Remove indirect MbedTLS_jll dependency from a few packages

A/Aria2/build_tarballs.jl

@@ -15,13 +15,13 @@ sources = [
 script = raw"""
 cd $WORKSPACE/srcdir/aria2-*/
 
-export CPPFLAGS="-I${includedir}"
-export LDFLAGS="-L${libdir}"
-
+# Note: we explicitly set `LIBSSH2_LIBS` to avoid pulling in mbedtls when
+# linking to older builds of libssh2.
 ./configure \
     --prefix=${prefix} --build=${MACHTYPE} --host=${target} \
     --with-pic --enable-shared --enable-libaria2 \
-    --with-openssl --with-libxml2 --with-libz --with-libssh2
+    --with-openssl --with-libxml2 --with-libz --with-libssh2 \
+    LIBSSH2_LIBS="-L${libdir} -lssh2 "
 
 make -j${nproc}
 make install
@@ -45,11 +45,6 @@ products = [
 dependencies = [
     Dependency(PackageSpec(name="Cares_jll")),
     Dependency(PackageSpec(name="LibSSH2_jll")),
-    # `MbedTLS_jll` is a dependency of `LibSSH2_jll`.  Strangely, we
-    # are getting a newer version in the build than the one
-    # `LibSSH2_jll` was compiled with.  So we explicitly select the
-    # right version here.
-    BuildDependency(PackageSpec(name="MbedTLS_jll", version=v"2.28")),
     Dependency(PackageSpec(name="OpenSSL_jll"); compat="3.0.8"),
     Dependency(PackageSpec(name="XML2_jll")),
     Dependency(PackageSpec(name="Zlib_jll")),

A/AzStorage/build_tarballs.jl

@@ -46,10 +46,6 @@ dependencies = [
     Dependency(PackageSpec(name="CompilerSupportLibraries_jll", uuid="e66e0078-7015-5450-92f7-15fbd957f2ae"); platforms=filter(!Sys.isbsd, platforms)),
     Dependency(PackageSpec(name="LLVMOpenMP_jll", uuid="1d63c593-3942-5779-bab2-d838dc0a180e"); platforms=filter(Sys.isbsd, platforms)),
     Dependency("LibCURL_jll", v"7.73.0"),
-    # MbedTLS is only an indirect dependency (through LibCURL), but we want to
-    # be sure to have the right version of MbedTLS for the corresponding version
-    # of Julia.
-    BuildDependency(PackageSpec(; name="MbedTLS_jll", version=v"2.24.0")),
 ]
 
 #=

N/NetCDFF/build_tarballs.jl

@@ -3,12 +3,12 @@
 using BinaryBuilder, Pkg
 
 name = "NetCDFF"
-version = v"4.6.0"
+version = v"4.6.1"
 
 # Collection of sources required to complete build
 sources = [
-    ArchiveSource("https://github.com/Unidata/netcdf-fortran/archive/refs/tags/v$(version).tar.gz",
-                  "8194aa70e400c0adfc456127c1d97af2c6489207171d13b10cd754a16da8b0ca"),
+    ArchiveSource("https://downloads.unidata.ucar.edu/netcdf-fortran/$(version)/netcdf-fortran-$(version).tar.gz",
+                  "b50b0c72b8b16b140201a020936aa8aeda5c79cf265c55160986cd637807a37a"),
 ]
 
 # Bash recipe for building across all platforms
@@ -29,10 +29,11 @@ rm ${prefix}/lib/*.a
 # platforms are passed in on the command line
 platforms = [
     Platform("x86_64", "linux"; libc = "glibc"),
-    Platform("x86_64", "macos"),
     Platform("aarch64", "linux"; libc="glibc"),
-    Platform("x86_64", "windows"),
+    Platform("x86_64", "macos"),
+    Platform("aarch64", "macos"),
     Platform("i686", "windows"),
+    Platform("x86_64", "windows"),
 ]
 platforms = expand_gfortran_versions(platforms)
 
@@ -45,10 +46,10 @@ products = [
 dependencies = [
     Dependency(PackageSpec(name="NetCDF_jll", uuid="7243133f-43d8-5620-bbf4-c2c921802cf3"); compat="400.902.5"),
     Dependency(PackageSpec(name="CompilerSupportLibraries_jll", uuid="e66e0078-7015-5450-92f7-15fbd957f2ae")),
-    # `MbedTLS_jll` is an indirect dependency through NetCDF, we need to specify
-    # a compatible build version for this to work.
-    BuildDependency(PackageSpec(; name="MbedTLS_jll", version=v"2.24.0")),
 ]
 
 # Build the tarballs, and possibly a `build.jl` as well.
-build_tarballs(ARGS, name, version, sources, script, platforms, products, dependencies; julia_compat="1.6")
+build_tarballs(ARGS, name, version, sources, script, platforms, products, dependencies;
+               # Note: for some reason GCC 4.8 is still linked to glibc 2.12, we
+               # need to use GCC 5 to have glibc 2.17.
+               julia_compat="1.6", preferred_gcc_version=v"5")

S/samtools/build_tarballs.jl

@@ -3,22 +3,24 @@
 using BinaryBuilder, Pkg
 
 name = "samtools"
-version = v"1.14"
+version = v"1.19.2"
 
 # Collection of sources required to complete build
 sources = [
-    GitSource("https://github.com/samtools/samtools.git", "c29621d3ae075573fce83e229a5e02348d4e8147"),
+    GitSource("https://github.com/samtools/samtools.git", "66830a3178c7dca941ec0f3b699477464bd44b76"),
 ]
 
