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2016-12-29gnu: r-biocstyle: Update to 2.2.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.2.1.
2016-12-29gnu: r-deseq2: Update to 1.14.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.14.1.
2016-12-29gnu: r-annotate: Update to 1.52.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.52.1. [propagated-inputs]: Add r-rcurl.
2016-12-29gnu: khard: Update to 0.11.3.Leo Famulari
* gnu/packages/mail.scm (khard): Update to 0.11.3. [arguments]: Build with python instead of python-2. Remove 'disable-egg-compression' phase. [propagated-inputs]: Don't use python-2 variants of propagated-inputs.
2016-12-29gnu: r-rsqlite: Update to 1.1-1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rsqlite): Update to 1.1-1. [propagated-inputs]: Add r-bh, r-memoise, r-plogr, and r-rcpp.
2016-12-29gnu: Add r-plogr.Ricardo Wurmus
* gnu/packages/statistics.scm (r-plogr): New variable.
2016-12-29gnu: r-hmisc: Update to 4.0-1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-hmisc): Update to 4.0-1. [propagated-inputs]: Remove r-cluster, r-foreign, r-lattice, r-nnet, and r-rpart; add r-base64.
2016-12-29gnu: Add r-base64.Ricardo Wurmus
* gnu/packages/statistics.scm (r-base64): New variable.
2016-12-29gnu: r-rmarkdown: Update to 1.3.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rmarkdown): Update to 1.3. [propagated-inputs]: Remove r-tibble; add r-rprojroot.
2016-12-29gnu: Add r-rprojroot.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rprojroot): New variable.
2016-12-29gnu: r-rcpparmadillo: Update to 0.7.600.1.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.7.600.1.0. * gnu/packages/maths.scm (armadillo-for-rcpparmadillo): Update to 7.600.1.
2016-12-29gnu: armadillo: Update to 7.600.2.Ricardo Wurmus
* gnu/packages/maths.scm (armadillo): Update to 7.600.2.
2016-12-29gnu: r-zoo: Update to 1.7-14.Ricardo Wurmus
* gnu/packages/statistics.scm (r-zoo): Update to 1.7-14. [propagated-inputs]: Remove r-lattice.
2016-12-29gnu: r-fastcluster: Update to 1.1.22.Ricardo Wurmus
* gnu/packages/statistics.scm (r-fastcluster): Update to 1.1.22.
2016-12-29gnu: r-plotly: Update to 4.5.6.Ricardo Wurmus
* gnu/packages/statistics.scm (r-plotly): Update to 4.5.6.
2016-12-29gnu: r-r-rsp: Update to 0.40.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-r-rsp): Update to 0.40.0.
2016-12-29gnu: r-r-utils: Update to 2.5.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-r-utils): Update to 2.5.0.
2016-12-29gnu: r-coda: Update to 0.19-1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-coda): Update to 0.19-1. [propagated-inputs]: Remove r-lattice.
2016-12-29gnu: r-chron: Update to 2.3-48.Ricardo Wurmus
* gnu/packages/statistics.scm (r-chron): Update to 2.3-48.
2016-12-29gnu: r-knitr: Update to 1.15.1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-knitr): Update to 1.15.1. [propagated-inputs]: Remove r-formatr.
2016-12-29gnu: r-bh: Update to 1.62.0-1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-bh): Update to 1.62.0-1.
2016-12-29gnu: r-svglite: Update to 1.2.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-svglite): Update to 1.2.0.
2016-12-29gnu: r-gdtools: Update to 0.1.3.Ricardo Wurmus
* gnu/packages/statistics.scm (r-gdtools): Update to 0.1.3.
2016-12-29gnu: r-ggplot2: Update to 2.2.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-ggplot2): Update to 2.2.0. [propagated-inputs]: Remove r-proto and r-svglite; add r-lazyeval and r-tibble.
2016-12-29gnu: r-scales: Update to 0.4.1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-scales): Update to 0.4.1.
2016-12-29gnu: r-mgcv: Update to 1.8-16.Ricardo Wurmus
* gnu/packages/statistics.scm (r-mgcv): Update to 1.8-16.
2016-12-29gnu: r-qtl: Update to 1.40-8.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.40-8.
2016-12-29gnu: r-hms: Update to 0.3.Ricardo Wurmus
* gnu/packages/statistics.scm (r-hms): Update to 0.3.
2016-12-29gnu: r-git2r: Update to 0.17.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-git2r): Update to 0.17.0.
2016-12-29gnu: r-ade4: Update to 1.7-5Ricardo Wurmus
* gnu/packages/statistics.scm (r-ade4): Update to 1.7-5.
2016-12-29gnu: r-xml: Update to 3.98-1.5.Ricardo Wurmus
* gnu/packages/statistics.scm (r-xml): Update to 3.98-1.5. [propagated-inputs]: Remove r-rcurl.
2016-12-29gnu: r-sparsem: Update to 1.74.Ricardo Wurmus
* gnu/packages/statistics.scm (r-sparsem): Update to 1.74.
2016-12-29gnu: r-data-table: Update to 1.10.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-data-table): Update to 1.10.0. [propagated-inputs]: Remove r-chron.
2016-12-29gnu: r-estimability: Update to 1.2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-estimability): Update to 1.2.
