Commit graph

70608 commits

Author SHA1 Message Date
Roel Janssen
a0df9b93ef
gnu: Add r-rcppnumerical.
* gnu/packages/bioconductor.scm (r-rcppnumerical): New variable.
2020-12-09 12:12:21 +01:00
zimoun
e9b60a2901
gnu: r-qvalue: Update to 2.22.0.
* gnu/packages/bioconductor.scm (r-qvalue): Update to 2.22.0.
2020-12-09 12:12:21 +01:00
zimoun
9af6fdf861
gnu: r-oligo: Update to 1.54.0.
* gnu/packages/bioconductor.scm (r-oligo): Update to 1.54.0.
2020-12-09 12:12:21 +01:00
zimoun
464df5ccbb
gnu: r-oligoclasses: Update to 1.52.0.
* gnu/packages/bioconductor.scm (r-oligoclasses): Update to 1.52.0.
2020-12-09 12:12:21 +01:00
zimoun
d72c4c98c8
gnu: r-geneplotter: Update to 1.68.0.
* gnu/packages/bioconductor.scm (r-geneplotter): Update to 1.68.0.
2020-12-09 12:12:20 +01:00
zimoun
c03c76344e
gnu: r-reportingtools: Update to 2.30.0.
* gnu/packages/bioconductor.scm (r-reportingtools): Update to 2.30.0.
2020-12-09 12:12:20 +01:00
zimoun
d1ff3604b7
gnu: r-regioner: Update to 1.22.0.
* gnu/packages/bioconductor.scm (r-regioner): Update to 1.22.0.
2020-12-09 12:12:20 +01:00
zimoun
fa7578b32f
gnu: r-hpar: Update to 1.32.1.
* gnu/packages/bioconductor.scm (r-hpar): Update to 1.32.1.
2020-12-09 12:12:20 +01:00
zimoun
7d56302332
gnu: r-annotate: Update to 1.68.0.
* gnu/packages/bioconductor.scm (r-annotate): Update to 1.68.0.
[propagated-inputs]: Remove 'r-rcurl', add 'r-httr'.
2020-12-09 12:12:20 +01:00
zimoun
8e6a2c328f
gnu: r-affxparser: Update to 1.62.0.
* gnu/packages/bioconductor.scm (r-affxparser): Update to 1.62.0.
2020-12-09 12:12:20 +01:00
zimoun
a92219b45f
gnu: r-affycoretools: Update to 1.62.0.
* gnu/packages/bioconductor.scm (r-affycoretools): Update to 1.62.0.
2020-12-09 12:12:20 +01:00
zimoun
3e82f9ccaf
gnu: r-affycontam: Update to 1.48.0.
* gnu/packages/bioconductor.scm (r-affycontam): Update to 1.48.0.
2020-12-09 12:12:20 +01:00
zimoun
fa2d16cc27
gnu: r-affycompatible: Update to 1.50.0.
* gnu/packages/bioconductor.scm (r-affycompatible): Update to 1.50.0.
2020-12-09 12:12:20 +01:00
zimoun
c472549f67
gnu: r-affycomp: Update to 1.66.0.
* gnu/packages/bioconductor.scm (r-affycomp): Update to 1.66.0.
2020-12-09 12:12:20 +01:00
zimoun
aa311eaa74
gnu: r-biocgenerics: Update to 0.36.0.
* gnu/packages/bioconductor.scm (r-biocgenerics): Update to 0.36.0.
2020-12-09 12:12:20 +01:00
zimoun
70ab99096d
gnu: r-biocversion: Update to 3.12.0.
* gnu/packages/bioconductor.scm (r-biocversion): Update to 3.12.0.
2020-12-09 12:12:20 +01:00
zimoun
a3e2e53837
gnu: r-cummerbund: Update to 2.32.0.
* gnu/packages/bioconductor.scm (r-cummerbund): Update to 2.32.0.
2020-12-09 12:12:20 +01:00
zimoun
5ef637ddc7
gnu: r-coverageview: Update to 1.28.0.
* gnu/packages/bioconductor.scm (r-coverageview): Update to 1.28.0.
2020-12-09 12:12:20 +01:00
zimoun
25f4e6520e
gnu: r-ideoviz: Update to 1.26.0.
* gnu/packages/bioconductor.scm (r-ideoviz): Update to 1.26.0.
2020-12-09 12:12:20 +01:00
Roel Janssen
0a79b24506
import: cran: Update the Bioconductor version to 3.12.
* guix/import/cran.scm (%bioconductor-version): Set to 3.12.
* guix/build-system/r.scm (bioconductor-uri):  Update to 3.12.
2020-12-09 12:12:19 +01:00
Efraim Flashner
533935ccf7
services: science.scm: Add missing copyright headers.
This module was always supposed to have the GPL3 header in place.
Follow-up to 8f19e63f76.

