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authorEfraim Flashner <efraim@flashner.co.il>2021-01-19 10:33:19 +0200
committerEfraim Flashner <efraim@flashner.co.il>2021-01-19 10:33:19 +0200
commit797585746b1e74aa47f06f0e757cbb6c0a262088 (patch)
tree4a8494c21dcd5bec70e4e47ccbf26e771941505f
parent63806fedf27024644c33e8c34fb594c5474bf3a1 (diff)
downloadguix-797585746b1e74aa47f06f0e757cbb6c0a262088.tar.gz
guix-797585746b1e74aa47f06f0e757cbb6c0a262088.zip
gnu: freebayes: Extend test timeout on slower architectures.
* gnu/packages/bioinformatics.scm (freebayes)[arguments]: Use custom 'check phase on aarch64-linux and armhf-linux to extend the test timeout.
-rw-r--r--gnu/packages/bioinformatics.scm12
1 files changed, 11 insertions, 1 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9d9cd05969..908ae8a194 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -143,6 +143,7 @@
#:use-module (gnu packages xml)
#:use-module (gnu packages xorg)
#:use-module (srfi srfi-1)
+ #:use-module (srfi srfi-26)
#:use-module (ice-9 match))
(define-public aragorn
@@ -15168,7 +15169,16 @@ manipulations on VCF files.")
(unpack "vcflib-src" "vcflib")
(unpack "intervaltree-src" "vcflib/intervaltree")
(unpack "test-simple-bash-src" "test/test-simple-bash"))
- #t))))))
+ #t)))
+ ;; The slow tests take longer than the specified timeout.
+ ,@(if (any (cute string=? <> (%current-system))
+ '("armhf-linux" "aarch64-linux"))
+ '((replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "meson" "test" "--timeout-multiplier" "5"))
+ #t)))
+ '()))))
(home-page "https://github.com/ekg/freebayes")
(synopsis "Haplotype-based variant detector")
(description "FreeBayes is a Bayesian genetic variant detector designed to
le='2016-07-13 23:42:35 +0200'>2016-07-13system: Change the shell of 'nobody' to 'nologin'....Fixes <http://bugs.gnu.org/23971>. Reported by Vincent Legoll <vincent.legoll@gmail.com>. * gnu/system/shadow.scm (%base-user-accounts): Add 'shell' field. Set 'home-directory' to "/nonexistent". Ludovic Courtès 2016-07-12services: <shepherd-service> no longer has an 'imported-modules' field....* gnu/services/shepherd.scm (<shepherd-service>)[imported-modules]: Remove. (%default-imported-modules): Make private. (shepherd-service-file): Use 'with-imported-modules'. (shepherd-configuration-file): Remove 'modules' and the calls to 'imported-modules' and 'compiled-modules'. Use 'with-imported-modules' instead. * doc/guix.texi (Shepherd Services): Adjust accordingly. * gnu/services/base.scm (file-system-shepherd-service): Use 'with-imported-modules'. Remove 'imported-modules' field. * gnu/system/mapped-devices.scm (device-mapping-service-type): Remove 'imported-modules'. (open-luks-device): Use 'with-imported-modules'. * gnu/tests.scm (marionette-shepherd-service): Remove 'imported-modules' field and use 'with-imported-modules'. Ludovic Courtès 2016-07-12gnu: Use 'gexp->file' in conjunction with 'with-imported-modules'....* gnu/services.scm (activation-script): Remove code to set '%load-path' and use 'with-imported-modules' instead. (cleanup-gexp): Likewise. * gnu/system/vm.scm (%vm-module-closure): New variable. (expression->derivation-in-linux-vm): Remove #:modules. [loader]: Remove code to set '%load-path'. [builder]: Use %VM-MODULE-CLOSURE. (qemu-image): Use 'with-imported-modules'. Ludovic Courtès 2016-07-12linux-container: Fix list of imported modules....This fixes a regression introduced in 958dd3ce68733bcd5c1231424c7e4ad39e67594a. * gnu/system/linux-container.scm (container-script)[script]: Add (guix combinators) to the list of imported modules. Ludovic Courtès 2016-07-12gnu: Switch to 'with-imported-modules'....