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* gnu: gource: Update to 0.49.Tobias Geerinckx-Rice2018-06-15
| | | | * gnu/packages/version-control.scm (gource): Update to 0.49.
* gnu: perl-xml-libxml-simple: Update to 0.99.Tobias Geerinckx-Rice2018-06-15
| | | | * gnu/packages/xml.scm (perl-xml-libxml-simple): Update to 0.99.
* gnu: fcitx-configtool: Update to 0.4.10.Tobias Geerinckx-Rice2018-06-15
| | | | * gnu/packages/fcitx.scm (fcitx-configtool): Update to 0.4.10.
* gnu: fcitx: Update to 4.2.9.6.Tobias Geerinckx-Rice2018-06-15
| | | | | * gnu/packages/fcitx.scm (fcitx): Update to 4.2.9.6. [native-inputs]: Add extra-cmake-modules.
* gnu: fcitx: Use HTTPS home page.Tobias Geerinckx-Rice2018-06-15
| | | | * gnu/packages/fcitx.scm (fcitx)[home-page]: Use HTTPS.
* gnu: perl-xml-xpath: Update to 1.42.Tobias Geerinckx-Rice2018-06-15
| | | | * gnu/packages/xml.scm (perl-xml-xpath): Update to 1.42.
* gnu: perl-xml-xpath: Propagate inputs.Tobias Geerinckx-Rice2018-06-15
| | | | | * gnu/packages/xml.scm (perl-xml-xpath)[inputs]: Rename this... [propagated-inputs]: ...to this.
* gnu: perl-xml-atom: Propagate inputs.Tobias Geerinckx-Rice2018-06-15
| | | | | | * gnu/packages/xml.scm (perl-xml-atom)[inputs]: Rename to... [propagated-inputs]: ...this, and... [native-inputs]: ...remove duplicate packages from here.
* gnu: nickle: Update to 2.81.Tobias Geerinckx-Rice2018-06-15
| | | | * gnu/packages/nickle.scm (nickle): Update to 2.81.
* gnu: r-cubature: Update to 1.4.Tobias Geerinckx-Rice2018-06-15
| | | | * gnu/packages/cran.scm (r-cubature): Update to 1.4.
* gnu: neofetch: Update to 4.0.2.Rutger Helling2018-06-15
| | | | * gnu/packages/admin.scm (neofetch): Update to 4.0.2.
* gnu: Add r-genomicinteractions.Ricardo Wurmus2018-06-15
| | | | * gnu/packages/bioconductor.scm (r-genomicinteractions): New variable.
* gnu: Add r-interactionset.Ricardo Wurmus2018-06-15
| | | | * gnu/packages/bioconductor.scm (r-interactionset): New variable.
* gnu: innoextract: Update to 1.7.Rutger Helling2018-06-15
| | | | * gnu/packages/compression.scm (innoextract): Update to 1.7.
* gnu: Add r-riboseqr.Ricardo Wurmus2018-06-15
| | | | * gnu/packages/bioconductor.scm (r-riboseqr): New variable.
* gnu: Add r-riboprofiling.Ricardo Wurmus2018-06-15
| | | | * gnu/packages/bioconductor.scm (r-riboprofiling): New variable.
* gnu: Add r-chipcomp.Ricardo Wurmus2018-06-15
| | | | * gnu/packages/bioconductor.scm (r-chipcomp): New variable.
* gnu: Add r-bsgenome-mmusculus-ucsc-mm9-masked.Ricardo Wurmus2018-06-15
| | | | | * gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm9-masked): New variable.
* gnu: Add r-bsgenome-hsapiens-ucsc-hg19-masked.Ricardo Wurmus2018-06-15
| | | | | * gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19-masked): New variable.
* gnu: Add r-bsgenome-dmelanogaster-ucsc-dm3-masked.Ricardo Wurmus2018-06-15
| | | | | * gnu/packages/bioconductor.scm (r-bsgenome-dmelanogaster-ucsc-dm3-masked): New variable.
* gnu: Add r-bayseq.Ricardo Wurmus2018-06-15
| | | | * gnu/packages/bioconductor.scm (r-bayseq): New variable.
