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2020-09-14gnu: r-diversitree: Update to 0.9-14.Ricardo Wurmus
* gnu/packages/cran.scm (r-diversitree): Update to 0.9-14.
2020-09-14gnu: r-seurat: Update to 3.2.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-seurat): Update to 3.2.1. [propagated-inputs]: Remove r-ape; add r-matrixstats.
2020-09-14gnu: r-rfast: Update to 2.0.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-rfast): Update to 2.0.1.
2020-09-14gnu: r-scatterpie: Update to 0.1.5.Ricardo Wurmus
* gnu/packages/cran.scm (r-scatterpie): Update to 0.1.5.
2020-09-14gnu: r-forecast: Update to 8.13.Ricardo Wurmus
* gnu/packages/cran.scm (r-forecast): Update to 8.13.
2020-09-14gnu: r-gamlss: Update to 5.2-0.Ricardo Wurmus
* gnu/packages/cran.scm (r-gamlss): Update to 5.2-0.
2020-09-14gnu: r-parameters: Update to 0.8.5.Ricardo Wurmus
* gnu/packages/cran.scm (r-parameters): Update to 0.8.5.
2020-09-14gnu: r-systemfonts: Update to 0.3.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-systemfonts): Update to 0.3.1.
2020-09-14gnu: r-dalex: Update to 2.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-dalex): Update to 2.0.
2020-09-14gnu: r-sf: Update to 0.9-6.Ricardo Wurmus
* gnu/packages/cran.scm (r-sf): Update to 0.9-6.
2020-09-14gnu: r-deldir: Update to 0.1-29.Ricardo Wurmus
* gnu/packages/cran.scm (r-deldir): Update to 0.1-29.
2020-09-14gnu: r-shinyjs: Update to 2.0.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-shinyjs): Update to 2.0.0. [native-inputs]: Add r-knitr.
2020-09-14gnu: r-etm: Update to 1.1.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-etm): Update to 1.1.1.
2020-09-14gnu: r-fields: Update to 11.4.Ricardo Wurmus
* gnu/packages/cran.scm (r-fields): Update to 11.4.
2020-09-14gnu: r-rnifti: Update to 1.2.2.Ricardo Wurmus
* gnu/packages/cran.scm (r-rnifti): Update to 1.2.2.
2020-09-14gnu: r-misc3d: Update to 0.9-0.Ricardo Wurmus
* gnu/packages/cran.scm (r-misc3d): Update to 0.9-0.
2020-09-14gnu: r-rcpphnsw: Update to 0.3.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-rcpphnsw): Update to 0.3.0.
2020-09-14gnu: r-ggeffects: Update to 0.16.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-ggeffects): Update to 0.16.0.
2020-09-14gnu: r-performance: Update to 0.5.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-performance): Update to 0.5.0.
2020-09-14gnu: r-mosaicdata: Update to 0.20.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-mosaicdata): Update to 0.20.1.
2020-09-14gnu: r-mosaiccore: Update to 0.8.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-mosaiccore): Update to 0.8.0. [propagated-inputs]: Remove r-lazyeval.
2020-09-14gnu: r-flextable: Update to 0.5.11.Ricardo Wurmus
* gnu/packages/cran.scm (r-flextable): Update to 0.5.11.
2020-09-14gnu: r-insight: Update to 0.9.5.Ricardo Wurmus
* gnu/packages/cran.scm (r-insight): Update to 0.9.5.
2020-09-14gnu: r-officer: Update to 0.3.14.Ricardo Wurmus
* gnu/packages/cran.scm (r-officer): Update to 0.3.14.
2020-09-14gnu: r-extradistr: Update to 1.9.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-extradistr): Update to 1.9.1.
2020-09-14gnu: r-tsa: Update to 1.3.Ricardo Wurmus
* gnu/packages/cran.scm (r-tsa): Update to 1.3. [propagated-inputs]: Add r-tseries.
2020-09-14gnu: r-xfun: Update to 0.17.Ricardo Wurmus
* gnu/packages/cran.scm (r-xfun): Update to 0.17.
2020-09-14gnu: r-processx: Update to 3.4.4.Ricardo Wurmus
* gnu/packages/cran.scm (r-processx): Update to 3.4.4.
2020-09-14gnu: r-xts: Update to 0.12.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-xts): Update to 0.12.1.
2020-09-14gnu: r-psych: Update to 2.0.8.Ricardo Wurmus
* gnu/packages/cran.scm (r-psych): Update to 2.0.8.
2020-09-14gnu: r-inline: Update to 0.3.16.Ricardo Wurmus
* gnu/packages/cran.scm (r-inline): Update to 0.3.16.
2020-09-14gnu: r-lmtest: Update to 0.9-38.Ricardo Wurmus
* gnu/packages/cran.scm (r-lmtest): Update to 0.9-38.
2020-09-14gnu: r-shape: Update to 1.4.5.Ricardo Wurmus
* gnu/packages/cran.scm (r-shape): Update to 1.4.5.
2020-09-14gnu: r-jsonlite: Update to 1.7.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-jsonlite): Update to 1.7.1.
2020-09-14gnu: r-callr: Update to 3.4.4.Ricardo Wurmus
* gnu/packages/cran.scm (r-callr): Update to 3.4.4.
2020-09-14gnu: r-ggpmisc: Update to 0.3.6.Ricardo Wurmus
* gnu/packages/cran.scm (r-ggpmisc): Update to 0.3.6. [propagated-inputs]: Add r-glue.
2020-09-14gnu: r-activedriverwgs: Update to 1.1.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-activedriverwgs): Update to 1.1.0. [propagated-inputs]: Remove r-plyr. [native-inputs]: Add r-knitr.
2020-09-14gnu: emacs-esup: Fix build.Mathieu Othacehe
* 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.
2020-09-14gnu: Add lsp-dsp-lib.Alexandros Theodotou
* gnu/packages/audio.scm (lsp-dsp-lib): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2020-09-14services: docker: Make docker command available.Efraim Flashner
* gnu/services/docker.scm (docker-service-type): Extend the profile-service-type and add the docker-cli package.
2020-09-14doc: Fix docker configuration options.Efraim Flashner
* doc/guix.texi (Docker Service): Fix typo in enable-proxy? default.
2020-09-14gnu: Add quickjs.Ryan Prior
* gnu/packages/javascript.scm (quickjs): New variable. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2020-09-14ui: 'show-what-to-build' displays download estimate more prominently.Ludovic Courtès
* 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'.
2020-09-14tests: Remove one 'delete-paths' call in 'tests/store.scm'.Ludovic Courtès
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.
2020-09-14authenticate: Cache the ACL and key pairs.Ludovic Courtès
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.
2020-09-14daemon: Spawn 'guix authenticate' once for all.Ludovic Courtès
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
2020-09-14daemon: Move 'Agent' to libutil.Ludovic Courtès
* 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.
2020-09-14daemon: Isolate signing and signature verification functions.Ludovic Courtès
* 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.
2020-09-14daemon: Generalize 'HookInstance' to 'Agent'.Ludovic Courtès
* 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.
2020-09-14guix: Fix download-svn-to-store.Paul Garlick
* 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.
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