Commit Graph

40425 Commits

Author SHA1 Message Date
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
Gabriel Hondet 88d7101798
gnu: Add emacs-general.
[[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>
2019-01-11 12:14:38 +01:00
Ludovic Courtès 84a2de36a1
services: Deprecate a few more service procedures.
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.
2019-01-11 12:14:38 +01:00
Ludovic Courtès babfd9447d
tests: Nitpick on Docker test.
This is a followup to 7d8a4eeacc.

* gnu/local.mk (GNU_SYSTEM_MODULES): Add gnu/tests/docker.scm.
* gnu/tests/docker.scm: Update copyright line.
2019-01-11 12:14:37 +01:00
Rutger Helling cb2ad4f508
gnu: wine-staging: Hard-code vulkan loader.
* gnu/packages/wine.scm (wine-staging-patchset-data): Fix indentation.
* gnu/packages/wine.scm (wine-staging)[arguments]: Add 'wrap-executable phase.
* gnu/packages/wine.scm (wine64-staging)[arguments]: Add 'wrap-executable
phase. Copy the real wine-preloader instead of the wrapped version.
2019-01-11 11:15:13 +01:00
Ricardo Wurmus e7c6bc45ed
gnu: jamm: Remove broken "build" phase.
* gnu/packages/bioinformatics.scm (jamm)[arguments]: Remove "build" phase.
2019-01-11 06:08:43 +01:00
Danny Milosavljevic 9757b57f4e
services: docker: Update comment.
* gnu/services/docker.scm (docker-shepherd-service): Update comment.
2019-01-11 02:53:28 +01:00
Leo Famulari adf0b482eb
gnu: gexiv2: Update to 0.10.10.
* gnu/packages/gnome.scm (gexiv2): Update to 0.10.10.
2019-01-10 18:45:41 -05:00
Ricardo Wurmus bf6fb59a33
build-system: texlive: Do not hide build output.
* guix/build/texlive-build-system.scm (compile-with-latex): Use "nonstopmode"
instead of "batchmode".
2019-01-10 22:43:09 +01:00
Ricardo Wurmus ac5c9f6ba6
build-system: texlive: Do not truncate lines.
* guix/build/texlive-build-system.scm (configure): Set environment variables
to prevent build output lines from being truncated.
2019-01-10 22:43:09 +01:00
Ricardo Wurmus d4d9a1ece0
gnu: Update texlive packages.
* guix/build-system/texlive.scm (%texlive-tag, %texlive-revision): Update to
texlive-2018.2, revision 49435.
* gnu/packages/tex.scm (texlive-dvips, texlive-generic-unicode-data,
texlive-generic-dehyph-exptl, texlive-generic-hyph-utf8, texlive-fontname,
texlive-fonts-cm, texlive-tex-plain, texlive-latex-base,
texlive-latex-graphics, texlive-latex-graphics, texlive-latex-oberdiek,
texlive-latex-tools, texlive-latex-l3kernel, texlive-latex-l3packages,
texlive-latex-fontspec, texlive-latex-amsmath, texlive-latex-amscls,
texlive-latex-babel, texlive-latex-cyrillic, texlive-latex-eqparbox,
texlive-latex-ifplatform, texlive-latex-etoolbox, texlive-latex-galois,
texlive-latex-polyglossia, texlive-tex-texinfo, texlive-latex-changebar,
texlive-latex-fancyhdr, texlive-latex-overpic, texlive-latex-parskip,
texlive-metapost, texlive-latex-ucs, texlive-generic-pdftex,
texlive-latex-media9, texlive-latex-ocgx2, texlive-latex-koma-script,
texlive-generic-listofitems, texlive-bibtex, texlive-context-base): Update
hashes.
(texlive-latex-fontspec)[arguments]: Remove custom build target.
(texlive-latex-dinbrief)[arguments]: Add build phase "fix-encoding-error".
(texlive-latex-xkeyval): New variable.
(texlive-latex-pstool)[source]: Fetch from new location.
[build-system]: Use trivial-build-system.
[arguments]: Write simple builder.
[propagated-inputs]: Add texlive-latex-l3kernel, texlive-latex-tools, and
texlive-latex-xkeyval.
[synopsis]: Fix typo.
2019-01-10 22:43:09 +01:00
Kei Kebreau c954fe6622
gnu: irssi: Update to 1.1.2 [fixes CVE-2019-5882].
* gnu/packages/irc.scm (irssi): Update to 1.1.2.
2019-01-10 16:05:42 -05:00
Danny Milosavljevic ffcd282702
gnu: docker: Booby-trap "Command" and "LookPath" calls.
* gnu/packages/docker.scm (docker)[arguments]<#:phases>[patch-paths]:
Booby-trap "Command" and "LookPath" calls.
2019-01-10 21:29:53 +01:00