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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>
2022-08-31py-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
2022-08-30New 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
2022-08-26[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
2022-08-26SDK: 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>
2022-08-26calculate 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
2022-08-25libzmq: 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
2022-08-25New package: py-mkdocs (#32363)Ryan Marcellino1-0/+30
2022-08-25fixed cp2k libcp2k.pc (#32349)AMD Toolchain Support1-10/+11
Co-authored-by: Prasanthi <pdonthir@amd.com>
2022-08-25new packages: r-cmdstanr and cmdstan (#32364)Glenn Johnson2-0/+117
2022-08-25new package: r-glmgampoi (#32366)Glenn Johnson1-0/+29
* new package: r-glmgampoi * Remove duplicate depends_on directive
2022-08-25new packages: r-scdblfinder and dependencies (#32367)Glenn Johnson4-0/+134
- r-bluster - r-metapod - r-scran
2022-08-25[ycsb] fixes build process and installation of YCSB (#32213)Matthieu Dorier1-15/+39
* [ycsb] fixes build process and installation of YCSB * [ycsb] fixing style * [ycsb] removed extra newline
generated by cgit v1.2.3-70-g09d2 (git 2.46.0) at 2024-11-20 04:28:35 +0000