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15
maintainers/maintainer-list.nix
View File

@ -69,6 +69,12 @@
fingerprint = "F466 A548 AD3F C1F1 8C88 4576 8702 7528 B006 D66D";
}];
};
_0xB10C = {
email = "nixpkgs@b10c.me";
name = "0xB10C";
github = "0xb10c";
githubId = 19157360;
};
_0xbe7a = {
email = "nix@be7a.de";
name = "Bela Stoyan";
@ -2156,6 +2162,13 @@
githubId = 51231053;
name = "Daniel";
};
calavera = {
email = "david.calavera@gmail.com";
github = "calavera";
githubId = 1050;
matrix = "@davidcalavera:matrix.org";
name = "David Calavera";
};
callahad = {
email = "dan.callahan@gmail.com";
github = "callahad";
@ -10165,7 +10178,7 @@
matrix = "@obfusk:matrix.org";
github = "obfusk";
githubId = 1260687;
name = "Felix C. Stegerman";
name = "FC Stegerman";
keys = [{
fingerprint = "D5E4 A51D F8D2 55B9 FAC6 A9BB 2F96 07F0 9B36 0F2D";
}];

44
nixos/doc/manual/from_md/release-notes/rl-2211.section.xml
View File

@ -130,6 +130,13 @@
PHP now defaults to PHP 8.1, updated from 8.0.
</para>
</listitem>
<listitem>
<para>
<literal>protonup</literal> has been aliased to and replaced
by <literal>protonup-ng</literal> due to upstream not
maintaining it.
</para>
</listitem>
<listitem>
<para>
Perl has been updated to 5.36, and its core module
@ -457,6 +464,14 @@
<link linkend="opt-services.uptime-kuma.enable">services.uptime-kuma</link>.
</para>
</listitem>
<listitem>
<para>
<link xlink:href="https://mepo.milesalan.com">Mepo</link>, a
fast, simple, hackable OSM map viewer for mobile and desktop
Linux. Available as
<link linkend="opt-programs.mepo.enable">programs.mepo.enable</link>.
</para>
</listitem>
</itemizedlist>
</section>
<section xml:id="sec-release-22.11-incompatibilities">
@ -804,6 +819,28 @@
</listitem>
</itemizedlist>
</listitem>
<listitem>
<para>
<literal>arangodb</literal> versions 3.3, 3.4, and 3.5 have
been removed because they are at EOL upstream. The default is
now 3.10.0. Support for aarch64-linux has been removed since
the target cannot be built reproducibly. By default
<literal>arangodb</literal> is now built for the
<literal>haswell</literal> architecture. If you wish to build
for a different architecture, you may override the
<literal>targetArchitecture</literal> argument with a value
from
<link xlink:href="https://github.com/arangodb/arangodb/blob/207ec6937e41a46e10aea34953879341f0606841/cmake/OptimizeForArchitecture.cmake#L594">this
list supported upstream</link>. Some architecture specific
optimizations are also conditionally enabled. You may alter
this behavior by overriding the
<literal>asmOptimizations</literal> parameter. You may also
add additional architecture support by adding more
<literal>-DHAS_XYZ</literal> flags to
<literal>cmakeFlags</literal> via
<literal>overrideAttrs</literal>.
</para>
</listitem>
<listitem>
<para>
The <literal>meta.mainProgram</literal> attribute of packages
@ -961,6 +998,13 @@
configure this behaviour.
</para>
</listitem>
<listitem>
<para>
<literal>mastodon</literal> now automatically removes remote
media attachments older than 30 days. This is configurable
through <literal>services.mastodon.mediaAutoRemove</literal>.
</para>
</listitem>
<listitem>
<para>
The Redis module now disables RDB persistence when

10
nixos/doc/manual/release-notes/rl-2211.section.md
View File

@ -53,6 +53,8 @@ In addition to numerous new and upgraded packages, this release has the followin
- PHP now defaults to PHP 8.1, updated from 8.0.
- `protonup` has been aliased to and replaced by `protonup-ng` due to upstream not maintaining it.
- Perl has been updated to 5.36, and its core module `HTTP::Tiny` was patched to verify SSL/TLS certificates by default.
- Improved performances of `lib.closePropagation` which was previously quadratic. This is used in e.g. `ghcWithPackages`. Please see backward incompatibilities notes below.
@ -149,6 +151,8 @@ Available as [services.patroni](options.html#opt-services.patroni.enable).
- [Uptime Kuma](https://uptime.kuma.pet/), a fancy self-hosted monitoring tool. Available as [services.uptime-kuma](#opt-services.uptime-kuma.enable).
- [Mepo](https://mepo.milesalan.com), a fast, simple, hackable OSM map viewer for mobile and desktop Linux. Available as [programs.mepo.enable](#opt-programs.mepo.enable).
<!-- To avoid merge conflicts, consider adding your item at an arbitrary place in the list instead. -->
## Backward Incompatibilities {#sec-release-22.11-incompatibilities}
@ -253,6 +257,8 @@ Available as [services.patroni](options.html#opt-services.patroni.enable).
* `systemd.network.networks.<name>.dhcpV6Config` no longer accepts the `ForceDHCPv6PDOtherInformation=` setting. Please use the `WithoutRA=` and `UseDelegatedPrefix=` settings in your `systemd.network.networks.<name>.dhcpV6Config` and the `DHCPv6Client=` setting in your `systemd.network.networks.<name>.ipv6AcceptRAConfig` to control when the DHCPv6 client is started and how the delegated prefixes are handled by the DHCPv6 client.
* `systemd.network.networks.<name>.networkConfig` no longer accepts the `IPv6Token=` setting. Use the `Token=` setting in your `systemd.network.networks.<name>.ipv6AcceptRAConfig` instead. The `systemd.network.networks.<name>.ipv6Prefixes.*.ipv6PrefixConfig` now also accepts the `Token=` setting.
- `arangodb` versions 3.3, 3.4, and 3.5 have been removed because they are at EOL upstream. The default is now 3.10.0. Support for aarch64-linux has been removed since the target cannot be built reproducibly. By default `arangodb` is now built for the `haswell` architecture. If you wish to build for a different architecture, you may override the `targetArchitecture` argument with a value from [this list supported upstream](https://github.com/arangodb/arangodb/blob/207ec6937e41a46e10aea34953879341f0606841/cmake/OptimizeForArchitecture.cmake#L594). Some architecture specific optimizations are also conditionally enabled. You may alter this behavior by overriding the `asmOptimizations` parameter. You may also add additional architecture support by adding more `-DHAS_XYZ` flags to `cmakeFlags` via `overrideAttrs`.
- The `meta.mainProgram` attribute of packages in `wineWowPackages` now defaults to `"wine64"`.
- The `paperless` module now defaults `PAPERLESS_TIME_ZONE` to your configured system timezone.
@ -296,6 +302,8 @@ Available as [services.patroni](options.html#opt-services.patroni.enable).
- ZFS module will not allow hibernation by default, this is a safety measure to prevent data loss cases like the ones described at [OpenZFS/260](https://github.com/openzfs/zfs/issues/260) and [OpenZFS/12842](https://github.com/openzfs/zfs/issues/12842). Use the `boot.zfs.allowHibernation` option to configure this behaviour.
- `mastodon` now automatically removes remote media attachments older than 30 days. This is configurable through `services.mastodon.mediaAutoRemove`.
- The Redis module now disables RDB persistence when `services.redis.servers.<name>.save = []` instead of using the Redis default.
- Neo4j was updated from version 3 to version 4. See this [migration guide](https://neo4j.com/docs/upgrade-migration-guide/current/) on how to migrate your Neo4j instance.
@ -364,7 +372,7 @@ Available as [services.patroni](options.html#opt-services.patroni.enable).
[systemd.oomd.enableRootSlice](options.html#opt-systemd.oomd.enableRootSlice),
[systemd.oomd.enableSystemSlice](options.html#opt-systemd.oomd.enableSystemSlice),
and [systemd.oomd.enableUserServices](options.html#opt-systemd.oomd.enableUserServices).
- The `tt-rss` service performs two database migrations when you first use its web UI after upgrade. Consider backing up its database before updating.
- The `pass-secret-service` package now includes systemd units from upstream, so adding it to the NixOS `services.dbus.packages` option will make it start automatically as a systemd user service when an application tries to talk to the libsecret D-Bus API.

3
nixos/modules/module-list.nix
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@ -186,6 +186,8 @@
./programs/less.nix
./programs/liboping.nix
./programs/light.nix
./programs/mdevctl.nix
./programs/mepo.nix
./programs/mosh.nix
./programs/mininet.nix
./programs/msmtp.nix
@ -320,6 +322,7 @@
./services/backup/znapzend.nix
./services/blockchain/ethereum/geth.nix
./services/blockchain/ethereum/erigon.nix
./services/blockchain/ethereum/lighthouse.nix
./services/backup/zrepl.nix
./services/cluster/corosync/default.nix
./services/cluster/hadoop/default.nix

3
nixos/modules/programs/less.nix
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@ -103,7 +103,8 @@ in
type = types.nullOr types.str;
default = null;
description = lib.mdDoc ''
When less closes a file opened in such a way, it will call another program, called the input postprocessor, which may perform any desired clean-up action (such as deleting the replacement file created by LESSOPEN).
When less closes a file opened in such a way, it will call another program, called the input postprocessor,
which may perform any desired clean-up action (such as deleting the replacement file created by LESSOPEN).
'';
};
};

18
nixos/modules/programs/mdevctl.nix Normal file
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@ -0,0 +1,18 @@
{ config, pkgs, lib, ... }:
with lib;
let
cfg = config.programs.mdevctl;
in {
options.programs.mdevctl = {
enable = mkEnableOption (lib.mdDoc "Mediated Device Management");
};
config = mkIf cfg.enable {
environment.systemPackages = with pkgs; [ mdevctl ];
environment.etc."mdevctl.d/scripts.d/notifiers/.keep".text = "";
environment.etc."mdevctl.d/scripts.d/callouts/.keep".text = "";
};
}

46
nixos/modules/programs/mepo.nix Normal file
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@ -0,0 +1,46 @@
{ pkgs, config, lib, ...}:
with lib;
let
cfg = config.programs.mepo;
in
{
options.programs.mepo = {
enable = mkEnableOption (mdDoc "Mepo");
locationBackends = {
gpsd = mkOption {
type = types.bool;
default = false;
description = mdDoc ''
Whether to enable location detection via gpsd.
This may require additional configuration of gpsd, see [here](#opt-services.gpsd.enable)
'';
};
geoclue = mkOption {
type = types.bool;
default = true;
description = mdDoc "Whether to enable location detection via geoclue";
};
};
};
config = mkIf cfg.enable {
environment.systemPackages = with pkgs; [
mepo
] ++ lib.optional cfg.locationBackends.geoclue geoclue2-with-demo-agent
++ lib.optional cfg.locationBackends.gpsd gpsd;
services.geoclue2 = mkIf cfg.locationBackends.geoclue {
enable = true;
appConfig.where-am-i = {
isAllowed = true;
isSystem = false;
};
};
services.gpsd.enable = cfg.locationBackends.gpsd;
};
meta.maintainers = with maintainers; [ laalsaas ];
}

22
nixos/modules/security/pam.nix
View File

@ -392,6 +392,24 @@ let
'';
};
failDelay = {
enable = mkOption {
type = types.bool;
default = false;
description = lib.mdDoc ''
If enabled, this will replace the `FAIL_DELAY` setting from `login.defs`.
Change the delay on failure per-application.
'';
};
delay = mkOption {
default = 3000000;
type = types.int;
example = 1000000;
description = lib.mdDoc "The delay time (in microseconds) on failure.";
};
};
gnupg = {
enable = mkOption {
type = types.bool;
@ -531,6 +549,7 @@ let
|| cfg.enableGnomeKeyring
|| cfg.googleAuthenticator.enable
|| cfg.gnupg.enable
|| cfg.failDelay.enable
|| cfg.duoSecurity.enable))
(
''
@ -551,6 +570,9 @@ let
optionalString cfg.gnupg.enable ''
auth optional ${pkgs.pam_gnupg}/lib/security/pam_gnupg.so ${optionalString cfg.gnupg.storeOnly " store-only"}
'' +
optionalString cfg.failDelay.enable ''
auth optional ${pkgs.pam}/lib/security/pam_faildelay.so delay=${toString cfg.failDelay.delay}
'' +
optionalString cfg.googleAuthenticator.enable ''
auth required ${pkgs.google-authenticator}/lib/security/pam_google_authenticator.so no_increment_hotp
'' +

26
nixos/modules/services/blockchain/ethereum/erigon.nix
View File

@ -13,6 +13,15 @@ in {
services.erigon = {
enable = mkEnableOption (lib.mdDoc "Ethereum implementation on the efficiency frontier");
group = mkOption {
type = types.str;
default = "ethereum";
description = lib.mdDoc ''
Group of the user running the lighthouse process. This is used to share the jwt
secret with the execution layer.
'';
};
settings = mkOption {
description = lib.mdDoc ''
Configuration for Erigon
@ -55,6 +64,19 @@ in {
};
config = mkIf cfg.enable {
users = {
users.erigon = {
name = "erigon";
group = cfg.group;
description = "Erigon user";
home = "/var/lib/erigon";
isSystemUser = true;
};
groups = mkIf (cfg.group == "ethereum") {
ethereum = {};
};
};
# Default values are the same as in the binary, they are just written here for convenience.
services.erigon.settings = {
datadir = mkDefault "/var/lib/erigon";
@ -77,10 +99,11 @@ in {
serviceConfig = {
ExecStart = "${pkgs.erigon}/bin/erigon --config ${configFile}";
User = "erigon";
Group = cfg.group;
Restart = "on-failure";
StateDirectory = "erigon";
CapabilityBoundingSet = "";
DynamicUser = true;
NoNewPrivileges = true;
PrivateTmp = true;
ProtectHome = true;
@ -97,7 +120,6 @@ in {
RestrictNamespaces = true;
LockPersonality = true;
RemoveIPC = true;
RestrictAddressFamilies = [ "AF_INET" "AF_INET6" ];
SystemCallFilter = [ "@system-service" "~@privileged" ];
};
};

335
nixos/modules/services/blockchain/ethereum/lighthouse.nix Normal file
View File

@ -0,0 +1,335 @@
{ config, lib, pkgs, ... }:
with lib;
let
cfg = config.services.lighthouse;
in {
options = {
services.lighthouse = {
beacon = mkOption {
description = lib.mdDoc "Beacon node";
default = {};
type = types.submodule {
options = {
enable = lib.mkEnableOption (lib.mdDoc "Lightouse Beacon node");
dataDir = mkOption {
type = types.str;
default = "/var/lib/lighthouse-beacon";
description = lib.mdDoc ''
Directory where data will be stored. Each chain will be stored under it's own specific subdirectory.
'';
};
address = mkOption {
type = types.str;
default = "0.0.0.0";
description = lib.mdDoc ''
Listen address of Beacon node.
'';
};
port = mkOption {
type = types.port;
default = 9000;
description = lib.mdDoc ''
Port number the Beacon node will be listening on.
'';
};
openFirewall = mkOption {
type = types.bool;
default = false;
description = lib.mdDoc ''
Open the port in the firewall
'';
};
disableDepositContractSync = mkOption {
type = types.bool;
default = false;
description = lib.mdDoc ''
Explictly disables syncing of deposit logs from the execution node.
This overrides any previous option that depends on it.
Useful if you intend to run a non-validating beacon node.
'';
};
group = mkOption {
type = types.str;
default = "ethereum";
description = lib.mdDoc ''
Group of the user running the lighthouse process. This is used to share the jwt
secret with the execution layer.
'';
};
execution = {
address = mkOption {
type = types.str;
default = "127.0.0.1";
description = lib.mdDoc ''
Listen address for the execution layer.
'';
};
port = mkOption {
type = types.port;
default = 8551;
description = lib.mdDoc ''
Port number the Beacon node will be listening on for the execution layer.
'';
};
jwtPath = mkOption {
type = types.str;
default = "";
description = lib.mdDoc ''
Path for the jwt secret required to connect to the execution layer.
'';
};
};
http = {
enable = lib.mkEnableOption (lib.mdDoc "Beacon node http api");
port = mkOption {
type = types.port;
default = 5052;
description = lib.mdDoc ''
Port number of Beacon node RPC service.
'';
};
address = mkOption {
type = types.str;
default = "127.0.0.1";
description = lib.mdDoc ''
Listen address of Beacon node RPC service.
'';
};
};
metrics = {
enable = lib.mkEnableOption (lib.mdDoc "Beacon node prometheus metrics");
address = mkOption {
type = types.str;
default = "127.0.0.1";
description = lib.mdDoc ''
Listen address of Beacon node metrics service.
'';
};
port = mkOption {
type = types.port;
default = 5054;
description = lib.mdDoc ''
Port number of Beacon node metrics service.
'';
};
};
extraArgs = mkOption {
type = types.str;
description = lib.mdDoc ''
Additional arguments passed to the lighthouse beacon command.
'';
default = "";
example = "";
};
};
};
};
validator = mkOption {
description = lib.mdDoc "Validator node";
default = {};
type = types.submodule {
options = {
enable = mkOption {
type = types.bool;
default = false;
description = lib.mdDoc "Enable Lightouse Validator node.";
};
dataDir = mkOption {
type = types.str;
default = "/var/lib/lighthouse-validator";
description = lib.mdDoc ''
Directory where data will be stored. Each chain will be stored under it's own specific subdirectory.
'';
};
beaconNodes = mkOption {
type = types.listOf types.str;
default = ["http://localhost:5052"];
description = lib.mdDoc ''
Beacon nodes to connect to.
'';
};
metrics = {
enable = lib.mkEnableOption (lib.mdDoc "Validator node prometheus metrics");
address = mkOption {
type = types.str;
default = "127.0.0.1";
description = lib.mdDoc ''
Listen address of Validator node metrics service.
'';
};
port = mkOption {
type = types.port;
default = 5056;
description = lib.mdDoc ''
Port number of Validator node metrics service.
'';
};
};
extraArgs = mkOption {
type = types.str;
description = lib.mdDoc ''
Additional arguments passed to the lighthouse validator command.
'';
default = "";
example = "";
};
};
};
};
network = mkOption {
type = types.enum [ "mainnet" "prater" "goerli" "gnosis" "kiln" "ropsten" "sepolia" ];
default = "mainnet";
description = lib.mdDoc ''
The network to connect to. Mainnet is the default ethereum network.
'';
};
extraArgs = mkOption {
type = types.str;
description = lib.mdDoc ''
Additional arguments passed to every lighthouse command.
'';
default = "";
example = "";
};
};
};
config = mkIf (cfg.beacon.enable || cfg.validator.enable) {
users = {
users.lighthouse-beacon = {
name = "lighthouse-beacon";
group = cfg.beacon.group;
description = "Lighthouse beacon node user";
home = "${cfg.beacon.dataDir}";
isSystemUser = true;
};
groups = mkIf (cfg.beacon.group == "ethereum") {
ethereum = {};
};
};
environment.systemPackages = [ pkgs.lighthouse ] ;
networking.firewall = mkIf cfg.beacon.enable {
allowedTCPPorts = mkIf cfg.beacon.openFirewall [ cfg.beacon.port ];
allowedUDPPorts = mkIf cfg.beacon.openFirewall [ cfg.beacon.port ];
};
systemd.services.lighthouse-beacon = mkIf cfg.beacon.enable {
description = "Lighthouse beacon node (connect to P2P nodes and verify blocks)";
wantedBy = [ "multi-user.target" ];
after = [ "network.target" ];
script = ''
# make sure the chain data directory is created on first run
mkdir -p ${cfg.beacon.dataDir}/${cfg.network}
${pkgs.lighthouse}/bin/lighthouse beacon_node \
--disable-upnp \
${lib.optionalString cfg.beacon.disableDepositContractSync "--disable-deposit-contract-sync"} \
--port ${toString cfg.beacon.port} \
--listen-address ${cfg.beacon.address} \
--network ${cfg.network} \
--datadir ${cfg.beacon.dataDir}/${cfg.network} \
--execution-endpoint http://${cfg.beacon.execution.address}:${toString cfg.beacon.execution.port} \
--execution-jwt ${cfg.beacon.execution.jwtPath} \
${lib.optionalString cfg.beacon.http.enable '' --http --http-address ${cfg.beacon.http.address} --http-port ${toString cfg.beacon.http.port}''} \
${lib.optionalString cfg.beacon.metrics.enable '' --metrics --metrics-address ${cfg.beacon.metrics.address} --metrics-port ${toString cfg.beacon.metrics.port}''} \
${cfg.extraArgs} ${cfg.beacon.extraArgs}
'';
serviceConfig = {
User = "lighthouse-beacon";
Group = cfg.beacon.group;
Restart = "on-failure";
StateDirectory = "lighthouse-beacon";
NoNewPrivileges = true;
PrivateTmp = true;
ProtectHome = true;
ProtectClock = true;
ProtectProc = "noaccess";
ProcSubset = "pid";
ProtectKernelLogs = true;
ProtectKernelModules = true;
ProtectKernelTunables = true;
ProtectControlGroups = true;
ProtectHostname = true;
RestrictSUIDSGID = true;
RestrictRealtime = true;
RestrictNamespaces = true;
LockPersonality = true;
RemoveIPC = true;
SystemCallFilter = [ "@system-service" "~@privileged" ];
};
};
systemd.services.lighthouse-validator = mkIf cfg.validator.enable {
description = "Lighthouse validtor node (manages validators, using data obtained from the beacon node via a HTTP API)";
wantedBy = [ "multi-user.target" ];
after = [ "network.target" ];
script = ''
# make sure the chain data directory is created on first run
mkdir -p ${cfg.validator.dataDir}/${cfg.network}
${pkgs.lighthouse}/bin/lighthouse validator_client \
--network ${cfg.network} \
--beacon-nodes ${lib.concatStringsSep "," cfg.validator.beaconNodes} \
--datadir ${cfg.validator.dataDir}/${cfg.network}
${optionalString cfg.validator.metrics.enable ''--metrics --metrics-address ${cfg.validator.metrics.address} --metrics-port ${toString cfg.validator.metrics.port}''} \
${cfg.extraArgs} ${cfg.validator.extraArgs}
'';
serviceConfig = {
Restart = "on-failure";
StateDirectory = "lighthouse-validator";
CapabilityBoundingSet = "";
DynamicUser = true;
NoNewPrivileges = true;
PrivateTmp = true;
ProtectHome = true;
ProtectClock = true;
ProtectProc = "noaccess";
ProcSubset = "pid";
ProtectKernelLogs = true;
ProtectKernelModules = true;
ProtectKernelTunables = true;
ProtectControlGroups = true;
ProtectHostname = true;
RestrictSUIDSGID = true;
RestrictRealtime = true;
RestrictNamespaces = true;
LockPersonality = true;
RemoveIPC = true;
RestrictAddressFamilies = [ "AF_INET" "AF_INET6" ];
SystemCallFilter = [ "@system-service" "~@privileged" ];
};
};
};
}

2
nixos/modules/services/misc/nix-daemon.nix
View File

@ -206,7 +206,7 @@ in
daemonIOSchedPriority = mkOption {
type = types.int;
default = 0;
default = 4;
example = 1;
description = lib.mdDoc ''
Nix daemon process I/O scheduling priority. This priority propagates

27
nixos/modules/services/monitoring/prometheus/default.nix
View File

@ -1796,6 +1796,33 @@ in
WorkingDirectory = workingDir;
StateDirectory = cfg.stateDir;
StateDirectoryMode = "0700";
# Hardening
AmbientCapabilities = lib.mkIf (cfg.port < 1024) [ "CAP_NET_BIND_SERVICE" ];
CapabilityBoundingSet = if (cfg.port < 1024) then [ "CAP_NET_BIND_SERVICE" ] else [ "" ];
DeviceAllow = [ "/dev/null rw" ];
DevicePolicy = "strict";
LockPersonality = true;
MemoryDenyWriteExecute = true;
NoNewPrivileges = true;
PrivateDevices = true;
PrivateTmp = true;
PrivateUsers = true;
ProtectClock = true;
ProtectControlGroups = true;
ProtectHome = true;
ProtectHostname = true;
ProtectKernelLogs = true;
ProtectKernelModules = true;
ProtectKernelTunables = true;
ProtectProc = "invisible";
ProtectSystem = "full";
RemoveIPC = true;
RestrictAddressFamilies = [ "AF_INET" "AF_INET6" "AF_UNIX" ];
RestrictNamespaces = true;
RestrictRealtime = true;
RestrictSUIDSGID = true;
SystemCallArchitectures = "native";
SystemCallFilter = [ "@system-service" "~@privileged" "~@resources" ];
};
};
# prometheus-config-reload will activate after prometheus. However, what we

2
nixos/modules/services/monitoring/teamviewer.nix
View File

@ -30,7 +30,7 @@ in
description = "TeamViewer remote control daemon";
wantedBy = [ "multi-user.target" ];
after = [ "NetworkManager-wait-online.service" "network.target" "dbus.service" ];
after = [ "network-online.target" "network.target" "dbus.service" ];
requires = [ "dbus.service" ];
preStart = "mkdir -pv /var/lib/teamviewer /var/log/teamviewer";

18
nixos/modules/services/networking/wireguard.nix
View File

@ -391,6 +391,19 @@ let
'';
};
# the target is required to start new peer units when they are added
generateInterfaceTarget = name: values:
let
mkPeerUnit = peer: (peerUnitServiceName name peer.publicKey (peer.dynamicEndpointRefreshSeconds != 0)) + ".service";
in
nameValuePair "wireguard-${name}"
rec {
description = "WireGuard Tunnel - ${name}";
wantedBy = [ "multi-user.target" ];
wants = [ "wireguard-${name}.service" ] ++ map mkPeerUnit values.peers;
after = wants;
};
generateInterfaceUnit = name: values:
# exactly one way to specify the private key must be set
#assert (values.privateKey != null) != (values.privateKeyFile != null);
@ -409,7 +422,6 @@ let
after = [ "network-pre.target" ];
wants = [ "network.target" ];
before = [ "network.target" ];
wantedBy = [ "multi-user.target" ];
environment.DEVICE = name;
path = with pkgs; [ kmod iproute2 wireguard-tools ];
@ -540,6 +552,8 @@ in
// (mapAttrs' generateKeyServiceUnit
(filterAttrs (name: value: value.generatePrivateKeyFile) cfg.interfaces));
});
systemd.targets = mapAttrs' generateInterfaceTarget cfg.interfaces;
}
);
}

49
nixos/modules/services/web-apps/mastodon.nix
View File

@ -425,6 +425,39 @@ in {
Do automatic database migrations.
'';
};
mediaAutoRemove = {
enable = lib.mkOption {
type = lib.types.bool;
default = true;
example = false;
description = lib.mdDoc ''
Automatically remove remote media attachments and preview cards older than the configured amount of days.
Recommended in https://docs.joinmastodon.org/admin/setup/.
'';
};
startAt = lib.mkOption {
type = lib.types.str;
default = "daily";
example = "hourly";
description = lib.mdDoc ''
How often to remove remote media.
The format is described in {manpage}`systemd.time(7)`.
'';
};
olderThanDays = lib.mkOption {
type = lib.types.int;
default = 30;
example = 14;
description = lib.mdDoc ''
How old remote media needs to be in order to be removed.
'';
};
};
};
};
@ -585,6 +618,22 @@ in {
path = with pkgs; [ file imagemagick ffmpeg ];
};
systemd.services.mastodon-media-auto-remove = lib.mkIf cfg.mediaAutoRemove.enable {
description = "Mastodon media auto remove";
environment = env;
serviceConfig = {
Type = "oneshot";
script = let
olderThanDays = toString cfg.mediaAutoRemove.olderThanDays;
in ''
${cfg.package}/bin/tootctl media remove --days=${olderThanDays}
${cfg.package}/bin/tootctl preview_cards remove --days=${olderThanDays}
'';
EnvironmentFile = "/var/lib/mastodon/.secrets_env";
startAt = cfg.mediaAutoRemove.startAt;
} // cfgService;
};
services.nginx = lib.mkIf cfg.configureNginx {
enable = true;
recommendedProxySettings = true; # required for redirections to work

2
nixos/modules/services/web-apps/wordpress.nix
View File

@ -409,6 +409,8 @@ in
"d '${stateDir hostName}' 0750 ${user} ${webserver.group} - -"
"d '${cfg.uploadsDir}' 0750 ${user} ${webserver.group} - -"
"Z '${cfg.uploadsDir}' 0750 ${user} ${webserver.group} - -"
"d '${cfg.fontsDir}' 0750 ${user} ${webserver.group} - -"
"Z '${cfg.fontsDir}' 0750 ${user} ${webserver.group} - -"
]) eachSite);
systemd.services = mkMerge [

26
nixos/modules/services/x11/display-managers/lightdm-greeters/mobile.nix Normal file
View File

@ -0,0 +1,26 @@
{ config, lib, pkgs, ... }:
with lib;
let
dmcfg = config.services.xserver.displayManager;
ldmcfg = dmcfg.lightdm;
cfg = ldmcfg.greeters.mobile;
in
{
options = {
services.xserver.displayManager.lightdm.greeters.mobile = {
enable = mkEnableOption (lib.mdDoc
"lightdm-mobile-greeter as the lightdm greeter"
);
};
};
config = mkIf (ldmcfg.enable && cfg.enable) {
services.xserver.displayManager.lightdm.greeters.gtk.enable = false;
services.xserver.displayManager.lightdm.greeter = mkDefault {
package = pkgs.lightdm-mobile-greeter.xgreeters;
name = "lightdm-mobile-greeter";
};
};
}

1
nixos/modules/services/x11/display-managers/lightdm.nix
View File

@ -83,6 +83,7 @@ in
./lightdm-greeters/pantheon.nix
./lightdm-greeters/tiny.nix
./lightdm-greeters/slick.nix
./lightdm-greeters/mobile.nix
(mkRenamedOptionModule [ "services" "xserver" "displayManager" "lightdm" "autoLogin" "enable" ] [
"services"
"xserver"

1
nixos/modules/system/boot/binfmt.nix
View File

@ -321,5 +321,6 @@ in {
"proc-sys-fs-binfmt_misc.mount"
"systemd-binfmt.service"
];
systemd.services.systemd-binfmt.restartTriggers = [ (builtins.toJSON config.boot.binfmt.registrations) ];
};
}

11
nixos/tests/chromium.nix
View File

@ -166,6 +166,8 @@ mapAttrs (channel: chromiumPkg: makeTest {
clipboard = machine.succeed(
ru("${pkgs.xclip}/bin/xclip -o")
)
if url == "chrome://gpu":
clipboard = "" # TODO: We cannot copy the text via Ctrl+a
print(f"{description} window content:\n{clipboard}")
with machine.nested(description):
yield clipboard
@ -246,11 +248,10 @@ mapAttrs (channel: chromiumPkg: makeTest {
machine.screenshot("after_copy_from_chromium")
if major_version < "107":
# TODO: Fix the chrome://gpu test for M107+
with test_new_win("gpu_info", "chrome://gpu", "chrome://gpu"):
# To check the text rendering (catches regressions like #131074):
machine.wait_for_text("Graphics Feature Status")
with test_new_win("gpu_info", "chrome://gpu", "GPU Internals"):
# To check the text rendering (catches regressions like #131074):
machine.wait_for_text("Graphics Feature Status")
# TODO: Fix copying all of the text to the clipboard
with test_new_win("version_info", "chrome://version", "About Version") as clipboard:

73
nixos/tests/podman/default.nix
View File

@ -1,5 +1,3 @@
# This test runs podman and checks if simple container starts
import ../make-test-python.nix (
{ pkgs, lib, ... }: {
name = "podman";
@ -8,31 +6,31 @@ import ../make-test-python.nix (
};
nodes = {
podman =
{ pkgs, ... }:
{
virtualisation.podman.enable = true;
# To test docker socket support
virtualisation.podman.dockerSocket.enable = true;
environment.systemPackages = [
pkgs.docker-client
];
users.users.alice = {
isNormalUser = true;
home = "/home/alice";
description = "Alice Foobar";
extraGroups = [ "podman" ];
};
users.users.mallory = {
isNormalUser = true;
home = "/home/mallory";
description = "Mallory Foobar";
};
podman = { pkgs, ... }: {
virtualisation.podman.enable = true;
users.users.alice = {
isNormalUser = true;
};
};
docker = { pkgs, ... }: {
virtualisation.podman.enable = true;
virtualisation.podman.dockerSocket.enable = true;
environment.systemPackages = [
pkgs.docker-client
];
users.users.alice = {
isNormalUser = true;
extraGroups = [ "podman" ];
};
users.users.mallory = {
isNormalUser = true;
};
};
};
testScript = ''
@ -45,6 +43,7 @@ import ../make-test-python.nix (
podman.wait_for_unit("sockets.target")
docker.wait_for_unit("sockets.target")
start_all()
with subtest("Run container as root with runc"):
@ -74,8 +73,10 @@ import ../make-test-python.nix (
podman.succeed("podman stop sleeping")
podman.succeed("podman rm sleeping")
# create systemd session for rootless
# start systemd session for rootless
podman.succeed("loginctl enable-linger alice")
podman.succeed(su_cmd("whoami"))
podman.sleep(1)
with subtest("Run container rootless with runc"):
podman.succeed(su_cmd("tar cv --files-from /dev/null | podman import - scratchimg"))
@ -120,22 +121,22 @@ import ../make-test-python.nix (
assert pid == "2"
with subtest("A podman member can use the docker cli"):
podman.succeed(su_cmd("docker version"))
docker.succeed(su_cmd("docker version"))
with subtest("Run container via docker cli"):
podman.succeed("docker network create default")
podman.succeed("tar cv --files-from /dev/null | podman import - scratchimg")
podman.succeed(
docker.succeed("docker network create default")
docker.succeed("tar cv --files-from /dev/null | podman import - scratchimg")
docker.succeed(
"docker run -d --name=sleeping -v /nix/store:/nix/store -v /run/current-system/sw/bin:/bin localhost/scratchimg /bin/sleep 10"
)
podman.succeed("docker ps | grep sleeping")
podman.succeed("podman ps | grep sleeping")
podman.succeed("docker stop sleeping")
podman.succeed("docker rm sleeping")
podman.succeed("docker network rm default")
docker.succeed("docker ps | grep sleeping")
docker.succeed("podman ps | grep sleeping")
docker.succeed("docker stop sleeping")
docker.succeed("docker rm sleeping")
docker.succeed("docker network rm default")
with subtest("A podman non-member can not use the docker cli"):
podman.fail(su_cmd("docker version", user="mallory"))
docker.fail(su_cmd("docker version", user="mallory"))
# TODO: add docker-compose test

10
pkgs/applications/audio/picard/default.nix
View File

@ -1,6 +1,7 @@
{ lib
, python3Packages
, fetchFromGitHub
, fetchpatch
, gettext
, chromaprint
, qt5
@ -27,6 +28,15 @@ pythonPackages.buildPythonApplication rec {
sha256 = "sha256-KUHciIlwaKXvyCCkAzdh1vpe9cunDizrMUl0SoCpxgY=";
};
patches = [
# fix for tests failing with newer mutagen, remove after >2.8.3
# https://tickets.metabrainz.org/browse/PICARD-2583
(fetchpatch {
url = "https://github.com/metabrainz/picard/commit/76c2dff6b61140bbc7675c9e9f62a086b885e539.patch";
hash = "sha256-V1/oq1tEcb1mtqbYAA9o7mJcw16vRO0IK3GGmJkwO1Q=";
})
];
nativeBuildInputs = [ gettext qt5.wrapQtAppsHook qt5.qtbase ]
++ lib.optionals (pyqt5.multimediaEnabled) [
qt5.qtmultimedia.bin

4
pkgs/applications/backup/vorta/default.nix
View File

@ -8,13 +8,13 @@
python3Packages.buildPythonApplication rec {
pname = "vorta";
version = "0.8.7";
version = "0.8.9";
src = fetchFromGitHub {
owner = "borgbase";
repo = "vorta";
rev = "refs/tags/v${version}";
sha256 = "sha256-9SfHZbNM+lRtwLO/0dE9C4cHb3pSPkxBUITYNEdPMQw=";
sha256 = "sha256-5RZXHMov3CX0zRprs7sgz0+cGEdESLrg4I2glRnTkcU=";
};
nativeBuildInputs = [ wrapQtAppsHook ];

31
pkgs/applications/blockchains/btcd/default.nix Normal file
View File

@ -0,0 +1,31 @@
{ lib, buildGoModule, fetchFromGitHub }:
buildGoModule rec {
pname = "btcd";
version = "0.23.3";
src = fetchFromGitHub {
owner = "btcsuite";
repo = pname;
rev = "v${version}";
sha256 = "sha256-LdK68Ianiyrs+HVMwrkiX2ruCWKkdpuY8ylxhNbm9qI=";
};
vendorSha256 = "sha256-3w8rb0sfAIFCXqPXOKb4QwoLd7WsbFv3phu/rJCEjeY=";
subPackages = [ "." "cmd/*" ];
preCheck = ''
DIR="github.com/btcsuite/btcd/"
# TestCreateDefaultConfigFile requires the sample-btcd.conf in $DIR
mkdir -p $DIR
cp sample-btcd.conf $DIR
'';
meta = with lib; {
description = "An alternative full node bitcoin implementation written in Go (golang)";
homepage = "https://github.com/btcsuite/btcd";
license = licenses.isc;
maintainers = with maintainers; [ _0xB10C ];
};
}

53
pkgs/applications/display-managers/lightdm-mobile-greeter/default.nix Normal file
View File

@ -0,0 +1,53 @@
{ lib
, fetchFromGitea
, gtk3
, libhandy_0
, lightdm
, lightdm-mobile-greeter
, linkFarm
, pkg-config
, rustPlatform
}:
rustPlatform.buildRustPackage rec {
pname = "lightdm-mobile-greeter";
version = "2022-10-30";
src = fetchFromGitea {
domain = "git.raatty.club";
owner = "raatty";
repo = "lightdm-mobile-greeter";
rev = "8c8d6dfce62799307320c8c5a1f0dd5c8c18e4d3";
hash = "sha256-SrAR2+An3BN/doFl/s8PcYZMUHLfVPXKZOo6ndO60nY=";
};
cargoHash = "sha256-NZ0jOkEBNa5oOydfyKm0XQB/vkAvBv9wHBbnM9egQFQ=";
buildInputs = [
gtk3
libhandy_0
lightdm
];
nativeBuildInputs = [
pkg-config
];
postInstall = ''
mkdir -p $out/share/xgreeters
substitute lightdm-mobile-greeter.desktop \
$out/share/xgreeters/lightdm-mobile-greeter.desktop \
--replace lightdm-mobile-greeter $out/bin/lightdm-mobile-greeter
'';
passthru.xgreeters = linkFarm "lightdm-mobile-greeter-xgreeters" [{
path = "${lightdm-mobile-greeter}/share/xgreeters/lightdm-mobile-greeter.desktop";
name = "lightdm-mobile-greeter.desktop";
}];
meta = with lib; {
description = "A simple log in screen for use on touch screens";
homepage = "https://git.raatty.club/raatty/lightdm-mobile-greeter";
maintainers = with maintainers; [ colinsane ];
platforms = platforms.linux;
license = licenses.mit;
};
}

4
pkgs/applications/editors/android-studio/default.nix
View File

@ -10,8 +10,8 @@ let
inherit tiling_wm;
};
stableVersion = {
version = "2021.3.1.16"; # "Android Studio Dolphin (2021.3.1)"
sha256Hash = "GnJbWFeG9DuUQzbK9wM2BEbj9LXm4jQFf/Eh5Q75HZo=";
version = "2021.3.1.17"; # "Android Studio Dolphin (2021.3.1)"
sha256Hash = "sha256-ia2wzg/6RreJTnv+2xQrH11SxDwXHmpsualaSfd3Vso=";
};
betaVersion = {
version = "2022.1.1.12"; # "Android Studio Electric Eel (2022.1.1) Beta 2"

6
pkgs/applications/editors/neovim/neovide/default.nix
View File

@ -31,16 +31,16 @@
}:
rustPlatform.buildRustPackage rec {
pname = "neovide";
version = "0.10.1";
version = "0.10.3";
src = fetchFromGitHub {
owner = "Kethku";
repo = "neovide";
rev = version;
sha256 = "sha256-PViSiK6+H79MLIOFe26cNqUZ6gZdqDC/S+ksTrbOm54=";
sha256 = "sha256-CcBiCcfOJzuq0DnokTUHpMdo7Ry29ugQ+N7Hk0R+cQE=";
};
cargoSha256 = "sha256-GvueDUY4Hzfih/MyEfhdz/QNVd9atTC8SCF+PyuJJic=";
cargoSha256 = "sha256-bS7yBnxAWPoTTabxI6W5Knl1DFiDztYSkEPJMa8bqlY=";
SKIA_SOURCE_DIR =
let

3
pkgs/applications/emulators/zsnes/default.nix
View File

@ -34,7 +34,8 @@ in stdenv.mkDerivation {
# Workaround build failure on -fno-common toolchains:
# ld: initc.o:(.bss+0x28): multiple definition of `HacksDisable'; cfg.o:(.bss+0x59e3): first defined here
NIX_CFLAGS_COMPILE = "-fcommon";
# Use pre-c++17 standard (c++17 forbids throw annotations)
NIX_CFLAGS_COMPILE = "-fcommon -std=c++14";
preConfigure = ''
cd src

27
pkgs/applications/graphics/json-plot/default.nix Normal file
View File

@ -0,0 +1,27 @@
{ lib
, fetchFromGitHub
, buildGoPackage
}:
# upstream is pretty stale, but it still works, so until they merge module
# support we have to use gopath: see sgreben/jp#29
buildGoPackage rec {
pname = "json-plot";
version = "1.1.12";
src = fetchFromGitHub {
owner = "sgreben";
repo = "jp";
rev = version;
hash = "sha256-WWARAh/CF3lGli3VLRzAGaCA8xQyryPi8WcuwvdInjk=";
};
goPackagePath = "github.com/sgreben/jp";
meta = with lib; {
description = "Dead simple terminal plots from JSON (or CSV) data. Bar charts, line charts, scatter plots, histograms and heatmaps are supported.";
homepage = "https://github.com/sgreben/jp";
license = licenses.mit;
maintainers = with maintainers; [ urandom ];
mainProgram = "jp";
};
}

1
pkgs/applications/graphics/synfigstudio/default.nix
View File

@ -103,6 +103,7 @@ stdenv.mkDerivation {
pkg-config
autoreconfHook
gettext
intltool
wrapGAppsHook
];
buildInputs = [

6
pkgs/applications/misc/auto-multiple-choice/default.nix
View File

@ -11,6 +11,7 @@
, graphicsmagick
, gsettings-desktop-schemas
, gtk3
, hicolor-icon-theme
, libnotify
, librsvg
, libxslt
@ -56,6 +57,8 @@ stdenv.mkDerivation rec {
"LANG_GTKSOURCEVIEW_DIR=/share/gtksourceview-4/language-specs"
# Pretend to be redhat so `install` doesn't try to chown/chgrp.
"SYSTEM_TYPE=rpm"
"GCC=${stdenv.cc.targetPrefix}cc"
"GCC_PP=${stdenv.cc.targetPrefix}c++"
];
preFixup = ''
@ -82,7 +85,7 @@ stdenv.mkDerivation rec {
XMLSimple
XMLWriter
]}:"$out/share/perl5 \
--prefix XDG_DATA_DIRS : "$out/share" \
--prefix XDG_DATA_DIRS : "$out/share:$XDG_ICON_DIRS:$GSETTINGS_SCHEMAS_PATH" \
--set TEXINPUTS ":.:$out/tex/latex"
'';
@ -101,6 +104,7 @@ stdenv.mkDerivation rec {
graphicsmagick
gsettings-desktop-schemas
gtk3
hicolor-icon-theme
libnotify
librsvg
libxslt

