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2017-11-18gnu: r-org-dm-eg-db: Update to 3.5.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Update to 3.5.0.
2017-11-18gnu: r-org-mm-eg-db: Update to 3.5.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Update to 3.5.0.
2017-11-18gnu: r-genomationdata: Update to 1.10.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.10.0.
2017-11-18gnu: Remove duplicates from (gnu packages statistics).Ricardo Wurmus
* gnu/packages/statistics.scm (r-cluster, r-codetools, r-kernsmooth): Remove duplicates.
2017-11-18gnu: Remove duplicate from (gnu packages gnupg).Ricardo Wurmus
* gnu/packages/gnupg.scm (perl-gnupg-interface): Remove duplicate.
2017-11-18gnu: Remove duplicate from (gnu packages bioinformatics).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationfilter): Remove duplicate.
2017-11-18gnu: Remove duplicate from (gnu packages cran).Ricardo Wurmus
* gnu/packages/cran.scm (r-bbmle): Remove duplicate.
2017-11-18gnu: Remove duplicates from (gnu packages java).Ricardo Wurmus
* gnu/packages/java.scm (java-commons-net, java-asm): Remove duplicates.
2017-11-18gnu: r-org-hs-eg-db: Clarify description.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db)[description]: Clarify.
2017-11-18gnu: r-org-hs-eg-db: Update to 3.5.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.5.0.
2017-11-18gnu: r-org-hs-eg-db: Remove duplicate package definition.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Remove duplicate variable.
2017-11-18gnu: linux-libre: Remove Tegra DRM from arm configuration.Mark H Weaver
The code fails to compile on armhf using our configuration. See <https://patchwork.kernel.org/patch/9688615/> for details. * gnu/packages/aux-files/linux-libre/4.14-arm.conf: Remove Tegra DRM support.
2017-11-18gnu: linux-libre: Remove Nouveau from arm configuration.Mark H Weaver
The Nouveau code fails to compile on armhf with our configuration. * gnu/packages/aux-files/linux-libre/4.14-arm.conf: Disable Nouveau.
2017-11-18gnu: dino: Update to 0.0-2-2a514d096.Ricardo Wurmus
* gnu/packages/messaging.scm (dino): Update to 0.0-2-2a514d096. [source]: Do not fetch libsignal-protocol-c submodule. [arguments]: Add phase "unpack-sources" to unpack our sources for libsignal-protocol-c. [native-inputs]: Add "libsignal-protocol-c-source".
2017-11-17build-system/go: Don't let Go executables refer to the Go compiler.Leo Famulari
* guix/build/go-build-system.scm (remove-store-reference, remove-go-references): New procedures. (%standard-phases): Add 'remove-go-references' phase. * guix/build-system/go.scm (go-build): Add allow-go-reference? key.
2017-11-17gnu: vim: Update to 8.0.1300.Leo Famulari
* gnu/packages/vim.scm (vim): Update to 8.0.1300.
2017-11-17gnu: tuxguitar: Build with icedtea-8.Ricardo Wurmus
* gnu/packages/music.scm (tuxguitar)[arguments]: Use icedtea-8.
2017-11-17gnu: java-swt: Update to 4.7.1a.Ricardo Wurmus
* gnu/packages/java.scm (java-swt): Update to 4.7.1a. [arguments]: Build with icedtea-8. [inputs]: Remove "icecat".
2017-11-17gnu: eolie: Update to 0.9.12.Ricardo Wurmus
* gnu/packages/gnome.scm (eolie): Update to 0.9.12. [inputs]: Add python-dateutil.
2017-11-17doc: Write "file system" instead of "partition" as appopriate.Marco van Hulten
* doc/guix.texi (Preparing for Installation): Write "file system" instead of "partition" as appopriate.
