concretizer: --force is now config and a common argument

`--force` was previously available only on `spack concretize`
but not on `spack spec`, `spack solve`, and other commands that
do concretization.

This means you can now preview a force-concretize on an environment
or spec with `spack spec -f` or `spack solve -f`.  You can also set
concretization to *always* force in config with:

```yaml
spack:
    concretizer:
        force: true
```

- [x] make `concretizer:force` a configuration option
- [x] add `--force` to common concretizer arguments

.github/workflows/valid-style.yml

@@ -121,7 +121,7 @@ jobs:
       uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
       with:
         repository: haampie/circular-import-fighter
-        ref: 38c5473f619493d060d813c72c80eac86b3d2aeb
+        ref: 9a2c728c97f594dec0210e7f85cb7167eaf29176
         path: circular-import-fighter
     - name: Install dependencies
       working-directory: circular-import-fighter

lib/spack/spack/__init__.py

@@ -10,7 +10,7 @@
 import spack.util.git
 
 #: PEP440 canonical <major>.<minor>.<micro>.<devN> string
-__version__ = "1.0.0.dev0"
+__version__ = "0.24.0.dev0"
 spack_version = __version__
 
 

lib/spack/spack/build_systems/cuda.py

@@ -15,7 +15,7 @@ class CudaPackage(PackageBase):
     """Auxiliary class which contains CUDA variant, dependencies and conflicts
     and is meant to unify and facilitate its usage.
 
-    Maintainers: ax3l, Rombur, davidbeckingsale, pauleonix
+    Maintainers: ax3l, Rombur, davidbeckingsale
     """
 
     # https://docs.nvidia.com/cuda/cuda-compiler-driver-nvcc/index.html#gpu-feature-list
@@ -47,12 +47,6 @@ class CudaPackage(PackageBase):
         "89",
         "90",
         "90a",
-        "100",
-        "100a",
-        "101",
-        "101a",
-        "120",
-        "120a",
     )
 
     # FIXME: keep cuda and cuda_arch separate to make usage easier until
@@ -105,56 +99,39 @@ def compute_capabilities(arch_list: Iterable[str]) -> List[str]:
     # CUDA version vs Architecture
     # https://en.wikipedia.org/wiki/CUDA#GPUs_supported
     # https://docs.nvidia.com/cuda/cuda-toolkit-release-notes/index.html#deprecated-features
-    # Tesla support:
     depends_on("cuda@:6.0", when="cuda_arch=10")
     depends_on("cuda@:6.5", when="cuda_arch=11")
     depends_on("cuda@2.1:6.5", when="cuda_arch=12")
     depends_on("cuda@2.1:6.5", when="cuda_arch=13")
 
-    # Fermi support:
     depends_on("cuda@3.0:8.0", when="cuda_arch=20")
     depends_on("cuda@3.2:8.0", when="cuda_arch=21")
 
-    # Kepler support:
     depends_on("cuda@5.0:10.2", when="cuda_arch=30")
     depends_on("cuda@5.0:10.2", when="cuda_arch=32")
     depends_on("cuda@5.0:11.8", when="cuda_arch=35")
     depends_on("cuda@6.5:11.8", when="cuda_arch=37")
 
-    # Maxwell support:
     depends_on("cuda@6.0:", when="cuda_arch=50")
     depends_on("cuda@6.5:", when="cuda_arch=52")
     depends_on("cuda@6.5:", when="cuda_arch=53")
 
-    # Pascal support:
     depends_on("cuda@8.0:", when="cuda_arch=60")
     depends_on("cuda@8.0:", when="cuda_arch=61")
     depends_on("cuda@8.0:", when="cuda_arch=62")
 
-    # Volta support:
     depends_on("cuda@9.0:", when="cuda_arch=70")
-    # Turing support:
     depends_on("cuda@9.0:", when="cuda_arch=72")
     depends_on("cuda@10.0:", when="cuda_arch=75")
 
-    # Ampere support:
     depends_on("cuda@11.0:", when="cuda_arch=80")
     depends_on("cuda@11.1:", when="cuda_arch=86")
     depends_on("cuda@11.4:", when="cuda_arch=87")
-    # Ada support:
     depends_on("cuda@11.8:", when="cuda_arch=89")
 
-    # Hopper support:
     depends_on("cuda@12.0:", when="cuda_arch=90")
     depends_on("cuda@12.0:", when="cuda_arch=90a")
 
-    # Blackwell support:
-    depends_on("cuda@12.8:", when="cuda_arch=100")
-    depends_on("cuda@12.8:", when="cuda_arch=100a")
-    depends_on("cuda@12.8:", when="cuda_arch=101")
-    depends_on("cuda@12.8:", when="cuda_arch=101a")
-    depends_on("cuda@12.8:", when="cuda_arch=120")
-    depends_on("cuda@12.8:", when="cuda_arch=120a")
     # From the NVIDIA install guide we know of conflicts for particular
     # platforms (linux, darwin), architectures (x86, powerpc) and compilers
     # (gcc, clang). We don't restrict %gcc and %clang conflicts to
@@ -186,7 +163,6 @@ def compute_capabilities(arch_list: Iterable[str]) -> List[str]:
         conflicts("%gcc@12:", when="+cuda ^cuda@:11.8")
         conflicts("%gcc@13:", when="+cuda ^cuda@:12.3")
         conflicts("%gcc@14:", when="+cuda ^cuda@:12.6")
-        conflicts("%gcc@15:", when="+cuda ^cuda@:12.8")
         conflicts("%clang@12:", when="+cuda ^cuda@:11.4.0")
         conflicts("%clang@13:", when="+cuda ^cuda@:11.5")
         conflicts("%clang@14:", when="+cuda ^cuda@:11.7")
@@ -195,7 +171,6 @@ def compute_capabilities(arch_list: Iterable[str]) -> List[str]:
         conflicts("%clang@17:", when="+cuda ^cuda@:12.3")
         conflicts("%clang@18:", when="+cuda ^cuda@:12.5")
         conflicts("%clang@19:", when="+cuda ^cuda@:12.6")
-        conflicts("%clang@20:", when="+cuda ^cuda@:12.8")
 
         # https://gist.github.com/ax3l/9489132#gistcomment-3860114
         conflicts("%gcc@10", when="+cuda ^cuda@:11.4.0")

lib/spack/spack/ci/__init__.py

@@ -14,7 +14,7 @@
 import zipfile
 from collections import namedtuple
 from typing import Callable, Dict, List, Set
-from urllib.request import Request
+from urllib.request import HTTPHandler, Request, build_opener
 
 import llnl.util.filesystem as fs
 import llnl.util.tty as tty
@@ -62,8 +62,6 @@
 
 PushResult = namedtuple("PushResult", "success url")
 
-urlopen = web_util.urlopen  # alias for mocking in tests
-
 
 def get_change_revisions():
     """If this is a git repo get the revisions to use when checking
@@ -629,19 +627,29 @@ def download_and_extract_artifacts(url, work_dir):
     if token:
         headers["PRIVATE-TOKEN"] = token
 
-    request = Request(url, headers=headers, method="GET")
+    opener = build_opener(HTTPHandler)
+
+    request = Request(url, headers=headers)
+    request.get_method = lambda: "GET"
+
+    response = opener.open(request, timeout=SPACK_CDASH_TIMEOUT)
+    response_code = response.getcode()
+
+    if response_code != 200:
+        msg = f"Error response code ({response_code}) in reproduce_ci_job"
+        raise SpackError(msg)
+
     artifacts_zip_path = os.path.join(work_dir, "artifacts.zip")
-    os.makedirs(work_dir, exist_ok=True)
 
-    try:
-        response = urlopen(request, timeout=SPACK_CDASH_TIMEOUT)
-        with open(artifacts_zip_path, "wb") as out_file:
-            shutil.copyfileobj(response, out_file)
-    except OSError as e:
-        raise SpackError(f"Error fetching artifacts: {e}")
+    if not os.path.exists(work_dir):
+        os.makedirs(work_dir)
 
-    with zipfile.ZipFile(artifacts_zip_path) as zip_file:
-        zip_file.extractall(work_dir)
+    with open(artifacts_zip_path, "wb") as out_file:
+        shutil.copyfileobj(response, out_file)
+
+    zip_file = zipfile.ZipFile(artifacts_zip_path)
+    zip_file.extractall(work_dir)
+    zip_file.close()
 
     os.remove(artifacts_zip_path)
 

lib/spack/spack/cmd/common/arguments.py

@@ -504,11 +504,22 @@ class ConfigSetAction(argparse.Action):
     """
 
     def __init__(
-        self, option_strings, dest, const, default=None, required=False, help=None, metavar=None
+        self,
+        option_strings,
+        dest,
+        const,
+        default=None,
+        required=False,
+        help=None,
+        metavar=None,
+        require_environment=False,
     ):
         # save the config option we're supposed to set
         self.config_path = dest
 
+        # save whether the option requires an active env
+        self.require_environment = require_environment
+
         # destination is translated to a legal python identifier by
         # substituting '_' for ':'.
         dest = dest.replace(":", "_")
@@ -524,6 +535,11 @@ def __init__(
         )
 
     def __call__(self, parser, namespace, values, option_string):
+        if self.require_environment and not ev.active_environment():
+            raise argparse.ArgumentTypeError(
+                f"argument '{self.option_strings[-1]}' requires an environment"
+            )
+
         # Retrieve the name of the config option and set it to
         # the const from the constructor or a value from the CLI.
         # Note that this is only called if the argument is actually
@@ -545,6 +561,16 @@ def add_concretizer_args(subparser):
     Just substitute ``_`` for ``:``.
     """
     subgroup = subparser.add_argument_group("concretizer arguments")
+    subgroup.add_argument(
+        "-f",
+        "--force",
+        action=ConfigSetAction,
+        require_environment=True,
+        dest="concretizer:force",
+        const=True,
+        default=False,
+        help="allow changes to concretized specs in spack.lock (in an env)",
+    )
     subgroup.add_argument(
         "-U",
         "--fresh",

lib/spack/spack/cmd/concretize.py

@@ -15,9 +15,6 @@
 
 
 def setup_parser(subparser):
-    subparser.add_argument(
-        "-f", "--force", action="store_true", help="re-concretize even if already concretized"
-    )
     subparser.add_argument(
         "--test",
         default=None,
@@ -43,7 +40,7 @@ def concretize(parser, args):
         tests = False
 
     with env.write_transaction():
-        concretized_specs = env.concretize(force=args.force, tests=tests)
+        concretized_specs = env.concretize(tests=tests)
         if not args.quiet:
             if concretized_specs:
                 tty.msg(f"Concretized {plural(len(concretized_specs), 'spec')}:")

lib/spack/spack/container/__init__.py

@@ -57,7 +57,7 @@ def validate(configuration_file):
     # Set the default value of the concretization strategy to unify and
     # warn if the user explicitly set another value
     env_dict.setdefault("concretizer", {"unify": True})
-    if env_dict["concretizer"]["unify"] is not True:
+    if not env_dict["concretizer"]["unify"] is True:
         warnings.warn(
             '"concretizer:unify" is not set to "true", which means the '
             "generated image may contain different variants of the same "

lib/spack/spack/environment/environment.py

@@ -1427,7 +1427,7 @@ def is_develop(self, spec):
         """Returns true when the spec is built from local sources"""
         return spec.name in self.dev_specs
 
-    def concretize(self, force=False, tests=False):
+    def concretize(self, tests=False):
         """Concretize user_specs in this environment.
 
         Only concretizes specs that haven't been concretized yet unless
@@ -1437,8 +1437,6 @@ def concretize(self, force=False, tests=False):
         write out a lockfile containing concretized specs.
 
         Arguments:
-            force (bool): re-concretize ALL specs, even those that were
-               already concretized
             tests (bool or list or set): False to run no tests, True to test
                 all packages, or a list of package names to run tests for some
 
@@ -1446,7 +1444,7 @@ def concretize(self, force=False, tests=False):
             List of specs that have been concretized. Each entry is a tuple of
             the user spec and the corresponding concretized spec.
         """
-        if force:
+        if spack.config.get("concretizer:force", False):
             # Clear previously concretized specs
             self.concretized_user_specs = []
             self.concretized_order = []

lib/spack/spack/installer.py

@@ -814,7 +814,7 @@ def get_depflags(self, pkg: "spack.package_base.PackageBase") -> int:
         # Include build dependencies if pkg is going to be built from sources, or
         # if build deps are explicitly requested.
         if include_build_deps or not (
-            cache_only or pkg.spec.installed and pkg.spec.dag_hash() not in self.overwrite
+            cache_only or pkg.spec.installed and not pkg.spec.dag_hash() in self.overwrite
         ):
             depflag |= dt.BUILD
         if self.run_tests(pkg):

lib/spack/spack/mirrors/mirror.py

@@ -64,7 +64,7 @@ def from_local_path(path: str):
     @staticmethod
     def from_url(url: str):
         """Create an anonymous mirror by URL. This method validates the URL."""
-        if urllib.parse.urlparse(url).scheme not in supported_url_schemes:
+        if not urllib.parse.urlparse(url).scheme in supported_url_schemes:
             raise ValueError(
                 f'"{url}" is not a valid mirror URL. '
                 f"Scheme must be one of {supported_url_schemes}."

lib/spack/spack/package_base.py

@@ -697,6 +697,9 @@ class PackageBase(WindowsRPath, PackageViewMixin, metaclass=PackageMeta):
     #: Verbosity level, preserved across installs.
     _verbose = None
 
+    #: index of patches by sha256 sum, built lazily
+    _patches_by_hash = None
+
     #: Package homepage where users can find more information about the package
     homepage: Optional[str] = None
 

lib/spack/spack/reporters/cdash.py

@@ -1,7 +1,6 @@
 # Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-import codecs
 import collections
 import hashlib
 import os
@@ -14,7 +13,7 @@
 import xml.sax.saxutils
 from typing import Dict, Optional
 from urllib.parse import urlencode
-from urllib.request import Request
+from urllib.request import HTTPSHandler, Request, build_opener
 
 import llnl.util.tty as tty
 from llnl.util.filesystem import working_dir
@@ -25,10 +24,10 @@
 import spack.spec
 import spack.tengine
 import spack.util.git
-import spack.util.web as web_util
 from spack.error import SpackError
 from spack.util.crypto import checksum
 from spack.util.log_parse import parse_log_events
+from spack.util.web import ssl_create_default_context
 
 from .base import Reporter
 from .extract import extract_test_parts
@@ -434,6 +433,7 @@ def upload(self, filename):
         # Compute md5 checksum for the contents of this file.
         md5sum = checksum(hashlib.md5, filename, block_size=8192)
 
+        opener = build_opener(HTTPSHandler(context=ssl_create_default_context()))
         with open(filename, "rb") as f:
             params_dict = {
                 "build": self.buildname,
@@ -443,21 +443,26 @@ def upload(self, filename):
             }
             encoded_params = urlencode(params_dict)
             url = "{0}&{1}".format(self.cdash_upload_url, encoded_params)
-            request = Request(url, data=f, method="PUT")
+            request = Request(url, data=f)
             request.add_header("Content-Type", "text/xml")
             request.add_header("Content-Length", os.path.getsize(filename))
             if self.authtoken:
                 request.add_header("Authorization", "Bearer {0}".format(self.authtoken))
             try:
-                response = web_util.urlopen(request, timeout=SPACK_CDASH_TIMEOUT)
+                # By default, urllib2 only support GET and POST.
+                # CDash expects this file to be uploaded via PUT.
+                request.get_method = lambda: "PUT"
+                response = opener.open(request, timeout=SPACK_CDASH_TIMEOUT)
                 if self.current_package_name not in self.buildIds:
-                    resp_value = codecs.getreader("utf-8")(response).read()
+                    resp_value = response.read()
+                    if isinstance(resp_value, bytes):
+                        resp_value = resp_value.decode("utf-8")
                     match = self.buildid_regexp.search(resp_value)
                     if match:
                         buildid = match.group(1)
                         self.buildIds[self.current_package_name] = buildid
             except Exception as e:
-                print(f"Upload to CDash failed: {e}")
+                print("Upload to CDash failed: {0}".format(e))
 
     def finalize_report(self):
         if self.buildIds:

lib/spack/spack/schema/concretizer.py

@@ -15,6 +15,7 @@
         "type": "object",
         "additionalProperties": False,
         "properties": {
+            "force": {"type": "boolean", "default": False},
             "reuse": {
                 "oneOf": [
                     {"type": "boolean"},

lib/spack/spack/test/ci.py

@@ -1,10 +1,8 @@
 # Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-import io
 import os
 import subprocess
-from urllib.error import HTTPError
 
 import pytest
 
@@ -17,7 +15,6 @@
 import spack.paths as spack_paths
 import spack.repo as repo
 import spack.util.git
-from spack.test.conftest import MockHTTPResponse
 
 pytestmark = [pytest.mark.usefixtures("mock_packages")]
 
