whitelisted but plausibly official, and no untrusted prebuilt binaries are used.

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 host for a legitimate bioinformatics tool, building from source; the host is non-whitelisted but plausibly official, and no untrusted prebuilt binaries are used.

1 higher static finding superseded - not the current verdict (shown for transparency)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:11 source=("http://zhanglab.ccmb.med.umich.edu/TM-align/${_pkgname}${pkgver}.tar.gz"

PKGBUILD

1 offending line(s) highlighted

      1# Maintainer: Athemis <alexander.minges[at]googlemail[dot]com>
    
      2pkgname=tmtools
    
      3_pkgname=TMtools
    
      4pkgver=20170708
    
      5pkgrel=1
    
      6pkgdesc="TM-align is a computer algorithm for protein structure alignment using dynamic programming and TM-score rotation matrix"
    
      7url="http://zhanglab.ccmb.med.umich.edu/TM-align/"
    
      8arch=('x86_64' 'i686')
    
      9license=('custom')
    
      10makedepends=('gcc-fortran')
    
      11source=("http://zhanglab.ccmb.med.umich.edu/TM-align/${_pkgname}${pkgver}.tar.gz"
    
      12        "LICENSE")
    
      13
    
      14sha256sums=('bb67e0924f34dc6f427de5f14734e3daa13be9f0394504efc8d5938da575f58d'
    
      15            '6702b261d43b8ce84af0aecabb2ff3c8a4187204f65b0b60c8d5fb5b9f24961b')
    
      16
    
      17prepare() {
    
      18cd "${srcdir}"
    
      19  # Remove pre-built binaries
    
      20  rm TMalign
    
      21  rm TMscore    
    
      22}
    
      23
    
      24build() {
    
      25  cd "${srcdir}"
    
      26  gfortran -march=native -O3 -pipe -ffast-math -lm -o TMalign TMalign.f
    
      27  gfortran -march=native -O3 -pipe -ffast-math -lm -o TMscore TMscore.f 
    
      28}
    
      29
    
      30package() {
    
      31  cd "${srcdir}"
    
      32  install -d ${pkgdir}/usr/bin
    
      33  install -d ${pkgdir}/usr/share/licenses/${pkgname}
    
      34  install -Dm755 TMalign ${pkgdir}/usr/bin
    
      35  install -Dm755 TMscore ${pkgdir}/usr/bin
    
      36  install -Dm644 LICENSE ${pkgdir}/usr/share/licenses/${pkgname}
    
      37}
    
      38
    
      39# vim:set ts=2 sw=2 et:
    
      40

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