4929a30f69
gnu: r-variantannotation: Update to 1.30.1.
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* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.30.1.
2019-05-29 00:02:10 +02:00
531940d388
import: cran: Ignore invalid packages from the system requirements.
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* guix/import/cran.scm (description->package): Filter invalid packages from
the list of system requirements.
2019-05-28 23:56:59 +02:00
e4519ee73d
gnu: r-atacseqqc: Update to 1.8.1.
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* gnu/packages/bioconductor.scm (r-atacseqqc): Update to 1.8.1.
2019-05-28 23:56:36 +02:00
13b49976b7
gnu: r-icobra: Update to 1.12.1.
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* gnu/packages/bioconductor.scm (r-icobra): Update to 1.12.1.
2019-05-28 23:56:31 +02:00
85d0bd5340
gnu: r-chippeakanno: Update to 3.18.1.
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* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.18.1.
2019-05-28 23:56:27 +02:00
f43ec9e96a
gnu: r-geosphere: Update to 1.5-10.
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* gnu/packages/cran.scm (r-geosphere): Update to 1.5-10.
2019-05-28 23:56:15 +02:00
0fe52daa59
gnu: r-ggfortify: Update to 0.4.7.
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* gnu/packages/cran.scm (r-ggfortify): Update to 0.4.7.
2019-05-28 23:56:08 +02:00
7a8577717f
gnu: r-wgcna: Update to 1.68.
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* gnu/packages/cran.scm (r-wgcna): Update to 1.68.
2019-05-28 23:56:04 +02:00
650e8defa0
gnu: r-bookdown: Update to 0.11.
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* gnu/packages/cran.scm (r-bookdown): Update to 0.11.
[propagated-inputs]: Add ghc-pandoc; remove r-yaml.
2019-05-28 23:55:44 +02:00
20656a0202
gnu: r-upsetr: Update to 1.4.0.
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* gnu/packages/cran.scm (r-upsetr): Update to 1.4.0.
2019-05-28 23:55:38 +02:00
41059f63df
gnu: r-epi: Update to 2.37.
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* gnu/packages/cran.scm (r-epi): Update to 2.37.
2019-05-28 23:55:33 +02:00
9a749cad19
gnu: r-etm: Update to 1.0.5.
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* gnu/packages/cran.scm (r-etm): Update to 1.0.5.
2019-05-28 23:55:27 +02:00
10dbc3fc54
gnu: r-cmprsk: Update to 2.2-8.
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* gnu/packages/cran.scm (r-cmprsk): Update to 2.2-8.
2019-05-28 23:55:21 +02:00
fa10f0d330
gnu: r-ks: Update to 1.11.5.
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* gnu/packages/cran.scm (r-ks): Update to 1.11.5.
2019-05-28 23:55:14 +02:00
1d7bde781f
gnu: r-bayesplot: Update to 1.7.0.
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* gnu/packages/cran.scm (r-bayesplot): Update to 1.7.0.
[propagated-inputs]: Add r-glue, r-tibble, and r-tidyselect.
2019-05-28 23:54:53 +02:00
27abdb11ae
gnu: r-refgenome: Update to 1.7.7.
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* gnu/packages/cran.scm (r-refgenome): Update to 1.7.7.
2019-05-28 23:54:46 +02:00
794c9e7d96
gnu: r-snakecase: Update to 0.11.0.
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* gnu/packages/cran.scm (r-snakecase): Update to 0.11.0.
2019-05-28 23:54:40 +02:00
9dd351233b
gnu: r-openxlsx: Update to 4.1.0.1.
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* gnu/packages/cran.scm (r-openxlsx): Update to 4.1.0.1.
2019-05-28 23:54:36 +02:00
d328379d62
gnu: r-pillar: Update to 1.4.1.
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* gnu/packages/cran.scm (r-pillar): Update to 1.4.1.
2019-05-28 23:54:32 +02:00
130314d8fa
gnu: r-tsp: Update to 1.1-7.