@@ -165,8 +162,38 @@ def test_import_signing_key(mock_gnupghome):
     ci.import_signing_key(signing_key)
 
 
-def test_download_and_extract_artifacts(tmpdir, monkeypatch):
-    monkeypatch.setenv("GITLAB_PRIVATE_TOKEN", "faketoken")
+class FakeWebResponder:
+    def __init__(self, response_code=200, content_to_read=[]):
+        self._resp_code = response_code
+        self._content = content_to_read
+        self._read = [False for c in content_to_read]
+
+    def open(self, request, data=None, timeout=object()):
+        return self
+
+    def getcode(self):
+        return self._resp_code
+
+    def read(self, length=None):
+        if len(self._content) <= 0:
+            return None
+
+        if not self._read[-1]:
+            return_content = self._content[-1]
+            if length:
+                self._read[-1] = True
+            else:
+                self._read.pop()
+                self._content.pop()
+            return return_content
+
+        self._read.pop()
+        self._content.pop()
+        return None
+
+
+def test_download_and_extract_artifacts(tmpdir, monkeypatch, working_env):
+    os.environ.update({"GITLAB_PRIVATE_TOKEN": "faketoken"})
 
     url = "https://www.nosuchurlexists.itsfake/artifacts.zip"
     working_dir = os.path.join(tmpdir.strpath, "repro")
@@ -174,13 +201,10 @@ def test_download_and_extract_artifacts(tmpdir, monkeypatch):
         spack_paths.test_path, "data", "ci", "gitlab", "artifacts.zip"
     )
 
-    def _urlopen_OK(*args, **kwargs):
-        with open(test_artifacts_path, "rb") as f:
-            return MockHTTPResponse(
-                "200", "OK", {"Content-Type": "application/zip"}, io.BytesIO(f.read())
-            )
+    with open(test_artifacts_path, "rb") as fd:
+        fake_responder = FakeWebResponder(content_to_read=[fd.read()])
 
-    monkeypatch.setattr(ci, "urlopen", _urlopen_OK)
+    monkeypatch.setattr(ci, "build_opener", lambda handler: fake_responder)
 
     ci.download_and_extract_artifacts(url, working_dir)
 
@@ -190,11 +214,7 @@ def _urlopen_OK(*args, **kwargs):
     found_install = fs.find(working_dir, "install.sh")
     assert len(found_install) == 1
 
-    def _urlopen_500(*args, **kwargs):
-        raise HTTPError(url, 500, "Internal Server Error", {}, None)
-
-    monkeypatch.setattr(ci, "urlopen", _urlopen_500)
-
+    fake_responder._resp_code = 400
     with pytest.raises(spack.error.SpackError):
         ci.download_and_extract_artifacts(url, working_dir)
 

lib/spack/spack/test/concretization/requirements.py

@@ -182,7 +182,7 @@ def test_requirement_adds_version_satisfies(
 
     # Sanity check: early version of T does not include U
     s0 = spack.concretize.concretize_one("t@2.0")
-    assert "u" not in s0
+    assert not ("u" in s0)
 
     conf_str = """\
 packages:

lib/spack/spack/util/spack_yaml.py

@@ -436,8 +436,8 @@ def _dump_annotated(handler, data, stream=None):
     width = max(clen(a) for a in _ANNOTATIONS)
     formats = ["%%-%ds  %%s\n" % (width + cextra(a)) for a in _ANNOTATIONS]
 
-    for fmt, annotation, line in zip(formats, _ANNOTATIONS, lines):
-        stream.write(fmt % (annotation, line))
+    for f, a, l in zip(formats, _ANNOTATIONS, lines):
+        stream.write(f % (a, l))
 
     if getvalue:
         return getvalue()

share/spack/gitlab/cloud_pipelines/.gitlab-ci.yml

@@ -539,6 +539,57 @@ data-vis-sdk-build:
     - artifacts: True
       job: data-vis-sdk-generate
 
+########################################
+# AWS ISC Applications (x86_64)
+########################################
+
+# Call this AFTER .*-generate
+.aws-isc-overrides:
+  # This controls image for generate step; build step is controlled by spack.yaml
+  # Note that generator emits OS info for build so these should be the same.
+  image: { "name": "ghcr.io/spack/e4s-amazonlinux-2:v2023-03-09", "entrypoint": [""] }
+
+.aws-isc:
+  extends: [ ".linux_x86_64_v3" ]
+  variables:
+    SPACK_CI_STACK_NAME: aws-isc
+
+aws-isc-generate:
+  extends: [ ".aws-isc", ".generate-x86_64", ".aws-isc-overrides", ".tags-x86_64_v4" ]
+
+aws-isc-build:
+  extends: [ ".aws-isc", ".build" ]
+  trigger:
+    include:
+      - artifact: jobs_scratch_dir/cloud-ci-pipeline.yml
+        job: aws-isc-generate
+    strategy: depend
+  needs:
+    - artifacts: True
+      job: aws-isc-generate
+
+# Parallel Pipeline for aarch64 (reuses override image, but generates and builds on aarch64)
+
+.aws-isc-aarch64:
+  extends: [ ".linux_aarch64" ]
+  variables:
+    SPACK_CI_STACK_NAME: aws-isc-aarch64
+
+aws-isc-aarch64-generate:
+  extends: [ ".aws-isc-aarch64", ".generate-aarch64", ".aws-isc-overrides" ]
+
+aws-isc-aarch64-build:
+  extends: [ ".aws-isc-aarch64", ".build" ]
+  trigger:
+    include:
+      - artifact: jobs_scratch_dir/cloud-ci-pipeline.yml
+        job: aws-isc-aarch64-generate
+    strategy: depend
+  needs:
+    - artifacts: True
+      job: aws-isc-aarch64-generate
+
+
 ########################################
 # Spack Tutorial
 ########################################

share/spack/gitlab/cloud_pipelines/stacks/aws-isc-aarch64/spack.yaml

@@ -56,7 +56,7 @@ spack:
   definitions:
 
   - compiler_specs:
-    - gcc@11
+    - gcc@11.2
     # Licensing OK?
     # - intel-oneapi-compilers@2022.1
     # - nvhpc

share/spack/gitlab/cloud_pipelines/stacks/aws-isc/spack.yaml

@@ -56,7 +56,7 @@ spack:
   definitions:
 
   - compiler_specs:
-    - gcc@11
+    - gcc@11.2
     # Licensing OK?
     # - intel-oneapi-compilers@2022.1
     # - nvhpc

share/spack/gitlab/cloud_pipelines/stacks/hep/spack.yaml

@@ -83,7 +83,7 @@ spack:
   - pythia8 +evtgen +fastjet +hdf5 +hepmc +hepmc3 +lhapdf ~madgraph5amc +python +rivet ~root # pythia8 and root circularly depend
   - rivet hepmc=3
   - root +davix +dcache +examples +fftw +fits +fortran +gdml +graphviz +gsl +http +math +minuit +mlp +mysql +opengl +postgres +pythia8 +python +r +roofit +root7 +rpath ~shadow +spectrum +sqlite +ssl +tbb +threads +tmva +unuran +vc +vdt +veccore +webgui +x +xml +xrootd
-  - sherpa +analysis ~blackhat +gzip +hepmc3 +hepmc3root +lhapdf +lhole +openloops +pythia ~python ~recola ~rivet +root +ufo cxxstd=20
+  - sherpa +analysis ~blackhat +gzip +hepmc3 +hepmc3root +lhapdf +lhole +openloops +pythia ~python ~recola ~rivet +root +ufo
   - tauola +hepmc3 +lhapdf cxxstd=20
   - thepeg hepmc=3 ~rivet
   - vecgeom +gdml +geant4 +root

share/spack/gitlab/cloud_pipelines/stacks/tutorial/spack.yaml

@@ -18,7 +18,7 @@ spack:
         - hdf5+hl+mpi ^mpich
         - trilinos
         - trilinos +hdf5 ^hdf5+hl+mpi ^mpich
-        - gcc@12
+        - gcc@12.3.0
         - mpileaks
         - lmod@8.7.18
         - environment-modules

var/spack/repos/builtin/packages/ace/package.py

@@ -32,7 +32,7 @@ def edit(self, spec, prefix):
         # Dictionary mapping: compiler-name : ACE config-label
         supported = {"intel": "_icc", "gcc": ""}
 
-        if self.compiler.name not in supported:
+        if not (self.compiler.name in supported):
             raise Exception(
                 "compiler " + self.compiler.name + " not supported in ace spack-package"
             )

var/spack/repos/builtin/packages/amrex/package.py

@@ -25,7 +25,6 @@ class Amrex(CMakePackage, CudaPackage, ROCmPackage):
     license("BSD-3-Clause")
 
     version("develop", branch="development")
-    version("25.02", sha256="2680a5a9afba04e211cd48d27799c5a25abbb36c6c3d2b6c13cd4757c7176b23")
     version("25.01", sha256="29eb35cf67d66b0fd0654282454c210abfadf27fcff8478b256e3196f237c74f")
     version("24.12", sha256="ca4b41ac73fabb9cf3600b530c9823eb3625f337d9b7b9699c1089e81c67fc67")
     version("24.11", sha256="31cc37b39f15e02252875815f6066046fc56a479bf459362b9889b0d6a202df6")
@@ -361,7 +360,7 @@ def cmake_args(self):
             args.append("-DAMReX_GPU_BACKEND=SYCL")
             # SYCL GPU backend only supported with Intel's oneAPI or DPC++ compilers
             sycl_compatible_compilers = ["icpx"]
-            if os.path.basename(self.compiler.cxx) not in sycl_compatible_compilers:
+            if not (os.path.basename(self.compiler.cxx) in sycl_compatible_compilers):
                 raise InstallError(
                     "AMReX's SYCL GPU Backend requires the oneAPI CXX (icpx) compiler."
                 )

var/spack/repos/builtin/packages/berkeleygw/package.py

@@ -118,7 +118,7 @@ class Berkeleygw(MakefilePackage):
     def edit(self, spec, prefix):
         # archive is a tar file, despite the .gz expension
         tar = which("tar")
-        tar("-x", "-o", "-f", self.stage.archive_file, "--strip-components=1")
+        tar("-x", "-f", self.stage.archive_file, "--strip-components=1")
 
         # get generic arch.mk template
         if spec.satisfies("+mpi"):

var/spack/repos/builtin/packages/charmpp/package.py

@@ -276,7 +276,7 @@ def charmarch(self):
     #            build-target=LIBS backend={0}'.format(b))
 
     def install(self, spec, prefix):
-        if "backend=mpi" not in self.spec or "backend=netlrts" not in self.spec:
+        if not ("backend=mpi" in self.spec) or not ("backend=netlrts" in self.spec):
             if self.spec.satisfies("+pthreads"):
                 raise InstallError(
                     "The pthreads option is only available on the Netlrts and MPI network layers."

var/spack/repos/builtin/packages/cp2k/package.py

@@ -159,7 +159,6 @@ class Cp2k(MakefilePackage, CMakePackage, CudaPackage, ROCmPackage):
     )
 
     depends_on("python@3", type="build")
-    depends_on("pkgconfig", type="build", when="build_system=cmake")
 
     depends_on("blas")
     depends_on("lapack")
@@ -197,14 +196,13 @@ class Cp2k(MakefilePackage, CMakePackage, CudaPackage, ROCmPackage):
             )
 
     with when("+libxc"):
-        depends_on("pkgconfig", type="build", when="@7.0: ^libxc@:6")
+        depends_on("pkgconfig", type="build", when="@7.0:")
         depends_on("libxc@4.0.3:4", when="@7.0:8.1")
         depends_on("libxc@5.1.3:5.1", when="@8.2:8")
         depends_on("libxc@5.1.7:5.1", when="@9:2022.2")
         depends_on("libxc@6.1:", when="@2023.1:")
         depends_on("libxc@6.2:", when="@2023.2:")
         depends_on("libxc@:6", when="@:2024.3")
-        depends_on("libxc@7 build_system=cmake", when="@2025.2:")
 
     with when("+spla"):
         depends_on("spla+cuda+fortran", when="+cuda")

var/spack/repos/builtin/packages/cppgsl/package.py

@@ -15,7 +15,6 @@ class Cppgsl(CMakePackage):
     license("MIT")
 
     version("main", branch="main")
-    version("4.1.0", sha256="0a227fc9c8e0bf25115f401b9a46c2a68cd28f299d24ab195284eb3f1d7794bd")
     version("4.0.0", sha256="f0e32cb10654fea91ad56bde89170d78cfbf4363ee0b01d8f097de2ba49f6ce9")
     version("3.1.0", sha256="d3234d7f94cea4389e3ca70619b82e8fb4c2f33bb3a070799f1e18eef500a083")
     version("2.1.0", sha256="ef73814657b073e1be86c8f7353718771bf4149b482b6cb54f99e79b23ff899d")
@@ -33,7 +32,6 @@ class Cppgsl(CMakePackage):
     )
 
     depends_on("cmake@3.1.3:", type="build")
-    depends_on("cmake@3.14:", type="build", when="@4.1:")
 
     def cmake_args(self):
         return [

var/spack/repos/builtin/packages/creduce/package.py

@@ -25,7 +25,7 @@ class Creduce(CMakePackage):
     depends_on("flex")
     depends_on("libxml2")
     depends_on("llvm")
-    depends_on("llvm@8.0", when="@:2.10")
+    depends_on("llvm@8.0.0", when="@:2.10")
     depends_on("perl")
     depends_on("perl-exporter-lite")
     depends_on("perl-file-which")

var/spack/repos/builtin/packages/cuda/package.py

@@ -21,16 +21,6 @@
 #    format returned by platform.system() and 'arch' by platform.machine()
 
 _versions = {
-    "12.8.0": {
-        "Linux-aarch64": (
-            "5bc211f00c4f544da6e3fc3a549b3eb0a7e038439f5f3de71caa688f2f6b132c",
-            "https://developer.download.nvidia.com/compute/cuda/12.8.0/local_installers/cuda_12.8.0_570.86.10_linux_sbsa.run",
-        ),
-        "Linux-x86_64": (
-            "610867dcd6d94c4e36c4924f1d01b9db28ec08164e8af6c764f21b84200695f8",
-            "https://developer.download.nvidia.com/compute/cuda/12.8.0/local_installers/cuda_12.8.0_570.86.10_linux.run",
-        ),
-    },
     "12.6.3": {
         "Linux-aarch64": (
             "213ea63a6357020978a8b0a79a8c9d12a2a5941afa1cdc69d5a3f933fa8bed04",

var/spack/repos/builtin/packages/cusz/package.py

@@ -19,10 +19,7 @@ class Cusz(CMakePackage, CudaPackage):
     conflicts("cuda_arch=none", when="+cuda")
 
     version("develop", branch="develop")
-    version("0.14.0", commit="e57fd7cd9df923164af9dd307b0b3d37dd9df137")
-    version("0.9.0rc3", commit="c3c3a74d006c6de3c145255241fb181682bd1492")
-    # 0.9.0rc1 was listed as 0.6.0 for a while in spack
-    version("0.9.0rc1", commit="cafed521dc338fe2159ebb5b09a36fc318524bf7")
+    version("0.6.0", commit="cafed521dc338fe2159ebb5b09a36fc318524bf7")
     version("0.3.1", commit="02be3cbd07db467decaf45ec9eb593ba6173c809")
     version("0.3", sha256="0feb4f7fd64879fe147624dd5ad164adf3983f79b2e0383d35724f8d185dcb11")
 
@@ -34,10 +31,6 @@ class Cusz(CMakePackage, CudaPackage):
 
     depends_on("cub", when="^cuda@:10.2.89")
 
