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48392 Commits

Author SHA1 Message Date
Ludovic Courtès befac35876
gnu: libraft: Fetch source from Git. 
* gnu/packages/cluster.scm (libraft)[source]: Switch to GIT-FETCH.
 2019-09-08 14:43:41 +02:00
Andrew Miloradovsky 45151bcb94
gnu: Add libraft 
* gnu/packages/cluster.scm (libraft): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-09-08 14:43:41 +02:00
Ludovic Courtès 74781c65f3
gnu: guix: Update to cc98b00. 
* gnu/packages/package-management.scm (guix): Update to cc98b00.
(guix-daemon)[arguments]: Remove 'install' phase; add
'change-default-guix' phase.
 2019-09-08 14:43:41 +02:00
Efraim Flashner 28ac73358f
gnu: micropython: Update to 1.11. 
* gnu/packages/python.scm (micropython): Update to 1.11.
 2019-09-08 14:43:15 +03:00
Efraim Flashner 78249ebf5b
gnu: wget2: Update to 1.99.2. 
* gnu/packages/wget.scm (wget2): Update to 1.99.2.
[source]: Download from gnu mirrors.
[arguments]: Remove custom 'bootstrap phase, update custom
'skip-network-tests phase. Don't build static library.
[inputs]: Add bzip2, gpgme, zlib.
[native-inputs]: Remove autoconf, automake, flex, gettext-minimal,
libtool, python-2.
 2019-09-08 13:53:26 +03:00
Efraim Flashner 7fb742215c
gnu: wget.scm: Use license: prefix. 
* gnu/packages/wget.scm (wget, wgetpaste, wget2)[license]: Use
'license:' prefix.
 2019-09-08 13:53:26 +03:00
Ludovic Courtès cc98b00857
etc: Remove references to libexec/guix* from SELinux policy. 
* etc/guix-daemon.cil.in: Remove references to libexec/guix*.
 2019-09-08 11:49:25 +02:00
Ludovic Courtès 82f903e70f
daemon: Remove 'NIX_LIBEXEC_DIR'. 
* nix/libstore/globals.hh (Settings)[nixLibexecDir]: Remove.
* nix/libstore/globals.cc (Settings::processEnvironment): Remove
reference to 'nixLibexecDir'.
* nix/local.mk (libstore_a_CPPFLAGS): Remove -DNIX_LIBEXEC_DIR flag.
* build-aux/pre-inst-env.in: Remove references to 'NIX_LIBEXEC_DIR'.
 2019-09-08 11:49:24 +02:00
Ludovic Courtès f6919ebdc6
daemon: Run 'guix substitute' directly and assume a single substituter. 
The daemon had a mechanism that allows it to handle a list of
substituters and try them sequentially; this removes it.

* nix/scripts/substitute.in: Remove.
* nix/local.mk (nodist_pkglibexec_SCRIPTS): Remove.
* config-daemon.ac: Don't output 'nix/scripts/substitute'.
* nix/libstore/build.cc (SubstitutionGoal)[subs, sub, hasSubstitute]:
Remove.
[tryNext]: Make private.
(SubstitutionGoal::SubstitutionGoal, SubstitutionGoal::init): Remove now
unneeded initializers.
(SubstitutionGoal::tryNext): Adjust to assume a single substituter: call
'amDone' upfront when we couldn't find substitutes.
(SubstitutionGoal::tryToRun): Adjust to run 'guix substitute' via
'settings.guixProgram'.
(SubstitutionGoal::finished): Call 'amDone(ecFailed)' upon failure
instead of setting 'state' to 'tryNext'.
* nix/libstore/globals.hh (Settings)[substituters]: Remove.
* nix/libstore/local-store.cc (LocalStore::~LocalStore): Adjust to
handle a single substituter.
(LocalStore::startSubstituter): Remove 'path' parameter.  Adjust to
invoke 'settings.guixProgram'.  Don't refer to 'run.program', which no
longer exists.
(LocalStore::querySubstitutablePaths): Adjust for 'runningSubstituters'
being a singleton instead of a list.
(LocalStore::querySubstitutablePathInfos): Likewise, and remove
'substituter' parameter.
* nix/libstore/local-store.hh (RunningSubstituter)[program]: Remove.
(LocalStore)[runningSubstituters]: Remove.
[runningSubstituter]: New field.
[querySubstitutablePathInfos]: Remove 'substituter' parameter.