* gnu/services/science.scm: Add Copyright headers.
2020-12-09 12:55:02 +02:00
Guillaume Le Vaillant
53c480006b
gnu: monero-gui: Update to 0.17.1.6.
* gnu/packages/finance.scm (monero-gui): Update to 0.17.1.6.
2020-12-09 11:34:25 +01:00
Guillaume Le Vaillant
5560bd7b6b
gnu: monero: Update to 0.17.1.6.
* gnu/packages/finance.scm (monero): Update to 0.17.1.6.
2020-12-09 11:34:25 +01:00
elaexuotee@wilsonb.com
8e2aad26ae
gnu: Add lemonbar-xft.
* gnu/packages/wm.scm (lemonbar-xft): New variable.

Signed-off-by: Christopher Baines <mail@cbaines.net>
2020-12-09 09:10:33 +00:00
Ryan Prior
9941036559
gnu: Add go-github-com-aws-sdk.
* gnu/packages/golang.scm (go-github-com-aws-sdk): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2020-12-09 09:45:35 +02:00
Ryan Prior
016501aec6
gnu: Add go-github-com-jmespath-go-jmespath.
* gnu/packages/golang.scm (go-github-com-jmespath-go-jmespath): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2020-12-09 09:45:35 +02:00
Ryan Prior
f7c2896e52
gnu: Add go-github-com-go-sql-driver-mysql.
* gnu/packages/golang.scm (go-github-com-go-sql-driver-mysql): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2020-12-09 09:45:31 +02:00
Leo Famulari
2b0185a74b
gnu: linux-libre 4.14: Update to 4.14.211.
* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.211.
(linux-libre-4.14-pristine-source): Update hash.
2020-12-09 01:08:15 -05:00
Leo Famulari
a2eae5ec4a
gnu: linux-libre 4.19: Update to 4.19.162.
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.162.
(linux-libre-4.19-pristine-source): Update hash.
2020-12-09 01:08:15 -05:00
Leo Famulari
66b1b55148
gnu: linux-libre 5.4: Update to 5.4.82.
* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.82.
(linux-libre-5.4-pristine-source): Update hash.
2020-12-09 01:08:14 -05:00
Leo Famulari
54f777ca4e
gnu: linux-libre: Update to 5.9.13.
* gnu/packages/linux.scm (linux-libre-5.9-version): Update to 5.9.13.
(linux-libre-5.9-pristine-source): Update hash.
2020-12-09 01:08:09 -05:00
Leo Famulari
02b21f35cc
gnu: OpenSSL: Update to 1.1.1i [fixes CVE-2020-1971].
* gnu/packages/tls.scm (openssl)[replacement]: Update replacement to 1.1.1i
(openssl-1.1.1g): Replace with ...
(openssl-1.1.1i): ... new variable.
2020-12-08 19:48:09 -05:00
Ludovic Courtès
456421fc0f
gnu: guix: Update to 799f066.
* gnu/packages/package-management.scm (guix): Update to 799f066.
2020-12-08 23:38:04 +01:00
Ludovic Courtès
799f066768
import: opam: Adjust test to latest 'opam->guix-package' changes.
This is a followup to a8dccd4bdc, which
broke the test.

* guix/import/opam.scm (get-opam-repository): Prevent inlining.
* tests/opam.scm ("opam->guix-package"): Mock 'get-opam-repository'.
2020-12-08 22:58:37 +01:00
Ludovic Courtès
bfe4cdf88e
daemon: Raise an error if substituter doesn't send the expected hash.
It was already impossible in practice for 'expectedHashStr' to be empty
if 'status' == "success".