-    patch("thrust-includes.patch", when="@0.10:0.14 ^cuda@12.8:")
-    patch("thrust-includes-0.9.patch", when="@0.9 ^cuda@12.8:")
-    conflicts("^cuda@12.8:", when="@:0.8")
-
     def cmake_args(self):
         cuda_arch = self.spec.variants["cuda_arch"].value
         args = ["-DBUILD_TESTING=OFF", ("-DCMAKE_CUDA_ARCHITECTURES=%s" % cuda_arch)]

var/spack/repos/builtin/packages/cusz/thrust-includes-0.9.patch

@@ -1,27 +0,0 @@
-diff --git a/src/stat/detail/compare.thrust.inl b/src/stat/detail/compare.thrust.inl
-index ce49408..ec8d650 100644
---- a/src/stat/detail/compare.thrust.inl
-+++ b/src/stat/detail/compare.thrust.inl
-@@ -18,6 +18,9 @@
- // #include <thrust/iterator/constant_iterator.h>
- #include <thrust/device_ptr.h>
- #include <thrust/execution_policy.h>
-+#include <thrust/functional.h>
-+#include <thrust/iterator/zip_iterator.h>
-+#include <thrust/transform_reduce.h>
- #include <thrust/tuple.h>
- 
- #include "cusz/type.h"
-diff --git a/src/stat/detail/maxerr.thrust.inl b/src/stat/detail/maxerr.thrust.inl
-index 2415655..9b31e88 100644
---- a/src/stat/detail/maxerr.thrust.inl
-+++ b/src/stat/detail/maxerr.thrust.inl
-@@ -18,6 +18,8 @@
- // #include <thrust/iterator/constant_iterator.h>
- #include <thrust/device_ptr.h>
- #include <thrust/execution_policy.h>
-+#include <thrust/extrema.h>
-+#include <thrust/transform.h>
- 
- #include "cusz/type.h"
- 

var/spack/repos/builtin/packages/cusz/thrust-includes.patch

@@ -1,27 +0,0 @@
-diff --git a/psz/src/stat/detail/compare.thrust.inl b/psz/src/stat/detail/compare.thrust.inl
-index f35c7df..719d68f 100644
---- a/psz/src/stat/detail/compare.thrust.inl
-+++ b/psz/src/stat/detail/compare.thrust.inl
-@@ -11,6 +11,9 @@
- 
- #include <thrust/device_ptr.h>
- #include <thrust/execution_policy.h>
-+#include <thrust/functional.h>
-+#include <thrust/iterator/zip_iterator.h>
-+#include <thrust/transform_reduce.h>
- #include <thrust/tuple.h>
- 
- #include "cusz/type.h"
-diff --git a/psz/src/stat/detail/maxerr.thrust.inl b/psz/src/stat/detail/maxerr.thrust.inl
-index f7a4db5..ce7925a 100644
---- a/psz/src/stat/detail/maxerr.thrust.inl
-+++ b/psz/src/stat/detail/maxerr.thrust.inl
-@@ -11,6 +11,8 @@
- 
- #include <thrust/device_ptr.h>
- #include <thrust/execution_policy.h>
-+#include <thrust/extrema.h>
-+#include <thrust/transform.h>
- 
- #include "cusz/type.h"
- #include "port.hh"

var/spack/repos/builtin/packages/dav-sdk/package.py

@@ -30,7 +30,7 @@ def dav_sdk_depends_on(spec, when=None, propagate=None):
     # Map the propagated variants to the dependency variant.  Some packages may need
     # overrides to propagate a dependency as something else, e.g., {"visit": "libsim"}.
     # Most call-sites will just use a list.
-    if type(propagate) is not dict:
+    if not type(propagate) is dict:
         propagate = dict([(v, v) for v in propagate])
 
     # Determine the base variant

var/spack/repos/builtin/packages/dla-future/package.py

@@ -73,7 +73,7 @@ class DlaFuture(CMakePackage, CudaPackage, ROCmPackage):
     generator("ninja")
 
     depends_on("cmake@3.22:", type="build")
-    depends_on("pkgconfig", type=("build", "link"))
+    depends_on("pkgconfig", type="build")
     depends_on("doxygen", type="build", when="+doc")
     depends_on("mpi")
 

var/spack/repos/builtin/packages/ecp-data-vis-sdk/package.py

@@ -30,7 +30,7 @@ def dav_sdk_depends_on(spec, when=None, propagate=None):
     # Map the propagated variants to the dependency variant.  Some packages may need
     # overrides to propagate a dependency as something else, e.g., {"visit": "libsim"}.
     # Most call-sites will just use a list.
-    if type(propagate) is not dict:
+    if not type(propagate) is dict:
         propagate = dict([(v, v) for v in propagate])
 
     # Determine the base variant

var/spack/repos/builtin/packages/fcgi/package.py

@@ -14,10 +14,12 @@ class Fcgi(AutotoolsPackage):
     homepage = "https://fastcgi-archives.github.io/"
     url = "https://github.com/FastCGI-Archives/fcgi2/archive/refs/tags/2.4.2.tar.gz"
 
+    depends_on("autoconf", type="build")
+    depends_on("automake", type="build")
+    depends_on("libtool", type="build")
+
     license("OML")
 
-    version("2.4.4", sha256="c0e0d9cc7d1e456d7278c974e2826f593ef5ca555783eba81e7e9c1a07ae0ecc")
-    version("2.4.3", sha256="5273bc54c28215d81b9bd78f937a9bcdd4fe94e41ccd8d7c991aa8a01b50b70e")
     version("2.4.2", sha256="1fe83501edfc3a7ec96bb1e69db3fd5ea1730135bd73ab152186fd0b437013bc")
     version(
         "2.4.1-SNAP-0910052249",
@@ -25,10 +27,7 @@ class Fcgi(AutotoolsPackage):
         url="https://github.com/FastCGI-Archives/FastCGI.com/raw/master/original_snapshot/fcgi-2.4.1-SNAP-0910052249.tar.gz",
     )
 
-    depends_on("c", type="build")
-    depends_on("cxx", type="build")
-    depends_on("autoconf", type="build")
-    depends_on("automake", type="build")
-    depends_on("libtool", type="build")
+    depends_on("c", type="build")  # generated
+    depends_on("cxx", type="build")  # generated
 
     parallel = False

var/spack/repos/builtin/packages/func/package.py

@@ -1,45 +0,0 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack.package import *
-
-
-class Func(CMakePackage):
-    """(Function Comparator) is a C++ tool for quickly profiling the performance
-    of various different abstracted implementations of mathematical function evaluations"""
-
-    homepage = "https://github.com/uofs-simlab/func"
-    url = "https://github.com/uofs-simlab/func/archive/refs/tags/v2.0.tar.gz"
-    git = "https://github.com/uofs-simlab/func"
-
-    license("GPL/LGPL")
-    maintainers("Chrismarsh")
-
-    version("master", branch="master")
-    version("2.2.0", sha256="bd4ecbc27096fa0b913fb46059e02298a96afd4912d549eb68b5c4c090999976")
-    version("2.1.0", sha256="150cc53fe90df16a1b06f34c3293f4aef4557ce42b30e1095e7570b1c367b9f7")
-    version("2.0", sha256="ca25b960c72bebc5b0be0fedc189ef24e669d21a7571fd59f751a187fb6c1cea")
-    version("1.0", sha256="60dbc353f82208efde08eeaea1fabd15e805b6c517a8e033d168027c89884fbf")
-
-    variant(
-        "armadillo",
-        default=True,
-        description="Use Armadillo to enable ChebyInterpTables or PadeTable tables.",
-    )
-    variant("openmp", default=True, description="Enable OpenMP")
-    variant("examples", default=False, description="Build examples")
-
-    depends_on("cxx", type="build")
-
-    depends_on("boost")
-    depends_on("armadillo", when="+armadillo")
-    depends_on("llvm-openmp", when="%apple-clang +openmp")
-
-    def cmake_args(self):
-        args = [
-            self.define_from_variant("FUNC_USE_OPENMP", "openmp"),
-            self.define_from_variant("FUNC_USE_ARMADILLO", "armadillo"),
-            self.define_from_variant("BUILD_EXAMPLES", "examples"),
-        ]
-        return args

var/spack/repos/builtin/packages/g4vg/package.py

@@ -1,36 +0,0 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack.package import *
-
-
-class G4vg(CMakePackage):
-    """Generate VecGeom geometry representations from in-memory Geant4 geometry."""
-
-    homepage = "https://github.com/celeritas-project/g4vg"
-    url = "https://github.com/celeritas-project/g4vg/releases/download/v1.0.1/g4vg-1.0.1.tar.gz"
-
-    maintainers("sethrj", "drbenmorgan")
-
-    license("Apache-2.0", checked_by="sethrj")
-
-    version("1.0.1", sha256="add7ce4bc37889cac2101323a997cea8574b18da6cbeffdab44a2b714d134e99")
-
-    variant("debug", default=False, description="Enable runtime debug assertions")
-    variant("shared", default=True, description="Build shared libraries")
-
-    depends_on("cxx", type="build")
-    depends_on("vecgeom@1.2.8:")
-    depends_on("geant4")
-
-    def cmake_args(self):
-        define = self.define
-        from_variant = self.define_from_variant
-        args = [
-            from_variant("BUILD_SHARED_LIBS", "shared"),
-            from_variant("G4VG_DEBUG", "debug"),
-            define("G4VG_BUILD_TESTS", False),
-        ]
-
-        return args

var/spack/repos/builtin/packages/gcc/package.py

@@ -38,99 +38,69 @@ class Gcc(AutotoolsPackage, GNUMirrorPackage, CompilerPackage):
     version("master", branch="master")
 
     version("14.2.0", sha256="a7b39bc69cbf9e25826c5a60ab26477001f7c08d85cec04bc0e29cabed6f3cc9")
+    version("14.1.0", sha256="e283c654987afe3de9d8080bc0bd79534b5ca0d681a73a11ff2b5d3767426840")
+
     version("13.3.0", sha256="0845e9621c9543a13f484e94584a49ffc0129970e9914624235fc1d061a0c083")
+    version("13.2.0", sha256="e275e76442a6067341a27f04c5c6b83d8613144004c0413528863dc6b5c743da")
+    version("13.1.0", sha256="61d684f0aa5e76ac6585ad8898a2427aade8979ed5e7f85492286c4dfc13ee86")
+
     version("12.4.0", sha256="704f652604ccbccb14bdabf3478c9511c89788b12cb3bbffded37341916a9175")
+    version("12.3.0", sha256="949a5d4f99e786421a93b532b22ffab5578de7321369975b91aec97adfda8c3b")
+    version("12.2.0", sha256="e549cf9cf3594a00e27b6589d4322d70e0720cdd213f39beb4181e06926230ff")
+    version("12.1.0", sha256="62fd634889f31c02b64af2c468f064b47ad1ca78411c45abe6ac4b5f8dd19c7b")
+
     version("11.5.0", sha256="a6e21868ead545cf87f0c01f84276e4b5281d672098591c1c896241f09363478")
+    version("11.4.0", sha256="3f2db222b007e8a4a23cd5ba56726ef08e8b1f1eb2055ee72c1402cea73a8dd9")
+    version("11.3.0", sha256="b47cf2818691f5b1e21df2bb38c795fac2cfbd640ede2d0a5e1c89e338a3ac39")
+    version("11.2.0", sha256="d08edc536b54c372a1010ff6619dd274c0f1603aa49212ba20f7aa2cda36fa8b")
+    version("11.1.0", sha256="4c4a6fb8a8396059241c2e674b85b351c26a5d678274007f076957afa1cc9ddf")
+
     version("10.5.0", sha256="25109543fdf46f397c347b5d8b7a2c7e5694a5a51cce4b9c6e1ea8a71ca307c1")
+    version("10.4.0", sha256="c9297d5bcd7cb43f3dfc2fed5389e948c9312fd962ef6a4ce455cff963ebe4f1")
+    version("10.3.0", sha256="64f404c1a650f27fc33da242e1f2df54952e3963a49e06e73f6940f3223ac344")
+    version("10.2.0", sha256="b8dd4368bb9c7f0b98188317ee0254dd8cc99d1e3a18d0ff146c855fe16c1d8c")
+    version("10.1.0", sha256="b6898a23844b656f1b68691c5c012036c2e694ac4b53a8918d4712ad876e7ea2")
+
     version("9.5.0", sha256="27769f64ef1d4cd5e2be8682c0c93f9887983e6cfd1a927ce5a0a2915a95cf8f")
+    version("9.4.0", sha256="c95da32f440378d7751dd95533186f7fc05ceb4fb65eb5b85234e6299eb9838e")
+    version("9.3.0", sha256="71e197867611f6054aa1119b13a0c0abac12834765fe2d81f35ac57f84f742d1")
+    version("9.2.0", sha256="ea6ef08f121239da5695f76c9b33637a118dcf63e24164422231917fa61fb206")
+    version("9.1.0", sha256="79a66834e96a6050d8fe78db2c3b32fb285b230b855d0a66288235bc04b327a0")
+
     version("8.5.0", sha256="d308841a511bb830a6100397b0042db24ce11f642dab6ea6ee44842e5325ed50")
+    version("8.4.0", sha256="e30a6e52d10e1f27ed55104ad233c30bd1e99cfb5ff98ab022dc941edd1b2dd4")
+    version("8.3.0", sha256="64baadfe6cc0f4947a84cb12d7f0dfaf45bb58b7e92461639596c21e02d97d2c")
+    version("8.2.0", sha256="196c3c04ba2613f893283977e6011b2345d1cd1af9abeac58e916b1aab3e0080")
+    version("8.1.0", sha256="1d1866f992626e61349a1ccd0b8d5253816222cdc13390dcfaa74b093aa2b153")
+
     version("7.5.0", sha256="b81946e7f01f90528a1f7352ab08cc602b9ccc05d4e44da4bd501c5a189ee661")
+    version("7.4.0", sha256="eddde28d04f334aec1604456e536416549e9b1aa137fc69204e65eb0c009fe51")
+    version("7.3.0", sha256="832ca6ae04636adbb430e865a1451adf6979ab44ca1c8374f61fba65645ce15c")
+    version("7.2.0", sha256="1cf7adf8ff4b5aa49041c8734bbcf1ad18cc4c94d0029aae0f4e48841088479a")
+    version("7.1.0", sha256="8a8136c235f64c6fef69cac0d73a46a1a09bb250776a050aec8f9fc880bebc17")
+
     version("6.5.0", sha256="7ef1796ce497e89479183702635b14bb7a46b53249209a5e0f999bebf4740945")
+    version("6.4.0", sha256="850bf21eafdfe5cd5f6827148184c08c4a0852a37ccf36ce69855334d2c914d4")
+    version("6.3.0", sha256="f06ae7f3f790fbf0f018f6d40e844451e6bc3b7bc96e128e63b09825c1f8b29f")
+    version("6.2.0", sha256="9944589fc722d3e66308c0ce5257788ebd7872982a718aa2516123940671b7c5")
+    version("6.1.0", sha256="09c4c85cabebb971b1de732a0219609f93fc0af5f86f6e437fd8d7f832f1a351")
+
     version("5.5.0", sha256="530cea139d82fe542b358961130c69cfde8b3d14556370b65823d2f91f0ced87")
+    version("5.4.0", sha256="608df76dec2d34de6558249d8af4cbee21eceddbcb580d666f7a5a583ca3303a")
+    version("5.3.0", sha256="b84f5592e9218b73dbae612b5253035a7b34a9a1f7688d2e1bfaaf7267d5c4db")
+    version("5.2.0", sha256="5f835b04b5f7dd4f4d2dc96190ec1621b8d89f2dc6f638f9f8bc1b1014ba8cad")
+    version("5.1.0", sha256="b7dafdf89cbb0e20333dbf5b5349319ae06e3d1a30bf3515b5488f7e89dca5ad")
+
     version("4.9.4", sha256="6c11d292cd01b294f9f84c9a59c230d80e9e4a47e5c6355f046bb36d4f358092")
+    version("4.9.3", sha256="2332b2a5a321b57508b9031354a8503af6fdfb868b8c1748d33028d100a8b67e")
+    version("4.9.2", sha256="2020c98295856aa13fda0f2f3a4794490757fc24bcca918d52cc8b4917b972dd")
+    version("4.9.1", sha256="d334781a124ada6f38e63b545e2a3b8c2183049515a1abab6d513f109f1d717e")
     version("4.8.5", sha256="22fb1e7e0f68a63cee631d85b20461d1ea6bda162f03096350e38c8d427ecf23")
+    version("4.8.4", sha256="4a80aa23798b8e9b5793494b8c976b39b8d9aa2e53cd5ed5534aff662a7f8695")
     version("4.7.4", sha256="92e61c6dc3a0a449e62d72a38185fda550168a86702dea07125ebd3ec3996282")
     version("4.6.4", sha256="35af16afa0b67af9b8eb15cafb76d2bc5f568540552522f5dc2c88dd45d977e8")
     version("4.5.4", sha256="eef3f0456db8c3d992cbb51d5d32558190bc14f3bc19383dd93acc27acc6befc")
 
