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2019-06-21gnu: Add openjdk12.Gábor Boskovits
* gnu/packages/java.scm(openjdk12): New variable.
2019-06-21gnu: emacs-fish-completion: Update to 1.1.Pierre Neidhardt
* gnu/packages/emacs-xyz.scm (emacs-fish-completion): Update to 1.1.
2019-06-21gnu: zn-poly: Install all libraries.Andreas Enge
* gnu/packages/sagemath.scm (zn-poly): Install the static and the dynamic library with its symlinks, and end a phase with #t.
2019-06-21gnu: khmer: Update to 3.0.0a3.Ricardo Wurmus
* 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.
2019-06-21gnu: icecat: Update to 60.7.2-guix1 [security fixes].Mark H Weaver
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.
2019-06-21gnu: ungoogled-chromium: Increase build timeout.Marius Bakke
* gnu/packages/chromium.scm (ungoogled-chromium)[properties]: New field.
2019-06-21gnu: linux-libre: Update to 5.1.12.Mark H Weaver
* gnu/packages/linux.scm (%linux-libre-version): Update to 5.1.12. (%linux-libre-hash): Update hash.
2019-06-21gnu: linux-libre@4.19: Update to 4.19.53.Mark H Weaver
* gnu/packages/linux.scm (%linux-libre-4.19-version): Update to 4.19.53. (%linux-libre-4.19-hash): Update hash.
2019-06-21gnu: linux-libre@4.14: Update to 4.14.128.Mark H Weaver
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.128. (%linux-libre-4.14-hash): Update hash.
2019-06-21gnu: ratpoints: Generate position-independent code.Andreas Enge
* gnu/packages/algebra.scm (ratpoints): Add "CCFLAGS=-fPIC" to make flags.
2019-06-21gnu: symmetrica: Generate position-independent code.Andreas Enge
* gnu/packages/algebra.scm (symmetrica): Add -fPIC compiler flag.
2019-06-21gnu: iml: Enable shared library.Andreas Enge
* gnu/packages/algebra.scm (iml): Add configure flag --enable-shared.
2019-06-21gnu: Add lcalc.Andreas Enge
* 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.
2019-06-21gnu: lrcalc: Add a patch for identifying include files.Andreas Enge
* gnu/packages/patches/lrcalc-includes.patch: New file. * gnu/packages/algebra.scm (lrcalc): Use patch. * gnu/local.mk (dist_patch_DATA): Register patch.
2019-06-21gnu: python-mpi4py: Update to 3.0.2.Paul Garlick
* gnu/packages/mpi.scm (python-mpi4py): Update to 3.0.2. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2019-06-20gnu: ungoogled-chromium: Disable parallel build.Marius Bakke
* gnu/packages/chromium.scm (ungoogled-chromium)[arguments]: Set #:parallel-build? #f. Adjust 'build' phase to account for it.
2019-06-20gnu: samba: Update to 4.10.5 [fixes CVE-2019-12435, CVE-2019-12436].Marius Bakke
* gnu/packages/samba.scm (samba): Update to 4.10.5.
2019-06-20gnu: ungoogled-chromium: Update to 75.0.3770.100-0.5d8abc3.Marius Bakke
* gnu/packages/chromium.scm (%chromium-version): Set to 75.0.3770.100. (%chromium-origin): Update hash.
2019-06-20gnu: openh264: Update to 2.0.0.Marius Bakke
* gnu/packages/video.scm (openh264): Update to 2.0.0. [source](uri): Adjust file name.
2019-06-20gnu: ungoogled-chromium: Install icons.Alex Griffin
* gnu/packages/chromium.scm (ungoogled-chromium)[arguments]: Install icons. Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2019-06-20gnu: Use HTTPS for sphinx-doc.org.Marius Bakke
* gnu/packages/sphinx.scm (python-sphinx, python-sphinxcontrib-websupport)[home-page]: Use HTTPS.
2019-06-20gnu: python-unidecode: Update to 1.1.0.Marius Bakke
* gnu/packages/python-xyz.scm (python-unidecode): Update to 1.1.0.
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.
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