6
pkgs/applications/misc/bb/default.nix
View File

@ -18,10 +18,14 @@ stdenv.mkDerivation rec {
sed -i -e '/^#include <malloc.h>$/d' *.c
'';
# error: 'regparm' is not valid on this platform
NIX_CFLAGS_COMPILE = lib.optionalString (stdenv.isDarwin && stdenv.isAarch64)
"-D__STRICT_ANSI__";
meta = with lib; {
homepage = "http://aa-project.sourceforge.net/bb";
description = "AA-lib demo";
license = licenses.gpl2;
license = licenses.gpl2Plus;
maintainers = [ maintainers.rnhmjoj ];
platforms = platforms.unix;
};

4
pkgs/applications/misc/cheat/default.nix
View File

@ -3,13 +3,13 @@
buildGoModule rec {
pname = "cheat";
version = "4.3.3";
version = "4.4.0";
src = fetchFromGitHub {
owner = "cheat";
repo = "cheat";
rev = version;
sha256 = "sha256-cOryo70eJj2PIJ6R09Kx6lfoguYcduIiWiOBpYp8eqY=";
sha256 = "sha256-lEMwPGXvgI8wtXska9ngAy9R2tr41Jq5yO6xQk9V5n4=";
};
subPackages = [ "cmd/cheat" ];

2
pkgs/applications/misc/clipqr/default.nix
View File

@ -12,6 +12,7 @@
, makeDesktopItem
, mesa
, pkg-config
, stdenv
}:
buildGoModule rec {
@ -66,5 +67,6 @@ buildGoModule rec {
license = licenses.mit;
maintainers = with maintainers; [ MatthieuBarthel ];
homepage = "https://gitlab.com/imatt-foss/clipqr";
broken = stdenv.isDarwin;
};
}

4
pkgs/applications/misc/fuzzel/default.nix
View File

@ -25,14 +25,14 @@ assert svgSupport -> enableCairo;
stdenv.mkDerivation rec {
pname = "fuzzel";
version = "1.7.0";
version = "1.8.2";
src = fetchFromGitea {
domain = "codeberg.org";
owner = "dnkl";
repo = "fuzzel";
rev = version;
sha256 = "1261gwxiky37pvzmmbrpml1psa22kkglb141ybj1fbnwg6j7jvlf";
sha256 = "sha256-5uXf5HfQ8bDQSMNCHHaC9sCX5P/D89T2ZOUiXTDx3bQ=";
};
nativeBuildInputs = [

4
pkgs/applications/misc/mangal/default.nix
View File

@ -2,13 +2,13 @@
buildGoModule rec {
pname = "mangal";
version = "4.0.1";
version = "4.0.2";
src = fetchFromGitHub {
owner = "metafates";
repo = pname;
rev = "v${version}";
hash = "sha256-pMiZgO/+koyIDm7ONZn0qEq+d6HeFfQFaU1Qjovqmc4=";
hash = "sha256-ssvd8gdF5h6EKLY/W+1zbZWcVQqy+UirIS0p0DBQj0E=";
};
proxyVendor = true;

53
pkgs/applications/misc/mepo/default.nix
View File

@ -4,38 +4,38 @@
, pkg-config
, zig
, makeWrapper
, busybox
, curl
, SDL2
, SDL2_gfx
, SDL2_image
, SDL2_ttf
, findutils
, jq
, ncurses
, inconsolata-nerdfont
, dmenu
, xdotool
, bemenu
, withX11 ? false
, gnome
, xorg
, util-linux
, gpsd
, geoclue2-with-demo-agent
}:
let
menuInputs = if withX11 then [ dmenu xdotool ] else [ bemenu ];
in stdenv.mkDerivation rec {
stdenv.mkDerivation rec {
pname = "mepo";
version = "0.4.2";
version = "1.1";
src = fetchFromSourcehut {
owner = "~mil";
repo = pname;
rev = version;
hash = "sha256-k6YXaqB3EwbDPlTvijZf10q+IYwt4/MiqGXL495KIcY=";
hash = "sha256-OIZ617QLjiTiDwcsn0DnRussYtjDkVyifr2mdSqA98A=";
};
nativeBuildInputs = [ pkg-config zig makeWrapper ];
buildInputs = [
curl SDL2 SDL2_gfx SDL2_image SDL2_ttf inconsolata-nerdfont jq ncurses
] ++ menuInputs;
curl SDL2 SDL2_gfx SDL2_image SDL2_ttf jq ncurses
];
preBuild = ''
export HOME=$TMPDIR
@ -54,30 +54,33 @@ in stdenv.mkDerivation rec {
runHook preInstall
zig build -Drelease-safe=true -Dcpu=baseline --prefix $out install
install -d $out/share/man/man1
$out/bin/mepo -docman > $out/share/man/man1/mepo.1
runHook postInstall
'';
postInstall = ''
wrapProgram $out/bin/mepo_dl.sh\
--suffix PATH : ${lib.makeBinPath [ jq ncurses ]}
wrapProgram $out/bin/mepo_ui_helper_menu.sh\
--suffix PATH : ${lib.makeBinPath menuInputs}
for script in $(grep -l jq out/bin/mepo_ui_menu_*.sh); do
wrapProgram $script --suffix PATH : $out/bin:${lib.makeBinPath [ jq ]}
done
for prog in $out/bin/mepo*; do
if [ ! -f $out/bin/.$(basename $prog)-wrapped ]; then
wrapProgram $prog --suffix PATH : $out/bin
fi
substituteInPlace $out/bin/mepo_ui_menu_user_pin_updater.sh \
--replace /usr/libexec/geoclue-2.0 ${geoclue2-with-demo-agent}/libexec/geoclue-2.0
substituteInPlace $out/bin/mepo_ui_central_menu.sh \
--replace "grep mepo_" "grep '^\.mepo_\|^mepo_'" \
--replace " ls " " ls -a " #circumvent wrapping for script detection
for program in $out/bin/* ; do
wrapProgram $program \
--suffix PATH : $out/bin:${lib.makeBinPath ([ jq ncurses curl busybox findutils util-linux gpsd gnome.zenity xorg.xwininfo ])}
done
'';
meta = with lib; {
description = "Fast, simple, and hackable OSM map viewer";
homepage = "https://sr.ht/~mil/mepo/";
longDescription = ''
It is recommended to use the corresponding NixOS module.
'';
homepage = "https://mepo.milesalan.com";
license = licenses.gpl3Plus;
maintainers = with maintainers; [ sikmir McSinyx ];
maintainers = with maintainers; [ sikmir McSinyx laalsaas ];
platforms = platforms.linux;
};
}

11
pkgs/applications/misc/safeeyes/default.nix
View File

@ -1,6 +1,5 @@
{ lib
, buildPythonApplication
, fetchPypi
, python3
, alsa-utils
, gobject-introspection
, libappindicator-gtk3
@ -10,14 +9,10 @@
, xprintidle
, xprop
, wrapGAppsHook
, babel
, psutil
, xlib
, pygobject3
, dbus-python
, croniter
}:
with python3.pkgs;
buildPythonApplication rec {
pname = "safeeyes";
version = "2.1.3";

6
pkgs/applications/networking/browsers/tor-browser-bundle-bin/default.nix
View File

@ -87,7 +87,7 @@ let
fteLibPath = makeLibraryPath [ stdenv.cc.cc gmp ];
# Upstream source
version = "11.5.6";
version = "11.5.7";
lang = "en-US";
@ -99,7 +99,7 @@ let
"https://tor.eff.org/dist/torbrowser/${version}/tor-browser-linux64-${version}_${lang}.tar.xz"
"https://tor.calyxinstitute.org/dist/torbrowser/${version}/tor-browser-linux64-${version}_${lang}.tar.xz"
];
sha256 = "sha256-DTMY6n7GXokOz6WSrvFUkC64Siuo1Zy80A4UDolmIME=";
sha256 = "sha256-K50T9Fe6tMuP1J5gfwK9f/25ZeakQ9vsJi4IOPa6fMk=";
};
i686-linux = fetchurl {
@ -109,7 +109,7 @@ let
"https://tor.eff.org/dist/torbrowser/${version}/tor-browser-linux32-${version}_${lang}.tar.xz"
"https://tor.calyxinstitute.org/dist/torbrowser/${version}/tor-browser-linux32-${version}_${lang}.tar.xz"
];
sha256 = "sha256-2/fGt+m/EDoeaSune32zmktHVHt8zH2wCr8+stewKCs=";
sha256 = "sha256-tbL/iTI3vR0gdMcLwOoWlfIDZNefIKA2hfvWKNNM9vE=";
};
};
in

4
pkgs/applications/networking/cluster/odo/default.nix
View File

@ -2,13 +2,13 @@
buildGoModule rec {
pname = "odo";
version = "3.1.0";
version = "3.2.0";
src = fetchFromGitHub {
owner = "redhat-developer";
repo = "odo";
rev = "v${version}";
sha256 = "sha256-+QLRm01JTV7nnMiIvitdkm38E08TsmU6EfrNTUCTddY=";
sha256 = "sha256-nevwmw2d8HARRwOy8dPsjtjQj+W3psknphcmebRjrNE=";
};
vendorSha256 = null;

9
pkgs/applications/networking/cluster/terraform-providers/providers.json
View File

@ -93,13 +93,14 @@
"version": "0.39.0"
},
"avi": {
"hash": "sha256-BQ4M1e7wWDCq2HEJIoAAqSUmq9hV66auvH47p3j2M8I=",
"hash": "sha256-0FcdVd7EGVHZ0iRonoGfjwYgXpJtUhqX5i925Ejhv54=",
"owner": "vmware",
"provider-source-address": "registry.terraform.io/vmware/avi",
"proxyVendor": true,
"repo": "terraform-provider-avi",
"rev": "v22.1.1",
"vendorHash": "sha256-otOArethLfanpp3KjQCutrlOxkcpr+6YHn5xWl31feE=",
"version": "22.1.1"
"rev": "v22.1.2",
"vendorHash": "sha256-yDkox74g0N8iniWHSNk6KjfM0HJa8H2HUxm6RxrdhkE=",
"version": "22.1.2"
},
"aviatrix": {
"hash": "sha256-1zHaSdDcGynLhgLMDRbRgRzt0IvQI25TDZrYzZwwQ34=",

4
pkgs/applications/networking/instant-messengers/discord/default.nix
View File

@ -3,7 +3,7 @@ let
versions = if stdenv.isLinux then {
stable = "0.0.21";
ptb = "0.0.34";
canary = "0.0.142";
canary = "0.0.143";
} else {
stable = "0.0.264";
ptb = "0.0.59";
@ -22,7 +22,7 @@ let
};
canary = fetchurl {
url = "https://dl-canary.discordapp.net/apps/linux/${version}/discord-canary-${version}.tar.gz";
sha256 = "sha256-/EWJC3hFIBqwHa9z4nMWR7CpoaqYY+pvw+1vcq4F0LU=";
sha256 = "sha256-K+yyg9GTAvggfn4JQCTmq016tMyyzq+nD7aL3+bWFlo=";
};
};
x86_64-darwin = {

134
pkgs/applications/networking/instant-messengers/element/element-web.nix
View File

@ -18,73 +18,93 @@ let
disable_guests = true; # disable automatic guest account registration at matrix.org
piwik = false; # disable analytics
};
configOverrides = writeText "element-config-overrides.json" (builtins.toJSON (noPhoningHome // conf));
in stdenv.mkDerivation rec {
pname = "element-web";
inherit (pinData) version;
unwrapped = stdenv.mkDerivation rec {
pname = "element-web";
inherit (pinData) version;
src = fetchFromGitHub {
owner = "vector-im";
repo = pname;
rev = "v${version}";
sha256 = pinData.webSrcHash;
src = fetchFromGitHub {
owner = "vector-im";
repo = pname;
rev = "v${version}";
sha256 = pinData.webSrcHash;
};
offlineCache = fetchYarnDeps {
yarnLock = src + "/yarn.lock";
sha256 = pinData.webYarnHash;
};
nativeBuildInputs = [ yarn fixup_yarn_lock jq nodejs ];
configurePhase = ''
runHook preConfigure
export HOME=$PWD/tmp
# with the update of openssl3, some key ciphers are not supported anymore
# this flag will allow those codecs again as a workaround
# see https://medium.com/the-node-js-collection/node-js-17-is-here-8dba1e14e382#5f07
# and https://github.com/vector-im/element-web/issues/21043
export NODE_OPTIONS=--openssl-legacy-provider
mkdir -p $HOME
fixup_yarn_lock yarn.lock
yarn config --offline set yarn-offline-mirror $offlineCache
yarn install --offline --frozen-lockfile --ignore-platform --ignore-scripts --no-progress --non-interactive
patchShebangs node_modules
runHook postConfigure
'';
buildPhase = ''
runHook preBuild
export VERSION=${version}
yarn build:res --offline
yarn build:module_system --offline
yarn build:bundle --offline
runHook postBuild
'';
installPhase = ''
runHook preInstall
cp -R webapp $out
cp ${jitsi-meet}/libs/external_api.min.js $out/jitsi_external_api.min.js
echo "${version}" > "$out/version"
jq -s '.[0] * $conf' "config.sample.json" --argjson "conf" '${builtins.toJSON noPhoningHome}' > "$out/config.json"
runHook postInstall
'';
meta = {
description = "A glossy Matrix collaboration client for the web";
homepage = "https://element.io/";
changelog = "https://github.com/vector-im/element-web/blob/v${version}/CHANGELOG.md";
maintainers = lib.teams.matrix.members;
license = lib.licenses.asl20;
platforms = lib.platforms.all;
};
};
in
if (conf == { }) then unwrapped else
stdenv.mkDerivation rec {
pname = "${unwrapped.pname}-wrapped";
inherit (unwrapped) version meta;
offlineCache = fetchYarnDeps {
yarnLock = src + "/yarn.lock";
sha256 = pinData.webYarnHash;
};
dontUnpack = true;
nativeBuildInputs = [ yarn fixup_yarn_lock jq nodejs ];
configurePhase = ''
runHook preConfigure
export HOME=$PWD/tmp
# with the update of openssl3, some key ciphers are not supported anymore
# this flag will allow those codecs again as a workaround
# see https://medium.com/the-node-js-collection/node-js-17-is-here-8dba1e14e382#5f07
# and https://github.com/vector-im/element-web/issues/21043
export NODE_OPTIONS=--openssl-legacy-provider
mkdir -p $HOME
fixup_yarn_lock yarn.lock
yarn config --offline set yarn-offline-mirror $offlineCache
yarn install --offline --frozen-lockfile --ignore-platform --ignore-scripts --no-progress --non-interactive
patchShebangs node_modules
runHook postConfigure
'';
buildPhase = ''
runHook preBuild
export VERSION=${version}
yarn build:res --offline
yarn build:module_system --offline
yarn build:bundle --offline
runHook postBuild
'';
nativeBuildInputs = [ jq ];
installPhase = ''
runHook preInstall
cp -R webapp $out
cp ${jitsi-meet}/libs/external_api.min.js $out/jitsi_external_api.min.js
echo "${version}" > "$out/version"
jq -s '.[0] * .[1]' "config.sample.json" "${configOverrides}" > "$out/config.json"
mkdir -p $out
ln -s ${unwrapped}/* $out
rm $out/config.json
jq -s '.[0] * $conf' "${unwrapped}/config.json" --argjson "conf" '${builtins.toJSON conf}' > "$out/config.json"
runHook postInstall
'';
meta = {
description = "A glossy Matrix collaboration client for the web";
homepage = "https://element.io/";
changelog = "https://github.com/vector-im/element-web/blob/v${version}/CHANGELOG.md";
maintainers = lib.teams.matrix.members;
license = lib.licenses.asl20;
platforms = lib.platforms.all;
};
}

14
pkgs/applications/networking/instant-messengers/gotktrix/default.nix
View File

@ -10,16 +10,16 @@
buildGoModule rec {
pname = "gotktrix";
version = "0.1.4";
version = "unstable-2022-09-29";
src = fetchFromGitHub {
owner = "diamondburned";
repo = pname;
rev = "v${version}";
sha256 = "sha256-ZaE7L43fA9L5WbTAsBiIxlwYgjl1hMrtfrraAROz+7k=";
rev = "3d9e8ac4810f7cb9d9ead7b4b13ffa6f5da8927f"; # compound
sha256 = "sha256-VIV4vSntu3oCIE23f5fiYj8cxcKY1n4M4Xkf0MGhvxI=";
};
vendorSha256 = "sha256-k6T44aH1NogyrbUnflfEHkp0zpOOH1YFly/X2kwbMzs=";
vendorSha256 = "sha256-R55tfTJL/bgNWTgmuBFRxIQleKS9zeDqvfez2VyzqjI=";
buildInputs = [
gtk4
@ -32,8 +32,12 @@ buildGoModule rec {
# Checking requires a working display
doCheck = false;
postInstall = ''
postPatch = ''
sed -i '/DBusActivatable/d' .nix/com.github.diamondburned.gotktrix.desktop
echo 'X-Purism-FormFactor=Workstation;Mobile;' >> .nix/com.github.diamondburned.gotktrix.desktop
'';
postInstall = ''
install -Dm444 .nix/com.github.diamondburned.gotktrix.desktop -t $out/share/applications/
install -Dm444 .github/logo-256.png -T $out/share/icons/hicolor/256x256/apps/gotktrix.png
'';

14
pkgs/applications/networking/instant-messengers/signald/0001-Fetch-buildconfig-during-gradle-build-inside-Nix-FOD.patch
View File

@ -1,4 +1,4 @@
From 8ed5f3c9117e08f7c2e4e1e01c2eee501675049b Mon Sep 17 00:00:00 2001
From 2c126682aaabd7f486dfb2ff75fe29b5d8697060 Mon Sep 17 00:00:00 2001
From: Maximilian Bosch <maximilian@mbosch.me>
Date: Sat, 26 Feb 2022 12:33:13 +0100
Subject: [PATCH] Fetch buildconfig during gradle build inside Nix FOD
@ -8,7 +8,7 @@ Subject: [PATCH] Fetch buildconfig during gradle build inside Nix FOD
1 file changed, 6 insertions(+), 1 deletion(-)
diff --git a/build.gradle b/build.gradle
index eaa6e0e..63c2947 100644
index 799e782..caceaac 100644
--- a/build.gradle
+++ b/build.gradle
@@ -83,6 +83,9 @@ static String getVersion() {
@ -22,11 +22,11 @@ index eaa6e0e..63c2947 100644
}
@@ -104,6 +107,8 @@ dependencies {
implementation 'io.prometheus:simpleclient_httpserver:0.15.0'
implementation 'io.prometheus:simpleclient_httpserver:0.16.0'
implementation 'com.squareup.okhttp3:logging-interceptor:4.9.3'
implementation 'io.sentry:sentry:5.7.3'
+ implementation 'com.github.gmazzo.buildconfig:com.github.gmazzo.buildconfig.gradle.plugin:3.0.3'
+ implementation 'org.jetbrains.kotlin:kotlin-scripting-jvm:1.4.31'
implementation 'io.sentry:sentry:6.4.0'
+ implementation 'com.github.gmazzo.buildconfig:com.github.gmazzo.buildconfig.gradle.plugin:3.1.0'
+ implementation 'org.jetbrains.kotlin:kotlin-scripting-jvm:1.7.10'
testImplementation 'org.junit.jupiter:junit-jupiter:5.8.2'
}
@ -38,5 +38,5 @@ index eaa6e0e..63c2947 100644
\ No newline at end of file
+}
--
2.36.0
2.36.2

14
pkgs/applications/networking/instant-messengers/signald/0002-buildconfig-local-deps-fixes.patch
View File

@ -1,4 +1,4 @@
From f319e1db47ae1eeddb6021cafe7b4f8551a702d7 Mon Sep 17 00:00:00 2001
From b068af1f3e49dedfb489e3ed957934ff651e98ee Mon Sep 17 00:00:00 2001
From: Maximilian Bosch <maximilian@mbosch.me>
Date: Sat, 26 Feb 2022 12:36:15 +0100
Subject: [PATCH 2/2] buildconfig/local deps fixes
@ -8,7 +8,7 @@ Subject: [PATCH 2/2] buildconfig/local deps fixes
1 file changed, 18 insertions(+), 8 deletions(-)
diff --git a/build.gradle b/build.gradle
index eaa6e0e..9a2f4e2 100644
index 799e782..6ecef3e 100644
--- a/build.gradle
+++ b/build.gradle
@@ -10,11 +10,21 @@ import org.gradle.nativeplatform.platform.internal.ArchitectureInternal
@ -48,11 +48,11 @@ index eaa6e0e..9a2f4e2 100644
dependencies {
@@ -104,6 +117,8 @@ dependencies {
implementation 'io.prometheus:simpleclient_httpserver:0.15.0'
implementation 'io.prometheus:simpleclient_httpserver:0.16.0'
implementation 'com.squareup.okhttp3:logging-interceptor:4.9.3'
implementation 'io.sentry:sentry:5.7.3'
+ implementation 'com.github.gmazzo.buildconfig:com.github.gmazzo.buildconfig.gradle.plugin:3.0.3'
+ implementation 'org.jetbrains.kotlin:kotlin-scripting-jvm:1.4.31'
implementation 'io.sentry:sentry:6.4.0'
+ implementation 'com.github.gmazzo.buildconfig:com.github.gmazzo.buildconfig.gradle.plugin:3.1.0'
+ implementation 'org.jetbrains.kotlin:kotlin-scripting-jvm:1.7.10'
testImplementation 'org.junit.jupiter:junit-jupiter:5.8.2'
}
@ -67,5 +67,5 @@ index eaa6e0e..9a2f4e2 100644
-}
\ No newline at end of file
--
2.36.0
2.36.2

10
pkgs/applications/networking/instant-messengers/signald/default.nix
View File

@ -4,18 +4,18 @@
let
pname = "signald";
version = "0.19.1";
version = "0.23.0";
src = fetchFromGitLab {
owner = pname;
repo = pname;
rev = version;
sha256 = "sha256-Ma6kIKRVM8UUU/TvfVp2RVl/FLxFgBQU3mEypnujJ+c=";
sha256 = "sha256-RN0OYjOmVtHKeFkviep952uf3qWuBj8lhcaP1Lk/gDo=";
};
jre' = jre_minimal.override {
jdk = jdk17_headless;
# from https://gitlab.com/signald/signald/-/blob/0.19.1/build.gradle#L173
# from https://gitlab.com/signald/signald/-/blob/0.23.0/build.gradle#L173
modules = [
"java.base"
"java.management"
@ -54,8 +54,8 @@ let
outputHashMode = "recursive";
# Downloaded jars differ by platform
outputHash = {
x86_64-linux = "sha256-q1gzauIL7aKalvPSfiK5IvkNkidCh+6jp5bpwxR+PZ0=";
aarch64-linux = "sha256-cM+7MaV0/4yAzobXX9FSdl/ZfLddwySayao96UdDgzk=";
x86_64-linux = "sha256-ANiNDdTuCuDEH5zUPsrVF6Uegdq3zVsMv+uMtYRX0jE=";
aarch64-linux = "sha256-V9zn4v/ZeLELAwFJ5y7OVAeJwZp4DmHm4KWxE6KpwGs=";
}.${stdenv.system} or (throw "Unsupported platform");
};

4
pkgs/applications/networking/mailreaders/mutt/default.nix
View File

@ -21,12 +21,12 @@
stdenv.mkDerivation rec {
pname = "mutt";
version = "2.2.7";
version = "2.2.8";
outputs = [ "out" "doc" "info" ];
src = fetchurl {
url = "http://ftp.mutt.org/pub/mutt/${pname}-${version}.tar.gz";
sha256 = "6xOFj1i7Np9He/ZS2Q6baq3dDWEKy+o0VQSeXvrTbfE=";
sha256 = "A/PSN6LuKh0WM2QXyaXxe0nPcEXu/qYCHwggu/hdClM=";
};
patches = lib.optional smimeSupport (fetchpatch {

7
pkgs/applications/science/biology/octopus/default.nix
View File

@ -1,4 +1,4 @@
{lib, stdenv, fetchFromGitHub, cmake, boost, gmp, htslib, zlib, xz, pkg-config}:
{lib, stdenv, fetchurl, fetchFromGitHub, cmake, boost, gmp, htslib, zlib, xz, pkg-config}:
stdenv.mkDerivation rec {
pname = "octopus";
@ -14,6 +14,11 @@ stdenv.mkDerivation rec {
nativeBuildInputs = [ cmake pkg-config ];
buildInputs = [ boost gmp htslib zlib xz ];
patches = [ (fetchurl {
url = "https://github.com/luntergroup/octopus/commit/17a597d192bcd5192689bf38c5836a98b824867a.patch";
sha256 = "sha256-VaUr63v7mzhh4VBghH7a7qrqOYwl6vucmmKzTi9yAjY=";
}) ];
postInstall = ''
mkdir $out/bin
mv $out/octopus $out/bin

8
pkgs/applications/science/logic/potassco/clingcon.nix
View File

@ -7,19 +7,15 @@
stdenv.mkDerivation rec {
pname = "clingcon";
version = "5.0.0";
version = "5.2.0";
src = fetchFromGitHub {
owner = "potassco";
repo = pname;
rev = "v${version}";
sha256 = "1g2xkz9nsgqnrw3fdf5jchl16f0skj5mm32va61scc2yrchll166";
sha256 = "sha256-wZfTneoQSqEnLAVE8WyPh9EABmOEhDgRm6yWAF1T7Nk=";
};
patches = [
./clingcon_limits.patch
];
postPatch = ''
cp ${catch2}/include/catch2/catch.hpp libclingcon/tests/catch.hpp
'';

24
pkgs/applications/science/logic/potassco/clingcon_limits.patch
View File

@ -1,24 +0,0 @@
diff --git i/libclingcon/clingcon/base.hh w/libclingcon/clingcon/base.hh
index 2d449fe..0b5fa17 100644
--- i/libclingcon/clingcon/base.hh
+++ w/libclingcon/clingcon/base.hh
@@ -28,6 +28,7 @@
#include <clingo.hh>
#include <optional>
#include <forward_list>
+#include <limits>
//! @file clingcon/base.hh
//! Basic data types.
diff --git i/libclingcon/clingcon/util.hh w/libclingcon/clingcon/util.hh
index df4cddd..308259e 100644
--- i/libclingcon/clingcon/util.hh
+++ w/libclingcon/clingcon/util.hh
@@ -30,6 +30,7 @@
#include <map>
#include <cstdlib>
#include <stdexcept>
+#include <limits>
//! @file clingcon/util.hh
//! Very general utility functions.

4
pkgs/applications/science/math/gmsh/default.nix
View File

@ -5,11 +5,11 @@ assert (!blas.isILP64) && (!lapack.isILP64);
stdenv.mkDerivation rec {
pname = "gmsh";
version = "4.10.5";
version = "4.11.0";
src = fetchurl {
url = "https://gmsh.info/src/gmsh-${version}-source.tgz";
sha256 = "sha256-zAMMWu5l59WPhQuLb1WmiUXIm8hx+U4SOSefWiEPxOo=";
sha256 = "sha256-PPLyRFXuCSUsmeZNTmRilW5o8P8fN7rKC3jICdbMVXo=";
};
buildInputs = [

17
pkgs/applications/science/math/sage/patches/disable-slow-glpk-test.patch Normal file
View File

@ -0,0 +1,17 @@
diff --git a/src/sage/graphs/generic_graph.py b/src/sage/graphs/generic_graph.py
index 0070705f78..ac19818f1b 100644
--- a/src/sage/graphs/generic_graph.py
+++ b/src/sage/graphs/generic_graph.py
@@ -6699,12 +6699,6 @@ class GenericGraph(GenericGraph_pyx):
sage: G = DiGraph(d6, format='dig6')
sage: G.edge_connectivity()
5
- sage: G.edge_disjoint_spanning_trees(5) # long time
- [Digraph on 28 vertices,
- Digraph on 28 vertices,
- Digraph on 28 vertices,
- Digraph on 28 vertices,
- Digraph on 28 vertices]
Small cases::

16
pkgs/applications/science/math/sage/sage-src.nix
View File

@ -138,6 +138,22 @@ stdenv.mkDerivation rec {
rev = "eb8cd42feb58963adba67599bf6e311e03424328";
sha256 = "sha256-0dKewOZe2n3PqSdxCJt18FkqwTdrD0VA5MXAMiTW8Tw=";
})
# https://trac.sagemath.org/ticket/34701
(fetchSageDiff {
name = "libgap-fix-gc-crashes-on-aarch64.patch";
base = "eb8cd42feb58963adba67599bf6e311e03424328"; # TODO: update when #34391 lands
rev = "90acc7f1c13a80b8aa673469a2668feb9cd4207f";
sha256 = "sha256-9BhQLFB3wUhiXRQsK9L+I62lSjvTfrqMNi7QUIQvH4U=";
})
# Sage uses mixed integer programs (MIPs) to find edge disjoint
# spanning trees. For some reason, aarch64 glpk takes much longer
# than x86_64 glpk to solve such MIPs. Since the MIP formulation
# has "numerous problems" and will be replaced by a polynomial
# algorithm soon, disable this test for now.
# https://trac.sagemath.org/ticket/34575
./patches/disable-slow-glpk-test.patch
];
patches = nixPatches ++ bugfixPatches ++ packageUpgradePatches;

4
pkgs/applications/version-management/git-and-tools/ghorg/default.nix
View File

@ -2,13 +2,13 @@
buildGoModule rec {
pname = "ghorg";
version = "1.8.8";
version = "1.9.0";
src = fetchFromGitHub {
owner = "gabrie30";
repo = "ghorg";
rev = "v${version}";
sha256 = "sha256-xB/TdeXC0V8dZs6N6Uq1+gzG84j9uhSrwkSbIMwUWSk=";
sha256 = "sha256-P9LwgEUz8QgUVQYISIx3Sa8ibFxNTGNNO5Vn014UB88=";
};
doCheck = false;

6
pkgs/applications/version-management/gitoxide/default.nix
View File

@ -12,16 +12,16 @@
rustPlatform.buildRustPackage rec {
pname = "gitoxide";
version = "0.16.0";
version = "0.17.0";
src = fetchFromGitHub {
owner = "Byron";
repo = "gitoxide";
rev = "v${version}";
sha256 = "sha256-4Yk3WXkm8jdabEisGKqVQlzjFrrf3pskRmuPa5K4vw4=";
sha256 = "sha256-UtQ9LcGE9mLowttAAwR1ujD+BSCosFk+GHQvDwG/CAQ=";
};
cargoSha256 = "sha256-mX58cb1Ywr7npmxgynDQ1x1PmO/62Bd+bONdv/Y1I2Q=";
cargoSha256 = "sha256-0cZy7hOaREtdFB0Ww1VSV4ILpB0utSBcKlC3t9fhum8=";
nativeBuildInputs = [ cmake pkg-config ];
buildInputs = if stdenv.isDarwin

7
pkgs/applications/virtualization/OVMF/default.nix
View File

@ -1,4 +1,4 @@
{ stdenv, nixosTests, lib, edk2, util-linux, nasm, acpica-tools
{ stdenv, nixosTests, lib, edk2, util-linux, nasm, acpica-tools, llvmPackages
, csmSupport ? false, seabios ? null
, secureBoot ? false
, httpSupport ? false
@ -33,7 +33,8 @@ edk2.mkDerivation projectDscPath (finalAttrs: {
outputs = [ "out" "fd" ];
nativeBuildInputs = [ util-linux nasm acpica-tools ];
nativeBuildInputs = [ util-linux nasm acpica-tools ]
++ lib.optionals stdenv.cc.isClang [ llvmPackages.bintools llvmPackages.llvm ];
strictDeps = true;
hardeningDisable = [ "format" "stackprotector" "pic" "fortify" ];
@ -44,6 +45,8 @@ edk2.mkDerivation projectDscPath (finalAttrs: {
++ lib.optionals httpSupport [ "-D NETWORK_HTTP_ENABLE=TRUE" "-D NETWORK_HTTP_BOOT_ENABLE=TRUE" ]
++ lib.optionals tpmSupport [ "-D TPM_ENABLE" "-D TPM2_ENABLE" "-D TPM2_CONFIG_ENABLE"];
NIX_CFLAGS_COMPILE = lib.optional stdenv.cc.isClang "-Qunused-arguments";
postPatch = lib.optionalString csmSupport ''
cp ${seabios}/Csm16.bin OvmfPkg/Csm/Csm16/Csm16.bin
'';

4
pkgs/applications/virtualization/crun/default.nix
View File

@ -38,13 +38,13 @@ let
in
stdenv.mkDerivation rec {
pname = "crun";
version = "1.6";
version = "1.7";
src = fetchFromGitHub {
owner = "containers";
repo = pname;
rev = version;
sha256 = "sha256-JO07bF2Xucz8lSvj7om17a/NT0I7Vru1vayZhPDFLIw=";
sha256 = "sha256-Ly6GBR7nF7J5Dwe1jrQxR4XYsao7KxBAxGn8fsJwmMs=";
fetchSubmodules = true;
};

3
pkgs/applications/window-managers/eww/default.nix
View File

@ -3,6 +3,7 @@
, fetchFromGitHub
, pkg-config
, gtk3
, gdk-pixbuf
, withWayland ? false
, gtk-layer-shell
, stdenv
@ -25,7 +26,7 @@ rustPlatform.buildRustPackage rec {
nativeBuildInputs = [ pkg-config ];
buildInputs = [ gtk3 ] ++ lib.optional withWayland gtk-layer-shell;
buildInputs = [ gtk3 gdk-pixbuf ] ++ lib.optional withWayland gtk-layer-shell;
buildNoDefaultFeatures = withWayland;
buildFeatures = lib.optional withWayland "wayland";

4
pkgs/data/icons/numix-icon-theme-circle/default.nix
View File

@ -2,13 +2,13 @@
stdenvNoCC.mkDerivation rec {
pname = "numix-icon-theme-circle";
version = "22.10.31";
version = "22.11.05";
src = fetchFromGitHub {
owner = "numixproject";
repo = pname;
rev = version;
sha256 = "sha256-FuXCQkSSSmIx6ZsVUqvOTGZrrvobITF9n9N0phoS49U=";
sha256 = "sha256-1SeXPkqBakqJMys5GQXdcSkI2I/VpnEWD1BZAHFWfCs=";
};
nativeBuildInputs = [ gtk3 ];

14
pkgs/desktops/cinnamon/cinnamon-gsettings-overrides/default.nix
View File

@ -2,6 +2,7 @@
, runCommand
, nixos-artwork
, glib
, gnome
, gtk3
, gsettings-desktop-schemas
, extraGSettingsOverrides ? ""
@ -35,9 +36,20 @@ let
cinnamon-session
cinnamon-settings-daemon
cinnamon-common
gnome.gnome-terminal
gtk3
] ++ extraGSettingsOverridePackages;
gsettingsOverrides = ''
# Use Fedora's default to make text readable and
# restore ununified menu.
# https://github.com/NixOS/nixpkgs/issues/200017
[org.gnome.Terminal.Legacy.Settings]
theme-variant='dark'
unified-menu=false
${extraGSettingsOverrides}
'';
in
# TODO: Having https://github.com/NixOS/nixpkgs/issues/54150 would supersede this
@ -53,7 +65,7 @@ runCommand "cinnamon-gsettings-overrides" { preferLocalBuild = true; }
chmod -R a+w "$data_dir"
cat - > "$schema_dir/nixos-defaults.gschema.override" <<- EOF
${extraGSettingsOverrides}
${gsettingsOverrides}
EOF
${glib.dev}/bin/glib-compile-schemas --strict "$schema_dir"

2
pkgs/development/compilers/edk2/default.nix
View File

@ -61,7 +61,7 @@ edk2 = buildStdenv.mkDerivation {
${"GCC5_${targetArch}_PREFIX"}=stdenv.cc.targetPrefix;
makeFlags = [ "-C BaseTools" ]
++ lib.optionals (stdenv.cc.isClang) [ "BUILD_CC=clang BUILD_CXX=clang++ BUILD_AS=clang" ];
++ lib.optionals (stdenv.cc.isClang) [ "CXX=llvm BUILD_AR=ar BUILD_CC=clang BUILD_CXX=clang++ BUILD_AS=clang BUILD_LD=ld" ];
NIX_CFLAGS_COMPILE = "-Wno-return-type" + lib.optionalString (stdenv.cc.isGNU) " -Wno-error=stringop-truncation";

2
pkgs/development/compilers/ocaml/generic.nix
View File

@ -138,7 +138,7 @@ stdenv.mkDerivation (args // {
'';
platforms = with platforms; linux ++ darwin;
broken = stdenv.isAarch64 && lib.versionOlder version "4.06";
broken = stdenv.isAarch64 && lib.versionOlder version (if stdenv.isDarwin then "4.10" else "4.06");
};
})

2
pkgs/development/compilers/openjdk/meta.nix
View File

@ -5,7 +5,7 @@ lib: version: with lib; {
maintainers = with maintainers; [ edwtjo asbachb ];
platforms = [ "i686-linux" "x86_64-linux" "aarch64-linux" "armv7l-linux" "armv6l-linux" ];
mainProgram = "java";
knownVulnerabilities = optionals (builtins.elem (versions.major version) [ "12" "13" "14" "15" "16" ]) [
knownVulnerabilities = optionals (builtins.elem (versions.major version) [ "12" "13" "14" "15" "16" "18" ]) [
"This OpenJDK version has reached its end of life."
];
}

20
pkgs/development/libraries/aspell/dictionaries.nix
View File

@ -105,6 +105,26 @@ let
homepage = "http://ftp.gnu.org/gnu/aspell/dict/0index.html";
} // (args.meta or {});
} // lib.optionalAttrs (stdenv.isDarwin && elem language [ "is" "nb" ]) {
# tar: Cannot open: Illegal byte sequence
unpackPhase = ''
runHook preUnpack
tar -xf $src --strip-components=1 || true
runHook postUnpack
'';
postPatch = getAttr language {
is = ''
cp icelandic.alias íslenska.alias
sed -i 's/ .slenska\.alias/ íslenska.alias/g' Makefile.pre
'';
nb = ''
cp bokmal.alias bokmål.alias
sed -i 's/ bokm.l\.alias/ bokmål.alias/g' Makefile.pre
'';
};
} // removeAttrs args [ "language" "filename" "sha256" "meta" ];
in buildDict buildArgs;

57
pkgs/development/libraries/bencode/default.nix Normal file
View File

@ -0,0 +1,57 @@
{ lib
, stdenv
, fetchFromGitHub
, catch2
, cmake
, expected-lite
, fmt
, gsl-lite
, ninja
}:
stdenv.mkDerivation rec {
pname = "bencode";
version = "0.5.0";
src = fetchFromGitHub {
owner = "fbdtemme";
repo = "bencode";
rev = "v${version}";
hash = "sha256-ePbQ6oTumQ+T5TOb+ReaOYa8Q3lvcMBZ6jTMoquTngg=";
};
nativeBuildInputs = [
cmake
ninja
];
buildInputs = [
catch2
expected-lite
fmt
gsl-lite
];
postPatch = ''
# Disable a test that requires an internet connection.
substituteInPlace tests/CMakeLists.txt \
--replace "add_subdirectory(cmake_fetch_content)" ""
'';
doCheck = true;
postInstall = ''
rm -rf $out/lib64
'';
meta = with lib; {
description = "A header-only C++20 bencode serialization/deserialization library";
homepage = "https://github.com/fbdtemme/bencode";
changelog = "https://github.com/fbdtemme/bencode/blob/${src.rev}/CHANGELOG.md";
license = licenses.mit;
maintainers = with maintainers; [ azahi ];
platforms = platforms.unix;
# Broken because the default stdenv on these targets doesn't support C++20.
broken = with stdenv; isDarwin || (isLinux && isAarch64);
};
}

9
pkgs/development/libraries/cmark/default.nix
View File

@ -13,10 +13,11 @@ stdenv.mkDerivation rec {
nativeBuildInputs = [ cmake ];
cmakeFlags = [
# Link the executable with the shared library
"-DCMARK_STATIC=OFF"
];
cmakeFlags =
# Link the executable with the shared library on system with shared libraries.
lib.optional (!stdenv.hostPlatform.isStatic) "-DCMARK_STATIC=OFF"
# Do not attempt to build .so library on static platform.
++ lib.optional stdenv.hostPlatform.isStatic "-DCMARK_SHARED=OFF";
doCheck = true;

2
pkgs/development/libraries/ffmpeg/generic.nix
View File

@ -71,7 +71,7 @@ stdenv.mkDerivation rec {
configureFlags = filter (v: v != null) ([
"--arch=${stdenv.hostPlatform.parsed.cpu.name}"
"--target_os=${stdenv.hostPlatform.parsed.kernel.name}"
"--pkg-config=${pkg-config.targetPrefix}pkg-config"
"--pkg-config=${buildPackages.pkg-config.targetPrefix}pkg-config"
# License
"--enable-gpl"
"--enable-version3"

5
pkgs/development/libraries/glib-networking/default.nix
View File

@ -14,6 +14,7 @@
, libproxy
, gnome
, gsettings-desktop-schemas
, bash
}:
stdenv.mkDerivation rec {
@ -36,12 +37,15 @@ stdenv.mkDerivation rec {
./installed-tests-path.patch
];
strictDeps = true;
nativeBuildInputs = [
meson
ninja
pkg-config
gettext
makeWrapper
glib # for gio-querymodules
];
buildInputs = [
@ -50,6 +54,7 @@ stdenv.mkDerivation rec {
p11-kit
libproxy
gsettings-desktop-schemas
bash # installed-tests shebangs
];
doCheck = false; # tests need to access the certificates (among other things)

4
pkgs/development/libraries/lzlib/default.nix
View File

@ -12,6 +12,10 @@ stdenv.mkDerivation rec {
sha256 = "sha256-3ea9WzJTXxeyjJrCS2ZgfgJQUGrBQypBEso8c/XWYsM=";
};
postPatch = lib.optionalString stdenv.isDarwin ''
substituteInPlace Makefile.in --replace '-Wl,--soname=' '-Wl,-install_name,$(out)/lib/'
'';
makeFlags = [ "CC:=$(CC)" ];
doCheck = true;

6
pkgs/development/libraries/science/biology/EBTKS/default.nix
View File

@ -11,6 +11,12 @@ stdenv.mkDerivation rec {
sha256 = "1a1qw6i47fs1izx60l1ysabpmyx9j5sjnbdv8b47wi2xcc9i3hpq";
};
# error: use of undeclared identifier 'finite'; did you mean 'isfinite'?
postPatch = ''
substituteInPlace templates/EBTKS/SimpleArray.h \
--replace "#define FINITE(x) finite(x)" "#define FINITE(x) isfinite(x)"
'';
nativeBuildInputs = [ cmake ];
buildInputs = [ libminc ];

4
pkgs/development/libraries/webkitgtk/default.nix
View File

@ -73,7 +73,9 @@ stdenv.mkDerivation (finalAttrs: {
outputs = [ "out" "dev" "devdoc" ];
separateDebugInfo = stdenv.isLinux;
# https://github.com/NixOS/nixpkgs/issues/153528
# Can't be linked within a 4GB address space.
separateDebugInfo = stdenv.isLinux && !stdenv.is32bit;
src = fetchurl {
url = "https://webkitgtk.org/releases/webkitgtk-${finalAttrs.version}.tar.xz";

