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39390 Commits

Author SHA1 Message Date
Ricardo Wurmus fb45934202
gnu: r-rstudioapi: Update to 0.9.0. 
* gnu/packages/statistics.scm (r-rstudioapi): Update to 0.9.0.
 2019-01-12 23:35:13 +01:00
Ricardo Wurmus 8f49d99a84
gnu: r-git2r: Update to 0.24.0. 
* gnu/packages/statistics.scm (r-git2r): Update to 0.24.0.
 2019-01-12 23:35:13 +01:00
Ricardo Wurmus c12e429348
gnu: r-httr: Update to 1.4.0. 
* gnu/packages/statistics.scm (r-httr): Update to 1.4.0.
 2019-01-12 23:35:13 +01:00
Ricardo Wurmus 02c89c5812
gnu: r-commonmark: Update to 1.7. 
* gnu/packages/statistics.scm (r-commonmark): Update to 1.7.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus fe8c44502b
gnu: r-checkmate: Update to 1.9.0. 
* gnu/packages/statistics.scm (r-checkmate): Update to 1.9.0.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus ca4861c602
gnu: r-backports: Update to 1.1.3. 
* gnu/packages/statistics.scm (r-backports): Update to 1.1.3.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus 23347dc353
gnu: r-dbplyr: Update to 1.3.0. 
* gnu/packages/statistics.scm (r-dbplyr): Update to 1.3.0.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus f12ed3664d
gnu: r-tibble: Update to 2.0.0. 
* gnu/packages/statistics.scm (r-tibble): Update to 2.0.0.
[propagated-inputs]: Add r-fansi and r-pkgconfig.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus c668a95861
gnu: r-rlang: Update to 0.3.1. 
* gnu/packages/statistics.scm (r-rlang): Update to 0.3.1.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus 495866a9d7
gnu: r-knitr: Update to 1.21. 
* gnu/packages/statistics.scm (r-knitr): Update to 1.21.
[propagated-inputs]: Add r-xfun.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus bf3aded0cf
gnu: r-markdown: Update to 0.9. 
* gnu/packages/statistics.scm (r-markdown): Update to 0.9.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus eae93bd3f2
gnu: r-bh: Update to 1.69.0-1. 
* gnu/packages/statistics.scm (r-bh): Update to 1.69.0-1.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus b6e27673e6
gnu: r-pheatmap: Update to 1.0.12. 
* gnu/packages/statistics.scm (r-pheatmap): Update to 1.0.12.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus ca2bc7e037
gnu: r-mgcv: Update to 1.8-26. 
* gnu/packages/statistics.scm (r-mgcv): Update to 1.8-26.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus 60f1bce09f
gnu: r-codetools: Update to 0.2-16. 
* gnu/packages/statistics.scm (r-codetools): Update to 0.2-16.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus 3dbd87f504
gnu: r-class: Update to 7.3-15. 
* gnu/packages/statistics.scm (r-class): Update to 7.3-15.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus 35cf4874cc
gnu: r-survival: Update to 2.43-3. 
* gnu/packages/statistics.scm (r-survival): Update to 2.43-3.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus 11a36548d9
gnu: r-argparse: Update to 2.0.0. 
* gnu/packages/cran.scm (r-argparse): Update to 2.0.0.
[propagated-inputs]: Add r-r6; remove r-proto.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus 527c605598
gnu: r-callr: Update to 3.1.1. 
* gnu/packages/cran.scm (r-callr): Update to 3.1.1.
[propagated-inputs]: Remove r-base64enc.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus b140569e18
gnu: r-readxl: Update to 1.2.0. 
* gnu/packages/cran.scm (r-readxl): Update to 1.2.0.
[propagated-inputs]: Add r-progress.
 2019-01-12 23:35:11 +01:00
Ricardo Wurmus 0aad198e2b
gnu: r-pracma: Update to 2.2.2. 
* gnu/packages/maths.scm (r-pracma): Update to 2.2.2.
 2019-01-12 23:35:11 +01:00
Ricardo Wurmus 44c69a536e
gnu: r-rcpparmadillo: Update to 0.9.200.5.0. 
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.9.200.5.0.
 2019-01-12 23:35:11 +01:00
Ricardo Wurmus 0e87bf0177
gnu: r-processx: Update to 3.2.1. 
* gnu/packages/cran.scm (r-processx): Update to 3.2.1.
[propagated-inputs]: Remove r-assertthat, r-crayon, and r-testthat.
 2019-01-12 23:35:11 +01:00
Ricardo Wurmus 2766d3436a
gnu: r-sjlabelled: Update to 1.0.16. 
* gnu/packages/cran.scm (r-sjlabelled): Update to 1.0.16.
[propagated-inputs]: Remove r-tibble and r-tidyselect.
 2019-01-12 23:35:11 +01:00
Ricardo Wurmus 813d9c51e3
gnu: r-broom: Update to 0.5.1. 
* gnu/packages/cran.scm (r-broom): Update to 0.5.1.
[propagated-inputs]: Add r-generics.
 2019-01-12 23:35:11 +01:00
Ricardo Wurmus 25c67ecfc6
gnu: Add r-generics. 
* gnu/packages/cran.scm (r-generics): New variable.
 2019-01-12 23:35:11 +01:00
Ricardo Wurmus 646e1ef059
gnu: r-curl: Update to 3.3. 
