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Commit Graph

70270 Commits

Author SHA1 Message Date
zimoun ee052d05f1 gnu: r-cghbase: Update to 1.50.0.
* gnu/packages/bioconductor.scm (r-cghbase): Update to 1.50.0.
2020-12-09 12:12:22 +01:00
zimoun 6e6c627230 gnu: r-marray: Update to 1.68.0.
* gnu/packages/bioconductor.scm (r-marray): Update to 1.68.0.
2020-12-09 12:12:22 +01:00
zimoun d068d96743 gnu: r-chippeakanno: Update to 3.24.0.
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.24.0.
2020-12-09 12:12:21 +01:00
zimoun f519b4dc01 gnu: r-graph: Update to 1.68.0.
* gnu/packages/bioconductor.scm (r-graph): Update to 1.68.0.
2020-12-09 12:12:21 +01:00
zimoun 1e6920c521 gnu: r-multtest: Update to 2.46.0.
* gnu/packages/bioconductor.scm (r-multtest): Update to 2.46.0.
2020-12-09 12:12:21 +01:00
Roel Janssen 341ebaaa01 gnu: r-diffbind: Update to 3.0.7.
* gnu/packages/bioconductor.scm (r-diffbind): Update to 3.0.7.
[propagated-inputs]: Add r-apeglm, r-ashr, and r-greylistchip; remove r-edger.
2020-12-09 12:12:21 +01:00
Roel Janssen 6e396c4bff gnu: Add r-greylistchip.
* gnu/packages/bioconductor.scm (r-greylistchip): New variable.
2020-12-09 12:12:21 +01:00
Roel Janssen c84762c446 gnu: Add r-ashr.
* gnu/packages/cran.scm (r-ashr): New variable.
2020-12-09 12:12:21 +01:00
Roel Janssen 755d16a3b0 gnu: Add r-mixsqp.
* gnu/packages/cran.scm (r-mixsqp): New variable.
2020-12-09 12:12:21 +01:00
Roel Janssen deda2319f7 gnu: Add r-etrunct.
* gnu/packages/cran.scm (r-etrunct): New variable.
2020-12-09 12:12:21 +01:00
Roel Janssen a7f4a8b4d0 gnu: Add r-invgamma.
* gnu/packages/cran.scm (r-invgamma): New variable.
2020-12-09 12:12:21 +01:00
Roel Janssen 3b399e514f gnu: Add r-apeglm.
* gnu/packages/bioconductor.scm (r-apeglm): New variable.
2020-12-09 12:12:21 +01:00
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