-    with default_args(deprecated=True):
-        version(
-            "14.1.0", sha256="e283c654987afe3de9d8080bc0bd79534b5ca0d681a73a11ff2b5d3767426840"
-        )
-
-        version(
-            "13.2.0", sha256="e275e76442a6067341a27f04c5c6b83d8613144004c0413528863dc6b5c743da"
-        )
-        version(
-            "13.1.0", sha256="61d684f0aa5e76ac6585ad8898a2427aade8979ed5e7f85492286c4dfc13ee86"
-        )
-
-        version(
-            "12.3.0", sha256="949a5d4f99e786421a93b532b22ffab5578de7321369975b91aec97adfda8c3b"
-        )
-        version(
-            "12.2.0", sha256="e549cf9cf3594a00e27b6589d4322d70e0720cdd213f39beb4181e06926230ff"
-        )
-        version(
-            "12.1.0", sha256="62fd634889f31c02b64af2c468f064b47ad1ca78411c45abe6ac4b5f8dd19c7b"
-        )
-
-        version(
-            "11.4.0", sha256="3f2db222b007e8a4a23cd5ba56726ef08e8b1f1eb2055ee72c1402cea73a8dd9"
-        )
-        version(
-            "11.3.0", sha256="b47cf2818691f5b1e21df2bb38c795fac2cfbd640ede2d0a5e1c89e338a3ac39"
-        )
-        version(
-            "11.2.0", sha256="d08edc536b54c372a1010ff6619dd274c0f1603aa49212ba20f7aa2cda36fa8b"
-        )
-        version(
-            "11.1.0", sha256="4c4a6fb8a8396059241c2e674b85b351c26a5d678274007f076957afa1cc9ddf"
-        )
-
-        version(
-            "10.4.0", sha256="c9297d5bcd7cb43f3dfc2fed5389e948c9312fd962ef6a4ce455cff963ebe4f1"
-        )
-        version(
-            "10.3.0", sha256="64f404c1a650f27fc33da242e1f2df54952e3963a49e06e73f6940f3223ac344"
-        )
-        version(
-            "10.2.0", sha256="b8dd4368bb9c7f0b98188317ee0254dd8cc99d1e3a18d0ff146c855fe16c1d8c"
-        )
-        version(
-            "10.1.0", sha256="b6898a23844b656f1b68691c5c012036c2e694ac4b53a8918d4712ad876e7ea2"
-        )
-
-        version("9.4.0", sha256="c95da32f440378d7751dd95533186f7fc05ceb4fb65eb5b85234e6299eb9838e")
-        version("9.3.0", sha256="71e197867611f6054aa1119b13a0c0abac12834765fe2d81f35ac57f84f742d1")
-        version("9.2.0", sha256="ea6ef08f121239da5695f76c9b33637a118dcf63e24164422231917fa61fb206")
-        version("9.1.0", sha256="79a66834e96a6050d8fe78db2c3b32fb285b230b855d0a66288235bc04b327a0")
-
-        version("8.4.0", sha256="e30a6e52d10e1f27ed55104ad233c30bd1e99cfb5ff98ab022dc941edd1b2dd4")
-        version("8.3.0", sha256="64baadfe6cc0f4947a84cb12d7f0dfaf45bb58b7e92461639596c21e02d97d2c")
-        version("8.2.0", sha256="196c3c04ba2613f893283977e6011b2345d1cd1af9abeac58e916b1aab3e0080")
-        version("8.1.0", sha256="1d1866f992626e61349a1ccd0b8d5253816222cdc13390dcfaa74b093aa2b153")
-
-        version("7.4.0", sha256="eddde28d04f334aec1604456e536416549e9b1aa137fc69204e65eb0c009fe51")
-        version("7.3.0", sha256="832ca6ae04636adbb430e865a1451adf6979ab44ca1c8374f61fba65645ce15c")
-        version("7.2.0", sha256="1cf7adf8ff4b5aa49041c8734bbcf1ad18cc4c94d0029aae0f4e48841088479a")
-        version("7.1.0", sha256="8a8136c235f64c6fef69cac0d73a46a1a09bb250776a050aec8f9fc880bebc17")
-
-        version("6.4.0", sha256="850bf21eafdfe5cd5f6827148184c08c4a0852a37ccf36ce69855334d2c914d4")
-        version("6.3.0", sha256="f06ae7f3f790fbf0f018f6d40e844451e6bc3b7bc96e128e63b09825c1f8b29f")
-        version("6.2.0", sha256="9944589fc722d3e66308c0ce5257788ebd7872982a718aa2516123940671b7c5")
-        version("6.1.0", sha256="09c4c85cabebb971b1de732a0219609f93fc0af5f86f6e437fd8d7f832f1a351")
-
-        version("5.4.0", sha256="608df76dec2d34de6558249d8af4cbee21eceddbcb580d666f7a5a583ca3303a")
-        version("5.3.0", sha256="b84f5592e9218b73dbae612b5253035a7b34a9a1f7688d2e1bfaaf7267d5c4db")
-        version("5.2.0", sha256="5f835b04b5f7dd4f4d2dc96190ec1621b8d89f2dc6f638f9f8bc1b1014ba8cad")
-        version("5.1.0", sha256="b7dafdf89cbb0e20333dbf5b5349319ae06e3d1a30bf3515b5488f7e89dca5ad")
-
-        version("4.9.3", sha256="2332b2a5a321b57508b9031354a8503af6fdfb868b8c1748d33028d100a8b67e")
-        version("4.9.2", sha256="2020c98295856aa13fda0f2f3a4794490757fc24bcca918d52cc8b4917b972dd")
-        version("4.9.1", sha256="d334781a124ada6f38e63b545e2a3b8c2183049515a1abab6d513f109f1d717e")
-        version("4.8.4", sha256="4a80aa23798b8e9b5793494b8c976b39b8d9aa2e53cd5ed5534aff662a7f8695")
-
     depends_on("c", type="build")
     depends_on("cxx", type="build")
 
@@ -578,9 +548,6 @@ class Gcc(AutotoolsPackage, GNUMirrorPackage, CompilerPackage):
         when="@13.2.0 target=aarch64:",
     )
 
-    # see https://gcc.gnu.org/gcc-11/changes.html 11.5 Caveats
-    patch("patch-5522dec054cb940fe83661b96249aa12c54c1d77.patch", when="@11.5.0 target=aarch64:")
-
     build_directory = "spack-build"
 
     compiler_languages = ["c", "cxx", "fortran", "d", "go"]

var/spack/repos/builtin/packages/gcc/patch-5522dec054cb940fe83661b96249aa12c54c1d77.patch

@@ -1,111 +0,0 @@
-From 5522dec054cb940fe83661b96249aa12c54c1d77 Mon Sep 17 00:00:00 2001
-From: Andre Vieira <andre.simoesdiasvieira@arm.com>
-Date: Fri, 8 Apr 2022 15:12:23 +0100
-Subject: [PATCH] aarch64: PR target/105157 Increase number of cores
- TARGET_CPU_DEFAULT can encode
-
-This addresses the compile-time increase seen in the PR target/105157. This was
-being caused by selecting the wrong core tuning, as when we added the latest
-AArch64 the TARGET_CPU_generic tuning was pushed beyond the 0x3f mask we used
-to encode both target cpu and attributes into TARGET_CPU_DEFAULT.
-
-gcc/ChangeLog:
-
-	PR target/105157
-	* config.gcc: Shift ext_mask by TARGET_CPU_NBITS.
-	* config/aarch64/aarch64.h (TARGET_CPU_NBITS): New macro.
-	(TARGET_CPU_MASK): Likewise.
-	(TARGET_CPU_DEFAULT): Use TARGET_CPU_NBITS.
-	* config/aarch64/aarch64.cc (aarch64_get_tune_cpu): Use TARGET_CPU_MASK.
-	(aarch64_get_arch): Likewise.
-	(aarch64_override_options): Use TARGET_CPU_NBITS.
----
- gcc/config.gcc                |  2 +-
- gcc/config/aarch64/aarch64.cc | 14 +++++++++-----
- gcc/config/aarch64/aarch64.h  |  8 +++++++-
- 3 files changed, 17 insertions(+), 7 deletions(-)
-
-diff --git a/gcc/config.gcc b/gcc/config.gcc
-index 7b58e1314ff0dc57701a77a7433de1a6e263c259..5382788e267214ccc1015d0bed85b718ebf00011 100644
---- a/gcc/config.gcc
-+++ b/gcc/config.gcc
-@@ -4261,7 +4261,7 @@ case "${target}" in
- 				ext_val=`echo $ext_val | sed -e 's/[a-z0-9]\+//'`
- 			  done
- 
--			  ext_mask="(("$ext_mask") << 6)"
-+			  ext_mask="(("$ext_mask") << TARGET_CPU_NBITS)"
- 			  if [ x"$base_id" != x ]; then
- 				target_cpu_cname="TARGET_CPU_$base_id | $ext_mask"
- 			  fi
-diff --git a/gcc/config/aarch64/aarch64.c b/gcc/config/aarch64/aarch64.c
-index 3e2a6fb64725d4e37ddd89f6987795733cfff35c..cf62bdd023b5799284fdcc337a50c01ccd21493f 100644
---- a/gcc/config/aarch64/aarch64.c
-+++ b/gcc/config/aarch64/aarch64.c
-@@ -18053,6 +18053,9 @@ aarch64_validate_mtune (const char *str, const struct processor **res)
-   return false;
- }
- 
-+static_assert (TARGET_CPU_generic < TARGET_CPU_MASK,
-+	       "TARGET_CPU_NBITS is big enough");
-+
- /* Return the CPU corresponding to the enum CPU.
-    If it doesn't specify a cpu, return the default.  */
- 
-@@ -18062,12 +18065,12 @@ aarch64_get_tune_cpu (enum aarch64_processor cpu)
-   if (cpu != aarch64_none)
-     return &all_cores[cpu];
- 
--  /* The & 0x3f is to extract the bottom 6 bits that encode the
--     default cpu as selected by the --with-cpu GCC configure option
-+  /* The & TARGET_CPU_MASK is to extract the bottom TARGET_CPU_NBITS bits that
-+     encode the default cpu as selected by the --with-cpu GCC configure option
-      in config.gcc.
-      ???: The whole TARGET_CPU_DEFAULT and AARCH64_CPU_DEFAULT_FLAGS
-      flags mechanism should be reworked to make it more sane.  */
--  return &all_cores[TARGET_CPU_DEFAULT & 0x3f];
-+  return &all_cores[TARGET_CPU_DEFAULT & TARGET_CPU_MASK];
- }
- 
- /* Return the architecture corresponding to the enum ARCH.
-@@ -18079,7 +18082,8 @@ aarch64_get_arch (enum aarch64_arch arch)
-   if (arch != aarch64_no_arch)
-     return &all_architectures[arch];
- 
--  const struct processor *cpu = &all_cores[TARGET_CPU_DEFAULT & 0x3f];
-+  const struct processor *cpu
-+    = &all_cores[TARGET_CPU_DEFAULT & TARGET_CPU_MASK];
- 
-   return &all_architectures[cpu->arch];
- }
-@@ -18166,7 +18170,7 @@ aarch64_override_options (void)
- 	{
- 	  /* Get default configure-time CPU.  */
- 	  selected_cpu = aarch64_get_tune_cpu (aarch64_none);
--	  aarch64_isa_flags = TARGET_CPU_DEFAULT >> 6;
-+	  aarch64_isa_flags = TARGET_CPU_DEFAULT >> TARGET_CPU_NBITS;
- 	}
- 
-       if (selected_tune)
-diff --git a/gcc/config/aarch64/aarch64.h b/gcc/config/aarch64/aarch64.h
-index efa46ac0b8799b5849b609d591186e26e5cb37ff..359b6e8561faa38f53a806b8c114c83ae37e7e17 100644
---- a/gcc/config/aarch64/aarch64.h
-+++ b/gcc/config/aarch64/aarch64.h
-@@ -813,10 +813,16 @@ enum target_cpus
-   TARGET_CPU_generic
- };
- 
-+/* Define how many bits are used to represent the CPU in TARGET_CPU_DEFAULT.
-+   This needs to be big enough to fit the value of TARGET_CPU_generic.
-+   All bits after this are used to represent the AARCH64_CPU_DEFAULT_FLAGS.  */
-+#define TARGET_CPU_NBITS 8
-+#define TARGET_CPU_MASK ((1 << TARGET_CPU_NBITS) - 1)
-+
- /* If there is no CPU defined at configure, use generic as default.  */
- #ifndef TARGET_CPU_DEFAULT
- #define TARGET_CPU_DEFAULT \
--  (TARGET_CPU_generic | (AARCH64_CPU_DEFAULT_FLAGS << 6))
-+  (TARGET_CPU_generic | (AARCH64_CPU_DEFAULT_FLAGS << TARGET_CPU_NBITS))
- #endif
- 
- /* If inserting NOP before a mult-accumulate insn remember to adjust the

var/spack/repos/builtin/packages/ginkgo/package.py

@@ -226,7 +226,7 @@ def cmake_args(self):
 
         if self.spec.satisfies("+sycl"):
             sycl_compatible_compilers = ["icpx"]
-            if os.path.basename(self.compiler.cxx) not in sycl_compatible_compilers:
+            if not (os.path.basename(self.compiler.cxx) in sycl_compatible_compilers):
                 raise InstallError("ginkgo +sycl requires icpx compiler.")
         return args
 

var/spack/repos/builtin/packages/hypre/package.py

@@ -322,7 +322,7 @@ def configure_args(self):
         if spec.satisfies("+sycl"):
             configure_args.append("--with-sycl")
             sycl_compatible_compilers = ["icpx"]
-            if os.path.basename(self.compiler.cxx) not in sycl_compatible_compilers:
+            if not (os.path.basename(self.compiler.cxx) in sycl_compatible_compilers):
                 raise InstallError(
                     "Hypre's SYCL GPU Backend requires the oneAPI CXX (icpx) compiler."
                 )

var/spack/repos/builtin/packages/icu4c/package.py

@@ -19,8 +19,6 @@ class Icu4c(AutotoolsPackage, MSBuildPackage):
 
     license("Unicode-TOU")
 
-    version("76.1", sha256="dfacb46bfe4747410472ce3e1144bf28a102feeaa4e3875bac9b4c6cf30f4f3e")
-    version("75.1", sha256="cb968df3e4d2e87e8b11c49a5d01c787bd13b9545280fc6642f826527618caef")
     version("74.2", sha256="68db082212a96d6f53e35d60f47d38b962e9f9d207a74cfac78029ae8ff5e08c")
     version("67.1", sha256="94a80cd6f251a53bd2a997f6f1b5ac6653fe791dfab66e1eb0227740fb86d5dc")
     version("66.1", sha256="52a3f2209ab95559c1cf0a14f24338001f389615bf00e2585ef3dbc43ecf0a2e")
@@ -42,7 +40,7 @@ class Icu4c(AutotoolsPackage, MSBuildPackage):
             variant(
                 "cxxstd",
                 default="11",
-                values=(conditional("11", "14", when="@:74"), "17"),
+                values=("11", "14", "17"),
                 multi=False,
                 description="Use the specified C++ standard when building",
             )

var/spack/repos/builtin/packages/isa-l/package.py

@@ -30,7 +30,6 @@ class IsaL(AutotoolsPackage):
     version("master", branch="master")
 
     # Current
-    version("2.31.1", sha256="e1d5573a4019738243b568ab1e1422e6ab7557c5cae33cc8686944d327ad6bb4")
     version("2.30.0", sha256="bcf592c04fdfa19e723d2adf53d3e0f4efd5b956bb618fed54a1108d76a6eb56")
     version("2.29.0", sha256="832d9747ef3f0c8c05d39e3d7fd6ee5299a844e1ee7382fc8c8b52a268f36eda")
     version("2.28.0", sha256="589202efdcfe437b1786750ec81bf93055e3b88a4bdf909d3b519f2a7134034b")

var/spack/repos/builtin/packages/leptonica/package.py

@@ -2,8 +2,6 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-import os
-
 from spack.package import *
 
 
@@ -16,7 +14,6 @@ class Leptonica(CMakePackage):
 
     license("custom")
 