* gnu: certbot, python-acme: Update to 0.25.1.Leo Famulari2018-06-14
| | | | | | | * gnu/packages/tls.scm (certbot): Update 0.25.1. (python-acme): Update to 0.25.1. [native-inputs]: Add python-pytest. [propagated-inputs]: Add python-requests-toolbelt.
* gnu: Go 1.10: Update to 1.10.3.Leo Famulari2018-06-14
| | | | * gnu/packages/golang.scm (go-1.10): Update to 1.10.3.
* gnu: Go 1.9: Update to 1.9.7.Leo Famulari2018-06-14
| | | | * gnu/packages/golang.scm (go-1.9): Update to 1.9.7.
* linux-initrd: Module check correctly handles hyphen vs. underscore.Ludovic Courtès2018-06-14
| | | | | | | | | | Fixes <https://bugs.gnu.org/31714>. Reported by Vagrant Cascadian <vagrant@debian.org> and Florian Pelz <pelzflorian@pelzflorian.de>. * gnu/system/mapped-devices.scm (check-device-initrd-modules): Pass LINUX-MODULES through 'normalize-module-name'. * gnu/build/linux-modules.scm (normalize-module-name): Export.
* gnu: emacs-racket-mode: Update and bug fix.Konrad Hinsen2018-06-14
| | | | | | | | | * gnu/packages/emacs.scm (emacs-racket-mode): Update and bug fix. - Update to the current commit - Bug fix: include Racket files in addition to Emacs Lisp files Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add vowpal-wabbit.Fis Trivial2018-06-14
| | | | | | * gnu/packages/machine-learning.scm (vowpal-wabbit): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add lightgbm.Fis Trivial2018-06-14
| | | | | | * gnu/packages/machine-learning.scm (lightgbm): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* self: Add 'guix-daemon' to the result.Ludovic Courtès2018-06-14
| | | | | | * gnu/packages/package-management.scm (guix-daemon): New variable. * guix/self.scm (whole-package): Add #:daemon and honor it. (compiled-guix): Pass #:daemon to 'whole-package'.
* gnu: libressl: Update to 2.7.4 [fixes CVE-2018-{0495,0732}].Gábor Boskovits2018-06-14
| | | | | | * gnu/packages/tls.scm (libressl): Update to 2.7.4. Signed-off-by: Leo Famulari <leo@famulari.name>
* gnu: botan: Update to 2.6.0 [fixes CVE-2018-{9127,9860}].Leo Famulari2018-06-14
| | | | * gnu/packages/crypto.scm (botan): Update to 2.6.0.
* gnu: vdirsyncer: Update to 0.6.6.Leo Famulari2018-06-14
| | | | | * gnu/packages/dav.scm (vdirsyncer): Update to 0.6.6. [arguments]: Simplify the man-page building.
* gnu: python-click-log: Update to 0.3.2.Leo Famulari2018-06-14
| | | | * gnu/packages/python.scm (python-click-log): Update to 0.3.2.
* gnu: GnuPG 1.4: Update to 1.4.23.Leo Famulari2018-06-14
| | | | | | | * gnu/packages/gnupg.scm (gnupg-1): Update to 1.4.23. [source]: Remove patch. * gnu/packages/patches/gnupg-1.4-CVE-2018-12020.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it.
* gnu: python-freezegun: Update to 0.3.10.Tobias Geerinckx-Rice2018-06-14
| | | | * gnu/packages/check.scm (python-freezegun): Update to 0.3.10.
* gnu: python-freezegun: Return #t from phase.Tobias Geerinckx-Rice2018-06-14
| | | | | * gnu/packages/check.scm (python-freezegun)[arguments]: Substitute INVOKE for SYSTEM*.
* gnu: cppcheck: Update to 1.84.Tobias Geerinckx-Rice2018-06-14
| | | | * gnu/packages/check.scm (cppcheck): Update to 1.84.
* gnu: qrencode: Update to 4.0.2.Tobias Geerinckx-Rice2018-06-14
| | | | * gnu/packages/aidc.scm (qrencode): Update to 4.0.2.
