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2019-11-15Revert "gnu: openmpi: Pass explicit "--with-*" configure flags."Ludovic Courtès
This reverts commit eaa52b5baa8fbb26a79890561d0c40344d1e1bf3, which would lead to build failures on systems other than x86_64-linux.
2019-11-15gnu: openmpi: Fix typo.Ludovic Courtès
* gnu/packages/mpi.scm (openmpi)[inputs]: For UCX, check the supported systems of UCX, not PSM2.
2019-11-15gnu: tomb: Use system's sudo.Eric Bavier
* gnu/packages/crypto.scm (tomb)[arguments]: Disallow references to the "sudo" input. Remove it's path from the wrapper.
2019-11-15gnu: tomb: Add lsof input for "ps" and "slam".Eric Bavier
* gnu/packages/crypto.scm (tomb)[inputs]: Add lsof. [arguments]: Add it to the wrapper PATH.
2019-11-15gnu: tomb: Update to 2.7.Eric Bavier
* gnu/packages/patches/tomb-fix-errors-on-open.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/crypto.scm (tomb): Update to 2.7. [source]: Use the patch.
2019-11-15gnu: CMake: Add version 3.15.5.Ivan Vilata-i-Balaguer
Add CMake version 3.15.5 but do not replace the existing version to avoid triggering the rebuild of all CMake-based packages. See <https://issues.guix.gnu.org/issue/38060>. * gnu/packages/cmake.scm (cmake-3.15.5): Add CMake 3.15.5. Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2019-11-15gnu: ungoogled-chromium: Update to 78.0.3904.97-0.acaf163.Marius Bakke
* gnu/packages/chromium.scm (%preserved-third-party-files): Adjust for Chromium 78. (%chromium-version): Set to 78.0.3904.97. (%ungoogled-revision): Set to acaf16383f264d8a2f24142ad054c9b4355771d3. (%debian-revision): Set to e43d74632091324774a5049668782dba7b09cf72. (%chromium-origin, %ungoogled-origin, %debian-origin): Update hashes. (gentoo-patches, %auxiliary-patches): Remove variables. (ungoogled-chromium-source): Adjust Debian patches for 78. Don't apply %AUXILIARY-PATCHES. (libvpx/chromium): New variable. (ungoogled-chromium)[arguments]: Add substitution for ICU headers. Adjust other substitutions for 78. Remove obsolete workaround. Increase ulimit in 'build' phase. Don't install '22x22' icon, which no longer exists. [inputs]: Change from LIBVPX to LIBVPX/CHROMIUM. [properties]: Remove HIDDEN?. (ungoogled-chromium-wayland)[inputs]: Don't remove inherited inputs. (ungoogled-chromium-is-deprecated, ungoogled-chromium-wayland-is-deprecated): Remove variables.
2019-11-15gnu: gn: Enable tests.Marius Bakke
* gnu/packages/build-tools.scm (gn)[arguments]: Remove #:tests?. Override 'check' phase.
2019-11-15gnu: gn: Update to 0.0-1666.6e5ba2e.Marius Bakke
* gnu/packages/build-tools.scm (gn): Update to 0.0-1666.6e5ba2e. [arguments]: Do not override LDFLAGS.
2019-11-15gnu: openmpi: Raise the priority of the PSM2 component.Ludovic Courtès
This allows us to get better performance by default on machines with OmniPath hardware. * gnu/packages/patches/openmpi-psm2-priority.patch: New file. * gnu/packages/mpi.scm (openmpi)[source]: Use it. * gnu/local.mk (dist_patch_DATA): Add it.
2019-11-15gnu: psm: Add "debug" output.Ludovic Courtès
* gnu/packages/linux.scm (psm)[outputs]: New field.
2019-11-15gnu: openmpi, slurm: Switch to hwloc 2.x.Ludovic Courtès
* gnu/packages/mpi.scm (openmpi)[inputs]: Switch to HWLOC-2. * gnu/packages/parallel.scm (slurm)[inputs]: Likewise.
2019-11-15gnu: hwloc: Update to 2.1.0.Ludovic Courtès
* gnu/packages/mpi.scm (hwloc-2.0): Rename to... (hwloc-2): ... this. Update to 2.1.0 (hwloc-2.0): Define as deprecated. * gnu/packages/opencl.scm (pocl)[inputs]: Adjust accordingly.
2019-11-15gnu: slurm: Build shared libraries only.Ludovic Courtès
* gnu/packages/parallel.scm (slurm)[arguments]: Pass "--disable-static".
2019-11-15gnu: slurm: Update to 19.05.3-2.Ludovic Courtès
* gnu/packages/parallel.scm (slurm): Update to 19.05.3-2. [source](snippet): Keep "contribs/mpi" and its reference in 'Makefile.am'. [inputs]: Remove OPENSSL. [arguments]: Remove "--with-ssl". Add 'install-libpmi' phase.
2019-11-15gnu: Add Intel MPI Benchmarks.Ludovic Courtès
* gnu/packages/mpi.scm (intel-mpi-benchmarks): New variable.
2019-11-15gnu: rdma-core: Update to 26.0.Ludovic Courtès
* gnu/packages/linux.scm (rdma-core): Update to 26.0. [arguments]: Add "-DRST2MAN_EXECUTABLE=..." to #:configure-flags. [native-inputs]: Add PYTHON-DOCUTILS.
2019-11-15gnu: rdma-core: Use the "write" ioctl mode.Ludovic Courtès
* gnu/packages/linux.scm (rdma-core)[arguments]: Add "-DIOCTL_MODE=write" to #:configure-flags.
2019-11-15gnu: openmpi: Pass explicit "--with-*" configure flags.Ludovic Courtès
* gnu/packages/mpi.scm (openmpi)[arguments]: Pass "--with-ucx", "--with-psm", and "--with-psm2".
