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2018-03-29gnu: r-mutationalpatterns: Update to 1.4.3.Roel Janssen
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.3; [propagated-inputs]: Remove r-gridextra.
2018-03-29gnu: kaiju: Update to 1.6.2.Roel Janssen
* gnu/packages/bioinformatics.scm (kaiju): Update to 1.6.2; [inputs]: Add zlib.
2018-03-29gnu: Add duperemove.Vasile Dumitrascu
* gnu/packages/disk.scm (duperemove): New variable. Co-authored-by: Ludovic Courtès <ludovic.courtes@inria.fr>
2018-03-29gnu: Add python-debug.Ludovic Courtès
Suggested by Pjotr Prins <pjotr.public12@thebird.nl>. * gnu/packages/python.scm (python-debug): New variable.
2018-03-29gnu: nano: Update to 2.9.5.Efraim Flashner
* gnu/packages/nano.scm (nano): Update to 2.9.5.
2018-03-29gnu: Add r-idr.Roel Janssen
* gnu/packages/cran.scm (r-idr): New variable.
2018-03-29gnu: Add r-amap.Roel Janssen
* gnu/packages/cran.scm (r-amap): New variable.
2018-03-29gnu: Add r-venndiagram.Roel Janssen
* gnu/packages/cran.scm (r-venndiagram): New variable.
2018-03-29gnu: Add r-pastecs.Roel Janssen
* gnu/packages/cran.scm (r-pastecs): New variable.
2018-03-29gnu: libusb4java: Adjust for building with libusb 1.0.22.Ricardo Wurmus
* gnu/packages/libusb.scm (libusb4java)[arguments]: Add phase to remove "-Werror" flag.
2018-03-29gnu: libusb-for-axoloti: Update patch.Ricardo Wurmus
* gnu/packages/patches/libusb-for-axoloti.patch: Update context for libusb 1.0.22.
2018-03-29gnu: Refactor boot-service-type and activation-service-type.Chris Marusich
* gnu/services.scm (boot-service-type) <compose>: Use the "identity" procedure instead of the "append" procedure because it more accurately reflects the intent, which is to simply return the single list of extensions to which fold-services applies the "compose" procedure. (activation-service-type) <compose>: Likewise.
2018-03-28gnu: node: Update to 9.10.0.Jelle Licht
* gnu/packages/node.scm (node): Update to 9.10.0.
2018-03-28gnu: http-parser: Update to 2.8.0.Jelle Licht
* gnu/packages/web.scm (http-parser): Update to 2.8.0.
2018-03-28gnu: xf86-video-ati: Update to 18.0.1.Marius Bakke
* gnu/packages/xorg.scm (xf86-video-ati): Update to 18.0.1.
2018-03-28gnu: xf86-input-libinput: Update to 0.27.0.Marius Bakke
* gnu/packages/xorg.scm (xf86-input-libinput): Update to 0.27.0.
2018-03-28gnu: ntp: Update to 4.2.8p11 [security-fixes].Leo Famulari
Fixes CVE-2016-1549 and CVE-2018-{7170,7182,7183,7184,7185}. * gnu/packages/ntp.scm (ntp): Update to 4.2.8p11.
2018-03-28gnu: openssl: Replace with OpenSSL 1.0.2o [fixes CVE-2018-0739].Leo Famulari
* gnu/packages/tls.scm (openssl)[replacement]: New field. (openssl-1.0.2o): New variable.
2018-03-28gnu: Add r-parsedate.Konrad Hinsen
* gnu/packages/cran.scm (r-parsedate): New variable. Signed-off-by: Ludovic Courtès <ludovic.courtes@inria.fr>
2018-03-28gnu: mu: Fix tests failures triggered by DST.Maxim Cournoyer
* gnu/packages/mail.scm (mu)[phases]: Add 'fix-date-tests. Signed-off-by: Ludovic Courtès <ludovic.courtes@inria.fr>
2018-03-28gnu: Add tcalc.Nadya Voronova
* gnu/packages/maths.scm (tcalc): New variables. Signed-off-by: Ludovic Courtès <ludovic.courtes@inria.fr>
2018-03-28gnu: culmus: Rename to font-culmus.Arun Isaac
* gnu/packages/fonts.scm (culmus): Rename to... (font-culmus): ...this. Re-indent.
2018-03-28gnu: culmus: Switch to font-build-system.Arun Isaac
* gnu/packages/fonts.scm (culmus): Switch to font-build-system. [arguments]: Replace system* with invoke.
2018-03-28gnu: font-linuxlibertine: Switch to font-build-system.Arun Isaac
* gnu/packages/fonts.scm (font-linuxlibertine): Switch to font-build-system. [arguments]: Replace system* with invoke.
2018-03-28gnu: font-lato: Switch to font-build-system.Arun Isaac
* gnu/packages/fonts.scm (font-lato): Switch to font-build-system. [source]: Use url-fetch/zipbomb.
2018-03-27gnu: icecat: Add fix for CVE-2018-5148.Mark H Weaver
* gnu/packages/gnuzilla.scm (icecat)[source]: Add the fix for CVE-2018-5148 from the upstream mozilla-esr52 repository.
2018-03-27gnu: mupdf: Fix CVE-2018-{6544,1000051}.Leo Famulari
* gnu/packages/patches/mupdf-CVE-2018-1000051.patch, gnu/packages/patches/mupdf-CVE-2018-6544.patch: New files. * gnu/local.mk (dist_patch_DATA): Add them. * gnu/packages/pdf.scm (mupdf)[source]: Use them.
