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* gnu: rclone: Update to 1.48.0.Tobias Geerinckx-Rice2019-06-21
| | | | * gnu/packages/sync.scm (rclone): Update to 1.48.0.
* gnu: Move ratpoints into "sagemath.scm"Nicolas Goaziou2019-06-21
| | | | | * gnu/packages/algebra.scm (ratpoints): Move package from here... * gnu/packages/sagemath.scm (ratpoints): ... to here.
* gnu: Add openjdk12.Gábor Boskovits2019-06-21
| | | | * gnu/packages/java.scm(openjdk12): New variable.
* gnu: emacs-fish-completion: Update to 1.1.Pierre Neidhardt2019-06-21
| | | | * gnu/packages/emacs-xyz.scm (emacs-fish-completion): Update to 1.1.
* gnu: zn-poly: Install all libraries.Andreas Enge2019-06-21
| | | | | * gnu/packages/sagemath.scm (zn-poly): Install the static and the dynamic library with its symlinks, and end a phase with #t.
* gnu: khmer: Update to 3.0.0a3.Ricardo Wurmus2019-06-21
| | | | | | | | * gnu/packages/bioinformatics.scm (khmer): Update to 3.0.0a3. [source]: Remove patch; remove seqan in snippet. [inputs]: Add seqan-1. * gnu/packages/patches/khmer-use-libraries.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it.
* gnu: icecat: Update to 60.7.2-guix1 [security fixes].Mark H Weaver2019-06-21
| | | | | | | Includes fixes for CVE-2019-11707 and CVE-2019-11708. * gnu/packages/gnuzilla.scm (%icecat-version): Update to 60.7.2-guix1. (icecat-source)[upstream-firefox-source]: Update hash.
* gnu: ungoogled-chromium: Increase build timeout.Marius Bakke2019-06-21
| | | | * gnu/packages/chromium.scm (ungoogled-chromium)[properties]: New field.
* gnu: linux-libre: Update to 5.1.12.Mark H Weaver2019-06-21
| | | | | * gnu/packages/linux.scm (%linux-libre-version): Update to 5.1.12. (%linux-libre-hash): Update hash.
* gnu: linux-libre@4.19: Update to 4.19.53.Mark H Weaver2019-06-21
| | | | | * gnu/packages/linux.scm (%linux-libre-4.19-version): Update to 4.19.53. (%linux-libre-4.19-hash): Update hash.
* gnu: linux-libre@4.14: Update to 4.14.128.Mark H Weaver2019-06-21
| | | | | * gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.128. (%linux-libre-4.14-hash): Update hash.
* gnu: ratpoints: Generate position-independent code.Andreas Enge2019-06-21
| | | | * gnu/packages/algebra.scm (ratpoints): Add "CCFLAGS=-fPIC" to make flags.
* gnu: symmetrica: Generate position-independent code.Andreas Enge2019-06-21
| | | | * gnu/packages/algebra.scm (symmetrica): Add -fPIC compiler flag.
* gnu: iml: Enable shared library.Andreas Enge2019-06-21
| | | | * gnu/packages/algebra.scm (iml): Add configure flag --enable-shared.
* gnu: Add lcalc.Andreas Enge2019-06-21
| | | | | | | | | * gnu/packages/sagemath.scm (lcalc): New variable. * gnu/packages/patches/lcalc-default-parameters-1.patch, gnu/packages/patches/lcalc-default-parameters-2.patch, gnu/packages/patches/lcalc-lcommon-h.patch, gnu/packages/patches/lcalc-using-namespace-std.patch: New files. * gnu/local.mk (dist_patch_DATA): Register patches.
* gnu: lrcalc: Add a patch for identifying include files.Andreas Enge2019-06-21
| | | | | | * gnu/packages/patches/lrcalc-includes.patch: New file. * gnu/packages/algebra.scm (lrcalc): Use patch. * gnu/local.mk (dist_patch_DATA): Register patch.
* gnu: python-mpi4py: Update to 3.0.2.Paul Garlick2019-06-21
| | | | | | * gnu/packages/mpi.scm (python-mpi4py): Update to 3.0.2. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: ungoogled-chromium: Disable parallel build.Marius Bakke2019-06-20
| | | | | * gnu/packages/chromium.scm (ungoogled-chromium)[arguments]: Set #:parallel-build? #f. Adjust 'build' phase to account for it.
* gnu: samba: Update to 4.10.5 [fixes CVE-2019-12435, CVE-2019-12436].Marius Bakke2019-06-20
| | | | * gnu/packages/samba.scm (samba): Update to 4.10.5.
* gnu: ungoogled-chromium: Update to 75.0.3770.100-0.5d8abc3.Marius Bakke2019-06-20
| | | | | * gnu/packages/chromium.scm (%chromium-version): Set to 75.0.3770.100. (%chromium-origin): Update hash.
* gnu: openh264: Update to 2.0.0.Marius Bakke2019-06-20
| | | | | * gnu/packages/video.scm (openh264): Update to 2.0.0. [source](uri): Adjust file name.
* gnu: ungoogled-chromium: Install icons.Alex Griffin2019-06-20
| | | | | | * gnu/packages/chromium.scm (ungoogled-chromium)[arguments]: Install icons. Signed-off-by: Marius Bakke <mbakke@fastmail.com>
* gnu: Use HTTPS for sphinx-doc.org.Marius Bakke2019-06-20
| | | | | * gnu/packages/sphinx.scm (python-sphinx, python-sphinxcontrib-websupport)[home-page]: Use HTTPS.
* gnu: python-unidecode: Update to 1.1.0.Marius Bakke2019-06-20
| | | | * gnu/packages/python-xyz.scm (python-unidecode): Update to 1.1.0.
* 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.
* 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".
* 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.
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