aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorRicardo Wurmus <rekado@elephly.net>2019-12-13 13:30:58 +0100
committerRicardo Wurmus <rekado@elephly.net>2019-12-13 22:41:36 +0100
commite44c4cd73cfb256c97a0f14f8b3731b35b024dd8 (patch)
treeb94e17f73f7601abd5e8b9c55e9029245db68e06
parentba4fcea499c74515925f2bc6a414ba64fff7754c (diff)
downloadguix-e44c4cd73cfb256c97a0f14f8b3731b35b024dd8.tar.gz
guix-e44c4cd73cfb256c97a0f14f8b3731b35b024dd8.zip
gnu: Add r-bio3d.
* gnu/packages/cran.scm (r-bio3d): New variable.
-rw-r--r--gnu/packages/cran.scm31
1 files changed, 31 insertions, 0 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index c2f0e156bd..1c3d40d76c 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16013,3 +16013,34 @@ graphics directly in the terminal window. This package provides a basic
plotting function (and equivalents of curve, density, acf and barplot) as well
as a boxplot function.")
(license license:lgpl3+)))
+
+(define-public r-bio3d
+ (package
+ (name "r-bio3d")
+ (version "2.4-0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "bio3d" version))
+ (sha256
+ (base32
+ "0ikpk1ppdp50m9kd289z616i382j9i7ji1zchyd4xqfyk8lnxf4s"))))
+ (properties `((upstream-name . "bio3d")))
+ (build-system r-build-system)
+ (inputs `(("zlib" ,zlib)))
+ (propagated-inputs `(("r-rcpp" ,r-rcpp)))
+ (home-page "http://thegrantlab.org/bio3d/")
+ (synopsis "Biological structure analysis")
+ (description
+ "This package provides utilities to process, organize and explore protein
+structure, sequence and dynamics data. Features include the ability to read
+and write structure, sequence and dynamic trajectory data, perform sequence
+and structure database searches, data summaries, atom selection, alignment,
+superposition, rigid core identification, clustering, torsion analysis,
+distance matrix analysis, structure and sequence conservation analysis, normal
+mode analysis, principal component analysis of heterogeneous structure data,
+and correlation network analysis from normal mode and molecular dynamics data.
+In addition, various utility functions are provided to enable the statistical
+and graphical power of the R environment to work with biological sequence and
+structural data.")
+ (license license:gpl2+)))
t-scheme)[origin]{snippet}: New snippet. Signed-off-by: Marius Bakke <marius@gnu.org> Maxime Devos 2022-09-07gnu: gnunet-scheme: Make scheme-gnunet.pdf reproducible....* gnu/packages/gnunet.scm (gnunet-scheme)[arguments]<#:phases>{reproducible-timestamp}: New phase. Signed-off-by: Marius Bakke <marius@gnu.org> Maxime Devos 2022-09-07gnu: gnunet-scheme: Update to 0.3....The old snippet doesn't apply anymore, so a different work-around was committed to gnunet-scheme. * gnu/packages/gnunet.scm (gnunet-scheme): Update to 0.3. [description]: Update description for new features. Signed-off-by: Marius Bakke <marius@gnu.org> Maxime Devos a href='/guix/commit/gnu/services/base.scm?id=264ca9452fae827d6621b28b8972f4b1d68401a1'>services: syslogd: Do not fsync at each line....Fixes <https://issues.guix.gnu.org/55707>. Previously Inetutils' syslogd would call 'fsync' after each line written to a file. This would significantly increase boot times on machines with slow-ish spinning HDDs, where each 'fsync' call would take between 0.1s and 0.4s (and we'd do two of them for each line, one for /var/log/messages and one for /var/log/debug). * gnu/services/base.scm (%default-syslog.conf): Add a '-' before each file name, except /var/log/secure. Change what goes to /var/log/debug. Ludovic Courtès 2022-06-05services: pam-limits: Add sudo and sshd....* gnu/services/base.scm (pam-limits-service-type): Add "sudo" and "sshd" to the list. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Kiran Shila 2022-05-18services: Add more description fields....