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* services: SSH services: Provide 'ssh' and 'sshd' Shepherd services.Leo Famulari2019-12-04
| | | | | * gnu/services/ssh.scm (lsh-shepherd-service, dropbear-shepherd-service, openssh-sheperd-service): Add 'ssh' and 'sshd' to provision.
* gnu: icecat: Update to 68.3.0-guix0-preview1 [security fixes].Mark H Weaver2019-12-04
| | | | | | | | | | | | | | 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.
* gnu: emacs-transient: Refer to the updated installation directory.Clément Lassieur2019-12-04
| | | | | * gnu/packages/emacs-xyz.scm (emacs-transient)[arguments]: Refer to the updated installation directory.
* gnuL librsvg-next: Unvendor some rust crates.Efraim Flashner2019-12-04
| | | | | | | | | * 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.
* gnu: emacs-emacsql: Fix build.Maxim Cournoyer2019-12-04
| | | | | | | * gnu/packages/emacs-xyz.scm (emacs-emacsql): Refer to the updated installation directory. Signed-off-by: Clément Lassieur <clement@lassieur.org>
* gnu: emacs-ert-runner: Fix build.Maxim Cournoyer2019-12-04
| | | | | | | * gnu/packages/emacs-xyz.scm (emacs-ert-runner): Refer to the updated installation directory. Signed-off-by: Clément Lassieur <clement@lassieur.org>
* gnu: emacs: Use load-path instead of EMACSLOADPATH.Maxim Cournoyer2019-12-04
| | | | | | | | | | | | 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>
* gnu: emacs: Fix guix-emacs.el indentation.Maxim Cournoyer2019-12-04
| | | | | | * gnu/packages/aux-files/emacs/guix-emacs.el: Fix indentation. Signed-off-by: Clément Lassieur <clement@lassieur.org>
* gnu: emacs: Simplify the EMACSLOADPATH search path specification.Maxim Cournoyer2019-12-04
| | | | | | | | | | | | 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>
* build: emacs-build-system: Unify the installation directory.Maxim Cournoyer2019-12-04
| | | | | | | | | | | | | | | | | | | | | | 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>
* build-system/linux-module: Accept a #:make-flags keyword.Tobias Geerinckx-Rice2019-12-04
| | | | | | | | Fixes bug#37882. * guix/build-system/linux-module.scm (linux-module-build): Accept a MAKE-FLAGS argument. <builder>: Pass it on.
* gnu: r-catterplots: Update to 0-3.ae17cd5.Ricardo Wurmus2019-12-04
| | | | * gnu/packages/statistics.scm (r-catterplots): Update to 0-3.ae17cd5.
* gnu: hexchat: Fix up inputs.Efraim Flashner2019-12-04
| | | | | * gnu/packages/messaging.scm (hexchat)[inputs]: Move glib:bin ... [native-inputs]: ... to here.
* gnu: ocaml-gen: Don't use unstable tarball.Efraim Flashner2019-12-04
| | | | * gnu/packages/ocaml.scm (ocaml-gen)[source]: Download using git-fetch.
* gnu: p7zip: Move *asm inputs to native-inputs.Efraim Flashner2019-12-04
| | | | | * gnu/packages/compression.scm (p7zip)[inputs]: Move yasm, nasm ... [native-inputs]: ... to here.
* gnu: lablgtk: Use a source file-name.Efraim Flashner2019-12-04
| | | | * gnu/packages/ocaml.scm (lablgtk)[source]: Add 'file-name'.
* gnu: r-rversions: Update to 2.0.1.Ricardo Wurmus2019-12-04
| | | | * gnu/packages/statistics.scm (r-rversions): Update to 2.0.1.
* gnu: r-survival: Update to 3.1-8.Ricardo Wurmus2019-12-04
| | | | * gnu/packages/statistics.scm (r-survival): Update to 3.1-8.
* gnu: r-all: Use bioconductor-uri.Ricardo Wurmus2019-12-04
| | | | * gnu/packages/bioconductor.scm (r-all)[source]: Use bioconductor-uri.
