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2019-01-12gnu: r-commonmark: Update to 1.7.Ricardo Wurmus
* gnu/packages/statistics.scm (r-commonmark): Update to 1.7.
2019-01-12gnu: r-checkmate: Update to 1.9.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-checkmate): Update to 1.9.0.
2019-01-12gnu: r-backports: Update to 1.1.3.Ricardo Wurmus
* gnu/packages/statistics.scm (r-backports): Update to 1.1.3.
2019-01-12gnu: r-dbplyr: Update to 1.3.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-dbplyr): Update to 1.3.0.
2019-01-12gnu: r-tibble: Update to 2.0.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-tibble): Update to 2.0.0. [propagated-inputs]: Add r-fansi and r-pkgconfig.
2019-01-12gnu: r-rlang: Update to 0.3.1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rlang): Update to 0.3.1.
2019-01-12gnu: r-knitr: Update to 1.21.Ricardo Wurmus
* gnu/packages/statistics.scm (r-knitr): Update to 1.21. [propagated-inputs]: Add r-xfun.
2019-01-12gnu: r-markdown: Update to 0.9.Ricardo Wurmus
* gnu/packages/statistics.scm (r-markdown): Update to 0.9.
2019-01-12gnu: r-bh: Update to 1.69.0-1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-bh): Update to 1.69.0-1.
2019-01-12gnu: r-pheatmap: Update to 1.0.12.Ricardo Wurmus
* gnu/packages/statistics.scm (r-pheatmap): Update to 1.0.12.
2019-01-12gnu: r-mgcv: Update to 1.8-26.Ricardo Wurmus
* gnu/packages/statistics.scm (r-mgcv): Update to 1.8-26.
2019-01-12gnu: r-codetools: Update to 0.2-16.Ricardo Wurmus
* gnu/packages/statistics.scm (r-codetools): Update to 0.2-16.
2019-01-12gnu: r-class: Update to 7.3-15.Ricardo Wurmus
* gnu/packages/statistics.scm (r-class): Update to 7.3-15.
2019-01-12gnu: r-survival: Update to 2.43-3.Ricardo Wurmus
* gnu/packages/statistics.scm (r-survival): Update to 2.43-3.
2019-01-12gnu: r-argparse: Update to 2.0.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-argparse): Update to 2.0.0. [propagated-inputs]: Add r-r6; remove r-proto.
2019-01-12gnu: r-callr: Update to 3.1.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-callr): Update to 3.1.1. [propagated-inputs]: Remove r-base64enc.
2019-01-12gnu: r-readxl: Update to 1.2.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-readxl): Update to 1.2.0. [propagated-inputs]: Add r-progress.
2019-01-12gnu: r-pracma: Update to 2.2.2.Ricardo Wurmus
* gnu/packages/maths.scm (r-pracma): Update to 2.2.2.
2019-01-12gnu: r-rcpparmadillo: Update to 0.9.200.5.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.9.200.5.0.
2019-01-12gnu: r-processx: Update to 3.2.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-processx): Update to 3.2.1. [propagated-inputs]: Remove r-assertthat, r-crayon, and r-testthat.
2019-01-12gnu: r-sjlabelled: Update to 1.0.16.Ricardo Wurmus
* gnu/packages/cran.scm (r-sjlabelled): Update to 1.0.16. [propagated-inputs]: Remove r-tibble and r-tidyselect.
2019-01-12gnu: r-broom: Update to 0.5.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-broom): Update to 0.5.1. [propagated-inputs]: Add r-generics.
2019-01-12gnu: Add r-generics.Ricardo Wurmus
* gnu/packages/cran.scm (r-generics): New variable.
2019-01-12gnu: r-curl: Update to 3.3.Ricardo Wurmus
* gnu/packages/cran.scm (r-curl): Update to 3.3. [inputs]: Add zlib. [native-inputs]: Add pkg-config.
2019-01-12gnu: r-readr: Update to 1.3.1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-readr): Update to 1.3.1. [propagated-inputs]: Add r-clipr and r-crayon.
2019-01-12gnu: r-mvabund: Update to 4.0.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-mvabund): Update to 4.0.1.
2019-01-12gnu: r-writexl: Update to 1.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-writexl): Update to 1.1.
2019-01-12gnu: r-jsonlite: Update to 1.6.Ricardo Wurmus
* gnu/packages/cran.scm (r-jsonlite): Update to 1.6.
