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2022-08-31gdk-pixbuf: only build tests when requested (#32452)Wouter Deconinck1-0/+3
The building of tests is optional [as of 2.42.9](https://gitlab.gnome.org/GNOME/gdk-pixbuf/-/commit/801eef111df624f4377baed9a90c94b6a2d4340c). This applies this option in the build. The reason the option was added was to deal with test build failures in sandboxed environments and with certain glibc versions (caused by glib gresources). For example, with the latest version glibc and in the latest version of docker these tests [cannot be built](https://github.com/moby/moby/issues/43595).
2022-08-31py-pandas: add v1.4.4 (#32459)Adam J. Stewart1-0/+2
2022-08-31llvm: fix 15.0.0rc builds on MacOS with command-line-tools (#32397)Satish Balay1-5/+18
* llvm: fix 15.0.0rc builds on MacOS with command-line-tools Ref: https://github.com/llvm/llvm-project/issues/57037 i.e use -DBUILTINS_CMAKE_ARGS=-DCOMPILER_RT_ENABLE_IOS=OFF. But this needs switching "compiler-rt" from "projects" to "runtimes". Also fixing the warnings below fixes compile errors CMake Warning at CMakeLists.txt:101 (message): Using LLVM_ENABLE_PROJECTS=libcxx is deprecated now, please use -DLLVM_ENABLE_RUNTIMES=libcxx or see the instructions at https://libcxx.llvm.org/BuildingLibcxx.html for building the runtimes. CMake Warning at CMakeLists.txt:101 (message): Using LLVM_ENABLE_PROJECTS=libcxxabi is deprecated now, please use -DLLVM_ENABLE_RUNTIMES=libcxxabi or see the instructions at https://libcxx.llvm.org/BuildingLibcxx.html for building the runtimes. CMake Warning at CMakeLists.txt:101 (message): Using LLVM_ENABLE_PROJECTS=libunwind is deprecated now, please use -DLLVM_ENABLE_RUNTIMES=libunwind or see the instructions at https://libcxx.llvm.org/BuildingLibcxx.html for building the runtimes. /private/var/folders/nt/_m1t_x7j76q6sl3xt91tqgs00000gn/T/balay/spack-stage/spack-stage-llvm-15.0.0-rc2-h2t5bohzyy7exz2ub3m42pfycjcmbndk/spack-build-h2t5boh/include/c++/v1/cstdlib:135:9: error: no member named 'at_quick_exit' in the global namespace using ::at_quick_exit _LIBCPP_USING_IF_EXISTS; ~~^ * Update var/spack/repos/builtin/packages/llvm/package.py Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-08-31ASP-based solver: allow to reuse installed externals (#31558)Massimiliano Culpo4-31/+146
fixes #31484 Before this change if anything was matching an external condition, it was considered "external" and thus something to be "built". This was happening in particular to external packages that were re-read from the DB, which then couldn't be reused, causing the problems shown in #31484. This PR fixes the issue by excluding specs with a "hash" from being considered "external" * Test that users have a way to select a virtual This ought to be solved by extending the "require" attribute to virtual packages, so that one can: ```yaml mpi: require: 'multi-provider-mpi' ``` * Prevent conflicts to be enforced on specs that can be reused. * Rename the "external_only" fact to "buildable_false", to better reflect its origin
2022-08-31py-breathe: add new version and improve version constraints (#31857)Seth R. Johnson1-1/+5
* py-breathe: add new version and improve version constraints * py-breathe: everyone loves versions ``` py-breathe, py-breathe in the air don't be afraid to care ```` * Update var/spack/repos/builtin/packages/py-breathe/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * add comment Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-08-31hdf5-vol-log: Update package versions and update HDF5 dependency to version ↵Larry Knox1-2/+4
1.13.2 (#32448) * Add HDF5 version 1.13.2. Remove HDF5 versions 1.13.0 and 1.13.1. * Correct formatting. * Update vol-log-based versions and HDF5 dependency version.
2022-08-31bdw-gc: add v8.2.2 (#32453)Ivan Maidanski1-1/+2
2022-08-30py-gpytorch: add v1.9.0 (#32445)Adam J. Stewart2-2/+29
2022-08-30py-kornia: add v0.6.7 (#32447)Adam J. Stewart1-0/+1
2022-08-30Environments: Add support for include URLs (#29026)Tamara Dahlgren22-221/+919
* Preliminary support for include URLs in spack.yaml (environment) files This commit adds support in environments for external configuration files obtained from a URL with a preference for grabbing raw text from GitHub and gitlab for efficient downloads of the relevant files. The URL can also be a link to a directory that contains multiple configuration files. Remote configuration files are retrieved and cached for the environment. Configuration files with the same name will not be overwritten once cached.