* gnu: r-hsmmsinglecell: Use bioconductor-uri.Ricardo Wurmus2019-12-04
| | | | | * gnu/packages/bioconductor.scm (r-hsmmsinglecell)[source]: Use bioconductor-uri.
* gnu: r-arrmdata: Use bioconductor-uri.Ricardo Wurmus2019-12-04
| | | | * gnu/packages/bioconductor.scm (r-arrmdata)[source]: Use bioconductor-uri.
* gnu: r-abadata: Use bioconductor-uri.Ricardo Wurmus2019-12-04
| | | | * gnu/packages/bioconductor.scm (r-abadata)[source]: Use bioconductor-uri.
* gnu: r-do-db: Use bioconductor-uri.Ricardo Wurmus2019-12-04
| | | | * gnu/packages/bioconductor.scm (r-do-db)[source]: Use bioconductor-uri.
* gnu: r-illuminahumanmethylationepicmanifest: Use bioconductor-uri.Ricardo Wurmus2019-12-04
| | | | | * gnu/packages/bioconductor.scm (r-illuminahumanmethylationepicmanifest)[source]: Use bioconductor-uri.
* gnu: r-fdb-infiniummethylation-hg19: Use bioconductor-uri.Ricardo Wurmus2019-12-04
| | | | | * gnu/packages/bioconductor.scm (r-fdb-infiniummethylation-hg19)[source]: Use bioconductor-uri.
* gnu: r-txdb-mmusculus-ucsc-mm10-knowngene: Use bioconductor-uri.Ricardo Wurmus2019-12-04
| | | | | | * gnu/packages/bioconductor.scm (r-txdb-mmusculus-ucsc-mm10-knowngene)[source]: Use bioconductor-uri. [arguments]: Enable substitution.
* gnu: r-txdb-mmusculus-ucsc-mm9-knowngene: Use bioconductor-uri.Ricardo Wurmus2019-12-04
| | | | | * gnu/packages/bioconductor.scm (r-txdb-mmusculus-ucsc-mm9-knowngene)[source]: Use bioconductor-uri.
* gnu: r-txdb-hsapiens-ucsc-hg38-knowngene: Use bioconductor-uri.Ricardo Wurmus2019-12-04
| | | | | * gnu/packages/bioconductor.scm (r-txdb-hsapiens-ucsc-hg38-knowngene)[source]: Use bioconductor-uri.
* gnu: r-txdb-hsapiens-ucsc-hg19-knowngene: Use bioconductor-uri.Ricardo Wurmus2019-12-04
| | | | | | * gnu/packages/bioconductor.scm (r-txdb-hsapiens-ucsc-hg19-knowngene)[source]: Use bioconductor-uri. [arguments]: Enable substitution.
* gnu: r-genelendatabase: Use bioconductor-uri.Ricardo Wurmus2019-12-04
| | | | | * gnu/packages/bioconductor.scm (r-genelendatabase)[source]: Use bioconductor-uri.
* gnu: r-bsgenome-hsapiens-ucsc-hg19: Use bioconductor-uri.Ricardo Wurmus2019-12-04
| | | | | | * gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19)[source]: Use bioconductor-uri. [arguments]: Enable substitution.
* gnu: r-org-mm-eg-db: Use bioconductor-uri.Ricardo Wurmus2019-12-04
| | | | | * gnu/packages/bioconductor.scm (r-org-mm-eg-db)[source]: Use bioconductor-uri.
* gnu: r-org-hs-eg-db: Use bioconductor-uri.Ricardo Wurmus2019-12-04
| | | | | * gnu/packages/bioconductor.scm (r-org-hs-eg-db)[source]: Use bioconductor-uri.
* gnu: r-org-dr-eg-db: Use bioconductor-uri.Ricardo Wurmus2019-12-04
| | | | | * gnu/packages/bioconductor.scm (r-org-dr-eg-db)[source]: Use bioconductor-uri.
* gnu: r-org-dm-eg-db: Use bioconductor-uri.Ricardo Wurmus2019-12-04
| | | | | * gnu/packages/bioconductor.scm (r-org-dm-eg-db)[source]: Use bioconductor-uri.