3
pkgs/development/lisp-modules-new/ql.nix
View File

@ -60,6 +60,9 @@ let
trivial-ssh-libssh2 = pkg: {
nativeLibs = [ libssh2 ];
};
mssql = pkg: {
nativeLibs = [ freetds ];
};
sqlite = pkg: {
nativeLibs = [ sqlite ];
};

34
pkgs/development/ocaml-modules/ppx_yojson_conv/default.nix Normal file
View File

@ -0,0 +1,34 @@
{
lib,
buildDunePackage,
fetchFromGitHub,
ppx_js_style,
ppx_yojson_conv_lib,
ppxlib,
}:
buildDunePackage rec {
pname = "ppx_yojson_conv";
version = "0.15.1";
duneVersion = "3";
minimumOCamlVersion = "4.08.0";
src = fetchFromGitHub {
owner = "janestreet";
repo = pname;
rev = "v${version}";
sha256 = "sha256-lSOUSMVgsRiArEhFTKpAj2yFBPbtaIc/SxdPA+24xXs=";
};
propagatedBuildInputs = [
ppx_js_style
ppx_yojson_conv_lib
ppxlib
];
meta = with lib; {
description = "A PPX syntax extension that generates code for converting OCaml types to and from Yojson";
homepage = "https://github.com/janestreet/ppx_yojson_conv";
maintainers = with maintainers; [djacu];
license = with licenses; [mit];
};
}

1
pkgs/development/php-packages/deployer/default.nix
View File

@ -30,6 +30,7 @@ mkDerivation rec {
description = "A deployment tool for PHP";
license = licenses.mit;
homepage = "https://deployer.org/";
mainProgram = "dep";
maintainers = with maintainers; teams.php.members;
};
}

2
pkgs/development/php-packages/php-parallel-lint/default.nix
View File

@ -22,7 +22,7 @@ mkDerivation {
buildPhase = ''
runHook preBuild
composer dump-autoload
box build
box compile
runHook postBuild
'';

18
pkgs/development/python-modules/amaranth/default.nix
View File

@ -2,6 +2,7 @@
, buildPythonPackage
, pythonOlder
, fetchFromGitHub
, fetchpatch
, setuptools
, setuptools-scm
, pyvcd
@ -31,6 +32,23 @@ buildPythonPackage rec {
sha256 = "P9AG3t30eGeeCN5+t7mjhRoOWIGZVzWQji9eYXphjA0=";
};
patches = [
(fetchpatch {
name = "fix-for-setuptools-64.0.2-preparation.patch";
url = "https://github.com/amaranth-lang/amaranth/commit/64771a065a280fa683c1e6692383bec4f59f20fa.patch";
hash = "sha256-Rsh9vVvUQj9nIcrsRirmR6XwFrfZ2VMaYJ4RCQ8sBE0=";
# This commit removes support for Python 3.6, which is unnecessary to fix
# the build when using new setuptools. Include only one file, which has a
# harmless comment change so that the subsequent patch applies cleanly.
includes = ["amaranth/_toolchain/cxx.py"];
})
(fetchpatch {
name = "fix-for-setuptools-64.0.2.patch";
url = "https://github.com/amaranth-lang/amaranth/pull/722/commits/e5a56b07c568e5f4cc2603eefebd14c5cc4e13d8.patch";
hash = "sha256-C8FyMSKHA7XsEMpO9eYNZx/X5rGaK7p3eXP+jSb6wVg=";
})
];
SETUPTOOLS_SCM_PRETEND_VERSION="${realVersion}";
nativeBuildInputs = [

41
pkgs/development/python-modules/construct-classes/default.nix Normal file
View File

@ -0,0 +1,41 @@
{ lib
, stdenv
, buildPythonPackage
, fetchFromGitHub
, poetry-core
, construct
, pytestCheckHook
}:
buildPythonPackage rec {
pname = "construct-classes";
version = "0.1.2";
format = "pyproject";
# no tests in PyPI tarball
src = fetchFromGitHub {
owner = "matejcik";
repo = "construct-classes";
rev = "v${version}";
sha256 = "sha256-l4sVacKTuQbhXCw2lVHCl1OzpCiKmEAm9nSQ8pxFuTo=";
};
nativeBuildInputs = [
poetry-core
];
propagatedBuildInputs = [
construct
];
checkInputs = [ pytestCheckHook ];
pythonImportsCheck = [ "construct_classes" ];
meta = with lib; {
description = "Parse your binary data into dataclasses.";
homepage = "https://github.com/matejcik/construct-classes";
license = licenses.mit;
maintainers = with maintainers; [ prusnak ];
};
}

38
pkgs/development/python-modules/gsd/default.nix
View File

@ -1,27 +1,47 @@
{ lib, buildPythonPackage, fetchFromGitHub, isPy27
, cython, numpy
{ lib
, buildPythonPackage
, cython
, fetchFromGitHub
, numpy
, pytestCheckHook
, pythonOlder
}:
buildPythonPackage rec {
version = "2.6.0";
pname = "gsd";
disabled = isPy27;
version = "2.6.1";
format = "setuptools";
disabled = pythonOlder "3.7";
src = fetchFromGitHub {
owner = "glotzerlab";
repo = pname;
rev = "refs/tags/v${version}";
sha256 = "sha256-GVb05uy5HKIn+fARFBN+mK54y2CtFBM8At21VUFr7tc=";
hash = "sha256-vQutfkSilfgRHuu/THWMG6bmkT1eKlAAniQM4DP8mqI=";
};
nativeBuildInputs = [ cython ];
propagatedBuildInputs = [ numpy ];
nativeBuildInputs = [
cython
];
propagatedBuildInputs = [
numpy
];
checkInputs = [
pytestCheckHook
];
pythonImportsCheck = [
"gsd"
];
checkInputs = [ pytestCheckHook ];
preCheck = ''
pushd gsd/test
'';
postCheck = ''
popd
'';
@ -30,6 +50,6 @@ buildPythonPackage rec {
description = "General simulation data file format";
homepage = "https://github.com/glotzerlab/gsd";
license = licenses.bsd2;
maintainers = [ maintainers.costrouc ];
maintainers = with maintainers; [ costrouc ];
};
}

3
pkgs/development/python-modules/poetry/default.nix
View File

@ -55,7 +55,8 @@ buildPythonPackage rec {
postPatch = ''
substituteInPlace pyproject.toml \
--replace 'crashtest = "^0.3.0"' 'crashtest = "*"'
--replace 'crashtest = "^0.3.0"' 'crashtest = "*"' \
--replace 'xattr = { version = "^0.9.7"' 'xattr = { version = "^0.10.0"'
'';
nativeBuildInputs = [

10
pkgs/development/python-modules/protonup/default.nix → pkgs/development/python-modules/protonup-ng/default.nix
View File

@ -1,13 +1,13 @@
{ lib, buildPythonPackage, pythonOlder, fetchPypi, requests, configparser }:
buildPythonPackage rec {
pname = "protonup";
version = "0.1.4";
pname = "protonup-ng";
version = "0.2.1";
disabled = pythonOlder "3.6";
src = fetchPypi {
inherit pname version;
sha256 = "0z5q0s9h51w2bqm9lkafml14g13v2dgm4nm9x06v7nxqc9msmyyy";
hash = "sha256-rys9Noa3+w4phttfcI1OGEDfHMy8s80bm8kM8TzssQA=";
};
postPatch = ''
@ -21,9 +21,9 @@ buildPythonPackage rec {
pythonImportsCheck = [ "protonup" ];
meta = with lib; {
homepage = "https://github.com/AUNaseef/protonup";
homepage = "https://github.com/cloudishBenne/protonup-ng";
description = "CLI program and API to automate the installation and update of GloriousEggroll's Proton-GE";
license = licenses.gpl3Only;
maintainers = with maintainers; [ flexagoon ];
maintainers = with maintainers; [ Madouura ];
};
}

4
pkgs/development/python-modules/pyinfra/default.nix
View File

@ -18,7 +18,7 @@
buildPythonPackage rec {
pname = "pyinfra";
version = "2.5.1";
version = "2.5.2";
format = "setuptools";
disabled = pythonOlder "3.7";
@ -27,7 +27,7 @@ buildPythonPackage rec {
owner = "Fizzadar";
repo = pname;
rev = "refs/tags/v${version}";
hash = "sha256-cN7nyjdnU/ls3HNhC2m1sunRrmZFT5pFZr+kEBcwHkU=";
hash = "sha256-35qM6u3I8yH1E8mrlaeFjhliOVTkMXH13b8S6e9ROig=";
};
propagatedBuildInputs = [

1
pkgs/development/python-modules/rpi-gpio/default.nix
View File

@ -18,6 +18,7 @@ buildPythonPackage rec {
homepage = "https://sourceforge.net/p/raspberry-gpio-python";
description = "Python module to control the GPIO on a Raspberry Pi";
license = licenses.mit;
platforms = platforms.linux;
maintainers = with maintainers; [ onny ];
};
}

2
pkgs/development/python-modules/tensorboard/default.nix
View File

@ -41,7 +41,7 @@ buildPythonPackage rec {
pushd unpacked/tensorboard-${version}
substituteInPlace tensorboard-${version}.dist-info/METADATA \
--replace "google-auth-oauthlib (<0.5,>=0.4.1)" "google-auth-oauthlib (<0.6,>=0.4.1)" \
--replace "google-auth-oauthlib (<0.5,>=0.4.1)" "google-auth-oauthlib (<1.0,>=0.4.1)" \
--replace "protobuf (<3.20,>=3.9.2)" "protobuf (>=3.9.2)"
popd

7
pkgs/development/python-modules/trezor/default.nix
View File

@ -7,6 +7,7 @@
, attrs
, click
, construct
, construct-classes
, ecdsa
, hidapi
, libusb1
@ -24,13 +25,13 @@
buildPythonPackage rec {
pname = "trezor";
version = "0.13.3";
version = "0.13.4";
disabled = !isPy3k;
src = fetchPypi {
inherit pname version;
sha256 = "055d32174d4ecf2353f7622ee44b8e82e3bef78fe40ce5cdbeafc785b422a049";
sha256 = "04a77b44005971819386bbd55242a1004b1f88fbbdb829deb039a1e0028a4af1";
};
nativeBuildInputs = [ installShellFiles ];
@ -39,6 +40,7 @@ buildPythonPackage rec {
attrs
click
construct
construct-classes
ecdsa
hidapi
libusb1
@ -58,6 +60,7 @@ buildPythonPackage rec {
disabledTestPaths = [
"tests/test_stellar.py" # requires stellar-sdk
"tests/test_firmware.py" # requires network downloads
];
pythonImportsCheck = [ "trezorlib" ];

3
pkgs/development/python-modules/zeroconf/default.nix
View File

@ -28,6 +28,9 @@ buildPythonPackage rec {
ifaddr
];
# OSError: [Errno 48] Address already in use
doCheck = !stdenv.isDarwin;
checkInputs = [
pytest-asyncio
pytestCheckHook

8
pkgs/development/r-modules/bioc-experiment-packages.nix generated
View File

@ -48,7 +48,7 @@ in with self; {
DMRcatedata = derive2 { name="DMRcatedata"; version="2.14.0"; sha256="0abmnnawn06m4dyh6hs5hcdlhwx5l5bmlygzizcy6968d9x5l4w9"; depends=[ExperimentHub GenomicFeatures Gviz IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylationEPICanno_ilm10b4_hg19 plyr readxl rtracklayer]; };
DREAM4 = derive2 { name="DREAM4"; version="1.31.0"; sha256="11ypc84agvq0q0v7bk0b25cm48awxay5hhhjd95gw9s7jk196i2p"; depends=[SummarizedExperiment]; };
DeSousa2013 = derive2 { name="DeSousa2013"; version="1.32.0"; sha256="1dx3568szd4i26jpl8i0klqqh0qgi8mgh5i4mmmkxwp44p10igzg"; depends=[affy AnnotationDbi Biobase cluster ConsensusClusterPlus frma frmaTools gplots hgu133plus2_db hgu133plus2frmavecs pamr rgl ROCR siggenes survival sva]; };
DmelSGI = derive2 { name="DmelSGI"; version="1.27.0"; sha256="134jwqnqprvma85slbahhx6jbbmfpxwfgnyk0kvx6xy28kvgkx6b"; depends=[abind gplots igraph knitr limma rhdf5 TSP]; };
DmelSGI = derive2 { name="DmelSGI"; version="1.28.1"; sha256="0644cwq481n5wk49q52jjwg3bkg2hpz6bcw8hf5y5v9vl2dsnwip"; depends=[abind gplots igraph knitr limma rhdf5 TSP]; };
DonaPLLP2013 = derive2 { name="DonaPLLP2013"; version="1.34.0"; sha256="088w2c7xyz6zsymwsm4s5999q6sry0xscrs9n8sv6qzqhpfisa5p"; depends=[EBImage]; };
DropletTestFiles = derive2 { name="DropletTestFiles"; version="1.6.0"; sha256="0lwcfprv17p9ng5x3arr9j67234y003n5g45aqcc39qiz075y8rv"; depends=[AnnotationHub ExperimentHub S4Vectors]; };
DrugVsDiseasedata = derive2 { name="DrugVsDiseasedata"; version="1.32.0"; sha256="0l4n4wfd24l0lx07b5x947ngp4wyyw2iajgyam4h9n99k8cjkmnl"; depends=[]; };
@ -173,7 +173,7 @@ in with self; {
RcisTarget_hg19_motifDBs_cisbpOnly_500bp = derive2 { name="RcisTarget.hg19.motifDBs.cisbpOnly.500bp"; version="1.16.0"; sha256="1wi7g1246p04ld97x11pkb7hy4490cq5pfw404xhcmavm6sbrsps"; depends=[data_table]; };
ReactomeGSA_data = derive2 { name="ReactomeGSA.data"; version="1.10.0"; sha256="1z0sridzwyfq3cxvmv97c5mg96z5aylwpma35kizzi1y5y7xjqnr"; depends=[edgeR limma ReactomeGSA Seurat]; };
RegParallel = derive2 { name="RegParallel"; version="1.14.0"; sha256="12ak24899dp4184xc2g549d22zxv297aaz1c5s3zva821bv43djq"; depends=[arm data_table doParallel foreach iterators stringr survival]; };
RforProteomics = derive2 { name="RforProteomics"; version="1.33.1"; sha256="0wsbalnq82h02hs6v71ng2b6gw1kpcjz1ypzcxv5fr13aaivl512"; depends=[BiocManager biocViews MSnbase R_utils]; };
RforProteomics = derive2 { name="RforProteomics"; version="1.34.1"; sha256="11i9r36n3jqwnf1q3fawgk26zvs7zkixq8hmfam7d4kaqj5f9kvz"; depends=[BiocManager biocViews MSnbase R_utils]; };
RnBeads_hg19 = derive2 { name="RnBeads.hg19"; version="1.28.0"; sha256="13vjqi6n6swz08qzadycn873rls1wkzprmf2rawx7mrbsy1cn5zh"; depends=[GenomicRanges]; };
RnBeads_hg38 = derive2 { name="RnBeads.hg38"; version="1.28.0"; sha256="0wdzm89rn5z33sk3jw9f8yq6f23k5m5pv6ysbf8irw6s1g6y3xr3"; depends=[GenomicRanges]; };
RnBeads_mm10 = derive2 { name="RnBeads.mm10"; version="2.4.1"; sha256="10gixzi25ka6arxapn04yxj39193f1b614ynnn1795hbz1njv7a4"; depends=[GenomicRanges]; };
@ -391,10 +391,11 @@ in with self; {
signatureSearchData = derive2 { name="signatureSearchData"; version="1.10.0"; sha256="1wq9pk2g4zriijrlc6bqizi4rvmag3m0nrnml3qhqhn1jcc065g3"; depends=[affy Biobase dplyr ExperimentHub limma magrittr R_utils rhdf5]; };
simpIntLists = derive2 { name="simpIntLists"; version="1.32.0"; sha256="07jscl1yd3dix0igsxw1fsyhsgqhqf0la6p6958jypy2chih4wp8"; depends=[]; };
spatialDmelxsim = derive2 { name="spatialDmelxsim"; version="1.2.0"; sha256="126agbyablnn3b2gh4fkvlqf1mm1krvk01bxl0x41f6l4dm5gj6a"; depends=[ExperimentHub SummarizedExperiment]; };
spatialLIBD = derive2 { name="spatialLIBD"; version="1.8.10"; sha256="11h39570h2rpxa3dw93wf16i574928gjyf4wzb5a3y6b3avzn4yg"; depends=[AnnotationHub benchmarkme BiocFileCache BiocGenerics cowplot DT ExperimentHub fields GenomicRanges ggplot2 golem IRanges jsonlite magick Matrix paletteer plotly png RColorBrewer rtracklayer S4Vectors scater sessioninfo shiny shinyWidgets SingleCellExperiment SpatialExperiment SummarizedExperiment tibble viridisLite]; };
spatialLIBD = derive2 { name="spatialLIBD"; version="1.8.11"; sha256="0yk749566rcvcw415s8ix185jf1vvmip2079mf81kjr8jsmlmz4c"; depends=[AnnotationHub benchmarkme BiocFileCache BiocGenerics cowplot DT ExperimentHub fields GenomicRanges ggplot2 golem IRanges jsonlite magick Matrix paletteer plotly png RColorBrewer rtracklayer S4Vectors scater sessioninfo shiny shinyWidgets SingleCellExperiment SpatialExperiment SummarizedExperiment tibble viridisLite]; };
spqnData = derive2 { name="spqnData"; version="1.8.0"; sha256="190jkvra5zsml0hxmw96nxg3fz5cnq6apcxcqsncq9raz30w8qqq"; depends=[SummarizedExperiment]; };
stemHypoxia = derive2 { name="stemHypoxia"; version="1.32.0"; sha256="0rfnka092sd0qb6vs7yawwkjw763rdaayyr7bv4618qqx2i6kllz"; depends=[]; };
stjudem = derive2 { name="stjudem"; version="1.36.0"; sha256="0a7qrs9r76zlzd6kmfid8wzvv3k47y3w95ydqphd5pic9c6r56a3"; depends=[]; };
synapterdata = derive2 { name="synapterdata"; version="1.34.0"; sha256="15lndkk8cgk5sy2ddc7g98nnjcd89j5a7c8kxz7jvd0j2vq1g0ga"; depends=[synapter]; };
systemPipeRdata = derive2 { name="systemPipeRdata"; version="2.0.1"; sha256="1g5641hkx2di7j2kgd13v1zih4ddm9wljrzi7swr0dxb01vqvckh"; depends=[BiocGenerics Biostrings jsonlite remotes]; };
tartare = derive2 { name="tartare"; version="1.10.0"; sha256="1857nmpd64zlbk0i7jk7ql04kkmyznr355jd3zml44x2zbip96mg"; depends=[AnnotationHub ExperimentHub]; };
timecoursedata = derive2 { name="timecoursedata"; version="1.6.0"; sha256="0f2m6d4q6ayk6sqz3d4gnh4w9c5z91m4j8pjfi1932q4a86smhr5"; depends=[SummarizedExperiment]; };
@ -418,6 +419,5 @@ in with self; {
MAQCsubsetAFX = derive2 { name="MAQCsubsetAFX"; version="1.30.0"; sha256="14mwg96g7aza81vc3hpmb41scmygl8vnsi6s8p48c8v92106asmb"; depends=[affy Biobase]; broken = true; };
MSstatsBioData = derive2 { name="MSstatsBioData"; version="1.13.0"; sha256="1jzypgfmd6d0fdj9ycp4jwihjpxyinr5kwi2x2dg2z6hvxx97gb8"; depends=[]; broken = true; };
brainImageRdata = derive2 { name="brainImageRdata"; version="1.12.0"; sha256="072x7yn1ambf6hfpir6qdxl8bybv64blpbi1jdp0bvqlk66zs7zv"; depends=[ExperimentHub]; broken = true; };
synapterdata = derive2 { name="synapterdata"; version="1.31.0"; sha256="03bdx8a1hrnlbcfq92d2yrjydw978pifbgr257r55p15khkigl86"; depends=[]; broken = true; };
tcgaWGBSData_hg19 = derive2 { name="tcgaWGBSData.hg19"; version="1.12.0"; sha256="1kmh4iyh2h7vc1mlwb3sridn4nwkqdschz5md5dk53mxkn2wxcmi"; depends=[bsseq ExperimentHub knitr]; broken = true; };
}