-    version("1.85.0", sha256="c01376bce0379d4ea4bc2ec5d5cbddaa49e2f06f88242619ab8c059e21adf233")
     version("1.84.1", sha256="ecd7a868403b3963c4e33623595d77f2c87667e2cfdd9b370f87729192061bef")
     version("1.83.1", sha256="4289d0a4224b614010072253531c0455a33a4d7c7a0017fe7825ed382290c0da")
     version("1.81.0", sha256="70ebc04ff8b9684205bd1d01843c635a8521255b74813bf7cce9a33368f7952c")
@@ -39,9 +36,3 @@ def cmake_args(self):
         args = [self.define("BUILD_SHARED_LIBS", "ON")]
 
         return args
-
-    @run_after("install")
-    def pkgconfig_fixup(self):
-        with working_dir(self.prefix.lib.pkgconfig):
-            if not os.path.exists("lept.pc"):
-                symlink(f"lept_{self.spec.variants['build_type'].value}.pc", "lept.pc")

var/spack/repos/builtin/packages/libdrm/package.py

@@ -20,7 +20,6 @@ class Libdrm(AutotoolsPackage, MesonPackage):
 
     license("MIT")
 
-    version("2.4.124", sha256="ac36293f61ca4aafaf4b16a2a7afff312aa4f5c37c9fbd797de9e3c0863ca379")
     version("2.4.123", sha256="a2b98567a149a74b0f50e91e825f9c0315d86e7be9b74394dae8b298caadb79e")
     version("2.4.122", sha256="d9f5079b777dffca9300ccc56b10a93588cdfbc9dde2fae111940dfb6292f251")
     version("2.4.121", sha256="909084a505d7638887f590b70791b3bbd9069c710c948f5d1f1ce6d080cdfcab")

var/spack/repos/builtin/packages/libpressio/package.py

@@ -309,7 +309,7 @@ class Libpressio(CMakePackage, CudaPackage):
     depends_on("sz3@3.1.8:", when="@0.98.1: +sz3")
     depends_on("bzip2", when="+bzip2")
     depends_on("qoz", when="+qoz")
-    depends_on("cusz@0.9", when="+cusz")
+    depends_on("cusz@0.6.0:", when="+cusz")
 
     extends("python", when="+python")
 

var/spack/repos/builtin/packages/llvm/package.py

@@ -55,160 +55,70 @@ class Llvm(CMakePackage, CudaPackage, LlvmDetection, CompilerPackage):
 
     version("main", branch="main")
     version("19.1.7", sha256="59abea1c22e64933fad4de1671a61cdb934098793c7a31b333ff58dc41bff36c")
+    version("19.1.6", sha256="f07fdcbb27b2b67aa95e5ddadf45406b33228481c250e65175066d36536a1ee2")
+    version("19.1.5", sha256="e2204b9903cd9d7ee833a2f56a18bef40a33df4793e31cc090906b32cbd8a1f5")
+    version("19.1.4", sha256="010e1fd3cabee8799bd2f8a6fbc68f28207494f315cf9da7057a2820f79fd531")
+    version("19.1.3", sha256="e5106e2bef341b3f5e41340e4b6c6a58259f4021ad801acf14e88f1a84567b05")
+    version("19.1.2", sha256="622cb6c5e95a3bb7e9876c4696a65671f235bd836cfd0c096b272f6c2ada41e7")
+    version("19.1.1", sha256="115dfd98a353d05bffdab3f80db22f159da48aca0124e8c416f437adcd54b77f")
+    version("19.1.0", sha256="0a08341036ca99a106786f50f9c5cb3fbe458b3b74cab6089fd368d0edb2edfe")
     version("18.1.8", sha256="09c08693a9afd6236f27a2ebae62cda656eba19021ef3f94d59e931d662d4856")
+    version("18.1.7", sha256="b60df7cbe02cef2523f7357120fb0d46cbb443791cde3a5fb36b82c335c0afc9")
+    version("18.1.6", sha256="01390edfae5b809e982b530ff9088e674c62b13aa92cb9dc1e067fa2cf501083")
+    version("18.1.5", sha256="d543309f55ae3f9b422108302b45c40f5696c96862f4bda8f5526955daa54284")
+    version("18.1.4", sha256="deca5a29e8b1d103ecc4badb3c304aca50d5cac6453364d88ee415dc55699dfb")
+    version("18.1.3", sha256="fc5a2fd176d73ceb17f4e522f8fe96d8dde23300b8c233476d3609f55d995a7a")
+    version("18.1.2", sha256="8d686d5ece6f12b09985cb382a3a530dc06bb6e7eb907f57c7f8bf2d868ebb0b")
+    version("18.1.1", sha256="62439f733311869dbbaf704ce2e02141d2a07092d952fc87ef52d1d636a9b1e4")
+    version("18.1.0", sha256="eb18f65a68981e94ea1a5aae4f02321b17da9e99f76bfdb983b953f4ba2d3550")
     version("17.0.6", sha256="81494d32e6f12ea6f73d6d25424dbd2364646011bb8f7e345ca870750aa27de1")
+    version("17.0.5", sha256="432c1eda3d1c9379cd52a9bee8e0ea6f7b204bff5075895f963fd8e575aa4fb8")
+    version("17.0.4", sha256="46200b79f52a02fe26d0a43fd856ab6ceff49ab2a0b7c240ac4b700a6ada700c")
+    version("17.0.3", sha256="1e3d9d04fb5fbd8d0080042ad72c7e2a5c68788b014b186647a604dbbdd625d2")
+    version("17.0.2", sha256="dcba3eb486973dce45b6edfe618f3f29b703ae7e6ef9df65182fb50fb6fe4235")
+    version("17.0.1", sha256="d51b10be66c10a6a81f4c594b554ffbf1063ffbadcb810af37d1f88d6e0b49dd")
     version("16.0.6", sha256="56b2f75fdaa95ad5e477a246d3f0d164964ab066b4619a01836ef08e475ec9d5")
+    version("16.0.5", sha256="e0fbca476693fcafa125bc71c8535587b6d9950293122b66b262bb4333a03942")
+    version("16.0.4", sha256="10c3fe1757d2e4f1cd7745dc548ecf687680a71824ec81701c38524c2a0753e2")
+    version("16.0.3", sha256="0bd71bc687a4e5a250c40afb0decefc50c85178fcce726137b682039de63919b")
+    version("16.0.2", sha256="97c3c6aafb53c4bb0ed2781a18d6f05e75445e24bb1dc57a32b74f8d710ac19f")
+    version("16.0.1", sha256="b5a9ff1793b1e2d388a3819bf35797002b1d2e40bb35a10c65605e0ea1435271")
+    version("16.0.0", sha256="cba969a0782a3a398658d439f047b5e548ea04724f4fbfdbe17cfc946f4cd3ed")
     version("15.0.7", sha256="42a0088f148edcf6c770dfc780a7273014a9a89b66f357c761b4ca7c8dfa10ba")
+    version("15.0.6", sha256="4d857d7a180918bdacd09a5910bf9743c9861a1e49cb065a85f7a990f812161d")
+    version("15.0.5", sha256="c47640269e0251e009ae18a25162df4e20e175885286e21d28c054b084b991a4")
+    version("15.0.4", sha256="e24b4d3bf7821dcb1c901d1e09096c1f88fb00095c5a6ef893baab4836975e52")
+    version("15.0.3", sha256="8ac8e4c0982bf236526d737d385db5e1e66543ab217a9355d54159659eae3774")
+    version("15.0.2", sha256="dc11d35e60ab61792baa607dff080c993b39de23fb93b3d3369ba15b0601c307")
+    version("15.0.1", sha256="20bccb964e39f604fdc16d1258f94d2053fbdcdab2b2f6d5e20e6095ec403c00")
+    version("15.0.0", sha256="36d83cd84e1caf2bcfda1669c029e2b949adb9860cff01e7d3246ac2348b11ae")
     version("14.0.6", sha256="98f15f842700bdb7220a166c8d2739a03a72e775b67031205078f39dd756a055")
+    version("14.0.5", sha256="a4a57f029cb81f04618e05853f05fc2d21b64353c760977d8e7799bf7218a23a")
+    version("14.0.4", sha256="1333236f9bee38658762076be4236cb5ebf15ae9b7f2bfce6946b96ae962dc73")
+    version("14.0.3", sha256="0e1d049b050127ecf6286107e9a4400b0550f841d5d2288b9d31fd32ed0683d5")
+    version("14.0.2", sha256="ca52232b3451c8e017f00eb882277707c13e30fac1271ec97015f6d0eeb383d1")
+    version("14.0.1", sha256="c8be00406e872c8a24f8571cf6f5517b73ae707104724b1fd1db2f0af9544019")
+    version("14.0.0", sha256="87b1a068b370df5b79a892fdb2935922a8efb1fddec4cc506e30fe57b6a1d9c4")
     version("13.0.1", sha256="09c50d558bd975c41157364421820228df66632802a4a6a7c9c17f86a7340802")
+    version("13.0.0", sha256="a1131358f1f9f819df73fa6bff505f2c49d176e9eef0a3aedd1fdbce3b4630e8")
     version("12.0.1", sha256="66b64aa301244975a4aea489f402f205cde2f53dd722dad9e7b77a0459b4c8df")
+    version("12.0.0", sha256="8e6c99e482bb16a450165176c2d881804976a2d770e0445af4375e78a1fbf19c")
     version("11.1.0", sha256="53a0719f3f4b0388013cfffd7b10c7d5682eece1929a9553c722348d1f866e79")
+    version("11.0.1", sha256="9c7ad8e8ec77c5bde8eb4afa105a318fd1ded7dff3747d14f012758719d7171b")
+    version("11.0.0", sha256="8ad4ddbafac4f2c8f2ea523c2c4196f940e8e16f9e635210537582a48622a5d5")
     version("10.0.1", sha256="c7ccb735c37b4ec470f66a6c35fbae4f029c0f88038f6977180b1a8ddc255637")
+    version("10.0.0", sha256="b81c96d2f8f40dc61b14a167513d87c0d813aae0251e06e11ae8a4384ca15451")
     version("9.0.1", sha256="be7b034641a5fda51ffca7f5d840b1a768737779f75f7c4fd18fe2d37820289a")
+    version("9.0.0", sha256="7807fac25330e24e9955ca46cd855dd34bbc9cc4fdba8322366206654d1036f2")
     version("8.0.1", sha256="5b18f6111c7aee7c0933c355877d4abcfe6cb40c1a64178f28821849c725c841")
+    version("8.0.0", sha256="d81238b4a69e93e29f74ce56f8107cbfcf0c7d7b40510b7879e98cc031e25167")
     version("7.1.0", sha256="71c93979f20e01f1a1cc839a247945f556fa5e63abf2084e8468b238080fd839")
+    version("7.0.1", sha256="f17a6cd401e8fd8f811fbfbb36dcb4f455f898c9d03af4044807ad005df9f3c0")
     version("6.0.1", sha256="aefadceb231f4c195fe6d6cd3b1a010b269c8a22410f339b5a089c2e902aa177")
+    version("6.0.0", sha256="1946ec629c88d30122afa072d3c6a89cc5d5e4e2bb28dc63b2f9ebcc7917ee64")
     version("5.0.2", sha256="fe87aa11558c08856739bfd9bd971263a28657663cb0c3a0af01b94f03b0b795")
-
-    with default_args(deprecated=True):
-        version(
-            "19.1.6", sha256="f07fdcbb27b2b67aa95e5ddadf45406b33228481c250e65175066d36536a1ee2"
-        )
-        version(
-            "19.1.5", sha256="e2204b9903cd9d7ee833a2f56a18bef40a33df4793e31cc090906b32cbd8a1f5"
-        )
-        version(
-            "19.1.4", sha256="010e1fd3cabee8799bd2f8a6fbc68f28207494f315cf9da7057a2820f79fd531"
-        )
-        version(
-            "19.1.3", sha256="e5106e2bef341b3f5e41340e4b6c6a58259f4021ad801acf14e88f1a84567b05"
-        )
-        version(
-            "19.1.2", sha256="622cb6c5e95a3bb7e9876c4696a65671f235bd836cfd0c096b272f6c2ada41e7"
-        )
-        version(
-            "19.1.1", sha256="115dfd98a353d05bffdab3f80db22f159da48aca0124e8c416f437adcd54b77f"
-        )
-        version(
-            "19.1.0", sha256="0a08341036ca99a106786f50f9c5cb3fbe458b3b74cab6089fd368d0edb2edfe"
-        )
-        version(
-            "18.1.7", sha256="b60df7cbe02cef2523f7357120fb0d46cbb443791cde3a5fb36b82c335c0afc9"
-        )
-        version(
-            "18.1.6", sha256="01390edfae5b809e982b530ff9088e674c62b13aa92cb9dc1e067fa2cf501083"
-        )
-        version(
-            "18.1.5", sha256="d543309f55ae3f9b422108302b45c40f5696c96862f4bda8f5526955daa54284"
-        )
-        version(
-            "18.1.4", sha256="deca5a29e8b1d103ecc4badb3c304aca50d5cac6453364d88ee415dc55699dfb"
-        )
-        version(
-            "18.1.3", sha256="fc5a2fd176d73ceb17f4e522f8fe96d8dde23300b8c233476d3609f55d995a7a"
-        )
-        version(
-            "18.1.2", sha256="8d686d5ece6f12b09985cb382a3a530dc06bb6e7eb907f57c7f8bf2d868ebb0b"
-        )
-        version(
-            "18.1.1", sha256="62439f733311869dbbaf704ce2e02141d2a07092d952fc87ef52d1d636a9b1e4"
-        )
-        version(
-            "18.1.0", sha256="eb18f65a68981e94ea1a5aae4f02321b17da9e99f76bfdb983b953f4ba2d3550"
-        )
-        version(
-            "17.0.5", sha256="432c1eda3d1c9379cd52a9bee8e0ea6f7b204bff5075895f963fd8e575aa4fb8"
-        )
-        version(
-            "17.0.4", sha256="46200b79f52a02fe26d0a43fd856ab6ceff49ab2a0b7c240ac4b700a6ada700c"
-        )
-        version(
-            "17.0.3", sha256="1e3d9d04fb5fbd8d0080042ad72c7e2a5c68788b014b186647a604dbbdd625d2"
-        )
-        version(
-            "17.0.2", sha256="dcba3eb486973dce45b6edfe618f3f29b703ae7e6ef9df65182fb50fb6fe4235"
-        )
-        version(
-            "17.0.1", sha256="d51b10be66c10a6a81f4c594b554ffbf1063ffbadcb810af37d1f88d6e0b49dd"
-        )
-        version(
-            "16.0.5", sha256="e0fbca476693fcafa125bc71c8535587b6d9950293122b66b262bb4333a03942"
-        )
-        version(
-            "16.0.4", sha256="10c3fe1757d2e4f1cd7745dc548ecf687680a71824ec81701c38524c2a0753e2"
-        )
-        version(
-            "16.0.3", sha256="0bd71bc687a4e5a250c40afb0decefc50c85178fcce726137b682039de63919b"
-        )
-        version(
-            "16.0.2", sha256="97c3c6aafb53c4bb0ed2781a18d6f05e75445e24bb1dc57a32b74f8d710ac19f"
-        )
-        version(
-            "16.0.1", sha256="b5a9ff1793b1e2d388a3819bf35797002b1d2e40bb35a10c65605e0ea1435271"
-        )
-        version(
-            "16.0.0", sha256="cba969a0782a3a398658d439f047b5e548ea04724f4fbfdbe17cfc946f4cd3ed"
-        )
-        version(
-            "15.0.6", sha256="4d857d7a180918bdacd09a5910bf9743c9861a1e49cb065a85f7a990f812161d"
-        )
-        version(
-            "15.0.5", sha256="c47640269e0251e009ae18a25162df4e20e175885286e21d28c054b084b991a4"
-        )
-        version(
-            "15.0.4", sha256="e24b4d3bf7821dcb1c901d1e09096c1f88fb00095c5a6ef893baab4836975e52"
-        )
-        version(
-            "15.0.3", sha256="8ac8e4c0982bf236526d737d385db5e1e66543ab217a9355d54159659eae3774"
-        )
-        version(
-            "15.0.2", sha256="dc11d35e60ab61792baa607dff080c993b39de23fb93b3d3369ba15b0601c307"
-        )
-        version(
-            "15.0.1", sha256="20bccb964e39f604fdc16d1258f94d2053fbdcdab2b2f6d5e20e6095ec403c00"
-        )
-        version(
-            "15.0.0", sha256="36d83cd84e1caf2bcfda1669c029e2b949adb9860cff01e7d3246ac2348b11ae"
-        )
-        version(
-            "14.0.5", sha256="a4a57f029cb81f04618e05853f05fc2d21b64353c760977d8e7799bf7218a23a"
-        )
-        version(
-            "14.0.4", sha256="1333236f9bee38658762076be4236cb5ebf15ae9b7f2bfce6946b96ae962dc73"
-        )
-        version(
-            "14.0.3", sha256="0e1d049b050127ecf6286107e9a4400b0550f841d5d2288b9d31fd32ed0683d5"
-        )
-        version(
-            "14.0.2", sha256="ca52232b3451c8e017f00eb882277707c13e30fac1271ec97015f6d0eeb383d1"
-        )
-        version(
-            "14.0.1", sha256="c8be00406e872c8a24f8571cf6f5517b73ae707104724b1fd1db2f0af9544019"
-        )
-        version(
-            "14.0.0", sha256="87b1a068b370df5b79a892fdb2935922a8efb1fddec4cc506e30fe57b6a1d9c4"
-        )
-        version(
-            "13.0.0", sha256="a1131358f1f9f819df73fa6bff505f2c49d176e9eef0a3aedd1fdbce3b4630e8"
-        )
-        version(
-            "12.0.0", sha256="8e6c99e482bb16a450165176c2d881804976a2d770e0445af4375e78a1fbf19c"
-        )
-        version(
-            "11.0.1", sha256="9c7ad8e8ec77c5bde8eb4afa105a318fd1ded7dff3747d14f012758719d7171b"
-        )
-        version(
-            "11.0.0", sha256="8ad4ddbafac4f2c8f2ea523c2c4196f940e8e16f9e635210537582a48622a5d5"
-        )
-        version(
-            "10.0.0", sha256="b81c96d2f8f40dc61b14a167513d87c0d813aae0251e06e11ae8a4384ca15451"
-        )
-        version("9.0.0", sha256="7807fac25330e24e9955ca46cd855dd34bbc9cc4fdba8322366206654d1036f2")
-        version("8.0.0", sha256="d81238b4a69e93e29f74ce56f8107cbfcf0c7d7b40510b7879e98cc031e25167")
-        version("7.0.1", sha256="f17a6cd401e8fd8f811fbfbb36dcb4f455f898c9d03af4044807ad005df9f3c0")
-        version("6.0.0", sha256="1946ec629c88d30122afa072d3c6a89cc5d5e4e2bb28dc63b2f9ebcc7917ee64")
-        version("5.0.1", sha256="84ca454abf262579814a2a2b846569f6e0cb3e16dc33ca3642b4f1dff6fbafd3")
-        version("5.0.0", sha256="1f1843315657a4371d8ca37f01265fa9aae17dbcf46d2d0a95c1fdb3c6a4bab6")
+    version("5.0.1", sha256="84ca454abf262579814a2a2b846569f6e0cb3e16dc33ca3642b4f1dff6fbafd3")
+    version("5.0.0", sha256="1f1843315657a4371d8ca37f01265fa9aae17dbcf46d2d0a95c1fdb3c6a4bab6")
 