* gnu/services.scm (simple-service): Add 'description' field. * gnu/services/base.scm (udev-rules-service): Likewise. * gnu/system/install.scm (configuration-template-service-type): Likewise. * gnu/tests.scm (marionette-service-type): Likewise. Ludovic Courtès 2022-05-02services: Make sure Shepherd destructors match constructors....This is a followup to b06ecc57515d4e3c8b2228e8142654e9a26ba6e1, 211fe3f66e6dfdaa64974931c458ab1d92afc182, and fd57ce267c4083fe98242caa31075d2bd62903bf. * gnu/services/base.scm (guix-publish-shepherd-service): Change 'stop' method to use 'make-systemd-destructor' when 'make-systemd-constructor' is used. * gnu/services/dict.scm (dicod-shepherd-service): Change 'stop' method to use 'make-inetd-destructor' when 'make-inetd-constructor' is used. * gnu/services/messaging.scm (bitlbee-shepherd-service): Likewise. Ludovic Courtès 2022-05-01gexp: Add 'references-file'....* gnu/services/base.scm (references-file): Remove. * guix/gexp.scm (references-file): New procedure. * tests/gexp.scm ("references-file"): New test. Ludovic Courtès 2022-04-29services: guix-publish: Use socket activation when possible....* gnu/services/base.scm (guix-publish-shepherd-service): Use 'make-systemd-constructor' when it's available and ADVERTISE? is false. Ludovic Courtès 2022-04-04services: Add 'log-cleanup' service to '%base-services' for build logs....* gnu/services/base.scm (%base-services): Add 'log-cleanup-service-type' instance. * doc/guix.texi (Log Rotation): Add example and mention '%base-services'. Ludovic Courtès 2022-03-10services: guix: Add 'generate-substitute-key?' field....* gnu/services/base.scm (<guix-configuration>)[generate-substitute-key?]: New field. (guix-activation): Honor it. * doc/guix.texi (Base Services): Document it. Ludovic Courtès 2022-02-25agetty-shepherd-service: Rename console agetty to "term-console" for clarity....* gnu/services/base.scm (agetty-shepherd-service)[provision]: Rename console agetty to "term-console". Danny Milosavljevic 2022-02-25services: %base-services: Adapt agetty-service-type to depend on syslogd...Fixes <https://issues.guix.gnu.org/30464>. * gnu/services/base.scm (%base-services): Reorder syslog-service for clarity. [shepherd-requirement]: New field. Danny Milosavljevic 2022-02-25services: agetty: Add shepherd-requirement....* gnu/services/base.scm (<agetty-configuration>): Add shepherd-requirement. * doc/guix.texi (agetty-configuration): Document it. Danny Milosavljevic 2022-02-20services: udev: Use a fixed location for the rules directory and config....Fixes <https://issues.guix.gnu.org/47681>. This change adjusts the location of the udev configuration file and rules directory to a fixed location. Since udev relies on inotify to discover change to its rules directory (/etc/udev/rules.d), by using a fixed directory layout, new udev rules can be automatically picked up without restarting the service. * gnu/services/base.scm (udev-rules-union): Build rules output directly in #$output. (udev-shepherd-service)[start]: Adjust the UDEV_CONFIG_FILE and EUDEV_RULES_DIRECTORY environment variables. [actions]: Remove field. The 'rules' action is no longer useful. (udev.conf): New variable. (udev-etc): New procedure. (udev-service-type): Extend the etc-service-type with it. Maxim Cournoyer 2022-01-20services: guix-publish: Add negative-ttl parameter....* gnu/services/base.scm (guix-publish-configuration): Add 'negative-ttl' field. (guix-publish-sheperd-service): Process it. * doc/guix.texi (Base Services)[guix-publish-service-type]: Add item for negative-ttl. Guillaume Le Vaillant 2022-01-18daemon: Always default to gzip for log compression....