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2016-05-24gnu: libxml2: Fix CVE-2016-3627 and CVE-2016-3705.Ludovic Courtès
* gnu/packages/patches/libxml2-CVE-2016-3627.patch, gnu/packages/patches/libxml2-CVE-2016-3705.patch: New files. * gnu/local.mk (dist_patch_DATA): Add them. * gnu/packages/xml.scm (libxml2)[replacement]: New field. (libxml2/fixed): New variable.
2016-05-24build: Use "%D%" in Makefile fragments.Mathieu Lirzin
* doc/local.mk: Use "%D%" for the directory of the fragment relative to the base 'Makefile.am'. * emacs/local.mk: Likewise. * gnu/local.mk: Likewise. * nix/local.mk: Likewise.
2016-05-24ui: Let users report translation bugs.Mathieu Lirzin
* guix/ui.scm (show-bug-report-information): Add a comment for translators.
2016-05-24gnu: Add emacs-clojure-mode.humanitiesNerd
* gnu/packages/emacs.scm (emacs-clojure-mode): New variable. Signed-off-by: Alex Kost <alezost@gmail.com>
2016-05-24gnu: Use 'emacs-minimal' instead of 'emacs-no-x'.Alex Kost
* gnu/packages/code.scm (cflow)[native-inputs]: Use 'emacs-minimal' instead of 'emacs-no-x'. * gnu/packages/databases.scm (recutils): Likewise. * gnu/packages/finance.scm (ledger): Likewise * gnu/packages/idutils.scm (idutils): Likewise. * gnu/packages/mail.scm (mu): Likewise. * gnu/packages/ocaml.scm (proof-general): Likewise. * gnu/packages/package-management.scm (guix-0.10.0): Likewise. * gnu/packages/plotutils.scm (asymptote): Likewise. * gnu/packages/scheme.scm (scmutils): Likewise. * gnu/packages/version-control.scm (vc-dwim): Likewise. * gnu/packages/emacs.scm (geiser): Likewise. (paredit): Likewise. (git-modes): Likewise. (magit): Likewise. (magit-svn): Likewise. (haskell-mode): Likewise. (let-alist): Likewise. (emacs-w3m): Likewise. (emacs-wget): Likewise. (emms): Likewise. (bbdb): Likewise. (emacs-mmm-mode): Likewise. (emacs-pdf-tools): Likewise. (emacs-popup)[native-inputs]: Remove as it is not needed for emacs-build-system. (emacs-rfcview): Likewise. (emacs-ffap-rfc-space): Likewise.
2016-05-24gnu: Move emacs for building from inputs to native-inputs.Alex Kost
* gnu/packages/emacs.scm (geiser): Move "emacs" from inputs to native-inputs. (paredit): Likewise. (haskell-mode): Likewise. (emacs-w3m): Likewise. (emacs-wget): Likewise. * gnu/packages/mail.scm (mu): Likewise. * gnu/packages/version-control.scm (vc-dwim): Likewise.
2016-05-24build-system/emacs: Use 'emacs-minimal' by default.Alex Kost
* guix/build-system/emacs.scm (default-emacs): Use 'emacs-minimal'. * gnu/packages/emacs.scm (emacs-auctex): Use 'emacs'.
2016-05-24gnu: Add emacs-minimal.Alex Kost
* gnu/packages/emacs.scm (emacs-minimal): New variable.
2016-05-24gnu: emacs: Remove *.elc and autoloads from the tarball.Alex Kost
* gnu/packages/emacs.scm (emacs)[source]: Add 'snippet' to remove compiled and generated elisp files.
2016-05-24gnu: enblend-enfuse: Update to 4.2.Efraim Flashner
* gnu/packages/photo.scm (enblend-enfuse): Update to 4.2. [native-inputs]: Add help2man, texlive-minimal.
2016-05-23gnu: grub: Re-enable test.Leo Famulari
* gnu/packages/grub.scm (grub)[arguments]: Re-enable test.