2022-08-30New package: py-mkdocstrings-python (#32421)Ryan Marcellino1-0/+21
2022-08-30added STAT 4.2.0 and updated deps (#32385)Gregory Lee3-3/+13
* added STAT 4.2.0 and updated deps * launchmon package fix and style fixes * launchmon package fix * Update var/spack/repos/builtin/packages/launchmon/package.py Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-08-30libatomic_ops: add v7.6.14 (#32418)Ivan Maidanski1-1/+2
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-08-30libxml2: fix building with nvhpc (#32440)Harmen Stoppels2-36/+1
2022-08-30root: new bugfix version 6.26.06 (#32230)Wouter Deconinck1-0/+13
2022-08-30oprnmx: fix to build with Fujitsu compiler. (#32389)Toyohisa Kameyama1-1/+1
2022-08-30coreutils: add support for external find (#32414)Olivier Cessenat1-0/+10
2022-08-30hipsycl: fix building on OSX. Patch boost to be backward-compatible. (#31311)David M. Rogers1-3/+7
Co-authored-by: frobnitzem <frobnitzem@users.noreply.github.com>
2022-08-30scorep: modify configure flags for Cray platforms (#32201)luker1-2/+4
2022-08-30visit: actually set the dev env for plugins again (#32427)Olivier Cessenat1-1/+4
2022-08-30esmf: update package for cce (cray) compiler (#32433)Jim Edwards2-4/+27
2022-08-29Initial commit for freesurfer package (#32395)robgics1-0/+40
* Initial commit for freesurfer package * Add myself as maintainer * Change URLs to https and move url function to proper place.
2022-08-29snphylo: update to new version (#32425)snehring1-2/+5
2022-08-29Switched LBANN to using an explicit variant to enable unit testing (#32429)Brian Van Essen1-4/+6
support rather than relying on the spack install --test root option, because it doesn't play nice in environments.
2022-08-29dealii:: fixed application of stdcxx variant (#32413)Luca Heltai1-0/+5
* Fixed imposition of stdcxx. * Fixed style.
2022-08-29celeritas: new version 0.1.1 (#32412)Seth R. Johnson1-0/+1
2022-08-29gdk-pixbuf: new bugfix version 2.42.9 (#32420)Wouter Deconinck1-0/+1
No changes of note. Just bugfixes. Full diff at https://gitlab.gnome.org/GNOME/gdk-pixbuf/-/compare/2.42.6...2.42.9?from_project_id=1548
2022-08-28New package: py-mkdocstrings (#32417)Ryan Marcellino1-0/+25
2022-08-28New package: py-mkdocs-jupyter (#32416)Ryan Marcellino1-0/+27
2022-08-27libxml2: add new versions (#32394)Sergey Kosukhin1-0/+10
* libxml2: add new versions * libxml2: apply patch preventing SIGFPE
2022-08-26py-radiant-mlhub: add v0.5 (#32406)Adam J. Stewart4-10/+29
2022-08-26add sra-tools and NCBI-VDT packages (#32403)downloadico2-0/+50
* ncbi-vdb: add ncbi-vdb package to spack ncbi-vdb provides the interface to the NCBI VDB * sra-tools: add sra-tools to spack
2022-08-26py-sphinx-rtd-theme: add version 1.0.0 (#32379)Richard Berger1-1/+5
2022-08-26Use threading.TIMEOUT_MAX when available (#32399)Betsy McPhail1-1/+8
This value was introduced in Python 3.2. Specifying a timeout greater than this value will raise an OverflowError.
2022-08-26[py-pybedtools] added version 0.9.0 (#32401)Jen Herting1-15/+14
2022-08-26New packages: roary plus 5 new perl-* (#32217)dlkuehn9-12/+210
* New package: roary
2022-08-26Configuration: Allow requirements for virtual packages (#32369)Massimiliano Culpo4-22/+149
Extend the semantics of package requirements to allow using them also under a virtual package attribute in packages.yaml These requirements are enforced whenever that virtual spec is present in the DAG.
2022-08-26SDK: Option to disable fortran support. (#32319)kwryankrattiger1-6/+9
This option was requested to support MacOS systems that do not have fortran installed.