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* gnu/packages/cran.scm (r-tsp): Update to 1.1-7.
2019-05-28 23:54:26 +02:00
6d3cfb88ea
gnu: r-jomo: Update to 2.6-8.
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* gnu/packages/cran.scm (r-jomo): Update to 2.6-8.
2019-05-28 23:54:18 +02:00
beb82eb9d0
gnu: r-ksamples: Update to 1.2-9.
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* gnu/packages/cran.scm (r-ksamples): Update to 1.2-9.
2019-05-28 23:54:12 +02:00
6edf0fb3db
gnu: r-lpsolve: Update to 5.6.13.1.
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* gnu/packages/cran.scm (r-lpsolve): Update to 5.6.13.1.
2019-05-28 23:54:07 +02:00
14532452b8
gnu: r-car: Update to 3.0-3.
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* gnu/packages/statistics.scm (r-car): Update to 3.0-3.
2019-05-28 23:54:00 +02:00
341643c6e1
gnu: r-fpc: Update to 2.2-1.
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* gnu/packages/statistics.scm (r-fpc): Update to 2.2-1.
[propagated-inputs]: Remove r-trimcluster.
2019-05-28 23:53:43 +02:00
f95690ceae
gnu: r-prabclus: Update to 2.2-7.1.
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* gnu/packages/statistics.scm (r-prabclus): Update to 2.2-7.1.
2019-05-28 23:53:33 +02:00
1498b5a2a4
gnu: r-zoo: Update to 1.8-6.
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* gnu/packages/statistics.scm (r-zoo): Update to 1.8-6.
2019-05-28 23:53:28 +02:00
3fca3fa1bc
gnu: r-rmarkdown: Update to 1.13.
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* gnu/packages/statistics.scm (r-rmarkdown): Update to 1.13.
[propagated-inputs]: Add r-xfun.
2019-05-28 23:53:15 +02:00
923c6ac139
gnu: r-evaluate: Update to 0.14.
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* gnu/packages/statistics.scm (r-evaluate): Update to 0.14.
2019-05-28 23:53:02 +02:00
fa86654824
self: Fix unquoting.
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This is a follow-up to commit dfc69e4b6d
2019-05-28 23:21:27 +02:00
67458e209d
gnu: python-attrs: Update to 19.1.0.
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* gnu/packages/python-xyz.scm (python-attrs): Update to 19.1.0.
Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
2019-05-28 21:48:10 +02:00
205eb40e5b
gnu: python-flask: Update to 1.0.3.
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* gnu/packages/python-web.scm (python-flask): Update to 1.0.3.
Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
2019-05-28 21:18:24 +02:00
458e92215f
gnu: d-feet: Fix missing input and update to 0.3.14.
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* gnu/packages/gnome.scm (d-feet): Update to 0.3.14.
[inputs]: Add hicolor-icon-theme since d-feet won't list anything without it.
2019-05-28 14:53:02 +02:00
e7f078c337
gnu: guix: Update to 35d1354.
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* gnu/packages/package-management.scm (guix): Update to 35d1354
2019-05-28 09:51:12 +02:00
70fa77d881
gnu: emacs-relint: Update to 1.8.
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* gnu/packages/emacs-xyz.scm (emacs-relint): Update to 1.8.
2019-05-27 23:22:34 +02:00
d8d896c5b5
gnu: emacs-xr: Update to 1.12.
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* gnu/packages/emacs-xyz.scm (emacs-xr): Update to 1.12.
2019-05-27 23:22:19 +02:00
35d1354fe8
publish: Display the compression method and level in use.
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* guix/scripts/publish.scm (guix-publish): Use 'info' instead of
'format' for the initial message. When COMPRESSION is true, display the
method and level in use.
2019-05-27 22:47:24 +02:00
c131bea276
lzlib: 'lzread!' never returns more than it was asked for.
