alignace

MEDIUM

maintainer orphaned 0 votes scanned 2026-09-17 00:27:14.276658

View on AUR

Why flagged

The PKGBUILD installs two prebuilt binaries: (1) AlignACE/ScanACE executables from the official Harvard AREP lab host (arep.med.harvard.edu), which is the legitimate upstream vendor; (2) a prebuilt i386 shared library libstdc++-2.9.0-30.i386.rpm from archive.download.redhat.com. The second source is a Red Hat archive mirror — archive.download.redhat.com is a known Red Hat/Fedora legacy archive host, not a random personal server, so it is more trustworthy than a truly unofficial host. However, the package still installs a prebuilt binary (libstdc++ shared library) that will be loaded at runtime, and the RPM is from a very old Red Hat 6.2 release (circa 2000). The MD5 checksums provide minimal integrity assurance. The core concern is that prebuilt executables and a prebuilt shared library are installed without source compilation, and the libstdc++ library from a 24-year-old RPM is an unusual dependency. This is a genuine supply-chain concern (executed binary from an archived host with no modern verification), but not clearly malicious. Medium is appropriate.

Triggered rules

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:10 source=("http://arep.med.harvard.edu/mrnadata/software/${pkgname}.tar.gz" "http://archive.download.redhat.com/pub/redhat/linux/6.2/it/os/i386/RedHat/RPMS/libstdc++-2.9.0-30.i386.rpm")
PKGBUILD:10 source=("http://arep.med.harvard.edu/mrnadata/software/${pkgname}.tar.gz" "http://archive.download.redhat.com/pub/redhat/linux/6.2/it/os/i386/RedHat/RPMS/libstdc++-2.9.0-30.i386.rpm")

Medium AI review llm_review

An AI model (anthropic/claude-4.6-sonnet-20260217) reviewed this and agrees it is MEDIUM (confidence 82%): The PKGBUILD installs two prebuilt binaries: (1) AlignACE/ScanACE executables from the official Harvard AREP lab host (arep.med.harvard.edu), which is the legitimate upstream vendor; (2) a prebuilt i386 shared library libstdc++-2.9.0-30.i386.rpm from archive.download.redhat.com. The second source is a Red Hat archive mirror — archive.download.redhat.com is a known Red Hat/Fedora legacy archive host, not a random personal server, so it is more trustworthy than a truly unofficial host. However, the package still installs a prebuilt binary (libstdc++ shared library) that will be loaded at runtime, and the RPM is from a very old Red Hat 6.2 release (circa 2000). The MD5 checksums provide minimal integrity assurance. The core concern is that prebuilt executables and a prebuilt shared library are installed without source compilation, and the libstdc++ library from a 24-year-old RPM is an unusual dependency. This is a genuine supply-chain concern (executed binary from an archived host with no modern verification), but not clearly malicious. Medium is appropriate.

PKGBUILD

1 offending line(s) highlighted

      1#Maintainer: allencch <allencch at hotmail dot com>
    
      2pkgname=alignace
    
      3pkgver=1.0
    
      4pkgrel=6
    
      5pkgdesc="Program that finds sequence elements conserved in a set of DNA sequences"
    
      6arch=('i686' 'x86_64')
    
      7url="http://arep.med.harvard.edu/mrnadata/mrnasoft.html"
    
      8license=('custom')
    
      9depends=("sh")
    
      10source=("http://arep.med.harvard.edu/mrnadata/software/${pkgname}.tar.gz" "http://archive.download.redhat.com/pub/redhat/linux/6.2/it/os/i386/RedHat/RPMS/libstdc++-2.9.0-30.i386.rpm")
    
      11md5sums=('6d2d9fb0929ce03974dca874b516cd07'
    
      12         '29ca50829f6d43c63d8fcc827b3daceb')
    
      13
    
      14package() {
    
      15	cd "${srcdir}/${pkgname}"
    
      16	mkdir -p "${pkgdir}/usr/bin"
    
      17	mkdir -p "${pkgdir}/usr/lib"
    
      18	install -m755 AlignACE "${pkgdir}/usr/bin"
    
      19	install -m755 ScanACE "${pkgdir}/usr/bin"
    
      20	install -m755 ../usr/lib/libstdc++-2-libc6.1-1-2.9.0.so "${pkgdir}/usr/lib"
    
      21}
    
      22

Scan history

Scanned at (UTC)	Severity	Rules
2026-09-17 00:27:14	Medium	2
2026-09-16 00:03:17	Medium	2
2026-09-15 00:25:31	Medium	2
2026-09-14 00:27:57	Medium	2
2026-09-13 00:19:54	Medium	2
2026-09-12 00:25:17	Medium	2
2026-09-11 00:19:22	Medium	2
2026-09-10 00:22:44	Medium	2
2026-09-09 00:04:09	Medium	2
2026-09-08 00:18:08	Medium	2
2026-09-07 00:30:15	Medium	2
2026-09-06 00:17:06	Medium	2
2026-09-05 00:16:27	Medium	2
2026-09-04 00:03:13	Medium	2
2026-09-03 00:15:47	Medium	2
2026-09-02 00:02:31	Medium	2
2026-09-01 00:11:19	Medium	2
2026-08-31 00:19:57	Medium	2
2026-08-30 00:04:14	Medium	2
2026-08-29 00:29:17	Medium	2