221
pkgs/development/r-modules/bioc-packages.nix generated
View File

@ -19,10 +19,10 @@ in with self; {
ALDEx2 = derive2 { name="ALDEx2"; version="1.28.1"; sha256="0xppx52sllbz4pli174422i4kkf37v0yl844088nbj3j9r6pfbj9"; depends=[BiocParallel GenomicRanges IRanges multtest Rfast S4Vectors SummarizedExperiment zCompositions]; };
AMARETTO = derive2 { name="AMARETTO"; version="1.12.0"; sha256="111dk19b9910icksyr592cvhc5gwvgknr5q4887j9yxbajd7hcmx"; depends=[BiocFileCache callr circlize ComplexHeatmap curatedTCGAData doParallel dplyr DT foreach ggplot2 glmnet gridExtra httr impute knitr limma Matrix matrixStats MultiAssayExperiment Rcpp readr reshape2 rmarkdown tibble]; };
AMOUNTAIN = derive2 { name="AMOUNTAIN"; version="1.22.0"; sha256="0vdfabsrisdd7qq28f5ivd0v8zz49szqn677i5lhwnlaix220c54"; depends=[]; };
ANCOMBC = derive2 { name="ANCOMBC"; version="1.6.2"; sha256="1d8i4d7zksx6fgzpm4dh9vksglb3kppx476mhn6d3342nswczcav"; depends=[DescTools doParallel doRNG dplyr energy foreach Hmisc magrittr MASS microbiome nlme nloptr phyloseq Rdpack rlang tibble tidyr]; };
ANCOMBC = derive2 { name="ANCOMBC"; version="1.6.4"; sha256="02vip6b6vkzwnwsmdxpmrkd8nb9diq05wvrs0yqvxxnvkj980ppz"; depends=[CVXR DescTools doParallel doRNG dplyr emmeans energy foreach Hmisc lme4 lmerTest magrittr MASS mia nloptr Rdpack rlang rngtools S4Vectors SingleCellExperiment SummarizedExperiment tibble tidyr]; };
ANF = derive2 { name="ANF"; version="1.18.0"; sha256="1fa2pbdapymrpz01ws0m2fbzf11d723x6rbsys29v06is57f5lpj"; depends=[Biobase igraph MASS RColorBrewer survival]; };
APAlyzer = derive2 { name="APAlyzer"; version="1.10.0"; sha256="1xixj6ck1akwc01gv7xsgnnflrkhflsrpq2cbxh5s7z6xj0f8k00"; depends=[DESeq2 dplyr GenomicAlignments GenomicFeatures GenomicRanges ggplot2 ggrepel HybridMTest repmis Rsamtools Rsubread rtracklayer SummarizedExperiment tidyr VariantAnnotation]; };
APL = derive2 { name="APL"; version="1.0.0"; sha256="1089klbirrnm99xw02bd0hfzqnhcq5fas9hw1l52x191j7b0363r"; depends=[ggplot2 ggrepel magrittr org_Hs_eg_db org_Mm_eg_db plotly reticulate rlang Seurat SingleCellExperiment SummarizedExperiment topGO viridisLite]; };
APL = derive2 { name="APL"; version="1.0.1"; sha256="0v6m5vcj5c1f0f9d8ksyhq58jgqfrjsgg4vf9pmbb36gvf3k81dk"; depends=[ggplot2 ggrepel magrittr org_Hs_eg_db org_Mm_eg_db plotly reticulate rlang Seurat SingleCellExperiment SummarizedExperiment topGO viridisLite]; };
ARRmNormalization = derive2 { name="ARRmNormalization"; version="1.36.0"; sha256="1pnvw8psbql787m8lrmhd9xbmgkc3dbc70yfds1aggv50dk3yjk1"; depends=[ARRmData]; };
ASAFE = derive2 { name="ASAFE"; version="1.22.0"; sha256="1l9iqw2imr6w2gwqrmg05jp6lj2xc7hbyhd144d4q8vw8z7ga4ns"; depends=[]; };
ASEB = derive2 { name="ASEB"; version="1.40.0"; sha256="1i0r4vimk6is4j4rr14ajp8papznpmmr0bhwd96s8w53cqdqph7p"; depends=[]; };
@ -42,8 +42,8 @@ in with self; {
AgiMicroRna = derive2 { name="AgiMicroRna"; version="2.46.0"; sha256="0jic89gyphbv7jzlfgm9bh1aq48lp86rq6hr34gsg9z0pa1192xa"; depends=[affy affycoretools Biobase limma preprocessCore]; };
AllelicImbalance = derive2 { name="AllelicImbalance"; version="1.34.0"; sha256="0w4xd0xzkwx7bbhrgqligpahlhg85rginknx520z891r8v0bim2z"; depends=[AnnotationDbi BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges gridExtra Gviz IRanges lattice latticeExtra nlme Rsamtools S4Vectors seqinr SummarizedExperiment VariantAnnotation]; };
AlphaBeta = derive2 { name="AlphaBeta"; version="1.10.0"; sha256="1ikdrigma02gnl6ggrc89bjsiqmd7knpb9kw7nqyrdnv3qjd9iag"; depends=[BiocParallel data_table dplyr expm ggplot2 gtools igraph optimx plotly stringr]; };
AlpsNMR = derive2 { name="AlpsNMR"; version="3.6.0"; sha256="0gmzabwidvh1ja8821sc2whn8nhw6g26694f35x1193kpr858qih"; depends=[baseline BiocParallel dplyr fs future ggplot2 glue htmltools magrittr matrixStats mixOmics pcaPP purrr readxl reshape2 rlang rmarkdown signal speaq stringr tibble tidyr vctrs]; };
AnVIL = derive2 { name="AnVIL"; version="1.8.3"; sha256="10wd56brz0y0zyi6qd9nx11s04a6h56yzdnfd2m28r8y6x9dxhg4"; depends=[BiocManager dplyr futile_logger httr jsonlite rapiclient rlang tibble tidyr tidyselect]; };
AlpsNMR = derive2 { name="AlpsNMR"; version="3.6.1"; sha256="09z2k6mqr837bh422mpy0k71hwsmc4s730f58fq9ya651cjzvdcs"; depends=[baseline BiocParallel dplyr fs future ggplot2 glue htmltools magrittr matrixStats mixOmics pcaPP purrr readxl reshape2 rlang rmarkdown signal speaq stringr tibble tidyr vctrs]; };
AnVIL = derive2 { name="AnVIL"; version="1.8.7"; sha256="16vqqm7p3v92b51ir9kmaa410p57bpqpxr4nvqngz2c8vvkm5l5g"; depends=[BiocManager dplyr futile_logger httr jsonlite rapiclient rlang tibble tidyr tidyselect]; };
AnVILBilling = derive2 { name="AnVILBilling"; version="1.6.0"; sha256="08bc1lsjkgs0hmrfi2fbk5swbi5ckgrv4vhsfkqqywfpnkq9k436"; depends=[bigrquery DBI dplyr DT ggplot2 lubridate magrittr plotly shiny shinytoastr]; };
AnVILPublish = derive2 { name="AnVILPublish"; version="1.6.0"; sha256="1iwvm60lricpsf4nr99wxhni0lwaa4z8aibr7lwj9gdwf2y43c9x"; depends=[AnVIL httr jsonlite readr rmarkdown whisker yaml]; };
Anaquin = derive2 { name="Anaquin"; version="2.20.0"; sha256="1jgpnls2djl1yzvnk64qc83mljmlci7wflwkza3wr0sv6r47b0dd"; depends=[DESeq2 ggplot2 knitr locfit plyr qvalue ROCR]; };
@ -66,7 +66,7 @@ in with self; {
BDMMAcorrect = derive2 { name="BDMMAcorrect"; version="1.14.0"; sha256="19b3jm2a5nz7p43sxa0b08zvc1lvjnqd5g052rj98n6knfb403k7"; depends=[ape ellipse ggplot2 Rcpp RcppArmadillo RcppEigen SummarizedExperiment vegan]; };
BEARscc = derive2 { name="BEARscc"; version="1.16.0"; sha256="0vslyhscqw1y519qmbilb1fw0482aplib8kb37pvmhy3ak1mcxqj"; depends=[data_table ggplot2 SingleCellExperiment]; };
BEAT = derive2 { name="BEAT"; version="1.34.0"; sha256="1hgqiy52l34z8zxzvq5j528sy3pf2l5q1mjsccs2nkxalpd31vmg"; depends=[Biostrings BSgenome GenomicRanges ShortRead]; };
BEclear = derive2 { name="BEclear"; version="2.12.0"; sha256="0x43yfnmb2d782g3g52nqdfs90i3zrrlqz8qy3ybmgv5f8n92p15"; depends=[abind BiocParallel data_table dixonTest futile_logger Matrix Rcpp Rdpack]; };
BEclear = derive2 { name="BEclear"; version="2.12.1"; sha256="0r8w71zwsrva7734d1a23qbwvd7p380h0i5d2lrdgdq4h5p7kzsm"; depends=[abind BiocParallel data_table dixonTest futile_logger ids Matrix Rcpp Rdpack]; };
BGmix = derive2 { name="BGmix"; version="1.56.0"; sha256="03f6nknp3n49yvg2d9qsmds676rva70pr4wjz0md228jczgjk0vj"; depends=[KernSmooth]; };
BHC = derive2 { name="BHC"; version="1.48.0"; sha256="1kqajd16981y5yaak2imaq1i7pilgqdr3nbhggsakh787j1d9rc5"; depends=[]; };
BLMA = derive2 { name="BLMA"; version="1.20.0"; sha256="1425r1gavszzdfh7zy9gnc20507vjqimadxrm9yi1y1knk5ikas2"; depends=[Biobase graph GSA limma metafor PADOG ROntoTools]; };
@ -89,7 +89,7 @@ in with self; {
BayesKnockdown = derive2 { name="BayesKnockdown"; version="1.22.0"; sha256="122vg0lvs3fkgwcvn259rk0m1vaz19pdfvhsj5m1hd3d2h44pv65"; depends=[Biobase]; };
BayesSpace = derive2 { name="BayesSpace"; version="1.6.0"; sha256="0086fw2chymjwxwgzax6lky84kaa34900ca2p90pbjqx14b161vf"; depends=[assertthat BiocFileCache BiocSingular coda DirichletReg ggplot2 Matrix mclust purrr Rcpp RcppArmadillo RcppDist RcppProgress RCurl rhdf5 S4Vectors scales scater scran SingleCellExperiment SummarizedExperiment xgboost]; };
BeadDataPackR = derive2 { name="BeadDataPackR"; version="1.48.0"; sha256="19f0y6drsrsrwysb16xx6mafgiw55fr35pwxkjxn0ks6jc5vx1cx"; depends=[]; };
BgeeCall = derive2 { name="BgeeCall"; version="1.12.1"; sha256="1g12cms66zb45p347h3b358vjhnq76galvwqwq86xby4hnwpdzkh"; depends=[biomaRt Biostrings data_table dplyr GenomicFeatures jsonlite rhdf5 rslurm rtracklayer sjmisc tximport]; };
BgeeCall = derive2 { name="BgeeCall"; version="1.12.2"; sha256="0l6smwy55mm4clb71l4bpch3bayyyf87nq1asbrv6s6fd22mmwil"; depends=[biomaRt Biostrings data_table dplyr GenomicFeatures jsonlite rhdf5 rslurm rtracklayer sjmisc tximport]; };
BgeeDB = derive2 { name="BgeeDB"; version="2.22.3"; sha256="1f6lrazaibbz21sqvj59rq6ps9m1riw2y0kyidbn29mxf4ibwh3k"; depends=[Biobase curl data_table digest dplyr graph R_utils RCurl RSQLite tidyr topGO]; };
BiFET = derive2 { name="BiFET"; version="1.16.0"; sha256="03ypbbn8i0f4bl4m6wfdcv702jydniak56wqjb1vlrckd9aphwzq"; depends=[GenomicRanges poibin]; };
BiGGR = derive2 { name="BiGGR"; version="1.32.0"; sha256="0n57bgl6xz5b1gpw4isimq2pqxmlabn7jzhbjg2fbxcklabdvrcw"; depends=[hyperdraw hypergraph LIM limSolve rsbml stringr]; };
@ -100,29 +100,29 @@ in with self; {
BioCor = derive2 { name="BioCor"; version="1.20.0"; sha256="004mksswampwisljcdz6fswwbgdjdii3y86gjzib0gf8v4w7w4q3"; depends=[BiocParallel GSEABase Matrix]; };
BioMM = derive2 { name="BioMM"; version="1.12.0"; sha256="1sxa6safl4dp2b89bmgshdvkc1s0kxrmld3xfv2wlxkf90b3b57h"; depends=[BiocParallel CMplot e1071 ggplot2 glmnet imager lattice nsprcomp precrec ranger rms topGO vioplot xlsx]; };
BioMVCClass = derive2 { name="BioMVCClass"; version="1.64.0"; sha256="078pnyygbvbfxziqspfr1nn78w67xyb4qmiwc34czga5psblvfwz"; depends=[Biobase graph MVCClass Rgraphviz]; };
BioNERO = derive2 { name="BioNERO"; version="1.4.0"; sha256="1nyzjbl0gcwvbj2nxfwykirikf8j3rsx5ny45bqjbcb4r23k65kj"; depends=[BiocParallel ComplexHeatmap DESeq2 dynamicTreeCut GENIE3 ggnetwork ggnewscale ggplot2 ggpubr igraph intergraph matrixStats minet NetRep networkD3 RColorBrewer reshape2 SummarizedExperiment sva WGCNA]; };
BioNERO = derive2 { name="BioNERO"; version="1.4.2"; sha256="0dsznfnhidbmf52rv8l26f1ms2k9yy4q4c6cf3x8ylc79c1sjrcp"; depends=[BiocParallel ComplexHeatmap dynamicTreeCut GENIE3 ggnetwork ggnewscale ggplot2 ggrepel igraph intergraph matrixStats minet NetRep networkD3 patchwork RColorBrewer reshape2 SummarizedExperiment sva WGCNA]; };
BioNet = derive2 { name="BioNet"; version="1.56.0"; sha256="0kcw71j4nmdkn373wk21ak6h0v4gycivnfrklb72kk1qcmsy1wrm"; depends=[AnnotationDbi Biobase graph igraph RBGL]; };
BioNetStat = derive2 { name="BioNetStat"; version="1.16.1"; sha256="0zs6pymvxb95sji0rnnzaz3whj7hsvj2kl4n4gzj7w1q0prbfpb2"; depends=[BiocParallel DT ggplot2 Hmisc igraph knitr markdown pathview pheatmap plyr psych RColorBrewer RJSONIO rmarkdown shiny shinyBS whisker yaml]; };
BioPlex = derive2 { name="BioPlex"; version="1.2.3"; sha256="0cn0x6ij2a3xy61bq0qy5amp0ipj4r4shh7g0vlwbkrclj9w347r"; depends=[BiocFileCache GenomeInfoDb GenomicRanges GEOquery graph SummarizedExperiment]; };
BioQC = derive2 { name="BioQC"; version="1.24.0"; sha256="0vb2nnzqvyv25pw8qshcmijravswafg0858pkgqjgiv7wsr2mn3m"; depends=[Biobase edgeR Rcpp]; };
BioTIP = derive2 { name="BioTIP"; version="1.10.0"; sha256="1sihi5zy7mlabh3ix1wvdqz8ibfq1avl8bnxjhvxyzq40zbcklh6"; depends=[cluster GenomicRanges igraph MASS psych scran stringr]; };
Biobase = derive2 { name="Biobase"; version="2.56.0"; sha256="1mnxky78an079p60427cjvk4fzilp0xzy6b85fq274qvdcrz8jbv"; depends=[BiocGenerics]; };
BiocCheck = derive2 { name="BiocCheck"; version="1.32.0"; sha256="1k1gxzmxx26hmwdxgagv93mv4jwyygkk8703ds6nvryzhqffzkbc"; depends=[BiocManager biocViews codetools graph httr knitr stringdist]; };
BiocDockerManager = derive2 { name="BiocDockerManager"; version="1.8.0"; sha256="0kl6r8ad728a8dvqx0safj7v5gj1rxxcdiw44jkr1pd5ddv0xbi6"; depends=[dplyr httr memoise readr whisker]; };
BiocCheck = derive2 { name="BiocCheck"; version="1.32.1"; sha256="0bq4xrz1spp0bmbccxydkw6yw03by5dysz85mn152ab6xixm52lw"; depends=[BiocManager biocViews codetools graph httr knitr stringdist]; };
BiocDockerManager = derive2 { name="BiocDockerManager"; version="1.8.1"; sha256="0a4dcga18bw5mvzmsml28bf4zclz32pp9iflnbvps7pdxvhmmg9d"; depends=[dplyr httr memoise readr whisker]; };
BiocFileCache = derive2 { name="BiocFileCache"; version="2.4.0"; sha256="1bdbmlixrd8wvs25nmzdksq5hwnsxf8b6ds9qwx01h284vky5vsw"; depends=[curl DBI dbplyr dplyr filelock httr rappdirs RSQLite]; };
BiocGenerics = derive2 { name="BiocGenerics"; version="0.42.0"; sha256="0iv9bnpw2hycndwbmjsszqfwrksz6dfr6qcz78jkssc9ldsgmdhc"; depends=[]; };
BiocIO = derive2 { name="BiocIO"; version="1.6.0"; sha256="16j826w4zrmbgpmq6nyglcrjailsfv48ih1rz1qn383g7v503ydp"; depends=[BiocGenerics S4Vectors]; };
BiocNeighbors = derive2 { name="BiocNeighbors"; version="1.14.0"; sha256="1a43hzmcpxviqa9723hkafr6gm358amfpqj9d56imclkkfkdz95x"; depends=[BiocParallel Matrix Rcpp RcppHNSW S4Vectors]; };
BiocOncoTK = derive2 { name="BiocOncoTK"; version="1.16.0"; sha256="1alplszw84vqa1mvzp996f94s40scmh4qwbrqhg43hrnyvbnq7pi"; depends=[bigrquery car ComplexHeatmap curatedTCGAData DBI dplyr DT GenomicFeatures GenomicRanges ggplot2 ggpubr graph httr IRanges magrittr plyr Rgraphviz rjson S4Vectors scales shiny SummarizedExperiment]; };
BiocParallel = derive2 { name="BiocParallel"; version="1.30.3"; sha256="1rs3wmasl9mx7f399iclvm0bnvggvjj2a88zbi294r5m8wxqlc92"; depends=[BH codetools futile_logger snow]; };
BiocPkgTools = derive2 { name="BiocPkgTools"; version="1.14.0"; sha256="1v0824vmg49q9lh0igdyniryyknw6vmh462rn25kmg9hdna0w99h"; depends=[BiocFileCache BiocManager biocViews dplyr DT gh graph htmltools htmlwidgets httr igraph jsonlite magrittr RBGL readr rlang rvest stringr tibble tidyr tidyselect xml2]; };
BiocParallel = derive2 { name="BiocParallel"; version="1.30.4"; sha256="1sf87gxyh41v82pip71qkqpmind357zyngzyg1f80iz65c85xk0k"; depends=[BH codetools futile_logger snow]; };
BiocPkgTools = derive2 { name="BiocPkgTools"; version="1.14.1"; sha256="0akryshjdn227a8ir8r0lb59v060h58rhy5vjmdxax8p81ajzxkd"; depends=[BiocFileCache BiocManager biocViews dplyr DT gh graph htmltools htmlwidgets httr igraph jsonlite magrittr RBGL readr rlang rvest stringr tibble tidyr tidyselect xml2]; };
BiocSet = derive2 { name="BiocSet"; version="1.10.0"; sha256="1ghba7020inrdxlbrrgds9gjymjxjma2p89b9lgkjin89zalqglh"; depends=[AnnotationDbi BiocIO dplyr KEGGREST ontologyIndex plyr rlang S4Vectors tibble tidyr]; };
BiocSingular = derive2 { name="BiocSingular"; version="1.12.0"; sha256="1sraycnn0jahpi8kni1y8ik00ga89fvwqjmbr8388968q22mvm3x"; depends=[beachmat BiocGenerics BiocParallel DelayedArray irlba Matrix Rcpp rsvd S4Vectors ScaledMatrix]; };
BiocSklearn = derive2 { name="BiocSklearn"; version="1.18.2"; sha256="0q9qlp12ycmhnvfqwn7mvrhd8ypwnbbf715ficgx1xnagh72dpgg"; depends=[basilisk reticulate SummarizedExperiment]; };
BiocStyle = derive2 { name="BiocStyle"; version="2.24.0"; sha256="1nwiib201b9q1x19ihqjqr5jl0vnid8wfgpi8sa3y02bn722g5a5"; depends=[BiocManager bookdown knitr rmarkdown yaml]; };
BiocVersion = derive2 { name="BiocVersion"; version="3.15.2"; sha256="0rs4nyza4hqqk204d037gi013135wgfhx5asq2dsdjc9vk5nwzfn"; depends=[]; };
BiocWorkflowTools = derive2 { name="BiocWorkflowTools"; version="1.22.0"; sha256="1jj4icpkhrv9f6yx3vghkpdil1pfghf3yvc9756wmndvhs100r5l"; depends=[BiocStyle bookdown git2r httr knitr rmarkdown rstudioapi stringr usethis]; };
Biostrings = derive2 { name="Biostrings"; version="2.64.0"; sha256="1sz52hz89l9w2y2bvyis7kczslk1xnskls9l2bn1s3dhnjzdzhg8"; depends=[BiocGenerics crayon GenomeInfoDb IRanges S4Vectors XVector]; };
Biostrings = derive2 { name="Biostrings"; version="2.64.1"; sha256="1wk8nlmp6f6fsjrcb4fb48s3ay38yywwad748i6lfkkcw2pdfw33"; depends=[BiocGenerics crayon GenomeInfoDb IRanges S4Vectors XVector]; };
BitSeq = derive2 { name="BitSeq"; version="1.40.0"; sha256="0pfsdc15zfn7sizf0zqh0wjg5yr84kd9lmdifykkbxk882gjy5fh"; depends=[IRanges Rhtslib Rsamtools S4Vectors]; };
BloodGen3Module = derive2 { name="BloodGen3Module"; version="1.4.0"; sha256="1dlb6jbzrdp417sm55y0h90sx2l62h4329l67w49z321yi7iyw1j"; depends=[circlize ComplexHeatmap ExperimentHub ggplot2 gtools limma matrixStats preprocessCore randomcoloR reshape2 SummarizedExperiment testthat V8]; };
BrainSABER = derive2 { name="BrainSABER"; version="1.6.0"; sha256="1rc4ff0rglbj1kax4fdn6mmv8jzz5qyapi9mjb4nh9ffaswfj09n"; depends=[BiocFileCache biomaRt data_table lsa S4Vectors shiny SummarizedExperiment]; };
@ -164,7 +164,7 @@ in with self; {
CNVMetrics = derive2 { name="CNVMetrics"; version="1.0.0"; sha256="15ihpsr804qrywf968h0zvskcz1w8117hlh6ly5lr30afs4kfq5g"; depends=[BiocParallel GenomicRanges gridExtra IRanges magrittr pheatmap S4Vectors]; };
CNVPanelizer = derive2 { name="CNVPanelizer"; version="1.28.0"; sha256="1d7srf01ds32nbn2m26nc2bffi59dc2pc9nn5whb7kkgawgbh4a9"; depends=[BiocGenerics exomeCopy foreach GenomeInfoDb GenomicRanges ggplot2 gplots IRanges NOISeq openxlsx plyr reshape2 Rsamtools S4Vectors shiny shinyFiles shinyjs stringr testthat]; };
CNVRanger = derive2 { name="CNVRanger"; version="1.12.0"; sha256="08w1nmpvyy302024g6xcb3vi4hr8kspxqx40qs234l6k62xsri4z"; depends=[BiocGenerics BiocParallel data_table edgeR GDSArray gdsfmt GenomeInfoDb GenomicRanges IRanges lattice limma plyr qqman RaggedExperiment rappdirs reshape2 S4Vectors SNPRelate SummarizedExperiment]; };
CNVfilteR = derive2 { name="CNVfilteR"; version="1.10.0"; sha256="0k10lza9kgkdfy8p3a4iksvs7spdvn1065avji5qgc524cxnpy0f"; depends=[assertthat Biostrings CopyNumberPlots GenomeInfoDb GenomicRanges IRanges karyoploteR pracma regioneR Rsamtools SummarizedExperiment VariantAnnotation]; };
CNVfilteR = derive2 { name="CNVfilteR"; version="1.10.1"; sha256="1sbgzsbiz0jhlswsj4xa517ay5pkjncikz653k6n7jiq71d2x81i"; depends=[assertthat Biostrings CopyNumberPlots GenomeInfoDb GenomicRanges IRanges karyoploteR pracma regioneR Rsamtools SummarizedExperiment VariantAnnotation]; };
CNVgears = derive2 { name="CNVgears"; version="1.4.0"; sha256="1n93vbxsb69j302rbbgb10z576hmhm0f8hwjv36xr92chy7x6fya"; depends=[data_table ggplot2]; };
CNViz = derive2 { name="CNViz"; version="1.4.0"; sha256="062rr0im9dfi7qgkwz3a34m63vd479n9m7d1nlm22fcalym5s08r"; depends=[CopyNumberPlots dplyr DT GenomicRanges karyoploteR magrittr plotly scales shiny]; };
CNVrd2 = derive2 { name="CNVrd2"; version="1.34.0"; sha256="1mdn5dljl8cw7sax4d0p6pv7kc9li8g3r19yybyhbv7wzh6q350j"; depends=[DNAcopy ggplot2 gridExtra IRanges rjags Rsamtools VariantAnnotation]; };
@ -184,11 +184,11 @@ in with self; {
CSSQ = derive2 { name="CSSQ"; version="1.8.0"; sha256="1kgadkqjcac127xbaxr38r2icfhdz6y4q1w9xpamj4mjb6d27hq7"; depends=[GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment]; };
CTDquerier = derive2 { name="CTDquerier"; version="2.3.1"; sha256="18pxg4qhgf03sq48yp5m0x0jq5y27pbpqqlcvpn2pj09dzx7camc"; depends=[BiocFileCache ggplot2 gridExtra igraph RCurl S4Vectors stringdist stringr]; };
CancerInSilico = derive2 { name="CancerInSilico"; version="2.16.0"; sha256="1xswflpx055x3lkakbvxaw6q8y4ndrpr9ma1wyia63ghvdnaian0"; depends=[BH Rcpp]; };
CancerSubtypes = derive2 { name="CancerSubtypes"; version="1.22.0"; sha256="1qgjzbppi5nzw7jvqd0i780fccwz0mf5i6r4shzdnkvszh8q98a7"; depends=[cluster ConsensusClusterPlus impute limma NMF sigclust survival]; };
CancerSubtypes = derive2 { name="CancerSubtypes"; version="1.22.1"; sha256="0dg35d0m1lvrqbq3v406qagjdpwi2kfsfvnby3mcj9lpn7vahg0x"; depends=[cluster ConsensusClusterPlus impute limma NMF sigclust survival]; };
Cardinal = derive2 { name="Cardinal"; version="2.14.0"; sha256="07048rzp4x6593836a9iag8xjq93a94z9zvj6cbp0bj15w3p62r6"; depends=[Biobase BiocGenerics BiocParallel dplyr EBImage irlba lattice magrittr Matrix matter mclust nlme ProtGenerics S4Vectors signal sp viridisLite]; };
Category = derive2 { name="Category"; version="2.62.0"; sha256="07js03cfdd6gzbzw14iavlqxynfcqszh988v6k1a3h074wxiivqd"; depends=[annotate AnnotationDbi Biobase BiocGenerics DBI genefilter graph GSEABase Matrix RBGL]; };
CausalR = derive2 { name="CausalR"; version="1.28.0"; sha256="1ij6z12a6irbd1hd8nzd01xipmrgrpj7gqm6gp5r3hd7gfdpsway"; depends=[igraph]; };
CeTF = derive2 { name="CeTF"; version="1.8.0"; sha256="0hs5jk6x6kamajs61122vr39n7x65rx5qk3sfj2lil9r4wlmmc13"; depends=[circlize clusterProfiler ComplexHeatmap DESeq2 dplyr GenomicTools GenomicTools_fileHandler GGally ggnetwork ggplot2 ggpubr ggrepel igraph Matrix network Rcpp RcppArmadillo RCy3 S4Vectors SummarizedExperiment]; };
CeTF = derive2 { name="CeTF"; version="1.8.0"; sha256="0hs5jk6x6kamajs61122vr39n7x65rx5qk3sfj2lil9r4wlmmc13"; depends=[circlize clusterProfiler ComplexHeatmap DESeq2 dplyr GenomicTools_fileHandler GGally ggnetwork ggplot2 ggpubr ggrepel igraph Matrix network Rcpp RcppArmadillo RCy3 S4Vectors SummarizedExperiment]; };
CellBarcode = derive2 { name="CellBarcode"; version="1.2.0"; sha256="1xan4ha7aiasch2h1lk7adj2dc3prpmiily1s6pfy0chwj0bi76n"; depends=[Biostrings Ckmeans_1d_dp data_table egg ggplot2 magrittr plyr Rcpp S4Vectors ShortRead stringr]; };
CellBench = derive2 { name="CellBench"; version="1.12.0"; sha256="1sw3z3n7vdvw2352amc7biz35dmyzx7fhxdmz1jr0gdf0fhwhr1s"; depends=[BiocFileCache BiocGenerics BiocParallel dplyr glue lubridate magrittr memoise purrr rappdirs rlang SingleCellExperiment tibble tidyr tidyselect]; };
CellMapper = derive2 { name="CellMapper"; version="1.22.0"; sha256="1sz81czvam86am9mrzs3kn4qn0qz6402i7n2bdic7hcchl00qbbd"; depends=[S4Vectors]; };
@ -208,7 +208,7 @@ in with self; {
ChIPanalyser = derive2 { name="ChIPanalyser"; version="1.18.0"; sha256="0vi7qngbyss7h6zzbqv5x31x09pnwkrhxgfsbmhazz6wczmwkcix"; depends=[BiocManager Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges RcppRoll ROCR rtracklayer S4Vectors]; };
ChIPexoQual = derive2 { name="ChIPexoQual"; version="1.20.0"; sha256="1r4s8awvwwj1g33jpnzfxji23mfy0chkhi14i0ml5sh090xijpaz"; depends=[BiocParallel biovizBase broom data_table dplyr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 hexbin IRanges RColorBrewer rmarkdown Rsamtools S4Vectors scales viridis]; };
ChIPpeakAnno = derive2 { name="ChIPpeakAnno"; version="3.30.1"; sha256="0a26glldxczcfymjvd45gv5m4hympziivm6wwx4ab9wld7n43l8y"; depends=[AnnotationDbi BiocGenerics biomaRt Biostrings DBI dplyr ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 graph InteractionSet IRanges KEGGREST matrixStats multtest RBGL regioneR Rsamtools rtracklayer S4Vectors SummarizedExperiment VennDiagram]; };
ChIPseeker = derive2 { name="ChIPseeker"; version="1.32.0"; sha256="001f85nk4myk9vgs05inlj2dfby4802p1iyzkfqg332yk52gsbl7"; depends=[AnnotationDbi BiocGenerics boot dplyr enrichplot GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 gplots gtools IRanges magrittr plotrix RColorBrewer rtracklayer S4Vectors TxDb_Hsapiens_UCSC_hg19_knownGene]; };
ChIPseeker = derive2 { name="ChIPseeker"; version="1.32.1"; sha256="0l2514wvlc8q7n1zjzfrghdg372sp73z39204bkif3g6pdkcvbcf"; depends=[AnnotationDbi BiocGenerics boot dplyr enrichplot GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggVennDiagram gplots gtools IRanges magrittr plotrix RColorBrewer rtracklayer S4Vectors TxDb_Hsapiens_UCSC_hg19_knownGene]; };
ChIPseqR = derive2 { name="ChIPseqR"; version="1.50.0"; sha256="09z03ym6iqllj007558pijksjz6bqizrq8r5y1s9f12919szydsv"; depends=[BiocGenerics Biostrings fBasics GenomicRanges HilbertVis IRanges S4Vectors ShortRead timsac]; };
ChIPsim = derive2 { name="ChIPsim"; version="1.50.0"; sha256="1rjh61721pxm3r0zh1jpk65f2ll7yyhk7d92hvp4hjmq8283xwsh"; depends=[Biostrings IRanges ShortRead XVector]; };
ChemmineOB = derive2 { name="ChemmineOB"; version="1.34.0"; sha256="1cxblrisvqmrng5zvsm2x9g2rjl088s9jmrxxapgbf5zxdv1h1lb"; depends=[BH BiocGenerics Rcpp zlibbioc]; };
@ -229,7 +229,7 @@ in with self; {
Cogito = derive2 { name="Cogito"; version="1.2.0"; sha256="0sahx7cdqqnpzwb0164c84xwr246aiv4jdv9b07mw3k4s45z3h37"; depends=[AnnotationDbi BiocManager entropy GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 jsonlite magrittr rmarkdown S4Vectors TxDb_Mmusculus_UCSC_mm9_knownGene]; };
ComPrAn = derive2 { name="ComPrAn"; version="1.4.0"; sha256="0wwx025sv07h4xf3nvvqijvyca5mwdb8vsb8kvp4g0rxngc6jm30"; depends=[data_table dplyr DT forcats ggplot2 magrittr purrr RColorBrewer rio rlang scales shiny shinydashboard shinyjs stringr tibble tidyr VennDiagram]; };
ComplexHeatmap = derive2 { name="ComplexHeatmap"; version="2.12.1"; sha256="0b4p3ijhdcydfp0j58xlb5dn7d3m2x420n91rl9diqpg4r2gl0s8"; depends=[circlize clue codetools colorspace digest doParallel foreach GetoptLong GlobalOptions IRanges matrixStats png RColorBrewer]; };
CompoundDb = derive2 { name="CompoundDb"; version="1.0.1"; sha256="1f5x08adrkf71bwfa1vddzbmi0dya4i1wyjh51gjfd54cdg7g53i"; depends=[AnnotationFilter Biobase BiocGenerics ChemmineR DBI dbplyr dplyr IRanges jsonlite MetaboCoreUtils MsCoreUtils ProtGenerics RSQLite S4Vectors Spectra tibble xml2]; };
CompoundDb = derive2 { name="CompoundDb"; version="1.0.2"; sha256="1lwl4n9zm196l8dc5wdp4xl1h5dncbswqsninzzdqjrdwbpflkfz"; depends=[AnnotationFilter Biobase BiocGenerics ChemmineR DBI dbplyr dplyr IRanges jsonlite MetaboCoreUtils MsCoreUtils ProtGenerics RSQLite S4Vectors Spectra tibble xml2]; };
ConsensusClusterPlus = derive2 { name="ConsensusClusterPlus"; version="1.60.0"; sha256="1021cix4mr9qsafskw4kk1l3wdzx9pk2gcwjifz6f4zqxss9v07p"; depends=[ALL Biobase cluster]; };
CopyNumberPlots = derive2 { name="CopyNumberPlots"; version="1.12.0"; sha256="01sxmgsjrwhg8j7gckmcjwjy0yfbhw2rnww8z4hk0ig5vcb8g778"; depends=[cn_mops GenomeInfoDb GenomicRanges IRanges karyoploteR regioneR rhdf5 Rsamtools SummarizedExperiment VariantAnnotation]; };
CopywriteR = derive2 { name="CopywriteR"; version="2.28.0"; sha256="1k11kvam96hpg71hz2n9cfzizmb7d1bmq5zfvm34s7fn09is60xb"; depends=[BiocParallel chipseq CopyhelpeR data_table DNAcopy futile_logger GenomeInfoDb GenomicAlignments GenomicRanges gtools IRanges matrixStats Rsamtools S4Vectors]; };
@ -240,7 +240,7 @@ in with self; {
CyTOFpower = derive2 { name="CyTOFpower"; version="1.2.0"; sha256="0dkz6wihnlvmrbjvw1rigcm5mff9vds0izqhcr4507cmvclw6984"; depends=[CytoGLMM diffcyt dplyr DT ggplot2 magrittr rlang shiny shinyFeedback shinyjs shinyMatrix SummarizedExperiment tibble tidyr]; };
CytoDx = derive2 { name="CytoDx"; version="1.16.0"; sha256="0rk3ksgycwxagkyvl3qm0sbcrzjwlmll9mrhiwyj6n3divw2qg81"; depends=[doParallel dplyr flowCore glmnet rpart rpart_plot]; };
CytoGLMM = derive2 { name="CytoGLMM"; version="1.4.0"; sha256="04k9gz1rbz2rkkdcn1g1ya6dcjslk4h8427dmy9mkz58nvyjg1ya"; depends=[BiocParallel caret cowplot doParallel dplyr factoextra flexmix ggplot2 ggrepel logging magrittr MASS Matrix mbest pheatmap RColorBrewer rlang speedglm stringr strucchange tibble tidyr]; };
CytoML = derive2 { name="CytoML"; version="2.8.0"; sha256="0vp7advfh1d8596hjpzayasjhga4mx0l104sgz2asscbrjm4v7rr"; depends=[base64enc BH Biobase corpcor cytolib data_table dplyr flowCore flowWorkspace ggcyto graph jsonlite lattice openCyto plyr RBGL Rcpp RcppArmadillo RcppParallel Rgraphviz Rhdf5lib RProtoBufLib RUnit tibble XML xml2 yaml]; };
CytoML = derive2 { name="CytoML"; version="2.8.1"; sha256="01yzdljpyq92bv318b5qs29f190226zwbqjnckvxmbb0k8m7s5hw"; depends=[base64enc BH Biobase corpcor cytolib data_table dplyr flowCore flowWorkspace ggcyto graph jsonlite lattice openCyto plyr RBGL Rcpp RcppArmadillo RcppParallel Rgraphviz Rhdf5lib RProtoBufLib RUnit tibble XML xml2 yaml]; };
CytoTree = derive2 { name="CytoTree"; version="1.6.0"; sha256="1dsdhwjkd3ngnw50fs6vz048afk47r95vhi0wqj8sip11nhndkd8"; depends=[Biobase BiocNeighbors cluster destiny flowCore FlowSOM flowUtils ggplot2 gmodels igraph limma Matrix matrixStats mclust pheatmap prettydoc RANN Rcpp Rtsne scatterpie scatterplot3d stringr sva umap]; };
DAMEfinder = derive2 { name="DAMEfinder"; version="1.8.0"; sha256="123ra94bij0m45j2fzqr7fjipj4ld9kgk0kir1zfdbbd5h8h4mdf"; depends=[BiocGenerics Biostrings bumphunter cowplot GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges limma plyr readr reshape2 Rsamtools S4Vectors stringr SummarizedExperiment VariantAnnotation]; };
DAPAR = derive2 { name="DAPAR"; version="1.28.5"; sha256="1z7p6h1j76k5dhqd1fs1swy2iyjh79h50nlagkdbxfpcc9vcfa3z"; depends=[Biobase DAPARdata foreach highcharter MSnbase]; };
@ -259,7 +259,7 @@ in with self; {
DEqMS = derive2 { name="DEqMS"; version="1.14.0"; sha256="04b35mhsz87dfj53clgxrb7igkyv41hqmblb4429l68l55wsxhp6"; depends=[ggplot2 limma matrixStats]; };
DEsingle = derive2 { name="DEsingle"; version="1.16.0"; sha256="0gw2zbq910jnn1pdpc5sgvvfmvg06hximz1qnvvmv9pb8g68r0zk"; depends=[bbmle BiocParallel gamlss MASS Matrix maxLik pscl VGAM]; };
DEsubs = derive2 { name="DEsubs"; version="1.22.0"; sha256="06vjby0wpaczaw9bj2g2inylfnw92acrqgpadr70q458v1kpshs5"; depends=[circlize DESeq2 EBSeq edgeR ggplot2 graph igraph jsonlite limma locfit Matrix NBPSeq pheatmap RBGL]; };
DExMA = derive2 { name="DExMA"; version="1.4.3"; sha256="1wqxwb1f11glz823zv8vkbx69cgrvp2912l4w1x94zpfdaxmj02y"; depends=[Biobase bnstruct DExMAdata GEOquery impute limma pheatmap plyr RColorBrewer scales snpStats sva swamp]; };
DExMA = derive2 { name="DExMA"; version="1.4.5"; sha256="08pxd01x829v6a20y2lvdsbmhq2as1c5pnsyzcjbpmb3d73aad70"; depends=[Biobase bnstruct DExMAdata GEOquery impute limma pheatmap plyr RColorBrewer scales snpStats sva swamp]; };
DFP = derive2 { name="DFP"; version="1.54.0"; sha256="19xjvfymjclnd0ck7n7al3f54s7f8z3aszi35i0cavr7xj3cgrj5"; depends=[Biobase]; };
DIAlignR = derive2 { name="DIAlignR"; version="2.4.0"; sha256="0mh27n8vsnsv10mq8jcslspyq86sfvwwgn8iib5w3f7qb47w5d7r"; depends=[ape bit64 data_table DBI dplyr ggplot2 magrittr mzR phangorn pracma Rcpp RcppEigen reticulate rlang RMSNumpress RSQLite signal tidyr zoo]; };
DMCFB = derive2 { name="DMCFB"; version="1.10.0"; sha256="0wka5s820k0vfw87dfycnkbr3c41wm4rmylwnkm8c0azjda8n126"; depends=[arm benchmarkme BiocParallel data_table fastDummies GenomicRanges IRanges MASS matrixStats rtracklayer S4Vectors speedglm SummarizedExperiment tibble]; };
@ -272,7 +272,7 @@ in with self; {
DNABarcodes = derive2 { name="DNABarcodes"; version="1.26.0"; sha256="0n2qlvpcjhrxr3br27gz9vhwcpf7sn6g4xdjazvvi3gqcgk90xc6"; depends=[BH Matrix Rcpp]; };
DNAcopy = derive2 { name="DNAcopy"; version="1.70.0"; sha256="10bh4p8nbl84rfngsm3bi9w542m159kff95f8c2hvjcxv5yw7iwc"; depends=[]; };
DNAshapeR = derive2 { name="DNAshapeR"; version="1.24.0"; sha256="0qayysdkifa7dpin6a64zqp0mfvfxj2z0g1vcp757jci2w903b6g"; depends=[Biostrings fields GenomicRanges Rcpp]; };
DOSE = derive2 { name="DOSE"; version="3.22.0"; sha256="11lg4ql0bi54p2wg3z1dw9rwqai37khgcqbs4cb7zf67ml8jadwp"; depends=[AnnotationDbi BiocParallel DO_db fgsea ggplot2 GOSemSim qvalue reshape2]; };
DOSE = derive2 { name="DOSE"; version="3.22.1"; sha256="1mch26kddrhhzgi4bssnyy7bvdhprrncmvxl6zn1cq7g07p5765i"; depends=[AnnotationDbi BiocParallel DO_db fgsea ggplot2 GOSemSim qvalue reshape2]; };
DRIMSeq = derive2 { name="DRIMSeq"; version="1.24.0"; sha256="1dph483ij43ayw0z5dbnp6gwp53ka7k5si1hp3miac7z8dqzv94l"; depends=[BiocGenerics BiocParallel edgeR GenomicRanges ggplot2 IRanges limma MASS reshape2 S4Vectors]; };
DSS = derive2 { name="DSS"; version="2.44.0"; sha256="12l5b3h9jd2ld6g4vncxy70a8vfi37byl5k85ix61ir0rbcqf6jn"; depends=[Biobase BiocParallel bsseq matrixStats]; };
DTA = derive2 { name="DTA"; version="2.42.0"; sha256="13x7z2zgxcnz8lpgdnsm5rp6j8yj6fkm03amymlnzihrqjdjpzw4"; depends=[LSD scatterplot3d]; };
@ -285,12 +285,12 @@ in with self; {
DegNorm = derive2 { name="DegNorm"; version="1.6.1"; sha256="0332mw9b0qvrnsvshjpcznglz406dqk44l7mjcrb1995ddld3221"; depends=[data_table doParallel foreach GenomicAlignments GenomicFeatures GenomicRanges ggplot2 heatmaply IRanges plotly plyr Rcpp RcppArmadillo Rsamtools S4Vectors viridis]; };
DelayedArray = derive2 { name="DelayedArray"; version="0.22.0"; sha256="11id63qza9dxl1364gllqafxmx25a0q22jv5q8h709bgc3f0grqy"; depends=[BiocGenerics IRanges Matrix MatrixGenerics S4Vectors]; };
DelayedDataFrame = derive2 { name="DelayedDataFrame"; version="1.12.0"; sha256="1nja5h0vxl2i34dhag7gyjdhyaisqagn11004i65pwbx5fmwq58d"; depends=[BiocGenerics DelayedArray S4Vectors]; };
DelayedMatrixStats = derive2 { name="DelayedMatrixStats"; version="1.18.0"; sha256="1qlwv69c0r2w3zkmsr8r7w6sr3hf1ha0sfcrsjx4ks8f0ww7aqsv"; depends=[DelayedArray IRanges Matrix MatrixGenerics matrixStats S4Vectors sparseMatrixStats]; };
DelayedMatrixStats = derive2 { name="DelayedMatrixStats"; version="1.18.2"; sha256="0zc7560d5lizkfai7yf4is246mjw8n5j2wrrikrrv3fabby44h7x"; depends=[DelayedArray IRanges Matrix MatrixGenerics matrixStats S4Vectors sparseMatrixStats]; };
DelayedRandomArray = derive2 { name="DelayedRandomArray"; version="1.4.0"; sha256="13g4dfsv4d5fdp8flxy7p7sc5l9jiby97zixpkda8q1smg2ggr93"; depends=[BH DelayedArray dqrng Rcpp]; };
DelayedTensor = derive2 { name="DelayedTensor"; version="1.2.0"; sha256="1paciar5cm61gx894awwxb7gzqnyiwmsfinfijff2qx210l0yz51"; depends=[BiocSingular DelayedArray DelayedRandomArray einsum HDF5Array irlba Matrix rTensor]; };
DepInfeR = derive2 { name="DepInfeR"; version="1.0.0"; sha256="03qvgk20dgxa95gkv2ya2dibiwshda3ssl5f95x5nn06lfgzk6m0"; depends=[BiocParallel glmnet matrixStats]; };
DepecheR = derive2 { name="DepecheR"; version="1.12.0"; sha256="0rixczdds5gpac50wap6s68kmpdj4208l38gcihkrysz5frbvqjp"; depends=[beanplot doSNOW dplyr FNN foreach ggplot2 gmodels gplots MASS matrixStats mixOmics moments Rcpp RcppEigen reshape2 robustbase viridis]; };
DiffBind = derive2 { name="DiffBind"; version="3.6.3"; sha256="0v435h9gd3bvld5573m6173lndnhfxc20x3s3drcgrxgsjdij12r"; depends=[amap apeglm ashr BiocParallel DESeq2 dplyr GenomicAlignments GenomicRanges ggplot2 ggrepel gplots GreyListChIP IRanges lattice limma locfit RColorBrewer Rcpp Rhtslib Rsamtools S4Vectors SummarizedExperiment systemPipeR]; };
DiffBind = derive2 { name="DiffBind"; version="3.6.5"; sha256="1c82szcbbai9yldzby90p0q7qi4n9g1wd2wl7h4imyqyj2n4yagx"; depends=[amap apeglm ashr BiocParallel DESeq2 dplyr GenomicAlignments GenomicRanges ggplot2 ggrepel gplots GreyListChIP IRanges lattice limma locfit RColorBrewer Rcpp Rhtslib Rsamtools S4Vectors SummarizedExperiment systemPipeR]; };
DiffLogo = derive2 { name="DiffLogo"; version="2.20.0"; sha256="08dr3ah0gakdkv133ipw1ib2w1p84hild0s4y9kp8z51qg0zk7mn"; depends=[cba]; };
DifferentialRegulation = derive2 { name="DifferentialRegulation"; version="1.0.7"; sha256="1q33zyhqc0dxfip5pcn4m5rvr4nivzic4wshdh8sk1hwpviwd90r"; depends=[BANDITS data_table doParallel doRNG foreach ggplot2 MASS Matrix Rcpp RcppArmadillo SingleCellExperiment SummarizedExperiment]; };
