emboss

maintainer mschu · 21 votes · scanned 2026-08-03 00:08:14.047287

LOW

Why flagged The source is a tarball from a plausibly project-owned FTP host (emboss.open-bio.org), building from official source; the non-whitelisted host is not inherently dangerous as it is the project's official distribution point.

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 a plausibly project-owned FTP host (emboss.open-bio.org), building from official source; the non-whitelisted host is not inherently dangerous as it is the project's official distribution point.

1 higher static finding superseded - not the current verdict (shown for transparency)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:16 source=("ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-$pkgver.tar.gz")

PKGBUILD

1 offending line(s) highlighted

      1# Maintainer: Michael Schubert <mschu.dev at gmail>
    
      2# Contributor: moostik <mooostik_at_gmail.com>
    
      3# Contributor: mick elliot <micke@sfu.ca>
    
      4pkgname=emboss
    
      5_pkgname=EMBOSS
    
      6pkgver=6.6.0
    
      7pkgrel=3
    
      8pkgdesc="A collection of molecular biology applications"
    
      9arch=('x86_64' 'i686')
    
      10url="http://emboss.sourceforge.net/"
    
      11depends=('gd' 'pcre' 'java-runtime')
    
      12optdepends=('libmariadbclient' 'postgresql-libs')
    
      13makedepends=('libmariadbclient' 'postgresql-libs' 'java-environment')
    
      14options=('!libtool')
    
      15license=('GPL2')
    
      16source=("ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-$pkgver.tar.gz")
    
      17sha256sums=('7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e')
    
      18
    
      19build() {
    
      20  cd "$srcdir/$_pkgname-$pkgver"
    
      21
    
      22  ./configure --prefix=/usr --enable-large --with-x
    
      23
    
      24  sed -i 's|$(bindir)/embossupdate|:|' Makefile
    
      25  JAVA_CFLAGS="-I$JAVA_HOME/include -I$JAVA_HOME/include/linux" make
    
      26}
    
      27
    
      28package() {
    
      29  cd "$srcdir/$_pkgname-$pkgver"
    
      30
    
      31  make DESTDIR="$pkgdir" install
    
      32
    
      33  # provided pcre headers conflict with pcre
    
      34  mv "$pkgdir"/usr/include "$pkgdir"/usr/emboss
    
      35  mkdir "$pkgdir"/usr/include
    
      36  mv "$pkgdir"/usr/emboss "$pkgdir"/usr/include/
    
      37  
    
      38  mv "$pkgdir"/usr/bin/{,emboss_}showdb # conflict with sqlite
    
      39  mv "$pkgdir"/usr/bin/{,emboss_}wordcount # conflict with texlive-latexextra
    
      40}
    
      41

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