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Author SHA1 Message Date
Eric Bavier 417df5bb57
gnu: tomb: Add lsof input for "ps" and "slam". 
* gnu/packages/crypto.scm (tomb)[inputs]: Add lsof.
[arguments]: Add it to the wrapper PATH.
 2019-11-15 14:59:16 -06:00
Eric Bavier 4535eb91c3
gnu: tomb: Update to 2.7. 
* 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.
 2019-11-15 14:59:07 -06:00
Ivan Vilata-i-Balaguer 528b52390d
gnu: CMake: Add version 3.15.5. 
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>
 2019-11-15 19:09:13 +01:00
Marius Bakke ba261f6318
gnu: ungoogled-chromium: Update to 78.0.3904.97-0.acaf163. 
* 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.
 2019-11-15 19:09:13 +01:00
Marius Bakke 97b672d99f
gnu: gn: Enable tests. 
* gnu/packages/build-tools.scm (gn)[arguments]: Remove #:tests?.  Override
'check' phase.
 2019-11-15 19:09:13 +01:00
Marius Bakke d922724521
gnu: gn: Update to 0.0-1666.6e5ba2e. 
* gnu/packages/build-tools.scm (gn): Update to 0.0-1666.6e5ba2e.
[arguments]: Do not override LDFLAGS.
 2019-11-15 19:09:13 +01:00
Ludovic Courtès faab7082ab
gnu: openmpi: Raise the priority of the PSM2 component. 
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.
 2019-11-15 17:52:45 +01:00
Ludovic Courtès 348caf3d2c
gnu: psm: Add "debug" output. 
* gnu/packages/linux.scm (psm)[outputs]: New field.
 2019-11-15 17:52:45 +01:00
Ludovic Courtès 58a536bb1b
gnu: openmpi, slurm: Switch to hwloc 2.x. 
* gnu/packages/mpi.scm (openmpi)[inputs]: Switch to HWLOC-2.
* gnu/packages/parallel.scm (slurm)[inputs]: Likewise.
 2019-11-15 17:52:45 +01:00
Ludovic Courtès 8c8e108978
gnu: hwloc: Update to 2.1.0. 
* 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.
 2019-11-15 17:52:45 +01:00
Ludovic Courtès 52cd164aad
gnu: slurm: Build shared libraries only. 
* gnu/packages/parallel.scm (slurm)[arguments]: Pass "--disable-static".
 2019-11-15 17:52:45 +01:00
Ludovic Courtès 7c96befa52
gnu: slurm: Update to 19.05.3-2. 
* 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.
 2019-11-15 17:52:44 +01:00
Ludovic Courtès c1ea4c0793
gnu: Add Intel MPI Benchmarks. 
* gnu/packages/mpi.scm (intel-mpi-benchmarks): New variable.
 2019-11-15 17:52:44 +01:00
Ludovic Courtès e68f954eb3
gnu: rdma-core: Update to 26.0. 
* gnu/packages/linux.scm (rdma-core): Update to 26.0.
[arguments]: Add "-DRST2MAN_EXECUTABLE=..." to #:configure-flags.
[native-inputs]: Add PYTHON-DOCUTILS.
 2019-11-15 17:52:44 +01:00
Ludovic Courtès 2b14c60d38
gnu: rdma-core: Use the "write" ioctl mode. 
* gnu/packages/linux.scm (rdma-core)[arguments]: Add "-DIOCTL_MODE=write"
to #:configure-flags.
 2019-11-15 17:52:44 +01:00
Ludovic Courtès eaa52b5baa
gnu: openmpi: Pass explicit "--with-*" configure flags. 
* gnu/packages/mpi.scm (openmpi)[arguments]: Pass "--with-ucx",
"--with-psm", and "--with-psm2".
 2019-11-15 17:52:44 +01:00
Ludovic Courtès 3b09bb191c
gnu: ucx: Do not install static libraries. 
* gnu/packages/fabric-management.scm (ucx)[arguments]: Pass
"--disable-static".