2018-03-27gnu: emacs-org, emacs-org-contrib: Update to 9.1.9.Nicolas Goaziou
* gnu/packages/emacs.scm (emacs-org): (emacs-org-contrib): Update to 20180327, a.k.a. release 9.1.9.
2018-03-27gnu: alpine: Update to 2.21.999.ng0
* gnu/packages/mail.scm (alpine): Update to 2.21.999. [source]: Change to new upstream location. [home-page]: Use new location. Signed-off-by: Ludovic Courtès <ludovic.courtes@inria.fr>
2018-03-27nss: Remove '%compat' from the defaults.Ludovic Courtès
* gnu/system/nss.scm (%compat): Add comment. (<name-service-switch>)[group, password, shadow]: Remove %COMPAT from the default value.
2018-03-27gnu: zstd: Update to 1.3.4.Tobias Geerinckx-Rice
* gnu/packages/compression.scm (zstd): Update to 1.3.4.
2018-03-27gnu: dovecot: Update to 2.3.1.Tobias Geerinckx-Rice
* gnu/packages/mail.scm (dovecot): Update to 2.3.1. [arguments]: Rename ‘patch-other-shebangs’ phase to the more accurate ‘patch-other-file-names’... then patch more file names.
2018-03-27gnu: lyx: Use HTTPS home page.Tobias Geerinckx-Rice
* gnu/packages/tex.scm (lyx)[home-page]: Use HTTPS.
2018-03-27gnu: openssl@1.1.0: Update to 1.1.0h [security fixes].Leo Famulari
Fixes CVE-2017-3738 and CVE-2018-{0733,0739}. * gnu/packages/tls.scm (openssl-next): Update to 1.1.0h.
2018-03-27gnu: Remove unnecessary import.Ludovic Courtès
* gnu/packages/guile.scm: Remove unnecessary import.
2018-03-27activation: Pass '-d HOME' to 'usermod'.Ludovic Courtès
Fixes a bug whereby changes to user home directories in the OS config would never be effective. Reported by Pierre Neidhardt <ambrevar@gmail.com>. * gnu/build/activation.scm (modify-user): Pass '-d HOME'.
2018-03-27gnu: bootstrap: Remove unneeded import.Ludovic Courtès
* gnu/packages/bootstrap.scm: Remove unneeded (guix build utils) import.
2018-03-27gnu: Remove Haskell packages provided by GHC.Timothy Sample
* gnu/packages/haskell.scm (ghc-array, ghc-binary, ghc-bytestring, ghc-directory, ghc-haskeline, ghc-process, ghc-transformers, ghc-transformers-0.4.2.0): Remove. (ghc-tar)[inputs]: Remove ghc-array. (ghc-hslogger)[inputs]: Remove ghc-directory. * gnu/packages/version-control.scm (darcs)[inputs]: Remove ghc-array, ghc-binary, and ghc-haskeline. * gnu/packages/wm.scm (xmonad)[inputs]: Remove ghc-directory. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2018-03-27gnu: supercollider: Update to 3.9.2.Tobias Geerinckx-Rice
* gnu/packages/audio.scm (supercollider): Update to 3.9.2.
2018-03-27gnu: gzdoom: Update to 3.3.0.Tobias Geerinckx-Rice
* gnu/packages/games.scm (gzdoom): Update to 3.3.0.
2018-03-27gnu: ccache: Update to 3.4.2.Tobias Geerinckx-Rice
* gnu/packages/ccache.scm (ccache): Update to 3.4.2.
2018-03-27gnu: jetring: Update to 0.27.Tobias Geerinckx-Rice
* gnu/packages/gnupg.scm (jetring): Update to 0.27.
2018-03-27gnu: libkomparediff2: Update to 17.12.3.Tobias Geerinckx-Rice
* gnu/packages/kde.scm (libkomparediff2): Update to 17.12.3.
2018-03-27gnu: radeontop: Update to 1.1.Tobias Geerinckx-Rice
* gnu/packages/linux.scm (radeontop): Update to 1.1.
2018-03-27gnu: ruby-rake: Update to 12.3.1.Tobias Geerinckx-Rice
* gnu/packages/ruby.scm (ruby-rake): Update to 12.3.1.
2018-03-27gnu: ruby-asciidoctor: Update to 1.5.6.2.Tobias Geerinckx-Rice
* gnu/packages/ruby.scm (ruby-asciidoctor): Update to 1.5.6.2.
2018-03-27gnu: python-plotly: Update to 2.4.1.Tobias Geerinckx-Rice
* gnu/packages/graph.scm (python-plotly): Update to 2.4.1.
2018-03-27gnu: python-django-crispy-forms: Update to 1.7.2.Tobias Geerinckx-Rice
* gnu/packages/django.scm (python-django-crispy-forms): Update to 1.7.2.
2018-03-27gnu: r-randomforest: Update to 4.6-14.Tobias Geerinckx-Rice
* gnu/packages/statistics.scm (r-randomforest): Update to 4.6-14.
2018-03-27gnu: r-blob: Update to 1.1.1.Tobias Geerinckx-Rice
* gnu/packages/statistics.scm (r-blob): Update to 1.1.1. [propagated-inputs]: Add r-prettyunits.
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