Dino = derive2 { name="Dino"; version="1.2.0"; sha256="1rcll2y034v1n183v819brazr6crr73klp8qmkq51p7jpsvx1450"; depends=[BiocParallel BiocSingular Matrix matrixStats S4Vectors scran Seurat SingleCellExperiment SummarizedExperiment]; };
@ -344,7 +344,7 @@ in with self; {
FRGEpistasis = derive2 { name="FRGEpistasis"; version="1.32.0"; sha256="14wskfc350zrna1ng8wkyb91y3h01jhk93ajw3if04nkghav193a"; depends=[fda MASS]; };
FScanR = derive2 { name="FScanR"; version="1.6.0"; sha256="0117fgbmig6zaik5j7axcw33rx2pjwhgla751sr4zi990a9p6igb"; depends=[]; };
FamAgg = derive2 { name="FamAgg"; version="1.24.0"; sha256="0pzqy8rx7hyz93v8gh4qf861axwidxwiv3w9i8j7g796mdmy66my"; depends=[BiocGenerics gap igraph kinship2 Matrix survey]; };
FastqCleaner = derive2 { name="FastqCleaner"; version="1.13.0"; sha256="140g8l2z2yvspz4cs01wbxd1k5bk36fmvdgbqx06y0qxyfprglzv"; depends=[Biostrings DT htmltools IRanges Rcpp S4Vectors shiny shinyBS ShortRead]; };
FastqCleaner = derive2 { name="FastqCleaner"; version="1.14.2"; sha256="0vna7kmfgn6m0irrp7aqgvswvfmxcd8bjpl6l35mwqq2rm8h25gf"; depends=[Biostrings DT htmltools IRanges Rcpp S4Vectors shiny shinyBS ShortRead]; };
FilterFFPE = derive2 { name="FilterFFPE"; version="1.6.0"; sha256="0x76a382lw0j06h8hlq2vrawnydjngn9w0dhymyrx94jkmsl15wl"; depends=[doParallel foreach GenomicRanges IRanges Rsamtools S4Vectors]; };
FindIT2 = derive2 { name="FindIT2"; version="1.2.3"; sha256="0fj6csbxx6dfcd8fhsiff04cagb2yyg79h8wklqqm0dr7agbfaj9"; depends=[BiocGenerics BiocParallel dplyr GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggrepel glmnet IRanges MultiAssayExperiment patchwork progress purrr qvalue rlang rtracklayer S4Vectors stringr SummarizedExperiment tibble tidyr withr]; };
FitHiC = derive2 { name="FitHiC"; version="1.22.0"; sha256="0iv14yx3g7shzl8qrjknyxbmiylj51sbd1wzr1ff9lc5shgl55kq"; depends=[data_table fdrtool Rcpp]; };
@ -356,11 +356,11 @@ in with self; {
GAPGOM = derive2 { name="GAPGOM"; version="1.11.0"; sha256="0sl97w5zx4zdrdbcwayqyvgxspaxpbils3mpsrim0zlspjrjcy6z"; depends=[AnnotationDbi Biobase BiocFileCache data_table dplyr fastmatch GEOquery GO_db GOSemSim graph igraph magrittr Matrix matrixStats org_Hs_eg_db org_Mm_eg_db plyr RBGL]; };
GARS = derive2 { name="GARS"; version="1.16.0"; sha256="1v3ps3v2zsr4p2q5wvxa1wm9mnxkhc2d9sgsz841ld0rbqzw7fjl"; depends=[cluster DaMiRseq ggplot2 MLSeq SummarizedExperiment]; };
GAprediction = derive2 { name="GAprediction"; version="1.22.0"; sha256="08xhky97f5x6kakdavzpqdxp053nrjfjr51r4gkfvcv4xj4dypk0"; depends=[glmnet Matrix]; };
GBScleanR = derive2 { name="GBScleanR"; version="1.0.0"; sha256="1vgjhms2gqsa9l2is6vy4qpp4hzrcda0hnimixl1i2wa4v2anz0w"; depends=[Biobase expm gdsfmt ggplot2 GWASTools Rcpp RcppParallel SeqArray tidyr]; };
GBScleanR = derive2 { name="GBScleanR"; version="1.0.6"; sha256="01wk8d1kbs7x26i2anxh8pjsvc9arr6b64qy4zzr32kwmlj0yvg7"; depends=[expm gdsfmt ggplot2 Rcpp RcppParallel SeqArray tidyr]; };
GCSConnection = derive2 { name="GCSConnection"; version="1.7.0"; sha256="1psmw3825whyzvbzqpqksgcl09b6kfyb8k5vny6ljkjbac1jzvnf"; depends=[googleAuthR googleCloudStorageR httr jsonlite Rcpp]; };
GCSFilesystem = derive2 { name="GCSFilesystem"; version="1.6.0"; sha256="0qk8xyg06f71y4r1q1zpcj89irh9i6cd9z6nqlx635x8if84sh6d"; depends=[]; };
GCSscore = derive2 { name="GCSscore"; version="1.10.0"; sha256="0cdhv2awcyg95cjwq088r9rsbmdi3vqnlnh0c74h7k2gjldl9r24"; depends=[affxparser Biobase BiocManager data_table devtools dplR RSQLite stringr]; };
GDCRNATools = derive2 { name="GDCRNATools"; version="1.16.2"; sha256="1zr1c32x8fj24mn240yx5v3q2p63j018hq90q06bh85y6jzq7zaw"; depends=[BiocParallel biomaRt clusterProfiler DESeq2 DOSE DT edgeR GenomicDataCommons ggplot2 gplots jsonlite limma org_Hs_eg_db pathview rjson shiny survival survminer XML]; };
GDCRNATools = derive2 { name="GDCRNATools"; version="1.16.6"; sha256="0zkw0g711g1w0dp75qwa3cfk3d8dfsp6v4f122j88xc1cjf5rarv"; depends=[BiocParallel biomaRt clusterProfiler DESeq2 DOSE DT edgeR GenomicDataCommons ggplot2 gplots jsonlite limma org_Hs_eg_db pathview rjson shiny survival survminer XML]; };
GDSArray = derive2 { name="GDSArray"; version="1.16.0"; sha256="1j6a0xlrx4cjqsfcm1k1vapddi5v2q5h05b617i839l9cp0ggd1s"; depends=[BiocGenerics DelayedArray gdsfmt S4Vectors SeqArray SNPRelate]; };
GEM = derive2 { name="GEM"; version="1.22.0"; sha256="0vxpncvnqhgggy0is4lvgf29lgh307jkgz4zjjspdq9ds6y40l1i"; depends=[ggplot2]; };
GENESIS = derive2 { name="GENESIS"; version="2.26.0"; sha256="1qn3x6j9lvyx130sx9wg7bxvacwbwp87x75inpxx9llc00p7sl9c"; depends=[Biobase BiocGenerics BiocParallel data_table gdsfmt GenomicRanges GWASTools igraph IRanges Matrix reshape2 S4Vectors SeqArray SeqVarTools SNPRelate]; };
@ -387,7 +387,7 @@ in with self; {
GOsummaries = derive2 { name="GOsummaries"; version="2.32.0"; sha256="0wkal7hsfz9msf8j7975vkqqzv5x681c891zj1b4mfk6dvn5xffa"; depends=[ggplot2 gProfileR gtable limma plyr Rcpp reshape2]; };
GPA = derive2 { name="GPA"; version="1.8.0"; sha256="0z4qh88x7gvm02186mnl6bkhg1f5swqci30gzj27lj1kx700jsf3"; depends=[DT ggplot2 ggrepel plyr Rcpp shiny shinyBS vegan]; };
GRENITS = derive2 { name="GRENITS"; version="1.48.0"; sha256="09c6d8hcawc6ky0pjhvc5yvd7fj1a1bl8n4hcw72nyfgbf20hygi"; depends=[ggplot2 Rcpp RcppArmadillo reshape2]; };
GRaNIE = derive2 { name="GRaNIE"; version="1.0.5"; sha256="086m5blc28w6ks63gvv1ix3qdbdbgnslniaik315jzsq735v6mc4"; depends=[BiocFileCache BiocManager BiocParallel Biostrings checkmate circlize colorspace ComplexHeatmap csaw data_table DESeq2 dplyr forcats futile_logger GenomeInfoDb GenomicRanges ggplot2 gridExtra igraph IRanges limma magrittr Matrix matrixStats patchwork progress purrr RColorBrewer readr reshape2 rlang robust S4Vectors scales stringr SummarizedExperiment tibble tidyr tidyselect tidyverse topGO viridis]; };
GRaNIE = derive2 { name="GRaNIE"; version="1.0.7"; sha256="1lvc78fbhbp4i6ix4bdmmlnzwma2n5w0v3099p1nghzwcl0jx7z2"; depends=[BiocFileCache BiocManager BiocParallel Biostrings checkmate circlize colorspace ComplexHeatmap csaw data_table DESeq2 dplyr forcats futile_logger GenomeInfoDb GenomicRanges ggplot2 gridExtra igraph IRanges limma magrittr Matrix matrixStats patchwork progress purrr RColorBrewer readr reshape2 rlang robust S4Vectors scales stringr SummarizedExperiment tibble tidyr tidyselect tidyverse topGO viridis]; };
GRmetrics = derive2 { name="GRmetrics"; version="1.22.0"; sha256="1qz2bj8wnp14mw5zm2207xk3zj98s2gk16fvhdzpy21y07irrx3j"; depends=[drc ggplot2 plotly S4Vectors SummarizedExperiment]; };
GRridge = derive2 { name="GRridge"; version="1.20.0"; sha256="16bra2nz4i4f40x2gfcky7ggz3alpvhwcbilv48r7nv4p6b31j8i"; depends=[glmnet graph Iso mvtnorm penalized survival]; };
GSALightning = derive2 { name="GSALightning"; version="1.24.0"; sha256="0p2k8k05283h7ls1aj5457ycqq46mxjjx7pmjijmj0kfzcmnqyv2"; depends=[data_table Matrix]; };
@ -399,11 +399,11 @@ in with self; {
GSEAmining = derive2 { name="GSEAmining"; version="1.6.0"; sha256="19r923086qr400f4p2kfn4ii09q2k2pqg9k4r035b9afqgd0x91a"; depends=[dendextend dplyr ggplot2 ggwordcloud gridExtra rlang stringr tibble tidytext]; };
GSRI = derive2 { name="GSRI"; version="2.44.0"; sha256="0z79l6m3z0ib9iy24hpiscmxasrx33y6swrdg0k1z48sdhy0gsf1"; depends=[Biobase fdrtool genefilter GSEABase les]; };
GSReg = derive2 { name="GSReg"; version="1.30.0"; sha256="0g0j4bh9h8qvki84gcp2s6yn2hhc38219jzihmf9jpjl66k74gs0"; depends=[AnnotationDbi GenomicFeatures Homo_sapiens org_Hs_eg_db]; };
GSVA = derive2 { name="GSVA"; version="1.44.2"; sha256="0q0216hq3zfqxsirfllvs1p7zlpm8j7gg9mvlgyqz8yjfz6p02sq"; depends=[Biobase BiocParallel BiocSingular DelayedArray DelayedMatrixStats GSEABase HDF5Array IRanges Matrix S4Vectors SingleCellExperiment sparseMatrixStats SummarizedExperiment]; };
GSVA = derive2 { name="GSVA"; version="1.44.5"; sha256="09szzrgyjcx33yh2327s8w4xaarvavajsb19jfdgdxc1bs5yhzl9"; depends=[Biobase BiocParallel BiocSingular DelayedArray DelayedMatrixStats GSEABase HDF5Array IRanges Matrix S4Vectors SingleCellExperiment sparseMatrixStats SummarizedExperiment]; };
GSgalgoR = derive2 { name="GSgalgoR"; version="1.6.0"; sha256="1wi6ww5rycc2zxhnm83amzrh7ffripmiqklcmxisv6jqgr64adp3"; depends=[cluster doParallel foreach matchingR nsga2R proxy survival]; };
GUIDEseq = derive2 { name="GUIDEseq"; version="1.26.0"; sha256="1ar20zr3mjfqs7fvd323mdrxylvsjazn6si4d8ilgbpq4xhdv58a"; depends=[BiocGenerics BiocParallel Biostrings BSgenome ChIPpeakAnno CRISPRseek data_table dplyr GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges hash IRanges limma matrixStats Rsamtools S4Vectors]; };
GWAS_BAYES = derive2 { name="GWAS.BAYES"; version="1.6.0"; sha256="01bj6gh95p95imyvvzjylnw42rcrzw3x8z0q8x2cx42zqf45dqc1"; depends=[caret doParallel GA ggplot2 Matrix memoise Rcpp RcppEigen reshape2]; };
GWASTools = derive2 { name="GWASTools"; version="1.42.0"; sha256="0n0gcapaj5y72a03624zhrd11h3b5q65yr1lp2ljpwp2xhl8rh4z"; depends=[Biobase data_table DBI DNAcopy gdsfmt GWASExactHW lmtest logistf quantsmooth RSQLite sandwich survival]; };
GWASTools = derive2 { name="GWASTools"; version="1.42.1"; sha256="0a9k2dsaxp5szqm71qd3l5jq0aqnbgp7w5n8d7qiywlkfw4l8lwm"; depends=[Biobase data_table DBI DNAcopy gdsfmt GWASExactHW lmtest logistf quantsmooth RSQLite sandwich survival]; };
GWENA = derive2 { name="GWENA"; version="1.6.0"; sha256="10cs5csg6dwqajsk461flq55siz6jfd90w5cyqdhyq4mcbv6zp1x"; depends=[cluster dplyr dynamicTreeCut ggplot2 gprofiler2 igraph magrittr matrixStats NetRep purrr RColorBrewer rlist stringr SummarizedExperiment tibble tidyr WGCNA]; };
GateFinder = derive2 { name="GateFinder"; version="1.16.0"; sha256="1wrx3rp1r4fjq8c56dk40izawzpsrmkrrdvivi67arx5pdjhjz30"; depends=[diptest flowCore flowFP mvoutlier splancs]; };
GenProSeq = derive2 { name="GenProSeq"; version="1.0.0"; sha256="0vmsjpdkfvq28bihmf47a2ihlfxzadjr5vm6clh25016rz0086pp"; depends=[CatEncoders DeepPINCS keras mclust reticulate tensorflow ttgsea word2vec]; };
@ -421,11 +421,11 @@ in with self; {
GeneStructureTools = derive2 { name="GeneStructureTools"; version="1.16.0"; sha256="1ciflsp0i96ljh4xz1b1bbf6za4hd2swnykmp0wvgayxxcwxdwjv"; depends=[Biostrings BSgenome_Mmusculus_UCSC_mm10 data_table GenomicRanges Gviz IRanges plyr rtracklayer S4Vectors stringdist stringr]; };
GeneTonic = derive2 { name="GeneTonic"; version="2.0.2"; sha256="08mq482px35a1b3cz64h8hlw2s4cabyddb1ly5hzbbgcqq9h18p3"; depends=[AnnotationDbi backbone bs4Dash circlize colorspace colourpicker ComplexHeatmap ComplexUpset dendextend DESeq2 dplyr DT dynamicTreeCut expm ggforce ggplot2 ggrepel GO_db igraph matrixStats plotly RColorBrewer rintrojs rlang rmarkdown S4Vectors scales shiny shinyAce shinycssloaders shinyWidgets SummarizedExperiment tidyr tippy viridis visNetwork]; };
GeneticsPed = derive2 { name="GeneticsPed"; version="1.58.0"; sha256="0vbkbjyb9r5gsbkn3c28y3bicmn82r1bfsah6ww6pf539xzipbzj"; depends=[gdata genetics MASS]; };
GenomeInfoDb = derive2 { name="GenomeInfoDb"; version="1.32.3"; sha256="17nwcq2ivj3bdibdywfyjq4n6z0djispbh9ahqa55sp31ksq41xh"; depends=[BiocGenerics GenomeInfoDbData IRanges RCurl S4Vectors]; };
GenomeInfoDb = derive2 { name="GenomeInfoDb"; version="1.32.4"; sha256="0z2bqr0zrl3r2kcqs72ny8p1psf8w1sgbr7qjjknxdv1qp8m2j7v"; depends=[BiocGenerics GenomeInfoDbData IRanges RCurl S4Vectors]; };
GenomicAlignments = derive2 { name="GenomicAlignments"; version="1.32.1"; sha256="09pg7822camyav5zvlpv360sj5gz8q1bhk528qa2da2qsz74a3cz"; depends=[BiocGenerics BiocParallel Biostrings GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors SummarizedExperiment]; };
GenomicDataCommons = derive2 { name="GenomicDataCommons"; version="1.20.2"; sha256="0igmcvb2sj4fzpm5f4wfj9ak3pijbiykzrxf2f10xg30wfr6v93z"; depends=[dplyr GenomicRanges httr IRanges jsonlite magrittr rappdirs readr rlang tibble xml2]; };
GenomicDataCommons = derive2 { name="GenomicDataCommons"; version="1.20.3"; sha256="09qjy79wvbahwyb2avvagp3pp4d2v3qr2balsjvg75g8j5fsy50f"; depends=[dplyr GenomicRanges httr IRanges jsonlite magrittr rappdirs readr rlang tibble xml2]; };
GenomicDistributions = derive2 { name="GenomicDistributions"; version="1.4.6"; sha256="05q36bbcg2acr93bzcmd6vfxl442ig7rk0d0kmzhp33fbrrz8k3a"; depends=[Biostrings broom data_table dplyr GenomeInfoDb GenomicRanges ggplot2 IRanges plyr reshape2 scales]; };
GenomicFeatures = derive2 { name="GenomicFeatures"; version="1.48.3"; sha256="0f14p1ma2y8l60p9sxmh5j0axws9by1cznczb2jxipphpb4slpl1"; depends=[AnnotationDbi Biobase BiocGenerics BiocIO biomaRt Biostrings DBI GenomeInfoDb GenomicRanges IRanges RCurl RSQLite rtracklayer S4Vectors XVector]; };
GenomicFeatures = derive2 { name="GenomicFeatures"; version="1.48.4"; sha256="15kn5lmdqp7rsh2zlixj7ashsqnv50bs36hapw36qbaz9vgvim4v"; depends=[AnnotationDbi Biobase BiocGenerics BiocIO biomaRt Biostrings DBI GenomeInfoDb GenomicRanges IRanges RCurl RSQLite rtracklayer S4Vectors XVector]; };
GenomicFiles = derive2 { name="GenomicFiles"; version="1.32.1"; sha256="06ycfna26klx27vvsnlpgv46bymfrc8z0zkpag7nm4m23153ivkz"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicRanges IRanges MatrixGenerics Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation]; };
GenomicInteractionNodes = derive2 { name="GenomicInteractionNodes"; version="1.0.0"; sha256="064mvbgrhf098pyqabqdi70yskri5pa3fd1yylzwmabx3g7wvsw8"; depends=[AnnotationDbi GenomeInfoDb GenomicFeatures GenomicRanges GO_db graph IRanges RBGL S4Vectors]; };
GenomicInteractions = derive2 { name="GenomicInteractions"; version="1.30.0"; sha256="0aph1hja5vfprxs3jl4zd1inhvih6m3v1p3jkm6w7xpj3jzvmgbx"; depends=[Biobase BiocGenerics data_table dplyr GenomeInfoDb GenomicRanges ggplot2 gridExtra Gviz igraph InteractionSet IRanges Rsamtools rtracklayer S4Vectors stringr]; };
@ -485,9 +485,9 @@ in with self; {
INPower = derive2 { name="INPower"; version="1.32.0"; sha256="0zszizdpb4b3lwp9561a1rq415vxns3w5dky2g1121p7b0pn3wdq"; depends=[mvtnorm]; };
INSPEcT = derive2 { name="INSPEcT"; version="1.26.0"; sha256="0jx887vhxwd8zlqajr9czvn9nx88ryyxlnl58hxrlajjpcjkz9ax"; depends=[Biobase BiocGenerics BiocParallel DESeq2 deSolve gdata GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges KernSmooth plgem pROC rootSolve Rsamtools rtracklayer S4Vectors shiny SummarizedExperiment TxDb_Mmusculus_UCSC_mm9_knownGene]; };
IONiseR = derive2 { name="IONiseR"; version="2.20.0"; sha256="0cgx1dcfh617l9vr4r3ky8w7f0snl0vpavfd9n1h5n68p0p42dwi"; depends=[BiocGenerics BiocParallel Biostrings bit64 dplyr ggplot2 magrittr rhdf5 ShortRead stringr tibble tidyr XVector]; };
IPO = derive2 { name="IPO"; version="1.21.0"; sha256="1kf84n6af1aqq2lcm1yffc4kkdnjyc0lw9yjqvifhl03ba8kbmp0"; depends=[BiocParallel CAMERA rsm xcms]; };
IPO = derive2 { name="IPO"; version="1.22.1"; sha256="00wzavqw8qldwqsj46z97wi32yxacwf64xjywr2ck6kjicz4d245"; depends=[BiocParallel CAMERA rsm xcms]; };
IRISFGM = derive2 { name="IRISFGM"; version="1.4.0"; sha256="13c9xk3gmqg0chzhmd6kj9fwmc11mc2j3wqin5202dkkn7x9b170"; depends=[AdaptGauss AnnotationDbi anocva clusterProfiler colorspace DEsingle DrImpute ggplot2 ggpubr ggraph igraph knitr Matrix MCL mixtools org_Hs_eg_db org_Mm_eg_db pheatmap Polychrome RColorBrewer Rcpp scater scran Seurat SingleCellExperiment]; };
IRanges = derive2 { name="IRanges"; version="2.30.0"; sha256="0hfx5n0b4pqrrc1w2dik596803ly8ffnxfs768iy5l5kr8wwyc8k"; depends=[BiocGenerics S4Vectors]; };
IRanges = derive2 { name="IRanges"; version="2.30.1"; sha256="1r01c9lczkchgd9hbxxd6wrd5avhy52mfqjck7l9avjq1jimvzv3"; depends=[BiocGenerics S4Vectors]; };
ISAnalytics = derive2 { name="ISAnalytics"; version="1.6.2"; sha256="10arh47m7pg81rry1hb4pdfd0b5rdcj81lz9i32xlxanh3sp8kjv"; depends=[BiocParallel bslib data_table datamods dplyr forcats fs ggplot2 ggrepel glue lifecycle lubridate magrittr psych purrr Rcapture readr readxl rlang shiny shinyWidgets stringr tibble tidyr]; };
ISoLDE = derive2 { name="ISoLDE"; version="1.24.0"; sha256="13cgy5hr4y6l3fkq2fx43wm4aypn5k3wp159kdqgp00lywd7pzxp"; depends=[]; };
ITALICS = derive2 { name="ITALICS"; version="2.56.0"; sha256="150kfwhf47ipr2aql5cxli2hhs3cmgcya9aag0il41xy0wgc96k5"; depends=[affxparser DBI GLAD ITALICSData oligo oligoClasses pd_mapping50k_xba240]; };
@ -533,7 +533,7 @@ in with self; {
Linnorm = derive2 { name="Linnorm"; version="2.20.0"; sha256="1002lllgns5klv3q2wsikkbypa2bafpka7a8mri0y5bfxncfr2zb"; depends=[amap apcluster ellipse fastcluster fpc ggdendro ggplot2 gmodels igraph limma MASS mclust Rcpp RcppArmadillo Rtsne statmod vegan zoo]; };
LiquidAssociation = derive2 { name="LiquidAssociation"; version="1.50.0"; sha256="123qlv58y4vhsjnqgxs0w8zylnvib0hjb3jlg5cl74xzdb2gfl0f"; depends=[Biobase geepack org_Sc_sgd_db yeastCC]; };
LoomExperiment = derive2 { name="LoomExperiment"; version="1.14.0"; sha256="1rnnvnbpxlvy85fdyz9zxsn4r6j4x8fydblz00jjl3mk9943538j"; depends=[BiocIO DelayedArray GenomicRanges HDF5Array Matrix rhdf5 S4Vectors SingleCellExperiment stringr SummarizedExperiment]; };
LowMACA = derive2 { name="LowMACA"; version="1.25.0"; sha256="040f9gngial6akqghv9fcv8x11f0xm3qmnfki5xc7ryl0j7a3ahm"; depends=[BiocParallel Biostrings data_table gridBase httr LowMACAAnnotation motifStack RColorBrewer reshape2 stringr]; };
LowMACA = derive2 { name="LowMACA"; version="1.26.2"; sha256="0inx7lgywi6687i5kdifmfx8b4q3gbbiz9vn0mlfp8kwhjirb551"; depends=[BiocParallel Biostrings cBioPortalData data_table gridBase httr LowMACAAnnotation motifStack plyr RColorBrewer reshape2 stringr]; };
LymphoSeq = derive2 { name="LymphoSeq"; version="1.24.0"; sha256="12habp9qw5pi6ylfwraqayxfhmrxx2334gcj0k3c8awgxnb20hc1"; depends=[Biostrings circlize data_table dplyr ggplot2 ggtree ineq LymphoSeqDB msa phangorn plyr RColorBrewer reshape stringdist UpSetR VennDiagram]; };
M3C = derive2 { name="M3C"; version="1.18.0"; sha256="120gd7gkgc98d1l6hl2ij799b3jksdnga5iyb44ps9mbc79hl012"; depends=[cluster corpcor doParallel doSNOW foreach ggplot2 Matrix matrixcalc Rtsne umap]; };
M3Drop = derive2 { name="M3Drop"; version="1.22.0"; sha256="0h8qj7hwkm007717yv2j6bx5ri0zi71yd2bdl45rh68j30qv62ab"; depends=[bbmle gplots Hmisc irlba Matrix matrixStats numDeriv RColorBrewer reldist statmod]; };
@ -571,7 +571,7 @@ in with self; {
MLSeq = derive2 { name="MLSeq"; version="2.14.0"; sha256="0ajkxa6wm215df6i8y7z9ha68m25p5kg5hzk2ni4v07w6mn3cikj"; depends=[Biobase caret DESeq2 edgeR foreach ggplot2 limma pamr plyr sSeq SummarizedExperiment testthat VennDiagram xtable]; };
MMAPPR2 = derive2 { name="MMAPPR2"; version="1.10.0"; sha256="1w8ajra7ip9yfmzinvdgxcm1n808saj0shfx0irflmz54a829kfr"; depends=[Biobase BiocGenerics BiocParallel data_table dplyr ensemblVEP GenomeInfoDb GenomicRanges gmapR IRanges magrittr Rsamtools S4Vectors stringr tidyr VariantAnnotation VariantTools]; };
MMDiff2 = derive2 { name="MMDiff2"; version="1.24.0"; sha256="031d3j2d6rqj5adaflbhq1q40h1573mg44vxk07hg3ky6w55mv82"; depends=[Biobase Biostrings BSgenome GenomicRanges ggplot2 locfit RColorBrewer Rsamtools S4Vectors shiny]; };
MMUPHin = derive2 { name="MMUPHin"; version="1.10.2"; sha256="0p4v0nh38rgpnisq4mbryx0z9bh35634y5f3zafsmi59smcfs2rr"; depends=[cowplot dplyr fpc ggplot2 igraph Maaslin2 metafor stringr tidyr]; };
MMUPHin = derive2 { name="MMUPHin"; version="1.10.3"; sha256="0kg4zwwwbxzzl4cddbcn2ww93z5z17n6d2imw2gfr8jcpzxysd3n"; depends=[cowplot dplyr fpc ggplot2 igraph Maaslin2 metafor stringr tidyr]; };
MODA = derive2 { name="MODA"; version="1.22.0"; sha256="1aa5g2zy251q3rpy83c4siyvdnrzw5cb3a136qrxd69z6pfpnkx3"; depends=[AMOUNTAIN cluster dynamicTreeCut igraph RColorBrewer WGCNA]; };
MOFA2 = derive2 { name="MOFA2"; version="1.6.0"; sha256="1cdx2zgmicn5qa59x794mjcnz9csgmsscl21qd9yhwc5n9fj0zqw"; depends=[basilisk corrplot cowplot DelayedArray dplyr forcats ggplot2 ggrepel HDF5Array magrittr pheatmap RColorBrewer reshape2 reticulate rhdf5 Rtsne stringi tidyr uwot]; };
MOGAMUN = derive2 { name="MOGAMUN"; version="1.6.0"; sha256="1wgpr6ci1hmzl1racszxfvgk95q5x4ca21rxhimimgag1gkk472b"; depends=[BiocParallel igraph RCy3 RUnit stringr]; };
@ -592,7 +592,7 @@ in with self; {
MSstatsQC = derive2 { name="MSstatsQC"; version="2.14.0"; sha256="0bgkwgcghdmccza7f4fkza3drjarl3b3prbzq7kf88k7k7zvknzr"; depends=[dplyr ggExtra ggplot2 MSnbase plotly qcmetrics]; };
MSstatsQCgui = derive2 { name="MSstatsQCgui"; version="1.16.0"; sha256="0nrhqznkg61vmv9g3zly0p26dvkbcf4lqx48yj9k8rbrfkg06bdk"; depends=[dplyr ggExtra gridExtra MSstatsQC plotly shiny]; };
MSstatsSampleSize = derive2 { name="MSstatsSampleSize"; version="1.10.0"; sha256="09cclwrf2s0ld3cvvs0drkfk8xgq6la9cc9mqn4kjw355zqwb7lp"; depends=[BiocParallel caret ggplot2 gridExtra MSstats reshape2]; };
MSstatsTMT = derive2 { name="MSstatsTMT"; version="2.4.0"; sha256="16x6mjn1xcbkqb6aymwgcawadpvcaf8bw7y475hk041n1bcl57yk"; depends=[checkmate data_table ggplot2 limma lme4 lmerTest MSstats MSstatsConvert]; };
MSstatsTMT = derive2 { name="MSstatsTMT"; version="2.4.1"; sha256="1g3vljkfddq95m31r53vcjnk785ikw8ml1clmfii10s66y852c4j"; depends=[checkmate data_table ggplot2 limma lme4 lmerTest MSstats MSstatsConvert]; };
MVCClass = derive2 { name="MVCClass"; version="1.70.0"; sha256="0apcjlq4i2mg8mlfqgvlcsqkiy51whzid3nd0m830jff0ywgh47g"; depends=[]; };
MWASTools = derive2 { name="MWASTools"; version="1.20.0"; sha256="17j82k7nrw8lsvvzlzaq6134gckkrxgff3yi8s4jwlzi1grzgjc7"; depends=[boot car ComplexHeatmap ggplot2 glm2 gridExtra igraph KEGGgraph KEGGREST ppcor qvalue RCurl SummarizedExperiment]; };
Maaslin2 = derive2 { name="Maaslin2"; version="1.10.0"; sha256="1qw2vmxg5z8lirj2pknfsybn9vhrifqh3j7p2xyhnjsbsfw5ix70"; depends=[biglm car chemometrics cplm data_table dplyr edgeR ggplot2 glmmTMB hash lme4 lmerTest logging lpsymphony MASS metagenomeSeq optparse pbapply pcaPP pheatmap pscl robustbase vegan]; };
@ -629,8 +629,8 @@ in with self; {
MiPP = derive2 { name="MiPP"; version="1.68.0"; sha256="080cc1y32yi046xsj05vppp1l3c2sdyjclw8p439kmakcrf0sigf"; depends=[Biobase e1071 MASS]; };
MiRaGE = derive2 { name="MiRaGE"; version="1.38.0"; sha256="0w4c41izigparfaddj5ffccxw7v33gc11zh0b1cdyz2hacmw03ly"; depends=[AnnotationDbi Biobase BiocGenerics BiocManager S4Vectors]; };
MicrobiomeProfiler = derive2 { name="MicrobiomeProfiler"; version="1.2.0"; sha256="0czli81lqbx1xkhj5yqlixjgszk4whvckhjpw9k70ggcx9svc249"; depends=[clusterProfiler config DT enrichplot ggplot2 golem htmltools magrittr shiny shinycustomloader shinyWidgets]; };
MicrobiotaProcess = derive2 { name="MicrobiotaProcess"; version="1.8.1"; sha256="0gv5vkrrp4lk9df2brjacqa313h78wayzal63d5mmszjfg9cd7s3"; depends=[ape Biostrings coin dplyr dtplyr foreach ggplot2 ggrepel ggsignif ggstar ggtree ggtreeExtra magrittr MASS patchwork pillar plyr rlang SummarizedExperiment tibble tidyr tidyselect tidytree treeio vegan zoo]; };
MineICA = derive2 { name="MineICA"; version="1.36.0"; sha256="0lwpykysp8arq6rhfq9w6w5phxmj41lk8xg473b2n4pcfc6sh34h"; depends=[annotate AnnotationDbi Biobase BiocGenerics biomaRt cluster colorspace fastICA foreach fpc ggplot2 GOstats graph gtools Hmisc igraph JADE lumi lumiHumanAll_db marray mclust plyr RColorBrewer Rgraphviz scales xtable]; };
MicrobiotaProcess = derive2 { name="MicrobiotaProcess"; version="1.8.2"; sha256="1v7drwwn1qflrxi25nllk84xr7v24qypdnq7pz7nkxganfdnw7xh"; depends=[ape Biostrings coin dplyr dtplyr foreach ggplot2 ggrepel ggsignif ggstar ggtree ggtreeExtra magrittr MASS patchwork pillar plyr rlang SummarizedExperiment tibble tidyr tidyselect tidytree treeio vegan zoo]; };
MineICA = derive2 { name="MineICA"; version="1.36.1"; sha256="0552rxj4blisxyzrjm59qxmqnrfg9x1kygr6d2knhnzyasprwl5p"; depends=[annotate AnnotationDbi Biobase BiocGenerics biomaRt cluster colorspace fastICA foreach fpc ggplot2 GOstats graph gtools Hmisc igraph JADE lumi lumiHumanAll_db marray mclust plyr RColorBrewer Rgraphviz scales xtable]; };
MinimumDistance = derive2 { name="MinimumDistance"; version="1.40.0"; sha256="0409nqlhjnx0l8zcy71zrawjbml1rmjkgch9a87zcc1j2phnpdch"; depends=[Biobase BiocGenerics data_table DNAcopy ff foreach GenomeInfoDb GenomicRanges IRanges lattice MatrixGenerics matrixStats oligoClasses S4Vectors SummarizedExperiment VanillaICE]; };
MobilityTransformR = derive2 { name="MobilityTransformR"; version="1.0.0"; sha256="0x3xxh54sdlb6dan9rrrg116vfr1q4b0z9fdjaqh52qbwchy1x82"; depends=[MetaboCoreUtils MSnbase Spectra xcms]; };
ModCon = derive2 { name="ModCon"; version="1.4.0"; sha256="1av9ragz32ss6y0hh36hc8zldg5qmgz4kxjkgi649v2l2fb5yn8h"; depends=[data_table]; };
@ -684,7 +684,7 @@ in with self; {
OMICsPCA = derive2 { name="OMICsPCA"; version="1.14.0"; sha256="0fldppwhjijw53s6q44g92n59pfmlz5049qsmna7nzqdh06l8wh6"; depends=[cluster clValid corrplot cowplot data_table factoextra FactoMineR fpc GenomeInfoDb ggplot2 HelloRanges IRanges kableExtra magick MASS MultiAssayExperiment NbClust OMICsPCAdata pdftools PerformanceAnalytics reshape2 rgl rmarkdown rtracklayer tidyr]; };
OPWeight = derive2 { name="OPWeight"; version="1.18.0"; sha256="1k4qfbg29lll9hpkzbcbhfipyjn4rdpfyhm2wmr8a9jcp04fpl43"; depends=[MASS qvalue tibble]; };
ORFhunteR = derive2 { name="ORFhunteR"; version="1.4.0"; sha256="1381knb35njc4dvbdr9jbkmyfyc87aacvham3ljmdq7llis0zz7b"; depends=[Biostrings BSgenome_Hsapiens_UCSC_hg38 data_table Peptides randomForest Rcpp rtracklayer stringr xfun]; };
ORFik = derive2 { name="ORFik"; version="1.16.3"; sha256="0yhi07fccw9gp71kkgr3k61khpmsggz5dx9bl4mykck0r83d29pr"; depends=[AnnotationDbi BiocGenerics BiocParallel biomartr Biostrings BSgenome cowplot data_table DESeq2 fst GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GGally ggplot2 gridExtra httr IRanges jsonlite R_utils Rcpp Rsamtools rtracklayer S4Vectors SummarizedExperiment xml2]; };
ORFik = derive2 { name="ORFik"; version="1.16.6"; sha256="0yiby6z7bx5n7p32nz8yhv630m3laawq07ck11lp6vw0sn9dg6s1"; depends=[AnnotationDbi BiocGenerics BiocParallel biomaRt biomartr Biostrings BSgenome cowplot data_table DESeq2 fst GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 gridExtra httr IRanges jsonlite R_utils Rcpp Rsamtools rtracklayer S4Vectors SummarizedExperiment xml2]; };
OSAT = derive2 { name="OSAT"; version="1.44.0"; sha256="1hd1qmxbsqr1x1k8iihji48n5dqqg0zpk0ccvgaq2qkdkf9ayp06"; depends=[]; };
OTUbase = derive2 { name="OTUbase"; version="1.46.0"; sha256="1s41amahlqpb5gffmxd4rgdc1wwdjfzsr3jikv7flbb48965rjin"; depends=[Biobase Biostrings IRanges S4Vectors ShortRead vegan]; };
OUTRIDER = derive2 { name="OUTRIDER"; version="1.14.0"; sha256="0app3h20d76nrrrm2yc856fsz6wvjm3rl0irlr8vfb85qws7zrfi"; depends=[BBmisc BiocGenerics BiocParallel data_table DESeq2 generics GenomicFeatures GenomicRanges ggplot2 heatmaply IRanges matrixStats pcaMethods pheatmap plotly plyr PRROC RColorBrewer Rcpp RcppArmadillo reshape2 S4Vectors scales SummarizedExperiment]; };
@ -693,7 +693,7 @@ in with self; {
OmicCircos = derive2 { name="OmicCircos"; version="1.34.0"; sha256="0644xcyk0li39xcyldqy927k06q6p6b8y07s3wl75dmd8gqwgvdp"; depends=[GenomicRanges]; };
OmicsLonDA = derive2 { name="OmicsLonDA"; version="1.12.0"; sha256="125ijszmi6igsxhdg4kmgkc1sbsvsqk6ybqab73d1ly17w612z5q"; depends=[BiocGenerics BiocParallel ggplot2 gss plyr pracma SummarizedExperiment zoo]; };
Omixer = derive2 { name="Omixer"; version="1.6.0"; sha256="12avwqrb27ljish8xk4gryjisa6zslx8b977k2dmgp19wm7f2f9x"; depends=[dplyr forcats ggplot2 gridExtra magrittr readr stringr tibble tidyselect]; };
OmnipathR = derive2 { name="OmnipathR"; version="3.4.0"; sha256="0vk0fv09j3ql78mzzhdxwxb2b83qqdz2qfd8wpp1vydmcx2vvgni"; depends=[checkmate crayon curl digest dplyr httr igraph jsonlite later logger magrittr progress purrr rappdirs readr readxl rlang stringr tibble tidyr tidyselect withr xml2 yaml]; };
OmnipathR = derive2 { name="OmnipathR"; version="3.4.7"; sha256="1042hif90kcq8vf0qmqkkhmx014ammg5m7j96mxkd139nrdc6hzs"; depends=[checkmate crayon curl digest dplyr httr igraph jsonlite later logger magrittr progress purrr rappdirs readr readxl rlang rmarkdown stringr tibble tidyr tidyselect withr xml2 yaml]; };
OncoScore = derive2 { name="OncoScore"; version="1.24.0"; sha256="02s6y5p1ncmlbaqf4fmgkvkbf913d6czz3gd9dqfwblsycxy2cxp"; depends=[biomaRt]; };
OncoSimulR = derive2 { name="OncoSimulR"; version="3.4.0"; sha256="0ixlyrj7112rn2dnrfx226kqxfsisi2rccan9rxfcz1l1slkjvwk"; depends=[car data_table dplyr ggplot2 ggrepel graph gtools igraph RColorBrewer Rcpp Rgraphviz smatr stringr]; };
OpenStats = derive2 { name="OpenStats"; version="1.8.0"; sha256="08r2id3f6gx5s1va4gr6m191c9y44m2c6s5lbxr8xhrnpi4c61p0"; depends=[AICcmodavg car Hmisc jsonlite knitr MASS nlme rlist summarytools]; };
@ -727,7 +727,7 @@ in with self; {
PSICQUIC = derive2 { name="PSICQUIC"; version="1.34.0"; sha256="0gkkxxbc2a7cin92qwn1masqfigyz9s4fhyy2daa17r3ckk4ccgx"; depends=[BiocGenerics biomaRt httr IRanges plyr RCurl]; };
PSMatch = derive2 { name="PSMatch"; version="1.0.0"; sha256="027r2r70n9v54m6kww6bzaqvf7ahn42vh7fdbbb4m6xzbl62frmq"; depends=[BiocGenerics BiocParallel igraph Matrix MsCoreUtils ProtGenerics QFeatures S4Vectors]; };
PWMEnrich = derive2 { name="PWMEnrich"; version="4.32.0"; sha256="031j563jcaakiasx1r8aflhqm0vq7j5628f9bv4kkyi5rhr3aix9"; depends=[BiocGenerics Biostrings evd gdata S4Vectors seqLogo]; };
PanomiR = derive2 { name="PanomiR"; version="1.0.1"; sha256="18cy3qxismfvb1r7ln386s84r81zl8z20zbam343dh1pzw7ll61y"; depends=[clusterProfiler dplyr forcats GSEABase igraph limma metap org_Hs_eg_db preprocessCore RColorBrewer rlang tibble withr]; };
PanomiR = derive2 { name="PanomiR"; version="1.0.2"; sha256="14cmhsns15620ggqp41hl1dahanvqdlydxgr1aysq0h1145yhw31"; depends=[clusterProfiler dplyr forcats GSEABase igraph limma metap org_Hs_eg_db preprocessCore RColorBrewer rlang tibble withr]; };
Path2PPI = derive2 { name="Path2PPI"; version="1.26.0"; sha256="0csqciqavnamyhsf7hx5c6x3ranr1h8wskzz09hf7rw65gxbn6jp"; depends=[igraph]; };
PathNet = derive2 { name="PathNet"; version="1.36.0"; sha256="1xbwzvbnjgxby7xwgpl20qnx172lpzhm5z8rm3q1n3ww0n4z7pfk"; depends=[]; };
PathoStat = derive2 { name="PathoStat"; version="1.22.0"; sha256="1f01vrncrw50jcvaivgqpjyc6h0ccphzifcw1aq03w39nrw55mz9"; depends=[ape BiocStyle ComplexHeatmap corpcor DESeq2 devtools dplyr DT edgeR ggplot2 glmnet gmodels knitr limma matrixStats phyloseq plotly plyr RColorBrewer rentrez reshape2 ROCR scales shiny shinyjs tidyr vegan webshot XML]; };
@ -741,12 +741,12 @@ in with self; {
PhyloProfile = derive2 { name="PhyloProfile"; version="1.10.5"; sha256="1ij0mjz9arpfp67vjv6mp3h2w1marwqqdbvb2sc7vmqd0wj8bnvg"; depends=[ape BiocStyle bioDist Biostrings colourpicker data_table DT energy ExperimentHub ggplot2 gridExtra OmaDB pbapply plyr RColorBrewer RCurl shiny shinyBS shinyFiles shinyjs xml2 yaml zoo]; };
Pi = derive2 { name="Pi"; version="2.8.0"; sha256="0vpvpq7ss4x6qcz525zl71ysfh65zcqp13qym03s0v6r491gndnv"; depends=[BiocGenerics caret dnet dplyr GenomeInfoDb GenomicRanges ggnetwork ggplot2 ggrepel glmnet igraph IRanges lattice MASS Matrix osfr plot3D purrr randomForest RCircos readr ROCR scales supraHex tibble tidyr]; };
Pigengene = derive2 { name="Pigengene"; version="1.22.0"; sha256="11bx3ivzfzh0bnmz77psz4vah0gm0vaa7pwbbkwjcra85sbzyxiz"; depends=[BiocStyle bnlearn C50 clusterProfiler DBI DOSE dplyr gdata ggplot2 GO_db graph impute MASS matrixStats openxlsx partykit pheatmap preprocessCore ReactomePA Rgraphviz WGCNA]; };
PloGO2 = derive2 { name="PloGO2"; version="1.8.0"; sha256="1fwzim2x1yrd8jqbjg3zjnq8rpva7xnywsqmbab6cplx0qdy185s"; depends=[GO_db GOstats httr lattice openxlsx xtable]; };
PloGO2 = derive2 { name="PloGO2"; version="1.8.2"; sha256="0icflih4wkddj87zvq1f188v0rqb57cw9l9vygmz7vvlxis2x9ny"; depends=[GO_db GOstats httr lattice openxlsx xtable]; };
PoDCall = derive2 { name="PoDCall"; version="1.4.0"; sha256="1k47igncvcz4sqpv59148nqcinabz5ifpl6xkcrry20gvbngnrca"; depends=[diptest DT ggplot2 gridExtra LaplacesDemon mclust purrr readr rlist shiny shinyjs]; };
PoTRA = derive2 { name="PoTRA"; version="1.12.0"; sha256="0k93zj0mfs8pkr5cnf2y7bg9ynnwwr1acylsav8dcyz8vkc9r25k"; depends=[BiocGenerics graph graphite igraph org_Hs_eg_db]; };
PrInCE = derive2 { name="PrInCE"; version="1.12.0"; sha256="02vnpdmns14g0qhizpify2p4mzkacj31ar31jmbxzg3bcbq2nz84"; depends=[Biobase dplyr forecast Hmisc LiblineaR magrittr MSnbase naivebayes progress purrr ranger Rdpack robustbase speedglm tester tidyr]; };
PrecisionTrialDrawer = derive2 { name="PrecisionTrialDrawer"; version="1.11.0"; sha256="1miw8rj1zn1xv97dkgs66k9g21i6gp3j2m1l1akysskczgam3i2c"; depends=[BiocParallel biomaRt brglm data_table DT GenomicRanges ggplot2 ggrepel googleVis httr IRanges jsonlite LowMACAAnnotation magrittr matrixStats RColorBrewer reshape2 S4Vectors shiny shinyBS stringr XML]; };
Prostar = derive2 { name="Prostar"; version="1.28.4"; sha256="0w4cs2llaszmi0d8px6l3ixi0x8mmyisrv190q4iamsv3lbbljsn"; depends=[DAPAR data_table DT highcharter htmlwidgets later MSnbase RColorBrewer rhandsontable shiny shinyAce shinyBS shinycssloaders shinyjqui shinyjs shinyWidgets]; };
Prostar = derive2 { name="Prostar"; version="1.28.6"; sha256="1kjwzb94g91g9nw2kx8dcqq7iwld3flkaxaisvjg5rzi3306s96g"; depends=[DAPAR data_table highcharter htmlwidgets later MSnbase RColorBrewer rhandsontable shiny shinyAce shinyBS shinycssloaders shinyjqui shinyWidgets]; };
ProtGenerics = derive2 { name="ProtGenerics"; version="1.28.0"; sha256="04hcgj4q8dbzp1a29rbww2bxxrg679pgys3m09p0ydkpsx76rq05"; depends=[]; };
ProteoDisco = derive2 { name="ProteoDisco"; version="1.2.0"; sha256="1929aarf9al6di1r6z2n2ggdzblmfidikwswfg53nqanwwms31wa"; depends=[BiocGenerics BiocParallel Biostrings checkmate cleaver dplyr GenomeInfoDb GenomicFeatures GenomicRanges IRanges ParallelLogger plyr rlang S4Vectors tibble tidyr VariantAnnotation XVector]; };
ProteoMM = derive2 { name="ProteoMM"; version="1.14.0"; sha256="0l5h4s77bv5wj6kj0zyj517acydqvd2sbxgl2fd22c1igwj9iqyl"; depends=[biomaRt gdata ggplot2 ggrepel gtools matrixStats]; };