     depends_on("c", type="build")
     depends_on("cxx", type="build")

var/spack/repos/builtin/packages/netlib-scalapack/package.py

@@ -113,7 +113,7 @@ class NetlibScalapack(ScalapackBase):
     """
 
     homepage = "https://www.netlib.org/scalapack/"
-    url = "https://github.com/Reference-ScaLAPACK/scalapack/archive/refs/tags/v2.2.2.tar.gz"
+    url = "https://www.netlib.org/scalapack/scalapack-2.0.2.tgz"
     git = "https://github.com/Reference-ScaLAPACK/scalapack"
     tags = ["e4s"]
 
@@ -121,9 +121,8 @@ class NetlibScalapack(ScalapackBase):
 
     license("BSD-3-Clause-Open-MPI")
 
-    version("2.2.2", sha256="a2f0c9180a210bf7ffe126c9cb81099cf337da1a7120ddb4cbe4894eb7b7d022")
-    version("2.2.0", sha256="8862fc9673acf5f87a474aaa71cd74ae27e9bbeee475dbd7292cec5b8bcbdcf3")
-    version("2.1.0", sha256="f03fda720a152030b582a237f8387014da878b84cbd43c568390e9f05d24617f")
+    version("2.2.0", sha256="40b9406c20735a9a3009d863318cb8d3e496fb073d201c5463df810e01ab2a57")
+    version("2.1.0", sha256="61d9216cf81d246944720cfce96255878a3f85dec13b9351f1fa0fd6768220a6")
     version("2.0.2", sha256="0c74aeae690fe5ee4db7926f49c5d0bb69ce09eea75beb915e00bba07530395c")
     version("2.0.1", sha256="a9b34278d4e10b40cbe084c6d87d09af8845e874250719bfbbc497b2a88bfde1")
     version("2.0.0", sha256="e51fbd9c3ef3a0dbd81385b868e2355900148eea689bf915c5383d72daf73114")
@@ -133,9 +132,3 @@ class NetlibScalapack(ScalapackBase):
     depends_on("fortran", type="build")  # generated
     # versions before 2.0.0 are not using cmake and requires blacs as
     # a separated package
-
-    def url_for_version(self, version):
-        if self.spec.satisfies("@2.2:"):
-            return super().url_for_version(version)
-        url_fmt = "https://www.netlib.org/scalapack/scalapack-{0}.tgz"
-        return url_fmt.format(version)

var/spack/repos/builtin/packages/petsc/package.py

@@ -582,7 +582,7 @@ def configure_options(self):
 
         if "+sycl" in spec:
             sycl_compatible_compilers = ["icpx"]
-            if os.path.basename(self.compiler.cxx) not in sycl_compatible_compilers:
+            if not (os.path.basename(self.compiler.cxx) in sycl_compatible_compilers):
                 raise InstallError("PETSc's SYCL GPU Backend requires oneAPI CXX (icpx) compiler.")
             options.append("--with-sycl=1")
             options.append("--with-syclc=" + self.compiler.cxx)
@@ -590,9 +590,6 @@ def configure_options(self):
         else:
             options.append("--with-sycl=0")
 
-        if spec.satisfies("^cuda@12.8.0"):
-            options.append("CUDAPPFLAGS=-Wno-deprecated-gpu-targets")
-
         if "trilinos" in spec:
             if spec.satisfies("^trilinos+boost"):
                 options.append("--with-boost=1")

var/spack/repos/builtin/packages/py-geojson/package.py

@@ -1,23 +0,0 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack.package import *
-
-
-class PyGeojson(PythonPackage):
-    """Python bindings and utilities for GeoJSON."""
-
-    homepage = "https://github.com/jazzband/geojson"
-    pypi = "geojson/geojson-3.1.0.tar.gz"
-
-    maintainers("Chrismarsh")
-
-    license("BSD-3-Clause", checked_by="Chrismarsh")
-
-    version("3.2.0", sha256="b860baba1e8c6f71f8f5f6e3949a694daccf40820fa8f138b3f712bd85804903")
-    version("3.1.0", sha256="58a7fa40727ea058efc28b0e9ff0099eadf6d0965e04690830208d3ef571adac")
-
-    depends_on("python@3.7:3.12", when="@3.1.0")
-    depends_on("python@3.7:3.13", when="@3.2.0")
-    depends_on("py-setuptools", type="build")

var/spack/repos/builtin/packages/py-jaxlib/package.py

@@ -164,9 +164,6 @@ class PyJaxlib(PythonPackage, CudaPackage, ROCmPackage):
     # https://github.com/google/jax/issues/19992
     conflicts("@0.4.4:", when="target=ppc64le:")
 
-    # Fails to build with freshly released CUDA (#48708).
-    conflicts("^cuda@12.8:", when="@:0.4.31")
-
     def url_for_version(self, version):
         url = "https://github.com/jax-ml/jax/archive/refs/tags/{}-v{}.tar.gz"
         if version >= Version("0.4.33"):

var/spack/repos/builtin/packages/py-metis/package.py

@@ -1,21 +0,0 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack.package import *
-
-
-class PyMetis(PythonPackage):
-    """Wrapper for the METIS library for partitioning graphs (and other stuff)."""
-
-    homepage = "https://github.com/kw/metis-python"
-    pypi = "metis/metis-0.2a5.tar.gz"
-
-    maintainers("Chrismarsh")
-
-    license("MIT", checked_by="Chrismarsh")
-
-    version("0.2a5", sha256="c98f4aa129141554bea8d9e62daea5fea8351439f723e8e27fe593c2b7c53903")
-
-    depends_on("py-setuptools", type="build")
-    depends_on("metis", type=("build", "run"))

var/spack/repos/builtin/packages/py-tensorflow/package.py

@@ -3,6 +3,7 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 import glob
+import os
 import sys
 import tempfile
 
@@ -45,11 +46,6 @@ class PyTensorflow(Package, CudaPackage, ROCmPackage, PythonExtension):
     license("Apache-2.0")
     maintainers("adamjstewart", "aweits")
 
-    version(
-        "2.18.0-rocm-enhanced",
-        sha256="85f44bed166927b2e22db28f5c4e4538da22221fedd9c2f47c763c52a0e40814",
-        url="https://github.com/ROCm/tensorflow-upstream/archive/refs/tags/v2.18.0-rocm-enhanced.tar.gz",
-    )
     version("2.18.0", sha256="d7876f4bb0235cac60eb6316392a7c48676729860da1ab659fb440379ad5186d")
     version("2.17.1", sha256="2d3cfb48510f92f3a52fb05b820481c6f066a342a9f5296fe26d72c4ea757700")
     version("2.17.0", sha256="9cc4d5773b8ee910079baaecb4086d0c28939f024dd74b33fc5e64779b6533dc")
@@ -444,25 +440,11 @@ class PyTensorflow(Package, CudaPackage, ROCmPackage, PythonExtension):
     conflicts("platform=darwin target=aarch64:", when="@:2.4")
     # https://github.com/tensorflow/tensorflow/pull/39225
     conflicts("target=aarch64:", when="@:2.2")
-
-    rocm_versions = [
-        "2.7.4-rocm-enhanced",
-        "2.11.0-rocm-enhanced",
-        "2.14-rocm-enhanced",
-        "2.16.1-rocm-enhanced",
-        "2.18.0-rocm-enhanced",
-    ]
-    rocm_conflicts = [
-        ":2.7.4-a",
-        "2.7.4.0:2.11.0-a",
-        "2.11.0.0:2.14-a",
-        "2.14-z:2.16.1-a",
-        "2.16.1-z:2.18.0-a",
-        "2.18.0-z:",
-    ]
-    conflicts("~rocm", when=f"@{','.join(rocm_versions)}")
-    conflicts("+rocm", when=f"@{','.join(rocm_conflicts)}")
-
+    conflicts(
+        "~rocm",
+        when="@2.7.4-rocm-enhanced,2.11.0-rocm-enhanced,2.14-rocm-enhanced,2.16.1-rocm-enhanced",
+    )
+    conflicts("+rocm", when="@:2.7.4-a,2.7.4.0:2.11.0-a,2.11.0.0:2.14-a,2.14-z:2.16.1-a,2.16.1-z:")
     # wheel 0.40 upgrades vendored packaging, trips over tensorflow-io-gcs-filesystem identifier
     conflicts("^py-wheel@0.40:", when="@2.11:2.13")
 
@@ -528,14 +510,13 @@ class PyTensorflow(Package, CudaPackage, ROCmPackage, PythonExtension):
     patch(
         "https://github.com/ROCm/tensorflow-upstream/commit/f4f4e8698b90755b0b5ea2d9da1933b0b988b111.patch?full_index=1",
         sha256="a4c0fd62a0af3ba113c8933fa531dd17fa6667e507202a144715cd87fbdaf476",
-        when="@2.16.1-rocm-enhanced +rocm",
+        when="@2.16.1-rocm-enhanced: +rocm",
     )
     patch(
         "https://github.com/ROCm/tensorflow-upstream/commit/8b7fcccb2914078737689347540cb79ace579bbb.patch?full_index=1",
         sha256="75a61a79ce3aae51fda920f677f4dc045374b20e25628626eb37ca19c3a3b4c4",
         when="@2.16.1-rocm-enhanced +rocm",
     )
-    patch("set_jit_true.patch", when="@2.18.0-rocm-enhanced +rocm")
     phases = ["configure", "build", "install"]
 
     def flag_handler(self, name, flags):
@@ -869,10 +850,17 @@ def post_configure_fixes(self):
             with open(".tf_configure.bazelrc", mode="a") as f:
                 f.write('build --action_env LD_LIBRARY_PATH="' + slibs + '"')
 
-        if spec.satisfies("+rocm"):
-            before = r"/usr/lib/llvm-\d+/bin/clang"
-            after = spec["llvm-amdgpu"].prefix.bin.clang
-            filter_file(before, after, ".bazelrc")
+        if spec.satisfies("@2.16.1-rocm-enhanced +rocm"):
+            if os.path.exists(spec["llvm-amdgpu"].prefix.bin.clang):
+                filter_file(
+                    "/usr/lib/llvm-17/bin/clang", spec["llvm-amdgpu"].prefix.bin.clang, ".bazelrc"
+                )
+            else:
+                filter_file(
+                    "/usr/lib/llvm-17/bin/clang",
+                    spec["llvm-amdgpu"].prefix.llvm.bin.clang,
+                    ".bazelrc",
+                )
 
         filter_file("build:opt --copt=-march=native", "", ".tf_configure.bazelrc")
         filter_file("build:opt --host_copt=-march=native", "", ".tf_configure.bazelrc")
@@ -950,11 +938,6 @@ def build(self, spec, prefix):
 
         args.append("--config=v2")
 
-        if self.spec.satisfies("@2.18.0-rocm-enhanced: +rocm"):
-            buildpath = join_path(
-                self.stage.source_path, "bazel-bin/tensorflow/tools/pip_package/wheel_house/"
-            )
-            args.append(f"--repo_env=OUTPUT_PATH={buildpath}")
         # https://github.com/tensorflow/tensorflow/issues/63298
         if self.spec.satisfies("@2.17:"):
             args.append("//tensorflow/tools/pip_package:wheel")

var/spack/repos/builtin/packages/py-tensorflow/set_jit_true.patch

@@ -1,22 +0,0 @@
-diff --git a/tensorflow/core/kernels/mlir_generated/build_defs.bzl b/tensorflow/core/kernels/mlir_generated/build_defs.bzl
-index f574a8da8fd..fc1fbf68bf8 100644
---- a/tensorflow/core/kernels/mlir_generated/build_defs.bzl
-+++ b/tensorflow/core/kernels/mlir_generated/build_defs.bzl
-@@ -360,7 +360,7 @@ def _gen_kernel_library(
-                 extra_args = extra_args,
-                 host_triple = host_triple,
-                 gpu_archs = gpu_archs,
--                jit = jit,
-+                jit = True,
-                 mlir_op = "{op}_{name}_{platform}_{type}_{output_type}.mlir".format(
-                     op = op,
-                     name = name,
-@@ -370,7 +370,7 @@ def _gen_kernel_library(
-                 ),
-                 tile_size = typed_tile_size,
-                 unroll_factors = typed_unroll_factors,
--                jit_i64_indexed_for_large_tensors = jit_i64_indexed_for_large_tensors,
-+                jit_i64_indexed_for_large_tensors = False,
-             )
- 
-             # We have to use a sh_test instead of build_test because it doesn't properly find the dependent targets.

var/spack/repos/builtin/packages/r-a4/package.py

@@ -13,9 +13,6 @@ class RA4(RPackage):
 
     bioc = "a4"
 
-    version("1.54.0", commit="56cb1bc42bc4994e42071af04dcb75ebc0b24437")
-    version("1.52.0", commit="1270e4dd069313355c941c0470cf79352dc55b7f")
-    version("1.50.1", commit="3dba5687e0d029febfadbafcdcca5e54a4341a5b")
     version("1.48.0", commit="89ef9f4afdde5270acecc7c65be3752b71237eba")
     version("1.46.0", commit="1b8f1300025fb0940e7f24cff7ffec9fca02d0e4")
     version("1.44.0", commit="5b0fc5a9971d8f3688ad1f88a4f5ee1498e91633")

var/spack/repos/builtin/packages/r-a4base/package.py

@@ -13,9 +13,6 @@ class RA4base(RPackage):
 
     bioc = "a4Base"
 
-    version("1.54.0", commit="e45169b98e872087736bddbbc213fcd1951ed8ce")
-    version("1.52.0", commit="7312ef9ce99a61742a8c684739ae3e96b4733c02")
-    version("1.50.0", commit="26439bbad1e79464154cc5eb6adbcc69b3a231a0")
     version("1.48.0", commit="26d5793de3163091125feeed1de82e5406777b60")
     version("1.46.0", commit="be70ae723bb6031cdf9540d62dc6113761074e88")
     version("1.44.0", commit="9ae69e03118c7b14df0e6c9e3b25362b09f25bbe")

var/spack/repos/builtin/packages/r-a4classif/package.py

@@ -14,9 +14,6 @@ class RA4classif(RPackage):
 
     bioc = "a4Classif"
 