2019-01-12import: cran: Suggest input changes.Ricardo Wurmus
* guix/import/cran.scm (latest-cran-release, latest-bioconductor-release): Return input-changes.
2019-01-12refresh: Suggest input changes when updating.Ricardo Wurmus
* guix/upstream.scm (<upstream-source>)[input-changes]: New field. (<upstream-input-change>): New record. (upstream-input-change?, upstream-input-change-name, upstream-input-change-type, upstream-input-change-action, changed-inputs): New procedures. (package-update): Pass along input changes. * guix/script/refresh.scm (update-package): Process input changes.
2019-01-12gnu: python-pillow: Update homepage.Kei Kebreau
* gnu/packages/python.scm (python-pillow)[homepage]: Update URL.
2019-01-12gnu: python-pillow: Update to 5.4.0Kei Kebreau
* gnu/packages/python.scm (python-pillow): Update to 5.4.0. [arguments]: Add 'patch-ldconfig' phase.
2019-01-12gnu: Sort package modules in (gnu packages guile).Ricardo Wurmus
* gnu/packages/guile.scm: Sort list of gnu/packages modules.
2019-01-12gnu: impressive: Update to 0.12.0.Ricardo Wurmus
* gnu/packages/pdf.scm (impressive): Update to 0.12.0.
2019-01-12gnu: Move Java compression packages to new module.Ricardo Wurmus
* gnu/packages/compression.scm (bitshuffle-for-snappy): Export variable. (java-snappy, java-snappy-1, java-iq80-snappy, java-jbzip2, java-tukaani-xz): Move these variables from here... * gnu/packages/java-compression.scm: ...to this new file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. * gnu/packages/java.scm, gnu/packages/bioinformatics.scm: Adjust module references.
2019-01-11gnu: Add Bochs.guy fleury iteriteka
* gnu/packages/virtualization.scm (bochs): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
2019-01-11gnu: Stellarium: Update to 0.18.3.Leo Famulari
* gnu/packages/astronomy.scm (stellarium): Update to 0.18.3. [arguments]: Skip a broken test.
2019-01-11gnu: opendht: Make argon2 a propagated input so that its .pc is found.Pierre Neidhardt
* gnu/packages/networking.scm (opendht)[inputs]: Remove argon2. [propagated-inputs]: Add it here.
2019-01-11gnu: opendht: Use jsoncpp and restbed.Pierre Neidhardt
* gnu/packages/crypto.scm (opendht): Move definition to networking.scm. * gnu/packages/networking.scm (opendht)[inputs]: Add jsoncpp and restbed.
2019-01-11gnu: Add restbed.Pierre Neidhardt
* gnu/packages/networking.scm (restbed): New variable.
2019-01-11gnu: libupnp: Update to 1.6.25.Pierre Neidhardt
* gnu/packages/upnp.scm (libupnp): Update to 1.6.25.
2019-01-11gnu: kinit: Use KDEINIT5_LIBRARY_PATH to search for dynlibs.Hartmut Goebel
Using LIBRARY_PATH was introduced in 16b8aff85bcdb9799496c4a27257210cd45158e5, but is wrong since this variable is used by the compiler (gcc) at link time. * gnu/packages/patches/kinit-kdeinit-libpath.patch: Change LIBRARY_PATH to KDEINIT5_LIBRARY_PATH. * gnu/packages/kde-frameworks.scm (kinit)[native-search-paths]: New field.
2019-01-11Revert "gnu: emacs-ghub: Update to 3.2.0."Jelle Licht
This change should be applied once we update our magit package. This reverts commit b96f0e6ff9f8f36d250b5ae94a908272babb35cf.