* nix/libstore/build.cc (SubstitutionGoal::finished): Throw 'SubstError'
when 'expectedHashStr' is empty.
2020-12-08 22:30:08 +01:00
Ludovic Courtès
5ff521452b
substitute: Cache and reuse connections while substituting.
That way, when fetching a series of substitutes from the same server(s),
the connection is reused instead of being closed/opened for each
substitutes, which saves on network round trips and TLS handshakes.

* guix/http-client.scm (http-fetch): Add #:keep-alive? and honor it.
* guix/progress.scm (progress-report-port): Add #:close? parameter and
honor it.
* guix/scripts/substitute.scm (at-most): Return the tail as a second
value.
(fetch): Add #:port and #:keep-alive? and honor them.
(%max-cached-connections): New variable.
(open-connection-for-uri/cached, call-with-cached-connection): New
procedures.
(with-cached-connection): New macro.
(process-substitution): Wrap 'fetch' call in 'with-cached-connection'.
Pass #:close? to 'progress-report-port'.
2020-12-08 22:30:08 +01:00
Ludovic Courtès
711df9ef3c
daemon: Run 'guix substitute --substitute' as an agent.
This avoids spawning one substitute process per substitution.

* nix/libstore/build.cc (class Worker)[substituter]: New field.
[outPipe, logPipe, pid]: Remove.
(class SubstitutionGoal)[expectedHashStr, status, substituter]: New fields.
(SubstitutionGoal::timedOut): Adjust to check 'substituter'.
(SubstitutionGoal::tryToRun): Remove references to 'outPipe' and
'logPipe'.  Run "guix substitute --substitute" as an 'Agent'.  Send the
request with 'writeLine'.
(SubstitutionGoal::finished): Likewise.
(SubstitutionGoal::handleChildOutput): Change to fill in
'expectedHashStr' and 'status'.
(SubstitutionGoal::handleEOF): Call 'wakeUp' unconditionally.
(SubstitutionGoal::~SubstitutionGoal): Adjust to check 'substituter'.
* guix/scripts/substitute.scm (process-substitution): Write "success\n"
to stdout upon success.
(%error-to-file-descriptor-4?): New variable.
(guix-substitute): Set 'current-error-port' to file descriptor 4
unless (%error-to-file-descriptor-4?) is false.
Remove "--substitute" arguments.  Loop reading line from stdin.
* tests/substitute.scm <top level>: Call '%error-to-file-descriptor-4?'.
(request-substitution): New procedure.
("substitute, no signature")
("substitute, invalid hash")
("substitute, unauthorized key")
("substitute, authorized key")
("substitute, unauthorized narinfo comes first")
("substitute, unsigned narinfo comes first")
("substitute, first narinfo is unsigned and has wrong hash")
("substitute, first narinfo is unsigned and has wrong refs")
("substitute, two invalid narinfos")
("substitute, narinfo with several URLs"): Adjust to new "guix
substitute --substitute" calling convention.
2020-12-08 22:30:08 +01:00
Ludovic Courtès
a618a8c620
daemon: Factorize substituter agent spawning.
* nix/libstore/local-store.hh (class LocalStore)[substituter]: New
method.
[runningSubstituter]: Turn into a shared_ptr.
* nix/libstore/local-store.cc (LocalStore::querySubstitutablePaths):
Call 'substituter' instead of using inline code.
(LocalStore::querySubstitutablePathInfos): Likewise.
(LocalStore::substituter): New method.
2020-12-08 22:30:08 +01:00
Ludovic Courtès
79c6614f58
daemon: Use 'Agent' to spawn 'guix substitute --query'.
* nix/libstore/local-store.hh (RunningSubstituter): Remove.
(LocalStore)[runningSubstituter]: Change to unique_ptr<Agent>.
[setSubstituterEnv, didSetSubstituterEnv]: Remove.
[getLineFromSubstituter, getIntLineFromSubstituter]: Take an 'Agent'.
* nix/libstore/local-store.cc (LocalStore::~LocalStore): Remove
reference to 'runningSubstituter'.
(LocalStore::setSubstituterEnv, LocalStore::startSubstituter): Remove.
(LocalStore::getLineFromSubstituter): Adjust to 'run' being an 'Agent'.
(LocalStore::querySubstitutablePaths): Spawn substituter agent if
needed.  Adjust to 'Agent' interface.
(LocalStore::querySubstitutablePathInfos): Likewise.
* nix/libstore/build.cc (SubstitutionGoal::tryToRun): Remove call to
'setSubstituterEnv' and add 'setenv' call for "_NIX_OPTIONS" instead.
(SubstitutionGoal::finished): Remove 'readLine' call for 'dummy'.
* guix/scripts/substitute.scm (%allow-unauthenticated-substitutes?):
Remove second argument to 'make-parameter'.
(process-query): Call 'warn-about-missing-authentication'
when (%allow-unauthenticated-substitutes?) is #t.
(guix-substitute): Wrap body in 'parameterize'.  Set 'guix-warning-port'
too.  No longer exit when 'substitute-urls' returns the empty list.  No
longer print newline initially.
* tests/substitute.scm (test-quit): Parameterize 'current-error-port' to
account for the port changes in 'guix-substitute'.
2020-12-08 22:30:08 +01:00
Ludovic Courtès
2e308238ad
daemon: 'Agent' constructor takes a list of environment variables.
* nix/libutil/util.hh (struct Agent)[Agent]: Add 'env' parameter.
* nix/libutil/util.cc (Agent::Agent): Honor it.
2020-12-08 22:30:07 +01:00
Ludovic Courtès
4a98735297
gnu: autotools: Add version 2.70.
* gnu/packages/autotools.scm (autoconf): Rename to...
(autoconf-2.69): ... this.
(autoconf): Define as an alias for AUTOCONF-2.69.
(autoconf-2.70): New variable.
2020-12-08 22:28:00 +01:00
Ludovic Courtès
e9edaf3639
database: Remove unnecessary module imports.
* guix/store/database.scm: Remove unnecessary imports added in
4b9eecd322.
2020-12-08 21:40:05 +01:00
Vincent Legoll
20e5658c04
gnu: ocaml-menhir: Update to 20200211.
* gnu/packages/ocaml.scm (ocaml-menhir): Update to 20200211.
[build-system]: Switch from gnu to dune.
[arguments]: Remove phases and make-flags.
[native-inputs]: Remove field.

