Commit Graph

46769 Commits

Author SHA1 Message Date
Ricardo Wurmus 22b2d8b97f
gnu: r-quantmod: Update to 0.4-15.
* gnu/packages/cran.scm (r-quantmod): Update to 0.4-15.
2019-06-29 01:34:43 +02:00
Ricardo Wurmus f5ec882390
gnu: r-tinytex: Update to 0.14.
* gnu/packages/cran.scm (r-tinytex): Update to 0.14.
2019-06-29 01:34:43 +02:00
Ricardo Wurmus db794146ac
gnu: r-xfun: Update to 0.8.
* gnu/packages/cran.scm (r-xfun): Update to 0.8.
2019-06-29 01:34:43 +02:00
Ricardo Wurmus 1f7e8d49c3
gnu: r-performanceanalytics: Update to 1.5.3.
* gnu/packages/cran.scm (r-performanceanalytics): Update to 1.5.3.
2019-06-29 01:34:43 +02:00
Ricardo Wurmus 4ae5f18a25
gnu: r-abbyyr: Update to 0.5.5.
* gnu/packages/cran.scm (r-abbyyr): Update to 0.5.5.
2019-06-29 01:34:43 +02:00
Ricardo Wurmus 5b86bcfa68
gnu: r-phangorn: Update to 2.5.5.
* gnu/packages/bioinformatics.scm (r-phangorn): Update to 2.5.5.
2019-06-29 01:34:43 +02:00
Ricardo Wurmus 7f17e60ab7
gnu: r-tximport: Update to 1.12.3.
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.12.3.
2019-06-29 01:34:43 +02:00
Ricardo Wurmus dafd290d21
gnu: r-genomicfeatures: Update to 1.36.3.
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.36.3.
2019-06-29 01:34:43 +02:00
Ricardo Wurmus c40bba2b36
gnu: r-genomicalignments: Update to 1.20.1.
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.20.1.
2019-06-29 01:34:43 +02:00
Ricardo Wurmus 888085c36c
gnu: r-biomart: Update to 2.40.1.
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.40.1.
2019-06-29 01:34:43 +02:00
Ricardo Wurmus f0c244229a
gnu: r-edger: Update to 3.26.5.
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.5.
2019-06-29 01:34:43 +02:00
Ricardo Wurmus 0253b5d881
gnu: r-systempiper: Update to 1.18.2.
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.18.2.
2019-06-29 01:34:42 +02:00
Ricardo Wurmus 3e265d968b
gnu: r-rsubread: Update to 1.34.4.
* gnu/packages/bioconductor.scm (r-rsubread): Update to 1.34.4.
2019-06-29 01:34:42 +02:00
Ricardo Wurmus 3c944fdace
gnu: r-genomicscores: Update to 1.8.1.
* gnu/packages/bioconductor.scm (r-genomicscores): Update to 1.8.1.
2019-06-29 01:34:42 +02:00
Ricardo Wurmus aff3ecbfda
gnu: r-dose: Update to 3.10.2.
* gnu/packages/bioconductor.scm (r-dose): Update to 3.10.2.
2019-06-29 01:34:42 +02:00
Marius Bakke 4289d1d71c
gnu: python-llvmlite: Build against LLVM 7.
This is a follow-up to commit c5296e205b.

* gnu/packages/llvm.scm (llvm-7, clang-runtime-7, clang-7): New public variables.
(python-llvmlite)[inputs]: Inherit from LLVM-7 instead of LLVM.
2019-06-28 20:53:20 +02:00
Jakob L. Kreuze 4ee2cce327
gnu: Add beets-bandcamp.
* gnu/packages/music.scm (beets-bandcamp): New variable.

Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>
2019-06-28 14:22:05 +02:00
Nicolas Goaziou 9d83e60e51
gnu: musescore: Update to 3.2.
* gnu/packages/music.scm (musescore): Update to 3.2.
2019-06-28 10:46:45 +02:00
Nicolas Goaziou 458f410bc2
gnu: snap: Update to 5.
* gnu/packages/education.scm (snap): Update to 5.
2019-06-28 10:11:12 +02:00
Efraim Flashner 5b786db86c
gnu: atlas: All phases return #t.
* gnu/packages/maths.scm (atlas)[arguments]: Ensure all custom phases
return #t.
2019-06-28 10:39:11 +03:00
Nicolas Goaziou 2668e06efd
gnu: krita: Update to 4.2.2.
* gnu/packages/kde.scm (krita): Update to 4.2.2.
[source]: Don't use NAME in source URI.
[arguments]: Remove obsolete configure flags.
[native-inputs]: Add pkg-config.
[inputs]: Add quazip, reorder alphabetically.
2019-06-28 09:34:25 +02:00
Nicolas Goaziou 09debcf5aa
gnu: Add quazip.
* gnu/packages/compression.scm (quazip): New variable.
2019-06-28 09:34:25 +02:00
Mark H Weaver fbb5b688b6
gnu: linux-libre@4.14: Update to 4.14.131.
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.131.
(%linux-libre-4.14-hash): Update hash.
2019-06-27 18:58:45 -04:00
Mark H Weaver 1ad3e3f9f1
gnu: linux-libre@4.9: Update to 4.9.184.
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.184.
2019-06-27 18:58:06 -04:00
Mark H Weaver 9969b436af
gnu: linux-libre@4.4: Update to 4.4.184.
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.184.
2019-06-27 18:57:10 -04:00
Ludovic Courtès 5cc1075a76
Merge branch 'master' into core-updates 2019-06-27 23:33:48 +02:00
Ricardo Wurmus bae0f8af21
gnu: pigx-scrnaseq: Update to 0.0.8.
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.8.
2019-06-27 23:23:29 +02:00
Rutger Helling 6ad087b821
gnu: mame: Update to 0.211.
* gnu/packages/emulators.scm (mame): Update to 0.211.
2019-06-27 13:28:33 +02:00
Ludovic Courtès c30d117822
tests: Avoid TCP port collision between lint.scm and guix-daemon.sh.
This could lead to random deadlocks in one of these two tests when
running "make check -j5".

* tests/guix-daemon.sh (tcp_socket): Change port to 9998 to avoid
collision with tests/lint.scm.
2019-06-27 11:14:42 +02:00
Ludovic Courtès 08c95ba28d
ui: 'show-derivation-outputs' accepts <derivation-input> records.
* guix/ui.scm (show-derivation-outputs): Handle <derivation-input>
records.
2019-06-27 11:14:42 +02:00
Ludovic Courtès d38d4ffa10
ui: 'show-what-to-build' accepts derivation inputs.
This is a followup to f8a9f99cd6.

* guix/ui.scm (show-what-to-build)[inputs]: New variables.
[substitutable-info]: Build the derivation list from INPUTS.
Pass INPUTS to 'derivation-build-plan'.
2019-06-27 11:14:42 +02:00
Ludovic Courtès 066eeae1a1
packages: 'specification->package+output' distinguishes "no output specified".
Until now the caller couldn't tell the different between a spec like
"foo:out" and one like "foo".  This change allows users to distinguish
between these two cases.

* gnu/packages.scm (specification->package+output): Disable output
membership test when OUTPUT = #f and SUB-DRV = #f.
* tests/packages.scm ("specification->package+output")
("specification->package+output invalid output")
("specification->package+output no default output")
("specification->package+output invalid output, no default"): New tests.
2019-06-27 11:14:41 +02:00
Ludovic Courtès 7c690a4738
derivations: 'build-derivations' can be passed derivation inputs.
* guix/derivations.scm (build-derivations): Accept <derivation-input>
records among DERIVATIONS.
* tests/derivations.scm ("build-derivations with specific output"): Test
it.
2019-06-27 11:14:41 +02:00
Ludovic Courtès fd951cd543
derivations: 'derivation' preserves pointer equality.
* guix/derivations.scm (derivation): Check if FILE is already in
%DERIVATION-CACHE and return it if it is.
2019-06-27 11:14:41 +02:00
Ludovic Courtès 5cf4b26d52
derivations: <derivation-input> now aggregates a <derivation>.
Consequently, the whole graph of <derivation> object is readily
available without having to go through 'read-derivation-from-file',
which could have cache misses if the requested <derivation> object had
been GC'd in the meantime.  This is an important property for the
performance of things like 'derivation-build-plan' that traverse the
derivation graph.

* guix/derivations.scm (<derivation-input>): Replace 'path' field by
'derivation'.
(derivation-input-path): Adjust accordingly.
(derivation-input-key): New procedure.
(derivation-input-output-paths): Adjust accordingly.
(coalesce-duplicate-inputs): Likewise.
(derivation-prerequisites): Use 'derivation-input-key' to compute keys
for INPUT-SET.
(derivation-build-plan): Likewise.
(read-derivation): Add optional 'read-derivation-from-file' parameter.
[make-input-drvs]: Call it.
(write-derivation)[write-input]: Adjust to new <derivation-input>.
(derivation/masked-inputs): Likewise, and remove redundant
'coalesce-duplicate-inputs' call.
(derivation)[input->derivation-input]: Change to consider only the
derivation case.  Update call to 'make-derivation-input'.
[input->source]: New procedure.
Separate sources from inputs.
(map-derivation): Adjust to new <derivation-input>.
* tests/derivations.scm ("parse & export"): Pass a second argument to
'read-derivation'.
("build-expression->derivation and derivation-prerequisites")
("derivation-prerequisites and valid-derivation-input?"): Adjust to new
<derivation-input>.
2019-06-27 11:14:41 +02:00
Ludovic Courtès a250061986
graph: Use 'derivation-input-derivation'.
* guix/scripts/graph.scm (derivation-dependencies): Use
'derivation-input-derivation'.
2019-06-27 11:14:41 +02:00
Ludovic Courtès 9844d0091e
ui: 'show-what-to-build' uses 'derivation-build-plan'.
* guix/ui.scm (show-what-to-build)[build-or-substitutable?]: Remove.
Use 'derivation-build-plan' instead of
'derivation-prerequisites-to-build', passing it all of DRV at once, and
remove 'fold2' shenanigans and postprocessing of BUILD.
2019-06-27 11:14:41 +02:00
Ludovic Courtès ba04f80e2e
derivations: Rewrite and replace 'derivations-prerequisites-to-build'.
The new 'derivation-build-plan' procedure has a more appropriate
signature: it takes a list of <derivation-inputs> instead of taking one
<derivation>.  Its body is also much simpler.

