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* gnu: python-click-log: Update to 0.3.2.•••* gnu/packages/python.scm (python-click-log): Update to 0.3.2. Leo Famulari2018-06-14
* 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 Famulari2018-06-14
* gnu: python-freezegun: Update to 0.3.10.•••* gnu/packages/check.scm (python-freezegun): Update to 0.3.10. Tobias Geerinckx-Rice2018-06-14
* gnu: python-freezegun: Return #t from phase.•••* gnu/packages/check.scm (python-freezegun)[arguments]: Substitute INVOKE for SYSTEM*. Tobias Geerinckx-Rice2018-06-14
* gnu: cppcheck: Update to 1.84.•••* gnu/packages/check.scm (cppcheck): Update to 1.84. Tobias Geerinckx-Rice2018-06-14
* gnu: qrencode: Update to 4.0.2.•••* gnu/packages/aidc.scm (qrencode): Update to 4.0.2. Tobias Geerinckx-Rice2018-06-14
* gnu: perl-dbi: Update to 1.641.•••* gnu/packages/databases.scm (perl-dbi): Update to 1.641. Tobias Geerinckx-Rice2018-06-14
* 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-Rice2018-06-14
* 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 Helling2018-06-14
* 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 Lassieur2018-06-14
* 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 Lassieur2018-06-14
* gnu: fio: Update to 3.7.•••* gnu/packages/benchmark.scm (fio): Update to 3.7. Ricardo Wurmus2018-06-14
* gnu: Add minimap2.•••* gnu/packages/bioinformatics.scm (minimap2): New variable. Ricardo Wurmus2018-06-14
* gnu: pigx-bsseq: Update to 0.0.9.•••* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.9. Ricardo Wurmus2018-06-14
* 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 Courtès2018-06-14
* 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 Courtès2018-06-14
* gnu: libgcrypt: Fix CVE-2018-0495.•••* gnu/packages/gnupg.scm (libgcrypt)[replacement]: New field. (libgcrypt/fixed): New package. Efraim Flashner2018-06-14
* gnu: Add python-dns-lexicon.•••* gnu/packages/python.scm (python-dns-lexicon, python2-dns-lexicon): New variables. Clément Lassieur2018-06-14
* gnu: Add python-pynamecheap.•••* gnu/packages/python.scm (python-pynamecheap, python2-pynamecheap): New variables. Clément Lassieur2018-06-14
* gnu: Add python-tldextract.•••* gnu/packages/python.scm (python-tldextract, python2-tldextract): New variables. Clément Lassieur2018-06-14
* gnu: Add python-requests-file.•••* gnu/packages/python.scm (python-requests-file, python2-requests-file): New variables. Clément Lassieur2018-06-14
* gnu: Add tmate.•••* gnu/packages/terminals.scm (tmate): New variable. Arun Isaac2018-06-14
* Fix typo in (gnu packages gtk) header.•••* gnu/packages/gtk.scm: Fix ‘Coypright’ typo. Tobias Geerinckx-Rice2018-06-14
* gnu: python-gnupg: Return #t from phase.•••* gnu/packages/gnupg.scm (python-gnupg)[arguments]: Substitute INVOKE for SYSTEM*. Tobias Geerinckx-Rice2018-06-14
* gnu: python-gnupg: Update to 0.4.3.•••* gnu/packages/gnupg.scm (python-gnupg): Update to 0.4.3. [arguments]: Remove obsolete substitution. Tobias Geerinckx-Rice2018-06-14
* gnu: sssd: Update to 1.16.2.•••* gnu/packages/sssd.scm (sssd): Update to 1.16.2. [native-inputs]: Add libxml2. Tobias Geerinckx-Rice2018-06-14