* gnu/services.scm (directory-union): Use 'with-imported-modules' instead of the '#:modules' argument of 'computed-file'. * gnu/services/base.scm (udev-rules-union): Likewise. * gnu/services/dbus.scm (system-service-directory): Likewise. * gnu/services/desktop.scm (wrapped-dbus-service): (polkit-directory): Likewise. * gnu/services/networking.scm (tor-configuration->torrc): Likewise. * gnu/services/xorg.scm (xorg-configuration-directory): Likewise. * gnu/system/install.scm (self-contained-tarball): Likewise. * gnu/system/linux-container.scm (container-script): Likewise. * gnu/system/linux-initrd.scm (expression->initrd): Likewise, and remove #:modules parameter. (flat-linux-module-directory): Use 'with-imported-modules'. (base-initrd): Likewise. * gnu/system/locale.scm (locale-directory): Likewise. * gnu/system/shadow.scm (default-skeletons): Likewise. * gnu/system/vm.scm (expression->derivation-in-linux-vm): Likewise. * gnu/tests/base.scm (run-basic-test): Likewise. * gnu/tests/install.scm (run-install): Likewise. * doc/guix.texi (Initial RAM Disk): Update 'expression->initrd' documentation. Ludovic Courtès 2016-06-29gnu: linux-initrd: Support NVMe devices....* gnu/system/linux-initrd.scm (base-initrd): Add nvme to linux-modules. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Jan Nieuwenhuizen 2016-06-27Merge branch 'master' into core-updatesLudovic Courtès 2016-06-21install: Pass a relative file name to 'local-file'....This is a followup to cbbbb7be0fbaa11ff75bce92f2d82131ff8db104. * gnu/system/install.scm (/etc/configuration-files): Pass a relative file name to 'local-file'. Ludovic Courtès 2016-06-07Merge branch 'master' into core-updatesLudovic Courtès 2016-06-06file-systems: Remove unneeded import....* gnu/system/file-systems.scm: Remove import of (guix gexp), unneeded since commit 060d62a740fc1932a3be505534feff099b59ac9f. Ludovic Courtès 2016-05-31install: 'cow-store' now bind-mounts the target's /tmp....Reported by Matthew Jordan <matthewjordandevops@yandex.com> at <https://lists.gnu.org/archive/html/guix-devel/2016-05/msg00967.html>. * gnu/system/install.scm (make-cow-store): Bind-mount TARGET's /tmp on /tmp. Ludovic Courtès 2016-05-13Merge branch 'master' into core-updatesLeo Famulari 2016-05-06system: Do not export PS1 in /etc/skel/.bashrc....* gnu/system/shadow.scm (default-skeletons)[bashrc]: Remove "export" for 'PS1'. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Alex Griffin 2016-05-04tests: Add whole-system test....* gnu/system/vm.scm (virtualized-operating-system): Export. * gnu/tests/base.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. * Makefile.am (check-system): New target. Ludovic Courtès 2016-05-04Add (gnu tests) and (gnu build marionette)....* gnu/build/marionette.scm, gnu/tests.scm: New files. * gnu/local.mk (GNU_SYSTEM_MODULES): Add them. * gnu/system/vm.scm (common-qemu-options): Remove '-serial stdio'. Ludovic Courtès 2016-05-02Merge branch 'master' into core-updatesMathieu Lirzin 2016-04-29guix system: Reduce size of image produced for 'vm' action....This reduces the size of the image produced by 'guix system vm' from 26 MiB to 9 MiB. * gnu/system/vm.scm (system-qemu-image/shared-store): (system-qemu-image/shared-store-script): Change the default value of #:disk-image-size to 30 MiB when not FULL-BOOT?. * guix/scripts/system.scm (system-derivation-for-action): Likewise for the 'vm' action. Ludovic Courtès 2016-04-18mapped-devices: LUKS partitions can be designated by their UUID....* gnu/system/mapped-devices.scm (device-mapping-service-type): Add 'modules' and 'imported-modules' fields to 'shepherd-service'. (open-luks-device): Use 'find-partition-by-luks-uuid' to lookup the partition when SOURCE is a bytevector. * gnu/system/linux-initrd.scm (base-initrd): Augment 'use-modules' form. * doc/guix.texi (Mapped Devices): Give example with a UUID. Ludovic Courtès 2016-04-18mapped-devices: 'mapped-device-service' takes a <mapped-device>....* gnu/system/mapped-devices.scm (device-mapping-service): Take a <mapped-device> instead of 3 parameters. (device-mapping-service-type): Adjust accordingly. * gnu/system.scm (device-mapping-services): Adjust accordingly. Ludovic Courtès 2016-04-18services: Move 'device-mapping-service' to (gnu system mapped-devices)....