2017-11-17gnu: Move database packages from python.scm to databases.scm.Ricardo Wurmus
* gnu/packages/python.scm (python-ccm, python2-ccm, python2-pysqlite, python-sqlalchemy, python2-sqlalchemy, python-sqlalchemy-utils, python2-sqlalchemy-utils, python-alembic, python2-alembic, python-pickleshare, python2-pickleshare, python-apsw, python2-apsw, python2-neo4j-driver, python2-py2neo, python-psycopg2, python2-psycopg2, python-sadisplay, python2-sadisplay, python-mysqlclient, python2-mysqlclient, python-hiredis, python2-hiredis, python-fakeredis, python2-fakeredis, python-redis, python2-redis, python-rq, python2-rq, python-trollius-redis, python2-trollius-redis, python-sqlparse, python2-sqlparse, python-sql, python2-sql): Move from here... * gnu/packages/databases.scm: ...to here. * gnu/packages/tryton.scm, gnu/packages/python-web.scm, gnu/packages/nutrition.scm, gnu/packages/medical.scm: Adjust accordingly.
2017-11-17gnu: python-scikit-learn: Move from python.scm to machine-learning.scm.Ricardo Wurmus
* gnu/packages/python.scm (python-scikit-learn, python2-scikit-learn): Move from here... * gnu/packages/machine-learning.scm: ...to here.
2017-11-17gnu: Move more web packages from python.scm to python-web.scm.Ricardo Wurmus
* gnu/packages/python.scm (python-pastescript, python2-pastescript, python-paste, python2-paste, python-werkzeug, python2-werkzeug, python-bottle, python2-bottle, python-wtforms, python2-wtforms): Move from here... * gnu/packages/python-web.scm: ...to here.
2017-11-17gnu: Move testing packages from python.scm to check.scm.Ricardo Wurmus
* gnu/packages/python.scm (python-behave-web-api, python2-behave-web-api, python-mock, python2-mock, python-mock-2, python-nose, python2-nose, python-nose2, python2-nose2, python-unittest2, python2-unittest2, python-pytest, python2-pytest, python-pytest-3.0, python2-pytest-3.0, python-pytest-cov, python2-pytest-cov, python-pytest-runner, python2-pytest-runner, python-pytest-mock, python2-pytest-mock, python-pytest-xdist, python2-pytest-xdist, python-scripttest, python2-scripttest, python-testtools, python2-testtools, python-testscenarios, python2-testscenarios, python-testresources, python2-testresources, python-subunit, python2-subunit, python-fixtures, python2-fixtures, python-testrepository, python2-testrepository, python-coverage, python2-coverage, python-cov-core, python2-cov-core, python-testpath, python2-testpath, python-testlib, python2-testlib, python-pytest-cache, python2-pytest-cache, python-pytest-localserver, python-pytest-xprocess, python-pytest-subtesthack, python2-pytest-subtesthack, python-hypothesis, python2-hypothesis, python-lit, python2-lit, python-pytest-pep8, python2-pytest-pep8, python-pytest-flakes, python2-pytest-flakes, python2-coverage-test-runner, python-pylint, python2-pylint, python-paramunittest, python2-python-paramunittest, python-pytest-warnings, python2-pytest-warnings, python-pytest-capturelog, python2-pytest-capturelog, python-pytest-catchlog, python2-pytest-catchlog, python-nosexcover, python2-nosexcover, python-discover, python2-discover, behave, python-rednose, python2-rednose, python-nose-randomly, python2-nose-randomly, python-nose-timer, python2-nose-timer): Move from here... * gnu/packages/check.scm: ...to here. * gnu/packages/admin.scm, gnu/packages/android.scm, gnu/packages/backup.scm, gnu/packages/bioinformatics.scm, gnu/packages/calendar.scm, gnu/packages/dav.scm, gnu/packages/django.scm, gnu/packages/freedesktop.scm, gnu/packages/haskell.scm, gnu/packages/image.scm, gnu/packages/irc.scm, gnu/packages/jrnl.scm, gnu/packages/ldc.scm, gnu/packages/libffi.scm, gnu/packages/mail.scm, gnu/packages/mpd.scm, gnu/packages/openstack.scm, gnu/packages/package-management.scm, gnu/packages/password-utils.scm, gnu/packages/python-crypto.scm, gnu/packages/python-web.scm, gnu/packages/rdf.scm, gnu/packages/statistics.scm, gnu/packages/storage.scm, gnu/packages/time.scm, gnu/packages/tls.scm, gnu/packages/tor.scm, gnu/packages/tryton.scm: Adjust accordingly.