2016-12-29gnu: r-rcpp: Update to 0.12.8.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rcpp): Update to 0.12.8.
2016-12-29gnu: r-yaml: Update to 2.1.14.Ricardo Wurmus
* gnu/packages/statistics.scm (r-yaml): Update to 2.1.14.
2016-12-29gnu: r-htmlwidgets: Update to 0.8.Ricardo Wurmus
* gnu/packages/web.scm (r-htmlwidgets): Update to 0.8.
2016-12-29gnu: r-curl: Update to 2.3.Ricardo Wurmus
* gnu/packages/web.scm (r-curl): Update to 2.3.
2016-12-29gnu: r-servr: Update to 0.5.Ricardo Wurmus
* gnu/packages/web.scm (r-servr): Update to 0.5.
2016-12-29Remove Emacs interface.Alex Kost
* emacs/guix-about.el: Remove file. * emacs/guix-backend.el: Likewise. * emacs/guix-base.el: Likewise. * emacs/guix-buffer.el: Likewise. * emacs/guix-build-log.el: Likewise. * emacs/guix-command.el: Likewise. * emacs/guix-config.el.in: Likewise. * emacs/guix-devel.el: Likewise. * emacs/guix-entry.el: Likewise. * emacs/guix-external.el: Likewise. * emacs/guix-geiser.el: Likewise. * emacs/guix-guile.el: Likewise. * emacs/guix-help-vars.el: Likewise. * emacs/guix-helper.scm.in: Likewise. * emacs/guix-history.el: Likewise. * emacs/guix-hydra-build.el: Likewise. * emacs/guix-hydra-jobset.el: Likewise. * emacs/guix-hydra.el: Likewise. * emacs/guix-info.el: Likewise. * emacs/guix-init.el: Likewise. * emacs/guix-license.el: Likewise. * emacs/guix-list.el: Likewise. * emacs/guix-location.el: Likewise. * emacs/guix-main.scm: Likewise. * emacs/guix-messages.el: Likewise. * emacs/guix-pcomplete.el: Likewise. * emacs/guix-popup.el: Likewise. * emacs/guix-prettify.el: Likewise. * emacs/guix-profiles.el: Likewise. * emacs/guix-read.el: Likewise. * emacs/guix-ui-generation.el: Likewise. * emacs/guix-ui-license.el: Likewise. * emacs/guix-ui-location.el: Likewise. * emacs/guix-ui-package.el: Likewise. * emacs/guix-ui-system-generation.el: Likewise. * emacs/guix-ui.el: Likewise. * emacs/guix-utils.el: Likewise. * emacs/local.mk: Likewise. * doc/emacs.texi: Likewise. * doc/guix.texi: Remove cross-references to Emacs nodes. (Package Management): Mention 'emacs-guix' package. * doc/contributing.texi (The Perfect Setup): Remove the reference. * doc/htmlxref.cnf: Add 'emacs-guix' URL. * Makefile.am: Remove Emacs stuff. * configure.ac: Likewise. * gnu/packages/package-management.scm (guix-0.12.0)[native-inputs]: Remove "emacs". [propagated-inputs]: Remove "geiser" and "emacs-magit-popup". Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2016-12-29gnu: r-colorspace: Update to 1.3-2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-colorspace): Update to 1.3-2.
2016-12-29gnu: Add r-statmod.Raoul Jean Pierre Bonnal
* gnu/packages/statistics.scm (r-statmod): New variable.
2016-12-29gnu: Add r-ggbeeswarm.Raoul Jean Pierre Bonnal
* gnu/packages/statistics.scm (r-ggbeeswarm): New variable.
2016-12-29gnu: Add r-sourcetools.Raoul Jean Pierre Bonnal
* gnu/packages/statistics.scm (r-sourcetools): New variable.
2016-12-29gnu: Add r-beeswarm.Raoul Jean Pierre Bonnal
* gnu/packages/statistics.scm (r-beeswarm): New variable.
2016-12-29gnu: Add r-vipor.Raoul Jean Pierre Bonnal
* gnu/packages/statistics.scm (r-vipor): New variable.
2016-12-29gnu: libpng-1.2: Update to 1.2.57 [security update].Leo Famulari
* gnu/packages/image.scm (libpng-1.2): Update to 1.2.57. [replacement]: New field.
2016-12-29gnu: libpng: Fix a null pointer dereference [fixes security issue].Leo Famulari
* gnu/packages/patches/libpng-fix-null-ptr-dereference.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/image.scm (libpng)[replacement]: New field. (libpng/fixed): New variable.
2016-12-29daemon: Allow fixed-output derivation builds with TMPDIR set.Ludovic Courtès
Fixes <http://bugs.gnu.org/25242>. Reported by Leo Famulari <leo@famulari.name>. The regression was introduced in 94d92c7796a3dd50c27d532315f7d497ac99f08e. * nix/libstore/build.cc (DerivationGoal::startBuilder): Set 'useChroot' as a function 'of isBuiltin(drv)'. (DerivationGoal::runChild): Use 'useChroot' instead of 'useChroot && !isBuiltin(drv)'.
2016-12-29import: elpa: Import dependencies as propagated-inputsCarlo Zancanaro
* guix/import/elpa.scm (elpa-package->sexp): Import dependencies as propagated-inputs. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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