* nix/libstore/globals.cc (Settings::Settings): Have 'logCompression' default to COMPRESSION_GZIP unconditionally. * gnu/services/base.scm (<guix-configuration>)[log-compression]: Default to 'gzip. * doc/guix.texi (Invoking guix-daemon, Base Services): Adjust accordingly. Ludovic Courtès 2022-01-16services: guix: Add tar and gzip to PATH....* gnu/services/base.scm (guix-shepherd-service): Add the PATH environment-variable and populate it with tar and gzip. Timothy Sample 2022-01-08services: networking: Add netmask to loopback address....Previously, we would get a fishy 127.0.0.1/0 interface: $ ip a show dev lo 1: lo: <LOOPBACK,UP,LOWER_UP> mtu 65536 qdisc noqueue state UNKNOWN group default qlen 1000 link/loopback 00:00:00:00:00:00 brd 00:00:00:00:00:00 inet 127.0.0.1/8 scope host lo valid_lft forever preferred_lft forever inet 127.0.0.1/0 scope global lo valid_lft forever preferred_lft forever inet6 ::1/128 scope host valid_lft forever preferred_lft forever With this change, we get nothing but the "/8" version: $ ip a show dev lo 1: lo: <LOOPBACK,MULTICAST,UP,LOWER_UP> mtu 65536 qdisc noqueue state UNKNOWN group default qlen 1000 link/loopback 00:00:00:00:00:00 brd 00:00:00:00:00:00 inet 127.0.0.1/8 scope global lo valid_lft forever preferred_lft forever inet6 ::1/128 scope host valid_lft forever preferred_lft forever Reported by Yann Dupont <Yann.Dupont@univ-nantes.fr>. * gnu/services/base.scm (assert-valid-address): Remove special cases for 127.0.0.1 and ::1. (%loopback-static-networking): Add "/8". Ludovic Courtès 2021-12-21services: static-networking: Enable multicast by default....Fixes: <https://issues.guix.gnu.org/52520>. * gnu/services/base.scm (network-set-up/linux): Enable it. Mathieu Othacehe 2021-12-20services: static-networking: Sanitize <network-address> values....This makes sure users do not mistakenly configuring a network with "/0" as its netmask. * gnu/services/base.scm (assert-valid-address): New procedure. (<network-address>)[value]: Add it as 'sanitize'. Ludovic Courtès 2021-12-12services: Define '%loopback-static-networking'....* gnu/services/base.scm (%loopback-static-networking): New variable. (%base-services): Use it. * gnu/system/hurd.scm (%base-services/hurd): Use it. * gnu/system/install.scm (%installation-services): Use it. * doc/guix.texi (Networking Setup): Document it. Ludovic Courtès 2021-12-12services: Define '%qemu-static-networking'....* gnu/services/base.scm (%qemu-static-networking): New variable. * gnu/system/hurd.scm (%base-services/hurd): Use it. * doc/guix.texi (Networking Setup): Document it. Ludovic Courtès 2021-12-12services: static-networking: Change interface to mimic netlink....* gnu/services/base.scm (<static-networking>)[interface, ip, netmask] [gateway]: Remove. [addresses, links, routes]: New fields. [requirement]: Default to '(udev). (<network-address>, <network-link>, <network-route>): New record types. (ensure-no-separate-netmask, %ensure-no-separate-netmask): Remove. (ipv6-address?, cidr->netmask, ip+netmask->cidr) (network-set-up/hurd, network-tear-down/hurd) (network-set-up/linux, network-tear-down/linux) (static-networking->hurd-pfinet-options): New procedures. (static-networking-shepherd-service): New procedure. (static-networking-shepherd-services): Rewrite in terms of the above. (static-networking-service): Deprecate. Adjust to new 'static-networking' API. (%base-services): Likewise. * gnu/system/install.scm (%installation-services): Likewise. * gnu/system/hurd.scm (%base-services/hurd): Likewise, and separate 'loopback' from 'networking'. * gnu/build/hurd-boot.scm (set-hurd-device-translators): Remove "servers/socket/2". * gnu/tests/networking.scm (run-openvswitch-test)["networking has started on ovs0"]: Check for 'networking instead of 'networking-ovs0, which is no longer provided. * doc/guix.texi (Networking Setup): Document the new interface. Remove documentation of 'static-networking-service'. (Virtualization Services): Change Ganeti example to use the new interface. Ludovic Courtès 2021-12-12services: static-networking: Use Guile-Netlink on GNU/Linux....