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* 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.
* 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.
* build: Require Guile-SQLite3.Ludovic Courtès2018-06-14
| | | | | | | | | | | | | | | 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.
* gnu: libgcrypt: Fix CVE-2018-0495.Efraim Flashner2018-06-14
| | | | | * gnu/packages/gnupg.scm (libgcrypt)[replacement]: New field. (libgcrypt/fixed): New package.
* gnu: Add python-dns-lexicon.Clément Lassieur2018-06-14
| | | | | * gnu/packages/python.scm (python-dns-lexicon, python2-dns-lexicon): New variables.
* gnu: Add python-pynamecheap.Clément Lassieur2018-06-14
| | | | | * gnu/packages/python.scm (python-pynamecheap, python2-pynamecheap): New variables.
* gnu: Add python-tldextract.Clément Lassieur2018-06-14
| | | | | * gnu/packages/python.scm (python-tldextract, python2-tldextract): New variables.
* gnu: Add python-requests-file.Clément Lassieur2018-06-14
| | | | | * gnu/packages/python.scm (python-requests-file, python2-requests-file): New variables.
* gnu: Add tmate.Arun Isaac2018-06-14
| | | | * gnu/packages/terminals.scm (tmate): New variable.
* Fix typo in (gnu packages gtk) header.Tobias Geerinckx-Rice2018-06-14
| | | | * gnu/packages/gtk.scm: Fix ‘Coypright’ typo.
* gnu: python-gnupg: Return #t from phase.Tobias Geerinckx-Rice2018-06-14
| | | | | * gnu/packages/gnupg.scm (python-gnupg)[arguments]: Substitute INVOKE for SYSTEM*.
* gnu: python-gnupg: Update to 0.4.3.Tobias Geerinckx-Rice2018-06-14
| | | | | * gnu/packages/gnupg.scm (python-gnupg): Update to 0.4.3. [arguments]: Remove obsolete substitution.
* gnu: sssd: Update to 1.16.2.Tobias Geerinckx-Rice2018-06-14
| | | | | * gnu/packages/sssd.scm (sssd): Update to 1.16.2. [native-inputs]: Add libxml2.
* gnu: pigx-scrnaseq: Update to 0.0.5.Ricardo Wurmus2018-06-13
| | | | | * gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.5. [inputs]: Add python-magic.
* gnu: emacs-orgalist: Update to 1.8.Nicolas Goaziou2018-06-13
| | | | * gnu/packages/emacs.scm (emacs-orgalist): Update to 1.8.
* gnu: emacspeak: Update to 48.0.Kei Kebreau2018-06-13
| | | | | | | | * gnu/packages/emacs.scm (emacspeak): Update to 48.0. [arguments]: Use 'invoke'. In the 'install' phase, add additional installation directories and fix the launch script substitution. [inputs]: Add emacs and perl. [native-inputs]: Remove emacs-minimal.
* gnu: r-factoextra: Fix syntax error.Ricardo Wurmus2018-06-13
| | | | * gnu/packages/cran.scm (r-factoextra)[description]: Fix syntax error.
* gnu: r-seurat: Update to 2.3.2.Ricardo Wurmus2018-06-13
| | | | | * gnu/packages/bioinformatics.scm (r-seurat): Update to 2.3.2. [propagated-inputs]: Add r-hdf5r.
* gnu: r-s4vectors: Update to 0.18.3.Ricardo Wurmus2018-06-13
| | | | * gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.18.3.
* gnu: r-biocviews: Update to 1.48.1.Ricardo Wurmus2018-06-13
| | | | * gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.1.
* gnu: r-rjson: Update to 0.2.20.Ricardo Wurmus2018-06-13
| | | | * gnu/packages/web.scm (r-rjson): Update to 0.2.20.
* gnu: r-zoo: Update to 1.8-2.Ricardo Wurmus2018-06-13
| | | | * gnu/packages/statistics.scm (r-zoo): Update to 1.8-2.
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