python-rna

MEDIUM

maintainer RaumZeit 5 votes base viennarna scanned 2026-11-06 18:13:05.055048

View on AUR

Why flagged

One or more source=() URLs point to a host outside the trusted allowlist (github.com, gitlab.com, codeberg.org, pypi.org, …).

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:23 source=(http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-${pkgver}.tar.gz)

PKGBUILD

1 offending line(s) highlighted

      1# Maintainer: Ronny Lorenz <ronny at tbi dot univie dot ac dot at>
    
      2
    
      3pkgbase=viennarna
    
      4pkgname=('viennarna' 'python-rna' 'perl-rna')
    
      5pkgver=2.8.0
    
      6pkgrel=1
    
      7pkgdesc="RNA Secondary Structure Prediction and Comparison"
    
      8arch=('x86_64' 'i686')
    
      9license=('Custom')
    
      10url="https://www.tbi.univie.ac.at/RNA"
    
      11groups=('viennarna-package')
    
      12makedepends=( 'perl'
    
      13              'python'
    
      14              'libtool'
    
      15              'check'
    
      16              'mpfr'
    
      17              'gsl'
    
      18              'lapack'
    
      19              'lapacke'
    
      20              'blas'
    
      21              'gcc-fortran')
    
      22
    
      23source=(http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-${pkgver}.tar.gz)
    
      24
    
      25options=('staticlibs' '!strip')
    
      26sha256sums=('4d239d1ccb46400fcb46cf12894d1fb5975b327f91bb3d904bc4283cbe87d476')
    
      27
    
      28prepare() {
    
      29  cd "${srcdir}/ViennaRNA-${pkgver}"
    
      30  ./configure \
    
      31      --with-cluster \
    
      32      --with-kinwalker \
    
      33      --prefix=/usr \
    
      34      INSTALLDIRS=vendor
    
      35}
    
      36
    
      37build() {
    
      38  cd "${srcdir}/ViennaRNA-${pkgver}"
    
      39  make
    
      40}
    
      41
    
      42check() {
    
      43  cd "$srcdir/ViennaRNA-${pkgver}"
    
      44  export LC_ALL=C
    
      45  make check
    
      46}
    
      47
    
      48package_viennarna() {
    
      49  depends=('perl'
    
      50           'mpfr'
    
      51           'gsl'
    
      52           'lapack'
    
      53           'blas')
    
      54  optdepends=('gri: create 2D plots of secondary structure landscape with RNA2Dfold')
    
      55  provides=('Kinfold=1.4'
    
      56            'RNAforester=2.0'
    
      57            'kinwalker=2.0'
    
      58            'RNAxplorer=0.9'
    
      59            "viennarna2=${pkgver}"
    
      60            "libRNA=${pkgver}")
    
      61  conflict=('kinwalker')
    
      62
    
      63  cd "${srcdir}/ViennaRNA-${pkgver}"
    
      64
    
      65  # install executables
    
      66  cd src/bin/
    
      67  make DESTDIR="${pkgdir}" install
    
      68  cd ../Kinfold
    
      69  make DESTDIR="${pkgdir}" install
    
      70  cd ../RNAforester
    
      71  install -Dm755 src/RNAforester "${pkgdir}/usr/bin/"
    
      72  install -Dm644 man/RNAforester.1* "${pkgdir}/usr/share/man/man1/"
    
      73  cd ../Utils
    
      74  make DESTDIR="${pkgdir}" install
    
      75  cd ../Cluster
    
      76  make DESTDIR="${pkgdir}" install
    
      77  cd ../Kinwalker
    
      78  make DESTDIR="${pkgdir}" install
    
      79  cd ../RNAlocmin
    
      80  make DESTDIR="${pkgdir}" install
    
      81  cd ../RNAxplorer
    
      82  make DESTDIR="${pkgdir}" install
    
      83  cd ../..
    
      84
    
      85  # install library and header files
    
      86  cd src/ViennaRNA
    
      87  make DESTDIR="${pkgdir}" install
    
      88  cd ../..
    
      89
    
      90  # install manpages, documentation, examples, and misc files
    
      91  cd man
    
      92  make DESTDIR="${pkgdir}" install
    
      93  cd ../doc
    
      94  make DESTDIR="${pkgdir}" install
    
      95  cd ../examples
    
      96  make DESTDIR="${pkgdir}" install
    
      97  cd ../misc
    
      98  make DESTDIR="${pkgdir}" install
    
      99  cd ..
    
      100
    
      101  # install pkg-config file
    
      102  install -Dm644 RNAlib2.pc "$pkgdir/usr/lib/pkgconfig/RNAlib2.pc"
    
      103
    
      104  install -Dm644 COPYING "$pkgdir/usr/share/licenses/$pkgname/LICENSE"
    
      105
    
      106  # cleanup after dirty install ...
    
      107  install -dm755 "$pkgdir"/usr/bin/vendor_perl
    
      108  for perlscript in "$pkgdir"/usr/share/ViennaRNA/bin/*.pl ; do
    
      109    mv "$perlscript" "$pkgdir/usr/bin/vendor_perl/"
    
      110  done
    
      111
    
      112  # no need for that file it is outdated anyway
    
      113  rm $pkgdir/usr/share/info/dir
    
      114}
    
      115
    
      116package_python-rna() {
    
      117  depends=('python' viennarna="${pkgver}")
    
      118  cd "${srcdir}/ViennaRNA-${pkgver}"
    
      119  cd interfaces/Python
    
      120  make DESTDIR="${pkgdir}" install
    
      121}
    
      122
    
      123package_perl-rna() {
    
      124  depends=('perl' viennarna="${pkgver}")
    
      125  cd "${srcdir}/ViennaRNA-${pkgver}"
    
      126  cd interfaces/Perl
    
      127  make DESTDIR="${pkgdir}" install
    
      128}
    
      129

Changes since previous scan

--- PKGBUILD @ 2026-06-19 19:07
+++ PKGBUILD @ 2026-11-06 18:13
@@ -2,7 +2,7 @@
 
 pkgbase=viennarna
 pkgname=('viennarna' 'python-rna' 'perl-rna')
-pkgver=2.7.2
+pkgver=2.8.0
 pkgrel=1
 pkgdesc="RNA Secondary Structure Prediction and Comparison"
 arch=('x86_64' 'i686')
@@ -23,7 +23,7 @@
 source=(http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-${pkgver}.tar.gz)
 
 options=('staticlibs' '!strip')
-sha256sums=('1ab5f4a4f76fc85a2243546088e45f5d85f2d7a56cc656e969b005cce9bfab5f')
+sha256sums=('4d239d1ccb46400fcb46cf12894d1fb5975b327f91bb3d904bc4283cbe87d476')
 
 prepare() {
   cd "${srcdir}/ViennaRNA-${pkgver}"

Scan history

Scanned at (UTC)	Severity	Rules
2026-11-06 18:13:05	Medium	1
2026-06-19 19:07:35	Clean	2
2026-06-19 18:54:17	Clean	2
2026-06-18 16:11:54	Medium	1