[startSubstituter]: Remove 'substituter' parameter.
* nix/nix-daemon/guix-daemon.cc (main): Remove references to
'settings.substituters'.
* nix/nix-daemon/nix-daemon.cc (performOp): Ignore the user's
"build-use-substitutes" value when 'settings.useSubstitutes' is false.
 2019-09-08 11:49:24 +02:00
Ludovic Courtès bc69ea2d60
daemon: Run 'guix offload' directly. 
* nix/scripts/offload.in: Remove.
* nix/local.mk (nodist_pkglibexec_SCRIPTS) [BUILD_DAEMON_OFFLOAD]:
Remove 'scripts/offload'.
* config-daemon.ac: Don't output 'nix/scripts/offload'.
* build-aux/pre-inst-env.in: Don't set 'NIX_BUILD_HOOK'.
* nix/libstore/build.cc (HookInstance::HookInstance): Run 'guix
offload'.
(DerivationGoal::tryBuildHook): Remove reference to 'NIX_BUILD_HOOK'.
* nix/nix-daemon/guix-daemon.cc (main) [HAVE_DAEMON_OFFLOAD_HOOK]: Don't
set 'NIX_BUILD_HOOK'.
* nix/nix-daemon/nix-daemon.cc (performOp) [!HAVE_DAEMON_OFFLOAD_HOOK]:
Leave 'settings.useBuildHook' unchanged.
 2019-09-08 11:49:24 +02:00
Ludovic Courtès 9fcc35c51f
daemon: Run 'guix perform-download' directly. 
* nix/scripts/download.in: Remove.
* nix/local.mk (nodist_pkglibexec_SCRIPTS): Remove 'scripts/download'.
* config-daemon.ac: Don't output 'nix/scripts/download'.
* nix/libstore/builtins.cc (builtinDownload): Invoke 'guix
perform-download' directly.
 2019-09-08 11:49:24 +02:00
Ludovic Courtès 0c684b7edf
daemon: Run 'guix authenticate' directly. 
* nix/scripts/authenticate.in: Remove.
* nix/local.mk (nodist_pkglibexec_SCRIPTS): Remove
scripts/authenticate.
* config-daemon.ac: Don't output 'nix/scripts/authenticate'.
* nix/libstore/local-store.cc (runAuthenticationProgram): Run 'guix
authenticate'.
 2019-09-08 11:49:24 +02:00
Ludovic Courtès 2e3e5d2198
daemon: Invoke 'guix gc --list-busy' instead of 'list-runtime-roots'. 
* nix/scripts/list-runtime-roots.in: Remove.
* guix/store/roots.scm (%proc-directory): New variable.
(proc-file-roots, proc-exe-roots, proc-cwd-roots)
(proc-fd-roots, proc-maps-roots, proc-environ-roots)
(referenced-files, canonicalize-store-item, busy-store-items): New
procedures, taken from 'list-runtime-roots.in'.
* nix/libstore/globals.hh (Settings)[guixProgram]: New field.
* nix/libstore/globals.cc (Settings::processEnvironment): Initialize
'guixProgram'.
* nix/libstore/gc.cc (addAdditionalRoots): Drop code related to
'NIX_ROOT_FINDER'.  Run "guix gc --list-busy".
* nix/local.mk (nodist_pkglibexec_SCRIPTS): Remove
'scripts/list-runtime-roots'.
* config-daemon.ac: Don't output nix/scripts/list-runtime-roots.
* build-aux/pre-inst-env.in: Don't set 'NIX_ROOT_FINDER'.
Set 'GUIX'.
* doc/guix.texi (Invoking guix gc): Document '--list-busy'.
* guix/scripts/gc.scm (show-help, %options): Add "--list-busy".
(guix-gc)[list-busy]: New procedure.
Handle the 'list-busy' action.
 2019-09-08 11:49:24 +02:00
raingloom 7fcc2f9355
gnu: Add fmit. 
* gnu/packages/music.scm (fmit): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2019-09-08 11:08:46 +02:00
Jan Nieuwenhuizen d7303a048d
bootstrap: mes-boot: Fix at 0.19. 
This allows updating Mes without triggering a rebuild.

* gnu/packages/commencement.scm (mes-boot): Fix 0.19.
 2019-09-08 10:49:15 +02:00
Efraim Flashner 799d8d3ca6
gnu: haskell-xyz.scm: Correctly hide packages. 
