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Author SHA1 Message Date
zimoun
3b6484097c
gnu: r-qdnaseq: Update to 1.26.0. 
* gnu/packages/bioconductor.scm (r-qdnaseq): Update to 1.26.0.
 2020-12-09 12:12:22 +01:00
zimoun
724000356e
gnu: r-cghcall: Update to 2.52.0. 
* gnu/packages/bioconductor.scm (r-cghcall): Update to 2.52.0.
 2020-12-09 12:12:22 +01:00
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