Merge branch 'spack:develop' into add-r-rtracklayer-conflicts-deprecations

Author: w8jcik

.ci/env

@@ -1,2 +1,2 @@
-SPACK_CHECKOUT_VERSION=c1ddfe76000468ee84120d13db12ad4f497091da
+SPACK_CHECKOUT_VERSION=c5f814bfb1801c7bb50bc17015ba999ab68e1e27
 SPACK_CHECKOUT_REPO=spack/spack

repos/spack_repo/builtin/packages/blaspp/package.py

@@ -68,6 +68,7 @@ class Blaspp(CMakePackage, CudaPackage, ROCmPackage):
     depends_on("cxx", type="build")  # generated
 
     depends_on("cmake@3.15.0:", type="build")
+    depends_on("cmake@3.21:", when="@2025.05.28:", type="build")
     depends_on("blas")
     depends_on("lapack")
     depends_on("llvm-openmp", when="+openmp %apple-clang")
@@ -118,6 +119,11 @@ def cmake_args(self):
             "-DLAPACK_LIBRARIES=%s" % spec["lapack"].libs.joined(";"),
         ]
 
+        # Older releases only link precompiled CUDA libraries.
+        if spec.satisfies("@2025.05.28:+cuda") and not spec.satisfies("cuda_arch=none"):
+            cuda_arch = spec.variants["cuda_arch"].value
+            args.append(self.define("CMAKE_CUDA_ARCHITECTURES", ";".join(cuda_arch)))
+
         if spec["blas"].name == "cray-libsci":
             args.append(self.define("BLA_VENDOR", "CRAY"))
 

repos/spack_repo/builtin/packages/brigand/package.py

@@ -25,7 +25,8 @@ class Brigand(CMakePackage):
     version("1.1.0", sha256="afdcc6909ebff6994269d3039c31698c2b511a70280072f73382b26855221f64")
     version("1.0.0", sha256="8daf7686ff39792f851ef1977323808b80aab31c5f38ef0ba4e6a8faae491f8d")
 
-    depends_on("cxx", type="build")  # generated
+    depends_on("c", type="build")
+    depends_on("cxx", type="build")
 
     def cmake_args(self):
         args = [self.define("BUILD_TESTING", self.run_tests)]

repos/spack_repo/builtin/packages/camp/package.py

@@ -99,6 +99,7 @@ class Camp(CMakePackage, CudaPackage, ROCmPackage):
 
     with when("+cuda"):
         depends_on("cub", when="^cuda@:10")
+        depends_on("cmake@3.18:", type="build")
 
     depends_on("blt", type="build")
     depends_on("blt@0.7.1:", type="build", when="@2025.09.0:")
@@ -138,10 +139,7 @@ def cmake_args(self):
 
             if not spec.satisfies("cuda_arch=none"):
                 cuda_arch = spec.variants["cuda_arch"].value
-                options.append("-DCMAKE_CUDA_ARCHITECTURES={0}".format(cuda_arch[0]))
-                options.append("-DCUDA_ARCH=sm_{0}".format(cuda_arch[0]))
-                flag = "-arch sm_{0}".format(cuda_arch[0])
-                options.append("-DCMAKE_CUDA_FLAGS:STRING={0}".format(flag))
+                options.append("-DCMAKE_CUDA_ARCHITECTURES={0}".format(";".join(cuda_arch)))
 
         options.append(self.define_from_variant("ENABLE_HIP", "rocm"))
         if spec.satisfies("+rocm"):

repos/spack_repo/builtin/packages/clingo/package.py

@@ -29,6 +29,7 @@ class Clingo(CMakePackage):
     version("master", branch="master", submodules=True)
     version("spack", commit="2a025667090d71b2c9dce60fe924feb6bde8f667", submodules=True)
 
+    version("5.8.1", sha256="28fe78322cefb92e0f68f350777e19407d07bbb5179ca725fc6f77d538f0d19a")
     version("5.8.0", sha256="4ddd5975e79d7a0f8d126039f1b923a371b1a43e0e0687e1537a37d6d6d5cc7c")
     version(
         "5.7.1",
@@ -56,12 +57,14 @@ class Clingo(CMakePackage):
 
     with when("@5.6:5.8,master"):
         depends_on("re2c@1.1.1:", type="build")
-        # forward compat issue: reference to undefined condition 'aspif'
-        depends_on("re2c@:3", type="build")
         depends_on("bison@2.5:", type="build", when="platform=linux")
         depends_on("bison@2.5:", type="build", when="platform=darwin")
         depends_on("bison@2.5:", type="build", when="platform=freebsd")
 
