coot

LOW

maintainer hgonomeg 3 votes scanned 2026-09-17 00:27:14.276658

View on AUR

Why flagged

The package downloads source code and data files from the project maintainer's official academic host; the non-whitelisted domain is plausibly project-owned, and the installed content consists of buildable source and non-executable data, posing minimal supply-chain risk.

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 code and data files from the project maintainer's official academic host; the non-whitelisted domain is plausibly project-owned, and the installed content consists of buildable source and non-executable data, posing minimal supply-chain risk.

1 higher static finding superseded - not the current verdict (shown for transparency)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:15 https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/$pkgname/dependencies/refmac-monomer-library.tar.gz

PKGBUILD

1 offending line(s) highlighted

      1# Maintainer: Jakub Smulski <hgonomeg@gmail.com>
    
      2# Maintainer: Alexander Minges <alexander.minges@gmail.com>
    
      3pkgname=coot
    
      4pkgver=1.3.1
    
      5pkgrel=1
    
      6pkgdesc="Crystallographic Object-Oriented Toolkit for model building, completion and validation"
    
      7arch=('i686' 'x86_64')
    
      8url="https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/"
    
      9license=('GPL')
    
      10replaces=('coot-data')
    
      11makedepends=('autoconf' 'automake' 'libtool' 'eigen' 'boost' 'bc' 'which')
    
      12depends=('eigen' 'openal' 'coordgen' 'maeparser' 'boost-libs' 'guile' 'gemmi' 'libccp4>=6.5.1-2' 'libclipper>=2.1.20170202-3' 'libvorbis' 'fftw2-float' 'gsl' 'swig'
    
      13         'libgl' 'gtk4' 'glib2' 'glm' 'cairo' 'libssm>=1.4' 'zlib' 'curl' 'python' 'python-gobject' 'sqlite' 'rdkit' 'mmdb2>=2.0.12-4')
    
      14source=($pkgname-$pkgver.tar.gz::https://github.com/pemsley/$pkgname/archive/refs/tags/Release-$pkgver.tar.gz
    
      15        https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/$pkgname/dependencies/refmac-monomer-library.tar.gz
    
      16        https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/$pkgname/dependencies/reference-structures.tar.gz
    
      17        )
    
      18
    
      19sha256sums=('39069510b2bd499a407d5cc9202d4df591b353c344dd21aaf30e2ceab8260025'
    
      20            '03562eec612103a48bd114cfe0d171943e88f94b84610d16d542cda138e5f36b'
    
      21            '44db38506f0f90c097d4855ad81a82a36b49cd1e3ffe7d6ee4728b15109e281a'
    
      22            )
    
      23prepare() {	
    
      24  cd "$srcdir/$pkgname-Release-$pkgver"
    
      25  #patch -Np1 -i "$srcdir/glm_nopkgconfig.patch"
    
      26}
    
      27
    
      28build() {
    
      29  cd "$srcdir/$pkgname-Release-$pkgver"
    
      30
    
      31  aclocal -I macros
    
      32  libtoolize --automake --copy
    
      33  autoconf
    
      34  automake --copy --add-missing --gnu
    
      35
    
      36  #CXXFLAGS="${CXXFLAGS} -fpermissive"
    
      37  CXXFLAGS="-Wreturn-type -Wl,--as-needed -Wno-sequence-point -Wsign-compare -Wno-unknown-pragmas -Wno-template-id-cdtor -Wno-deprecated-declarations"
    
      38  PYTHON=python3
    
      39
    
      40  ./configure --prefix=/usr \
    
      41              --disable-static \
    
      42              --with-enhanced-ligand-tools \
    
      43              --with-gemmi=/usr \
    
      44              --with-sound
    
      45  make
    
      46}
    
      47
    
      48package() {
    
      49  cd "$srcdir/$pkgname-Release-$pkgver"
    
      50  make DESTDIR="$pkgdir/" install
    
      51  #sed -i 's|COOT_PYTHON_DIR=|COOT_PYTHON_DIR=/usr/lib/python2.7/site-packages/coot|' src/$pkgname
    
      52  sed -i 's|COOT_REFMAC_LIB_DIR=|COOT_REFMAC_LIB_DIR=/usr/share/coot/lib/|' src/$pkgname
    
      53  install -p -m 755 src/$pkgname $pkgdir/usr/bin
    
      54
    
      55  # remove shebang from python scripts
    
      56  # for lib in $(find $pkgdir/usr/lib/python2.7/site-packages/$pkgname/ -name "*.py"); do
    
      57  #  sed '/\/usr\/bin\/env/d' $lib > $lib.new &&
    
      58  #  touch -r $lib $lib.new &&
    
      59  #  mv $lib.new $lib
    
      60  # done
    
      61
    
      62  # chmod 644 $pkgdir/usr/lib/python2.7/site-packages/$pkgname/$pkgname.py
    
      63
    
      64  install -d $pkgdir/usr/share/$pkgname/reference-structures
    
      65  install -Dm644 $srcdir/reference-structures/*.pdb $pkgdir/usr/share/$pkgname/reference-structures/
    
      66
    
      67  install -d $pkgdir/usr/share/$pkgname/lib/data/monomers
    
      68  cp -r $srcdir/monomers/* $pkgdir/usr/share/$pkgname/lib/data/monomers/
    
      69}
    
      70

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