[Foldseek] update to v6

F/Foldseek/build_tarballs.jl

@@ -1,39 +1,37 @@
-# TODO
-# - use Zstd_jll ? (static lib?) (now uses builtin zstd lib)
-
-# Build fails
-# - x86_64-freebsd
-#   compilation error, seems like a clash between KASSERT macro defined in lib/kerasify/keras_model.h
-#   and usage in freebsd headers, e.g. at line 190 of
-#   /opt/x86_64-unknown-freebsd12.2/x86_64-unknown-freebsd12.2/sys-root//usr/include/sys/time.h
-#   see: https://github.com/JuliaPackaging/Yggdrasil/pull/6195#issuecomment-1416227398
-
 using BinaryBuilder, Pkg
 
 name = "Foldseek"
-
-# foldseek seem to use as versioning scheme of "major version + first 7
-# characters of the tagged commit"
-version = v"5"
-# version_commitprefix = "53465f0"
+version = v"6"
 
 # url = "https://github.com/steineggerlab/foldseek"
 # description = "Fast and sensitive comparisons of large protein structure sets"
 
 sources = [
-    # Foldseek 5-53465f0
-    # Note: this is the same commit as v"4" in Yggdrasil
+    # Foldseek 6-29e2557
     GitSource("https://github.com/steineggerlab/foldseek",
-              "53465f07cdeed1f7fda08ee7f188327cb57c37ba"),
+              "29e2557970c39c8e689601ecaae2279fff4faa17"),
     DirectorySource("./bundled"),
 ]
 
+# TODO
+# - use Zstd_jll ? (static lib?) (now uses builtin zstd lib)
+
+# Build fails
+# - x86_64-freebsd
+#   compilation error, seems like a clash between KASSERT macro defined in lib/kerasify/keras_model.h
+#   and usage in freebsd headers, e.g. at line 190 of
+#   /opt/x86_64-unknown-freebsd12.2/x86_64-unknown-freebsd12.2/sys-root//usr/include/sys/time.h
+#   see: https://github.com/JuliaPackaging/Yggdrasil/pull/6195#issuecomment-1416227398
+
 script = raw"""
 cd $WORKSPACE/srcdir/foldseek*/
 
 # patch lib/mmseqs/CMakeLists.txt so it doesn't set -march unnecessarily on ARM
 atomic_patch -p1 ../patches/mmseqs-arm-simd-march-cmakefile.patch
 
+# remove rustup check in corrosion's FindRust.cmake
+atomic_patch -p1 ../patches/corrosion-remove-rustup-check.patch
+
 ARCH_FLAGS=
 if [[ "${target}" == x86_64-* || "${target}" == i686-* ]]; then
     ARCH_FLAGS="-DHAVE_SSE2=1 -DHAVE_SSE4_1=1 -DHAVE_AVX2=1"
@@ -43,10 +41,22 @@ elif [[ "${target}" == aarch64-* ]]; then
     ARCH_FLAGS="-DHAVE_ARM8=1"
 fi
 
+# hack around corrosion (cmake cargo interop package) using a wrong
+# target string when cross-compiling
+CARGO_TARGET=
+if [[ "${target}" == *-linux-* ]]; then
+    # cargo uses an extra 'unknown' in the target string,
+    # e.g. 'x86_64-linux-gnu' becomes 'x86_64-unknown-linux-gnu' in cargo
+    CARGO_TARGET=$(echo ${target} | cut -d- -f1)-unknown-$(echo ${target} | cut -d- -f2-)
+else
+    CARGO_TARGET=${target}
+fi
+
 mkdir build && cd build
 cmake .. \
     -DCMAKE_INSTALL_PREFIX=$prefix -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TARGET_TOOLCHAIN} -DCMAKE_BUILD_TYPE=RELEASE \
-    -DNATIVE_ARCH=0 ${ARCH_FLAGS}
+    -DNATIVE_ARCH=0 ${ARCH_FLAGS} \
+    -DRust_COMPILER=$(which ${RUSTC}) -DRust_CARGO_TARGET=${CARGO_TARGET}
 make -j${nproc}
 make install
 
@@ -72,4 +82,4 @@ dependencies = Dependency[
 ]
 
 build_tarballs(ARGS, name, version, sources, script, platforms, products, dependencies;
-               julia_compat="1.6", preferred_gcc_version = v"8")
+               julia_compat="1.6", preferred_gcc_version = v"8", compilers=[:c, :rust])

F/Foldseek/bundled/patches/corrosion-remove-rustup-check.patch

@@ -0,0 +1,21 @@
+diff --git a/lib/corrosion/cmake/FindRust.cmake b/lib/corrosion/cmake/FindRust.cmake
+index ba2bd8a..4757f45 100644
+--- a/lib/corrosion/cmake/FindRust.cmake
++++ b/lib/corrosion/cmake/FindRust.cmake
+@@ -271,11 +271,11 @@ else()
+         RESULT_VARIABLE _RUSTC_VERSION_RESULT
+     )
+
+-    if(NOT (_RUSTC_VERSION_RESULT EQUAL "0"))
+-        _findrust_failed("`${_Rust_COMPILER_TEST} --version` failed with ${_RUSTC_VERSION_RESULT}\n"
+-            "rustc stderr:\n${_RUSTC_VERSION_STDERR}"
+-            )
+-    endif()
++    #if(NOT (_RUSTC_VERSION_RESULT EQUAL "0"))
++    #    _findrust_failed("`${_Rust_COMPILER_TEST} --version` failed with ${_RUSTC_VERSION_RESULT}\n"
++    #        "rustc stderr:\n${_RUSTC_VERSION_STDERR}"
++    #        )
++    #endif()
+
+     if (_RUSTC_VERSION_RAW MATCHES "rustup [0-9\\.]+")
+         if (_USER_SPECIFIED_RUSTC)