namd

LOW

maintainer michael_wzq 2 votes scanned 2026-09-17 00:27:14.276658

View on AUR

Why flagged

The package downloads a source tarball from a non-whitelisted but plausibly project-owned academic host (charm.cs.illinois.edu) for building the software, which is a normal AUR practice; the main source is locally provided, and all actions are part of standard build procedures without evidence of malicious behavior.

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 source tarball from a non-whitelisted but plausibly project-owned academic host (charm.cs.illinois.edu) for building the software, which is a normal AUR practice; the main source is locally provided, and all actions are part of standard build procedures without evidence of malicious behavior.

1 higher static finding superseded - not the current verdict (shown for transparency)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:29 source=("http://charm.cs.illinois.edu/distrib/charm-${_charmver}.tar.gz"

PKGBUILD

1 offending line(s) highlighted

      1# Maintainer: Viktor Drobot (aka dviktor) linux776 [at] gmail [dot] com
    
      2
    
      3pkgname=namd
    
      4pkgver=3.0.1
    
      5_charmver=8.0.0
    
      6pkgrel=1
    
      7pkgdesc="Scalable molecular dynamic engine"
    
      8url="http://www.ks.uiuc.edu/Research/namd/"
    
      9license=(LicenseRef-NAMD)
    
      10arch=(x86_64)
    
      11depends=(
    
      12	bash
    
      13	fftw
    
      14	gcc-libs
    
      15	glibc
    
      16	perl
    
      17	python-numpy
    
      18	python-scipy
    
      19	tcl
    
      20	zlib
    
      21)
    
      22makedepends=(gcc make patch)
    
      23b2sums=('e12efa3b229b4568bea586f3fe613ec1b0561c946e4fd0c06f937e95eac0c6d1f266cf95e26feac46a5257645ba3671e433f306ea4ede783c2883f1db5613f82'
    
      24        '21c13ba66436c11721f0a20abf13a32cb4e89908e71bff53022adcbbf0984c8a88f2b27e51a7086d873aa17164ae8865d440d08cc1281838d6ac7cdb38eb9110'
    
      25        '04d8df9bacbbd1cf6718a591b52686623cb9be3884c023ff4c70c2d6d4524003ebea132dbfb75fd345dd2ae97115ae66fc69deaf59a9803870ab95abb0e88535')
    
      26options=(!buildflags)
    
      27
    
      28# You MUST download the package from the NAMD url and put it in the PKGBUILD folder!
    
      29source=("http://charm.cs.illinois.edu/distrib/charm-${_charmver}.tar.gz"
    
      30        "local://NAMD_${pkgver}_Source.tar.gz"
    
      31        "Make.charm.patch")
    
      32
    
      33prepare() {
    
      34  # cd "${srcdir}/NAMD_${pkgver}_Source" || exit
    
      35
    
      36  # move Charm++ in place
    
      37  cp -ru "${srcdir}/charm-${_charmver}" "${srcdir}/NAMD_${pkgver}_Source/charm-${_charmver}"
    
      38
    
      39  # apply patch
    
      40  # patch -Np0 -i "${srcdir}/namd.patch"
    
      41
    
      42	# apply patch
    
      43	patch "${srcdir}/NAMD_${pkgver}_Source/Make.charm" ../Make.charm.patch
    
      44}
    
      45
    
      46build() {
    
      47  # build Charm++
    
      48  cd "${srcdir}/NAMD_${pkgver}_Source/charm-${_charmver}" || exit
    
      49
    
      50  ./build charm++ "multicore-linux-${CARCH}" --with-production --force
    
      51
    
      52  # go to the NAMD build
    
      53  cd "${srcdir}/NAMD_${pkgver}_Source" || exit
    
      54
    
      55  # configure and build NAMD
    
      56	# remove old directory
    
      57	rm -rf "${srcdir}/NAMD_${pkgver}_Source/Linux-${CARCH}-g++"
    
      58  ./config "Linux-${CARCH}-g++" --charm-arch "multicore-linux-${CARCH}" --tcl-prefix /usr --fftw-prefix /usr --with-fftw3
    
      59  cd "Linux-${CARCH}-g++" || exit
    
      60  make
    
      61}
    
      62
    
      63package() {
    
      64  cd "${srcdir}/NAMD_${pkgver}_Source/Linux-${CARCH}-g++" || exit
    
      65
    
      66  make release
    
      67
    
      68  # prepare directories
    
      69  mkdir -p "${pkgdir}/usr/bin"
    
      70  mkdir -p "${pkgdir}/usr/share/${pkgname}"
    
      71
    
      72  cd "NAMD_${pkgver}_Linux-${CARCH}-multicore" || exit
    
      73
    
      74  # install binaries
    
      75  install -Dm755 charmrun "${pkgdir}/usr/bin/charmrun"
    
      76  install -Dm755 flipbinpdb "${pkgdir}/usr/bin/flipbinpdb"
    
      77  install -Dm755 flipdcd "${pkgdir}/usr/bin/flipdcd"
    
      78  install -Dm755 namd3 "${pkgdir}/usr/bin/namd3"
    
      79  install -Dm755 psfgen "${pkgdir}/usr/bin/psfgen"
    
      80  install -Dm755 sortreplicas "${pkgdir}/usr/bin/sortreplicas"
    
      81
    
      82  # install license
    
      83  install -Dm644 license.txt "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE"
    
      84
    
      85  # install other stuff
    
      86  cp -ar lib README.txt announce.txt notes.txt "${pkgdir}/usr/share/${pkgname}/"
    
      87}
    
      88

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