Commit graph

66614 commits

Author SHA1 Message Date
Ricardo Wurmus
98f76dbcfb
gnu: r-mass: Update to 7.3-53.
* gnu/packages/statistics.scm (r-mass): Update to 7.3-53.
2020-09-14 19:07:47 +02:00
Ricardo Wurmus
1c1b941902
gnu: r-diversitree: Update to 0.9-14.
* gnu/packages/cran.scm (r-diversitree): Update to 0.9-14.
2020-09-14 19:07:47 +02:00
Ricardo Wurmus
8731d274ae
gnu: r-seurat: Update to 3.2.1.
* gnu/packages/cran.scm (r-seurat): Update to 3.2.1.
[propagated-inputs]: Remove r-ape; add r-matrixstats.
2020-09-14 19:07:47 +02:00
Ricardo Wurmus
e6711231ed
gnu: r-rfast: Update to 2.0.1.
* gnu/packages/cran.scm (r-rfast): Update to 2.0.1.
2020-09-14 19:07:47 +02:00
Ricardo Wurmus
0982ffa898
gnu: r-scatterpie: Update to 0.1.5.
* gnu/packages/cran.scm (r-scatterpie): Update to 0.1.5.
2020-09-14 19:07:47 +02:00
Ricardo Wurmus
df2210be8b
gnu: r-forecast: Update to 8.13.
* gnu/packages/cran.scm (r-forecast): Update to 8.13.
2020-09-14 19:07:47 +02:00
Ricardo Wurmus
ad10a45225
gnu: r-gamlss: Update to 5.2-0.
* gnu/packages/cran.scm (r-gamlss): Update to 5.2-0.
2020-09-14 19:07:47 +02:00
Ricardo Wurmus
bf37420fe7
gnu: r-parameters: Update to 0.8.5.
* gnu/packages/cran.scm (r-parameters): Update to 0.8.5.
2020-09-14 19:07:47 +02:00
Ricardo Wurmus
515b746945
gnu: r-systemfonts: Update to 0.3.1.
* gnu/packages/cran.scm (r-systemfonts): Update to 0.3.1.
2020-09-14 19:07:46 +02:00
Ricardo Wurmus
3f67fb11cf
gnu: r-dalex: Update to 2.0.
* gnu/packages/cran.scm (r-dalex): Update to 2.0.
2020-09-14 19:07:46 +02:00
Ricardo Wurmus
ef59d57841
gnu: r-sf: Update to 0.9-6.
* gnu/packages/cran.scm (r-sf): Update to 0.9-6.
2020-09-14 19:07:46 +02:00
Ricardo Wurmus
b426f79602
gnu: r-deldir: Update to 0.1-29.
* gnu/packages/cran.scm (r-deldir): Update to 0.1-29.
2020-09-14 19:07:46 +02:00
Ricardo Wurmus
0435f7eec1
gnu: r-shinyjs: Update to 2.0.0.
* gnu/packages/cran.scm (r-shinyjs): Update to 2.0.0.
[native-inputs]: Add r-knitr.
2020-09-14 19:07:46 +02:00
Ricardo Wurmus
11f448ba74
gnu: r-etm: Update to 1.1.1.
* gnu/packages/cran.scm (r-etm): Update to 1.1.1.
2020-09-14 19:07:46 +02:00
Ricardo Wurmus
ffe714b5f4
gnu: r-fields: Update to 11.4.
* gnu/packages/cran.scm (r-fields): Update to 11.4.
2020-09-14 19:07:46 +02:00
Ricardo Wurmus
0f93324a83
gnu: r-rnifti: Update to 1.2.2.
* gnu/packages/cran.scm (r-rnifti): Update to 1.2.2.
2020-09-14 19:07:46 +02:00
Ricardo Wurmus
0b73771ad9
gnu: r-misc3d: Update to 0.9-0.
* gnu/packages/cran.scm (r-misc3d): Update to 0.9-0.
2020-09-14 19:07:46 +02:00
Ricardo Wurmus
015e15c836
gnu: r-rcpphnsw: Update to 0.3.0.
* gnu/packages/cran.scm (r-rcpphnsw): Update to 0.3.0.
2020-09-14 19:07:46 +02:00
Ricardo Wurmus
a1e92714ce
gnu: r-ggeffects: Update to 0.16.0.
* gnu/packages/cran.scm (r-ggeffects): Update to 0.16.0.
2020-09-14 19:07:46 +02:00
Ricardo Wurmus
7975d2c3b8
gnu: r-performance: Update to 0.5.0.
* gnu/packages/cran.scm (r-performance): Update to 0.5.0.
2020-09-14 19:07:46 +02:00
Ricardo Wurmus
5efeef3f01
gnu: r-mosaicdata: Update to 0.20.1.
* gnu/packages/cran.scm (r-mosaicdata): Update to 0.20.1.
2020-09-14 19:07:46 +02:00
Ricardo Wurmus
9e3712958f
gnu: r-mosaiccore: Update to 0.8.0.
* gnu/packages/cran.scm (r-mosaiccore): Update to 0.8.0.
[propagated-inputs]: Remove r-lazyeval.
2020-09-14 19:07:46 +02:00
Ricardo Wurmus
6880269b94
gnu: r-flextable: Update to 0.5.11.
* gnu/packages/cran.scm (r-flextable): Update to 0.5.11.
2020-09-14 19:07:45 +02:00
Ricardo Wurmus
07c1620f81
gnu: r-insight: Update to 0.9.5.
* gnu/packages/cran.scm (r-insight): Update to 0.9.5.
