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2019-06-20gnu: dbus: Fix CVE-2019-12749.Marius Bakke
* gnu/packages/patches/dbus-CVE-2019-12749.patch: New file. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. * gnu/packages/glib.scm (dbus)[replacement]: New field. (dbus/fixed): New variable.
2019-06-20gnu: pigx-rnaseq: Update to 0.0.7.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.7. [inputs]: Add coreutils and sed.
2019-06-20licenses: Add Historical Permission Notice and Disclaimer licenseGiovanni Biscuolo
* gnu/licenses.scm (hpnd): New variable.
2019-06-20gnu: Add iml.Andreas Enge
* gnu/packages/algebra.scm (iml): New variable.
2019-06-20gnu: Add ppl.Andreas Enge
* gnu/packages/maths.scm (ppl): New variable.
2019-06-20services: opensmtpd: Extend the PAM service.Kristofer Buffington
* gnu/services/mail.scm (%opensmtpd-pam-services): New variable. (opensmtpd-service-type)[extensions]: Add it, extending PAM-ROOT-SERVICE-TYPE. Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>
2019-06-20gnu: ngs-sdk: Update to 2.9.6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 2.9.6.
2019-06-20gnu: sra-tools: Update to 2.9.6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.9.6.
2019-06-20gnu: ncbi-vdb: Update to 2.9.6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.9.6. [arguments]: Pass HAVE_HDF5 make flag; add build phase "patch-krypto-flags".
2019-06-20import: hackage: Add two expected failing test cases.Robert Vollmert
This adds failing test cases for two hackage import bugs: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=25138 https://debbugs.gnu.org/cgi/bugreport.cgi?bug=35743 * tests/hackage.scm: Make comment style consistent. Add two cabal parsing tests, marked as expected failures. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2019-06-20utils: canonical-newline-port: Fix handling of carriage return at buffer end.Robert Vollmert
Prior to this change the added test fails for me locally at byte 1024. It might depend on some default buffer sizes. Fixes <https://bugs.gnu.org/35863>. * tests/utils.scm ("canonical-newline-port-1024"): Add test. * guix/utils.scm (canonical-newline-port): Correct comments on CR/LF. Remove CR even when they're at the end of the buffer. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2019-06-20gnu: guile: Add 2.2.5.Ludovic Courtès
* gnu/packages/guile.scm (guile-2.2.5): New variable.
2019-06-20gnu: python-jupyter-console: Update to 6.0.0.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-jupyter-console): Update to 6.0.0. [arguments]: Enable tests. [propagated-inputs]: Replace python-prompt-toolkit-1 with python-prompt-toolkit.
2019-06-20gnu: python2-jupyter-console: Split from python-jupyter-console.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python2-jupyter-console): Implement without package-with-python2.
2019-06-20Revert "gnu: Add libgd."Nicolas Goaziou
This reverts commit 059e4c9a15b52f7e4b262e3317eac238bf53103d.
2019-06-20gnu: Add lrcalc.Andreas Enge
* gnu/packages/algebra.scm (lrcalc): New variable.
2019-06-20gnu: Add eclib.Andreas Enge
* gnu/packages/algebra.scm (eclib): New variable.
2019-06-20gnu: Add m4rie.Andreas Enge
* gnu/packages/algebra.scm (m4rie): New variable.
2019-06-20gnu: weechat: update to 2.5Josh Holland
* gnu/packages/irc.scm (weechat): update to 2.5 Signed-off-by: Gábor Boskovits <boskovits@gmail.com>
2019-06-20gnu: Add python-fpylll.Nicolas Goaziou
* gnu/packages/algebra.scm (python-fpylll): New variable.
2019-06-20gnu: fplll: Update to 5.2.1.Nicolas Goaziou
* gnu/packages/algebra.scm (fplll): Update to 5.2.1. [source]: Use Github tagged release: the original tarball no longer exists. [native-inputs]: Add Autoconf and al. [homepage]: Update it, the previous one no longer exists. [description]: Expound description.
2019-06-20services: Fix typo in (gnu services mail) exports.Tobias Geerinckx-Rice
* gnu/services/mail.scm (define-module): Re-spell ‘%default-imap4d-config-file’.
2019-06-20gnu: Add symmetrica.Nicolas Goaziou
* gnu/packages/algebra.scm (symmetrica): New variable. * gnu/packages/patches/symmetrica-bruch.patch: * gnu/packages/patches/symmetrica-int32.patch: * gnu/packages/patches/symmetrica-return_values.patch: * gnu/packages/patches/symmetrica-sort_sum_rename.patch: New files. * gnu/local.mk (dist_patch_DATA): Add patches.
2019-06-20gnu: zathura: Install icons.Alex Griffin
* gnu/packages/pdf.scm (zathura)[native-inputs]: Add librsvg to build and install the application icons. Signed-off-by: Gábor Boskovits <boskovits@gmail.com>
2019-06-20gnu: Add libgd.Nicolas Goaziou
* gnu/packages/image.scm (libgd): New variable.
2019-06-20gnu: Move ratpoints into a different module.Nicolas Goaziou
* gnu/packages/maths.scm (ratpoints): Move... * gnu/packages/algebra.scm: ...here.