* gnu: perl-dbi: Update to 1.641.Tobias Geerinckx-Rice2018-06-14
| | | | * gnu/packages/databases.scm (perl-dbi): Update to 1.641.
* gnu: python-nose-timer: Update to 0.7.2.Tobias Geerinckx-Rice2018-06-14
| | | | | | | | * gnu/packages/check.scm (python-nose-timer): Update to 0.7.2. [source]: Remove patch... * gnu/packages/patches/python-nose-timer-drop-ordereddict.patch: ...delete file... * gnu/local.mk (dist_patch_DATA): ...and remove it.
* gnu: openrct2: Downgrade to 0.1.1.Rutger Helling2018-06-14
| | | | | | | | * gnu/packages/games.scm (openrct2): Downgrade to 0.1.1 due to audio not working on 0.1.2+. Needs fixing before upgrade. [arguments]: Add "-DDOWNLOAD_TITLE_SEQUENCES=OFF" configure-flag. Remove 'fixgcc7 and 'get-rid-of-errors phases. [native-inputs]: Remove gcc@7.
* gnu: emacs-password-store: Update to 1.7.2.Clément Lassieur2018-06-14
| | | | | * gnu/packages/emacs.scm (emacs-password-store): Update to 1.7.2. [propagated-inputs]: Add emacs-with-editor.
* gnu: password-store: Update to 1.7.2.Clément Lassieur2018-06-14
| | | | | | | * gnu/packages/password-utils.scm (password-store): Update to 1.7.2. [source]: Remove 'password-store-gnupg-compat.patch'. * gnu/packages/patches/password-store-gnupg-compat.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it.
* gnu: fio: Update to 3.7.Ricardo Wurmus2018-06-14
| | | | * gnu/packages/benchmark.scm (fio): Update to 3.7.
* gnu: Add minimap2.Ricardo Wurmus2018-06-14
| | | | * gnu/packages/bioinformatics.scm (minimap2): New variable.
* gnu: pigx-bsseq: Update to 0.0.9.Ricardo Wurmus2018-06-14
| | | | * gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.9.
* Remove 'guix-register' and its traces.Ludovic Courtès2018-06-14
| | | | | | | | | | | | | | | | | | | * Makefile.am (SH_TESTS): Remove tests/guix-register.sh. * build-aux/pre-inst-env.in (GUIX_REGISTER): Remove. * gnu/build/install.scm (directives): Remove outdated comment. * gnu/build/vm.scm (root-partition-initializer): Update comment. * gnu/packages/package-management.scm (guix-register): Remove. * guix/config.scm.in (%sbindir, %guix-register-program): Remove. * guix/scripts/system.scm (install): Adjust docstring. * guix/self.scm (make-config.scm): Remove #:guix. Do not generate %sbindir and %guix-register-program. (specification->package): Remove "guix". * nix/guix-register/guix-register.cc: Remove. * nix/libstore/store-api.cc (decodeValidPathInfo): Remove. * nix/libstore/store-api.hh (decodeValidPathInfo): Remove declaration. * nix/local.mk (sbin_PROGRAMS, guix_register_SOURCES) (guix_register_CPPFLAGS, guix_register_LDFLAGS): Remove. * tests/guix-register.sh: Remove.
* database: Allow for deterministic database construction.Ludovic Courtès2018-06-14
| | | | | | | | | | Fixes <https://bugs.gnu.org/21073>. * guix/store/database.scm (sqlite-register): Add #:time. (%epoch): New variable. (register-items): Add #:registration-time. Pass #:time to 'sqlite-register'. * gnu/build/install.scm (register-closure): Pass #:registration-time.
* install: Use 'reset-timestamps' from (guix store database).Ludovic Courtès2018-06-14
| | | | | * gnu/build/install.scm (reset-timestamps): Remove. * gnu/build/vm.scm: Use 'reset-timestamps' from (guix store database).
* database: Add 'register-items'.Ludovic Courtès2018-06-14
| | | | | | | | * guix/build/store-copy.scm (store-info): Export. * guix/store/database.scm (register-items): New procedure. (register-path): Implement in terms of 'register-items'. * gnu/build/install.scm (register-closure): Use 'register-items' instead of 'for-each' and 'register-path'.
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