2019-01-11guix build: Re-purpose '--verbosity' and add '--debug'.Ludovic Courtès
The previous '--verbosity' option was misleading and rarely what users were looking for. The new option provides a consistent way to choose whether or not to display the build log. * guix/scripts/build.scm (show-build-options-help): Remove "--verbosity" and add "--debug". (set-build-options-from-command-line): Use the 'debug key of OPTS for #:verbosity. (%standard-build-options): Change "verbosity" to "debug". Use 'string->number*' instead of 'string->number'. (%default-options): Change 'verbosity to 'debug and add a 'verbosity key. (show-help): Add '--verbosity'. (%options): Likewise, and change '--quiet' to set the 'verbosity key of RESULT. (guix-build): Use 'with-status-verbosity' instead of parameterizing CURRENT-BUILD-OUTPUT-PORT, honor the 'verbosity key of OPTS, and remove 'quiet?'. * guix/scripts/environment.scm (show-help, %options): Add '--verbosity'. (%default-options): Add 'debug'. (guix-environment): Honor the 'verbosity key of OPTS. * guix/scripts/pack.scm (%default-options): Add 'debug. (%options, show-help): Add '--verbosity'. (guix-pack): Honor the 'verbosity key of OPTS. * guix/scripts/package.scm (%default-options): Add 'debug. (show-help, %options): Add '--verbosity'. Mark '--verbose' as deprecated and change it to set 'verbosity. (guix-package): Honor the 'verbosity key of OPTS and remove 'verbose?'. * guix/scripts/pull.scm (%default-options): Add 'debug. (show-help, %options): Add '--verbosity'. (guix-pull): Honor the 'verbosity key of OPTS. * guix/scripts/system.scm (show-help, %options): Add '--verbosity'. (%default-options): Add 'debug. (guix-system): Honor the 'verbosity key of OPTS. * guix/scripts/archive.scm (%default-options): Add 'debug, 'print-build-trace?, 'print-extended-build-trace?, and 'multiplexed-build-output?. (show-help, %options): Add '--verbosity'. (export-from-store): Remove call to 'set-build-options-from-command-line'. (guix-archive): Wrap body in 'with-status-verbosity'. Add call to 'set-build-options-from-command-line. * doc/guix.texi (Common Build Options): Document '--verbosity' and '--debug'. (Additional Build Options): Adjust description of '--quiet'.
2019-01-11status: Add 'with-status-verbosity'.Ludovic Courtès
* guix/status.scm (logger-for-level, call-with-status-verbosity): New procedures. (with-status-verbosity): New macro. * guix/scripts/environment.scm (guix-environment): Use 'with-status-verbosity' instead of 'with-status-report'. * guix/scripts/pack.scm (guix-pack): Likewise. * guix/scripts/package.scm (guix-package): Likewise. * guix/scripts/pull.scm (guix-pull): Likewise. * guix/scripts/system.scm (guix-system): Likewise. * build-aux/run-system-tests.scm (run-system-tests): Likewise.
2019-01-11refresh: Turn on warnings when '--manifest' is used.Ludovic Courtès
* guix/scripts/refresh.scm (guix-refresh): Set WARN? when '-m' is used.
2019-01-11refresh: Refactor option handling and '--recursive'.Ludovic Courtès
This allows us to combine '--recursive' with other options (-u, -m, etc.), turns off warnings when '--recursive' is used, and avoids the hazards of I/O in the presence of multithreading. * guix/scripts/refresh.scm (options->packages): New procedure, with code formerly in 'guix-refresh'. (refresh-recursive): Remove. (guix-refresh)[keep-newest, core-package?, args-packages, packages]: Remove. [warn?]: Set to #f when RECURSIVE? is true. Call 'options->packages' in monadic context.
2019-01-11gnu: Add emacs-general.Gabriel Hondet
[[PGP Signed Part:Good signature from 31BC8105F659D425 Gabriel Hondet <gabrielhondet@gmail.com> (trust undefined) created at 2019-01-06T10:42:43+0100 using RSA]] * gnu/packages/emacs.scm (emacs-general): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2019-01-11services: Deprecate a few more service procedures.Ludovic Courtès
These procedures were already either undocumented (and de facto deprecated) or documented as deprecated or redundant. * gnu/services/base.scm (guix-service, guix-publish-service): Mark as deprecated. * gnu/services/mcron.scm (mcron-service): Likewise. * gnu/services/networking.scm (tor-service): Likewise. * doc/guix.texi (Scheduled Job Execution): Remove 'mcron-service' and adjust example. (Networking Services): Remove 'tor-service'. * gnu/tests/base.scm (%mcron-os): Use 'mcron-service-type' instead of 'mcron-service'. * gnu/tests/networking.scm (%tor-os): Use 'tor-service-type' instead of 'tor-service'. * tests/guix-system.sh: Likewise.
2019-01-11tests: Nitpick on Docker test.Ludovic Courtès
This is a followup to 7d8a4eeacc534c8742e0b22d855aa73e5ab66b7f. * gnu/local.mk (GNU_SYSTEM_MODULES): Add gnu/tests/docker.scm. * gnu/tests/docker.scm: Update copyright line.
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