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* gnu: spice-protocol: Update to 0.12.14.•••* gnu/packages/spice.scm (spice-protocol): Update to 0.12.14. Tobias Geerinckx-Rice2018-06-151-2/+2
* gnu: python-pyrfc3339: Update to 1.1.•••* gnu/packages/time.scm (python-pyrfc3339): Update to 1.1. Tobias Geerinckx-Rice2018-06-151-2/+2
* gnu: gource: Update to 0.49.•••* gnu/packages/version-control.scm (gource): Update to 0.49. Tobias Geerinckx-Rice2018-06-151-2/+2
* gnu: perl-xml-libxml-simple: Update to 0.99.•••* gnu/packages/xml.scm (perl-xml-libxml-simple): Update to 0.99. Tobias Geerinckx-Rice2018-06-151-2/+2
* gnu: fcitx-configtool: Update to 0.4.10.•••* gnu/packages/fcitx.scm (fcitx-configtool): Update to 0.4.10. Tobias Geerinckx-Rice2018-06-151-2/+2
* gnu: fcitx: Update to 4.2.9.6.•••* gnu/packages/fcitx.scm (fcitx): Update to 4.2.9.6. [native-inputs]: Add extra-cmake-modules. Tobias Geerinckx-Rice2018-06-151-3/+9
* gnu: fcitx: Use HTTPS home page.•••* gnu/packages/fcitx.scm (fcitx)[home-page]: Use HTTPS. Tobias Geerinckx-Rice2018-06-151-1/+1
* gnu: perl-xml-xpath: Update to 1.42.•••* gnu/packages/xml.scm (perl-xml-xpath): Update to 1.42. Tobias Geerinckx-Rice2018-06-151-2/+2
* gnu: perl-xml-xpath: Propagate inputs.•••* gnu/packages/xml.scm (perl-xml-xpath)[inputs]: Rename this... [propagated-inputs]: ...to this. Tobias Geerinckx-Rice2018-06-151-1/+1
* gnu: perl-xml-atom: Propagate inputs.•••* gnu/packages/xml.scm (perl-xml-atom)[inputs]: Rename to... [propagated-inputs]: ...this, and... [native-inputs]: ...remove duplicate packages from here. Tobias Geerinckx-Rice2018-06-151-6/+4
* gnu: nickle: Update to 2.81.•••* gnu/packages/nickle.scm (nickle): Update to 2.81. Tobias Geerinckx-Rice2018-06-151-2/+3
* gnu: r-cubature: Update to 1.4.•••* gnu/packages/cran.scm (r-cubature): Update to 1.4. Tobias Geerinckx-Rice2018-06-151-2/+2
* gnu: neofetch: Update to 4.0.2.•••* gnu/packages/admin.scm (neofetch): Update to 4.0.2. Rutger Helling2018-06-151-2/+3
* gnu: Add r-genomicinteractions.•••* gnu/packages/bioconductor.scm (r-genomicinteractions): New variable. Ricardo Wurmus2018-06-151-2/+42
* gnu: Add r-interactionset.•••* gnu/packages/bioconductor.scm (r-interactionset): New variable. Ricardo Wurmus2018-06-151-0/+32
* gnu: innoextract: Update to 1.7.•••* gnu/packages/compression.scm (innoextract): Update to 1.7. Rutger Helling2018-06-151-2/+2
* gnu: Add r-riboseqr.•••* gnu/packages/bioconductor.scm (r-riboseqr): New variable. Ricardo Wurmus2018-06-151-0/+28
* gnu: Add r-riboprofiling.•••* gnu/packages/bioconductor.scm (r-riboprofiling): New variable. Ricardo Wurmus2018-06-151-0/+39
* gnu: Add r-chipcomp.•••* gnu/packages/bioconductor.scm (r-chipcomp): New variable. Ricardo Wurmus2018-06-151-0/+34
* gnu: Add r-bsgenome-mmusculus-ucsc-mm9-masked.•••* gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm9-masked): New variable. Ricardo Wurmus2018-06-151-0/+35
* gnu: Add r-bsgenome-hsapiens-ucsc-hg19-masked.•••* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19-masked): New variable. Ricardo Wurmus2018-06-151-0/+35
* gnu: Add r-bsgenome-dmelanogaster-ucsc-dm3-masked.•••* gnu/packages/bioconductor.scm (r-bsgenome-dmelanogaster-ucsc-dm3-masked): New variable. Ricardo Wurmus2018-06-151-0/+35
* gnu: Add r-bayseq.•••* gnu/packages/bioconductor.scm (r-bayseq): New variable. Ricardo Wurmus2018-06-151-0/+26
* gnu: certbot, python-acme: Update to 0.25.1.•••* 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. Leo Famulari2018-06-141-3/+5
* gnu: Go 1.10: Update to 1.10.3.•••* gnu/packages/golang.scm (go-1.10): Update to 1.10.3. Leo Famulari2018-06-141-2/+2
* gnu: Go 1.9: Update to 1.9.7.•••* gnu/packages/golang.scm (go-1.9): Update to 1.9.7. Leo Famulari2018-06-141-2/+2
* gnu: emacs-racket-mode: Update and bug fix.•••* 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> Konrad Hinsen2018-06-141-3/+5