* gnu/packages/haskell-xyz.scm (ghc-attoparsec-bootstrap,
ghc-integer-logarithms-bootstrap, ghc-scientific-bootstrap,
ghc-semigroups-bootstrap, ghc-unordered-containers-bootstrap,
ghc-wcwidth-bootstrap)[properties]: Fix typo, make 'hidden?' a tuple.
 2019-09-08 11:18:39 +03:00
Ricardo Wurmus e0819e5ca2
gnu: Add emacs-tao-theme. 
* gnu/packages/emacs-xyz.scm (emacs-tao-theme): New variable.
 2019-09-08 09:27:26 +02:00
Vagrant Cascadian bc5aa38667
gnu: Add odt2txt. 
* gnu/packages/textutils (odt2txt): New variable.
* gnu/packages/package-management (diffoscope)[native-inputs]: Add odt2txt.
  [use-modules]: Remove accidentally added libreoffice package module.
 2019-09-08 00:21:21 -07:00
Vagrant Cascadian d54ca1cd4d
gnu: Add sng. 
* gnu/packages/images (sng): New variable.
* gnu/packages/package-management (diffoscope)[native-inputs]: Add sng.
 2019-09-07 23:44:04 -07:00
Vagrant Cascadian 68fea604b0
gnu: Add pngsuite. 
* gnu/packages/image (pngsuite): New variable.
 2019-09-07 23:44:01 -07:00
Vagrant Cascadian 37ecf2d905
gnu: diffoscope: Enable even more tests. 
* gnu/packages/package-management (diffoscope)[native-inputs]: Add additional
  dependencies for tests.
  [use-module]: Add corresponding package modules.
 2019-09-07 20:28:48 -07:00
Vagrant Cascadian 3dd20da0cb
gnu: diffoscope: Enable additional tests. 
* gnu/packages/package-management (diffoscope) [native-inputs]: Add additional
  packages used for tests.
 2019-09-07 20:28:35 -07:00
Vagrant Cascadian 3ec8c0ca94
gnu: diffoscope: Update to 123. 
* gnu/packages/package-management (diffoscope): Update to 123.
  [arguments]: Update phase writable-test-data to include tests directory.
    Add phase remove-ocaml-test.
 2019-09-07 20:28:18 -07:00
Vagrant Cascadian 9f74bd317f
gnu: python-debian: Update to 0.1.36. 
* gnu/packages/python-xyz (python-debian): Update to 0.1.36.
  [source]: Switch to using git-fetch.
  [arguments]: Add phase to delete tests depending on tools not yet present in
  guix.
  [propagated-inputs]: Add python-chardet.
 2019-09-07 20:27:34 -07:00
Ricardo Wurmus f791b1eecc
gnu: r-rsubread: Update to 1.34.7. 
* gnu/packages/bioconductor.scm (r-rsubread): Update to 1.34.7.
 2019-09-08 00:30:33 +02:00
Ricardo Wurmus a39222d7e2
gnu: r-regioner: Update to 1.16.3. 
* gnu/packages/bioconductor.scm (r-regioner): Update to 1.16.3.
 2019-09-08 00:30:33 +02:00
Ricardo Wurmus d40ebbf228
gnu: r-gprofiler: Update to 0.6.8. 
* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.8.
 2019-09-08 00:30:33 +02:00
Ricardo Wurmus 8e70b33c56
gnu: r-annotationhub: Update to 2.16.1. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.16.1.
 2019-09-08 00:30:33 +02:00
Ricardo Wurmus f70599cb78
gnu: r-edger: Update to 3.26.8. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.8.
 2019-09-08 00:30:33 +02:00
Ricardo Wurmus 801dc98f1f
gnu: r-ggraph: Update to 2.0.0. 
* gnu/packages/cran.scm (r-ggraph): Update to 2.0.0.
[propagated-inputs]: Add r-graphlayouts, r-rlang, and r-tidygraph; remove
r-plyr.
 2019-09-08 00:30:33 +02:00
Ricardo Wurmus 995a20e892
gnu: r-msigdbr: Update to 7.0.1. 
* gnu/packages/cran.scm (r-msigdbr): Update to 7.0.1.
 2019-09-08 00:30:33 +02:00
Ricardo Wurmus f396d343b7
gnu: r-ggeffects: Update to 0.12.0. 
* gnu/packages/cran.scm (r-ggeffects): Update to 0.12.0.