* gnu/services/base.scm (static-networking-shepherd-service): Define 'set-up-via-ioctl', 'tear-down-via-ioctl', 'set-up-via-netlink', 'tear-down-via-netlink', and 'helpers' and use them in 'start' and 'stop'. Add (ip *) modules to 'modules'. Ludovic Courtès 2021-11-30services: Accept <inferior-package>s in lieu of <package>s....* gnu/services/authentication.scm (fprintd-configuration) (nslcd-configuration): Substitute file-like objects for package ones. * gnu/services/cgit.scm (cgit-configuration, opaque-cgit-configuration): Likewise. * gnu/services/cups.scm (package-list?, cups-configuration): Likewise. * gnu/services/dns.scm (verify-knot-configuration) (ddclient-configuration): Likewise. * gnu/services/docker.scm (docker-configuration): Likewise. * gnu/services/file-sharing.scm (transmission-daemon-configuration): Likewise. * gnu/services/getmail.scm (getmail-configuration): Likewise. * gnu/services/mail.scm (dovecot-configuration) (opaque-dovecot-configuration): Likewise. * gnu/services/messaging.scm (prosody-configuration) (opaque-prosody-configuration): Likewise. * gnu/services/monitoring.scm (zabbix-server-configuration) (zabbix-agent-configuration): Likewise. * gnu/services/networking.scm (opendht-configuration): Likewise. * gnu/services/pm.scm (tlp-configuration): Likewise. * gnu/services/telephony.scm (jami-configuration): Likewise. * gnu/services/virtualization.scm (libvirt-configuration) (qemu-guest-agent-configuration): Likewise. * gnu/services/vpn.scm (openvpn-client-configuration): Likewise. Tobias Geerinckx-Rice 2021-11-23gnu: system: Make old-style swap use default flags....* gnu/services/base.scm (swap-service-type): Use default flags (0) if SWAP is not a new-style <swap-space> record. Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr> Josselin Poiret 2021-11-23system: Add swap flags....* gnu/system/file-systems.scm (swap-space)[priority, discard?]: Add them. * guix/build/syscalls.scm (SWAP_FLAG_PREFER, SWAP_FLAG_PRIO_MASK, SWAP_FLAG_PRIO_SHIFT, SWAP_FLAG_DISCARD): Add them. * gnu/build/file-systems.scm (swap-space->flags-bit-mask): Add it. * gnu/services/base.scm (swap-service-type): Use it. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Josselin Poiret 2021-11-23system: Rework swap space support, add dependencies....* gnu/system/file-systems.scm (swap-space): Add it. * gnu/system.scm (operating-system)[swap-devices]: Update comment. * gnu/services/base.scm (swap-space->shepherd-service-name, swap-deprecated->shepherd-service-name, swap->shepherd-service-name): Add them. * gnu/services/base.scm (swap-service-type, swap-service): Use the new records. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Josselin Poiret 2021-08-29services: base: Honor file-system-create-mount-point? at all times....Fixes <https://issues.guix.gnu.org/40158>. * gnu/services/base.scm (file-system-shepherd-service): Update doc. Return a shepherd service for the mount point when either MOUNT? or CREATE? is true. [start]: Only mount when MOUNT? is true. (file-system-shepherd-services): Also consider file systems with create-mount-point? set to #t. Maxim Cournoyer 2021-08-07services: pam-limits: fix limits.conf location...* gnu/services/base.scm: fix limits.conf location This fixes #49771 Signed-off-by: Julien Lepiller <julien@lepiller.eu> muradm 2021-08-04services: guix: Use "match-record" in activation....It's more explicit to specify used fields instead of depending on their position. * gnu/services/base.scm (guix-activation): Replace "match" with "match-record". Brice Waegeneire 2021-07-13services: gpm: Use "make-forkexec-contstructor"....