2020-09-14 19:07:45 +02:00
Ricardo Wurmus
9a22da3790
gnu: r-officer: Update to 0.3.14.
* gnu/packages/cran.scm (r-officer): Update to 0.3.14.
2020-09-14 19:07:45 +02:00
Ricardo Wurmus
16cc10eafb
gnu: r-extradistr: Update to 1.9.1.
* gnu/packages/cran.scm (r-extradistr): Update to 1.9.1.
2020-09-14 19:07:45 +02:00
Ricardo Wurmus
8d8db33f71
gnu: r-tsa: Update to 1.3.
* gnu/packages/cran.scm (r-tsa): Update to 1.3.
[propagated-inputs]: Add r-tseries.
2020-09-14 19:07:45 +02:00
Ricardo Wurmus
60e4d97295
gnu: r-xfun: Update to 0.17.
* gnu/packages/cran.scm (r-xfun): Update to 0.17.
2020-09-14 19:07:45 +02:00
Ricardo Wurmus
cb4243eaba
gnu: r-processx: Update to 3.4.4.
* gnu/packages/cran.scm (r-processx): Update to 3.4.4.
2020-09-14 19:07:45 +02:00
Ricardo Wurmus
302dacec7e
gnu: r-xts: Update to 0.12.1.
* gnu/packages/cran.scm (r-xts): Update to 0.12.1.
2020-09-14 19:07:45 +02:00
Ricardo Wurmus
dee6078a86
gnu: r-psych: Update to 2.0.8.
* gnu/packages/cran.scm (r-psych): Update to 2.0.8.
2020-09-14 19:07:45 +02:00
Ricardo Wurmus
c5199f2918
gnu: r-inline: Update to 0.3.16.
* gnu/packages/cran.scm (r-inline): Update to 0.3.16.
2020-09-14 19:07:45 +02:00
Ricardo Wurmus
5473d23f59
gnu: r-lmtest: Update to 0.9-38.
* gnu/packages/cran.scm (r-lmtest): Update to 0.9-38.
2020-09-14 19:07:45 +02:00
Ricardo Wurmus
54c91e4a66
gnu: r-shape: Update to 1.4.5.
* gnu/packages/cran.scm (r-shape): Update to 1.4.5.
2020-09-14 19:07:45 +02:00
Ricardo Wurmus
8c7a185779
gnu: r-jsonlite: Update to 1.7.1.
* gnu/packages/cran.scm (r-jsonlite): Update to 1.7.1.
2020-09-14 19:07:45 +02:00
Ricardo Wurmus
adde909369
gnu: r-callr: Update to 3.4.4.
* gnu/packages/cran.scm (r-callr): Update to 3.4.4.
2020-09-14 19:07:44 +02:00
Ricardo Wurmus
c629dce1df
gnu: r-ggpmisc: Update to 0.3.6.
* gnu/packages/cran.scm (r-ggpmisc): Update to 0.3.6.
[propagated-inputs]: Add r-glue.
2020-09-14 19:07:44 +02:00
Ricardo Wurmus
e1ce10e385
gnu: r-activedriverwgs: Update to 1.1.0.
* gnu/packages/bioconductor.scm (r-activedriverwgs): Update to 1.1.0.
[propagated-inputs]: Remove r-plyr.
[native-inputs]: Add r-knitr.
2020-09-14 19:07:44 +02:00
Mathieu Othacehe
327f6aec55
gnu: emacs-esup: Fix build.
* gnu/packages/emacs-xyz.scm (emacs-esup): Update to 0.7.1-1.0de8af8.
[native-inputs]: Add "emacs-buttercup" and "emacs-undercover", remove
"emacs-el-mock".
[propagated-inputs]: Add "emacs-dash".
[arguments]: Fix testing.
2020-09-14 18:12:41 +02:00
Alexandros Theodotou
913faed8ba
gnu: Add lsp-dsp-lib.
* gnu/packages/audio.scm (lsp-dsp-lib): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2020-09-14 17:23:32 +03:00
Efraim Flashner
8422a67dc1
services: docker: Make docker command available.
* gnu/services/docker.scm (docker-service-type): Extend the
profile-service-type and add the docker-cli package.
2020-09-14 17:21:16 +03:00
Efraim Flashner
ef7381f463
doc: Fix docker configuration options.
* doc/guix.texi (Docker Service): Fix typo in enable-proxy? default.
2020-09-14 17:21:12 +03:00
Ryan Prior
4a2cb3fa0e
gnu: Add quickjs.
* gnu/packages/javascript.scm (quickjs): New variable.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2020-09-14 16:12:36 +02:00
Ludovic Courtès
846403ef62
ui: 'show-what-to-build' displays download estimate more prominently.
* guix/ui.scm (show-what-to-build): When VERBOSITY is 1, add a newline
before the "would/will be downloaded" line, and wrap that message in
'highlight'.
2020-09-14 15:42:56 +02:00
Ludovic Courtès
8eeeedcb35
tests: Remove one 'delete-paths' call in 'tests/store.scm'.
This makes the test slightly less expensive.