* guix/derivations.scm (derivation-build-plan): New procedure.
(derivation-prerequisites-to-build): Express in terms of
'derivation-build-plan' and mark as deprecated.
* tests/derivations.scm: Change 'derivation-prerequisites-to-build'
tests to 'derivation-build-plan' and adjust accordingly.
2019-06-27 11:14:41 +02:00
Ludovic Courtès c89985d91d
derivations: Add 'derivation-input'.
* guix/derivations.scm (derivation-input): New procedure.
* tests/grafts.scm (make-derivation-input): Remove.
("graft-derivation, unused outputs not depended on"): Use
'derivation-input'.
2019-06-27 11:14:41 +02:00
Ludovic Courtès 4311cf965c
ui: Add 'display-search-results' and use it.
* guix/ui.scm (display-search-results): New procedure.
* guix/scripts/package.scm (find-packages-by-description): Remove
'unzip2' call and return a list of pairs.
(process-query): Change to use 'display-search-results'.
* guix/scripts/system/search.scm (find-service-types): Remove 'unzip2'
call and return a list of pairs.
(guix-system-search): Use 'display-search-results'.
2019-06-27 11:14:41 +02:00
Ludovic Courtès 4593f5a654
syscalls: Add 'terminal-rows'.
* guix/build/syscalls.scm (terminal-dimension): New procedure.
(terminal-columns): Rewrite in terms of 'terminal-dimension'.
(terminal-rows): New procedure.
* tests/syscalls.scm ("terminal-rows"): New test.
2019-06-27 11:14:40 +02:00
Ludovic Courtès 8874faaaac
ui: 'relevance' considers regexps connected with a logical and.
* guix/ui.scm (relevance)[score]: Change to return 0 when one of REGEXPS
doesn't match.
* tests/ui.scm ("package-relevance"): New test.
2019-06-27 11:14:40 +02:00
Ludovic Courtès c25b44d640
accounts: Use 'fsync' instead of 'fdatasync'.
* gnu/build/accounts.scm (catch-ENOSYS): Remove.
(database-writer): Use 'fsync' instead of 'fdatasync'.
2019-06-27 11:14:40 +02:00
Rutger Helling b09e4960be
gnu: dosbox: Update to 0.74-3.
* gnu/packages/emulators.scm (dosbox): Update to 0.74-3.
2019-06-27 10:24:11 +02:00
Arun Isaac 4ffed73419
gnu: rep-gtk: Update to 0.90.8.3.
* gnu/packages/sawfish.scm (rep-gtk): Update to 0.90.8.3.
[source]: Use HTTPS URI.
[arguments]: Add remove-autogen phase.
[native-inputs]: Add autoconf, automake and libtool.
[home-page]: Update URI.
2019-06-27 12:22:04 +05:30
Benjamin Slade edccf761e3
gnu: sawfish: Update to 1.12.0.
* gnu/packages/sawfish.scm (sawfish): Update to 1.12.0.
[source]: Use HTTPS URI.
[home-page]: Update URI.

Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2019-06-27 12:21:09 +05:30
Vagrant Cascadian 7a70e7ca04
gnu: electron-cash: Update to 4.0.7.
* gnu/packages/finance (electron-cash): Update to 4.0.7.
2019-06-26 20:14:45 -07:00
Tobias Geerinckx-Rice ba912479e8
Revert "gnu: openssh: Don't create the PRIVSEP_PATH directory."
This reverts commit 46475f72ab.
2019-06-27 00:21:16 +02:00
Tobias Geerinckx-Rice 1ebb908d44
Revert "gnu: openssh: Clean-up custom install phase."
This reverts commit 7754136e46.
2019-06-27 00:21:16 +02:00
Nicolas Goaziou cac6c3bad5
gnu: supertux: Fix homepage.
* gnu/packages/games.scm (supertux)[homepage]: Fix URL.
2019-06-26 19:45:34 +02:00