* gnu/services/base.scm (gpm-shepherd-service)[start]: Replace custom logic with "make-forkexec-constructor". Brice Waegeneire 2021-06-29services: kmscon: Add keyboard-layout fields....* gnu/services/base.scm (<kmscon-configuration>): Add keyboard-layout fields. * doc/guix.texi (Base Services): Document them. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org> luhui 2021-06-19services: guix: Authorize 'bordeaux.guix.gnu.org.pub' by default....This follows on from the changes in 4985a4272497bf9ba87a2190353d915da9b55906. * gnu/services/base.scm (%default-authorized-guix-keys): Add bordeaux.guix.gnu.org.pub. Signed-off-by: Christopher Baines <mail@cbaines.net> Jack Hill 2021-06-14services: Remove deprecated service procedures....These service procedures were deprecated in January 2019, for instance in commit 65a67bf711b14bc7200f6730c0f173375ca12974. * gnu/services/avahi.scm (avahi-service): Remove. * gnu/services/base.scm (console-keymap, guix-service) (guix-publish-service, gpm-service, urandom-seed-service): Remove. * gnu/services/desktop.scm (upower-service, colord-service): Remove. * gnu/services/mcron.scm (mcron-service): Remove. * gnu/services/messaging.scm (bitlbee-service): Remove. * gnu/services/networking.scm (dhcp-client-service, ntp-service) (tor-service): Remove. * gnu/services/xorg.scm (slim-service, gdm-service): Remove. Ludovic Courtès 2021-04-03services: guix-publish: Add zstd compression by default....That way, the default config with (advertises? #t) and without a cache will offer zstd-compressed substitutes, which should lead to much higher throughput than gzip. * gnu/services/base.scm (default-compression): When 'guix-publish-configuration-cache' returns true, use higher level compression ratios. Add "zstd". * doc/guix.texi (Base Services): Mention zstd. Ludovic Courtès 2021-04-01services: kmscon: Add font-engine and font-size fields....* gnu/services/base.scm (<kmscon-configuration>): Add font-engine and font-size fields. (kmscon-service-type): Honor them. * doc/guix.texi (Base Services): Document them. qblade 2021-03-18services: Enable "protected hardlinks" and "protected symlinks" by default....References: https://sysctl-explorer.net/fs/protected_hardlinks/ https://sysctl-explorer.net/fs/protected_symlinks/ * gnu/services/sysctl.scm (%default-sysctl-settings): New public variable. (<sysctl-configuration>): Use %default-sysctl-settings as the default value. * gnu/services/base.scm (%base-services): Add sysctl-service-type. * doc/guix.texi (Miscellaneous Services): Document the new defaults. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Leo Famulari 2021-01-13services: shepherd: 'shepherd-service-type' requires documentation....* gnu/services/shepherd.scm (shepherd-service-type): Require a 'description' form. * gnu/services/base.scm (root-file-system-service-type) (rngd-service-type, host-name-service-type): (virtual-terminal-service-type, console-keymap-service-type) (syslog-service-type, swap-service-type) (kmscon-service-type): Add description. * gnu/services/networking.scm (dhcp-client-service-type): Likewise. * gnu/system/install.scm (cow-store-service-type): Likewise. * gnu/system/linux-container.scm (dummy-networking-service-type): Likewise. * gnu/system/mapped-devices.scm (device-mapping-service-type): Likewise. * tests/guix-system.sh: Likewise. Ludovic Courtès 2020-12-15services: 'references-file' depends on Guile-Gcrypt....Regression introduced in 6a060ff27ff68384d7c90076baa36c349fff689d. Reported by clone11 on #guix. * gnu/services/base.scm (references-file): Wrap gexp in 'with-extensions'. Ludovic Courtès