@ -772,7 +772,7 @@ in with self; {
RCASPAR = derive2 { name="RCASPAR"; version="1.42.0"; sha256="0zzg0gsg6hcinskdj3625vk1pbzaxsfxf2m9d17gzc2jydjysfbz"; depends=[]; };
RCM = derive2 { name="RCM"; version="1.12.0"; sha256="0v1dv69qlv0knaf96imi94mbpr8qz2a46hjn6rw7yfzfgsprnx7s"; depends=[alabama DBI edgeR ggplot2 MASS nleqslv phyloseq RColorBrewer reshape2 tensor tseries VGAM]; };
RCSL = derive2 { name="RCSL"; version="1.4.0"; sha256="1b15jjd6v2slw94fd54y2xf638yrzqaw6qs4vzwan5ima6yl0bhk"; depends=[ggplot2 igraph NbClust pracma RcppAnnoy Rtsne umap]; };
RCX = derive2 { name="RCX"; version="1.0.0"; sha256="1dm12izq57h2si7xry28p01ih7cbr7lq56rw7x5k3pr4iwzvv2lh"; depends=[igraph jsonlite plyr]; };
RCX = derive2 { name="RCX"; version="1.0.1"; sha256="1xrarll3fh8a3zgv507944klyq7kym87rpn7rk1kfsxs3zd94fsq"; depends=[igraph jsonlite plyr]; };
RCy3 = derive2 { name="RCy3"; version="2.16.0"; sha256="0xbvi9k4lvva4njmgcjz2yjbhjp7n6if5622swnkyb01s178a7vi"; depends=[base64enc base64url BiocGenerics fs glue graph httr IRdisplay IRkernel RColorBrewer RCurl RJSONIO uchardet uuid XML]; };
RCyjs = derive2 { name="RCyjs"; version="2.18.0"; sha256="105spxlmmr23h43hrym10h5jgizq3m5g1kmxzf42q8jzns042dqs"; depends=[base64enc BiocGenerics BrowserViz graph httpuv]; };
RDRToolbox = derive2 { name="RDRToolbox"; version="1.46.0"; sha256="13c7701g9n6irqpfc1bcamg2pys8vsryq1y6q9mw28im73wf0caw"; depends=[MASS rgl]; };
@ -812,7 +812,7 @@ in with self; {
RSeqAn = derive2 { name="RSeqAn"; version="1.16.0"; sha256="0i16z4vqp7mqjjkn8xzzxadh88r3ikl04h7jkjnn777cn4596svm"; depends=[Rcpp]; };
RTCA = derive2 { name="RTCA"; version="1.48.0"; sha256="06bcy13i6j2y4fxizhg9k6yv2grvb2fi4w98f3q4pf8b6w6hcczb"; depends=[Biobase gtools RColorBrewer]; };
RTCGA = derive2 { name="RTCGA"; version="1.26.0"; sha256="1r8ivxgqi9c33rzg0bx699grgzpikiqhbdznnck1daj66ab78shs"; depends=[assertthat data_table dplyr ggplot2 ggthemes knitr purrr rvest scales stringi survival survminer viridis XML xml2]; };
RTCGAToolbox = derive2 { name="RTCGAToolbox"; version="2.26.0"; sha256="19af2phrnlw86sqffhxzk43da1hxi6qm3xx0w0yhmx69fncqnml0"; depends=[BiocGenerics data_table DelayedArray GenomeInfoDb GenomicRanges httr limma RaggedExperiment RCircos RCurl RJSONIO S4Vectors stringr SummarizedExperiment survival TCGAutils XML]; };
RTCGAToolbox = derive2 { name="RTCGAToolbox"; version="2.26.1"; sha256="12h5lj1a6v8cbmxvg8cw0iqzci3sl6ixv49qzzyz5srq4kidh40j"; depends=[BiocGenerics data_table DelayedArray GenomeInfoDb GenomicRanges httr limma RaggedExperiment RCircos RCurl RJSONIO S4Vectors stringr SummarizedExperiment survival TCGAutils XML]; };
RTN = derive2 { name="RTN"; version="2.20.0"; sha256="06gxc3qpvkd488m4wsy0xqwgdpfakas934k3pqs8knq5ivc5hy2a"; depends=[car data_table igraph IRanges limma minet mixtools pheatmap pwr RedeR S4Vectors snow SummarizedExperiment viper]; };
RTNduals = derive2 { name="RTNduals"; version="1.20.0"; sha256="0lglzmd4hsc4nlf6j7c5ixgkvs5dxgb1jmr3b5080flcn24s5a3p"; depends=[RTN]; };
RTNsurvival = derive2 { name="RTNsurvival"; version="1.20.0"; sha256="1vw185sskn59b647gfk1hqdmbm4kkb856wmv8dqlnw88mj5pls14"; depends=[data_table dunn_test egg ggplot2 pheatmap RColorBrewer RTN RTNduals scales survival]; };
@ -822,7 +822,7 @@ in with self; {
RUVnormalize = derive2 { name="RUVnormalize"; version="1.30.0"; sha256="02jphy9y90jcl1i2pmsai188whb7ivb4zq0l2whzsz8hyanqgbwv"; depends=[Biobase RUVnormalizeData]; };
RVS = derive2 { name="RVS"; version="1.18.0"; sha256="0yzzbj31gb86gvcchs6bbi69hbd39f2y4d3zv1g4lmyhbxzqw6zb"; depends=[GENLIB gRain kinship2 snpStats]; };
RadioGx = derive2 { name="RadioGx"; version="2.0.0"; sha256="0biajaa10skv55r7g8gfa1gkz9cav1g9rr9bj6zfqdcyg4i9a9hi"; depends=[assertthat Biobase BiocGenerics BiocParallel caTools CoreGx data_table downloader magicaxis matrixStats RColorBrewer reshape2 S4Vectors scales SummarizedExperiment]; };
RaggedExperiment = derive2 { name="RaggedExperiment"; version="1.20.0"; sha256="04vq9g7c7j15dpfcgs9v2ml32sw42bwa312p8lzs4jq6xkc6h52f"; depends=[BiocGenerics GenomeInfoDb GenomicRanges IRanges Matrix MatrixGenerics S4Vectors SummarizedExperiment]; };
RaggedExperiment = derive2 { name="RaggedExperiment"; version="1.20.1"; sha256="0j784nixky7rzfzwzmgfv7cd7x3lv1dkhnqg9j8g7jxgc8prha2v"; depends=[BiocGenerics GenomeInfoDb GenomicRanges IRanges Matrix MatrixGenerics S4Vectors SummarizedExperiment]; };
RandomWalkRestartMH = derive2 { name="RandomWalkRestartMH"; version="1.16.0"; sha256="1cy4c1gw7gmz15hvl2bx6r4r1hjslymw74gmqir068qgbnn9jz86"; depends=[dnet igraph Matrix]; };
RankProd = derive2 { name="RankProd"; version="3.22.0"; sha256="0rq14h9kjj84krgvfa09jbc5s8yks37fjbcv8z88daaib0j3fq2d"; depends=[gmp Rmpfr]; };
RareVariantVis = derive2 { name="RareVariantVis"; version="2.24.0"; sha256="0m6r8ldilv8hl3qhvbxafv928f7xma7w1rj7nv0hzi21hg741kp1"; depends=[BiocGenerics BSgenome BSgenome_Hsapiens_UCSC_hg19 GenomeInfoDb GenomicFeatures GenomicRanges GenomicScores googleVis gtools IRanges phastCons100way_UCSC_hg19 S4Vectors SummarizedExperiment TxDb_Hsapiens_UCSC_hg19_knownGene VariantAnnotation]; };
@ -843,13 +843,13 @@ in with self; {
ReactomeGraph4R = derive2 { name="ReactomeGraph4R"; version="1.4.0"; sha256="07psjmygwvjkrz4dsgsa6hbw15dn97lkl5h1hk386yj94d5aplbk"; depends=[data_table doParallel foreach getPass jsonlite magrittr neo4r purrr ReactomeContentService4R rlang]; };
ReactomePA = derive2 { name="ReactomePA"; version="1.40.0"; sha256="1fd72m2afxbbvbgwy8knp6fiq1h561plmsh4r8a08w21ngmkz2s5"; depends=[AnnotationDbi DOSE enrichplot ggplot2 ggraph graphite igraph reactome_db]; };
ReadqPCR = derive2 { name="ReadqPCR"; version="1.42.0"; sha256="1999bn50w4sm8lr8ly6n773kswffcyrj3l6if37z1c17krfp58vl"; depends=[Biobase]; };
RedeR = derive2 { name="RedeR"; version="2.0.0"; sha256="1ai4cq48i3bpgkla2bf2fyrms5y15bmkf2c5qnjlh0lq274d160l"; depends=[igraph]; };
RedeR = derive2 { name="RedeR"; version="2.0.1"; sha256="163rxsnj00nyxy96jx36z08wahbxr5lgh5r7rlk2kc1r5mv9hypn"; depends=[igraph]; };
RefPlus = derive2 { name="RefPlus"; version="1.66.0"; sha256="0q0jklcbf7przhaxdb4w2qalin7ypds8s6v1yjlriqj62zkvd9bk"; depends=[affy affyPLM Biobase preprocessCore]; };
RegEnrich = derive2 { name="RegEnrich"; version="1.6.0"; sha256="0nfdnbw69dl6zba3mrvjb1v4h8avgn30kzpfwl5fi5n07x6s7xpb"; depends=[BiocParallel BiocSet DESeq2 DOSE dplyr fgsea ggplot2 limma magrittr randomForest reshape2 S4Vectors SummarizedExperiment tibble WGCNA]; };
RepViz = derive2 { name="RepViz"; version="1.12.0"; sha256="1y60br7rk1834izrsi74cnmw90klxdxgbwhlxcqsmvr3r1nblgwq"; depends=[biomaRt GenomicRanges IRanges Rsamtools S4Vectors]; };
Repitools = derive2 { name="Repitools"; version="1.42.0"; sha256="1jasydq3wai7zxkgjph7fgy77i65qrsf520chaq474xf1j9hr9j8"; depends=[BiocGenerics Biostrings BSgenome cluster DNAcopy edgeR GenomeInfoDb GenomicAlignments GenomicRanges gplots gsmoothr IRanges MASS Ringo Rsamtools Rsolnp rtracklayer S4Vectors]; };
ReportingTools = derive2 { name="ReportingTools"; version="2.36.0"; sha256="0r8cdqzfh1jxkghhk3j8x3y9kkmdyg9ibfhsic15jqkmp1im6khh"; depends=[annotate AnnotationDbi Biobase BiocGenerics Category DESeq2 edgeR ggbio ggplot2 GOstats GSEABase hwriter IRanges knitr lattice limma PFAM_db R_utils XML]; };
ResidualMatrix = derive2 { name="ResidualMatrix"; version="1.6.0"; sha256="1pjr3gva0jwj2pgqr4k4nl1ir1153hhrk1d400r30w0di472hns4"; depends=[DelayedArray Matrix S4Vectors]; };
ResidualMatrix = derive2 { name="ResidualMatrix"; version="1.6.1"; sha256="1530706c7b53h9m8smgnaj63rgdbm3hd09n7jwy6zc0y6qcffckd"; depends=[DelayedArray Matrix S4Vectors]; };
Rfastp = derive2 { name="Rfastp"; version="1.6.0"; sha256="06zzmdym2x72a99853qvh1a4snbmgysnmi6yckakdg6isizxm14p"; depends=[ggplot2 Rcpp reshape2 Rhtslib rjson zlibbioc]; };
Rgin = derive2 { name="Rgin"; version="1.15.0"; sha256="1x5zj2d5rvsr2xh0ifpnrys9v91dal1xxhv5mmk16rs8wzwqpqba"; depends=[RcppEigen]; };
Rgraphviz = derive2 { name="Rgraphviz"; version="2.40.0"; sha256="1r6ff7w2bmyfl1vzjvpgnhb8f5arwjlpab8fw5ph8fgyiqbcx94l"; depends=[graph]; };
@ -892,7 +892,7 @@ in with self; {
SEPIRA = derive2 { name="SEPIRA"; version="1.16.0"; sha256="0dz7d0vvzg9ak2gs2pgciqabpjgqwhs236gfa48m71cy13khsdpz"; depends=[corpcor limma]; };
SEtools = derive2 { name="SEtools"; version="1.10.0"; sha256="0s382ph3v3ynx5j90rzsh6ix9h8776m7dmn0pr8shc9gy5ixv54z"; depends=[BiocParallel data_table DESeq2 edgeR Matrix openxlsx S4Vectors sechm SummarizedExperiment sva]; };
SGSeq = derive2 { name="SGSeq"; version="1.30.0"; sha256="0hz45367i70wl97silnimicdvs3g41zyf8syc6igz6471wbwkxwp"; depends=[AnnotationDbi BiocGenerics Biostrings GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges igraph IRanges Rsamtools rtracklayer RUnit S4Vectors SummarizedExperiment]; };
SIAMCAT = derive2 { name="SIAMCAT"; version="2.0.0"; sha256="10bgschq9lihylbhmyr89rplxs5rxa84qhv93ms807syx6kk733f"; depends=[beanplot corrplot glmnet gridBase gridExtra infotheo lgr LiblineaR lmerTest matrixStats mlr3 mlr3learners mlr3tuning paradox phyloseq pROC progress PRROC RColorBrewer scales stringr]; };
SIAMCAT = derive2 { name="SIAMCAT"; version="2.0.1"; sha256="05r9sv41l812hnz6dq2hzgk29y25raqqzn0mcw4lcqv6zlm60k0s"; depends=[beanplot corrplot glmnet gridBase gridExtra infotheo lgr LiblineaR lmerTest matrixStats mlr3 mlr3learners mlr3tuning paradox phyloseq pROC progress PRROC RColorBrewer scales stringr]; };
SICtools = derive2 { name="SICtools"; version="1.26.0"; sha256="1vj5y3xysvf113f2iy2n10yzm3xy30m7g3brirydrj9vk73ssdcs"; depends=[Biostrings doParallel GenomicRanges IRanges matrixStats plyr Rsamtools stringr]; };
SIM = derive2 { name="SIM"; version="1.66.0"; sha256="0kvayxf4h7l9410v0gafbg31xkc8xcl1cbilfgln4l5pv42wnrl4"; depends=[globaltest quantreg quantsmooth]; };
SIMAT = derive2 { name="SIMAT"; version="1.28.0"; sha256="06f4py4gk2gqdas1gwz43by1m4k5b617l58a36rm294w9hvwi03b"; depends=[ggplot2 mzR Rcpp reshape2]; };
@ -914,9 +914,9 @@ in with self; {
SPONGE = derive2 { name="SPONGE"; version="1.18.1"; sha256="071w946cdvc8x277893ji74l336j99j73k3cxawi64k39c1qqsnd"; depends=[Biobase biomaRt caret ComplexHeatmap cvms data_table doRNG dplyr expm foreach ggplot2 ggpubr ggridges glmnet gRbase igraph iterators logging MASS MetBrewer miRBaseConverter ppcor randomForest rlang stringr tidyr tidyverse tnet]; };
SPOTlight = derive2 { name="SPOTlight"; version="1.0.0"; sha256="1h6w02ya3fcg13rb0phzfx6qdw4mhbgsq6jai1h2jab8whcggfpn"; depends=[ggplot2 Matrix matrixStats NMF nnls SingleCellExperiment]; };
SPsimSeq = derive2 { name="SPsimSeq"; version="1.6.0"; sha256="11symjnpyp6yb26071gnzgp3immhjyyzirwb6j7gnh8hmgzmcpz9"; depends=[edgeR fitdistrplus Hmisc limma mvtnorm phyloseq SingleCellExperiment WGCNA]; };
SQLDataFrame = derive2 { name="SQLDataFrame"; version="1.10.0"; sha256="0pkpjmhff9jlsnj1xs05j066lks4qmkzh09xlnc34wvgx7qrg20n"; depends=[BiocGenerics DBI dbplyr dplyr lazyeval RSQLite S4Vectors tibble]; };
SQLDataFrame = derive2 { name="SQLDataFrame"; version="1.10.3"; sha256="0fxl2if1bnw79md4lkz8lq51j7hi05bhf2k66605xwgfmz5q9lyf"; depends=[BiocGenerics DBI dbplyr dplyr lazyeval RSQLite S4Vectors tibble]; };
SQUADD = derive2 { name="SQUADD"; version="1.46.0"; sha256="13g381j3xbzdh6xwmgf3d1jsr39zd523q1kldpw3cmp01asykcwm"; depends=[RColorBrewer]; };
SRAdb = derive2 { name="SRAdb"; version="1.58.0"; sha256="1r21llikjjicbqsrcp3yaqsp45nbzbrccsn4gpgdk90gx7p325by"; depends=[GEOquery graph RCurl RSQLite]; };
SRAdb = derive2 { name="SRAdb"; version="1.58.1"; sha256="11590a9zayqy4h1f9mfq9mdfj0d4i3amlb4q5vpc5ibir7l9a4bk"; depends=[GEOquery graph RCurl RSQLite]; };
STAN = derive2 { name="STAN"; version="2.24.0"; sha256="18qa8fa6n9n965h0rwbsyfd14snh2n96rwfi1l1dg7wdrksyr8wx"; depends=[BiocGenerics GenomeInfoDb GenomicRanges Gviz IRanges poilog Rsolnp S4Vectors]; };
STATegRa = derive2 { name="STATegRa"; version="1.32.0"; sha256="157jm77mh12p5wdik1xm00p8r7x692gw5sb2dphkjf6fkc53sxk0"; depends=[affy Biobase calibrate edgeR foreach ggplot2 gplots gridExtra limma MASS]; };
STRINGdb = derive2 { name="STRINGdb"; version="2.8.4"; sha256="1jn6080v6097zpqsr4gfbx31gqqdhpzjrk63avk3v3xwawmf2379"; depends=[gplots hash igraph plotrix plyr png RColorBrewer RCurl sqldf]; };
@ -925,10 +925,10 @@ in with self; {
SWATH2stats = derive2 { name="SWATH2stats"; version="1.26.0"; sha256="0n6ap58lbn3rbaqb50244byam2fc62q85zl2a5bws5bsfccnvzk3"; depends=[biomaRt data_table ggplot2 reshape2]; };
SamSPECTRAL = derive2 { name="SamSPECTRAL"; version="1.50.0"; sha256="0p4a9f4aa714jn1z4r9177jqin11qi3ln3pdjb0vblcj435yhpdm"; depends=[]; };
Scale4C = derive2 { name="Scale4C"; version="1.18.0"; sha256="0n63sp8jalm8il1vyl1ls9cbbzs3jb227kq6rdw436mmnk5d7hik"; depends=[GenomicRanges IRanges smoothie SummarizedExperiment]; };
ScaledMatrix = derive2 { name="ScaledMatrix"; version="1.4.0"; sha256="0p6065mbn77hphpjfchz3r3raspl127f11n39mwh9bih4zg375cl"; depends=[DelayedArray Matrix S4Vectors]; };
ScaledMatrix = derive2 { name="ScaledMatrix"; version="1.4.1"; sha256="05gxr41nb1jqhv357rfha4062kszvrmkr36mhkjsf7kgnzf0p8hz"; depends=[DelayedArray Matrix S4Vectors]; };
Sconify = derive2 { name="Sconify"; version="1.16.0"; sha256="0nm6z5dmnqd1bw1xpw7ljjlrbccqjmpcb1ds83yjy5wc9i0m2jdb"; depends=[dplyr flowCore FNN ggplot2 magrittr readr Rtsne tibble]; };
SemDist = derive2 { name="SemDist"; version="1.30.0"; sha256="01pjcxhbyhbdcfw8jrjq04n4xi659ah3mx176rf0x7dll732y161"; depends=[annotate AnnotationDbi GO_db]; };
SeqArray = derive2 { name="SeqArray"; version="1.36.2"; sha256="04lk3khzlfxi8wmrv2c5sag21y650a35k58zcgqbfxaimvyq7jhp"; depends=[Biostrings gdsfmt GenomeInfoDb GenomicRanges IRanges S4Vectors]; };
SeqArray = derive2 { name="SeqArray"; version="1.36.3"; sha256="0b1zcays48s23k3z7p0k7l6sb89a8zn73xpdg38hbna016g92wjx"; depends=[Biostrings gdsfmt GenomeInfoDb GenomicRanges IRanges S4Vectors]; };
SeqGSEA = derive2 { name="SeqGSEA"; version="1.36.0"; sha256="0jpj0hksbbgzfr0k5f4zwm2ivdwrm00mcz8n8q0m35k44bj311b0"; depends=[Biobase biomaRt DESeq2 doParallel]; };
SeqGate = derive2 { name="SeqGate"; version="1.6.0"; sha256="0fa5spf66d1x0747ikgk822mpcjbvb0y4slmq636njxgi6n739wk"; depends=[BiocManager GenomicRanges S4Vectors SummarizedExperiment]; };
SeqSQC = derive2 { name="SeqSQC"; version="1.18.0"; sha256="1687klbjypwhd6qg7s965s7n47wf0kyfsn734wg27zv6mvfhck9r"; depends=[e1071 ExperimentHub gdsfmt GenomicRanges GGally ggplot2 IRanges rbokeh RColorBrewer reshape2 rmarkdown S4Vectors SNPRelate]; };
@ -940,7 +940,7 @@ in with self; {
SigsPack = derive2 { name="SigsPack"; version="1.10.0"; sha256="1c3xnk90gy60jzjgydg0vr1xmlcad4dkk45skyh42abzqxlwj5yd"; depends=[Biobase Biostrings BSgenome GenomeInfoDb GenomicRanges quadprog rtracklayer SummarizedExperiment VariantAnnotation]; };
SimBindProfiles = derive2 { name="SimBindProfiles"; version="1.34.0"; sha256="1ndim53fhx0naj1r5zwq4d655nbdvclfi40m3fqg891hzz370sd6"; depends=[Biobase limma mclust Ringo]; };
SimFFPE = derive2 { name="SimFFPE"; version="1.8.0"; sha256="0i2ah49bajhjf0yjjhm84vpc8brs8y3c016l4sbwhpb2nhcqgvgj"; depends=[Biostrings doParallel dplyr foreach GenomicRanges IRanges Rsamtools truncnorm]; };
SingleCellExperiment = derive2 { name="SingleCellExperiment"; version="1.18.0"; sha256="0s1aqbvlfnzijzfywjfpinqmxqj269dq2d3zlgf4xw9c1nwwnv7p"; depends=[BiocGenerics DelayedArray GenomicRanges S4Vectors SummarizedExperiment]; };
SingleCellExperiment = derive2 { name="SingleCellExperiment"; version="1.18.1"; sha256="13iq480xbgqriyjrlknamym1wspdh54i9jahgvk726ksfzf19vx0"; depends=[BiocGenerics DelayedArray GenomicRanges S4Vectors SummarizedExperiment]; };
SingleCellSignalR = derive2 { name="SingleCellSignalR"; version="1.8.0"; sha256="0c0fsr1b0mc5a7qfa7cjipx50fscb120747c9xjp5n55jv5hwd9c"; depends=[BiocManager circlize data_table edgeR foreach gplots igraph limma multtest pheatmap Rtsne scran SIMLR stringr]; };
SingleMoleculeFootprinting = derive2 { name="SingleMoleculeFootprinting"; version="1.4.0"; sha256="0kayi1cahn57ysdhykk4h3a93ajnr41p7xbf1v04mvbz9gq9piqf"; depends=[BiocGenerics Biostrings BSgenome data_table GenomeInfoDb GenomicRanges IRanges plyr QuasR RColorBrewer]; };
SingleR = derive2 { name="SingleR"; version="1.10.0"; sha256="0qbyc6ygw2xv3li9187i3axsw6ihwpa7pkvxvy9cagv7xck45c5y"; depends=[beachmat BiocNeighbors BiocParallel BiocSingular DelayedArray DelayedMatrixStats Matrix Rcpp S4Vectors SummarizedExperiment]; };
@ -954,7 +954,7 @@ in with self; {
SpeCond = derive2 { name="SpeCond"; version="1.50.0"; sha256="051p6npzjpwagd0bnzpbdjcmgkasr8d74a42ppmlc9hsfg8pzqcw"; depends=[Biobase fields hwriter mclust RColorBrewer]; };
Spectra = derive2 { name="Spectra"; version="1.6.0"; sha256="0kzz7par5zwk4qypicmz39d6bc4aqmflzzxfrpng2y3id7f15jks"; depends=[BiocGenerics BiocParallel fs IRanges MsCoreUtils ProtGenerics S4Vectors]; };
SpectralTAD = derive2 { name="SpectralTAD"; version="1.12.0"; sha256="0svv4mp6qk2k3clz8qdigzhawh4cglzwrb8frh5c6mgrgdbf53g5"; depends=[BiocParallel cluster dplyr GenomicRanges HiCcompare magrittr Matrix PRIMME]; };
SpidermiR = derive2 { name="SpidermiR"; version="1.26.0"; sha256="0v1sdcwrhvnkr497i6qifzvzg2sr3ml5w2pwrp6nhlfhp1g0l4ah"; depends=[AnnotationDbi gdata ggplot2 gplots gridExtra httr igraph lattice latticeExtra MAGeCKFlute miRNAtap miRNAtap_db org_Hs_eg_db TCGAbiolinks]; };
SpidermiR = derive2 { name="SpidermiR"; version="1.26.1"; sha256="0zwnl1pyclg994l8ikp13zlzh13daph113d8brg37cjmrvag4abm"; depends=[AnnotationDbi gdata httr igraph miRNAtap miRNAtap_db org_Hs_eg_db]; };
SplicingFactory = derive2 { name="SplicingFactory"; version="1.4.0"; sha256="11kkr4c2ilwbr2h80aqiphxihwzs4sr23hq3q6w22w3wqqp7w24k"; depends=[SummarizedExperiment]; };
SplicingGraphs = derive2 { name="SplicingGraphs"; version="1.36.0"; sha256="1c8m8ab5jrwa8fryrdww4r41svkv864l2pr1hy1kil3njyaam0ml"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph igraph IRanges Rgraphviz Rsamtools S4Vectors]; };
StarBioTrek = derive2 { name="StarBioTrek"; version="1.22.0"; sha256="10wf96rn0d1srwkp980www7w5jjxzrq1li8d7n7069z3ja01p4ca"; depends=[AnnotationDbi e1071 ggplot2 graphite igraph MLmetrics reshape2 ROCR SpidermiR]; };
@ -975,7 +975,7 @@ in with self; {
TCC = derive2 { name="TCC"; version="1.36.0"; sha256="077gj5f1iwb3xwy29p5q5fr3459nq9swybn7504dyxb93259qxzi"; depends=[baySeq DESeq2 edgeR ROC]; };
TCGAbiolinks = derive2 { name="TCGAbiolinks"; version="2.24.3"; sha256="0visvfhzaf0p1rb5vjkmw1c91zfxpks8nl9nbl9xlnpm8lkmmkms"; depends=[biomaRt data_table downloader dplyr GenomicRanges ggplot2 httr IRanges jsonlite knitr plyr purrr R_utils readr rvest S4Vectors stringr SummarizedExperiment TCGAbiolinksGUI_data tibble tidyr XML xml2]; };
TCGAbiolinksGUI = derive2 { name="TCGAbiolinksGUI"; version="1.22.0"; sha256="1rav6nmbq8sn60x6cdc5zmvwwpiyfjc6n8hlzyjsg2yy3h3ij0qp"; depends=[caret clusterProfiler colourpicker data_table downloader DT ELMER ggplot2 ggrepel maftools pathview plotly readr sesame shiny shinyBS shinydashboard shinyFiles shinyjs stringr SummarizedExperiment TCGAbiolinks TCGAbiolinksGUI_data]; };
TCGAutils = derive2 { name="TCGAutils"; version="1.16.0"; sha256="0xh2z8055az6hnr2a3rsjlz9x7i4vz82dywk67xzmjf7954b1qhc"; depends=[AnnotationDbi BiocGenerics GenomeInfoDb GenomicDataCommons GenomicFeatures GenomicRanges IRanges MultiAssayExperiment RaggedExperiment rvest S4Vectors stringr SummarizedExperiment xml2]; };
TCGAutils = derive2 { name="TCGAutils"; version="1.16.1"; sha256="0lsnqxv0zbx4b3dfm3x5bf7i88y9wpq39faff84lrqk4nz9v4svn"; depends=[AnnotationDbi BiocGenerics GenomeInfoDb GenomicDataCommons GenomicFeatures GenomicRanges IRanges MultiAssayExperiment RaggedExperiment rvest S4Vectors stringr SummarizedExperiment xml2]; };
TCseq = derive2 { name="TCseq"; version="1.20.0"; sha256="0wqkbvg41xbkfc0xs44ckpzagwyfmqrdr69fj7am51khzv7gznrk"; depends=[BiocGenerics cluster e1071 edgeR GenomicAlignments GenomicRanges ggplot2 IRanges locfit reshape2 Rsamtools SummarizedExperiment]; };
TDARACNE = derive2 { name="TDARACNE"; version="1.46.0"; sha256="1ryrnaaq15sgji2j4js5vgsr2j7dl4dd0shmz7qayyq0k7ai2yaq"; depends=[Biobase Rgraphviz]; };
TEKRABber = derive2 { name="TEKRABber"; version="1.0.1"; sha256="0pilrjrvd43jr8h6s2zcc6rk0p4q2l3bhz6lm344a7y5wyvccly6"; depends=[apeglm biomaRt DESeq2 Rcpp SCBN SummarizedExperiment]; };
@ -983,12 +983,12 @@ in with self; {
TFARM = derive2 { name="TFARM"; version="1.18.0"; sha256="0rmw7r6k8mb5672aap26liqblrmasxvccxd4fjw2sdb449wbd9dl"; depends=[arules fields GenomicRanges gplots stringr]; };
TFBSTools = derive2 { name="TFBSTools"; version="1.34.0"; sha256="0l6j1r2cx7jfd39qzbyynk4jvzd81ys6yypzxjc97js4kkyrx29w"; depends=[Biobase BiocGenerics BiocParallel Biostrings BSgenome caTools CNEr DBI DirichletMultinomial GenomeInfoDb GenomicRanges gtools IRanges RSQLite rtracklayer S4Vectors seqLogo TFMPvalue XML XVector]; };
TFEA_ChIP = derive2 { name="TFEA.ChIP"; version="1.16.0"; sha256="0ckc4azfd9li5qd07ylprmds8qyq78bf8blbqgrkrgig9jpzn92s"; depends=[biomaRt dplyr GenomicFeatures GenomicRanges IRanges org_Hs_eg_db R_utils]; };
TFHAZ = derive2 { name="TFHAZ"; version="1.18.0"; sha256="1c5nh7gvdr18dv52hddqcfvmnhpm4qk3bckag17r17a2capk9xij"; depends=[GenomicRanges IRanges S4Vectors]; };
TFHAZ = derive2 { name="TFHAZ"; version="1.18.4"; sha256="07vfy39fa0nx685wj248q19h0733p773vhad893ds4ikbylmy6mg"; depends=[GenomicRanges IRanges ORFik S4Vectors]; };
TFutils = derive2 { name="TFutils"; version="1.16.0"; sha256="1awzxj668ldh44fl0izvbm73cgm60rw93rfqfbhsflsx984rhzj9"; depends=[AnnotationDbi BiocFileCache dplyr DT GSEABase httr magrittr miniUI org_Hs_eg_db readxl rjson Rsamtools shiny]; };
TIN = derive2 { name="TIN"; version="1.28.0"; sha256="1kgs45dif5fdmxlzhd6971mlhg0y1a41srnrx7irm4s4wckrpg4n"; depends=[aroma_affymetrix data_table impute squash stringr WGCNA]; };
TMixClust = derive2 { name="TMixClust"; version="1.18.0"; sha256="11ypr523hzbrynr1l68l7grn32499bl3j5wb7ic5i265r2kjcz4w"; depends=[Biobase BiocParallel cluster flexclust gss mvtnorm SPEM zoo]; };
TNBC_CMS = derive2 { name="TNBC.CMS"; version="1.12.0"; sha256="12w43p3fpcn98h3p9brkc9fdsn0wn73bzyrz63gm43q1jw0zpizd"; depends=[e1071 forestplot GGally ggplot2 ggpubr GSVA pheatmap pracma quadprog R_utils RColorBrewer SummarizedExperiment survival]; };
TOAST = derive2 { name="TOAST"; version="1.10.0"; sha256="1m9zg2k0z22369ly48swccmgqwfw20rv2bm18d23zdafmkb7jklj"; depends=[corpcor doParallel EpiDISH GGally ggplot2 limma nnls quadprog SummarizedExperiment tidyr]; };
TOAST = derive2 { name="TOAST"; version="1.10.1"; sha256="08pqriz9x32ixkjajh2wlh1cb7y8xmxna7by2qm5pjrrzblq96bh"; depends=[corpcor doParallel EpiDISH GGally ggplot2 limma nnls quadprog SummarizedExperiment tidyr]; };
TPP = derive2 { name="TPP"; version="3.24.0"; sha256="0w0gwhvc2mra0jd81pskhqsdayikz3fpbcx0sf45iac918dd2m4l"; depends=[Biobase biobroom broom data_table doParallel dplyr foreach futile_logger ggplot2 gridExtra knitr limma magrittr MASS mefa nls2 openxlsx plyr purrr RColorBrewer RCurl reshape2 rmarkdown stringr tibble tidyr VennDiagram VGAM]; };
TPP2D = derive2 { name="TPP2D"; version="1.12.0"; sha256="1567r1v92skhlvjysh5v32h6c50grm8qm7wbwdvr52pjqc7kvfb4"; depends=[BiocParallel doParallel dplyr foreach ggplot2 limma MASS openxlsx RCurl stringr tidyr]; };
TREG = derive2 { name="TREG"; version="1.0.1"; sha256="1d0ynkj1iiirigrzbnfclzcvvz1yx8c0ykqhz5vg8bhaw1h0ry3j"; depends=[Matrix purrr rafalib SummarizedExperiment]; };
@ -1022,7 +1022,7 @@ in with self; {
UMI4Cats = derive2 { name="UMI4Cats"; version="1.6.0"; sha256="0216qwriwjm0m7rzq8qjrvhnmn0fyqsv13cx24is53wqkqbqnavm"; depends=[annotate BiocFileCache BiocGenerics Biostrings BSgenome cowplot DESeq2 dplyr fda GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges magick magrittr org_Hs_eg_db R_utils rappdirs Rbowtie2 RColorBrewer regioneR reshape2 rlang Rsamtools S4Vectors scales ShortRead stringr SummarizedExperiment TxDb_Hsapiens_UCSC_hg19_knownGene zoo]; };
UNDO = derive2 { name="UNDO"; version="1.38.0"; sha256="0fasad2y0cnrdlfarqxlmgn30hjfqksddnvq5yia3ps50wzj7xyr"; depends=[Biobase BiocGenerics boot MASS nnls]; };
Ularcirc = derive2 { name="Ularcirc"; version="1.14.0"; sha256="0pqinw35vd94gk78i45rdyl4gyp6q8dmzc5kz72mcfg702wh7g8h"; depends=[AnnotationDbi AnnotationHub BiocGenerics Biostrings BSgenome data_table DT GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 ggrepel gsubfn mirbase_db moments Organism_dplyr plotgardener R_utils S4Vectors shiny shinydashboard shinyFiles shinyjs yaml]; };
UniProt_ws = derive2 { name="UniProt.ws"; version="2.36.0"; sha256="0s63wpgcmg98ykccb8bcwnjzawz9isc4mxz4cirhb9dxl95axq3h"; depends=[AnnotationDbi BiocFileCache BiocGenerics httr rappdirs RSQLite]; };
UniProt_ws = derive2 { name="UniProt.ws"; version="2.36.5"; sha256="1q5wdfww4pdsqyxjvv2dw88b3kwddvj94p17yxbnnrs4ra6jcfdn"; depends=[AnnotationDbi BiocFileCache BiocGenerics cellxgenedp httpcache httr jsonlite progress RSQLite]; };
Uniquorn = derive2 { name="Uniquorn"; version="2.16.0"; sha256="0hf2gs0aw0jw9qw1bqhsvxvw5grppbi3wxbfiynkbvza11aglifw"; depends=[doParallel foreach GenomicRanges IRanges R_utils stringr VariantAnnotation WriteXLS]; };
VAExprs = derive2 { name="VAExprs"; version="1.2.1"; sha256="19jhjayyaga1lyswhbibgva32mdmfvkdidcvxgl22728c6ppkg61"; depends=[CatEncoders DeepPINCS DiagrammeR keras mclust purrr scater SingleCellExperiment SummarizedExperiment tensorflow]; };
VCFArray = derive2 { name="VCFArray"; version="1.12.0"; sha256="17zgwv8nc192jyzlym09zyqppbg6zlid60xzh921mvp41sprf2j9"; depends=[BiocGenerics DelayedArray GenomicFiles GenomicRanges Rsamtools S4Vectors VariantAnnotation]; };
@ -1090,7 +1090,7 @@ in with self; {
arrayQualityMetrics = derive2 { name="arrayQualityMetrics"; version="3.52.0"; sha256="0dqfl9agfr11mn38ibrf4jrfbhy4vcvn7ajd2mp7w2nmrfr0720i"; depends=[affy affyPLM beadarray Biobase genefilter gridSVG Hmisc hwriter lattice latticeExtra limma RColorBrewer setRNG svglite vsn XML]; };
artMS = derive2 { name="artMS"; version="1.14.0"; sha256="0mdcvlpnjkkgp08kh3smx49pw1bav5zsynp4vak6m937ngccnzsr"; depends=[AnnotationDbi bit64 circlize cluster corrplot data_table dplyr getopt ggdendro ggplot2 ggrepel gplots limma MSstats openxlsx org_Hs_eg_db pheatmap plotly plyr RColorBrewer scales seqinr stringr tidyr UpSetR VennDiagram yaml]; };
atSNP = derive2 { name="atSNP"; version="1.12.0"; sha256="0dmv34xqwr3l2rznapxmyrkyf1w78qzxdv88s5nn8s1m8qdkgwkz"; depends=[BiocFileCache BiocParallel BSgenome data_table ggplot2 lifecycle motifStack rappdirs Rcpp testthat]; };
atena = derive2 { name="atena"; version="1.2.0"; sha256="1jbnlxrk8npflym008cgrazamlsh6y624g1d6x648kcjd8zwvj6n"; depends=[AnnotationHub BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicRanges IRanges Matrix Rsamtools S4Vectors scales sparseMatrixStats SQUAREM SummarizedExperiment]; };
atena = derive2 { name="atena"; version="1.2.2"; sha256="0b89wb7cc44c8jd6868dn8pwgid768bprkncsi87qkdz0abbhzhp"; depends=[AnnotationHub BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicRanges IRanges Matrix Rsamtools S4Vectors scales sparseMatrixStats SQUAREM SummarizedExperiment]; };
attract = derive2 { name="attract"; version="1.48.0"; sha256="0f1fsv278kpnxvqg9qa5rw2k3zr8zws0ab73ldl60h6pv9cy8x82"; depends=[AnnotationDbi Biobase cluster GOstats KEGGREST limma org_Hs_eg_db reactome_db]; };
autonomics = derive2 { name="autonomics"; version="1.4.0"; sha256="00k04pp81s6s3dyzykh0cqn27gxyk2brkl0k8g40b8rh13s1w8qy"; depends=[abind assertive BiocFileCache BiocGenerics colorspace data_table edgeR ggplot2 ggrepel gridExtra limma magrittr matrixStats MultiAssayExperiment pcaMethods R_utils rappdirs readxl rlang S4Vectors scales stringi SummarizedExperiment tidyr]; };
awst = derive2 { name="awst"; version="1.4.0"; sha256="0iw3zycmj95rmdx7f2w0j4yxkzd90y87lrzgdn9cyvvzi5avflav"; depends=[SummarizedExperiment]; };
@ -1102,7 +1102,7 @@ in with self; {
banocc = derive2 { name="banocc"; version="1.20.0"; sha256="10vaggq1w5jkxd8r2k1mhymzvb7x3h8afwn2pvmcpj022ka7xhbx"; depends=[coda mvtnorm rstan stringr]; };
barcodetrackR = derive2 { name="barcodetrackR"; version="1.4.0"; sha256="0yxa15xkgqazw31vq4wm8v747bw4qb18m6i602pvynk0n5bgg3d3"; depends=[circlize cowplot dplyr ggdendro ggplot2 ggridges magrittr plyr proxy RColorBrewer rlang S4Vectors scales shiny SummarizedExperiment tibble tidyr vegan viridis]; };
basecallQC = derive2 { name="basecallQC"; version="1.20.0"; sha256="07mcg0bs13apabhsip997nj6riqdrv9247azg379z6anaa0b0vpd"; depends=[data_table dplyr DT ggplot2 knitr lazyeval magrittr prettydoc raster rmarkdown ShortRead stringr tidyr XML yaml]; };
basilisk = derive2 { name="basilisk"; version="1.8.0"; sha256="1p90wq8a9wrpqpgmcy4zgh5skdw65gg2gsb3lnx78zk9khq0yyzh"; depends=[basilisk_utils dir_expiry reticulate]; };
basilisk = derive2 { name="basilisk"; version="1.8.1"; sha256="134xix2iq5l7783dng2jjklxd3m5lh4snb7bjhslrs2r1j3p8jpk"; depends=[basilisk_utils dir_expiry reticulate]; };
basilisk_utils = derive2 { name="basilisk.utils"; version="1.8.0"; sha256="1jnqv0rlljkq27rd4ixl763v335f2aanm4fzr386yc81fj4vnmhk"; depends=[dir_expiry]; };
batchelor = derive2 { name="batchelor"; version="1.12.3"; sha256="00ix3hvhgalxg63qnynv2waa273jk336lg47k72qwxfzimsxfjxc"; depends=[beachmat BiocGenerics BiocNeighbors BiocParallel BiocSingular DelayedArray DelayedMatrixStats igraph Matrix Rcpp ResidualMatrix S4Vectors ScaledMatrix scuttle SingleCellExperiment SummarizedExperiment]; };
bayNorm = derive2 { name="bayNorm"; version="1.14.0"; sha256="12896sryq5bfbqglpk3dg9cdsq6rk3jhzdqcpyasvk6w7v1w8bin"; depends=[BB BiocParallel doSNOW fitdistrplus foreach iterators locfit MASS Matrix Rcpp RcppArmadillo RcppProgress SingleCellExperiment SummarizedExperiment]; };
@ -1112,7 +1112,7 @@ in with self; {
beadarray = derive2 { name="beadarray"; version="2.46.0"; sha256="09n38fmckc0zbsv150x8k7l0xqbbjjkxnyqx84lfxqjxs592dvjy"; depends=[AnnotationDbi BeadDataPackR Biobase BiocGenerics GenomicRanges ggplot2 hexbin illuminaio IRanges limma reshape2]; };
beadarraySNP = derive2 { name="beadarraySNP"; version="1.62.0"; sha256="0f07mjxm3d5636rd668i5710r57zkhn1j642ivghs61bjgmb3a01"; depends=[Biobase quantsmooth]; };
beer = derive2 { name="beer"; version="1.0.0"; sha256="15s7ygx63by28hjks3b5w5ig72zvlzb8lxp1mv9vzzxjhp8jq33p"; depends=[BiocParallel cli edgeR PhIPData progressr rjags SummarizedExperiment]; };
benchdamic = derive2 { name="benchdamic"; version="1.2.0"; sha256="0x06nm0wxndcib7y4q8w9yzs55m6vgqy89ynnkvpplikkxxh2nqn"; depends=[ALDEx2 BiocParallel corncob cowplot DESeq2 edgeR ffpe ggdendro ggplot2 limma MAST metagenomeSeq MGLM phyloseq plyr RColorBrewer reshape2 Seurat SummarizedExperiment zinbwave]; };
benchdamic = derive2 { name="benchdamic"; version="1.2.5"; sha256="16mrc5mybi8sz0v7xh5z4i5vd7p9wg8cry83gj62ka3vznd7y9qk"; depends=[ALDEx2 ANCOMBC BiocParallel cowplot dearseq DESeq2 edgeR ggdendro ggplot2 ggridges limma MAST metagenomeSeq MGLM NOISeq phyloseq plyr RColorBrewer reshape2 Seurat SummarizedExperiment tidytext TreeSummarizedExperiment zinbwave]; };
bgx = derive2 { name="bgx"; version="1.62.0"; sha256="0q2y4n6bcc9pvz5sgfkw1lrb00rrp7q29i1vh7srdfmfhgpyz6bk"; depends=[affy Biobase gcrma Rcpp]; };
bigPint = derive2 { name="bigPint"; version="1.12.0"; sha256="1hp69j2qcidrxqs3dxjjngb09nbzp5x2yy4jz1rjmv6ghif9ccfj"; depends=[DelayedArray dplyr GGally ggplot2 gridExtra hexbin Hmisc htmlwidgets plotly plyr RColorBrewer reshape shiny shinycssloaders shinydashboard stringr SummarizedExperiment tidyr]; };
bigmelon = derive2 { name="bigmelon"; version="1.22.0"; sha256="1msch4qbifkdqv0bbw03xj6d9w28z91mf4ki41rqg6048cq17h2k"; depends=[Biobase BiocGenerics gdsfmt GEOquery illuminaio methylumi minfi wateRmelon]; };
@ -1124,16 +1124,16 @@ in with self; {
biocGraph = derive2 { name="biocGraph"; version="1.58.0"; sha256="1y59a7c4ahhn1g2wz2hkx83izfn8i85mmxxp63jdd0rg7zwhr6nn"; depends=[BiocGenerics geneplotter graph Rgraphviz]; };
biocViews = derive2 { name="biocViews"; version="1.64.1"; sha256="0ixcx9qqpmwmnhml3klk5z075km8g2l4q0iqc1dbniga87qgyl38"; depends=[Biobase BiocManager graph RBGL RCurl RUnit XML]; };
biocthis = derive2 { name="biocthis"; version="1.6.0"; sha256="1hdgjp00d2si3mr7m1d289i9wn7g927z6n8n27d5sm94lb91qln0"; depends=[BiocManager fs glue rlang styler usethis]; };
biodb = derive2 { name="biodb"; version="1.4.0"; sha256="02i0n29bp9d9p1ibslxca5m37qsgny2hlgg7d364lf7kc6y2bqni"; depends=[BiocFileCache chk jsonlite lgr lifecycle openssl plyr progress R6 rappdirs Rcpp RCurl RSQLite stringr testthat withr XML yaml]; };
biodb = derive2 { name="biodb"; version="1.4.2"; sha256="0f3clqmrpaawhjjyb4x5mnbhsam56r0av05b5cl5p4waylp8qbs1"; depends=[BiocFileCache chk jsonlite lgr lifecycle openssl plyr progress R6 rappdirs Rcpp RCurl RSQLite stringr testthat withr XML yaml]; };
biodbChebi = derive2 { name="biodbChebi"; version="1.2.0"; sha256="14sgjlklrvdz6wrsk8qbfmv98q8wcr229w1ra1kif7agvdqdw0ad"; depends=[biodb R6]; };
biodbExpasy = derive2 { name="biodbExpasy"; version="1.0.0"; sha256="1a2g0i5jb6i3qvldiy1msdcpv3w65jpay2iavzmzsp228jp49v5f"; depends=[biodb chk R6 stringr]; };
biodbHmdb = derive2 { name="biodbHmdb"; version="1.2.0"; sha256="16vmp1z1b0jsap7xd7wcr0fbpl75srrswmqhcq26biy23w1r93kj"; depends=[biodb R6 Rcpp testthat]; };
biodbKegg = derive2 { name="biodbKegg"; version="1.2.0"; sha256="0fd2x5mbs9ir9k9nz9nqjmj08032d31w8mh61v8h25x5973qzaj4"; depends=[biodb chk lifecycle R6]; };
biodbKegg = derive2 { name="biodbKegg"; version="1.2.1"; sha256="0227nnqfyylghn3gb5ps26ak18hvbjhplxrnwg2lcccd5mi67hwh"; depends=[biodb chk lifecycle R6]; };
biodbLipidmaps = derive2 { name="biodbLipidmaps"; version="1.2.0"; sha256="0zbw7jmkq3zaf2mp86yizsfm4nyamgi2fnlhn5bl0wvd01jrjlc0"; depends=[biodb lifecycle R6]; };
biodbMirbase = derive2 { name="biodbMirbase"; version="1.0.0"; sha256="1ci7wf0wkqvrwqw04z57i0l9ldgzgmhwfwv69yrrz1a9yjfq82q6"; depends=[biodb chk R6 stringr]; };
biodbNcbi = derive2 { name="biodbNcbi"; version="1.0.0"; sha256="1ymngw0wy2jr853v0r1gf3nb1q596f03gjhxxf0x2pkblpp85mqz"; depends=[biodb chk R6 XML]; };