 2019-09-08 00:30:33 +02:00
Ricardo Wurmus 9a4706828c
gnu: r-ggformula: Update to 0.9.2. 
* gnu/packages/cran.scm (r-ggformula): Update to 0.9.2.
 2019-09-08 00:30:33 +02:00
Ricardo Wurmus c90eebf791
gnu: r-insight: Update to 0.5.0. 
* gnu/packages/cran.scm (r-insight): Update to 0.5.0.
 2019-09-08 00:30:33 +02:00
Ricardo Wurmus f11920c759
gnu: r-ggpubr: Update to 0.2.3. 
* gnu/packages/cran.scm (r-ggpubr): Update to 0.2.3.
 2019-09-08 00:30:32 +02:00
Ricardo Wurmus 9960ad55be
gnu: r-geometry: Update to 0.4.4. 
* gnu/packages/cran.scm (r-geometry): Update to 0.4.4.
 2019-09-08 00:30:32 +02:00
Ricardo Wurmus 02efab6917
gnu: r-feather: Update to 0.3.4. 
* gnu/packages/cran.scm (r-feather): Update to 0.3.4.
 2019-09-08 00:30:32 +02:00
Ricardo Wurmus 5e7c6e54c8
gnu: r-matrixstats: Update to 0.55.0. 
* gnu/packages/statistics.scm (r-matrixstats): Update to 0.55.0.
 2019-09-08 00:30:32 +02:00
Ricardo Wurmus de162a1509
gnu: r-rcpparmadillo: Update to 0.9.700.2.0. 
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.9.700.2.0.
 2019-09-08 00:30:32 +02:00
Ricardo Wurmus 2b705168e9
gnu: r-devtools: Update to 2.2.0. 
* gnu/packages/statistics.scm (r-devtools): Update to 2.2.0.
[propagated-inputs]: Add r-covr, r-crayon, r-desc, r-dt, r-ellipsis, r-glue,
and r-rversions.
 2019-09-08 00:30:32 +02:00
Ricardo Wurmus e5cf3722c6
gnu: r-gdtools: Update to 0.2.0. 
* gnu/packages/statistics.scm (r-gdtools): Update to 0.2.0.
[inputs]: Add freetype.
[propagated-inputs]: Add r-systemfonts; remove r-withr.
 2019-09-08 00:30:32 +02:00
Ricardo Wurmus 9567bd8dd9
gnu: Add r-tidygraph. 
* gnu/packages/cran.scm (r-tidygraph): New variable.
 2019-09-08 00:30:32 +02:00
Ricardo Wurmus 9390300915
gnu: Add r-graphlayouts. 
* gnu/packages/cran.scm (r-graphlayouts): New variable.
 2019-09-08 00:30:32 +02:00
Ricardo Wurmus 6983178b06
gnu: Add r-systemfonts. 
* gnu/packages/cran.scm (r-systemfonts): New variable.
 2019-09-08 00:30:32 +02:00
Ricardo Wurmus 7a5ed348c0
gnu: Add r-covr. 
* gnu/packages/cran.scm (r-covr): New variable.
 2019-09-08 00:30:32 +02:00
Julien Lepiller 1d03a9198d
tests: opam: Fix input type in import test. 
* tests/opam.scm: Expect propagated-inputs instead of inputs.
 2019-09-07 22:25:14 +02:00
Arun Isaac 9d280ef2a8
gnu: poussetaches: Update to 0.0.2. 
* gnu/packages/web.scm (poussetaches): Update to 0.0.2.
 2019-09-08 00:02:59 +05:30
Julien Lepiller e877f4d012
gnu: nml: Fix for newer pillow version. 
* gnu/packages/game-development.scm (nml)[arguments]: Add a phase to fix
for newer pillow.
 2019-09-07 20:14:50 +02:00
Ludovic Courtès 8ba31e8bd1
doc: Use @lisp instead of @example for Scheme snippets. 
This is a followup to f8c143a713, which
allows syntax highlighting of @lisp snippets in the HTML output.

* doc/guix.texi, doc/contributing.texi: Use @lisp instead of @example
for all the Scheme snippets.
 2019-09-07 18:42:08 +02:00
Ludovic Courtès 7854bbeb3f
doc: Work around (htmlprag) parser issue. 
* doc/build.scm (guile-lib/htmlprag-fixed): New variable.
(syntax-highlighted-html): Use it instead of GUILE-LIB.
 2019-09-07 18:42:08 +02:00