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2019-12-04gnu: Remove duplicate nlohmann-json-cpp package.Marius Bakke
* gnu/packages/serialization.scm (nlohmann-json-cpp): Move variable ... * gnu/packages/cpp.scm (nlohmann-json-cpp): ... here. Mark as deprecated by JSON-MODERN-CXX. * gnu/packages/jupyter.scm (xeus)[inputs]: Change NLOHMANN-JSON-CPP to JSON-MODERN-CXX. * gnu/packages/video.scm (mkvtoolnix)[inputs]: Likewise.
2019-12-04gnu: sunxi-tools: Simplify build.Danny Milosavljevic
* gnu/packages/admin.scm (sunxi-tools-source): New procedure. (sunxi-target-tools): New variable. (sunxi-tools)[source]: Use sunxi-tools-source. [native-inputs]: Remove cross-gcc, cross-libc, cross-libc-static. Add sunxi-target-tools. [arguments]<#:make-flags>: Modify. [arguments]<#:phases>[set-environment-up]: Delete phase. [build-armhf]: Delete phase. [install]: Modify.
2019-12-04machine: ssh: <machine-ssh-configuration> can include the host key.Ludovic Courtès
* gnu/machine/ssh.scm (<machine-ssh-configuration>)[host-key]: New field. (machine-ssh-session): Pass #:host-key to 'open-ssh-session'. * doc/guix.texi (Invoking guix deploy): Document it.
2019-12-04ssh: 'open-ssh-session' can be passed the expected host key.Ludovic Courtès
* guix/ssh.scm (open-ssh-session): Add #:host-key parameter. Pass #:knownhosts to 'make-session'. When HOST-KEY is true, call 'authenticate-server*' instead of 'authenticate-server'.
2019-12-04ssh: Always authenticate the server [security fix].Ludovic Courtès
Until now, users of 'open-ssh-session', including "guix deploy" and "GUIX_DAEMON_SOCKET=ssh://…" (but not "guix offload"), would not authenticate the SSH server they're talking to. * guix/ssh.scm (open-ssh-session): Call 'authenticate-server'.
2019-12-04ssh: Add 'authenticate-server*' and use it for offloading.Ludovic Courtès
* guix/scripts/offload.scm (host-key->type+key): Remove. (open-ssh-session): Replace server authentication code with a call to 'authenticate-server*'. * guix/ssh.scm (host-key->type+key, authenticate-server*): New procedures.
2019-12-04gnu: bitlbee: Use Python 3.Timotej Lazar
* gnu/packages/messaging.scm (bitlbee)[inputs]: Replace python-2 with python. [arguments]: Set the PYTHON environment variable before configuring. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2019-12-04services: Add GNOME Keyring service.Leo Prikler
* gnu/services/desktop.scm: (<gnome-keyring-configuration>): New record type. (pam-gnome-keyring): New procedure. (gnome-keyring-service-type): New variable. * doc/guix.texi (Desktop Services): Document it. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2019-12-04substitute: Remove unused procedure.Ludovic Courtès
This became unused with commit a9468b422b6df2349a3f4d1451c9302c3d77011b. * guix/scripts/substitute.scm (assert-valid-signature): Remove.
2019-12-04gnu: ncmpc: Update to 0.36.Leo Famulari
* gnu/packages/mpd.scm (ncmpc): Update to 0.36.
2019-12-04gnu: MPD: Update to 0.21.16.Leo Famulari
* gnu/packages/mpd.scm (mpd): Update to 0.21.16.
2019-12-04gnu: tmux: Update to 3.0a.Leo Famulari
* gnu/packages/tmux.scm (tmux): Update to 3.0a.
2019-12-04services: SSH services: Provide 'ssh' and 'sshd' Shepherd services.Leo Famulari
* gnu/services/ssh.scm (lsh-shepherd-service, dropbear-shepherd-service, openssh-sheperd-service): Add 'ssh' and 'sshd' to provision.
2019-12-04gnu: icecat: Update to 68.3.0-guix0-preview1 [security fixes].Mark H Weaver
Includes fixes for CVE-2019-11745, CVE-2019-17005, CVE-2019-17008, CVE-2019-17009, CVE-2019-17010, CVE-2019-17011, and CVE-2019-17012. * gnu/packages/patches/icecat-gnuzilla-fixes.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. * gnu/packages/gnuzilla.scm (%icecat-version, %icecat-build-id): Update. (icecat-source): Update hash for the firefox source tarball. Update to the latest from gnuzilla.git. Don't apply icecat-gnuzilla-fixes.patch. Remove determinism fix in makeicecat that is now upstream. Tweak a status message. (icecat)[arguments]: Add "--with-unsigned-addon-scopes=app" configure flag. * gnu/packages/patches/icecat-makeicecat.patch: Adapt.