* gnu/services/base.scm (device-mapping-service-type) (device-mapping-service): Move to... * gnu/system/mapped-devices.scm (device-mapping-service-type): (device-mapping-service): ... here. New variables. Ludovic Courtès 2016-04-18system: Move 'luks-device-mapping' to (gnu system mapped-devices)....* gnu/system.scm (open-luks-device, close-luks-device) (luks-device-mapping): Move to... * gnu/system/mapped-devices.scm: ... here. New file. Ludovic Courtès 2016-04-18system: Add (gnu system mapped-devices)....* gnu/system/file-systems.scm (<mapped-device>, <mapped-device-type>): Move to... * gnu/system/mapped-devices.scm: ... here. New file. * gnu/system.scm, gnu/services/base.scm, gnu/system/linux-initrd.scm: Use it. * gnu-system.am (GNU_SYSTEM_MODULES): Add it. * gnu.scm (%public-modules): Add it. Ludovic Courtès 2016-04-17install: Use 'beta' instead of 'alpha'....Suggested by Jelle Licht <jlicht@fsfe.org>. * gnu/system/install.scm (installation-services): Say 'beta' instead of 'alpha' and make the warning less scary. Ludovic Courtès 2016-04-06Merge branch 'master' into core-updatesLudovic Courtès 2016-04-03gnu: fontconfig: Find fonts in the system profile....Fixes <http://bugs.gnu.org/22927>. Reported by myglc2 <myglc2@gmail.com>. This also reverts commit e71ef7adaece7e132a5059139122b45083ea1b39. * gnu/packages/fontutils.scm (fontconfig)[arguments]: Add /run/current-system/profile/share/fonts to --with-add-fonts configure flag. * gnu/system/shadow.scm (default-skeletons): Do not create "fonts.conf" file. Alex Kost 2016-03-24install: Use 'info-reader' instead of Texinfo 4....* gnu/system/install.scm (installation-os)[packages]: Remove TEXINFO-4 since %BASE-PACKAGES already provides the Info reader. (log-to-info): Use INFO-READER instead of TEXINFO-4. Ludovic Courtès 2016-03-24install: Remove cgroup and elogind file systems....* gnu/system/install.scm (installation-os): Explicitly list three file systems instead of using %BASE-FILE-SYSTEMS. Ludovic Courtès 2016-03-24install: Add /tmp as a tmpfs....Fixes <http://bugs.gnu.org/23056>. Reported by Michael Downey <shaggy814@yandex.com> and Kei <kei@openmailbox.org>. * gnu/system/install.scm (installation-os)[file-systems]: Add "/tmp". Ludovic Courtès 2016-03-23doc: Add "lightweight desktop" OS config example....* gnu/system/examples/desktop.tmpl (packages): Remove XFCE and RATPOISON. (services): Add 'gnome-desktop-service' and 'xfce-desktop-service'. * gnu/system/examples/lightweight-desktop.tmpl: New file. * Makefile.am (EXAMPLES): Add it. * doc.am (OS_CONFIG_EXAMPLES_TEXI): Add doc/os-config-lightweight-desktop.texi. * gnu/system/install.scm (/etc/configuration-files)[directory]: Add lightweight-desktop.tmpl. Ludovic Courtès 2016-03-20system: Make sure fonts are searched for in the system profile....This fixes a bug whereby fonts in /run/current-system/profile would be invisible to Fontconfig. * gnu/packages/fontutils.scm (fontconfig): Add comment about system profile not being searched. * gnu/system/shadow.scm (default-skeletons)[fonts.conf-content, fonts.conf]: New variable. Add FONTS.CONF to the skeletons. Ludovic Courtès 2016-03-20system: Allow account skeletons to be directories....* gnu/system/shadow.scm (skeleton-directory): Use 'copy-recursively' instead of 'copy-file'. * gnu/build/activation.scm (copy-account-skeletons): Likewise. Ludovic Courtès 2016-03-07gnu: system: Add elogind cgroup mount....* gnu/system/file-systems.scm (%elogind-file-systems): Add elogind cgroup mount. Andy Wingo 2016-02-22vm: Only pass "-enable-kvm" to qemu if /dev/kvm is present....Fixes <http://bugs.gnu.org/22633>. * gnu/build/vm.scm (load-in-linux-vm): Only pass "-enable-kvm" flag to qemu if "/dev/kvm" is present. * gnu/system/vm.scm (common-kvm-options): Same as above. Christopher Allan Webber