* tests/store.scm ("add-text-to-store vs. delete-paths")
("add-to-store vs. delete-paths"): Delete and merge into...
("add-text-to-store/add-to-store vs. delete-paths"): ... this test.
2020-09-14 15:42:56 +02:00
Ludovic Courtès
7d516c17da
authenticate: Cache the ACL and key pairs.
In practice we're always using the same key pair,
/etc/guix/signing-key.{pub,sec}.  Keeping them in cache allows us to
avoid redundant I/O and parsing when signing multiple store items in a
row.

* guix/scripts/authenticate.scm (load-key-pair): New procedure.
(sign-with-key): Remove 'key-file' parameter and add 'public-key' and
'secret-key'.  Adjust accordingly.
(validate-signature): Add 'acl' parameter and pass it to
'authorized-key?'.
(guix-authenticate)[call-with-reply]: New procedure.
[with-reply]: New macro.
Call 'current-acl' upfront and cache its result.  Add 'key-pairs' as an
argument to 'loop' and use it as a cache of key pairs.
2020-09-14 15:42:55 +02:00
Ludovic Courtès
64cf660f87
daemon: Spawn 'guix authenticate' once for all.
Previously, we'd spawn 'guix authenticate' once for each item that has
to be signed (when exporting) or authenticated (when importing).  Now,
we spawn it once for all and then follow a request/reply protocol.  This
reduces the wall-clock time of:

  guix archive --export -r $(guix build coreutils -d)

from 30s to 2s.

* guix/scripts/authenticate.scm (sign-with-key): Return the signature
instead of displaying it.  Raise a &formatted-message instead of calling
'leave'.
(validate-signature): Likewise.
(read-command): New procedure.
(define-enumerate-type, reply-code): New macros.
(guix-authenticate)[send-reply]: New procedure.
Change to read commands from current-input-port.
* nix/libstore/local-store.cc (runAuthenticationProgram): Remove.
(authenticationAgent, readInteger, readAuthenticateReply): New
functions.
(signHash, verifySignature): Rewrite in terms of the agent.
* tests/store.scm ("import not signed"): Remove 'pk' call.
("import signed by unauthorized key"): Check the error message of C.
* tests/guix-authenticate.sh: Rewrite using the new protocol.

fixlet
2020-09-14 15:42:55 +02:00
Ludovic Courtès
ee9dff34f9
daemon: Move 'Agent' to libutil.
* nix/libstore/build.cc (DerivationGoal::tryBuildHook): Add "offload" to
'args' and pass settings.guixProgram as the first argument to
Agent::Agent.
(pathNullDevice, commonChildInit, Agent, Agent::Agent)
(Agent::~Agent): Move to...
* nix/libutil/util.cc: ... here.
* nix/libutil/util.hh (struct Agent, commonChildInit): New
declarations.
2020-09-14 15:42:55 +02:00
Ludovic Courtès
27cc51c269
daemon: Isolate signing and signature verification functions.
* nix/libstore/local-store.cc (signHash, verifySignature): New
functions.
(LocalStore::exportPath): Use 'signHash' instead of inline code.
(LocalStore::importPath): Use 'verifySignature' instead of inline code.
2020-09-14 15:42:55 +02:00
Ludovic Courtès
7809071c82
daemon: Generalize 'HookInstance' to 'Agent'.
* nix/libstore/build.cc (HookInstance): Rename to...
(Agent): ... this.  Rename 'toHook' and 'fromHook' similarly and update
users.  Change constructor to require a command and an argument list.
(DerivationGoal::tryBuildHook): Pass arguments to the 'Agent'
constructor.
2020-09-14 15:42:55 +02:00