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* gnu: dbus: Fix CVE-2019-12749.Marius Bakke2019-06-20
| | | | | | | * 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.
* gnu: pigx-rnaseq: Update to 0.0.7.Ricardo Wurmus2019-06-20
| | | | | * gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.7. [inputs]: Add coreutils and sed.
* licenses: Add Historical Permission Notice and Disclaimer licenseGiovanni Biscuolo2019-06-20
| | | | * gnu/licenses.scm (hpnd): New variable.
* gnu: Add iml.Andreas Enge2019-06-20
| | | | * gnu/packages/algebra.scm (iml): New variable.
* gnu: Add ppl.Andreas Enge2019-06-20
| | | | * gnu/packages/maths.scm (ppl): New variable.
* services: opensmtpd: Extend the PAM service.Kristofer Buffington2019-06-20
| | | | | | | | * 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>
* gnu: ngs-sdk: Update to 2.9.6.Ricardo Wurmus2019-06-20
| | | | * gnu/packages/bioinformatics.scm (ngs-sdk): Update to 2.9.6.
* gnu: sra-tools: Update to 2.9.6.Ricardo Wurmus2019-06-20
| | | | * gnu/packages/bioinformatics.scm (sra-tools): Update to 2.9.6.
* gnu: ncbi-vdb: Update to 2.9.6.Ricardo Wurmus2019-06-20
| | | | | * gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.9.6. [arguments]: Pass HAVE_HDF5 make flag; add build phase "patch-krypto-flags".
* import: hackage: Add two expected failing test cases.Robert Vollmert2019-06-20
| | | | | | | | | | | 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>
* utils: canonical-newline-port: Fix handling of carriage return at buffer end.Robert Vollmert2019-06-20
| | | | | | | | | | | | | 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>
* gnu: guile: Add 2.2.5.Ludovic Courtès2019-06-20
| | | | * gnu/packages/guile.scm (guile-2.2.5): New variable.
* gnu: python-jupyter-console: Update to 6.0.0.Ricardo Wurmus2019-06-20
| | | | | | | * 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.
* gnu: python2-jupyter-console: Split from python-jupyter-console.Ricardo Wurmus2019-06-20
| | | | | * gnu/packages/python-xyz.scm (python2-jupyter-console): Implement without package-with-python2.
* Revert "gnu: Add libgd."Nicolas Goaziou2019-06-20
| | | | This reverts commit 059e4c9a15b52f7e4b262e3317eac238bf53103d.
* gnu: Add lrcalc.Andreas Enge2019-06-20
| | | | * gnu/packages/algebra.scm (lrcalc): New variable.
* gnu: Add eclib.Andreas Enge2019-06-20
| | | | * gnu/packages/algebra.scm (eclib): New variable.
* gnu: Add m4rie.Andreas Enge2019-06-20
| | | | * gnu/packages/algebra.scm (m4rie): New variable.
* gnu: weechat: update to 2.5Josh Holland2019-06-20
| | | | | | * gnu/packages/irc.scm (weechat): update to 2.5 Signed-off-by: Gábor Boskovits <boskovits@gmail.com>
* gnu: Add python-fpylll.Nicolas Goaziou2019-06-20
| | | | * gnu/packages/algebra.scm (python-fpylll): New variable.
* gnu: fplll: Update to 5.2.1.Nicolas Goaziou2019-06-20
| | | | | | | | * 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.
* services: Fix typo in (gnu services mail) exports.Tobias Geerinckx-Rice2019-06-20
| | | | | * gnu/services/mail.scm (define-module): Re-spell ‘%default-imap4d-config-file’.
* gnu: Add symmetrica.Nicolas Goaziou2019-06-20
| | | | | | | | | * 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.
* gnu: zathura: Install icons.Alex Griffin2019-06-20
| | | | | | | * gnu/packages/pdf.scm (zathura)[native-inputs]: Add librsvg to build and install the application icons. Signed-off-by: Gábor Boskovits <boskovits@gmail.com>
* gnu: Add libgd.Nicolas Goaziou2019-06-20
| | | | * gnu/packages/image.scm (libgd): New variable.