2022-08-26New package: py-mkdocs-material (#32387)Ryan Marcellino1-0/+27
2022-08-26New package: py-mkdocs-autorefs (#32386)Ryan Marcellino1-0/+21
2022-08-26Add pic variant to bacio (#32388)Dom Heinzeller1-0/+7
* Add pic variant to bacio * Fix black style error
2022-08-26add eztrace 2.0 release (#32350)François Trahay1-1/+1
* [EZTrace] Version uptate to 2.0 * Update var/spack/repos/builtin/packages/eztrace/package.py Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-08-26Update archspec to latest commit (#32368)Massimiliano Culpo3-6/+105
Modifications: - [x] Add graviton3 - [x] Optimize __eq__ for microarchitectures
2022-08-26calculate make_jobs in ninja (#32384)Tom Scogland1-2/+4
This is in case ninja's setup_dependent_package is called before its module is initialized by build_environment
2022-08-26Improve error message for yaml config file (#32382)Chris White1-1/+9
* improve error message * Update lib/spack/spack/config.py Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-08-25libzmq: add patch for gcc-12; conflict for older gcc-11 versions (#32381)Wouter Deconinck1-2/+9
Per #32214, the existing patch `92b2c...` for `gcc@11:` only applies cleanly for `libzmq@4.3.3:4.3.4`. This PR adds a conflict for earlier versions, as they cannot be patched due to different context. For `gcc@11`, this leaves the most recent two versions available (a satisfactory compromise). For `gcc@12`, however, there is another existing conflict that makes these most recent two versions unavailable. This PR adds an upstream patch for the single most recent version that allows compilation with `gcc@12` for that most recent version. Starting point: - `gcc@11` concretizes on all versions, attempts to apply patch on `@4.2.3:4.3.4`, and only succeeds to apply patch on `@4.3.3:4.3.4`, - `gcc@12` concretizes on `@:4.3.1` (and `@master`), attempts to apply patch on `@4.2.3:4.3.1`, fails to apply patch on all. Ending point: - `gcc@11` concretizes on `@4.3.3:4.3.4` (and `@master`), attempts and succeeds to apply patch on `@4.3.3:4.3.4`, - `gcc@12` concretizes on `@4.3.4` (and `@master`), attempts and succeeds to apply patch on `@4.3.4`. Verified with environment build: ```yaml spack: specs: - libzmq@4.3.4%gcc@12.1.0 - libzmq@4.3.4%gcc@11.3.0 - libzmq@4.3.3%gcc@11.3.0 view: false ``` which returns the following: ```console 16:14:47 wdconinc@menelaos ~/git/spack (libzmq-patch-gcc12 *+$%=) $ spack install --fresh ==> Installing environment libzmq [+] /opt/software/linux-ubuntu22.04-skylake/gcc-12.1.0/libmd-1.0.4-egpgd6eoaqtsl5fja2iwsl6gyc4o32p5 [+] /opt/software/linux-ubuntu22.04-skylake/gcc-12.1.0/libsodium-1.0.18-af3rsfnvck6anxf7eeog3f2bph44tjia [+] /opt/software/linux-ubuntu22.04-skylake/gcc-12.1.0/pkgconf-1.8.0-z5of2hj2c6ygd3kxr4cwv7u7t42sxair [+] /opt/software/linux-ubuntu22.04-skylake/gcc-11.3.0/libmd-1.0.4-tec234gco2sd7n52dkwbrad43sdhaw4o [+] /opt/software/linux-ubuntu22.04-skylake/gcc-11.3.0/libsodium-1.0.18-uljf675u3yrn5c7fdjdpa5c7qnnkynke [+] /opt/software/linux-ubuntu22.04-skylake/gcc-11.3.0/pkgconf-1.8.0-l4hzc2g4pnn7dwyttphmxivt3xghvpoq [+] /opt/software/linux-ubuntu22.04-skylake/gcc-12.1.0/libbsd-0.11.5-fi3ri64moy45ksr4sf5pcwd6k23dsa4o [+] /opt/software/linux-ubuntu22.04-skylake/gcc-11.3.0/libbsd-0.11.5-2matmm7im7oygrr77k7wznttv4rbupfz ==> Installing libzmq-4.3.4-t7ad54q3atrnte4rzq7g7cfjcw5227pr ==> No