2016-05-24graph: Add 'node-reachable-count'.Ludovic Courtès
* guix/graph.scm (node-reachable-count): New procedure. * tests/graph.scm ("node-reachable-count"): New test.
2016-05-24graph: Expose 'traverse/depth-first'.Ludovic Courtès
* guix/graph.scm (traverse/depth-first): New procedure, based on code formerly in 'node-transitive-edges'. (node-transitive-edges): Rewrite in terms of it.
2016-05-24refresh: Make 'list-dependents' a monadic procedure.Ludovic Courtès
* guix/scripts/refresh.scm (list-dependents): Remove use of 'with-store' and 'run-with-store'. (guix-refresh): Wrap body in with-store/run-with-store.
2016-05-23gnu: vdirsyncer: Update to 0.11.0.Leo Famulari
* gnu/packages/dav.scm (vdirsyncer): Update to 0.11.0.
2016-05-23gnu: git: Update to 2.8.3.Leo Famulari
* gnu/packages/version-control.scm (git): Update to 2.8.3. (git-manpages)[source]: Update hash.
2016-05-23gnu: Add r-zoo.Roel Janssen
* gnu/packages/statistics.scm (r-zoo): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
2016-05-23gnu: borg: Update to 1.0.3.Leo Famulari
* gnu/packages/backup.scm (borg): Update to 1.0.3. [source]: Remove pypi-uri.
2016-05-23union: Compare inode numbers in 'file=?'.Ludovic Courtès
* guix/build/union.scm (file=?): Compare the inode of ST1 and ST2.
2016-05-23cve: Remove now unnecessary HTTP caching.Ludovic Courtès
* guix/cve.scm (call-with-cve-port): Use 'http-fetch' instead of 'http-fetch/cached'.
2016-05-23cve: Keep a summarized sexp in cache instead of the full XML.Ludovic Courtès
This avoids ~20s of XML parsing when running 'guix lint -c cve'. * guix/cve.scm (vulnerability->sexp, sexp->vulnerability) (fetch-vulnerabilities): New procedures. (current-vulnerabilities): Use 'fetch-vulnerabilities'.
2016-05-23gnu: Add poppler-qt5.Roel Janssen
* gnu/packages/pdf.scm (poppler-qt5): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2016-05-23gnu: Add slurm-drmaa.Ricardo Wurmus
* gnu/packages/parallel.scm (slurm-drmaa): New variable.
2016-05-23gnu: Add ParDRe.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pardre): New variable.
2016-05-22gnu: gnu-pw-mgr: Update to 2.0.Efraim Flashner
* gnu/packages/gnu-pw-mgr.scm (gnu-pw-mgr): Update to 2.0.
2016-05-22gnu: imagemagick: Update to 6.9.4-4.Leo Famulari
* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.4-4.
2016-05-22gnu: Add python2-rope.Lukas Gradl
* gnu/packages/python.scm (python2-rope): New variable.
2016-05-21gnu: Add gnome-calendar.Kei Yamashita
* gnu/packages/gnome.scm (gnome-calendar): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2016-05-21gnu: Add envstore.Matthew Jordan
* gnu/package/shellutils.scm: New file. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2016-05-21gnu: Add sicp.Jan Nieuwenhuizen
* gnu/packages/scheme.scm (sicp): New variable. Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2016-05-21gnu: Add dia.Roel Janssen
* gnu/packages/gnome.scm (dia): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2016-05-21build: Fix 'AM_V_at' typo.Mathieu Lirzin
* Makefile.am (hydra-jobs.scm): Fix 'AM_V_at' typo.
2016-05-21grafts: Rename files whose name matches a graft.Ludovic Courtès
Fixes <http://bugs.gnu.org/23132>. Reported by Mark H Weaver <mhw@netris.org>. * guix/build/graft.scm (rename-matching-files): New procedure. (rewrite-directory): Use it. * tests/grafts.scm ("graft-derivation, renaming"): New test.