2019-06-20gnu: spdlog: Clarify license.Meiyo Peng
* gnu/packages/logging.scm (spdlog): Clarify license of the bundled fmt library. Signed-off-by: Gábor Boskovits <boskovits@gmail.com>
2019-06-20gnu: bind: Update to 9.14.3 [fixes CVE-2019-6471].Tobias Geerinckx-Rice
* gnu/packages/dns.scm (isc-bind): Update to 9.14.3.
2019-06-20gnu: zn_poly: Rename to zn-poly, according to our naming conventions.Andreas Enge
Reported by Nicolas Goaziou <mail@nicolasgoaziou.fr>. This is a follow-up to commit 01822e3ebf24031d6438fc4e7ad3a869ea12fdf4. * gnu/packages/sagemath.scm (zn_poly): Rename to... * gnu/packages/sagemath.scm (zn-poly): ...this.
2019-06-19gnu: Add brial.Andreas Enge
* gnu/packages/sagemath.scm (brial): New variable.
2019-06-19gnu: Add m4ri.Andreas Enge
* gnu/packages/algebra.scm (m4ri): New variable.
2019-06-19gnu: Add crispy-doom.Dan Frumin
* gnu/packages/games.scm (crispy-doom): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2019-06-19gnu: emacs-unpackaged-el: Add patch for missing require statement.Brian Leung
* gnu/packages/emacs-xyz.scm (emacs-unpackaged-el)[source]: Add patch. * gnu/packages/patches/emacs-unpackaged-req.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2019-06-19gnu: Add numix-theme.Giacomo Leidi
* gnu/packages/gnome.scm (numix-theme): New variable Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2019-06-19grafts: Avoid 'query-valid-derivers' RPC.Ludovic Courtès
Previously we'd make 502 'query-valid-derivers' RPCs for "guix build vim -d", and after this patch, we don't do any. Furthermore, the previous strategy was "stateful" in the sense that 'item->deriver' could return a derivation that is not the one that was actually computed by this process, but an "equivalent" one (due to fixed-output derivations); which one is chosen would depend on the state of the store. This in turn means that we'd have to call 'read-derivation-from-file' to actually read .drv files (as opposed to getting them from %DERIVATION-CACHE). This is costly and doesn't work with GUIX_DAEMON_SOCKET=ssh://…. * guix/grafts.scm (item->deriver): Remove. (reference-origin): New procedure. (cumulative-grafts): Use it instead of 'item->deriver'.
2019-06-19derivations: Add 'derivation-input-derivation'.Ludovic Courtès
* guix/derivations.scm (derivation-input-derivation): New procedure. (derivation-prerequisites): Use it.
2019-06-19gnu: Add python-pandocfilters.Nicolas Goaziou
* gnu/packages/textutils.scm (python-pandocfilters): New variable.
2019-06-19gnu: Add ratpoints.Nicolas Goaziou
* gnu/packages/maths.scm (ratpoints): New variable. * gnu/packages/patches/ratpoints-sturm_and_rp_private.patch: New file. * gnu/local.mk (dist_patch_DATA): Reference patch.
2019-06-19gnu: Add gf2x.Andreas Enge
* gnu/packages/algebra.scm (gf2x): New variable.
2019-06-19gnu: Add zn_poly.Andreas Enge
* gnu/packages/sagemath.scm (zn_poly): New variable.
2019-06-19gnu: Add pynac.Andreas Enge
* gnu/packages/sagemath.scm (pynac): New variable.
2019-06-19gnu: python-gmpy2: Update to 2.1.0b1.Andreas Enge
The gmpy2 package has become a standard package in sage-8.7, and the latest stable release is too old. * gnu/packages/sagemath.scm (python-gmpy2): Update to 2.1.0b1.
2019-06-19gnu: balsa: Update to 2.5.7.Tobias Geerinckx-Rice
* gnu/packages/mail.scm (balsa): Update to 2.5.7. [inputs]: Build with gtksourceview@3.
2019-06-19gnu: nano: Update to 4.3.Tobias Geerinckx-Rice
* gnu/packages/nano.scm (nano): Update to 4.3.
2019-06-19gnu: notmuch: Update to 0.29.1.Tobias Geerinckx-Rice
* gnu/packages/mail.scm (notmuch): Update to 0.29.1.
2019-06-19gnu: mpd: Update to 0.21.10.Tobias Geerinckx-Rice
* gnu/packages/mpd.scm (mpd): Update to 0.21.10.
2019-06-19gnu: perl-xml-sax: Update to 1.02.Tobias Geerinckx-Rice
* gnu/packages/xml.scm (perl-xml-sax): Update to 1.02.
2019-06-19gnu: shadow: Update home page.Tobias Geerinckx-Rice
* gnu/packages/admin.scm (shadow)[home-page]: Update to new project home.
2019-06-19gnu: shadow: Update to 4.7.Tobias Geerinckx-Rice
* gnu/packages/admin.scm (shadow): Update to 4.7.
2019-06-19gnu: ansible: Update to 2.8.1.Tobias Geerinckx-Rice
* gnu/packages/admin.scm (ansible): Update to 2.8.1.
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