foldseek

LOW

maintainer imjiaoyuan 0 votes scanned 2026-08-20 17:11:42.006138

View on AUR

Why flagged

Uploaded within the last 14 days with 2 or fewer community votes — little peer review so far.

Triggered rules

Low Few votes, recently uploaded zero_votes_recent

Uploaded within the last 14 days with 2 or fewer community votes — little peer review so far.

PKGBUILD

      1# Maintainer: imjiaoyuan <imjiaoyuan@gmail.com>
    
      2
    
      3pkgname=foldseek
    
      4_tag=10-941cd33
    
      5pkgver=10_941cd33
    
      6pkgrel=2
    
      7pkgdesc="Fast and sensitive comparison of large protein structure sets"
    
      8arch=('x86_64')
    
      9url="https://github.com/steineggerlab/foldseek"
    
      10license=('GPL-3.0-or-later')
    
      11depends=('zlib' 'gcc-libs')
    
      12makedepends=('cmake' 'rust')
    
      13conflicts=('foldseek-bin')
    
      14source=("$pkgname-$pkgver.tar.gz::$url/archive/${_tag}.tar.gz")
    
      15sha256sums=('0db8bf072c9ec895efc6aa3626c746f4ca020acc9b92e9b2292b56c8c9f8a943')
    
      16
    
      17# foldseek vendors mmseqs2 plus a Rust block-aligner crate built through
    
      18# corrosion (offline, from the tarball), so a Rust toolchain is needed at
    
      19# build time. HAVE_SSE4_1 picks the portable SSE4.1 paths for both the C++
    
      20# and the Rust side (simd_sse2 feature) instead of upstream's default
    
      21# NATIVE_ARCH, which would bake the build machine's CPU capabilities into
    
      22# the binary; ProstT5/ggml follow the same selection automatically.
    
      23
    
      24prepare() {
    
      25  cd "$srcdir/$pkgname-${_tag}"
    
      26  # cmake 4: drop CMP0060 OLD (upstream only needs it for static builds) and
    
      27  # raise the pre-3.5 cmake_minimum_required calls cmake 4 refuses to load
    
      28  sed -i '/cmake_policy(SET CMP0060 OLD)/d' CMakeLists.txt
    
      29  sed -i 's/cmake_minimum_required(VERSION 2\.8\.12 FATAL_ERROR)/cmake_minimum_required(VERSION 3.15 FATAL_ERROR)/' lib/mmseqs/CMakeLists.txt
    
      30  sed -i 's/cmake_minimum_required(VERSION 2\.8\.12)/cmake_minimum_required(VERSION 3.15)/' lib/mmseqs/lib/tinyexpr/CMakeLists.txt
    
      31  sed -i 's/cmake_minimum_required(VERSION 3\.0 FATAL_ERROR)/cmake_minimum_required(VERSION 3.15 FATAL_ERROR)/' lib/foldcomp/CMakeLists.txt
    
      32}
    
      33
    
      34build() {
    
      35  cd "$srcdir/$pkgname-${_tag}"
    
      36  cmake -B build -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr -DHAVE_SSE4_1=1
    
      37  cmake --build build
    
      38}
    
      39
    
      40package() {
    
      41  cd "$srcdir/$pkgname-${_tag}"
    
      42  install -Dm755 build/src/foldseek "$pkgdir/usr/bin/foldseek"
    
      43  install -Dm644 LICENSE.md "$pkgdir/usr/share/licenses/$pkgname/LICENSE.md"
    
      44}
    
      45

Changes since previous scan

--- PKGBUILD @ 2026-08-18 00:03
+++ PKGBUILD @ 2026-08-20 17:11
@@ -3,14 +3,13 @@
 pkgname=foldseek
 _tag=10-941cd33
 pkgver=10_941cd33
-pkgrel=1
+pkgrel=2
 pkgdesc="Fast and sensitive comparison of large protein structure sets"
 arch=('x86_64')
 url="https://github.com/steineggerlab/foldseek"
-license=('GPL3')
+license=('GPL-3.0-or-later')
 depends=('zlib' 'gcc-libs')
 makedepends=('cmake' 'rust')
-provides=('foldseek')
 conflicts=('foldseek-bin')
 source=("$pkgname-$pkgver.tar.gz::$url/archive/${_tag}.tar.gz")
 sha256sums=('0db8bf072c9ec895efc6aa3626c746f4ca020acc9b92e9b2292b56c8c9f8a943')
@@ -22,14 +21,24 @@
 # NATIVE_ARCH, which would bake the build machine's CPU capabilities into
 # the binary; ProstT5/ggml follow the same selection automatically.
 
+prepare() {
+  cd "$srcdir/$pkgname-${_tag}"
+  # cmake 4: drop CMP0060 OLD (upstream only needs it for static builds) and
+  # raise the pre-3.5 cmake_minimum_required calls cmake 4 refuses to load
+  sed -i '/cmake_policy(SET CMP0060 OLD)/d' CMakeLists.txt
+  sed -i 's/cmake_minimum_required(VERSION 2\.8\.12 FATAL_ERROR)/cmake_minimum_required(VERSION 3.15 FATAL_ERROR)/' lib/mmseqs/CMakeLists.txt
+  sed -i 's/cmake_minimum_required(VERSION 2\.8\.12)/cmake_minimum_required(VERSION 3.15)/' lib/mmseqs/lib/tinyexpr/CMakeLists.txt
+  sed -i 's/cmake_minimum_required(VERSION 3\.0 FATAL_ERROR)/cmake_minimum_required(VERSION 3.15 FATAL_ERROR)/' lib/foldcomp/CMakeLists.txt
+}
+
 build() {
-  cd "$srcdir/$pkgname-$pkgver"
+  cd "$srcdir/$pkgname-${_tag}"
   cmake -B build -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr -DHAVE_SSE4_1=1
   cmake --build build
 }
 
 package() {
-  cd "$srcdir/$pkgname-$pkgver"
+  cd "$srcdir/$pkgname-${_tag}"
   install -Dm755 build/src/foldseek "$pkgdir/usr/bin/foldseek"
   install -Dm644 LICENSE.md "$pkgdir/usr/share/licenses/$pkgname/LICENSE.md"
 }

Scan history

Scanned at (UTC)	Severity	Rules
2026-08-20 17:11:42	Low	1
2026-08-18 00:03:42	Clean	2
2026-08-17 09:35:23	Low	1
2026-08-17 07:35:18	Low	1