 # Bash recipe for building across all platforms
 script = raw"""
 cd $WORKSPACE/srcdir/samtools/
 autoheader
 autoconf -Wno-syntax
-export CPPFLAGS="-I${includedir}"
-if [[ "${target}" != *-darwin* ]]; then
-    # Need to pass `-lcurl` because it's needed by libhts
-    export LIBS="-lcurl"
+if [[ "${target}" == x86_64-linux-musl ]]; then
+    # Need to pass `-lcurl -lnghttp2` because it's needed by libhts
+    # TODO: find a way to avoid this.
+    export LIBS="-lcurl -lnghttp2"
+elif [[ "${target}" == *-freebsd* ]]; then
+     export CPPFLAGS="-I${includedir}"
 fi
 ./configure --prefix=${prefix} --build=${MACHTYPE} --host=${target}
 make -j${nproc}
@@ -27,7 +29,7 @@ make install
 
 # These are the platforms we will build for by default, unless further
 # platforms are passed in on the command line
-platforms = supported_platforms(; experimental=true, exclude=Sys.iswindows)
+platforms = supported_platforms(; exclude=Sys.iswindows)
 
 # The products that we will ensure are always built
 products = [
@@ -37,13 +39,11 @@ products = [
 # Dependencies that must be installed before this package can be built
 dependencies = [
     Dependency(PackageSpec(name="Ncurses_jll", uuid="68e3532b-a499-55ff-9963-d1c0c0748b3a"))
-    Dependency(PackageSpec(name="htslib_jll", uuid="f06fe41e-9474-5571-8c61-5634d2b2700c"))
-    # `MbedTLS_jll` is an indirect dependency through `htslib_jll` (-> `LibCURL_jll` ->
-    # `MbedTLS_jll`).  For some reasons that aren't clear to me at the moment, we are
-    # getting a version of `MbedTLS_jll` which doesn't match the one `LibCURL_jll` was
-    # compiled with.
-    BuildDependency(PackageSpec(; name="MbedTLS_jll", version="2.24"))
+    Dependency(PackageSpec(name="htslib_jll", uuid="f06fe41e-9474-5571-8c61-5634d2b2700c"); compat="1.19.1")
 ]
 
 # Build the tarballs, and possibly a `build.jl` as well.
-build_tarballs(ARGS, name, version, sources, script, platforms, products, dependencies; julia_compat="1.6")
+build_tarballs(ARGS, name, version, sources, script, platforms, products, dependencies;
+               # Note: for some reason GCC 4.8 is still linked to glibc 2.12, we
+               # need to use at least GCC 5 to have glibc 2.17.
+               julia_compat="1.6", preferred_gcc_version=v"6")

T/TempestModel/build_tarballs.jl

@@ -6,7 +6,7 @@ const YGGDRASIL_DIR = "../.."
 include(joinpath(YGGDRASIL_DIR, "platforms", "mpi.jl"))
 
 name = "TempestModel"
-version = v"0.1.1"
+version = v"0.1.2"
 tempestmodel_version = v"0.1"
 sources = [
     GitSource("https://github.com/paullric/tempestmodel",
@@ -83,7 +83,7 @@ platforms = [
 ] 
 platforms = expand_cxxstring_abis(platforms)
 
-platforms, platform_dependencies = MPI.augment_platforms(platforms)
+platforms, platform_dependencies = MPI.augment_platforms(platforms; MPItrampoline_compat="5.3.1", OpenMPI_compat="4.1.6, 5")
 
 # Avoid platforms where the MPI implementation isn't supported
 # OpenMPI
@@ -124,16 +124,17 @@ products = [
 ]
 
 dependencies = [
-    Dependency("MKL_jll"),
-    Dependency("NetCDF_jll"; compat="400.701.400 - 400.799"),
+    # MKL 2023 is the last version which supports x86_64 macOS, so we use that version for
+    # building. We don't set compat bounds for the time being because apart from that MKL is
+    # moderately stable and their versioning scheme is calendar-based, rather than something
+    # semver-like.
+    Dependency("MKL_jll", v"2023.2.0"),
+    Dependency("NetCDF_jll"; compat="400.902.208 - 400.999"),
     # Updating to a newer HDF5 version is likely possible without problems but requires rebuilding this package
-    Dependency("HDF5_jll"; compat="~1.12"),
-    # `MbedTLS_jll` is an indirect dependency through NetCDF, we need to specify
-    # a compatible build version for this to work.
-    BuildDependency(PackageSpec(; name="MbedTLS_jll", version=v"2.24.0")),
+    Dependency("HDF5_jll"; compat="~1.14.3"),
 ]
 append!(dependencies, platform_dependencies)
 
 build_tarballs(ARGS, name, version, sources, script, platforms, products, dependencies;
-    augment_platform_block, julia_compat="1.6",
+    augment_platform_block, julia_compat="1.6", preferred_gcc_version=v"5",
 )

V/VMEC/build_tarballs.jl

@@ -101,8 +101,6 @@ products = [
 
 # Dependencies that must be installed before this package can be built
 dependencies = [
-    # MbedTLS is an indirect dependency, fix the version for building 
-    BuildDependency(PackageSpec(name = "MbedTLS_jll")),
     Dependency("SCALAPACK_jll"),
     Dependency("OpenBLAS_jll"),
     Dependency("MKL_jll"),