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2020-12-09gnu: r-diffbind: Update to 3.0.7.Roel Janssen
* gnu/packages/bioconductor.scm (r-diffbind): Update to 3.0.7. [propagated-inputs]: Add r-apeglm, r-ashr, and r-greylistchip; remove r-edger.
2020-12-09gnu: Add r-greylistchip.Roel Janssen
* gnu/packages/bioconductor.scm (r-greylistchip): New variable.
2020-12-09gnu: Add r-ashr.Roel Janssen
* gnu/packages/cran.scm (r-ashr): New variable.
2020-12-09gnu: Add r-mixsqp.Roel Janssen
* gnu/packages/cran.scm (r-mixsqp): New variable.
2020-12-09gnu: Add r-etrunct.Roel Janssen
* gnu/packages/cran.scm (r-etrunct): New variable.
2020-12-09gnu: Add r-invgamma.Roel Janssen
* gnu/packages/cran.scm (r-invgamma): New variable.
2020-12-09gnu: Add r-apeglm.Roel Janssen
* gnu/packages/bioconductor.scm (r-apeglm): New variable.
2020-12-09gnu: Add r-rcppnumerical.Roel Janssen
* gnu/packages/bioconductor.scm (r-rcppnumerical): New variable.
2020-12-09gnu: r-qvalue: Update to 2.22.0.zimoun
* gnu/packages/bioconductor.scm (r-qvalue): Update to 2.22.0.
2020-12-09gnu: r-oligo: Update to 1.54.0.zimoun
* gnu/packages/bioconductor.scm (r-oligo): Update to 1.54.0.
2020-12-09gnu: r-oligoclasses: Update to 1.52.0.zimoun
* gnu/packages/bioconductor.scm (r-oligoclasses): Update to 1.52.0.
2020-12-09gnu: r-geneplotter: Update to 1.68.0.zimoun
* gnu/packages/bioconductor.scm (r-geneplotter): Update to 1.68.0.
2020-12-09gnu: r-reportingtools: Update to 2.30.0.zimoun
* gnu/packages/bioconductor.scm (r-reportingtools): Update to 2.30.0.
2020-12-09gnu: r-regioner: Update to 1.22.0.zimoun
* gnu/packages/bioconductor.scm (r-regioner): Update to 1.22.0.
2020-12-09gnu: r-hpar: Update to 1.32.1.zimoun
* gnu/packages/bioconductor.scm (r-hpar): Update to 1.32.1.
2020-12-09gnu: r-annotate: Update to 1.68.0.zimoun
* gnu/packages/bioconductor.scm (r-annotate): Update to 1.68.0. [propagated-inputs]: Remove 'r-rcurl', add 'r-httr'.
2020-12-09gnu: r-affxparser: Update to 1.62.0.zimoun
* gnu/packages/bioconductor.scm (r-affxparser): Update to 1.62.0.
2020-12-09gnu: r-affycoretools: Update to 1.62.0.zimoun
* gnu/packages/bioconductor.scm (r-affycoretools): Update to 1.62.0.
2020-12-09gnu: r-affycontam: Update to 1.48.0.zimoun
* gnu/packages/bioconductor.scm (r-affycontam): Update to 1.48.0.
2020-12-09gnu: r-affycompatible: Update to 1.50.0.zimoun
* gnu/packages/bioconductor.scm (r-affycompatible): Update to 1.50.0.
2020-12-09gnu: r-affycomp: Update to 1.66.0.zimoun
* gnu/packages/bioconductor.scm (r-affycomp): Update to 1.66.0.
2020-12-09gnu: r-biocgenerics: Update to 0.36.0.zimoun
* gnu/packages/bioconductor.scm (r-biocgenerics): Update to 0.36.0.
2020-12-09gnu: r-biocversion: Update to 3.12.0.zimoun
* gnu/packages/bioconductor.scm (r-biocversion): Update to 3.12.0.
2020-12-09gnu: r-cummerbund: Update to 2.32.0.zimoun
* gnu/packages/bioconductor.scm (r-cummerbund): Update to 2.32.0.
2020-12-09gnu: r-coverageview: Update to 1.28.0.zimoun
* gnu/packages/bioconductor.scm (r-coverageview): Update to 1.28.0.
2020-12-09gnu: r-ideoviz: Update to 1.26.0.zimoun
* gnu/packages/bioconductor.scm (r-ideoviz): Update to 1.26.0.
