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2019-01-07gnu: Add r-densityclust.Ricardo Wurmus
* gnu/packages/cran.scm (r-densityclust): New variable.
2019-01-07gnu: Add r-sparsesvd.Ricardo Wurmus
* gnu/packages/cran.scm (r-sparsesvd): New variable.
2019-01-07gnu: Add r-docopt.Ricardo Wurmus
* gnu/packages/cran.scm (r-docopt): New variable.
2019-01-07gnu: Add r-rvcheck.Ricardo Wurmus
* gnu/packages/cran.scm (r-rvcheck): New variable.
2019-01-07gnu: Add r-tidytree.Ricardo Wurmus
* gnu/packages/cran.scm (r-tidytree): New variable.
2019-01-07gnu: Add r-colorramps.Ricardo Wurmus
* gnu/packages/cran.scm (r-colorramps): New variable.
2019-01-07gnu: Add r-wordcloud.Ricardo Wurmus
* gnu/packages/cran.scm (r-wordcloud): New variable.
2019-01-07gnu: Add r-waveslim.Ricardo Wurmus
* gnu/packages/cran.scm (r-waveslim): New variable.
2019-01-07gnu: Add r-tiff.Ricardo Wurmus
* gnu/packages/cran.scm (r-tiff): New variable.
2019-01-07gnu: Add r-fftwtools.Ricardo Wurmus
* gnu/packages/cran.scm (r-fftwtools): New variable.
2019-01-07gnu: Add r-softimpute.Ricardo Wurmus
* gnu/packages/cran.scm (r-softimpute): New variable.
2019-01-07gnu: Add r-adgoftest.Ricardo Wurmus
* gnu/packages/cran.scm (r-adgoftest): New variable.
2019-01-07gnu: Add r-gsl.Ricardo Wurmus
* gnu/packages/cran.scm (r-gsl): New variable.
2019-01-07gnu: Add r-stabledist.Ricardo Wurmus
* gnu/packages/cran.scm (r-stabledist): New variable.
2019-01-07gnu: perl-lingua-translit: Update to 0.28.Efraim Flashner
* gnu/packages/perl.scm (perl-lingua-translit): Update to 0.28.
2019-01-07gnu: Add containerd.Danny Milosavljevic
* gnu/packages/docker.scm (containerd): New variable.
2019-01-07gnu: Add dummy linker for arm-elf.Danny Milosavljevic
* gnu/packages/bootstrap.scm (glibc-dynamic-linker): Add case for arm-elf.
2019-01-07gnu: Move R packages from geo.scm to cran.scm.Ricardo Wurmus
* gnu/packages/geo.scm (r-maps, r-mapproj, r-rgooglemaps, r-geosphere, r-ggmap): Move from here... * gnu/packages/cran.scm: ...to here.
2019-01-07gnu: emacs-ess: Move to (gnu packages statistics).Ricardo Wurmus
* gnu/packages/emacs.scm (emacs-ess): Move from here... * gnu/packages/statistics.scm (emacs-ess): ...to here.
2019-01-07gnu: python-rpy2: Move to (gnu packages statistics).Ricardo Wurmus
* gnu/packages/python.scm (python-rpy2): Move from here... * gnu/packages/statistics.scm (python-rpy2): ...to here.
2019-01-07gnu: Remove reference to (gnu packages statistics).Ricardo Wurmus
* gnu/packages/web.scm: Remove obsolete use-module clause.
2019-01-07gnu: r-rmysql: Move from databases.scm to cran.scmRicardo Wurmus
* gnu/packages/databases.scm (r-rmysql): Move from here... * gnu/packages/cran.scm (r-rmysql): ...to here.
2019-01-07gnu: biber: Update to 2.12.Jelle Licht
* gnu/packages/tex.scm (biber): Update to 2.12. [source]: Use 'git-fetch'. Add patch. [inputs]: Add perl-file-slurper. Remove perl-file-slurp. * gnu/packages/patches/biber-fix-encoding-write.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it.
2019-01-07gnu: r-feather: Move from serialization.scm to cran.scm.Ricardo Wurmus
* gnu/packages/serialization.scm (r-feather): Move from here... * gnu/packages/cran.scm (r-feather): ...to here.
2019-01-07gnu: Fix top-level circular references between emacs.scm and llvm.scm.Ludovic Courtès
Previously, loading either of these two modules could fail somewhat non-deterministically because each top-level was referencing a variable defined by the other module's top-level. * gnu/packages/emacs.scm (package-elisp-from-package): Move to... * gnu/packages/llvm.scm (package-elisp-from-package): Here. Keep private.
2019-01-07gnu: perl-file-slurper: Update to 0.012.Jelle Licht
* gnu/packages/perl.scm (perl-file-slurper): Update to 0.012. [native-inputs]: Add perl-test-warnings.
2019-01-07gnu: Move R packages from web.scm to cran.scm.Ricardo Wurmus
* gnu/packages/web.scm (r-httpuv, r-jsonlite, r-servr, r-htmltools, r-htmlwidgets, r-htmltable, r-curl, r-hwriter, r-rjson, r-shiny, r-shinydashboard, r-shinyfiles, r-crosstalk, r-rook, r-miniui): Move these from here... * gnu/packages/cran.scm: ...to here.
2019-01-07Revert "gnu: Use package-elisp-from-package for clangs emacs lisp files"Pierre Neidhardt
This reverts commit 5bc2e14add6433adbade3ccdf28c60e57334c20a.
2019-01-07gnu: mantis: Limit to x86_64-linux.Efraim Flashner
* gnu/packages/bioinformatics.scm (mantis)[supported-systems]: New field.