biodbNci = derive2 { name="biodbNci"; version="1.0.0"; sha256="19gv91mqscdzpxcia32hc03v62icjd79c8bkkmi2nmvaa4zsyjii"; depends=[biodb chk R6 Rcpp testthat]; };
biodbUniprot = derive2 { name="biodbUniprot"; version="1.2.0"; sha256="13mcbj5sfpqify27cxzr566akm0riv27a7qkq64f848ca9y13lpa"; depends=[biodb R6]; };
biodbUniprot = derive2 { name="biodbUniprot"; version="1.2.1"; sha256="1cxmjq5f92is9ckqm61fj6syb2yw9i1pxj54yr268l2l67kz89vn"; depends=[biodb R6]; };
biomaRt = derive2 { name="biomaRt"; version="2.52.0"; sha256="0yn3kanyrplc89a900xiz33nw1v23mkljvd5isizgs8gzvwzf8xg"; depends=[AnnotationDbi BiocFileCache digest httr progress rappdirs stringr XML xml2]; };
biomformat = derive2 { name="biomformat"; version="1.24.0"; sha256="12wqjipxhngmlnrdmx329dqmkmy2wa4nkkrhwaqv2nwy90dncs9n"; depends=[jsonlite Matrix plyr rhdf5]; };
biomvRCNS = derive2 { name="biomvRCNS"; version="1.36.0"; sha256="0i576g7pkivqaxff1pkb760mdpx8v9fh071aic1mwfnlfa7k87ln"; depends=[GenomicRanges Gviz IRanges mvtnorm]; };
@ -1153,12 +1153,12 @@ in with self; {
brendaDb = derive2 { name="brendaDb"; version="1.10.0"; sha256="0wg52zq664zdv8lh4s6662wrwwxf9blrpag7b89ywz8p8rsnnmvm"; depends=[BiocFileCache BiocParallel crayon curl dplyr magrittr purrr rappdirs Rcpp rlang stringr tibble tidyr xml2]; };
bridge = derive2 { name="bridge"; version="1.60.0"; sha256="0w8l5fzid3iz7pb8wdggx2xli2jgcgyxvgnij2jl5blkg1dfzhc5"; depends=[rama]; };
bsseq = derive2 { name="bsseq"; version="1.32.0"; sha256="1jpfib2vb6hd7pgh3d33jgch24lba175zmbalwsbgvlmmyyf1ki5"; depends=[beachmat Biobase BiocGenerics BiocParallel Biostrings BSgenome data_table DelayedArray DelayedMatrixStats GenomeInfoDb GenomicRanges gtools HDF5Array IRanges limma locfit permute R_utils Rcpp rhdf5 S4Vectors scales SummarizedExperiment]; };
bugsigdbr = derive2 { name="bugsigdbr"; version="1.2.0"; sha256="1ib6aq0c07bjazh0clvn2nqx0vwpf1srp354rr162r37cix7mxlr"; depends=[BiocFileCache vroom]; };
bugsigdbr = derive2 { name="bugsigdbr"; version="1.2.2"; sha256="0jrvxlpc18gr5ba5r4pqrwzy9q6v03q26v150b2cb5b5nz4k8mbk"; depends=[BiocFileCache vroom]; };
bumphunter = derive2 { name="bumphunter"; version="1.38.0"; sha256="0k92ps9chqsimbc7vsr8swg679zfv8nfn5zahbqq4nknhhy7hwxw"; depends=[AnnotationDbi BiocGenerics doRNG foreach GenomeInfoDb GenomicFeatures GenomicRanges IRanges iterators limma locfit matrixStats S4Vectors]; };
cBioPortalData = derive2 { name="cBioPortalData"; version="2.8.2"; sha256="09bjlyr4l7iifgk39kkn3bq9lddvsgg2qj362xxy6z8igzblm05x"; depends=[AnVIL BiocFileCache digest dplyr GenomeInfoDb GenomicRanges httr IRanges MultiAssayExperiment RaggedExperiment readr RTCGAToolbox S4Vectors SummarizedExperiment TCGAutils tibble tidyr]; };
cTRAP = derive2 { name="cTRAP"; version="1.14.1"; sha256="1dsn2g0qnvv2qvkd9c1la20585z7pvhzzbr30y45sh271s27pa12"; depends=[AnnotationDbi AnnotationHub binr cowplot data_table dplyr DT fastmatch fgsea ggplot2 ggrepel highcharter htmltools httr limma pbapply purrr qs R_utils readxl reshape2 rhdf5 rlang scales shiny shinycssloaders tibble]; };
caOmicsV = derive2 { name="caOmicsV"; version="1.25.0"; sha256="10i4imjihmssdwfys21fsqng8zfp7sxzkc58m8qmnh6s5sccb3sz"; depends=[bc3net igraph]; };
cageminer = derive2 { name="cageminer"; version="1.2.2"; sha256="03k9al48cvnhvb9dis8dji14if0lih473zrm53srxx3bsxrdcyps"; depends=[BioNERO GenomeInfoDb GenomicRanges ggbio ggplot2 ggtext IRanges reshape2]; };
cageminer = derive2 { name="cageminer"; version="1.2.5"; sha256="1aq9q9cl75zscddmr3ijzyr9cn9cjdirvi0rl4jlnrpqkyh60x1i"; depends=[BioNERO GenomeInfoDb GenomicRanges ggbio ggplot2 ggtext IRanges reshape2]; };
calm = derive2 { name="calm"; version="1.10.0"; sha256="0fmi5s7g9xcbznd4g4hngp1rgy4anwdqxi1isp40anyhgmn3i3kj"; depends=[mgcv]; };
canceR = derive2 { name="canceR"; version="1.30.01"; sha256="1fv3dl7r67xhzzdrcwqyhr3g5pz8im0ll2rnyixskp1w55b98kjg"; depends=[Biobase circlize Formula geNetClassifier GSEABase httr phenoTest plyr R_methodsS3 R_oo rpart RUnit survival tkrplot]; };
cancerclass = derive2 { name="cancerclass"; version="1.40.0"; sha256="1s80w8ksf735ps677c7dcwkkpq1ynjqmp2r4biqav4j1y50nbi57"; depends=[binom Biobase]; };
@ -1178,7 +1178,7 @@ in with self; {
cellity = derive2 { name="cellity"; version="1.24.0"; sha256="0ywghrfj6m6hcz9yvpq0ww3p05rxdrfjna7il9faa76va5m8ssly"; depends=[AnnotationDbi e1071 ggplot2 mvoutlier org_Hs_eg_db org_Mm_eg_db robustbase topGO]; };
cellmigRation = derive2 { name="cellmigRation"; version="1.4.0"; sha256="09c6rmraajiqx7hgxmjyx4h32gdjy849ymyid0zvxqq4cfrx0pbs"; depends=[doParallel FactoMineR FME foreach Hmisc matrixStats reshape2 sp SpatialTools tiff vioplot]; };
cellscape = derive2 { name="cellscape"; version="1.20.0"; sha256="1k0z7sw4d3wxy4sz42b6aplq2njm673sfqgzzyf6m8iax2rvgvhs"; depends=[dplyr gtools htmlwidgets jsonlite plyr reshape2 stringr]; };
cellxgenedp = derive2 { name="cellxgenedp"; version="1.0.0"; sha256="1wwprws57cnan2a97yb7flqvq5syawad374d6sksjvalad5ii6xh"; depends=[cpp11 curl dplyr DT httr jsonlite shiny]; };
cellxgenedp = derive2 { name="cellxgenedp"; version="1.0.1"; sha256="1p2ajvsnrsz3kl1xkpvja5pxk3qycx0dvmnrwxwij3z15kgbcm2b"; depends=[cpp11 curl dplyr DT httr jsonlite shiny]; };
censcyt = derive2 { name="censcyt"; version="1.4.0"; sha256="03cr3l893b6250339d60xpf5mqcjl38fa9cpihy5gl83iy3dz9x4"; depends=[BiocParallel broom_mixed diffcyt dirmult dplyr edgeR fitdistrplus lme4 magrittr MASS mice multcomp purrr rlang S4Vectors stringr SummarizedExperiment survival tibble tidyr]; };
cfDNAPro = derive2 { name="cfDNAPro"; version="1.2.0"; sha256="1bbmp324nl2ijbifhqyw074s2na391c359iyq03w73yd86w8fcc0"; depends=[dplyr ggplot2 magrittr quantmod rlang Rsamtools stringr]; };
cghMCR = derive2 { name="cghMCR"; version="1.54.0"; sha256="0761pjajxgavxmrljzwksw0awdqrqxbi9cadqgixc0sj94rz82rd"; depends=[BiocGenerics CNTools DNAcopy limma]; };
@ -1195,10 +1195,10 @@ in with self; {
circRNAprofiler = derive2 { name="circRNAprofiler"; version="1.10.0"; sha256="1gwm416shhv2p3gh1n6kv1rvx0n0imy25b7z62z4s8b3gs3nfp5j"; depends=[AnnotationHub Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 DESeq2 dplyr edgeR GenomeInfoDb GenomicRanges ggplot2 gwascat IRanges magrittr R_utils readr reshape2 rlang rtracklayer S4Vectors seqinr stringi stringr universalmotif]; };
cisPath = derive2 { name="cisPath"; version="1.36.0"; sha256="07h948mxn2zjylv2y5q5w6rwqqmmha21xgwqpckzhgjh310jj674"; depends=[]; };
cleanUpdTSeq = derive2 { name="cleanUpdTSeq"; version="1.34.0"; sha256="1n1j9cz2v5bd0dbmpbb7pggixjsvyx3dfqjkmmqxir3dddbp6d0c"; depends=[Biostrings BSgenome BSgenome_Drerio_UCSC_danRer7 e1071 GenomeInfoDb GenomicRanges IRanges S4Vectors seqinr stringr]; };
cleaver = derive2 { name="cleaver"; version="1.34.0"; sha256="0apg7cqsw4fzchdvval82h14xfbs89bv0cfq1ynwi1pbnhkxngp0"; depends=[Biostrings IRanges S4Vectors]; };
cleaver = derive2 { name="cleaver"; version="1.34.1"; sha256="1ycrx0n2ignhmgb87is4qm6sv1z0m6a5c8sg3xn0cw9y4abjkgdf"; depends=[Biostrings IRanges S4Vectors]; };
cliProfiler = derive2 { name="cliProfiler"; version="1.2.0"; sha256="08hvj9zk42hf4r0cdd5pqxm2mk15salhk031fqbbks048hnqs42v"; depends=[Biostrings BSgenome dplyr GenomicRanges ggplot2 rtracklayer S4Vectors]; };
clippda = derive2 { name="clippda"; version="1.46.0"; sha256="1nhkf1nchxf26b05bdi4qz1asyrbxgi80irx80w1scijn33yv3d7"; depends=[Biobase lattice limma rgl scatterplot3d statmod]; };
clipper = derive2 { name="clipper"; version="1.36.0"; sha256="1s2cwy1spds18yf9vsjdx5ywg9ww69hd5indq7syndcqh449mzyw"; depends=[Biobase corpcor graph gRbase igraph KEGGgraph Matrix qpgraph RBGL Rcpp]; };
clipper = derive2 { name="clipper"; version="1.36.1"; sha256="0c58kwrlfbrnzwgh3amjby1bbk519rx4l6767b2ivx6qrpxcng6p"; depends=[Biobase corpcor graph gRbase igraph KEGGgraph Matrix qpgraph RBGL Rcpp]; };
cliqueMS = derive2 { name="cliqueMS"; version="1.10.0"; sha256="1fp5222wi91wk1fnw29gaiv02asidhrxzaq3da9isgjjvvr1gx63"; depends=[BH igraph matrixStats MSnbase qlcMatrix Rcpp RcppArmadillo xcms]; };
clonotypeR = derive2 { name="clonotypeR"; version="1.34.0"; sha256="15nnj6c23bcnln1xsmxs7f13m13lvn6did7lvp7ij8gcb0vg2g6q"; depends=[]; };
clst = derive2 { name="clst"; version="1.44.0"; sha256="0smr6kh6rk10zd2k8si79l3wdl2gdk6h3fh345a8m19rkv6sy455"; depends=[lattice ROC]; };
@ -1219,13 +1219,13 @@ in with self; {
coRdon = derive2 { name="coRdon"; version="1.14.0"; sha256="1kiw6kbbwqmr89mzppmgral0zxd5shmp53xyvbcr26fxs0xn1np2"; depends=[Biobase Biostrings data_table dplyr ggplot2 purrr stringr]; };
codelink = derive2 { name="codelink"; version="1.64.0"; sha256="0r1srzx7z2833yvbnmdmbpkhy7irs4hdy2901bzqcwp91b4n6q75"; depends=[annotate Biobase BiocGenerics limma]; };
cogena = derive2 { name="cogena"; version="1.30.0"; sha256="0xibcmnbaxsgq06wmh45263gp2f8m9llk2v5m2n1qlvcykyr7vwr"; depends=[amap apcluster Biobase biwt class cluster corrplot devtools doParallel dplyr fastcluster foreach ggplot2 gplots kohonen mclust reshape2 stringr tibble tidyr]; };
cogeqc = derive2 { name="cogeqc"; version="1.0.0"; sha256="1qy3hbr7z5hzgl4zdaxs1a1sna0xrwcl09iyvqdjh8fg9hv546yn"; depends=[Biostrings dplyr ggplot2 ggtree igraph patchwork reshape2 rlang]; };
cogeqc = derive2 { name="cogeqc"; version="1.0.7"; sha256="1dxywmwn0wsfvhpsyvrrav33bf4d0lszrll1f83514ycc9xvzqby"; depends=[Biostrings ggplot2 ggtree igraph patchwork reshape2]; };
cola = derive2 { name="cola"; version="2.2.0"; sha256="1940aqpqnb31kkypnhrrp7lbsv70bxcqkcrjgjmc1ag58148mnka"; depends=[BiocGenerics brew circlize clue cluster ComplexHeatmap crayon digest doParallel eulerr foreach GetoptLong GlobalOptions httr impute irlba knitr markdown matrixStats mclust microbenchmark png RColorBrewer Rcpp skmeans xml2]; };
comapr = derive2 { name="comapr"; version="1.0.0"; sha256="1m8jzgnkghwn7ci8jqr7zs4sj6lisnxri0wiw92m1vz9zibz3w5q"; depends=[BiocParallel circlize dplyr foreach GenomeInfoDb GenomicRanges ggplot2 gridExtra Gviz IRanges Matrix plotly plyr RColorBrewer reshape2 rlang S4Vectors scales SummarizedExperiment tidyr]; };
combi = derive2 { name="combi"; version="1.8.0"; sha256="12rv2ic1y4ab4mj5jlrfgph9fbm44sqla8kqsjn2fwfw2zfzyfq4"; depends=[alabama BB Biobase cobs DBI ggplot2 limma Matrix nleqslv phyloseq reshape2 SummarizedExperiment tensor vegan]; };
compEpiTools = derive2 { name="compEpiTools"; version="1.30.0"; sha256="1b7aasmm56ckfhb8b6im0p6yvlbn6njmn2jyvc8n1x0bxrpy3nv3"; depends=[AnnotationDbi BiocGenerics Biostrings GenomeInfoDb GenomicFeatures GenomicRanges GO_db gplots IRanges methylPipe Rsamtools S4Vectors topGO XVector]; };
compartmap = derive2 { name="compartmap"; version="1.14.0"; sha256="0iq19ca8jmdviacrm5aw6bicgnrkc84s1ywva8mc7lgwnc2fjrnw"; depends=[BiocSingular DelayedArray DelayedMatrixStats GenomicRanges ggplot2 HDF5Array Matrix RaggedExperiment reshape2 RMTstat rtracklayer scales SummarizedExperiment]; };
compcodeR = derive2 { name="compcodeR"; version="1.32.0"; sha256="1xhjizalbi6ngr2jc2znbb83fxjns8yxc52k06yhfhrmmnjm73zi"; depends=[ape caTools edgeR ggplot2 gplots gtools KernSmooth knitr lattice limma markdown MASS matrixStats modeest phylolm ROCR sm stringr vioplot]; };
compcodeR = derive2 { name="compcodeR"; version="1.32.1"; sha256="09jc7h0i5821piga3prqkhzk8zp29iac7r9z9m2rxlsv7lk2ynnk"; depends=[ape caTools edgeR ggplot2 gplots gtools KernSmooth knitr lattice limma markdown MASS matrixStats modeest phylolm ROCR sm stringr vioplot]; };
conclus = derive2 { name="conclus"; version="1.3.3"; sha256="1lgr0k1wf6a0dn4zvb6hpknr3dh10r3v81l3zlwnyfii5bnpi4a6"; depends=[AnnotationDbi Biobase BiocFileCache biomaRt clusterProfiler dbscan doParallel dplyr factoextra foreach fpc GEOquery ggplot2 gridExtra org_Hs_eg_db org_Mm_eg_db pheatmap rlang Rtsne scales scater scran SingleCellExperiment stringr SummarizedExperiment]; };
condiments = derive2 { name="condiments"; version="1.4.0"; sha256="15b6zpj9ivj8i2rykd39ywmb8gyllgfkbmswrjb5jhkinqcj53lf"; depends=[BiocParallel distinct dplyr Ecume igraph magrittr matrixStats mgcv pbapply RANN SingleCellExperiment slingshot SummarizedExperiment TrajectoryUtils]; };
consensus = derive2 { name="consensus"; version="1.14.0"; sha256="0hw9z5mqgnb0zy9sx5w96zsnnzywmlg7pqvvbs6lk33wyi7q42k6"; depends=[gplots matrixStats RColorBrewer]; };
@ -1313,21 +1313,21 @@ in with self; {
doseR = derive2 { name="doseR"; version="1.12.0"; sha256="1g793np07a9npv7vl8fwr9ijd7hbka6k101py3m99rw4wnp6dv0w"; depends=[digest edgeR lme4 matrixStats mclust RUnit S4Vectors SummarizedExperiment]; };
dpeak = derive2 { name="dpeak"; version="1.8.0"; sha256="07cv8yd95diwz9aw4d4wqhb5v75rjh8rcii62x0dqb0nf6x47gcn"; depends=[BSgenome IRanges MASS Rcpp]; };
drawProteins = derive2 { name="drawProteins"; version="1.16.0"; sha256="1rg0kji5rn4zp111cl09dkdd6bichrgd87kqa1623mcxa9xcn7np"; depends=[dplyr ggplot2 httr readr tidyr]; };
drugTargetInteractions = derive2 { name="drugTargetInteractions"; version="1.4.0"; sha256="1njw15cmzicwnjcm4lhj15yhwzk0dqj8jsyqxy0yhc83vd0lny2n"; depends=[AnnotationFilter BiocFileCache biomaRt dplyr ensembldb rappdirs RSQLite S4Vectors UniProt_ws]; };
drugTargetInteractions = derive2 { name="drugTargetInteractions"; version="1.4.1"; sha256="1i9c9c7c83z3i3ldm7qz4wmf4p8aaafakcfyfgzdafhaacxgz4y9"; depends=[AnnotationFilter BiocFileCache biomaRt dplyr ensembldb rappdirs RSQLite S4Vectors UniProt_ws]; };
dupRadar = derive2 { name="dupRadar"; version="1.26.1"; sha256="0lffngmhbld8w2j1njbrk1y41iwbigm1ssac23hlq3p0djad4fxn"; depends=[KernSmooth Rsubread]; };
dyebias = derive2 { name="dyebias"; version="1.56.0"; sha256="0xciqggk4vm31y9zq05iirkrhb9wy5m8pzzdjkzd4k80dvsiny30"; depends=[Biobase marray]; };
easier = derive2 { name="easier"; version="1.2.0"; sha256="088lgpdc1mzhm10k19l2pch0q7zy9ydf78rc4av3w939kazkz9f3"; depends=[arules BiocParallel coin DESeq2 dorothea dplyr easierData ggplot2 ggrepel matrixStats progeny quantiseqr reshape2 rlang ROCR rstatix]; };
easier = derive2 { name="easier"; version="1.2.2"; sha256="1l2245qcbji1cv2rzvl3sf8xailr4rr0hiw0lqafk885qdqlxg7v"; depends=[BiocParallel coin DESeq2 dorothea dplyr easierData ggplot2 ggpubr ggrepel matrixStats progeny quantiseqr reshape2 rlang ROCR rstatix]; };
easyRNASeq = derive2 { name="easyRNASeq"; version="2.32.0"; sha256="1dy1prn7qjvw7kjmq5cgdd0yvpw167f9m2azg1wxn2xfrdyb5ipr"; depends=[Biobase BiocFileCache BiocGenerics BiocParallel biomaRt Biostrings edgeR GenomeInfoDb genomeIntervals GenomicAlignments GenomicRanges IRanges locfit LSD rappdirs Rsamtools S4Vectors ShortRead SummarizedExperiment]; };
easyreporting = derive2 { name="easyreporting"; version="1.8.0"; sha256="1jpgaa55zqnhqla0kid200c63ghwv0apm7p1g1z5ybrfxdlfrrkv"; depends=[rlang rmarkdown shiny]; };
ecolitk = derive2 { name="ecolitk"; version="1.68.0"; sha256="07dax788x8p5dxwkw24hnlzkcpy72swzxl4ynhivjwixwy248diz"; depends=[Biobase]; };
edge = derive2 { name="edge"; version="2.28.0"; sha256="1dld7pz3wwmfp4blnn6fh98dfybgw8b38vmydmfdrzim51p1h036"; depends=[Biobase MASS qvalue snm sva]; };
edge = derive2 { name="edge"; version="2.28.1"; sha256="1yp80qc6ji11ln8zxs3g3rm6k0jh2v20sqfm5h2pqlfw3nn5yqal"; depends=[Biobase MASS qvalue snm sva]; };
edgeR = derive2 { name="edgeR"; version="3.38.4"; sha256="1ww69xrg9qrmq7dix2k48j6akgn58ss3340hm7pjvzx508x1j6n6"; depends=[limma locfit Rcpp]; };
eegc = derive2 { name="eegc"; version="1.22.0"; sha256="16ixc3bn5qkqy5w38428avzrd078xq5h2r8g0csms9b09hxmj65z"; depends=[AnnotationDbi clusterProfiler DESeq2 DOSE edgeR ggplot2 gplots igraph limma org_Hs_eg_db org_Mm_eg_db pheatmap R_utils S4Vectors sna wordcloud]; };
eiR = derive2 { name="eiR"; version="1.36.0"; sha256="0pnv2cfdkagq31v2q7x9yfzi1q79nj76k1i0d92wzkxh8j2rnmhh"; depends=[BiocGenerics ChemmineR DBI digest RcppAnnoy RCurl RUnit snow snowfall]; };
eisaR = derive2 { name="eisaR"; version="1.8.0"; sha256="1c1nmrc6xvmxk40wiwrqysvnslrfr318lypd6qbgh7h3z5n70s0w"; depends=[BiocGenerics edgeR GenomicRanges IRanges limma S4Vectors SummarizedExperiment]; };
enhancerHomologSearch = derive2 { name="enhancerHomologSearch"; version="1.2.0"; sha256="06wycza921fqycwff7fbyjxp64p7lyqinjglvwgv9jk85pxm1dxp"; depends=[BiocFileCache BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicRanges httr IRanges jsonlite Matrix motifmatchr Rcpp rtracklayer S4Vectors]; };
enrichTF = derive2 { name="enrichTF"; version="1.12.0"; sha256="0fv50ma7jaqqbrzaznzvk6vza76if40f5vbxvl22s1ymk5chwk50"; depends=[BiocGenerics BSgenome clusterProfiler GenomeInfoDb GenomicRanges ggplot2 ggpubr heatmap3 IRanges JASPAR2018 magrittr motifmatchr pipeFrame R_utils rmarkdown rtracklayer S4Vectors TFBSTools]; };
enrichplot = derive2 { name="enrichplot"; version="1.16.1"; sha256="17ln1wbkq8sp7jw0dpkccj5qcsl382sgd7zic04dk99z9ag3mh02"; depends=[aplot DOSE ggplot2 ggraph ggtree GOSemSim igraph magrittr plyr purrr RColorBrewer reshape2 scatterpie shadowtext yulab_utils]; };
enrichplot = derive2 { name="enrichplot"; version="1.16.2"; sha256="0qh7bci3rn6y2fl45izrdb62jcm6j0zxxg4pyp4mvvgjvka5lnss"; depends=[aplot DOSE ggplot2 ggraph ggtree GOSemSim igraph magrittr plyr purrr RColorBrewer reshape2 scatterpie shadowtext yulab_utils]; };
ensemblVEP = derive2 { name="ensemblVEP"; version="1.38.0"; sha256="1xllmsdxz0v0fg62piwxh2r96k1s4fykkznpn6dzqg749x1nzb68"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicRanges S4Vectors SummarizedExperiment VariantAnnotation]; };
ensembldb = derive2 { name="ensembldb"; version="2.20.2"; sha256="12n21dcimdhgyjzk33m6xbv0m9ihgyzcf66vr1jr5ycv3rq2s7xc"; depends=[AnnotationDbi AnnotationFilter Biobase BiocGenerics Biostrings curl DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges ProtGenerics Rsamtools RSQLite rtracklayer S4Vectors]; };
epiNEM = derive2 { name="epiNEM"; version="1.20.0"; sha256="1bi0pjmdvlvfjvl6m6r7hd3bd6jdh18i3bnk3s6vpnb52hi35a07"; depends=[BoolNet e1071 graph gtools igraph latex2exp lattice latticeExtra minet mnem pcalg RColorBrewer]; };
@ -1352,12 +1352,12 @@ in with self; {
evaluomeR = derive2 { name="evaluomeR"; version="1.12.0"; sha256="0wvha5ppx937b6qhxf95j0bwav07gq1bs2hw2q487mssksd7s1r2"; depends=[class cluster corrplot flexmix fpc ggdendro ggplot2 kableExtra MASS matrixStats mclust MultiAssayExperiment plotrix prabclus randomForest Rdpack reshape2 SummarizedExperiment]; };
exomeCopy = derive2 { name="exomeCopy"; version="1.42.0"; sha256="0wfigjicbz22dijibbcz38j7javlj891q2f9mgwjpg6pwb0xi178"; depends=[GenomeInfoDb GenomicRanges IRanges Rsamtools]; };
exomePeak2 = derive2 { name="exomePeak2"; version="1.8.1"; sha256="1vr5sijfddzss96zw560i46dgjw5jwrmi5dbgqjvbrrrr371sbk2"; depends=[BiocGenerics BiocParallel Biostrings BSgenome DESeq2 GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges magrittr mclust Rsamtools rtracklayer S4Vectors speedglm SummarizedExperiment]; };
extraChIPs = derive2 { name="extraChIPs"; version="1.0.3"; sha256="0y4dx6ckq9vglilzfwzagw4rpl2y5qfnf41mghxh4r5av1xadrzp"; depends=[BiocIO BiocParallel broom ComplexUpset csaw dplyr edgeR EnrichedHeatmap forcats GenomeInfoDb GenomicInteractions GenomicRanges ggforce ggplot2 ggrepel ggside glue Gviz InteractionSet IRanges limma RColorBrewer rlang Rsamtools rtracklayer S4Vectors scales stringr SummarizedExperiment tibble tidyr tidyselect vctrs VennDiagram]; };
extraChIPs = derive2 { name="extraChIPs"; version="1.0.4"; sha256="1b6kfs0lngvl6wy6a5d5qavls8jakbkjhyq7acrjgqnd94cqndr5"; depends=[BiocIO BiocParallel broom ComplexUpset csaw dplyr edgeR EnrichedHeatmap forcats GenomeInfoDb GenomicInteractions GenomicRanges ggforce ggplot2 ggrepel ggside glue Gviz InteractionSet IRanges limma RColorBrewer rlang Rsamtools rtracklayer S4Vectors scales stringr SummarizedExperiment tibble tidyr tidyselect vctrs VennDiagram]; };
fCCAC = derive2 { name="fCCAC"; version="1.22.0"; sha256="1dn8srjg505725l3arx3cajd2zf0lipq9sqhqrym7km4vlpj58qn"; depends=[ComplexHeatmap fda genomation GenomicRanges ggplot2 IRanges RColorBrewer S4Vectors]; };
fCI = derive2 { name="fCI"; version="1.26.0"; sha256="17gdknml04m18ds0yjik8h8c778r0jqpd182yhzfzq2gldngnaya"; depends=[FNN gtools psych rgl VennDiagram zoo]; };
fabia = derive2 { name="fabia"; version="2.42.0"; sha256="04apwymadah5vidbyg0ayp1lx6955c2626zgb6lhj6jhkhzqqxdv"; depends=[Biobase]; };
factDesign = derive2 { name="factDesign"; version="1.72.0"; sha256="0q6bd3fv6s3br19wivaf2qpcxafw244nvipxixp8ss7a4zgn4qf7"; depends=[Biobase]; };
famat = derive2 { name="famat"; version="1.5.0"; sha256="03gqkfss1prrchsawyfflzdw6bynjrwk3sxy78xzibh7w0ikkzsh"; depends=[clusterProfiler dplyr DT GO_db gprofiler2 KEGGREST magrittr ontologyIndex org_Hs_eg_db plotly reactome_db rWikiPathways shiny shinyBS shinydashboard stringr tidyr]; };
famat = derive2 { name="famat"; version="1.6.6"; sha256="1fj4j3i632dysj5mj03dlbhjs7zmyrh485z5sqdxkj5cr3gjiw24"; depends=[BiasedUrn clusterProfiler dplyr DT GO_db gprofiler2 KEGGREST magrittr mgcv ontologyIndex org_Hs_eg_db plotly reactome_db rWikiPathways shiny shinyBS shinydashboard stringr tidyr]; };
farms = derive2 { name="farms"; version="1.48.0"; sha256="1mnmgd846ayjx1g31pwk186pq6pv0sdq114axpq41728ai3v347c"; depends=[affy Biobase MASS]; };
fastLiquidAssociation = derive2 { name="fastLiquidAssociation"; version="1.32.0"; sha256="0q6zx6kwgv3lzl2gi8f6c9yzc6vl7kafjfbqnaa7q3a2h26dw9y4"; depends=[doParallel Hmisc impute LiquidAssociation preprocessCore WGCNA]; };
fastreeR = derive2 { name="fastreeR"; version="1.0.0"; sha256="1skqg527nfpwknyj9k369l4qkzdm02dn262g8v3m4y75i9dw9s58"; depends=[ape data_table dynamicTreeCut R_utils rJava stringr]; };
@ -1376,7 +1376,7 @@ in with self; {
flowBin = derive2 { name="flowBin"; version="1.32.0"; sha256="10h7jhadmr1l8qw94fsxcrq581ir9136w91ah84c95m7297nr5r8"; depends=[BiocGenerics class flowCore flowFP limma snow]; };
flowCHIC = derive2 { name="flowCHIC"; version="1.30.0"; sha256="0zj76ymr6cs27pg0k9gwzr67y5c3iav40fs4rjcjsi26bv5vxpsy"; depends=[EBImage flowCore ggplot2 hexbin vegan]; };
flowCL = derive2 { name="flowCL"; version="1.34.0"; sha256="05dcxl99sw6d1ngq3wl61y1knmyrf4l9b7nrfmcbigb1isxgjy26"; depends=[graph Rgraphviz]; };
flowClean = derive2 { name="flowClean"; version="1.34.0"; sha256="15kq27136qqplmnj281hi29aakw63r1ip1whj2r87pwhkyz4ifmi"; depends=[bit changepoint flowCore sfsmisc]; };
flowClean = derive2 { name="flowClean"; version="1.34.1"; sha256="0zqgccbfqm6hpi07i5nq5gd626imb6w5xkfb6q8pc0nkkz48mrfh"; depends=[bit changepoint flowCore sfsmisc]; };
flowClust = derive2 { name="flowClust"; version="3.34.0"; sha256="055vm9s8aha92znhpjqkipzprw8bkrinwjaik4ygmhym7w6vbblk"; depends=[Biobase BiocGenerics flowCore graph]; };
flowCore = derive2 { name="flowCore"; version="2.8.0"; sha256="17nci6rc4i0vs0ibw5q8zy30ap7q4550qpq4ifkbblqbyzxlzkhr"; depends=[BH Biobase BiocGenerics cytolib matrixStats Rcpp RcppArmadillo RProtoBufLib S4Vectors]; };
flowCut = derive2 { name="flowCut"; version="1.6.0"; sha256="0p8mgx1q3hw9pfhg41mv9pigx0rakvhsdx5f3dlsqdv2ll85gi98"; depends=[Cairo e1071 flowCore flowDensity]; };
@ -1407,9 +1407,9 @@ in with self; {
frma = derive2 { name="frma"; version="1.48.0"; sha256="1w0q34jkmzqwdjxl4xrvg5nmv11n4l2qf180fwrknvp8am6nf6yx"; depends=[affy Biobase BiocGenerics DBI MASS oligo oligoClasses preprocessCore]; };
frmaTools = derive2 { name="frmaTools"; version="1.48.0"; sha256="0paas86hfqkvcgv00bbgidcaps8p3gvmfy8prq4rcda4lv8i67bl"; depends=[affy Biobase DBI preprocessCore]; };
funtooNorm = derive2 { name="funtooNorm"; version="1.20.0"; sha256="02wkjj2nbghwa0ybmh58hl7r2863h9nw95rsd42xzvcp9vxkpfzz"; depends=[GenomeInfoDb IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest matrixStats minfi pls]; };
gCrisprTools = derive2 { name="gCrisprTools"; version="2.2.1"; sha256="1bq9k3695hxv05f9viw27c73yqmbxhnf60ghk2qv4ixys8lf6fi1"; depends=[Biobase ComplexHeatmap ggplot2 limma rmarkdown RobustRankAggreg SummarizedExperiment]; };
gCrisprTools = derive2 { name="gCrisprTools"; version="2.2.2"; sha256="023csgiik16k72jnb3322qvbrz0vl6pkmdmki29jlj1wmdfz7x6j"; depends=[Biobase ComplexHeatmap ggplot2 limma rmarkdown RobustRankAggreg SummarizedExperiment]; };
gaga = derive2 { name="gaga"; version="2.42.0"; sha256="17a2a73lgmgmrkznysd23c1qbddxcsnjdma7xa0pfjwrwskcisxb"; depends=[Biobase coda EBarrays mgcv]; };
gage = derive2 { name="gage"; version="2.46.0"; sha256="03hx188h98qrbpjlf8v9sg2vqyfv49rp4c18ir11pg6hwqqrxh7b"; depends=[AnnotationDbi GO_db graph KEGGREST]; };
gage = derive2 { name="gage"; version="2.46.1"; sha256="01y04jcy7a9fksyhj0nq37n1inkrpqf4qv117lflvipbx0dsw4gl"; depends=[AnnotationDbi GO_db graph KEGGREST]; };
gaggle = derive2 { name="gaggle"; version="1.64.0"; sha256="1w2819cx7s2hazifhv8iw54jjcvzacjwcpix045ay4fa98ryg7fz"; depends=[graph rJava RUnit]; };
gaia = derive2 { name="gaia"; version="2.39.0"; sha256="023mw2dy6dni7h7a1ild1y6l741kp9bmjzzfyi70jipji1jig4pa"; depends=[]; };
garfield = derive2 { name="garfield"; version="1.24.0"; sha256="1dp8z778ca4pj8da9nlhm80845mv4k7njnz5q4cdy7w1bhlfcjb7"; depends=[]; };
@ -1446,8 +1446,8 @@ in with self; {
ggmanh = derive2 { name="ggmanh"; version="1.0.0"; sha256="0bcdjvhablnxvakin5a4yhdpv5y5n9rqm21yz51mwjdfgz00p2mb"; depends=[gdsfmt ggplot2 ggrepel RColorBrewer rlang scales SeqArray]; };
ggmsa = derive2 { name="ggmsa"; version="1.2.3"; sha256="12s6bs8b8lgcllc540dn4mjdvij2cx28l7zgnz8yzcb05dqnisbr"; depends=[aplot Biostrings dplyr ggalt ggforce ggplot2 ggtree magrittr R4RNA RColorBrewer seqmagick statebins tidyr]; };
ggspavis = derive2 { name="ggspavis"; version="1.2.0"; sha256="0m0wfswz1jn7zhq527qa7q1x028zzrhg1zkw781w5p5i7ky0qzqf"; depends=[ggplot2 ggside SingleCellExperiment SpatialExperiment SummarizedExperiment]; };
ggtree = derive2 { name="ggtree"; version="3.4.2"; sha256="1wc1322cwlankwpmmxj04866insv8dfv2xzgz4ny5ab9ylxkzb2d"; depends=[ape aplot dplyr ggfun ggplot2 magrittr purrr rlang scales tidyr tidytree treeio yulab_utils]; };
ggtreeExtra = derive2 { name="ggtreeExtra"; version="1.6.0"; sha256="02qbjw8yq9p1qw4gh9dz38iw0qpry8jizp22h2l8wrnkxxg0bllg"; depends=[ggnewscale ggplot2 ggtree rlang tidytree]; };
ggtree = derive2 { name="ggtree"; version="3.4.4"; sha256="0h1qlhn4rj7jgd9vrja7lykaglyfvnzwkghvsqj1mvp4niwli7y5"; depends=[ape aplot dplyr ggfun ggplot2 magrittr purrr rlang scales tidyr tidytree treeio yulab_utils]; };
ggtreeExtra = derive2 { name="ggtreeExtra"; version="1.6.1"; sha256="0jhk2wqw8mi99n9063wllbl4ajrz1lzqdn7b827316q7ynh8z6ma"; depends=[ggnewscale ggplot2 ggtree rlang tidytree]; };
girafe = derive2 { name="girafe"; version="1.48.0"; sha256="0633w8dyzrwqgnzj7zhr1hwqh617qpcp7cvs33pgsyxmdh52i32p"; depends=[Biobase BiocGenerics Biostrings genomeIntervals intervals IRanges Rsamtools S4Vectors ShortRead]; };
glmGamPoi = derive2 { name="glmGamPoi"; version="1.8.0"; sha256="0k1qyljg89jvc4g3ixv8n50a1fmw3yfa7xjdvrfhbk3xsm6n1lh9"; depends=[beachmat BiocGenerics DelayedArray DelayedMatrixStats HDF5Array matrixStats Rcpp RcppArmadillo SummarizedExperiment]; };
glmSparseNet = derive2 { name="glmSparseNet"; version="1.14.1"; sha256="0xpbxgrfrgysnfcj757a0i9235pivwpga5xz052izyw2p5nfrlr2"; depends=[biomaRt digest dplyr forcats futile_logger futile_options ggplot2 glmnet glue httr Matrix MultiAssayExperiment readr reshape2 stringr SummarizedExperiment survminer]; };
@ -1469,7 +1469,7 @@ in with self; {
graphite = derive2 { name="graphite"; version="1.42.0"; sha256="0nl5mkgrvf7vsqjy48ij9b1dmxfvp9lf8cpay55h93c4qz4x606g"; depends=[AnnotationDbi graph httr rappdirs rlang]; };
groHMM = derive2 { name="groHMM"; version="1.30.1"; sha256="0v2mk7xcy483w2nygpmyjp73kj3v5pkk1kf1wr41n33dxqlddqai"; depends=[GenomeInfoDb GenomicAlignments GenomicRanges IRanges MASS rtracklayer S4Vectors]; };
gscreend = derive2 { name="gscreend"; version="1.10.0"; sha256="1dymj9s11nqjv25a3adnhllkgi5dw5lvhgxkg6sd7qpkh1bvbmrx"; depends=[BiocParallel fGarch nloptr SummarizedExperiment]; };
gsean = derive2 { name="gsean"; version="1.16.0"; sha256="1vp51nm7bydwljfl9bz4rvqdb5w7yj9zvm74373p2r1pad24r511"; depends=[fgsea PPInfer]; };
gsean = derive2 { name="gsean"; version="1.16.1"; sha256="1wmz760qyg281i62xmizy3p2ajfb4s99wnss9h9yys2skmqcl1vg"; depends=[fgsea PPInfer]; };
gtrellis = derive2 { name="gtrellis"; version="1.28.0"; sha256="1s4xczzv6hz2kyv32xgcq84540w75qr3f644w1s4c3kwxgyq2gff"; depends=[circlize GenomicRanges GetoptLong IRanges]; };
gwascat = derive2 { name="gwascat"; version="2.28.1"; sha256="19ymdxj8966i4yk0zalfw23938cpv4q7pywg4qb242p44na5y9sl"; depends=[AnnotationDbi AnnotationHub BiocFileCache Biostrings GenomeInfoDb GenomicFeatures GenomicRanges IRanges readr S4Vectors snpStats VariantAnnotation]; };
gwasurvivr = derive2 { name="gwasurvivr"; version="1.14.0"; sha256="1cdknh3ib417ni76wcbns54syqycslj0nzip4pw3sqnsif361ak0"; depends=[GWASTools matrixStats SNPRelate SummarizedExperiment survival VariantAnnotation]; };
@ -1544,7 +1544,7 @@ in with self; {
les = derive2 { name="les"; version="1.46.0"; sha256="07c805gcyc7b462hbkvkkjajk8sn735j1js452lz67ixf03pwcaq"; depends=[boot fdrtool gplots RColorBrewer]; };
levi = derive2 { name="levi"; version="1.14.0"; sha256="1dh314yd0zpnmi2vfnf41fhzpg76cgwgzkbm93vcxwrszj53cljc"; depends=[colorspace dplyr DT ggplot2 httr igraph knitr RColorBrewer Rcpp reshape2 rmarkdown shiny shinydashboard shinyjs testthat xml2]; };
lfa = derive2 { name="lfa"; version="1.26.0"; sha256="044866h4fnxmzb3sh9vmrd2smgsbcqgvd19dgwxisi418cad577l"; depends=[corpcor]; };
limma = derive2 { name="limma"; version="3.52.2"; sha256="0m8p8pqmf48f2zdf3qs66hmychbc58g2hfg1wyxzsv180m6xkk65"; depends=[]; };
limma = derive2 { name="limma"; version="3.52.4"; sha256="14xy3qyra2crz31sxgz768mhnhhvcpfhfcigf4xsii643lqcz75h"; depends=[]; };
limmaGUI = derive2 { name="limmaGUI"; version="1.72.0"; sha256="1sq20bdnc9j93iink9cs1p50alzgqfjcxikr8p0dfvd96c4js5b7"; depends=[limma R2HTML tkrplot xtable]; };
lineagespot = derive2 { name="lineagespot"; version="1.0.0"; sha256="0bn0rr7c8x576p53d7p7q0hs7dh5y7dm4z5dgcrp9m8pqgdq3n9h"; depends=[data_table httr MatrixGenerics stringr SummarizedExperiment VariantAnnotation]; };
lionessR = derive2 { name="lionessR"; version="1.10.0"; sha256="182hyz7acnlmprfn3555d1li73abahkylznrnqzizyi20r3nwczq"; depends=[S4Vectors SummarizedExperiment]; };
@ -1594,7 +1594,7 @@ in with self; {
metabCombiner = derive2 { name="metabCombiner"; version="1.6.0"; sha256="1vnh0bqfzknpflk0j5y9jxggmc3m4irxyfbkm9jf6k5a30fnmmxb"; depends=[caret dplyr matrixStats mgcv rlang S4Vectors tidyr]; };
metabolomicsWorkbenchR = derive2 { name="metabolomicsWorkbenchR"; version="1.6.0"; sha256="0mg7wrg8qgv11w7179nrw5w7209qjqbirm9niz2ygw1pidg0slc8"; depends=[data_table httr jsonlite MultiAssayExperiment struct SummarizedExperiment]; };
metabomxtr = derive2 { name="metabomxtr"; version="1.30.0"; sha256="0z02b91gd71b5ksfk2ql5jldicsqh66z2yvv5yyws98xl0qqrrxw"; depends=[Biobase BiocParallel Formula ggplot2 multtest optimx plyr]; };
metagene = derive2 { name="metagene"; version="2.28.0"; sha256="131ymnrwj1ywdf78yd3fffsl6yis9dsizvjhddkqssavz2d4xy71"; depends=[BiocParallel data_table EnsDb_Hsapiens_v86 ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 gplots IRanges magrittr matrixStats purrr R6 Rsamtools rtracklayer stringr]; };
metagene = derive2 { name="metagene"; version="2.28.1"; sha256="1r6kjwbwhksmk9kpvpmn9zwlfllznpam880ma4imsz6pgzfxsskw"; depends=[BiocParallel data_table EnsDb_Hsapiens_v86 ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 gplots IRanges magrittr matrixStats purrr R6 Rsamtools rtracklayer stringr]; };
metagene2 = derive2 { name="metagene2"; version="1.12.0"; sha256="1606i1kw8i4q1m07x2yax2mfmj9knzd7jiqgzq3fn792z1yj1bsb"; depends=[BiocParallel data_table dplyr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges magrittr purrr R6 reshape2 Rsamtools rtracklayer]; };
metagenomeSeq = derive2 { name="metagenomeSeq"; version="1.38.0"; sha256="0v8h8ld4gzq0v90hfprw3v8j2hlac44wxyj2m6qmz0y5hml97k02"; depends=[Biobase foreach glmnet gplots limma Matrix matrixStats RColorBrewer Wrench]; };
metahdep = derive2 { name="metahdep"; version="1.54.0"; sha256="1y8pr873jy1ax8n8qp8kihagddk5j03pjwmxff03amnqrnxyphlv"; depends=[]; };
@ -1633,7 +1633,7 @@ in with self; {
microRNA = derive2 { name="microRNA"; version="1.54.0"; sha256="1bd38qxcd0lb44wgnns5jsn65b3mvgxfalfz7wpysv6sikmlagx4"; depends=[Biostrings]; };
microbiome = derive2 { name="microbiome"; version="1.18.0"; sha256="1z9arkjp5xszlg07mzb4p163i74jfbd9p4gbwv5syivnpl040k12"; depends=[Biostrings compositions dplyr ggplot2 phyloseq reshape2 Rtsne scales tibble tidyr vegan]; };
microbiomeDASim = derive2 { name="microbiomeDASim"; version="1.10.0"; sha256="05lj8ihx8cpx2casxbpyn7n3zwia0bmj0lyn9prqial56s0zmsaj"; depends=[Biobase ggplot2 MASS Matrix metagenomeSeq mvtnorm pbapply phyloseq tmvtnorm]; };
microbiomeExplorer = derive2 { name="microbiomeExplorer"; version="1.6.0"; sha256="0h4flm07n56biviramydxjzcrzxq5n0rr1295mjsxngnpg83kvp8"; depends=[Biobase biomformat broom car DESeq2 dplyr DT forcats heatmaply knitr limma lubridate magrittr matrixStats metagenomeSeq plotly purrr RColorBrewer readr reshape2 rlang rmarkdown shiny shinycssloaders shinydashboard shinyjs shinyWidgets stringr tibble tidyr vegan]; };
microbiomeExplorer = derive2 { name="microbiomeExplorer"; version="1.6.1"; sha256="0sccij5f0h6gg3gi3qsirqc3v17qc6wv6rvh601rgn0zhbdf6hl7"; depends=[Biobase biomformat broom car DESeq2 dplyr DT forcats heatmaply knitr limma lubridate magrittr matrixStats metagenomeSeq plotly purrr RColorBrewer readr reshape2 rlang rmarkdown shiny shinycssloaders shinydashboard shinyjs shinyWidgets stringr tibble tidyr vegan]; };
microbiomeMarker = derive2 { name="microbiomeMarker"; version="1.2.2"; sha256="0bd5a92na9hk2hpmqphpdhn24pk1p2gk5nsbslp8yk5c4161qxmk"; depends=[ALDEx2 ANCOMBC Biobase BiocGenerics BiocParallel biomformat Biostrings caret coin ComplexHeatmap DESeq2 dplyr edgeR ggplot2 ggsignif ggtree IRanges limma magrittr MASS metagenomeSeq multtest patchwork phyloseq plotROC pROC purrr rlang S4Vectors tibble tidyr tidytree vegan yaml]; };