* gnu: r-org-ce-eg-db: Use bioconductor-uri.Ricardo Wurmus2019-12-04
| | | | | * gnu/packages/bioconductor.scm (r-org-ce-eg-db)[source]: Use bioconductor-uri.
* gnu: r-bsgenome-mmusculus-ucsc-mm10: Use bioconductor-uri.Ricardo Wurmus2019-12-04
| | | | | | * gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm10)[source]: Use bioconductor-uri. [arguments]: Enable substitution.
* gnu: r-bsgenome-mmusculus-ucsc-mm9-masked: Use bioconductor-uri.Ricardo Wurmus2019-12-04
| | | | | * gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm9-masked)[source]: Use bioconductor-uri.
* gnu: r-bsgenome-mmusculus-ucsc-mm9: Use bioconductor-uri.Ricardo Wurmus2019-12-04
| | | | | | * gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm9)[source]: Use bioconductor-uri. [arguments]: Enable substitution.
* gnu: r-bsgenome-hsapiens-ucsc-hg19-masked: Use bioconductor-uri.Ricardo Wurmus2019-12-04
| | | | | * gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19-masked)[source]: Use bioconductor-uri.
* gnu: r-bsgenome-hsapiens-1000genomes-hs37d5: Use bioconductor-uri.Ricardo Wurmus2019-12-04
| | | | | | * gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-1000genomes-hs37d5)[source]: Use bioconductor-uri. [arguments]: Enable substitution.
* gnu: r-bsgenome-dmelanogaster-ucsc-dm3-masked: Use bioconductor-uri.Ricardo Wurmus2019-12-04
| | | | | * gnu/packages/bioconductor.scm (r-bsgenome-dmelanogaster-ucsc-dm3-masked)[source]: Use bioconductor-uri.
* gnu: r-bsgenome-dmelanogaster-ucsc-dm3: Use bioconductor-uri.Ricardo Wurmus2019-12-04
| | | | | | * gnu/packages/bioconductor.scm (r-bsgenome-dmelanogaster-ucsc-dm3)[source]: Use bioconductor-uri. [arguments]: Enable substitution.
* gnu: r-bsgenome-dmelanogaster-ucsc-dm6: Use bioconductor-uri.Ricardo Wurmus2019-12-04
| | | | | | * gnu/packages/bioconductor.scm (r-bsgenome-dmelanogaster-ucsc-dm6)[source]: Use bioconductor-uri. [arguments]: Permit substitution.
* gnu: r-bsgenome-celegans-ucsc-ce10: Use bioconductor-uri.Ricardo Wurmus2019-12-04
| | | | | | * gnu/packages/bioconductor.scm (r-bsgenome-celegans-ucsc-ce10)[source]: Use bioconductor-uri. [arguments]: Permit substitution.
* gnu: emacs-olivetti: Update to 1.8.1.Brett Gilio2019-12-04
| | | | | | * gnu/packages/emacs-xyz.scm (emacs-olivetti): Update to 1.8.1. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: emacs-irony-mode: Update to 1.4.0.Brett Gilio2019-12-04
| | | | | | * gnu/packages/emacs-xyz.scm (emacs-irony-mode): Update to 1.4.0. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: emacs-elisp-demos: Update to 2019.12.01.Brett Gilio2019-12-04
| | | | | | * gnu/packages/emacs-xyz.scm (emacs-elisp-demos): Update to 2019.12.01. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: emacs-doom-modeline: Update to 2.8.0.Brett Gilio2019-12-04
| | | | | | * gnu/packages/emacs-xyz.scm (emacs-doom-modeline): Update to 2.8.0. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: python-pandas: Move to (gnu packages python-science).Ricardo Wurmus2019-12-04
| | | | | | | | | * gnu/packages/python-xyz.scm (python-pandas, python2-pandas): Move from here... * gnu/packages/python-science.scm (python-pandas, python2-pandas): ...to here. * gnu/packages/benchmark.scm, gnu/packages/databases.scm, gnu/packages/graph.scm, gnu/packages/parallel.scm, gnu/packages/serialization.scm: Import (gnu packages python-science).
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