2019-12-04gnu: emacs-transient: Refer to the updated installation directory.Clément Lassieur
* gnu/packages/emacs-xyz.scm (emacs-transient)[arguments]: Refer to the updated installation directory.
2019-12-04gnuL librsvg-next: Unvendor some rust crates.Efraim Flashner
* gnu/packages/gnome.scm (computed-origin-method, librsvg-next-source): New variables. (librsvg-next)[source]: Use computed librsvg-next-source. [arguments]: Import %cargo-build-modules. Enable 'patch-source-shebangs, 'patch-generated-source-shebangs, 'patch-user-bin-file phases. Change custom phase to patch cargo checksums and Cargo.lock.
2019-12-04gnu: emacs-emacsql: Fix build.Maxim Cournoyer
* gnu/packages/emacs-xyz.scm (emacs-emacsql): Refer to the updated installation directory. Signed-off-by: Clément Lassieur <clement@lassieur.org>
2019-12-04gnu: emacs-ert-runner: Fix build.Maxim Cournoyer
* gnu/packages/emacs-xyz.scm (emacs-ert-runner): Refer to the updated installation directory. Signed-off-by: Clément Lassieur <clement@lassieur.org>
2019-12-04gnu: emacs: Use load-path instead of EMACSLOADPATH.Maxim Cournoyer
This enables the use of the subdirs.el feature of Emacs, where specifying a directory in EMACSLOADPATH translates into a `load-path' variable containing the directory and all its sub-directories. * gnu/packages/aux-files/emacs/guix-emacs.el (guix-emacs-autoload-packages): Use `load-path' directly instead of parsing EMACSLOADPATH. Reported-by: Leo Prikler <leo.prikler@student.tugraz.at> Signed-off-by: Clément Lassieur <clement@lassieur.org>
2019-12-04gnu: emacs: Fix guix-emacs.el indentation.Maxim Cournoyer
* gnu/packages/aux-files/emacs/guix-emacs.el: Fix indentation. Signed-off-by: Clément Lassieur <clement@lassieur.org>
2019-12-04gnu: emacs: Simplify the EMACSLOADPATH search path specification.Maxim Cournoyer
The EMACSLOADPATH can be greatly simplified by relying on a subdirs.el file that causes Emacs to search recursively a directory found in EMACSLOADPATH. * gnu/packages/emacs.scm (emacs)[native-search-paths]: Remove the match-all file pattern regexp. Remove the versioned site-lisp directory from searched files, as it appears unused by Emacs. Reported-by: Leo Prikler <leo.prikler@student.tugraz.at> Signed-off-by: Clément Lassieur <clement@lassieur.org>
2019-12-04build: emacs-build-system: Unify the installation directory.Maxim Cournoyer
This change aims to reduce the length of the EMACSLOADPATH environment variable, which was found to cause issues such as <https://bugs.gnu.org/38309>. It should also enable discovery of newly installed packages without refreshing the session's EMACSLOADPATH of the user profile (e.g., when launching Emacs from the desktop manager application launcher), as discussed in <https://bugs.gnu.org/38309>. * guix/build/emacs-build-system.scm (%legacy-install-suffix): Rename to... (%install-dir): ...this. (%install-suffix): Remove variable. (build): Adjust installation target directory. (patch-el-files): Likewise. (install): Likewise. (move-doc): Likewise. (make-autoloads): Likewise. Signed-off-by: Clément Lassieur <clement@lassieur.org>
2019-12-04build-system/linux-module: Accept a #:make-flags keyword.Tobias Geerinckx-Rice
Fixes bug#37882. * guix/build-system/linux-module.scm (linux-module-build): Accept a MAKE-FLAGS argument. <builder>: Pass it on.
2019-12-04gnu: r-catterplots: Update to 0-3.ae17cd5.Ricardo Wurmus
* gnu/packages/statistics.scm (r-catterplots): Update to 0-3.ae17cd5.
2019-12-04gnu: hexchat: Fix up inputs.Efraim Flashner
* gnu/packages/messaging.scm (hexchat)[inputs]: Move glib:bin ... [native-inputs]: ... to here.