2017-11-17gnu: Add qmidiroute.Ricardo Wurmus
* gnu/packages/music.scm (qmidiroute): New variable.
2017-11-17gnu: cheese: Update to 3.26.0.Rutger Helling
* gnu/packages/gnome.scm (cheese): Update to 3.26.0 Signed-off-by: Leo Famulari <leo@famulari.name>
2017-11-17gnu: Add emacs-transmission.Oleg Pykhalov
* gnu/packages/emacs.scm (emacs-transmission): New variable.
2017-11-17gnu: cool-retro-term: Fix qml path.Oleg Pykhalov
* gnu/packages/terminals.scm (cool-retro-term): Fix qml path.
2017-11-17gnu: eog: Update to 3.26.2.Rutger Helling
* gnu/packages/gnome.scm (eog): Update to 3.26.2. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-11-17gnu: gnome-disk-utility: Update to 3.26.2.Rutger Helling
* gnu/packages/gnome.scm (gnome-disk-utility): Update to 3.26.2. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-11-17gnu: nftables: Update to 0.8.Rutger Helling
* gnu/packages/linux.scm (nftables): Update to 0.8. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-11-17gnu: libnftnl: Update to 1.0.8.Rutger Helling
* gnu/packages/linux.scm (libnftnl): Update to 1.0.8. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-11-17workers: Display backtrace in pre-unwind handler.Ludovic Courtès
* guix/workers.scm (worker-thunk): Add (const #f) as the 'catch' handler, and move previous handler as pre-unwind handler. Protect against 'make-stack' returning #f.
2017-11-17workers: Add test with exceptions.Ludovic Courtès
* tests/workers.scm ("exceptions"): New test.
2017-11-17workers: 'pool-idle?' returns true only if the workers are idle.Ludovic Courtès
Fixes <https://bugs.gnu.org/28779>. Reported by Eric Bavier <bavier@cray.com>. * guix/workers.scm (<pool>)[busy]: New field. (worker-thunk): Add #:idle and #:busy and use them. (make-pool): Pass #:busy and #:idle to 'worker-thunk'. Pass a 'busy' value to '%make-pool'. * guix/workers.scm (pool-idle?): Check whether 'pool-busy' returns zero and adjust docstring.
2017-11-16gnu: Add qucs-s.Theodoros Foradis
* gnu/packages/engineering.scm (qucs-s): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-11-16gnu: syslinux: Add explicit dependency on mtools.Ludovic Courtès
Suggested by Adam Van Ymeren <adam@vany.ca> at <https://bugs.gnu.org/28974>. * gnu/packages/bootloaders.scm (syslinux)[inputs]: Add MTOOLS. [ARGUMENTS]: In 'patch-files' phase, patch references to 'mcopy' and 'mattrib'.
2017-11-16gnu: wget: Add wget2.Rutger Helling
* gnu/packages/wget.scm (wget2): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-11-16gnu: spectrwm: Update to 3.1.0.ng0
* gnu/packages/wm.scm (spectrwm): Update to 3.1.0. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-11-16gnu: xpra: Fix paths.Rutger Helling
* gnu/packages/xorg.scm (xpra): [arguments]: Add '--without-opengl', '--without-Xdummy' and '--without-Xdummy-wrapper' to #:configure-flags. Add substitutions to #phases for proper paths. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-11-16gnu: messaging: Enable OMEMO for dino.Rutger Helling
* gnu/packages/messaging.scm (dino): Update to commit f6ac5bbd26638412a2289fd1d28ef12de1d7e8b5. [inputs]: Add libsignal-protocol-c and libgcrypt. [arguments]: Change #configure-flags to "-DSHARED_SIGNAL_PROTOCOL=yes". Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-11-16gnu: messaging: Add libsignal-protocol-c.Rutger Helling
* gnu/packages/messaging.scm (libsignal-protocol-c): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-11-16ui: Add source file name to the package search metrics.Ludovic Courtès
* guix/ui.scm (%package-metrics): Include 'package-location'. Increase score of the other fields.