 2019-11-15 17:52:44 +01:00
Ludovic Courtès b35f621e45
gnu: ucx: Enable InfiniBand support through Verbs. 
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".
 2019-11-15 17:52:44 +01:00
Kyle Meyer f3560c626d
gnu: git-annex: Update to 7.20191114. 
* gnu/packages/haskell-apps.scm (git-annex): Update to 7.20191114.

Signed-off-by: Mathieu Othacehe <m.othacehe@gmail.com>
 2019-11-15 14:48:32 +01:00
Pierre Langlois bcdf11d6ff
gnu: rtmidi: Update to 4.0.0. 
* 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>
 2019-11-15 14:29:57 +01:00
John Soo ae5525c591
gnu: freecad: Update to 0.18.4. 
* gnu/packages/engineering.scm (freecad): Update to 0.18.4.

Signed-off-by: Mathieu Othacehe <m.othacehe@gmail.com>
 2019-11-15 13:50:03 +01:00
Efraim Flashner cda79c7cc9
make-bootstrap: Adjust copied linux headers. 
* guix/build/make-bootstrap.scm (copy-linux-headers): Remove header
file 'a.out.h' is no longer part of the linux kernel headers.
 2019-11-15 13:00:23 +02:00
Mathieu Othacehe b02a9523b3
gnu: emacs-flycheck-cpplint: Set cpplint path. 
* gnu/packages/emacs-xyz.scm (emacs-flycheck-cpplint)[inputs]: Add cpplint.
[arguments]: Add a set-cpplint-path phase to set the path of cpplint.
 2019-11-15 11:04:23 +01:00
Mathieu Othacehe 7e08be71ac
gnu: Add cpplint. 
* gnu/packages/cpp.scm (cpplint): New variable.
 2019-11-15 10:50:19 +01:00
Tobias Geerinckx-Rice 37d473c5d1
gnu: fluidsynth: Update to 2.0.9. 
* gnu/packages/audio.scm (fluidsynth): Update to 2.0.9.
 2019-11-14 18:01:41 +01:00
Tobias Geerinckx-Rice daa03aca15
gnu: perl-type-tiny: Update to 1.006000. 
* gnu/packages/perl.scm (perl-type-tiny): Update to 1.006000.
 2019-11-14 18:01:40 +01:00
Tobias Geerinckx-Rice 84748e719d
gnu: msitools: Update to 0.100. 
* gnu/packages/package-management.scm (msitools): Update to 0.100.
 2019-11-14 18:01:40 +01:00
Tobias Geerinckx-Rice 3b27ffec0f
gnu: perl-mail-dkim: Update to 0.58. 
* gnu/packages/mail.scm (perl-mail-dkim): Update to 0.58.
 2019-11-14 18:01:40 +01:00
Jan Nieuwenhuizen 99b340f5ee
gnu: Add m2-planet. 
* gnu/packages/mes.scm (m2-planet): New variable.
 2019-11-14 16:41:55 +01:00
Pierre Neidhardt 5a17042e70
gnu: Add emacs-helm-fish-completion. 
* gnu/packages/emacs-xyz.scm (emacs-helm-fish-completion): New variable.
 2019-11-14 15:39:56 +01:00
Ricardo Wurmus 4dcf32b56b
gnu: r-gprofiler: Update to 0.7.0. 
* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.7.0.
 2019-11-14 10:14:10 +01:00
Ricardo Wurmus f40fedd8fd
gnu: r-hexbin: Update to 1.28.0. 
* gnu/packages/statistics.scm (r-hexbin): Update to 1.28.0.
 2019-11-14 10:14:10 +01:00
Ricardo Wurmus d458b2a9e5
gnu: r-r-oo: Update to 1.23.0. 
* gnu/packages/statistics.scm (r-r-oo): Update to 1.23.0.
 2019-11-14 10:14:09 +01:00
Ricardo Wurmus f046f43bb8
gnu: r-glmnet: Update to 3.0. 
* gnu/packages/statistics.scm (r-glmnet): Update to 3.0.
[inputs]: Move gfortran from here...
[native-inputs]: ...to here.