2020-12-09import: cran: Update the Bioconductor version to 3.12.Roel Janssen
* guix/import/cran.scm (%bioconductor-version): Set to 3.12. * guix/build-system/r.scm (bioconductor-uri): Update to 3.12.
2020-12-09services: science.scm: Add missing copyright headers.Efraim Flashner
This module was always supposed to have the GPL3 header in place. Follow-up to 8f19e63f760fe02f9969225da2f3f3c36801218f. * gnu/services/science.scm: Add Copyright headers.
2020-12-09gnu: monero-gui: Update to 0.17.1.6.Guillaume Le Vaillant
* gnu/packages/finance.scm (monero-gui): Update to 0.17.1.6.
2020-12-09gnu: monero: Update to 0.17.1.6.Guillaume Le Vaillant
* gnu/packages/finance.scm (monero): Update to 0.17.1.6.
2020-12-09gnu: Add lemonbar-xft.elaexuotee@wilsonb.com
* gnu/packages/wm.scm (lemonbar-xft): New variable. Signed-off-by: Christopher Baines <mail@cbaines.net>
2020-12-09gnu: Add go-github-com-aws-sdk.Ryan Prior
* gnu/packages/golang.scm (go-github-com-aws-sdk): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2020-12-09gnu: Add go-github-com-jmespath-go-jmespath.Ryan Prior
* gnu/packages/golang.scm (go-github-com-jmespath-go-jmespath): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2020-12-09gnu: Add go-github-com-go-sql-driver-mysql.Ryan Prior
* gnu/packages/golang.scm (go-github-com-go-sql-driver-mysql): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2020-12-09gnu: linux-libre 4.14: Update to 4.14.211.Leo Famulari
* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.211. (linux-libre-4.14-pristine-source): Update hash.
2020-12-09gnu: linux-libre 4.19: Update to 4.19.162.Leo Famulari
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.162. (linux-libre-4.19-pristine-source): Update hash.
2020-12-09gnu: linux-libre 5.4: Update to 5.4.82.Leo Famulari
* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.82. (linux-libre-5.4-pristine-source): Update hash.
2020-12-09gnu: linux-libre: Update to 5.9.13.Leo Famulari
* gnu/packages/linux.scm (linux-libre-5.9-version): Update to 5.9.13. (linux-libre-5.9-pristine-source): Update hash.
2020-12-08gnu: OpenSSL: Update to 1.1.1i [fixes CVE-2020-1971].Leo Famulari
* gnu/packages/tls.scm (openssl)[replacement]: Update replacement to 1.1.1i (openssl-1.1.1g): Replace with ... (openssl-1.1.1i): ... new variable.
2020-12-08gnu: guix: Update to 799f066.Ludovic Courtès
* gnu/packages/package-management.scm (guix): Update to 799f066.
2020-12-08import: opam: Adjust test to latest 'opam->guix-package' changes.Ludovic Courtès
This is a followup to a8dccd4bdc1e58219d4ba08fe1649bf0b8325f44, which broke the test. * guix/import/opam.scm (get-opam-repository): Prevent inlining. * tests/opam.scm ("opam->guix-package"): Mock 'get-opam-repository'.
2020-12-08daemon: Raise an error if substituter doesn't send the expected hash.Ludovic Courtès
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.
2020-12-08substitute: Cache and reuse connections while substituting.Ludovic Courtès
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'.
2020-12-08daemon: Run 'guix substitute --substitute' as an agent.Ludovic Courtès
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.
2020-12-08daemon: Factorize substituter agent spawning.Ludovic Courtès
* 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.
2020-12-08daemon: Use 'Agent' to spawn 'guix substitute --query'.Ludovic Courtès
* 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'.
2020-12-08daemon: 'Agent' constructor takes a list of environment variables.Ludovic Courtès
* nix/libutil/util.hh (struct Agent)[Agent]: Add 'env' parameter. * nix/libutil/util.cc (Agent::Agent): Honor it.
2020-12-08gnu: autotools: Add version 2.70.Ludovic Courtès
* 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.
2020-12-08database: Remove unnecessary module imports.Ludovic Courtès
* guix/store/database.scm: Remove unnecessary imports added in 4b9eecd322e566783369795ebea63a479b51f486.
2020-12-08gnu: ocaml-menhir: Update to 20200211.Vincent Legoll
* 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>
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