* gnu: pigx-scrnaseq: Update to 0.0.5.•••* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.5. [inputs]: Add python-magic. Ricardo Wurmus2018-06-13
* gnu: emacs-orgalist: Update to 1.8.•••* gnu/packages/emacs.scm (emacs-orgalist): Update to 1.8. Nicolas Goaziou2018-06-13
* gnu: emacspeak: Update to 48.0.•••* 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. Kei Kebreau2018-06-13
* gnu: r-factoextra: Fix syntax error.•••* gnu/packages/cran.scm (r-factoextra)[description]: Fix syntax error. Ricardo Wurmus2018-06-13
* gnu: r-seurat: Update to 2.3.2.•••* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.3.2. [propagated-inputs]: Add r-hdf5r. Ricardo Wurmus2018-06-13
* gnu: r-s4vectors: Update to 0.18.3.•••* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.18.3. Ricardo Wurmus2018-06-13
* gnu: r-biocviews: Update to 1.48.1.•••* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.1. Ricardo Wurmus2018-06-13
* gnu: r-rjson: Update to 0.2.20.•••* gnu/packages/web.scm (r-rjson): Update to 0.2.20. Ricardo Wurmus2018-06-13
* gnu: r-zoo: Update to 1.8-2.•••* gnu/packages/statistics.scm (r-zoo): Update to 1.8-2. Ricardo Wurmus2018-06-13
* gnu: r-rmarkdown: Update to 1.10.•••* gnu/packages/statistics.scm (r-rmarkdown): Update to 1.10. [propagated-inputs]: Add r-tinytex. Ricardo Wurmus2018-06-13
* gnu: r-highr: Update to 0.7.•••* gnu/packages/statistics.scm (r-highr): Update to 0.7. Ricardo Wurmus2018-06-13
* gnu: r-stringi: Update to 1.2.3.•••* gnu/packages/statistics.scm (r-stringi): Update to 1.2.3. Ricardo Wurmus2018-06-13
* gnu: r-munsell: Update to 0.5.0.•••* gnu/packages/statistics.scm (r-munsell): Update to 0.5.0. Ricardo Wurmus2018-06-13
* gnu: r-rgooglemaps: Update to 1.4.2.•••* gnu/packages/geo.scm (r-rgooglemaps): Update to 1.4.2. Ricardo Wurmus2018-06-13
* gnu: r-reticulate: Update to 1.8.•••* gnu/packages/cran.scm (r-reticulate): Update to 1.8. Ricardo Wurmus2018-06-13
* gnu: r-later: Update to 0.7.3.•••* gnu/packages/cran.scm (r-later): Update to 0.7.3. Ricardo Wurmus2018-06-13
* gnu: r-radiant-data: Update to 0.9.5.•••* gnu/packages/cran.scm (r-radiant-data): Update to 0.9.5. [propagated-inputs]: Remove r-plyr; add r-glue, r-plotly, r-readxl, r-rlang, and r-writexl. Ricardo Wurmus2018-06-13
* gnu: r-cubature: Update to 1.3-13.•••* gnu/packages/cran.scm (r-cubature): Update to 1.3-13. Ricardo Wurmus2018-06-13
* gnu: r-extradistr: Update to 1.8.9.•••* gnu/packages/cran.scm (r-extradistr): Update to 1.8.9. Ricardo Wurmus2018-06-13
* gnu: r-statnet-common: Update to 4.1.2.•••* gnu/packages/cran.scm (r-statnet-common): Update to 4.1.2. [propagated-inputs]: Add r-coda. Ricardo Wurmus2018-06-13
* gnu: r-stringdist: Update to 0.9.5.1.•••* gnu/packages/cran.scm (r-stringdist): Update to 0.9.5.1. Ricardo Wurmus2018-06-13
* gnu: r-rcpproll: Update to 0.3.0.•••* gnu/packages/cran.scm (r-rcpproll): Update to 0.3.0. Ricardo Wurmus2018-06-13
* gnu: r-extremes: Update to 2.0-9.•••* gnu/packages/cran.scm (r-extremes): Update to 2.0-9. Ricardo Wurmus2018-06-13
* gnu: r-sp: Update to 1.3-1.•••* gnu/packages/cran.scm (r-sp): Update to 1.3-1. Ricardo Wurmus2018-06-13