From c1637311b6331588734791a87376023338b6a4a3 Mon Sep 17 00:00:00 2001 From: Timothy Sample Date: Wed, 13 Nov 2019 22:59:24 -0500 Subject: gnu: ngless: Update to 1.0.1. * gnu/packages/bioinformatics.scm (ngless): Update to 1.0.1. [arguments]: Add a 'create-Versions.hs' phase that patches the Makefile and invokes 'make' to generate a required file. [inputs]: Remove 'ghc-chart', 'ghc-chart-cairo', and 'ghc-conduit-combinators'; add 'ghc-diagrams-core', 'ghc-diagrams-lib', 'ghc-diagrams-svg', and 'ghc-tar-conduit'. --- gnu/packages/bioinformatics.scm | 30 ++++++++++++++++++++++++------ 1 file changed, 24 insertions(+), 6 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 07c70fb82c..511146bb6e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13890,7 +13890,7 @@ datasets.") (define-public ngless (package (name "ngless") - (version "0.9.1") + (version "1.0.1") (source (origin (method git-fetch) @@ -13900,7 +13900,7 @@ datasets.") (file-name (git-file-name name version)) (sha256 (base32 - "0mc2gi7h4lx74zylvyp76mvc0w6706j858ii9vlgzqsw6acpr117")))) + "06ygv8q2zjqsnrid1302yrlhhvb8ik48nq6n0higk3i1mdc8r0dg")))) (build-system haskell-build-system) (arguments `(#:haddock? #f ; The haddock phase fails with: NGLess/CmdArgs.hs:20:1: @@ -13908,7 +13908,24 @@ datasets.") ; import Options.Applicative #:phases (modify-phases %standard-phases - (add-after 'unpack 'create-cabal-file + (add-after 'unpack 'create-Versions.hs + (lambda _ + (substitute* "Makefile" + (("BWA_VERSION = .*") + (string-append "BWA_VERSION = " + ,(package-version bwa) "\n")) + (("SAM_VERSION = .*") + (string-append "SAM_VERSION = " + ,(package-version samtools) "\n")) + (("PRODIGAL_VERSION = .*") + (string-append "PRODIGAL_VERSION = " + ,(package-version prodigal) "\n")) + (("MINIMAP2_VERSION = .*") + (string-append "MINIMAP2_VERSION = " + ,(package-version minimap2) "\n"))) + (invoke "make" "NGLess/Dependencies/Versions.hs") + #t)) + (add-after 'create-Versions.hs 'create-cabal-file (lambda _ (invoke "hpack") #t)) ;; These tools are expected to be installed alongside ngless. (add-after 'install 'link-tools @@ -13937,15 +13954,15 @@ datasets.") ("ghc-async" ,ghc-async) ("ghc-atomic-write" ,ghc-atomic-write) ("ghc-bytestring-lexing" ,ghc-bytestring-lexing) - ("ghc-chart" ,ghc-chart) - ("ghc-chart-cairo" ,ghc-chart-cairo) ("ghc-conduit" ,ghc-conduit) ("ghc-conduit-algorithms" ,ghc-conduit-algorithms) - ("ghc-conduit-combinators" ,ghc-conduit-combinators) ("ghc-conduit-extra" ,ghc-conduit-extra) ("ghc-configurator" ,ghc-configurator) ("ghc-convertible" ,ghc-convertible) ("ghc-data-default" ,ghc-data-default) + ("ghc-diagrams-core" ,ghc-diagrams-core) + ("ghc-diagrams-lib" ,ghc-diagrams-lib) + ("ghc-diagrams-svg" ,ghc-diagrams-svg) ("ghc-double-conversion" ,ghc-double-conversion) ("ghc-edit-distance" ,ghc-edit-distance) ("ghc-either" ,ghc-either) @@ -13966,6 +13983,7 @@ datasets.") ("ghc-safeio" ,ghc-safeio) ("ghc-strict" ,ghc-strict) ("ghc-tar" ,ghc-tar) + ("ghc-tar-conduit" ,ghc-tar-conduit) ("ghc-unliftio" ,ghc-unliftio) ("ghc-unliftio-core" ,ghc-unliftio-core) ("ghc-vector" ,ghc-vector) -- cgit v1.2.3 udovic Courtès 2021-09-25tests: Adjust to SRFI-64 as found in Guile 3.0.7....In Guile 3.0.7, 'test-runner-current' is set to #f upon 'test-end'. Consequently, the previous strategy, where we'd call 'test-runner-current' after 'test-end', no longer works. Instead, set the test runner in each test right before 'test-begin'. * gnu/build/marionette.scm (system-test-runner): New procedure. * gnu/tests/audio.scm (run-mpd-test): Replace (exit (= ...)) idiom by (test-runner-current (system-test-runner)). * gnu/tests/base.scm (run-basic-test) (run-cleanup-test, run-mcron-test, run-nss-mdns-test): Likewise. * gnu/tests/ci.scm (run-laminar-test): Likewise. * gnu/tests/cups.scm (run-cups-test): Likewise. * gnu/tests/databases.scm (run-memcached-test) (run-postgresql-test, run-mysql-test): Likewise. * gnu/tests/desktop.scm (run-elogind-test): Likewise. * gnu/tests/dict.scm (run-dicod-test): Likewise. * gnu/tests/docker.scm (run-docker-test): Likewise. (run-docker-system-test): Likewise. * gnu/tests/file-sharing.scm (run-transmission-daemon-test): Likewise. * gnu/tests/ganeti.scm (run-ganeti-test): Likewise. * gnu/tests/guix.scm (run-guix-build-coordinator-test): Likewise. (run-guix-data-service-test): Likewise. * gnu/tests/ldap.scm (run-ldap-test): Likewise. * gnu/tests/linux-modules.scm (run-loadable-kernel-modules-test-base): Likewise. * gnu/tests/mail.scm (run-opensmtpd-test) (run-exim-test, run-dovecot-test, run-getmail-test): Likewise. * gnu/tests/messaging.scm (run-xmpp-test) (run-bitlbee-test, run-quassel-test): Likewise. * gnu/tests/monitoring.scm (run-prometheus-node-exporter-server-test) (run-zabbix-server-test): Likewise. * gnu/tests/networking.scm (run-inetd-test, run-openvswitch-test) (run-dhcpd-test, run-tor-test, run-iptables-test, run-ipfs-test): Likewise. * gnu/tests/nfs.scm (run-nfs-test) (run-nfs-server-test, run-nfs-root-fs-test): Likewise. * gnu/tests/package-management.scm (run-nix-test): Likewise. * gnu/tests/reconfigure.scm (run-switch-to-system-test) (run-upgrade-services-test, run-install-bootloader-test): Likewise. * gnu/tests/rsync.scm (run-rsync-test): Likewise. * gnu/tests/security-token.scm (run-pcscd-test): Likewise. * gnu/tests/singularity.scm (run-singularity-test): Likewise. * gnu/tests/ssh.scm (run-ssh-test): Likewise. * gnu/tests/telephony.scm (run-jami-test): Likewise. * gnu/tests/version-control.scm (run-cgit-test): Likewise. (run-git-http-test, run-gitolite-test, run-gitile-test): Likewise. * gnu/tests/virtualization.scm (run-libvirt-test, run-childhurd-test): Likewise. * gnu/tests/web.scm (run-webserver-test, run-php-fpm-test) (run-hpcguix-web-server-test, run-tailon-test, run-patchwork-test): Likewise. Ludovic Courtès 2021-05-31tests: Fix loadable-kernel-modules-service tests....* gnu/tests/linux-modules.scm (run-loadable-kernel-modules-service-test): Actually load the modules with kernel-module-loader-service-type. Use a singleton service instead of defining a custom one. * doc/guix.texi (Service Reference): To give an example of linux-loadable-module-service-type use a singleton instead of defining a new service. Brice Waegeneire 2021-05-11gnu: Allow services to install kernel-loadable modules....* gnu/system.scm (operating-system-directory-base-entries): Remove code to handle generation of "kernel" for linux-libre kernels. (operating-system-default-essential-services): Instantiate linux-builder-service-type. (package-for-kernel): Move ... * gnu/services.scm: ... to here. (linux-builder-service-type): New variable. (linux-builder-configuration): New type. (linux-loadable-module-service-type): New variable. * gnu/tests/linux-modules.scm (run-loadable-kernel-modules-test): Move code to ... (run-loadable-kernel-modules-test-base): ... new procedure here. (run-loadable-kernel-modules-service-test): New procedure. (%test-loadable-kernel-modules-service-0): New variable. (%test-loadable-kernel-modules-service-1): New variable. (%test-loadable-kernel-modules-service-2): New variable. * doc/guix.texi: Document linux-loadable-module-service-type. Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org> raid5atemyhomework