* gnu: Add vowpal-wabbit.•••* gnu/packages/machine-learning.scm (vowpal-wabbit): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Fis Trivial2018-06-141-0/+29
* gnu: Add lightgbm.•••* gnu/packages/machine-learning.scm (lightgbm): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Fis Trivial2018-06-141-0/+47
* self: Add 'guix-daemon' to the result.•••* 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'. Ludovic Courtès2018-06-141-0/+47
* gnu: libressl: Update to 2.7.4 [fixes CVE-2018-{0495,0732}].•••* gnu/packages/tls.scm (libressl): Update to 2.7.4. Signed-off-by: Leo Famulari <leo@famulari.name> Gábor Boskovits2018-06-141-2/+2
* gnu: botan: Update to 2.6.0 [fixes CVE-2018-{9127,9860}].•••* gnu/packages/crypto.scm (botan): Update to 2.6.0. Leo Famulari2018-06-141-2/+2
* gnu: vdirsyncer: Update to 0.6.6.•••* gnu/packages/dav.scm (vdirsyncer): Update to 0.6.6. [arguments]: Simplify the man-page building. Leo Famulari2018-06-141-3/+2
* gnu: python-click-log: Update to 0.3.2.•••* gnu/packages/python.scm (python-click-log): Update to 0.3.2. Leo Famulari2018-06-141-2/+2
* gnu: GnuPG 1.4: Update to 1.4.23.•••* 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. Leo Famulari2018-06-142-53/+2
* gnu: python-freezegun: Update to 0.3.10.•••* gnu/packages/check.scm (python-freezegun): Update to 0.3.10. Tobias Geerinckx-Rice2018-06-141-2/+2
* gnu: python-freezegun: Return #t from phase.•••* gnu/packages/check.scm (python-freezegun)[arguments]: Substitute INVOKE for SYSTEM*. Tobias Geerinckx-Rice2018-06-141-1/+1
* gnu: cppcheck: Update to 1.84.•••* gnu/packages/check.scm (cppcheck): Update to 1.84. Tobias Geerinckx-Rice2018-06-141-2/+2
* gnu: qrencode: Update to 4.0.2.•••* gnu/packages/aidc.scm (qrencode): Update to 4.0.2. Tobias Geerinckx-Rice2018-06-141-2/+3
* gnu: perl-dbi: Update to 1.641.•••* gnu/packages/databases.scm (perl-dbi): Update to 1.641. Tobias Geerinckx-Rice2018-06-141-2/+2
* gnu: python-nose-timer: Update to 0.7.2.•••* 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. Tobias Geerinckx-Rice2018-06-142-51/+2
* gnu: openrct2: Downgrade to 0.1.1.•••* 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. Rutger Helling2018-06-141-18/+8
* gnu: emacs-password-store: Update to 1.7.2.•••* gnu/packages/emacs.scm (emacs-password-store): Update to 1.7.2. [propagated-inputs]: Add emacs-with-editor. Clément Lassieur2018-06-141-2/+3
* gnu: password-store: Update to 1.7.2.•••* 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. Clément Lassieur2018-06-142-31/+2
* gnu: fio: Update to 3.7.•••* gnu/packages/benchmark.scm (fio): Update to 3.7. Ricardo Wurmus2018-06-141-5/+5
* gnu: Add minimap2.•••* gnu/packages/bioinformatics.scm (minimap2): New variable. Ricardo Wurmus2018-06-141-0/+59
* gnu: pigx-bsseq: Update to 0.0.9.•••* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.9. Ricardo Wurmus2018-06-141-2/+2
* Remove 'guix-register' and its traces.•••* 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. Ludovic Courtès2018-06-141-36/+0
* build: Require Guile-SQLite3.•••The next commits make (sqlite3) an indirect dependency of (gnu build install), which is itself used by (guix scripts system), hence this new requirement. * configure.ac: Error out when $guix_cv_have_recent_guile_sqlite3 is false. Remove HAVE_GUILE_SQLITE3 Automake conditional. * Makefile.am (MODULES, SCM_TESTS): Remove HAVE_GUILE_SQLITE3 conditions. * doc/guix.texi (Requirements): Add Guile-SQLite3. * README: Ditto. * gnu/packages/package-management.scm (guix)[propagated-inputs]: Add GUILE-SQLITE3. [arguments]: In 'wrap-program' phase, take guile-sqlite3 into account. Ludovic Courtès2018-06-141-1/+3
* gnu: libgcrypt: Fix CVE-2018-0495.•••* gnu/packages/gnupg.scm (libgcrypt)[replacement]: New field. (libgcrypt/fixed): New package. Efraim Flashner2018-06-141-0/+14
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