[propagated-inputs]: Add r-shape.
 2019-11-14 10:14:09 +01:00
Ricardo Wurmus 3a3ece336b
gnu: r-dt: Update to 0.10. 
* gnu/packages/statistics.scm (r-dt): Update to 0.10.
 2019-11-14 10:14:09 +01:00
Ricardo Wurmus 85d44cf6de
gnu: r-rmarkdown: Update to 1.17. 
* gnu/packages/statistics.scm (r-rmarkdown): Update to 1.17.
 2019-11-14 10:14:08 +01:00
Ricardo Wurmus a713371db1
gnu: r-hms: Update to 0.5.2. 
* gnu/packages/statistics.scm (r-hms): Update to 0.5.2.
 2019-11-14 10:14:08 +01:00
Ricardo Wurmus 2295a17e64
gnu: r-roxygen2: Update to 7.0.0. 
* gnu/packages/statistics.scm (r-roxygen2): Update to 7.0.0.
[propagated-inputs]: Add r-rlang.
 2019-11-14 10:14:08 +01:00
Ricardo Wurmus 30301c0993
gnu: r-r6: Update to 2.4.1. 
* gnu/packages/statistics.scm (r-r6): Update to 2.4.1.
 2019-11-14 10:14:08 +01:00
Ricardo Wurmus 3d2c2a55fd
gnu: r-testthat: Update to 2.3.0. 
* gnu/packages/statistics.scm (r-testthat): Update to 2.3.0.
[propagated-inputs]: Add r-ellipsis and r-pkgload.
 2019-11-14 10:14:08 +01:00
Ricardo Wurmus bc697e716d
gnu: r-knitr: Update to 1.26. 
* gnu/packages/statistics.scm (r-knitr): Update to 1.26.
 2019-11-14 10:14:08 +01:00
Ricardo Wurmus 44ffff99d3
gnu: r-survival: Update to 3.1-7. 
* gnu/packages/statistics.scm (r-survival): Update to 3.1-7.
 2019-11-14 10:14:08 +01:00
Ricardo Wurmus f4061505dc
gnu: r-farver: Update to 2.0.1. 
* gnu/packages/cran.scm (r-farver): Update to 2.0.1.
[propagated-inputs]: Remove r-rcpp.
 2019-11-14 10:14:08 +01:00
Ricardo Wurmus f72874fe26
gnu: r-ggeffects: Update to 0.13.0. 
* gnu/packages/cran.scm (r-ggeffects): Update to 0.13.0.
[propagated-inputs]: Remove r-scales.
 2019-11-14 10:14:08 +01:00
Ricardo Wurmus 389f169a7e
gnu: r-learnr: Update to 0.10.0. 
* gnu/packages/cran.scm (r-learnr): Update to 0.10.0.
[propagated-inputs]: Add r-checkmate, r-ellipsis, and r-renv.
 2019-11-14 10:14:08 +01:00
Ricardo Wurmus a6412edf29
gnu: r-ggfortify: Update to 0.4.8. 
* gnu/packages/cran.scm (r-ggfortify): Update to 0.4.8.
 2019-11-14 10:14:08 +01:00
Ricardo Wurmus 17c5b6fcce
gnu: r-kernlab: Update to 0.9-29. 
* gnu/packages/cran.scm (r-kernlab): Update to 0.9-29.
 2019-11-14 10:14:07 +01:00
Ricardo Wurmus e6f1468c93
gnu: r-bookdown: Update to 0.15. 
* gnu/packages/cran.scm (r-bookdown): Update to 0.15.
 2019-11-14 10:14:07 +01:00
Ricardo Wurmus d4f4b30bbc
gnu: r-future: Update to 1.15.0. 
* gnu/packages/cran.scm (r-future): Update to 1.15.0.
 2019-11-14 10:14:07 +01:00
Ricardo Wurmus 610f2acc7c
gnu: r-rbamtools: Update to 2.16.17. 
* gnu/packages/cran.scm (r-rbamtools): Update to 2.16.17.
 2019-11-14 10:14:06 +01:00