2019-12-04gnu: ocaml-gen: Don't use unstable tarball.Efraim Flashner
* gnu/packages/ocaml.scm (ocaml-gen)[source]: Download using git-fetch.
2019-12-04gnu: p7zip: Move *asm inputs to native-inputs.Efraim Flashner
* gnu/packages/compression.scm (p7zip)[inputs]: Move yasm, nasm ... [native-inputs]: ... to here.
2019-12-04gnu: lablgtk: Use a source file-name.Efraim Flashner
* gnu/packages/ocaml.scm (lablgtk)[source]: Add 'file-name'.
2019-12-04gnu: r-rversions: Update to 2.0.1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rversions): Update to 2.0.1.
2019-12-04gnu: r-survival: Update to 3.1-8.Ricardo Wurmus
* gnu/packages/statistics.scm (r-survival): Update to 3.1-8.
2019-12-04gnu: r-all: Use bioconductor-uri.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-all)[source]: Use bioconductor-uri.
2019-12-04gnu: r-hsmmsinglecell: Use bioconductor-uri.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-hsmmsinglecell)[source]: Use bioconductor-uri.
2019-12-04gnu: r-arrmdata: Use bioconductor-uri.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-arrmdata)[source]: Use bioconductor-uri.
2019-12-04gnu: r-abadata: Use bioconductor-uri.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-abadata)[source]: Use bioconductor-uri.
2019-12-04gnu: r-do-db: Use bioconductor-uri.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-do-db)[source]: Use bioconductor-uri.
2019-12-04gnu: r-illuminahumanmethylationepicmanifest: Use bioconductor-uri.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-illuminahumanmethylationepicmanifest)[source]: Use bioconductor-uri.
2019-12-04gnu: r-fdb-infiniummethylation-hg19: Use bioconductor-uri.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-fdb-infiniummethylation-hg19)[source]: Use bioconductor-uri.
2019-12-04gnu: r-txdb-mmusculus-ucsc-mm10-knowngene: Use bioconductor-uri.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-txdb-mmusculus-ucsc-mm10-knowngene)[source]: Use bioconductor-uri. [arguments]: Enable substitution.
2019-12-04gnu: r-txdb-mmusculus-ucsc-mm9-knowngene: Use bioconductor-uri.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-txdb-mmusculus-ucsc-mm9-knowngene)[source]: Use bioconductor-uri.
2019-12-04gnu: r-txdb-hsapiens-ucsc-hg38-knowngene: Use bioconductor-uri.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-txdb-hsapiens-ucsc-hg38-knowngene)[source]: Use bioconductor-uri.
2019-12-04gnu: r-txdb-hsapiens-ucsc-hg19-knowngene: Use bioconductor-uri.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-txdb-hsapiens-ucsc-hg19-knowngene)[source]: Use bioconductor-uri. [arguments]: Enable substitution.
2019-12-04gnu: r-genelendatabase: Use bioconductor-uri.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-genelendatabase)[source]: Use bioconductor-uri.
2019-12-04gnu: r-bsgenome-hsapiens-ucsc-hg19: Use bioconductor-uri.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19)[source]: Use bioconductor-uri. [arguments]: Enable substitution.
2019-12-04gnu: r-org-mm-eg-db: Use bioconductor-uri.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-org-mm-eg-db)[source]: Use bioconductor-uri.
2019-12-04gnu: r-org-hs-eg-db: Use bioconductor-uri.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-org-hs-eg-db)[source]: Use bioconductor-uri.
2019-12-04gnu: r-org-dr-eg-db: Use bioconductor-uri.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-org-dr-eg-db)[source]: Use bioconductor-uri.
2019-12-04gnu: r-org-dm-eg-db: Use bioconductor-uri.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-org-dm-eg-db)[source]: Use bioconductor-uri.
2019-12-04gnu: r-org-ce-eg-db: Use bioconductor-uri.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-org-ce-eg-db)[source]: Use bioconductor-uri.
2019-12-04gnu: r-bsgenome-mmusculus-ucsc-mm10: Use bioconductor-uri.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm10)[source]: Use bioconductor-uri. [arguments]: Enable substitution.
2019-12-04gnu: r-bsgenome-mmusculus-ucsc-mm9-masked: Use bioconductor-uri.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm9-masked)[source]: Use bioconductor-uri.
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