Commit graph

66698 commits

Author SHA1 Message Date
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
Paul Garlick 735808b12c
guix: Fix download-svn-to-store.
* guix/svn-download.scm (download-svn-to-store): Add a subdirectory to
the download path.  The subdirectory is used as the target for the 'svn
export' command, avoiding a 'directory exists' error when attempting to
use the parent directory directly.
2020-09-14 14:24:29 +01:00
Mathieu Othacehe bc5dcd9ef5
gnu: cuirass: Update to 0.0.1-45.cf11b73.
* gnu/packages/ci.scm (cuirass): Update to 0.0.1-45.cf11b73.
2020-09-14 14:43:33 +02:00
Stefan 8c4f1aa85f
gnu: grub: Support loading files from TFTP if the root filesystem is NFS.
* gnu/bootloader/grub.scm (grub-root-search): Set the root to "(tftp)" if
the searched-for file is stored on NFS.
2020-09-14 14:25:04 +02:00
Ricardo Wurmus f6807498be
gnu: Add altermime.
* gnu/packages/mail.scm (altermime): New variable.
2020-09-14 13:17:46 +02:00
zimoun c22c6de453
gnu: rapicorn: Use pandoc instead of ghc-pandoc.
* gnu/packages/graphics.scm (rapicorn)[native-inputs]: Replace ghc-pandoc with
pandoc.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-09-14 10:51:27 +02:00
zimoun 885332832c
gnu: ganeti: Use pandoc instead of ghc-pandoc.
* gnu/packages/text-editors.scm (ganeti)[native-inputs]: Replace ghc-pandoc
with pandoc.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-09-14 10:51:27 +02:00
zimoun 5dc5a3116b
gnu: manuskript: Use pandoc instead of ghc-pandoc.
* gnu/packages/text-editors.scm (manuskript)[inputs]: Replace ghc-pandoc with
pandoc.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-09-14 10:51:26 +02:00
zimoun 991c61678b
gnu: emacs-org-web-tools: Use pandoc instead of ghc-pandoc.
* gnu/packages/emacs-xyz.scm (emacs-org-webtools)[inputs]: Replace ghc-pandoc
with pandoc.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-09-14 10:51:26 +02:00
zimoun d37279ee1e
gnu: emacs-ox-pandoc: Use pandoc instead of ghc-pandoc.
* gnu/packages/emacs-xyz.scm (emacs-ox-pandoc)[inputs]: Replace ghc-pandoc
with pandoc.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-09-14 10:51:26 +02:00
zimoun 8cc8e584ab
gnu: ruby-pandoc-ruby: Use pandoc instead of ghc-pandoc.
* gnu/packages/ruby.scm (ruby-pandoc-ruby)[native-inputs]: Replace ghc-pandoc
with pandoc.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-09-14 10:51:26 +02:00
Christopher Baines 2932591b8a
database: register-items: reduce transaction scope.
It was made transactional in a4678c6ba1, with
the reasoning to prevent broken intermediate states from being visible. I
think this means something like an entry being in ValidPaths, but the Refs not
being inserted.

Using a transaction for this makes sense, but I think using one single
transaction for the whole register-items call is unnecessary to avoid broken
states from being visible, and could block other writes to the store database
while register-items is running. Because the deduplication and resetting
timestamps happens within the transaction as well, even though these things
don't involve the database, writes to the database will still be blocked while
this is happening.

To reduce the potential for register-items to block other writers to the
database for extended periods, this commit moves the transaction to just wrap
the call to sqlite-register. This is the one place where writes occur, so that
should prevent the broken intermediate states issue above. The one difference
this will make is some of the registered items will be visible to other
connections while others may be still being added. I think this is OK, as it's
equivalent to just registering different items.

* guix/store/database.scm (register-items): Reduce transaction scope.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-09-14 10:51:26 +02:00
Caleb Ristvedt a05c31ab30
database: document extra registration requirements.
It's necessary that store items be locked and protected from garbage
collection while they are being registered.  This documents that.

* guix/store/database.scm (register-path, register-items): document GC
  protection and locking requirements.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-09-14 10:51:26 +02:00
Caleb Ristvedt 14c422c12c
deduplication: pass store directory to replace-with-link.
This causes with-writable-file to take into consideration the actual store
being used, as passed to 'deduplicate', rather than
whatever (%store-directory) may return.

* guix/store/deduplication.scm (replace-with-link): new keyword argument
  'store'.  Pass to with-writable-file.
  (with-writable-file, call-with-writable-file): new store argument.
  (deduplicate): pass store to replace-with-link.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-09-14 10:51:26 +02:00
Caleb Ristvedt 1d40e6fdd1
.dir-locals.el: fix call-with-{retrying-}transaction indenting.
* .dir-locals.el (call-with-transaction, call-with-retrying-transaction):
  change scheme-indent-function property from 2 to 1.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-09-14 10:51:26 +02:00
Pierre Neidhardt 24244f3fbf
gnu: python-wrapper: Mention pip in description.
* gnu/packages/python.scm (python-wrapper)[description]: Mention that `pip'
won't work properly if both python and python-wrapper are installed.
2020-09-14 10:35:05 +02:00
Danny Milosavljevic 2be5c2652a
build-system: linux-module: Delete some huge items that we probably don't need.
* guix/build-system/linux-module.scm (make-linux-module-builder): Delete
some huge items that we probably don't need.
2020-09-14 10:15:43 +02:00