2019-01-07gnu: package-elisp-from-package: Clarify docstring.Pierre Neidhardt
* gnu/packages/emacs.scm (package-elisp-from-package)[docstring]: Clarify.
2019-01-07gnu: Use package-elisp-from-package for clangs emacs lisp filesTim Gesthuizen
Use package-elisp-from-package for emacs-clang-format and emacs-clang-rename. Also remove package-from-clang-elisp-file as it is not needed anymore. * gnu/packages/llvm.scm (emacs-clang-format): Use package-elisp-from-package * gnu/packages/llvm.scm (emacs-clang-rename): Use package-elisp-from-package * gnu/packages/llvm.scm (package-from-clang-elisp-file): Remove function
2019-01-07gnu: Add package-elisp-from-packageTim Gesthuizen
Add a function to generate package definitions that packages single elisp files from other packages. * gnu/packages/emacs.scm (package-elisp-from-package): New function
2019-01-07gnu: python2-fastlmm: Move to machine-learning.scm.Ludovic Courtès
This is a step towards removing OCaml modules from the closure of (gnu packages python). * gnu/packages/python.scm (python2-fastlmm): Move to... * gnu/packages/machine-learning.scm (python2-fastlmm): ... here.
2019-01-07gnu: Remove unnecessary build-side module imports.Ludovic Courtès
* gnu/packages/batik.scm, gnu/packages/boost.scm, gnu/packages/calendar.scm, gnu/packages/gl.scm, gnu/packages/lua.scm, gnu/packages/qt.scm, gnu/packages/simulation.scm, gnu/packages/terminals.scm: Remove unnecessary import of (guix build utils). * gnu/packages/emacs.scm: Remove unnecessary imports of (guix ...). * gnu/packages/libcanberra.scm: Use (srfi srfi-1) instead of (guix build utils) for 'alist-delete'. * gnu/packages/wxwidgets.scm: Likewise.
2019-01-07gnu: Move Emacs modes for Dedukti to ocaml.scm.Ludovic Courtès
This removes OCaml-related modules from the closure of (gnu packages emacs). * gnu/packages/emacs.scm (emacs-dedukti-mode, emacs-flycheck-dedukti): Move to ... * gnu/packages/ocaml.scm: ... here.
2019-01-07gnu: Move OCaml packages away from maths.scm.Ludovic Courtès
This removes (gnu packages ocaml) and related build system modules from the closure of (gnu packages maths). * gnu/packages/maths.scm (ocaml-gsl, ocaml4.01-gsl, cubicle): Move to... * gnu/packages/ocaml.scm: ... here.
2019-01-07gnu: Add rmlint.Pierre Neidhardt
* gnu/packages/disk.scm (rmlint): New variable.
2019-01-07gnu: Add prosody-http-upload.Clément Lassieur
* gnu/packages/messaging.scm (prosody-http-upload): New variable.
2019-01-07gnu: Add mantis.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (mantis): New variable.
2019-01-07gnu: Add sdsl-lite.Ricardo Wurmus
* gnu/packages/datastructures.scm (sdsl-lite): New variable.
2019-01-07gnu: autoconf-archive: Update to 2019.01.06.Efraim Flashner
* gnu/packages/autotools.scm (autoconf-archive): Update to 2019.01.06.
2019-01-07gnu: Add jose.Manolis Ragkousis
* gnu/packages/jose.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
2019-01-07gnu: Add slurp.Rutger Helling
* gnu/packages/image.scm (slurp): New variable.
2019-01-07gnu: libarchive: Replace with libarchive 3.3.3 and fix ↵Alex Vong
CVE-2018-{1000877,1000878,1000880}. * gnu/packages/backup.scm (libarchive)[source, home-page]: Use HTTPS. [replacement]: New field. (libarchive-3.3.3): New variable. * gnu/packages/patches/libarchive-CVE-2018-1000877.patch, gnu/packages/patches/libarchive-CVE-2018-1000878.patch, gnu/packages/patches/libarchive-CVE-2018-1000880.patch: New files. * gnu/local.mk (dist_patch_DATA): Add them.
2019-01-06gnu: Add kitty.Gabriel Hondet
* gnu/packages/terminals.scm (kitty): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2019-01-06hydra: Compute jobs in an inferior.Ludovic Courtès
Previously we would rely on auto-compilation of all the Guix modules. The complete evaluation would take ~15mn on berlin.guixsd.org and require lots of RAM. This approach should be faster since potentially only part of the modules are rebuilt. Furthermore, as a side-effect, it builds the derivations that 'guix pull' uses. * build-aux/hydra/gnu-system.scm: Remove 'eval-when' form. (hydra-jobs): New procedure. * gnu/ci.scm (package->alist, qemu-jobs, system-test-jobs) (tarball-jobs): Return strings for the 'license' field. * guix/self.scm (compiled-guix)[*cli-modules*]: Add (gnu ci).
2019-01-06hydra: Move job definitions to (gnu ci).Ludovic Courtès
* build-aux/hydra/gnu-system.scm: Move code to... * gnu/ci.scm: ... here. New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
2019-01-06gnu: gama: Update to 2.02.Efraim Flashner
* gnu/packages/gps.scm (gama): Update to 2.02.
2019-01-06gnu: moe: Update to 1.10.Efraim Flashner
* gnu/packages/moe.scm (moe): Update to 1.10. [license]: Fix license, gpl2+.
2019-01-06gnu: recutils: Update to 1.8.Efraim Flashner
* gnu/packages/databases.scm (recutils): Update to 1.8. [source]: Remove snippet. [arguments]: Remove custom 'set-bash4.4-header-location phase. Enable parallel tests. [inputs]: Move check ... [native-inputs]: ... to here. Add pkg-config.
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