* gnu/packages/cran.scm (r-curl): Update to 3.3.
[inputs]: Add zlib.
[native-inputs]: Add pkg-config.
 2019-01-12 23:35:11 +01:00
Ricardo Wurmus ef91530362
gnu: r-readr: Update to 1.3.1. 
* gnu/packages/statistics.scm (r-readr): Update to 1.3.1.
[propagated-inputs]: Add r-clipr and r-crayon.
 2019-01-12 23:35:11 +01:00
Ricardo Wurmus 48102ce123
gnu: r-mvabund: Update to 4.0.1. 
* gnu/packages/cran.scm (r-mvabund): Update to 4.0.1.
 2019-01-12 23:35:11 +01:00
Ricardo Wurmus 04a18a81ae
gnu: r-writexl: Update to 1.1. 
* gnu/packages/cran.scm (r-writexl): Update to 1.1.
 2019-01-12 23:35:11 +01:00
Ricardo Wurmus a2315c6702
gnu: r-jsonlite: Update to 1.6. 
* gnu/packages/cran.scm (r-jsonlite): Update to 1.6.
 2019-01-12 23:35:11 +01:00
Ricardo Wurmus 91e05559bd
import: cran: Suggest input changes. 
* guix/import/cran.scm (latest-cran-release, latest-bioconductor-release):
Return input-changes.
 2019-01-12 23:35:11 +01:00
Ricardo Wurmus 7e634c2f53
refresh: Suggest input changes when updating. 
* 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.
 2019-01-12 23:35:11 +01:00
Kei Kebreau ea600ff709
gnu: python-pillow: Update homepage. 
* gnu/packages/python.scm (python-pillow)[homepage]: Update URL.
 2019-01-12 16:39:26 -05:00
Kei Kebreau acbf312573
gnu: python-pillow: Update to 5.4.0 
* gnu/packages/python.scm (python-pillow): Update to 5.4.0.
[arguments]: Add 'patch-ldconfig' phase.
 2019-01-12 16:38:36 -05:00
Ricardo Wurmus 146c6b62bf
gnu: Sort package modules in (gnu packages guile). 
* gnu/packages/guile.scm: Sort list of gnu/packages modules.
 2019-01-12 12:14:31 +01:00
Ricardo Wurmus 7d8baff97b
gnu: impressive: Update to 0.12.0. 
* gnu/packages/pdf.scm (impressive): Update to 0.12.0.
 2019-01-12 12:14:31 +01:00
Ricardo Wurmus 24155bf40d
gnu: Move Java compression packages to new module. 
* 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.
 2019-01-12 12:14:28 +01:00
guy fleury iteriteka 1704367719
gnu: Add Bochs. 
* gnu/packages/virtualization.scm (bochs): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2019-01-11 17:09:20 -05:00
Leo Famulari 81c64748ba
gnu: Stellarium: Update to 0.18.3. 
* gnu/packages/astronomy.scm (stellarium): Update to 0.18.3.
[arguments]: Skip a broken test.
 2019-01-11 17:07:55 -05:00
Pierre Neidhardt 1ac0c1b899
gnu: opendht: Make argon2 a propagated input so that its .pc is found. 
* gnu/packages/networking.scm (opendht)[inputs]: Remove argon2.
[propagated-inputs]: Add it here.
 2019-01-11 19:48:00 +01:00
Pierre Neidhardt e0fa641380
gnu: opendht: Use jsoncpp and restbed. 
* gnu/packages/crypto.scm (opendht): Move definition to networking.scm.
* gnu/packages/networking.scm (opendht)[inputs]: Add jsoncpp and restbed.
 2019-01-11 19:48:00 +01:00
Pierre Neidhardt 362fba83dd
gnu: Add restbed. 
* gnu/packages/networking.scm (restbed): New variable.
 2019-01-11 19:48:00 +01:00
Pierre Neidhardt 50e1843b3a
gnu: libupnp: Update to 1.6.25. 
* gnu/packages/upnp.scm (libupnp): Update to 1.6.25.
 2019-01-11 19:48:00 +01:00
Hartmut Goebel 46b082f97f
gnu: kinit: Use KDEINIT5_LIBRARY_PATH to search for dynlibs. 
Using LIBRARY_PATH was introduced in
16b8aff85b, 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.
 2019-01-11 16:35:52 +01:00
Jelle Licht 5a26f879c3
Revert "gnu: emacs-ghub: Update to 3.2.0." 
This change should be applied once we update our magit package.

This reverts commit b96f0e6ff9.
 2019-01-11 13:32:31 +01:00
Ludovic Courtès f1de676ea8
guix build: Re-purpose '--verbosity' and add '--debug'. 
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'.
 2019-01-11 12:14:38 +01:00
Ludovic Courtès 7804c45b9c
status: Add 'with-status-verbosity'. 
* 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.
 2019-01-11 12:14:38 +01:00
Ludovic Courtès 7489207ff7
refresh: Turn on warnings when '--manifest' is used. 
* guix/scripts/refresh.scm (guix-refresh): Set WARN? when '-m' is used.
 2019-01-11 12:14:38 +01:00
Ludovic Courtès fca43e14f7
refresh: Refactor option handling and '--recursive'. 
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.
 2019-01-11 12:14:38 +01:00