Signed-off-by: Christopher Baines <mail@cbaines.net>
2020-12-08 20:18:11 +00:00
Efraim Flashner
2d1a621b8d
gnu: mruby: Update to 2.1.2.
* gnu/packages/ruby.scm (mruby): Update to 2.1.2.
2020-12-08 22:09:30 +02:00
L p R n d n
8a55a3994c
gnu: Add mypaint.
* gnu/packages/image.scm (mypaint): New variable.

Signed-off-by: Christopher Baines <mail@cbaines.net>
2020-12-08 20:06:38 +00:00
Christopher Baines
c9c3569ad9
gnu: libmypaint: Update to 1.6.1.
Needed by mypaint@2.0.1.

* gnu/packages/gimp.scm (libmypaint): Update to 1.6.1.
2020-12-08 20:06:34 +00:00
Leo Famulari
e1d3b07ffc
gnu: isync: Use OpenSSL 1.1.
* gnu/packages/mail.scm (isync)[inputs]: Replace openssl-1.0 with openssl.
2020-12-08 13:25:27 -05:00
Efraim Flashner
adbb62f16e
gnu: fcitx5-material-color-theme: Add source file-name.
* gnu/packages/fcitx5.scm (fcitx5-material-color-theme)[source]: Add
file-name field.
2020-12-08 18:14:31 +02:00
Julien Lepiller
ccc4d287b7
guix: opam: Add coq support in the importer.
* guix/import/opam.scm (get-opam-repository): Add support for coq
repositories.
(ocaml-name->guix-name): Properly name coq package.
* doc/guix.texi (Invoking guix import): Document it.
2020-12-08 16:53:07 +01:00
Julien Lepiller
a8dccd4bdc
guix: opam: Add --repo argument to importer.
* guix/scripts/import/opam.scm (guix-import-opam): Pass --repo argument
to recursive and non-recursive importers.
* guix/import/opam.scm (get-opam-repository): Select proper repository
location depending on a new repo argument.
(opam->guix-package): Use get-opam-repository in the procedure body.
2020-12-08 16:47:22 +01:00