2017-11-16gnu: Move more packages from python to python-web.Ludovic Courtès
* gnu/packages/python.scm (python-requests, python2-requests) (python-requests-2.7, python-oauthlib, python2-oauthlib) (python-furl, python2-furl, python-wsgi-intercept) (python-publicsuffix, python2-publicsuffix) (python-publicsuffix2, python2-publicsuffix2): Move to... * gnu/packages/python-web.scm: ... here. * gnu/packages/bioinformatics.scm, gnu/packages/finance.scm: gnu/packages/maths.scm, gnu/packages/terminals.scm, gnu/packages/video.scm, gnu/packages/virtualization.scm: Adjust accordingly.
2017-11-16gnu: Move Python packages from crypto to python-crypto.Ludovic Courtès
* gnu/packages/crypto.scm (python-asn1crypto, python2-asn1crypto) (python-pynacl, python2-roca-detect): Move to python-crypto.scm. * gnu/packages/gnupg.scm (python2-pgpdump): Move to python-crypto.scm. * gnu/packages/python-crypto.scm (python-asn1crypto, python2-asn1crypto) (python-pynacl, python2-pgpdump, python2-roca-detect): New variables.
2017-11-16gnu: Move crypto packages from python to python-crypto.Ludovic Courtès
* gnu/packages/python.scm (python-passlib, python2-passlib) (python-py-bcrypt, python2-py-bcrypt) (python-paramiko, python2-paramiko, python-ecdsa, python2-ecdsa) (python-pycrypto, python2-pycrypto, python-keyring, python2-keyring) (python-certifi, python2-certifi) (python-cryptography-vectors, python2-cryptography-vectors) (python-cryptography, python2-cryptography) (python-pyopenssl, python2-pyopenssl) (python-axolotl-curve25519, python2-axolotl-curve25519) (python-axolotl, python2-axolotl, python2-slowaes) (python-pyaes, python2-pyaes): Move to... * gnu/packages/python-crypto.scm: ... here. New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. * gnu/packages/admin.scm, gnu/packages/backup.scm, gnu/packages/crypto.scm, gnu/packages/finance.scm, gnu/packages/irc.scm, gnu/packages/jrnl.scm, gnu/packages/messaging.scm, gnu/packages/openstack.scm, gnu/packages/python-web.scm, gnu/packages/tls.scm, gnu/packages/xorg.scm: Adjust accordingly.
2017-11-16cve: Use 'http-fetch/cached' instead of having custom caching.Ludovic Courtès
That way CVE fetching benefits from 'If-Modified-Since' handling. * guix/http-client.scm (http-fetch/cached): Add #:write-cache and #:cache-miss parameters and honor them. * guix/cve.scm (%current-year-ttl, %past-year-ttl): Reduce. (call-with-cve-port): Remove. (write-cache): New procedure. (fetch-vulnerabilities): Rewrite in terms of 'http-fetch/cached'.
2017-11-16download: Improve efficiency of 'write-request' over TLS.Ludovic Courtès
This is another instance of <https://bugs.gnu.org/22966>. The Microsoft-IIS/7.5 server at static.nvd.nist.gov would sometimes hang when receiving our requests byte by byte. * guix/build/download.scm (tls-wrap) [!guile-2.0]: Add 'setvbuf' call.
2017-11-16gnu: linux-libre: Update to 4.14.Mark H Weaver
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.14. (%linux-libre-hash): Update hash. * gnu/packages/aux-files/linux-libre/4.13-arm.conf, gnu/packages/aux-files/linux-libre/4.13-i686.conf, gnu/packages/aux-files/linux-libre/4.13-x86_64.conf: Delete files. * gnu/packages/aux-files/linux-libre/4.14-arm.conf, gnu/packages/aux-files/linux-libre/4.14-i686.conf, gnu/packages/aux-files/linux-libre/4.14-x86_64.conf: New files. * Makefile.am (AUX_FILES): Update accordingly.
2017-11-16gnu: linux-libre@4.9: Update to 4.9.62.Mark H Weaver
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.62.
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