2016-05-21grafts: Preserve empty directories when grafting.Ludovic Courtès
* guix/build/graft.scm (rewrite-directory)[rewrite-leaf]: Add case for 'directory. Pass #:directories? #t to 'find-files'.
2016-05-21substitute: Gracefully handle invalid store file names.Ludovic Courtès
Before, something like: echo have /gnu/foo | ./test-env guix substitute --query would lead to an ugly backtrace. * guix/scripts/substitute.scm (narinfo-cache-file): Call 'leave' when 'store-hash-part' returns #f.
2016-05-21graph: Allow store file names for 'derivation' and 'references' graphs.Ludovic Courtès
* guix/scripts/graph.scm (%derivation-node-type)[convert]: Add 'derivation-path?' and catch-all clauses. (%reference-node-type)[convert]: Add 'store-path?' and catch-all clauses. (assert-package, nodes-from-package): New procedures. (%package-node-type, %bag-node-type,%bag-with-origins-node-type) (%bag-emerged-node-type): Add 'convert' field (guix-graph): Rename 'packages' to 'items' and allow 'store-path?' arguments. * guix/graph.scm (<node-type>)[convert]: Adjust comment. * doc/guix.texi (Invoking guix graph): Document it.
2016-05-21derivations: 'derivation' sorts items in the resulting object.Ludovic Courtès
* guix/derivations.scm (derivation-input<?): New procedure. (write-derivation)[coalesce-duplicate-inputs]: Remove. Remove calls to 'sort'. (coalesce-duplicate-inputs): New procedure. (derivation-hash): Sort INPUTS and use 'coalesce-duplicate-inputs'. (derivation)[input->derivation-input] [coalesce-duplicate-inputs]: New procedures. Sort OUTPUTS, INPUTS, and ENV-VARS. * tests/derivations.scm ("read-derivation vs. derivation"): New test.
2016-05-21graph: Use absolute file name canonicalization.Ludovic Courtès
* guix/scripts/graph.scm (guix-graph): Wrap in 'with-fluids'.
2016-05-20gnu: linux-libre: Update to 4.5.5.Mark H Weaver
* gnu/packages/linux.scm (linux-libre): Update to 4.5.5.
2016-05-20gnu: linux-libre-4.4: Update to 4.4.11.Mark H Weaver
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.11.
2016-05-20ant-build-system: Add unpack phase.Ricardo Wurmus
* guix/build/ant-build-system.scm (unpack): New procedure. (%standard-phases): Use it.
2016-05-20gnu: Add default gcc-objc++.Ricardo Wurmus
* gnu/packages/gcc.scm (gcc-objc++): New variable.
2016-05-20gnu: Add gcc-objc++-4.9.Ricardo Wurmus
* gnu/packages/gcc.scm (gcc-objc++-4.9): New variable.
2016-05-20gnu: Add default gcc-objc.Ricardo Wurmus
* gnu/packages/gcc.scm (gcc-objc): New variable.
2016-05-20gnu: Add gcc-objc-4.9.Ricardo Wurmus
* gnu/packages/gcc.scm (gcc-objc-4.9): New variable.
2016-05-20gnu: r-rcpparmadillo: Update to 0.6.700.6.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.6.700.6.0. * gnu/packages/maths.scm (armadillo-for-rcpparmadillo): Update to 6.700.6.
2016-05-20gnu: armadillo: Update to 6.700.7.Ricardo Wurmus
* gnu/packages/maths.scm (armadillo): Update to 6.700.7.
2016-05-20gnu: r-genomation: Update to 1.4.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.4.2.
2016-05-20gnu: r-jsonlite: Update to 0.9.20.Ricardo Wurmus
* gnu/packages/web.scm (r-jsonlite): Update to 0.9.20.
2016-05-20gnu: r-plotly: Update to 3.6.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-plotly): Update to 3.6.0.
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