binary for libzmq-4.3.4-t7ad54q3atrnte4rzq7g7cfjcw5227pr found: installing from source ==> Fetching https://mirror.spack.io/_source-cache/archive/c5/c593001a89f5a85dd2ddf564805deb860e02471171b3f204944857336295c3e5.tar.gz ==> Fetching https://mirror.spack.io/_source-cache/archive/31/310b8aa57a8ea77b7ac74debb3bf928cbafdef5e7ca35beaac5d9c61c7edd239 ==> Fetching https://github.com/zeromq/libzmq/pull/4334.patch?full_index=1 ==> Applied patch https://github.com/zeromq/libzmq/commit/92b2c38a2c51a1942a380c7ee08147f7b1ca6845.patch?full_index=1 ==> Applied patch https://github.com/zeromq/libzmq/pull/4334.patch?full_index=1 ==> libzmq: Executing phase: 'autoreconf' ==> libzmq: Executing phase: 'configure' ==> libzmq: Executing phase: 'build' ==> libzmq: Executing phase: 'install' ==> libzmq: Successfully installed libzmq-4.3.4-t7ad54q3atrnte4rzq7g7cfjcw5227pr Fetch: 0.61s. Build: 1m 31.57s. Total: 1m 32.18s. [+] /opt/software/linux-ubuntu22.04-skylake/gcc-12.1.0/libzmq-4.3.4-t7ad54q3atrnte4rzq7g7cfjcw5227pr ==> Installing libzmq-4.3.3-pxrd6piprucu65bkro2ixms6d3x2eudz ==> No binary for libzmq-4.3.3-pxrd6piprucu65bkro2ixms6d3x2eudz found: installing from source ==> Fetching https://mirror.spack.io/_source-cache/archive/9d/9d9285db37ae942ed0780c016da87060497877af45094ff9e1a1ca736e3875a2.tar.gz ==> Using cached archive: /home/wdconinc/.spack/cache/_source-cache/archive/31/310b8aa57a8ea77b7ac74debb3bf928cbafdef5e7ca35beaac5d9c61c7edd239 ==> Applied patch https://github.com/zeromq/libzmq/commit/92b2c38a2c51a1942a380c7ee08147f7b1ca6845.patch?full_index=1 ==> libzmq: Executing phase: 'autoreconf' ==> libzmq: Executing phase: 'configure' ==> libzmq: Executing phase: 'build' ==> libzmq: Executing phase: 'install' ==> libzmq: Successfully installed libzmq-4.3.3-pxrd6piprucu65bkro2ixms6d3x2eudz Fetch: 0.93s. Build: 11.55s. Total: 12.48s. [+] /opt/software/linux-ubuntu22.04-skylake/gcc-11.3.0/libzmq-4.3.3-pxrd6piprucu65bkro2ixms6d3x2eudz ==> Installing libzmq-4.3.4-hiil6dzy2reb4nk555zztwh44rpbyv4h ==> No binary for libzmq-4.3.4-hiil6dzy2reb4nk555zztwh44rpbyv4h found: installing from source ==> Using cached archive: /home/wdconinc/.spack/cache/_source-cache/archive/c5/c593001a89f5a85dd2ddf564805deb860e02471171b3f204944857336295c3e5.tar.gz ==> Using cached archive: /home/wdconinc/.spack/cache/_source-cache/archive/31/310b8aa57a8ea77b7ac74debb3bf928cbafdef5e7ca35beaac5d9c61c7edd239 ==> Applied patch https://github.com/zeromq/libzmq/commit/92b2c38a2c51a1942a380c7ee08147f7b1ca6845.patch?full_index=1 ==> libzmq: Executing phase: 'autoreconf' ==> libzmq: Executing phase: 'configure' ==> libzmq: Executing phase: 'build' ==> libzmq: Executing phase: 'install' ==> libzmq: Successfully installed libzmq-4.3.4-hiil6dzy2reb4nk555zztwh44rpbyv4h Fetch: 0.01s. Build: 10.77s. Total: 10.78s. [+] /opt/software/linux-ubuntu22.04-skylake/gcc-11.3.0/libzmq-4.3.4-hiil6dzy2reb4nk555zztwh44rpbyv4h ```
2022-08-25py-pytorch-lightning: add v1.7.3 (#32383)Adam J. Stewart1-0/+1
2022-08-25phylip: adding workarounds for gcc10+ (#32376)snehring1-0/+16
* phylip: adding workarounds for gcc10+ * phylip: switch to spec.satisfies
2022-08-25zig: add v0.9.1 (#32380)Massimiliano Culpo1-1/+13
2022-08-25charliecloud: add versions 0.28 and 0.29 (#32378)Richard Berger1-1/+3
generated by cgit v1.2.3-70-g09d2 (git 2.46.0) at 2024-11-20 06:21:49 +0000