* gnu: Move ratpoints into a different module.Nicolas Goaziou2019-06-20
| | | | | * gnu/packages/maths.scm (ratpoints): Move... * gnu/packages/algebra.scm: ...here.
* gnu: spdlog: Clarify license.Meiyo Peng2019-06-20
| | | | | | | * gnu/packages/logging.scm (spdlog): Clarify license of the bundled fmt library. Signed-off-by: Gábor Boskovits <boskovits@gmail.com>
* gnu: bind: Update to 9.14.3 [fixes CVE-2019-6471].Tobias Geerinckx-Rice2019-06-20
| | | | * gnu/packages/dns.scm (isc-bind): Update to 9.14.3.
* gnu: zn_poly: Rename to zn-poly, according to our naming conventions.Andreas Enge2019-06-20
| | | | | | | | 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.
* gnu: Add brial.Andreas Enge2019-06-19
| | | | * gnu/packages/sagemath.scm (brial): New variable.
* gnu: Add m4ri.Andreas Enge2019-06-19
| | | | * gnu/packages/algebra.scm (m4ri): New variable.
* gnu: Add crispy-doom.Dan Frumin2019-06-19
| | | | | | * gnu/packages/games.scm (crispy-doom): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: emacs-unpackaged-el: Add patch for missing require statement.Brian Leung2019-06-19
| | | | | | | | * 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>
* gnu: Add numix-theme.Giacomo Leidi2019-06-19
| | | | | | * gnu/packages/gnome.scm (numix-theme): New variable Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* grafts: Avoid 'query-valid-derivers' RPC.Ludovic Courtès2019-06-19
| | | | | | | | | | | | | | | | | | | | 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'.
* derivations: Add 'derivation-input-derivation'.Ludovic Courtès2019-06-19
| | | | | * guix/derivations.scm (derivation-input-derivation): New procedure. (derivation-prerequisites): Use it.
* gnu: Add python-pandocfilters.Nicolas Goaziou2019-06-19
| | | | * gnu/packages/textutils.scm (python-pandocfilters): New variable.
* gnu: Add ratpoints.Nicolas Goaziou2019-06-19
| | | | | | * 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.
* gnu: Add gf2x.Andreas Enge2019-06-19
| | | | * gnu/packages/algebra.scm (gf2x): New variable.
* gnu: Add zn_poly.Andreas Enge2019-06-19
| | | | * gnu/packages/sagemath.scm (zn_poly): New variable.
* gnu: Add pynac.Andreas Enge2019-06-19
| | | | * gnu/packages/sagemath.scm (pynac): New variable.
* gnu: python-gmpy2: Update to 2.1.0b1.Andreas Enge2019-06-19
| | | | | | | 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.
* gnu: balsa: Update to 2.5.7.Tobias Geerinckx-Rice2019-06-19
| | | | | * gnu/packages/mail.scm (balsa): Update to 2.5.7. [inputs]: Build with gtksourceview@3.
* gnu: nano: Update to 4.3.Tobias Geerinckx-Rice2019-06-19
| | | | * gnu/packages/nano.scm (nano): Update to 4.3.
* gnu: notmuch: Update to 0.29.1.Tobias Geerinckx-Rice2019-06-19
| | | | * gnu/packages/mail.scm (notmuch): Update to 0.29.1.
* gnu: mpd: Update to 0.21.10.Tobias Geerinckx-Rice2019-06-19
| | | | * gnu/packages/mpd.scm (mpd): Update to 0.21.10.
* gnu: perl-xml-sax: Update to 1.02.Tobias Geerinckx-Rice2019-06-19
| | | | * gnu/packages/xml.scm (perl-xml-sax): Update to 1.02.
* gnu: shadow: Update home page.Tobias Geerinckx-Rice2019-06-19
| | | | * gnu/packages/admin.scm (shadow)[home-page]: Update to new project home.
* gnu: shadow: Update to 4.7.Tobias Geerinckx-Rice2019-06-19
| | | | * gnu/packages/admin.scm (shadow): Update to 4.7.
* gnu: ansible: Update to 2.8.1.Tobias Geerinckx-Rice2019-06-19
| | | | * gnu/packages/admin.scm (ansible): Update to 2.8.1.
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