-    version("1.54.0", commit="9540e623465e1b67f1f2dc1cb566f47b76952a16")
-    version("1.52.0", commit="0366c84be3eddd933ed36acc07bd57b1fea4ae4a")
-    version("1.50.0", commit="1a416537c532a37a46a2719aa591e244cca6e779")
     version("1.48.0", commit="1e2ff90d5af6332beac630395a7494c8fd30aff4")
     version("1.46.0", commit="96794183a76ab7da7a1863ccd421640254447af5")
     version("1.44.0", commit="df0fce781f9bc480a1159d958c9a63c314a9ed01")

var/spack/repos/builtin/packages/r-a4core/package.py

@@ -13,9 +13,6 @@ class RA4core(RPackage):
 
     bioc = "a4Core"
 
-    version("1.54.0", commit="247927f7b6fdec427fac10291eeb4ebe8d5cb279")
-    version("1.52.0", commit="13a748dc52233ee90f6ff8f957ecba0b2b0d94d2")
-    version("1.50.0", commit="efe662190be692270d9bbb2c5e00baf46b23a442")
     version("1.48.0", commit="3dd09f0a662745fcfd3fee7048301f3524e8ac5c")
     version("1.46.0", commit="8999fe146be6d04ae36c725d2b6324a6ce8ceb83")
     version("1.44.0", commit="61a7f3a51a41af615bfd4c22984e4c4a82874e8c")

var/spack/repos/builtin/packages/r-a4preproc/package.py

@@ -13,9 +13,6 @@ class RA4preproc(RPackage):
 
     bioc = "a4Preproc"
 
-    version("1.54.0", commit="8b1a156f988e90f2cc8e4c6a17d4ac6452a46ce3")
-    version("1.52.0", commit="cfc6b6f66815c8d812144266298cab96a3c6c9b2")
-    version("1.50.0", commit="7f02ff9d1b65409c110ca2b695dceba6231c06cf")
     version("1.48.0", commit="d3bf8b82d7cabd2ef77253bb9a741dcde3ca3a41")
     version("1.46.0", commit="8463958692c73fd655a6dfec39ea99c915513719")
     version("1.44.0", commit="252381265b96b83803a93e0c2014dd6b0574e57f")

var/spack/repos/builtin/packages/r-a4reporting/package.py

@@ -13,9 +13,6 @@ class RA4reporting(RPackage):
 
     bioc = "a4Reporting"
 
-    version("1.54.0", commit="87a5a7498541f9fec60983c78d0ade920266e4d9")
-    version("1.52.0", commit="ce1eea6021b3e829ced7dcef8bf42440344ea8cf")
-    version("1.50.0", commit="5facc73ff067e1c1fa0e07d20e4151bcefad9b36")
     version("1.48.0", commit="de8c4b76f6b7ef502d77d55289df0d64fe70447c")
     version("1.46.0", commit="00b82d25bef4d518ae92f615d3a6f7931c0618dc")
     version("1.44.0", commit="bfe83507daf53e2e327474ea3012f0dc920efac1")

var/spack/repos/builtin/packages/r-absseq/package.py

@@ -16,9 +16,6 @@ class RAbsseq(RPackage):
 
     bioc = "ABSSeq"
 
-    version("1.60.0", commit="39efc102aaf3f65155be949ea0e2b4fae112d969")
-    version("1.58.0", commit="05f507feb439ca16983c24de32fcbd784476be40")
-    version("1.56.0", commit="60fbebd28c1be53f1d991b46eed5925a27c30f72")
     version("1.54.0", commit="5e7de8c2a6532073012660f22243c9f7a5568ef6")
     version("1.52.0", commit="07038c047775e17d5d29909927d2143efb63e9cb")
     version("1.50.0", commit="4f384d04ebaae6ea0b56e5cff9a9dcdcb6c8afb0")

var/spack/repos/builtin/packages/r-acde/package.py

@@ -21,9 +21,6 @@ class RAcde(RPackage):
 
     bioc = "acde"
 
-    version("1.36.0", commit="d779819cf0900a11ce15bd6a80ff794c4b6430a1")
-    version("1.34.0", commit="e99a19bb1d0c95a574b37376e3471f7dca12b1a3")
-    version("1.32.0", commit="1f7d0ce5c9c8666a73934bc4c0ec4a3e0db30ec6")
     version("1.30.0", commit="4c16b9fd6c91a433bf1345252e022571c4983cb5")
     version("1.28.0", commit="0edccca7be2475fa2ae3b3c36d0d64924c37b3c0")
     version("1.26.0", commit="dfef9a435062e948efd5eda22942a0d500baa992")

var/spack/repos/builtin/packages/r-acgh/package.py

@@ -15,9 +15,6 @@ class RAcgh(RPackage):
 
     bioc = "aCGH"
 
-    version("1.84.0", commit="e992a615337d0d2b4c4d369fa9b33f5f3a32ed1c")
-    version("1.82.0", commit="617c195db8de204f147370dcf1624df2ea48dff4")
-    version("1.80.0", commit="5ec9dd3644069574dd2ffd81c9ca0ac5d86e3d21")
     version("1.78.0", commit="75df3a4839af66ce177d1bbc3cec4ac03c21dc8e")
     version("1.76.0", commit="c6068522854ed0b1c3feb006619ef25590f70ad6")
     version("1.74.0", commit="e7ba380af0da138788eb6c86f5dbe453269c0810")

var/spack/repos/builtin/packages/r-acme/package.py

@@ -20,9 +20,6 @@ class RAcme(RPackage):
 
     bioc = "ACME"
 
-    version("2.62.0", commit="f631445a51969d2f11ed1698e8ad7fc4cee1fbf6")
-    version("2.60.0", commit="7a1f0e4c6e89d68a3887fba157374892f9dd2c8d")
-    version("2.58.0", commit="1b192d9040fd42346790d900bf02f6b4c7313696")
     version("2.56.0", commit="083af1249e67db11fd471babe67b146eb9c1700c")
     version("2.54.0", commit="8d39d9d6623adf427f5eba308790e1de01213870")
     version("2.52.0", commit="14a97c722d0201654af9e583e7e462b458c28a77")

var/spack/repos/builtin/packages/r-adsplit/package.py

@@ -15,9 +15,6 @@ class RAdsplit(RPackage):
 
     bioc = "adSplit"
 
-    version("1.76.0", commit="3bfef6d1d8a4e11632aeeadf25a00801564d5949")
-    version("1.74.0", commit="3df3361641cc343e106525e33bfcea675ec05e3a")
-    version("1.72.0", commit="194ddb23b683bc8633c9522456acc49c85b369b5")
     version("1.70.0", commit="a08a994215a459b856eae051c778e2b9144f52d9")
     version("1.68.0", commit="705977b5e1cb7dd69793cc673fa215baaba42af5")
     version("1.66.0", commit="64580a6f7a9bc6b16334267c90df48fbb839cc16")

var/spack/repos/builtin/packages/r-affxparser/package.py

@@ -19,9 +19,6 @@ class RAffxparser(RPackage):
 
     bioc = "affxparser"
 
-    version("1.78.0", commit="fab9ee2c921c61e84245601eb19d2b7c5c3acc3e")
-    version("1.76.0", commit="4f86ff876074195c1de2f4b36d74d98409b7055a")
-    version("1.74.0", commit="cada520ac224840d0de93d05c8924ad2006d77c3")
     version("1.72.0", commit="6e976af32f77835143f6b4e0c01c6016dc1b331c")
     version("1.70.0", commit="28f94cd3477e9500942be89cbcb5cad1bbb369fe")
     version("1.68.1", commit="821a01a2df18115a3b7864b3f45418255b7123eb")

var/spack/repos/builtin/packages/r-affy/package.py

@@ -14,9 +14,6 @@ class RAffy(RPackage):
 
     bioc = "affy"
 
-    version("1.84.0", commit="1174adf7e83ee46603189397cd557044802cda01")
-    version("1.82.0", commit="fb130de33532f6d15fe99ba02ff35cce07922308")
-    version("1.80.0", commit="a0d64dfdadfff1a1d7a4c39ba73e843e5e3fc6da")
     version("1.78.0", commit="cc7eac358b6e10ee86a7a93d2e436758f6fbd9b5")
     version("1.76.0", commit="3bb309388d5d6402c356d4a5270ee83c5b88942f")
     version("1.74.0", commit="2266c4a46eda7e5b64f7f3e17e8b61e7b85579ff")
@@ -30,7 +27,6 @@ class RAffy(RPackage):
 
     depends_on("c", type="build")  # generated
 
-    depends_on("r@2.8.0:", type=("build", "run"))
     depends_on("r@2.8.0:4.0", type=("build", "run"), when="@:1.68.0")
     depends_on("r-biocgenerics@0.1.12:", type=("build", "run"))
     depends_on("r-biobase@2.5.5:", type=("build", "run"))

var/spack/repos/builtin/packages/r-affycomp/package.py

@@ -13,9 +13,6 @@ class RAffycomp(RPackage):
 
     bioc = "affycomp"
 
-    version("1.82.0", commit="646461c2af419067de1d95691ca27e2ace50a436")
-    version("1.80.0", commit="2b69f9c6ec9f7c90287e254ba5bb9d658ce5820f")
-    version("1.78.0", commit="65cc8f00be57876705853adf0670b05a4ed6bf12")
     version("1.76.0", commit="8bfc628de26a739c5e0cb47aa22bfda7c8d0a922")
     version("1.74.0", commit="1160d6395f23085456938ba2bd38fb45597fc92f")
     version("1.72.0", commit="c52baea98b80abd4a99380ac9d4b68ef91869d40")

var/spack/repos/builtin/packages/r-affycontam/package.py

@@ -13,9 +13,6 @@ class RAffycontam(RPackage):
 
     bioc = "affyContam"
 
-    version("1.64.0", commit="c7cf836b166f981f9d87bf38cb2d8e2a6ab1bf6b")
-    version("1.62.0", commit="b0ced2ce1dff00e6eab4f0e091cebd6994298588")
-    version("1.60.0", commit="f2e21b7d4d700e135ae3bd0fa3531e001a7aa950")
     version("1.58.0", commit="5e91d79d7653a4f484b62eae7fd7e908de8cb9b6")
     version("1.56.0", commit="e2b8a4fba1648255eadce954a848f2dd8e22bcb3")
     version("1.54.0", commit="c5208b48b8881983ff53a4713244327e8ad13b78")

var/spack/repos/builtin/packages/r-affycoretools/package.py

@@ -14,9 +14,6 @@ class RAffycoretools(RPackage):
 
     bioc = "affycoretools"
 
-    version("1.78.0", commit="2eb1cc5d748832ecd4f8e610397b43c88099ccd4")
-    version("1.76.0", commit="4733a16c9629a62c5dc6fb3fef3a6e6def049a02")
-    version("1.74.0", commit="c04ad6fe6a8809b769bdff4cefb6d47a23e7a891")
     version("1.72.0", commit="229ae09efc1a66e64ea395019c32d16387bf81ac")
     version("1.70.0", commit="f09a788aa83e1e052a7c5f148a451a99fe9c9c96")
     version("1.68.1", commit="69546b1fe5edd71eca130d53d33f0fb0fcf62c97")

var/spack/repos/builtin/packages/r-affydata/package.py

@@ -14,9 +14,6 @@ class RAffydata(RPackage):
 
     bioc = "affydata"
 
-    version("1.54.0", commit="b3765c212d7721c189cd7326c18c4141b5227da0")
-    version("1.52.0", commit="54b35381b1b13161e0d0ef10627efc26ed8dc0c5")
-    version("1.50.0", commit="203e040f737bdeb65d8cd2123dc76036f23e4e3a")
     version("1.48.0", commit="037b86c86c114761ff1bcca64ab4e0bcd68063d3")
     version("1.46.0", commit="870745b886df9f1fbbd6130d266c0ef96f3afa66")
     version("1.44.0", commit="f18304a356cee8cd7297bab362b13c40e50439df")

var/spack/repos/builtin/packages/r-affyexpress/package.py

@@ -14,7 +14,6 @@ class RAffyexpress(RPackage):
 
     bioc = "AffyExpress"
 
-    version("1.58.0", commit="3b0f72dc19d923a87cc462673d933e58760a9cc9")
     version("1.56.0", commit="e07085833de2bbf81537410cad526d39f8a82478")
     version("1.50.0", commit="8b98703b63396df9692afb0e15b594658125cc96")
     version("1.48.0", commit="dbaed516b7529ef4f7588aafaf3c5f1d53a9bb92")

var/spack/repos/builtin/packages/r-affyilm/package.py

@@ -15,9 +15,6 @@ class RAffyilm(RPackage):
 
     bioc = "affyILM"
 
-    version("1.58.0", commit="0ceee74b89a9e2dcd8793371cb37e60a9c9a79da")
-    version("1.56.0", commit="ee6044051fce374b0c7ec858e5d300bba28cfafa")
-    version("1.54.0", commit="4586915a1be400f54e37506ebc1ddffb91480e89")
     version("1.52.0", commit="08ed8c60921ba1b9e04fa90e156eef1a3c899d15")
     version("1.50.0", commit="185cd8e4712a3378ce7a156d4940224bbb2c4122")
     version("1.48.0", commit="4603a4c4d6c2330a8a56a7bb657dc56c51a9393a")

var/spack/repos/builtin/packages/r-affyio/package.py

@@ -14,9 +14,6 @@ class RAffyio(RPackage):
 
     bioc = "affyio"
 
-    version("1.76.0", commit="ed8b074ada05f3b3eeba3032b1214179e3034a42")
-    version("1.74.0", commit="1d0948e7a76a00da985b9fdd38d36fa0ca85c2af")
-    version("1.72.0", commit="2f97a7e3710e44886b0b732d1c0dbb3165e9b84c")
     version("1.70.0", commit="95560567e27088863c64e868a8e5069fc725b8d7")
     version("1.68.0", commit="33080c5eeb14c0ca40f0d231706af4e0c2c1ef8b")
     version("1.66.0", commit="3a0b90704fc46cddd99a72b985a6bdb348f69b50")
@@ -31,6 +28,5 @@ class RAffyio(RPackage):
     depends_on("c", type="build")  # generated
 
     depends_on("r@2.6.0:", type=("build", "run"))
+    depends_on("r-zlibbioc", type=("build", "run"))
     depends_on("zlib-api")
-
-    depends_on("r-zlibbioc", type=("build", "run"), when="@:1.77.0")

var/spack/repos/builtin/packages/r-affypdnn/package.py

@@ -13,8 +13,6 @@ class RAffypdnn(RPackage):
 
     bioc = "affypdnn"
 
-    version("1.62.0", commit="22a6e97303bd60c8b365b51c38e4312d5b7ee995")
-    version("1.60.0", commit="9f8998fa4405fbbaea6f7a7eb6d3c1b29c3f5e09")
     version("1.58.0", commit="83d8b6b0d9606845bd77dbf7164dd5b160f32ccf")
     version("1.56.0", commit="5fd9c5265fb895a1f646cf72e8d5169669d979f2")
     version("1.54.0", commit="ea971b1b9cc443695a6614bef92e8e116ee87d55")

var/spack/repos/builtin/packages/r-affyplm/package.py

@@ -16,9 +16,6 @@ class RAffyplm(RPackage):
 
     bioc = "affyPLM"
 
-    version("1.82.0", commit="16d738761d115c14f72a083266e501edb72ce548")
-    version("1.80.0", commit="b0584edcaba058d5cfb06d64e22a4859c7d15b60")
-    version("1.78.0", commit="1fa54e253098269e93b3e8f88bc592041b855334")
     version("1.76.0", commit="45557df5a32f56aa5240439737c5718738fb4c27")
     version("1.74.0", commit="5f76ef92e69deabc19c5395eaec4adb85c66b63d")
     version("1.72.0", commit="394c0a8e213f188d0b1d01e20516df8bf1bc5c09")

var/spack/repos/builtin/packages/r-affyqcreport/package.py

@@ -14,7 +14,6 @@ class RAffyqcreport(RPackage):
 
     bioc = "affyQCReport"
 
-    version("1.70.0", commit="9e49c8c376d8b1d79981628920e5adc238bddeca")
     version("1.68.0", commit="34b42a16f87a90a595146f4a1802ed04f6bfccca")
     version("1.62.0", commit="92d4124b688b90a6a9b8a21ab9d13d92b368cee4")
     version("1.60.0", commit="d0c15b1c56fc1caf6f114877ea6c1b8483a0dcfa")

var/spack/repos/builtin/packages/r-affyrnadegradation/package.py

@@ -17,9 +17,6 @@ class RAffyrnadegradation(RPackage):
 
     bioc = "AffyRNADegradation"
 