2019-11-15gnu: ucx: Do not install static libraries.Ludovic Courtès
* gnu/packages/fabric-management.scm (ucx)[arguments]: Pass "--disable-static".
2019-11-15gnu: ucx: Enable InfiniBand support through Verbs.Ludovic Courtès
Until now, InfiniBand support was missing, as reported by "ucx_info -d" on a machine with InfiniBand networking. * gnu/packages/fabric-management.scm (ucx)[arguments]: Build with "--with-verbs".
2019-11-15gnu: git-annex: Update to 7.20191114.Kyle Meyer
* gnu/packages/haskell-apps.scm (git-annex): Update to 7.20191114. Signed-off-by: Mathieu Othacehe <m.othacehe@gmail.com>
2019-11-15gnu: rtmidi: Update to 4.0.0.Pierre Langlois
* gnu/packages/audio.scm (rtmidi): Update to 4.0.0. [source]: Download tarball from upstream URL rather than the powertab github fork. [arguments]: Enable tests. Remove 'build and 'install phases and add a new 'noconfigure phase to prevent the bootstrap script from invoking configure. [home-page]: Update homepage to upstream URL. * gnu/packages/music.scm (powertabeditor)[arguments]: Add phase that substitutes the rtmidi #include directive to find the header. Signed-off-by: Mathieu Othacehe <m.othacehe@gmail.com>
2019-11-15gnu: freecad: Update to 0.18.4.John Soo
* gnu/packages/engineering.scm (freecad): Update to 0.18.4. Signed-off-by: Mathieu Othacehe <m.othacehe@gmail.com>
2019-11-15gnu: emacs-flycheck-cpplint: Set cpplint path.Mathieu Othacehe
* gnu/packages/emacs-xyz.scm (emacs-flycheck-cpplint)[inputs]: Add cpplint. [arguments]: Add a set-cpplint-path phase to set the path of cpplint.
2019-11-15gnu: Add cpplint.Mathieu Othacehe
* gnu/packages/cpp.scm (cpplint): New variable.
2019-11-14gnu: fluidsynth: Update to 2.0.9.Tobias Geerinckx-Rice
* gnu/packages/audio.scm (fluidsynth): Update to 2.0.9.
2019-11-14gnu: perl-type-tiny: Update to 1.006000.Tobias Geerinckx-Rice
* gnu/packages/perl.scm (perl-type-tiny): Update to 1.006000.
2019-11-14gnu: msitools: Update to 0.100.Tobias Geerinckx-Rice
* gnu/packages/package-management.scm (msitools): Update to 0.100.
2019-11-14gnu: perl-mail-dkim: Update to 0.58.Tobias Geerinckx-Rice
* gnu/packages/mail.scm (perl-mail-dkim): Update to 0.58.
2019-11-14gnu: Add m2-planet.Jan Nieuwenhuizen
* gnu/packages/mes.scm (m2-planet): New variable.
2019-11-14gnu: Add emacs-helm-fish-completion.Pierre Neidhardt
* gnu/packages/emacs-xyz.scm (emacs-helm-fish-completion): New variable.
2019-11-14gnu: r-gprofiler: Update to 0.7.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.7.0.
2019-11-14gnu: r-hexbin: Update to 1.28.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-hexbin): Update to 1.28.0.
2019-11-14gnu: r-r-oo: Update to 1.23.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-r-oo): Update to 1.23.0.
2019-11-14gnu: r-glmnet: Update to 3.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-glmnet): Update to 3.0. [inputs]: Move gfortran from here... [native-inputs]: ...to here. [propagated-inputs]: Add r-shape.
2019-11-14gnu: r-dt: Update to 0.10.Ricardo Wurmus
* gnu/packages/statistics.scm (r-dt): Update to 0.10.
2019-11-14gnu: r-rmarkdown: Update to 1.17.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rmarkdown): Update to 1.17.
2019-11-14gnu: r-hms: Update to 0.5.2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-hms): Update to 0.5.2.
2019-11-14gnu: r-roxygen2: Update to 7.0.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-roxygen2): Update to 7.0.0. [propagated-inputs]: Add r-rlang.
2019-11-14gnu: r-r6: Update to 2.4.1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-r6): Update to 2.4.1.
2019-11-14gnu: r-testthat: Update to 2.3.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-testthat): Update to 2.3.0. [propagated-inputs]: Add r-ellipsis and r-pkgload.
2019-11-14gnu: r-knitr: Update to 1.26.Ricardo Wurmus
* gnu/packages/statistics.scm (r-knitr): Update to 1.26.
2019-11-14gnu: r-survival: Update to 3.1-7.Ricardo Wurmus
* gnu/packages/statistics.scm (r-survival): Update to 3.1-7.
2019-11-14gnu: r-farver: Update to 2.0.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-farver): Update to 2.0.1. [propagated-inputs]: Remove r-rcpp.
2019-11-14gnu: r-ggeffects: Update to 0.13.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-ggeffects): Update to 0.13.0. [propagated-inputs]: Remove r-scales.
2019-11-14gnu: r-learnr: Update to 0.10.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-learnr): Update to 0.10.0. [propagated-inputs]: Add r-checkmate, r-ellipsis, and r-renv.
2019-11-14gnu: r-ggfortify: Update to 0.4.8.Ricardo Wurmus
* gnu/packages/cran.scm (r-ggfortify): Update to 0.4.8.
2019-11-14gnu: r-kernlab: Update to 0.9-29.Ricardo Wurmus
* gnu/packages/cran.scm (r-kernlab): Update to 0.9-29.
2019-11-14gnu: r-bookdown: Update to 0.15.Ricardo Wurmus
* gnu/packages/cran.scm (r-bookdown): Update to 0.15.
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