+    # Lexers use a re2c condition that 4.3+ rejects ("undefined condition 'aspif'"),
+    # fixed upstream in 5.8.1 and master. See https://github.com/potassco/clingo/issues/591
+    depends_on("re2c@:3", type="build", when="@5.6:5.8.0")
+
     with when("@6:"):
         depends_on("re2c@3:", type="build")
         depends_on("cmake@3.22.1:", type="build")

repos/spack_repo/builtin/packages/glibmm/package.py

@@ -20,7 +20,8 @@ class Glibmm(AutotoolsPackage):
     version("2.16.0", sha256="99795b9c6e58e490df740a113408092bf47a928427cbf178d77c35adcb6a57a3")
     version("2.4.8", sha256="78b97bfa1d001cc7b398f76bf09005ba55b45ae20780b297947a1a71c4f07e1f")
 
-    depends_on("cxx", type="build")  # generated
+    depends_on("c", type="build")
+    depends_on("cxx", type="build")
 
     depends_on("libsigcpp")
     # https://libsigcplusplus.github.io/libsigcplusplus/index.html

repos/spack_repo/builtin/packages/hdf5/package.py

@@ -377,6 +377,14 @@ def flag_handler(self, name, flags):
                 # in C99:
                 cmake_flags.append("-Wno-error=implicit-function-declaration")
                 # Note that this flag will cause an error if building %nvhpc.
+            if spec.satisfies("@:1.10.8 %gcc@14:"):
+                cmake_flags.extend(
+                    [
+                        "-Wno-error=implicit-int",
+                        "-Wno-error=incompatible-pointer-types",
+                        "-Wno-error=int-conversion",
+                    ]
+                )
             if spec.satisfies("@:1.8.12~shared"):
                 # More recent versions set CMAKE_POSITION_INDEPENDENT_CODE to
                 # True and build with PIC flags.
@@ -580,6 +588,9 @@ def cmake_args(self):
             self.define_from_variant("HDF5_BUILD_TOOLS", "tools"),
         ]
 
+        if spec.satisfies("@:1.10.8 %gcc@14:"):
+            args.append(self.define("HDF5_DISABLE_COMPILER_WARNINGS", True))
+
         # Always enable this option. This does not actually enable any
         # features: it only *allows* the user to specify certain combinations
         # of other arguments that would normally be rejected as unsupported

repos/spack_repo/builtin/packages/hdf_eos2/package.py

@@ -152,8 +152,16 @@ def flag_handler(self, name, flags):
                 flags.append("-Wno-error=implicit-int")
                 flags.append("-std=gnu17")
 
-            # Testing shows we need one extra flag for gcc@14
-            if self.spec.satisfies("%gcc@14:"):
+            # Newer compilers promote -Wincompatible-pointer-types from a warning
+            # to an error. This is not gcc-specific: clang 16+, and oneAPI's
+            # clang-based icx, reject the same code (58 errors in EHapi/GDapi/
+            # PTapi/SWapi.c passing 'long *' where 'int32 *' is expected).
+            if (
+                self.spec.satisfies("%clang@16:")
+                or self.spec.satisfies("%apple-clang@15:")
+                or self.spec.satisfies("%oneapi")
+                or self.spec.satisfies("%gcc@14:")
+            ):
                 flags.append("-Wno-error=incompatible-pointer-types")
         return flags, None, None
 
@@ -180,9 +188,15 @@ def setup_build_environment(self, env: EnvironmentModifications) -> None:
                 or self.spec.satisfies("%oneapi")
                 or self.spec.satisfies("%gcc@14:")
             ):
+                # NOTE: this env.set REPLACES the cflags computed in
+                # flag_handler above (the build uses CC=h4cc with these CFLAGS),
+                # so every flag needed there must be repeated here.
                 env.set(
                     "CFLAGS",
-                    "-Wno-error=implicit-function-declaration -Wno-error=implicit-int -std=gnu17",
+                    "-Wno-error=implicit-function-declaration "
+                    "-Wno-error=implicit-int "
+                    "-Wno-error=incompatible-pointer-types "
+                    "-std=gnu17",
                 )
 
     @run_before("configure", when="@3.0")

repos/spack_repo/builtin/packages/hssp/package.py

@@ -34,7 +34,8 @@ class Hssp(AutotoolsPackage):
     version("3.0.2", sha256="76b4275c8cde120509d7920609fca983f2b04249a649d0aa802c69fd09e5f8cf")
     version("3.0.1", sha256="62a703d15bdfec82fdbd2a4275e1973b6a1ac6ccd4dbec75036f16faacaa9dce")
 
-    depends_on("cxx", type="build")  # generated
+    depends_on("c", type="build")
+    depends_on("cxx", type="build")
 
     depends_on("autoconf", type="build")
     depends_on("automake", type="build")

repos/spack_repo/builtin/packages/ilmbase/package.py

@@ -36,4 +36,5 @@ class Ilmbase(AutotoolsPackage):
         url="http://download.savannah.nongnu.org/releases/openexr/ilmbase-0.9.0.tar.gz",
     )
 
-    depends_on("cxx", type="build")  # generated
+    depends_on("c", type="build")
+    depends_on("cxx", type="build")