-    version("1.52.0", commit="14b087a0fbe2796398ceaebe6232553bce90a2f1")
-    version("1.50.0", commit="2be3cbcdb710b069e82610c123c73a4cc4651a30")
-    version("1.48.0", commit="dfc274be6d53250bc516c9772022c771706c7545")
     version("1.46.0", commit="431ae61c9b3809829697ef71672c57171d93311e")
     version("1.44.0", commit="63881f41fc67cc7322b189446dcffb4e1060e303")
     version("1.42.0", commit="5775f41f538b3c8ee4d07d38cec1b49c548cebe6")

var/spack/repos/builtin/packages/r-agdex/package.py

@@ -13,9 +13,6 @@ class RAgdex(RPackage):
 
     bioc = "AGDEX"
 
-    version("1.54.0", commit="0dc73a6f55bf53ddea0689df48dc72d4983faf87")
-    version("1.52.0", commit="69fe01a6ce7045afe612daea363365b6deaeaed7")
-    version("1.50.0", commit="5b2ecdae7bbafee5c48de5b7181a55bda95143ba")
     version("1.48.0", commit="917920b397493b0ea40093044ebe36fff7c389ad")
     version("1.46.0", commit="d7c38e8bdcaa7b0261117c605e7f61e2b07e8316")
     version("1.44.0", commit="9d3eb90eaf7bf093c7fa73facb3df89506a85185")

var/spack/repos/builtin/packages/r-agilp/package.py

@@ -12,9 +12,6 @@ class RAgilp(RPackage):
 
     bioc = "agilp"
 
-    version("3.38.0", commit="5ed3359c61678afed7709bd3795702b9e94f46f3")
-    version("3.36.0", commit="204ae1003390b0b4efa5aa7d43f96c256e59fc9e")
-    version("3.34.0", commit="12c94ca5c5c1b6bc909571c1bee897a6268d9e39")
     version("3.32.0", commit="8291f7b7c1b6167952568f51593116afc6d0fc27")
     version("3.30.0", commit="a2c898dc901ccdda4b8582caff079ab20b1bfc28")
     version("3.28.0", commit="2c6dfccc76473b5bef13b75fa59adf46b3381f55")

var/spack/repos/builtin/packages/r-agimicrorna/package.py

@@ -13,9 +13,6 @@ class RAgimicrorna(RPackage):
 
     bioc = "AgiMicroRna"
 
-    version("2.56.0", commit="5e277127c2557b8cff752d3fca9f3a41b373d497")
-    version("2.54.0", commit="2c8850f9b62308a3932d74548689b24741347bab")
-    version("2.52.0", commit="73e65fb29170d1bee3b849f82a25ae7da3c6cd3b")
     version("2.50.0", commit="a812b0f4f215b093ca685889b65de60c6701b695")
     version("2.48.0", commit="4c163b1b730150a3a60a3815bd8c08fa04d71fc1")
     version("2.46.0", commit="8c6d73e1c3f1f9cc019bdb219b19e6179bb1efe4")

var/spack/repos/builtin/packages/r-aims/package.py

@@ -16,9 +16,6 @@ class RAims(RPackage):
 
     bioc = "AIMS"
 
-    version("1.38.0", commit="b7d238e6573f1921a4f255f9c7cd673a31482c1c")
-    version("1.36.0", commit="8c8f6120501a37595034c1c1759ccfb751e995e1")
-    version("1.34.0", commit="61910444b05ce6e438467177202a93046c700e32")
     version("1.32.0", commit="019415a6362e805465d43c157606e1774aed9e51")
     version("1.30.0", commit="2ab61159c5aa0902cc33fc1502f7853b66912cce")
     version("1.28.0", commit="84608df638b5694c08158ed77ad2c8a64c4e594b")

var/spack/repos/builtin/packages/r-aldex2/package.py

@@ -24,9 +24,6 @@ class RAldex2(RPackage):
 
     license("GPL-3.0-only")
 
-    version("1.38.0", commit="701515c185aa747e53c863afbb3730a9a331e242")
-    version("1.36.0", commit="c7a4c4bfc66baba750ef58163193f6b53830cf9b")
-    version("1.34.0", commit="eda12f9208ed90e9e2c2d6a47415a5c73c107e4b")
     version("1.32.0", commit="ba32b9a9b6a8f42906ea094318f00116f15e42eb")
     version("1.30.0", commit="cb6670515a8722f9cfedac12a8c2747a5298ee46")
     version("1.28.1", commit="f8d8ba6d2439bff75ab80f5466c9a047c31ed0a6")

var/spack/repos/builtin/packages/r-allelicimbalance/package.py

@@ -13,9 +13,6 @@ class RAllelicimbalance(RPackage):
 
     bioc = "AllelicImbalance"
 
-    version("1.44.0", commit="c46bcc17963050a7fd01a23615de796fd3e8bd4b")
-    version("1.42.0", commit="4dc686c08a02d051ba1d8e82c909c2c751dc5613")
-    version("1.40.0", commit="e3fc91108af4816a237b588b23cc40133f6eee30")
     version("1.38.0", commit="75a3b0fefe635a0892eae338d0fdd4a9e091f957")
     version("1.36.0", commit="cb4910c1fd58cc4272c21251a8f120990e1aa431")
     version("1.34.0", commit="290708ccc4ceae1fbb9e9257cb254916449d389b")

var/spack/repos/builtin/packages/r-alsace/package.py

@@ -18,7 +18,6 @@ class RAlsace(RPackage):
     bioc = "alsace"
 
     version("1.30.0", commit="d0e09b283da2b4869d5d6e6801399676246bc5bc")
-    version("1.28.0", commit="03344a1f12a5c86e61a8d69b68d9d16c3ed07561")
     version("1.26.0", commit="40a76404acb1466723a78a55d87c67eec3e6f306")
     version("1.20.0", commit="47f1cf8daafc864e5e3418009f349ce85d6b0389")
     version("1.18.0", commit="c9fc43c7b441de43b14ef1be69926c4c4a566191")

var/spack/repos/builtin/packages/r-altcdfenvs/package.py

@@ -12,9 +12,6 @@ class RAltcdfenvs(RPackage):
 
     bioc = "altcdfenvs"
 
-    version("2.68.0", commit="53038c86c7c743272e00a71b5fcb4252b068cf13")
-    version("2.66.0", commit="34a3f5bc0b36543e20de6dd2035db3776677e8e2")
-    version("2.64.0", commit="86cec42b52c7b2450ae6dbc7b0ab73a98c32fc3b")
     version("2.62.0", commit="aedf0e9f98639d60b327e50957e504cf24b64bbb")
     version("2.60.0", commit="0bc0b4493b8e9fe2eb47fb8e9377123ce8f472bb")
     version("2.58.0", commit="08255a777ffa1e1414d3dd3062d95bfdd3dfd47c")

var/spack/repos/builtin/packages/r-analysispageserver/package.py

@@ -14,8 +14,6 @@ class RAnalysispageserver(RPackage):
 
     bioc = "AnalysisPageServer"
 
-    version("1.22.0", commit="2a18bb215ccaef5da08ea4d0e37cfb591b9dc783")
-    version("1.20.0", commit="aafd0364f9f5d9778a36bda9f2c399360af4d8ad")
     version("1.18.1", commit="08bd85e872d3f2b0c1fa148cf30bcd2d1a29b630")
     version("1.16.0", commit="67b063523f80e2af1d26262367ff50f34e195174")
     version("1.14.0", commit="620c0ea1e129ddd1a0866e2c9d7c3fcf06a8baf4")

var/spack/repos/builtin/packages/r-anaquin/package.py

@@ -16,9 +16,6 @@ class RAnaquin(RPackage):
 
     bioc = "Anaquin"
 
-    version("2.30.0", commit="281f04476cf037429251e74e461e0d8827975560")
-    version("2.28.0", commit="b547d11c1108c18f8e28a805cdf5ffa43c27783d")
-    version("2.26.0", commit="ca9494432f5e2acbd32a74fff6ad271c05f9e4d9")
     version("2.24.0", commit="0eefabdc4036b98505032c460d08375839b1fc3e")
     version("2.22.0", commit="d848a9bd7bf9d1d62202cc477300bf1a65b3e36c")
     version("2.20.0", commit="61598dd3430b09b57f31d7d550ea95126a2d73c8")

var/spack/repos/builtin/packages/r-aneufinder/package.py

@@ -14,9 +14,6 @@ class RAneufinder(RPackage):
 
     bioc = "AneuFinder"
 
-    version("1.34.0", commit="b69e323eefb2a3485fcd46491b2229042eb57335")
-    version("1.32.0", commit="c7a1f1812e203a0e52db7f8228cf361abc954486")
-    version("1.30.0", commit="f0c9ccfd4bb3761460efdf8fcd5c4d0faf8467ff")
     version("1.28.0", commit="e17d810171bdab1c6a26a3ab7b7931db4e073e7e")
     version("1.26.0", commit="7cd59a1e24c6512f2e4fcbe2c53a0d3cd2d06217")
     version("1.24.0", commit="4c6906eee514eba3e8ac159654a6953e37a99bba")

var/spack/repos/builtin/packages/r-aneufinderdata/package.py

@@ -13,9 +13,6 @@ class RAneufinderdata(RPackage):
 
     bioc = "AneuFinderData"
 
-    version("1.34.0", commit="4c07ed4ce577a25fc8f1e20da0962a2f3f978620")
-    version("1.32.0", commit="79c9b4efa2db70e46af1b52d3dc7fb992beef35d")
-    version("1.30.0", commit="573710c04570ea62746a161cb8083c6690be95d6")
     version("1.28.0", commit="d04255e60173ce478d31b1e1e5c73e6ed9e3b20c")
     version("1.26.0", commit="4b810599b62a3fb39239bfd98ed960c93989e86b")
     version("1.24.0", commit="cf6f3852702aab28e3170fc56b695d00b7389666")

var/spack/repos/builtin/packages/r-annaffy/package.py

@@ -17,9 +17,6 @@ class RAnnaffy(RPackage):
 
     license("LGPL-2.1-or-later")
 
-    version("1.78.0", commit="095b5607fc77e49ba5dbad76ff3857f3a1ad9e5b")
-    version("1.76.0", commit="9a349617a9ebce7ebc81d64fd733497bf27b968f")
-    version("1.74.0", commit="15d4c6a754cb51daaca554255fc41f39dc303006")
     version("1.72.0", commit="7cb439706a7e93fb5b44ead374010077a44ea78b")
     version("1.70.0", commit="c99e81259adb39b5d8e954fd7afe7f93675229bc")
     version("1.68.0", commit="fa930c0bbdca9828a130ab06d86c65d451380830")

var/spack/repos/builtin/packages/r-annotate/package.py

@@ -12,9 +12,6 @@ class RAnnotate(RPackage):
 
     bioc = "annotate"
 
-    version("1.84.0", commit="6188ffbe46daf9b0fbf49de8ac81068df775c136")
-    version("1.82.0", commit="9710d81c5d0316382c076fbfa0648c4945f72d6c")
-    version("1.80.0", commit="45a42c3691e7707f96286c7c3234332a8ea39870")
     version("1.78.0", commit="ca6415a463ec682f340ba5d1dc6246a92e836143")
     version("1.76.0", commit="0181d5c41d594e36be06adb6a02302db0ad2c507")
     version("1.74.0", commit="200c71743417792880f8171d59b2ac0ddd3902a8")

var/spack/repos/builtin/packages/r-annotationdbi/package.py

@@ -13,9 +13,6 @@ class RAnnotationdbi(RPackage):
 
     bioc = "AnnotationDbi"
 
-    version("1.68.0", commit="6a2aa3361bb114fbfe7a25b51bcaed36450a57e0")
-    version("1.66.0", commit="989c1dcf56db17646e79bd7caa70484e4cda73d1")
-    version("1.64.1", commit="e5b997eac9f538d6ad5418fbe90716848d8c5f2e")
     version("1.62.0", commit="7ca03a0332d0a284ea27d16edb7b386c86cf99ea")
     version("1.60.0", commit="cd61bd1b1538e2f1f411fd7087820749ecf39da8")
     version("1.58.0", commit="05fcf7a28a6b15b195da23474d7ba89bd0cfd891")

var/spack/repos/builtin/packages/r-annotationfilter/package.py

@@ -14,9 +14,6 @@ class RAnnotationfilter(RPackage):
 
     bioc = "AnnotationFilter"
 
-    version("1.30.0", commit="1204cb5c19fde6628e99279ffca8e1b0b2a1219b")
-    version("1.28.0", commit="61709ad226a834e6c80b02199c170d7784f23196")
-    version("1.26.0", commit="be933b32635c36571f43c1aa6ec3b1efab0dd1da")
     version("1.24.0", commit="172d9c149d9025154f7b26982d07f571499b03e8")
     version("1.22.0", commit="c9fea4a829ce9419b6e0af987915b2d469358597")
     version("1.20.0", commit="2818aff6502fd6fe819521cd8d97695ef6f9198e")

var/spack/repos/builtin/packages/r-annotationforge/package.py

@@ -13,9 +13,6 @@ class RAnnotationforge(RPackage):
 
     bioc = "AnnotationForge"
 
-    version("1.48.0", commit="a22ccaf712a0737cf10fd5981a1a48f9c4e1395d")
-    version("1.46.0", commit="50d67131ed398f517b87263a6d5adfc189835ee5")
-    version("1.44.0", commit="1a9bb5fb6d66be5002b00b5abf5023ce81755b33")
     version("1.42.0", commit="2eac005012b11317c33c8b0062b968b2ac378308")
     version("1.40.0", commit="f77d3a942eb6b18c18888b7af3f0e652596cf19f")
     version("1.38.1", commit="2dcedf353bc57bf80818e6adb1f7129c21886f6b")

var/spack/repos/builtin/packages/r-annotationhub/package.py

@@ -19,9 +19,6 @@ class RAnnotationhub(RPackage):
 
     bioc = "AnnotationHub"
 
-    version("3.14.0", commit="f93a396134b69cb408946569c721dbe7ea7e1978")
-    version("3.12.0", commit="7c17d78eb590e7e3b6abeb678d8a4a38657a9765")
-    version("3.10.1", commit="290bd8e0792ec6f8f90d600eecbfae2c93fea227")
     version("3.8.0", commit="975022dd33706824bd02f67cc9c3a42f3567f4a5")
     version("3.6.0", commit="3315a73b7803a92412ed18209dd37b378195b86f")
     version("3.4.0", commit="e74e54ca44f50c2c15c60f8620e3d1721f8f5b6d")

var/spack/repos/builtin/packages/r-aroma-light/package.py

@@ -15,9 +15,6 @@ class RAromaLight(RPackage):
 
     bioc = "aroma.light"
 
-    version("3.36.0", commit="d421a4eb2af87b0b58c10aad160385d8fc034a43")
-    version("3.34.0", commit="8ae145cc50f51ae6b0321f085169cbd276987e63")
-    version("3.32.0", commit="21984e1f4fbeb51744bb462844748041c1a3b7e6")
     version("3.30.0", commit="a1882c2126622cb389a7ef1ef5b5c565e603a282")
     version("3.28.0", commit="7749dd7033e9885ec2546a5cac0562bac2fea04d")
     version("3.26.0", commit="7ead7517a77bc8b4b4b42aace69957a17e8fe016")

var/spack/repos/builtin/packages/r-assorthead/package.py

@@ -1,14 +0,0 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack.package import *
-
-
-class RAssorthead(RPackage):
-    """Assorted header-only C++ libraries for Bioconductor."""
-
-    bioc = "assorthead"
-
-    version("1.0.1", commit="4aa44624adb6981c75db9f5e200114784f343e32")

var/spack/repos/builtin/packages/r-bamsignals/package.py

@@ -15,9 +15,6 @@ class RBamsignals(RPackage):
 
     bioc = "bamsignals"
 
-    version("1.38.0", commit="579649b2878b7d70ad42926273863d21ef4b8ee4")
-    version("1.36.0", commit="5b8df63f3f42a02c6df75030d590a55919ff82c0")
-    version("1.34.0", commit="58fa17f3b093788c8799c23718fba8b0f0126476")
     version("1.32.0", commit="34bfc4e8b58e47c3b94347fd2976aeae07fc28c2")
     version("1.30.0", commit="aac37dffd6f6876b4626866e3d40bb7af75620fe")
     version("1.28.0", commit="27b70be6f73747d9d32054da043f4a37ea55b917")