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Fixes a bug whereby 'lzread!' could return more than COUNT.
* guix/lzlib.scm (lzread!): Rewrite in a semi-functional style.
2019-05-27 22:47:24 +02:00
2e5c71b2a2
gnu: guix: Add dependency on lzlib.
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* gnu/packages/package-management.scm (guix)[inputs]: Add LZLIB.
2019-05-27 22:47:24 +02:00
73ac9098b1
self: Add dependency on lzlib.
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* guix/self.scm (compiled-guix): Pass #:lzlib to 'make-config.scm'.
(make-config.scm): Add #:lzlib and honor it.
(specification->package): Add "lzlib".
2019-05-27 22:47:24 +02:00
66229b04ae
publish: Add support for lzip.
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* guix/scripts/publish.scm (show-help, %options): Support '-C METHOD'
and '-C METHOD:LEVEL'.
(default-compression): New procedure.
(bake-narinfo+nar): Add lzip.
(nar-response-port): Likewise.
(string->compression-type): New procedure.
(make-request-handler): Generalize /nar/gzip handler to handle /nar/lzip
as well.
* tests/publish.scm ("/nar/lzip/*"): New test.
("/*.narinfo with lzip compression"): New test.
* doc/guix.texi (Invoking guix publish): Document it.
(Requirements): Mention lzlib.
2019-05-27 22:47:24 +02:00
4e48923e75
utils: Support compression and decompression with lzip.
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* guix/utils.scm (lzip-port): New procedure.
(decompressed-port, compressed-port, compressed-output-port): Add 'lzip
case.
* tests/utils.scm <top level>: Call 'test-compression/decompression' for
'lzip as well.
2019-05-27 22:47:24 +02:00
4c7ebe318f
utils: Test 'compressed-port' and 'decompressed-port' for both gzip and xz.
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* tests/utils.scm (test-compression/decompression): New procedure.
<top level>: Call it for both 'xz and 'gzip.
2019-05-27 22:47:24 +02:00
2a991f3ae4
lzlib: Add 'make-lzip-input-port/compressed'.
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* guix/lzlib.scm (lzwrite!, make-lzip-input-port/compressed): New
procedures.
* tests/lzlib.scm ("make-lzip-input-port/compressed"): New test.
* guix/tests.scm (%seed): Export.
2019-05-27 22:47:24 +02:00
e13354a7ca
lzlib: Adjust 'lz-compress-read' docstring.
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* guix/lzlib.scm (lz-compress-read): The integer return can be zero;
adjust docstring accordingly.
2019-05-27 22:47:23 +02:00
8916034a34
gnu: r-shiny: Fix JavaScript minification.
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Fixes <https://bugs.gnu.org/35923 >.
* gnu/packages/cran.scm (r-shiny)[native-inputs]: Add uglify-js.
2019-05-27 22:09:22 +02:00
ed72a133db
gnu: Add osmctools
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* gnu/packages/geo.scm (osmctools): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
2019-05-27 14:32:13 -04:00
521d736ae9
gnu: go@1.4: Update to 1.4-bootstrap-20171003.
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* gnu/packages/golang.scm (go-1.4): Use the bootstrap branch that is
still supported upstream.
[version]: Update to 1.4-bootstrap-20171003.
[arguments]: Remove obsolete fix for timezone test which is now included
upstream. Don't manually disable cgo because it is disabled by default.
Manually enable test suite because future releases will disable tests by
default.
Signed-off-by: Leo Famulari <leo@famulari.name>
2019-05-27 14:26:46 -04:00
8d1647b228
gnu: python-alembic: Update to 1.0.10.
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* gnu/packages/databases.scm (python-alembic): Update to 1.0.10.
2019-05-27 18:16:25 +02:00
f644f63655
doc: Update default value of terminal-outputs.
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* doc/guix.texi: (terminal-outputs) Update default value.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2019-05-27 16:44:53 +02:00
Ricardo Wurmus