midasHLA = derive2 { name="midasHLA"; version="1.4.0"; sha256="1xvqrsp6rkcnr8fnjr9g62krwwshiy3xapxlmbi4bhm6605b0ccy"; depends=[assertthat broom dplyr formattable HardyWeinberg kableExtra knitr magrittr MultiAssayExperiment qdapTools rlang S4Vectors stringi SummarizedExperiment tibble]; };
miloR = derive2 { name="miloR"; version="1.4.0"; sha256="1jz9p3grnczx0bpdw6j64x21in8zgm3qy19hmm296har2rx9m5zs"; depends=[BiocGenerics BiocNeighbors BiocParallel BiocSingular cowplot dplyr edgeR ggbeeswarm ggplot2 ggraph ggrepel gtools igraph irlba limma Matrix matrixStats patchwork RColorBrewer S4Vectors SingleCellExperiment stringr SummarizedExperiment tibble tidyr]; };
@ -1657,7 +1657,7 @@ in with self; {
mosaics = derive2 { name="mosaics"; version="2.34.0"; sha256="196wz422a284akariq5iicknaqqcm50v63b57gsi2pzmv6qfmf5y"; depends=[GenomeInfoDb GenomicAlignments GenomicRanges IRanges lattice MASS Rcpp Rsamtools S4Vectors]; };
mosbi = derive2 { name="mosbi"; version="1.2.0"; sha256="00l9kykr9n8ys3riw4pjqsdskf8klv9j62v0nr66z66646c1a7vp"; depends=[akmbiclust BH biclust fabia igraph isa2 QUBIC RColorBrewer Rcpp RcppParallel xml2]; };
motifStack = derive2 { name="motifStack"; version="1.40.0"; sha256="0d2ihx73chczbv6f91n04qb372plrdv7k4qws8shyw1fmvb1rq0z"; depends=[ade4 Biostrings ggplot2 htmlwidgets TFBSTools XML]; };
motifbreakR = derive2 { name="motifbreakR"; version="2.10.0"; sha256="0sad73jjx52qzp1fmygp6xqvaxwl5szi69f00f94i1pdyq70qhlg"; depends=[BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicRanges Gviz IRanges matrixStats MotifDb motifStack rtracklayer S4Vectors stringr SummarizedExperiment TFMPvalue VariantAnnotation]; };
motifbreakR = derive2 { name="motifbreakR"; version="2.10.2"; sha256="0xmakbas2hhp0lknnfkdh73pm5z2dm4mrzixkx1sf69q7gq2g8gg"; depends=[BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicRanges Gviz IRanges matrixStats MotifDb motifStack rtracklayer S4Vectors stringr SummarizedExperiment TFMPvalue VariantAnnotation]; };
motifcounter = derive2 { name="motifcounter"; version="1.20.0"; sha256="06yy1ngf703ba6m9vs2jk3w1bds1s8hd4nlr3xrxfj3h7gs9dlak"; depends=[Biostrings]; };
motifmatchr = derive2 { name="motifmatchr"; version="1.18.0"; sha256="1ssn00mxwk23zr5na0vcmxvm69i68f0ga0wqlv1nk2isg0wpv878"; depends=[Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges Matrix Rcpp RcppArmadillo Rsamtools S4Vectors SummarizedExperiment TFBSTools]; };
mpra = derive2 { name="mpra"; version="1.18.0"; sha256="0hbsaw39k7yryl1bf45kzsnwv479minydvxc6kd0sr9qsvlhn6dc"; depends=[BiocGenerics limma S4Vectors scales statmod SummarizedExperiment]; };
@ -1701,7 +1701,7 @@ in with self; {
netboxr = derive2 { name="netboxr"; version="1.7.1"; sha256="06pc0qw275r1ksj07hvkfvcvxl9dg539wja07j7lbqvnp6hzl0xd"; depends=[clusterProfiler data_table DT gplots igraph jsonlite plyr RColorBrewer]; };
nethet = derive2 { name="nethet"; version="1.28.0"; sha256="1c6is3w1saw5i2akmxf6272qlbxpf40ayfh19jialmmqsdhik01z"; depends=[CompQuadForm GeneNet ggm ggplot2 glasso glmnet GSA huge ICSNP limma mclust multtest mvtnorm network]; };
netprioR = derive2 { name="netprioR"; version="1.22.0"; sha256="0wbhcr0qkcsnakfpx49hkjhwbmrc9n76rbs75pc3da4z9wv89qg3"; depends=[doParallel dplyr foreach ggplot2 gridExtra Matrix pROC sparseMVN]; };
netresponse = derive2 { name="netresponse"; version="1.56.0"; sha256="0ciw89zvahyirjnpc69rdipxzlil6fjd5qmk61fdmr1scvvpv2iv"; depends=[BiocStyle ggplot2 graph igraph mclust minet plyr qvalue RColorBrewer reshape2 Rgraphviz rmarkdown]; };
netresponse = derive2 { name="netresponse"; version="1.56.1"; sha256="0vzvmbb01f4dqy6g9yvwl078zmrnvzgdx12d91k43cw289z3ykvz"; depends=[BiocStyle ggplot2 graph igraph mclust minet plyr qvalue RColorBrewer reshape2 Rgraphviz rmarkdown]; };
networkBMA = derive2 { name="networkBMA"; version="2.35.0"; sha256="0xa0b977apbr6p9kqk38582af635kp99csj32bsn2bf8pjsmd4d2"; depends=[BH BMA leaps Rcpp RcppArmadillo RcppEigen]; };
ngsReports = derive2 { name="ngsReports"; version="1.12.4"; sha256="16nc7yl9gaxj7j3dggnd02jn157nndjgxpbvjwa78gxag1lp5fld"; depends=[BiocGenerics Biostrings checkmate dplyr DT forcats ggdendro ggplot2 lifecycle lubridate pander plotly readr reshape2 rmarkdown scales stringr tibble tidyr tidyselect zoo]; };
nnNorm = derive2 { name="nnNorm"; version="2.60.0"; sha256="09xr73xpfzj0w9wx23bqzkcnxlvgc50lazbfpd5phl0ravsl5spl"; depends=[marray nnet]; };
@ -1735,7 +1735,7 @@ in with self; {
oppar = derive2 { name="oppar"; version="1.24.0"; sha256="0p5r98v5f969hllm0ywqfi67gaxlgxba506qvlq2rd870bv5bgmk"; depends=[Biobase GSEABase GSVA]; };
oppti = derive2 { name="oppti"; version="1.10.0"; sha256="0rwgyq4qx4bgz1rl6z93yiadpslnj8v1aj84pdhjdd7gcn0xyc4g"; depends=[devtools ggplot2 knitr limma parallelDist pheatmap RColorBrewer reshape]; };
optimalFlow = derive2 { name="optimalFlow"; version="1.8.0"; sha256="0h6a1cv7gc9pbahn3jpxayxqn9gl9qdygvmppz0za4bmi7jsc03i"; depends=[dbscan doParallel dplyr ellipse flowMeans foreach optimalFlowData randomForest Rfast rgl rlang robustbase transport]; };
orthogene = derive2 { name="orthogene"; version="1.2.0"; sha256="1azq3l8cjzfa3n3hrmww6ms4ala6w4qscxrr2vf7c1lwr47r86v3"; depends=[babelgene data_table DelayedArray DelayedMatrixStats dplyr ggplot2 ggpubr ggtree gprofiler2 grr homologene jsonlite Matrix Matrix_utils patchwork repmis]; };
orthogene = derive2 { name="orthogene"; version="1.2.1"; sha256="1ckzzqglidwb8kmmd93aq2fm8ip95ac3hrf7f8kq27v2z62ykmjk"; depends=[babelgene data_table DelayedArray DelayedMatrixStats dplyr ggplot2 ggpubr ggtree gprofiler2 grr homologene jsonlite Matrix patchwork repmis]; };
pRoloc = derive2 { name="pRoloc"; version="1.36.0"; sha256="11nznxcw06v9z5l9zlkqqpqzb5iaabvfbww0d0y1blgzhf06mfpz"; depends=[Biobase BiocGenerics BiocParallel biomaRt caret class coda dendextend e1071 FNN ggplot2 gtools hexbin kernlab knitr LaplacesDemon lattice MASS mclust mixtools MLInterfaces MSnbase mvtnorm nnet plyr proxy randomForest RColorBrewer Rcpp RcppArmadillo sampling scales]; };
pRolocGUI = derive2 { name="pRolocGUI"; version="2.6.0"; sha256="0j48nky1gl1jggpikq60zxcnd4l3ka7l7wwsg0mn3i99ak1x55xh"; depends=[Biobase BiocGenerics colorspace colourpicker dplyr DT ggplot2 MSnbase pRoloc scales shiny shinydashboard shinydashboardPlus shinyhelper shinyjs shinyWidgets]; };
packFinder = derive2 { name="packFinder"; version="1.8.0"; sha256="0swvwh8wx871yppzi5mail4hrm8cvfyic4yqnwr32sihipsr9sgq"; depends=[ape Biostrings GenomicRanges IRanges kmer S4Vectors]; };
@ -1752,7 +1752,7 @@ in with self; {
pathRender = derive2 { name="pathRender"; version="1.64.0"; sha256="07mad39y9l4c1mb66psi5d9vqd7lwkin3psrszqhl5kd6fi6z3in"; depends=[AnnotationDbi cMAP graph RColorBrewer Rgraphviz]; };
pathVar = derive2 { name="pathVar"; version="1.26.0"; sha256="1q7dryn1h98cfr03xc7bm84rc0xsdhpc1mizd169cyck0jj70siq"; depends=[data_table EMT ggplot2 gridExtra Matching mclust]; };
pathifier = derive2 { name="pathifier"; version="1.34.0"; sha256="0aanvd9sgicnbl87wwfr7sdh6bjy6knhcx1x1d5g34pqbzkwfzwq"; depends=[princurve R_oo]; };
pathview = derive2 { name="pathview"; version="1.36.0"; sha256="1472k107f21cflbx2fip92g8gl9wlwxgwfvgvl73ma0y0jzs0qdq"; depends=[AnnotationDbi graph KEGGgraph KEGGREST org_Hs_eg_db png Rgraphviz XML]; };
pathview = derive2 { name="pathview"; version="1.36.1"; sha256="11g4zhy4qfq0gmy588334f7s2w1acs2dz9kimax5ya2b8jjibk71"; depends=[AnnotationDbi graph KEGGgraph KEGGREST org_Hs_eg_db png Rgraphviz XML]; };
pathwayPCA = derive2 { name="pathwayPCA"; version="1.12.0"; sha256="13ny1z0i7zywpk8lk8qpbj2zpgznq3l4q1vyg1r0rc265p8c3031"; depends=[lars survival]; };
paxtoolsr = derive2 { name="paxtoolsr"; version="1.30.0"; sha256="0kzszgk69078kg5v6blnr1bbhhin8rx62s40xx1abm6pm0k87kli"; depends=[httr igraph jsonlite plyr R_utils rappdirs readr rJava rjson XML]; };
pcaExplorer = derive2 { name="pcaExplorer"; version="2.22.0"; sha256="0xkafpi6y5n8hljdaj183hd5z4ik7lpbklg2cbx1hwfz4n4hh1bl"; depends=[AnnotationDbi base64enc biomaRt DESeq2 DT genefilter GenomicRanges ggplot2 ggrepel GO_db GOstats heatmaply IRanges knitr limma NMF pheatmap plotly plyr rmarkdown S4Vectors scales shiny shinyAce shinyBS shinydashboard SummarizedExperiment threejs tidyr topGO]; };
@ -1760,19 +1760,20 @@ in with self; {
pcxn = derive2 { name="pcxn"; version="2.18.0"; sha256="08w3b8ngbrv7nhc6ybmzwkahk89ixxq67f9zjwinajw3svfi7yw8"; depends=[pcxnData pheatmap]; };
pdInfoBuilder = derive2 { name="pdInfoBuilder"; version="1.60.0"; sha256="14lhkhkgslwls86p7y04k0vjg5yqd2js9j4hnvkn89zydv7r29r0"; depends=[affxparser Biobase BiocGenerics Biostrings DBI IRanges oligo oligoClasses RSQLite S4Vectors]; };
peakPantheR = derive2 { name="peakPantheR"; version="1.10.0"; sha256="0ais6q8vl16x9prf8xsairrhjaaq246zw5n90g2zmh0nnb6674hw"; depends=[bslib doParallel DT foreach ggplot2 gridExtra minpack_lm MSnbase mzR pracma scales shiny shinycssloaders stringr XML]; };
peco = derive2 { name="peco"; version="1.8.0"; sha256="12mq87cyndl7zgwn155vbd8lh3yil9l6slmyjin971hlw53qvikn"; depends=[assertthat circular conicfit doParallel foreach scater SingleCellExperiment SummarizedExperiment]; };
peco = derive2 { name="peco"; version="1.8.0"; sha256="12mq87cyndl7zgwn155vbd8lh3yil9l6slmyjin971hlw53qvikn"; depends=[assertthat circular conicfit doParallel foreach genlasso scater SingleCellExperiment SummarizedExperiment]; };
pengls = derive2 { name="pengls"; version="1.2.0"; sha256="0zk8f9yzxc1mnyyv1g2rfjlcc0hz2dgavjrlgfqajzss4m5dilqs"; depends=[BiocParallel glmnet nlme]; };
pepStat = derive2 { name="pepStat"; version="1.30.0"; sha256="1fj32n61zxm7ls7qk0ncpmm1g2xpf60i0310axniyxlxcbyds0b3"; depends=[Biobase data_table fields GenomicRanges ggplot2 IRanges limma plyr]; };
pepXMLTab = derive2 { name="pepXMLTab"; version="1.30.0"; sha256="11fnm35cbnwy9l09mci9846xcv2mxvknv9hb1bs1i8381q8ysvws"; depends=[XML]; };
periodicDNA = derive2 { name="periodicDNA"; version="1.6.0"; sha256="0ak5i5pqhjyz99lhbiqxjymsars3pajfwd2snzlyc7xd1fjxg06s"; depends=[BiocParallel Biostrings BSgenome cowplot GenomeInfoDb GenomicRanges ggplot2 IRanges magrittr rtracklayer S4Vectors zoo]; };
pgca = derive2 { name="pgca"; version="1.20.0"; sha256="1mrn054flab2v18za40fhfxn691g3gq93p1ciyxfakbyb89ryi5x"; depends=[]; };
phantasus = derive2 { name="phantasus"; version="1.16.2"; sha256="0r860hs25higr4crq1jf0s9a8pzrxbswdmz2zyx5bx0p1b78m6si"; depends=[AnnotationDbi assertthat Biobase ccaPP curl data_table DESeq2 fgsea GEOquery ggplot2 gtable htmltools httpuv httr jsonlite limma Matrix opencpu pheatmap protolite rhdf5 Rook scales stringr svglite]; };
phemd = derive2 { name="phemd"; version="1.12.0"; sha256="0nn0qgb0rz4j2xsjq0wydjhg5pmf2ra67rm9fdm4m1izmzwa0nhs"; depends=[Biobase BiocGenerics cluster cowplot destiny ggplot2 igraph maptree monocle phateR pheatmap pracma RANN RColorBrewer reticulate Rtsne S4Vectors scatterplot3d Seurat SingleCellExperiment SummarizedExperiment transport VGAM]; };
phenoTest = derive2 { name="phenoTest"; version="1.44.0"; sha256="0dm3h7ax83j3izcij7cdf8wg9cl4409vwnmzfbymf33y2l2z8csx"; depends=[annotate AnnotationDbi Biobase biomaRt BMA Category ellipse genefilter ggplot2 gplots GSEABase Heatplus hgu133a_db Hmisc hopach limma mgcv survival xtable]; };
phenopath = derive2 { name="phenopath"; version="1.20.0"; sha256="114v90my05q89bgyjgl2ix62h3l4xcy96j2fncmpa89l7zax9fr2"; depends=[dplyr ggplot2 Rcpp SummarizedExperiment tibble tidyr]; };
philr = derive2 { name="philr"; version="1.22.0"; sha256="1mj6mzl74dbpdhc5laiax5h20i0rh9n2rkip7vgwr5qc26a16kcw"; depends=[ape ggplot2 ggtree phangorn tidyr]; };
phosphonormalizer = derive2 { name="phosphonormalizer"; version="1.20.0"; sha256="0mcgxwg3igji0a3nwhjby10yy6p1hlh1pfcx973vi7fy3w5inm19"; depends=[matrixStats plyr]; };
phyloseq = derive2 { name="phyloseq"; version="1.40.0"; sha256="0hcyv4ziyaw74mc9vf7bad3q9izi9p0whg3hspbs6w8b3hp34y2k"; depends=[ade4 ape Biobase BiocGenerics biomformat Biostrings cluster data_table foreach ggplot2 igraph multtest plyr reshape2 scales vegan]; };
piano = derive2 { name="piano"; version="2.12.0"; sha256="04ipkyj3y6gy1x5q4i6khwwca36q8m2vqgxpn8lcidp0b0i9klkg"; depends=[Biobase BiocGenerics DT fgsea gplots htmlwidgets igraph marray relations scales shiny shinydashboard shinyjs visNetwork]; };
piano = derive2 { name="piano"; version="2.12.1"; sha256="0my7pkd565mkx8b8v008yayh5a0wkp25hwy7fpslygs5ycmr872h"; depends=[Biobase BiocGenerics DT fgsea gplots htmlwidgets igraph marray relations scales shiny shinydashboard shinyjs visNetwork]; };
pickgene = derive2 { name="pickgene"; version="1.68.0"; sha256="1zdiaw0n72sc98qz5fl5xq34s1sqjmp45p2m8m882cv17d81fdgm"; depends=[MASS]; };
pipeComp = derive2 { name="pipeComp"; version="1.6.0"; sha256="0m3kp996x248jvcy3d2d8hfw53vzj24k1jkcdw02lcc8p0rcy0zm"; depends=[aricode BiocParallel circlize clue cluster ComplexHeatmap cowplot dplyr ggplot2 intrinsicDimension knitr Matrix matrixStats randomcoloR RColorBrewer reshape2 Rtsne S4Vectors scales scater scran Seurat SingleCellExperiment SummarizedExperiment uwot viridisLite]; };
pipeFrame = derive2 { name="pipeFrame"; version="1.12.0"; sha256="13xxkk7ja7f7kzn5pxcikdczc5y8f42l4xx3qbw837jxl5sxk2fy"; depends=[Biostrings BSgenome digest GenomeInfoDb magrittr rmarkdown visNetwork]; };
@ -1824,12 +1825,12 @@ in with self; {
qcmetrics = derive2 { name="qcmetrics"; version="1.34.0"; sha256="1xr2j7d7k8fi4bfvgzmi100zhln7a7jq0jw0vn0b1jjs5zwlcikc"; depends=[Biobase knitr pander S4Vectors xtable]; };
qmtools = derive2 { name="qmtools"; version="1.0.0"; sha256="17absfbzih3jam158byykpywlphvzjp3f59dzkjzx7x0wfps4mlz"; depends=[ggplot2 heatmaply igraph MsCoreUtils patchwork rlang scales SummarizedExperiment VIM]; };
qpcrNorm = derive2 { name="qpcrNorm"; version="1.54.0"; sha256="06k1ymzylfsrfbs9cz6m8snrl841fbrrklymfxyrqd20kgfw13xi"; depends=[affy Biobase limma]; };
qpgraph = derive2 { name="qpgraph"; version="2.30.0"; sha256="14vsykbb54pcm12bhdnvq1a7vvnmqw0bz93zqp5v687j01h6b4ps"; depends=[annotate AnnotationDbi Biobase BiocParallel GenomeInfoDb GenomicFeatures GenomicRanges graph IRanges Matrix mvtnorm qtl Rgraphviz S4Vectors]; };
qpgraph = derive2 { name="qpgraph"; version="2.30.2"; sha256="095d3qbi7852islcr30h5s5pny0ci8k60isbczajnfrf79zgad15"; depends=[annotate AnnotationDbi Biobase BiocParallel GenomeInfoDb GenomicFeatures GenomicRanges graph IRanges Matrix mvtnorm qtl Rgraphviz S4Vectors]; };
qrqc = derive2 { name="qrqc"; version="1.50.0"; sha256="0dv6x2g5xkncvzrh37mxlf6hin46qdbj0hrnm83fapw2jb5bfy05"; depends=[Biostrings biovizBase brew ggplot2 plyr reshape Rhtslib testthat xtable]; };
qsea = derive2 { name="qsea"; version="1.22.0"; sha256="0ir752k7is9ns6jxvdsxpjw6byxywl8kakvvfpya763rck014rw0"; depends=[BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicRanges gtools HMMcopy IRanges limma Rsamtools rtracklayer zoo]; };
qsmooth = derive2 { name="qsmooth"; version="1.12.0"; sha256="0fvmb4dd6hfh0m0zssisd3fgd2j93js45gqklpvldpcm76g0dnw7"; depends=[Hmisc SummarizedExperiment sva]; };
qsvaR = derive2 { name="qsvaR"; version="1.0.0"; sha256="1gm2n5085jvz615lcd5qdpqlpk1wmrr395hgaixqgzxagwr5v6ll"; depends=[ggplot2 SummarizedExperiment sva]; };
quantiseqr = derive2 { name="quantiseqr"; version="1.4.0"; sha256="1ffjx3p0kyh023szmijv52fdb19lakk5f5x353rsb1ry7qg6ivdh"; depends=[Biobase ggplot2 limSolve MASS preprocessCore rlang SummarizedExperiment tidyr]; };
quantiseqr = derive2 { name="quantiseqr"; version="1.4.1"; sha256="0yvrgqnf3n5fb49sqcmi34hcvzbnkhndd5i9jq5haw23ns9czmva"; depends=[Biobase ggplot2 limSolve MASS preprocessCore rlang SummarizedExperiment tidyr]; };
quantro = derive2 { name="quantro"; version="1.30.0"; sha256="1zfrz7lxyrbf0c8d277npzj1h4six9whkqplvcjmn3li0xj5qng3"; depends=[Biobase doParallel foreach ggplot2 iterators minfi RColorBrewer]; };
quantsmooth = derive2 { name="quantsmooth"; version="1.62.0"; sha256="027am11ilisdn82k0f62dj0csninfxph1bsv5ff71hsjd9wghars"; depends=[quantreg]; };
qusage = derive2 { name="qusage"; version="2.30.0"; sha256="0ljch8y7985c0q9mfkl0sxdacwyqflszi34qm8gc9lrjf67p0q21"; depends=[Biobase emmeans fftw limma nlme]; };
@ -1838,7 +1839,7 @@ in with self; {
rBiopaxParser = derive2 { name="rBiopaxParser"; version="2.36.0"; sha256="05yh4zcqjwra301xala6b3wjx3i8dliifg1kydpy36gxm2qiy5l2"; depends=[data_table XML]; };
rCGH = derive2 { name="rCGH"; version="1.26.0"; sha256="1a0dwqcs4mpwqqqxw07vphmvbqwh6989ifd7jkls0jcpn2zxsk9g"; depends=[aCGH affy AnnotationDbi DNAcopy GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 IRanges lattice limma mclust org_Hs_eg_db plyr shiny TxDb_Hsapiens_UCSC_hg18_knownGene TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Hsapiens_UCSC_hg38_knownGene]; };
rDGIdb = derive2 { name="rDGIdb"; version="1.22.0"; sha256="11zqkxvbha38riah0j25crg9lwmwp9017a37ap95bh65cvxr9870"; depends=[httr jsonlite]; };
rGADEM = derive2 { name="rGADEM"; version="2.44.0"; sha256="013xdwz0c3n0n9hxf8kkx570qry961pgdjsp023531pl5ww2ing4"; depends=[Biostrings BSgenome GenomicRanges IRanges seqLogo]; };
rGADEM = derive2 { name="rGADEM"; version="2.44.1"; sha256="052z9iavnmkaz9jzz7ycpb8z7qqq3s5k6a04icrwl00wff7zqa2q"; depends=[Biostrings BSgenome GenomicRanges IRanges seqLogo]; };
rGREAT = derive2 { name="rGREAT"; version="1.28.0"; sha256="0px72r8mjimf5mxfwb9qz46kqpgjw5gaqq41hy0212ymjd8whaky"; depends=[GenomicRanges GetoptLong IRanges RCurl rjson]; };
rGenomeTracks = derive2 { name="rGenomeTracks"; version="1.2.0"; sha256="06fgw2sfnpbnaaa1clj4ahvx19pqkylyka62mdhh34sq9majxisq"; depends=[imager reticulate rGenomeTracksData]; };
rRDP = derive2 { name="rRDP"; version="1.30.0"; sha256="091picbs0cmvn1a0pmgpxg5j2gxcdj24d1vm1gz6dch8x9sl2ly2"; depends=[Biostrings]; };
@ -1869,9 +1870,9 @@ in with self; {
regutools = derive2 { name="regutools"; version="1.8.0"; sha256="1r8qxl5md44vvywfvfpkqg5jqb8zkw7hwdh2qpii20jxfd8nf77c"; depends=[AnnotationDbi AnnotationHub BiocFileCache Biostrings DBI GenomicRanges Gviz IRanges RCy3 RSQLite S4Vectors]; };
restfulSE = derive2 { name="restfulSE"; version="1.18.0"; sha256="09alrj7q373w01vylnymna8hjsgs5gg9ngadglasncnk3yswjg3d"; depends=[AnnotationDbi AnnotationHub bigrquery Biobase DBI DelayedArray dplyr ExperimentHub GO_db magrittr reshape2 rhdf5client rlang S4Vectors SummarizedExperiment]; };
rexposome = derive2 { name="rexposome"; version="1.18.2"; sha256="07vmprnv5rg42ddq3bwh3d9m488rnfsn82wpkd3l5lx4mlzp81g5"; depends=[Biobase circlize corrplot FactoMineR ggplot2 ggrepel glmnet gplots gridExtra gtools Hmisc imputeLCMD lme4 lsr mice pryr reshape2 S4Vectors scales scatterplot3d stringr]; };
rfPred = derive2 { name="rfPred"; version="1.34.0"; sha256="17kd733z728dla5vvhf7l6hg50fb9h5sz5ipi4asr88slm62dwma"; depends=[data_table GenomicRanges IRanges Rsamtools]; };
rfPred = derive2 { name="rfPred"; version="1.34.2"; sha256="1ccicwvsfb0b4cmiykswmrhjzpycbfwvfpwz3n23yq594i7658v7"; depends=[data_table GenomeInfoDb GenomicRanges IRanges Rsamtools]; };
rfaRm = derive2 { name="rfaRm"; version="1.8.0"; sha256="1brzplaw5nrwmayfjdqbwyd6xqq2h8421njpi63w6njjc41j9mhh"; depends=[Biostrings data_table httr IRanges magick rsvg rvest S4Vectors stringi xml2]; };
rgoslin = derive2 { name="rgoslin"; version="1.0.0"; sha256="1aki1v99ww3m86fd5fjll4wiwxwpzljn9f7k7mz3x4rd9bj3zyb9"; depends=[dplyr Rcpp]; };
rgoslin = derive2 { name="rgoslin"; version="1.0.99"; sha256="01gkgpqz5xb785par8xrx8mf8icbazxcskn9x2ailk5laaxd73sp"; depends=[dplyr Rcpp]; };
rgsepd = derive2 { name="rgsepd"; version="1.28.0"; sha256="08b11x5qhkq5q17mbr4a2q5r6hz8rrd2xgssclm0flwp2czvnldx"; depends=[AnnotationDbi biomaRt DESeq2 GO_db goseq gplots org_Hs_eg_db SummarizedExperiment]; };
rhdf5 = derive2 { name="rhdf5"; version="2.40.0"; sha256="00cp90mnb8p83jiflm6x4x0qf4p7gvgh47jk9jry6j3qyvfqaiff"; depends=[rhdf5filters Rhdf5lib]; };
rhdf5client = derive2 { name="rhdf5client"; version="1.18.0"; sha256="1mxbpnyqhzvxqc34fyd31pai242ivzs0l28z2zssj8ja463fif9f"; depends=[DelayedArray httr R6 rjson S4Vectors]; };
@ -1885,7 +1886,7 @@ in with self; {
rnaEditr = derive2 { name="rnaEditr"; version="1.6.0"; sha256="1js6a0y5hmkilsq1vgnkjk798z6dnz0acphgfq40p7i6182w1bx8"; depends=[BiocGenerics bumphunter corrplot GenomeInfoDb GenomicRanges IRanges logistf plyr S4Vectors survival]; };
rnaseqcomp = derive2 { name="rnaseqcomp"; version="1.26.0"; sha256="1gpdlv980nid6nsjg1prahdxwp1a8ij00xgzf08ir4ywpvy61ilz"; depends=[RColorBrewer]; };
roar = derive2 { name="roar"; version="1.32.0"; sha256="0zq1praf5h9294cvmrb06l3chx8v40xw2sfvhlnh1516x9sjkwfc"; depends=[BiocGenerics GenomeInfoDb GenomicAlignments GenomicRanges IRanges rtracklayer S4Vectors SummarizedExperiment]; };
rols = derive2 { name="rols"; version="2.24.3"; sha256="0xnvlcv6f6adhbj6hmx8dvsjs66k6mqh3bvcxip031b1z1d5qkc4"; depends=[Biobase BiocGenerics httr jsonlite progress]; };
rols = derive2 { name="rols"; version="2.24.4"; sha256="1hgd4zl8r3xxl5jc8yqyxdqsqpvn9dkmkf79ndqzldq8hmgrpdn9"; depends=[Biobase BiocGenerics httr jsonlite progress]; };
ropls = derive2 { name="ropls"; version="1.28.2"; sha256="07gpx15r8c3wljiwxnff2zp7wxbhzz9r7njk8zg8hpy2q5qm3i6c"; depends=[Biobase MultiAssayExperiment MultiDataSet SummarizedExperiment]; };
rprimer = derive2 { name="rprimer"; version="1.0.0"; sha256="040fy6zjvjjgz9syczvy8dpv02jnl3pv8vb75n40622z0c2hl1nx"; depends=[Biostrings bslib DT ggplot2 IRanges mathjaxr patchwork reshape2 S4Vectors shiny shinycssloaders shinyFeedback]; };
rpx = derive2 { name="rpx"; version="2.4.1"; sha256="169yyyjvr46kis18yxlsznbdb5mdxnlxi6l9nrq5z49wnwx69vav"; depends=[BiocFileCache curl jsonlite RCurl xml2]; };
@ -1923,7 +1924,7 @@ in with self; {
scPCA = derive2 { name="scPCA"; version="1.10.0"; sha256="1ia5z1qf2jvilamkw3vgxshw14bzl4xk19s1bm9f4p08ghvx6px0"; depends=[assertthat BiocParallel cluster coop DelayedArray dplyr elasticnet kernlab Matrix MatrixGenerics matrixStats origami purrr Rdpack RSpectra ScaledMatrix sparsepca stringr tibble]; };
scPipe = derive2 { name="scPipe"; version="1.18.0"; sha256="13wam3qbp9c8qgsp7hm7jq7q0a1ala6mw2xnp3nfbyz39aiwbix9"; depends=[AnnotationDbi BiocGenerics biomaRt dplyr GenomicRanges GGally ggplot2 glue hash magrittr MASS mclust org_Hs_eg_db org_Mm_eg_db Rcpp reshape Rhtslib rlang robustbase rtracklayer S4Vectors scales scater SingleCellExperiment stringr SummarizedExperiment testthat zlibbioc]; };
scReClassify = derive2 { name="scReClassify"; version="1.2.0"; sha256="1afwxnvn17a5awcggifas7zaiw2r556l9iq1yl4kq06s73c1dfws"; depends=[e1071 randomForest SingleCellExperiment SummarizedExperiment]; };
scRecover = derive2 { name="scRecover"; version="1.12.0"; sha256="0p3j54ii9assvhpyy8x8zwibv56h7mf4clvahgp0shp0qg4x7zjv"; depends=[bbmle BiocParallel doParallel foreach gamlss kernlab MASS Matrix penalized preseqR pscl Rmagic rsvd SAVER]; };
scRecover = derive2 { name="scRecover"; version="1.12.0"; sha256="0p3j54ii9assvhpyy8x8zwibv56h7mf4clvahgp0shp0qg4x7zjv"; depends=[bbmle BiocParallel doParallel foreach gamlss kernlab MASS Matrix penalized preseqR pscl rsvd SAVER]; };
scRepertoire = derive2 { name="scRepertoire"; version="1.6.0"; sha256="0an485i5myfiv2zzwd3ql7ckawid894md3k2603mz2yz6qfsl8yj"; depends=[doParallel dplyr ggalluvial ggplot2 igraph plyr powerTCR reshape2 rlang SeuratObject stringdist stringr SummarizedExperiment vegan]; };
scShapes = derive2 { name="scShapes"; version="1.2.0"; sha256="1ammb3a7ddys5zl2maggx3xqvdycy9dn9fl4kffrnqv4abfkvs9c"; depends=[BiocParallel dgof emdbook magrittr MASS Matrix pscl VGAM]; };
scTGIF = derive2 { name="scTGIF"; version="1.10.0"; sha256="0vmr6fginvs1zdzzqmvw8yz25s3w58fwb9ifk8rca922af4m72jx"; depends=[Biobase BiocStyle ggplot2 GSEABase igraph knitr msigdbr nnTensor plotly RColorBrewer Rcpp rmarkdown S4Vectors scales schex SingleCellExperiment SummarizedExperiment tagcloud tibble]; };
@ -1943,10 +1944,10 @@ in with self; {
scone = derive2 { name="scone"; version="1.20.0"; sha256="05id34n6min03ha1chg5mrvx399qm2mby9kxkaz5w8fbidp97851"; depends=[aroma_light BiocParallel boot class cluster compositions diptest edgeR fpc gplots hexbin limma MatrixGenerics matrixStats mixtools rARPACK RColorBrewer rhdf5 RUVSeq SingleCellExperiment SummarizedExperiment]; };
scoreInvHap = derive2 { name="scoreInvHap"; version="1.18.0"; sha256="10ipfhmp93jjw5ijqiv34vkl79i0wmc9mwwrz2j641qlbkyxziaq"; depends=[BiocParallel Biostrings GenomicRanges snpStats SummarizedExperiment VariantAnnotation]; };
scp = derive2 { name="scp"; version="1.6.0"; sha256="09gjq6n7rp4wngfq1yplcrkjrc7yw9w6rg7d2jr6lfj1x74p8syn"; depends=[dplyr magrittr matrixStats MsCoreUtils MultiAssayExperiment QFeatures rlang S4Vectors SingleCellExperiment SummarizedExperiment]; };
scran = derive2 { name="scran"; version="1.24.0"; sha256="0xg7dl35915a65pmzkxdacsm4iqf97ayljdjljcvqx1ycmn7x68w"; depends=[beachmat BH BiocGenerics BiocParallel BiocSingular bluster DelayedArray DelayedMatrixStats dqrng edgeR igraph limma Matrix metapod Rcpp S4Vectors scuttle SingleCellExperiment statmod SummarizedExperiment]; };
scran = derive2 { name="scran"; version="1.24.1"; sha256="1a6vlq8i5gh7zxm6igmy75187pkx42z28qjag50m49xy5valw3ni"; depends=[beachmat BH BiocGenerics BiocParallel BiocSingular bluster DelayedArray DelayedMatrixStats dqrng edgeR igraph limma Matrix metapod Rcpp S4Vectors scuttle SingleCellExperiment statmod SummarizedExperiment]; };
scruff = derive2 { name="scruff"; version="1.14.0"; sha256="0y5p27ih1v4qz47i83zvwwk1d4qkw6i9hwkfpdma3fw87ffxdy0q"; depends=[AnnotationDbi BiocGenerics BiocParallel Biostrings data_table GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggbio ggplot2 ggthemes plyr Rsamtools Rsubread rtracklayer S4Vectors scales ShortRead SingleCellExperiment stringdist SummarizedExperiment]; };
scry = derive2 { name="scry"; version="1.8.0"; sha256="16mj21r91jy8ircdz8rfrdli9gjy0hrx90kf6ghs305d3d4dl193"; depends=[BiocSingular DelayedArray glmpca HDF5Array Matrix SingleCellExperiment SummarizedExperiment]; };
scuttle = derive2 { name="scuttle"; version="1.6.2"; sha256="0nnmq3wf436xaw4arc4y3ldvn6ilsg52xzbccmid0icb8z3y2kzn"; depends=[beachmat BiocGenerics BiocParallel DelayedArray DelayedMatrixStats GenomicRanges Matrix Rcpp S4Vectors SingleCellExperiment SummarizedExperiment]; };
scuttle = derive2 { name="scuttle"; version="1.6.3"; sha256="1w1jy5fqkp2d03lp84d49fsksnl0pcg0wgqyd49d5k1mipdw4671"; depends=[beachmat BiocGenerics BiocParallel DelayedArray DelayedMatrixStats GenomicRanges Matrix Rcpp S4Vectors SingleCellExperiment SummarizedExperiment]; };
sechm = derive2 { name="sechm"; version="1.4.1"; sha256="1rimldsflmaa0ljrhi4am91hvkx6k8xvx5b0q3yl5ndblv2i6rvc"; depends=[circlize ComplexHeatmap matrixStats randomcoloR S4Vectors seriation SummarizedExperiment]; };
segmentSeq = derive2 { name="segmentSeq"; version="2.30.0"; sha256="16ijs06ccm36z634qyrs3pjcnv0ssdzbvd4r76n55qq0mb10fgcq"; depends=[abind baySeq GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors ShortRead]; };
segmenter = derive2 { name="segmenter"; version="1.2.0"; sha256="1q3dx6j3d85f94ki67lga81d7nk0swy5y8ip3fab186i3amdlwjk"; depends=[bamsignals ChIPseeker chromhmmData ComplexHeatmap GenomicRanges IRanges S4Vectors SummarizedExperiment]; };
@ -2027,7 +2028,7 @@ in with self; {
subSeq = derive2 { name="subSeq"; version="1.26.0"; sha256="1fwnjw0bqjqwb39i4cy34ipa6nw6jmk01d4la7r3fmf57xz73sp7"; depends=[Biobase data_table digest dplyr ggplot2 magrittr qvalue tidyr]; };
supersigs = derive2 { name="supersigs"; version="1.4.0"; sha256="0llhk099ql7xv5wcb710pgz6r5ljiac5g9bjwwvzvg3rnjnsq9im"; depends=[assertthat Biostrings caret dplyr rlang rsample SummarizedExperiment tidyr]; };
supraHex = derive2 { name="supraHex"; version="1.34.0"; sha256="1677sffcndrymh8dlahl7qh35zs9k5h0h4x040a7lal1iaqzgxdi"; depends=[ape dplyr hexbin igraph magrittr MASS purrr readr stringr tibble tidyr]; };
surfaltr = derive2 { name="surfaltr"; version="1.2.1"; sha256="1k6rq0rg2lvmghsw1cw3lnmyb8jfdgiyfi0dybx8pq4dyxf67fgh"; depends=[biomaRt Biostrings dplyr ggplot2 httr msa protr readr seqinr stringr testthat xml2]; };
surfaltr = derive2 { name="surfaltr"; version="1.2.2"; sha256="1dx8nfvyknqahszg94064mkvb45b79biibagqz6w24lmymdvxv0v"; depends=[biomaRt Biostrings dplyr ggplot2 httr msa protr readr seqinr stringr testthat xml2]; };
survcomp = derive2 { name="survcomp"; version="1.46.0"; sha256="1b39s6v0awmznfs2gkklps1x3pnk0b4420vhrhgfv5lakz89f1zi"; depends=[bootstrap ipred KernSmooth prodlim rmeta SuppDists survival survivalROC]; };
survtype = derive2 { name="survtype"; version="1.12.0"; sha256="0ihq2js9j2wkbqpgvpk8mzd0rrjvwmmdph84nhm20z04mfbsl4k5"; depends=[clustvarsel pheatmap SummarizedExperiment survival survminer]; };
sva = derive2 { name="sva"; version="3.44.0"; sha256="0ka259rn0la0hjslj7w24q1dyyh79h84nw6mxp7armqbfjb207a4"; depends=[BiocParallel edgeR genefilter limma matrixStats mgcv]; };
@ -2037,7 +2038,8 @@ in with self; {
switchBox = derive2 { name="switchBox"; version="1.32.0"; sha256="0fyysinxa14fx2lwmpishyva7jn4m4k9cipxmbhinf2v5z5h3qj5"; depends=[gplots pROC]; };
switchde = derive2 { name="switchde"; version="1.22.0"; sha256="0mgif3d6pkhivk8yrjdp4xm6kad5vm9g18mvn617zd71zfqd902y"; depends=[dplyr ggplot2 SingleCellExperiment SummarizedExperiment]; };
synapsis = derive2 { name="synapsis"; version="1.2.0"; sha256="1m8js52l8spp3w40pypbha1ydgbjz0ypylk08gjxclw3jp9abwjy"; depends=[EBImage]; };
synergyfinder = derive2 { name="synergyfinder"; version="3.4.1"; sha256="0si3n6g3c98y9zp1qc43b4zalf15ljzkchghapb82pgs5bfjv12l"; depends=[dplyr drc furrr future ggforce ggplot2 ggrepel gstat kriging lattice magrittr metR mice nleqslv pbapply plotly purrr reshape2 sp SpatialExtremes stringr tidyr tidyverse vegan]; };
synapter = derive2 { name="synapter"; version="2.20.1"; sha256="193j8r44msr0hhb9hvpk5yl0i2ns1lpzbfb585jfiji6w37lskrp"; depends=[Biobase Biostrings cleaver lattice MSnbase multtest qvalue RColorBrewer readr rmarkdown]; };
synergyfinder = derive2 { name="synergyfinder"; version="3.4.5"; sha256="01m56wbb9qlyv4fj939h68g31vm0c1rfj0xammc5g2lwwwnnascz"; depends=[dplyr drc furrr future ggforce ggplot2 ggrepel gstat kriging lattice magrittr metR mice nleqslv pbapply plotly purrr reshape2 sp SpatialExtremes stringr tidyr tidyverse vegan]; };
synlet = derive2 { name="synlet"; version="1.26.0"; sha256="0zygs6gskgddb68as4yh3bw1kjlsxk60rym1f6yxj5vzln0ka53c"; depends=[doBy dplyr ggplot2 magrittr RankProd RColorBrewer reshape2]; };
systemPipeR = derive2 { name="systemPipeR"; version="2.2.2"; sha256="1yybbff29gwv6rm0nw4yjw73bbl5prfj8gj4zky917smjfd459im"; depends=[BiocGenerics Biostrings crayon GenomicRanges ggplot2 htmlwidgets magrittr Rsamtools S4Vectors ShortRead stringr SummarizedExperiment yaml]; };
systemPipeShiny = derive2 { name="systemPipeShiny"; version="1.6.1"; sha256="1b0x9vy7mkppf20c0i5p65wjicz12njx7in9w4vjqggvixbc9cjn"; depends=[assertthat bsplus crayon dplyr drawer DT ggplot2 glue htmltools magrittr openssl plotly R6 rlang RSQLite rstudioapi shiny shinyAce shinydashboard shinydashboardPlus shinyFiles shinyjqui shinyjs shinytoastr shinyWidgets spsComps spsUtil stringr styler tibble vroom yaml]; };
@ -2049,12 +2051,12 @@ in with self; {
tRanslatome = derive2 { name="tRanslatome"; version="1.34.0"; sha256="0pv11lrg0fsfpv933k7zjlqswb5zqqxx12cwrfkz91v3x3ivsbza"; depends=[anota Biobase DESeq2 edgeR GOSemSim gplots Heatplus limma org_Hs_eg_db plotrix RankProd sigPathway topGO]; };
tanggle = derive2 { name="tanggle"; version="1.2.0"; sha256="1r04qmxq9ww0ly4mzpkxqv7xyva3mqy02lh3vw13v4dp9d9zaf7c"; depends=[ape ggplot2 ggtree phangorn]; };
target = derive2 { name="target"; version="1.10.0"; sha256="00dwbwzv6y9nfs1cc2jv39b0fcjcbzwfnqmv3zicwfq1lsa4z9mv"; depends=[BiocGenerics GenomicRanges IRanges matrixStats shiny]; };
tenXplore = derive2 { name="tenXplore"; version="1.17.1"; sha256="1k8v0igw44c5fbj1dsjkda98v1c8y9sdw8mjarmy5axlrz3cpcbf"; depends=[AnnotationDbi matrixStats ontoProc org_Mm_eg_db restfulSE shiny SummarizedExperiment]; };
tenXplore = derive2 { name="tenXplore"; version="1.18.1"; sha256="0abybqmmn5ah189c38j7l1msm985vdzk42a1cw0pkskvan62hw50"; depends=[AnnotationDbi matrixStats ontoProc org_Mm_eg_db restfulSE shiny SummarizedExperiment]; };
ternarynet = derive2 { name="ternarynet"; version="1.40.0"; sha256="02r53h6224f8jwwvnv1n09s8i8akhq2qf562crq14m8qk5xw4scf"; depends=[BiocParallel igraph]; };
terraTCGAdata = derive2 { name="terraTCGAdata"; version="1.0.0"; sha256="16sc6n1cgrxr425024k37vzy1n2pij8n7lzxq383r73wyp5z3zkc"; depends=[AnVIL BiocFileCache dplyr GenomicRanges MultiAssayExperiment RaggedExperiment readr S4Vectors TCGAutils tidyr]; };
tidySingleCellExperiment = derive2 { name="tidySingleCellExperiment"; version="1.6.3"; sha256="1b90n9sirpff8dh8kh8m2p4lnpfpqfh0zwvhpk5ymnw7j7x1vw7n"; depends=[cli dplyr ellipsis fansi ggplot2 lifecycle magrittr pillar plotly purrr rlang S4Vectors SingleCellExperiment stringr SummarizedExperiment tibble tidyr tidyselect ttservice vctrs]; };
tidySummarizedExperiment = derive2 { name="tidySummarizedExperiment"; version="1.6.1"; sha256="0y30479w9nim6yap55fcg99qi4599rnliacqaiq693qwnrglksmg"; depends=[cli dplyr ellipsis fansi ggplot2 lifecycle magrittr pillar plotly purrr rlang S4Vectors stringr SummarizedExperiment tibble tidyr tidyselect vctrs]; };
tidybulk = derive2 { name="tidybulk"; version="1.8.0"; sha256="02dgny3zshn1g2lpr2s888yg230q6impi8dffr3x9c8yjak213xp"; depends=[dplyr GenomicRanges lifecycle magrittr preprocessCore purrr readr rlang scales stringi stringr SummarizedExperiment tibble tidyr tidyselect]; };
tidybulk = derive2 { name="tidybulk"; version="1.8.2"; sha256="0ma28j78hcmhwzz6fcc9gp0rpwd1j2wf5nwhnc1xq66sm0wn299g"; depends=[dplyr GenomicRanges lifecycle magrittr preprocessCore purrr readr rlang scales stringi stringr SummarizedExperiment tibble tidyr tidyselect]; };
tigre = derive2 { name="tigre"; version="1.50.0"; sha256="0a4nn8q6iz20xfpwjvdp387cc3w0wdd9rpn6p8gh3dkqh8wsnggd"; depends=[annotate AnnotationDbi Biobase BiocGenerics DBI gplots RSQLite]; };
tilingArray = derive2 { name="tilingArray"; version="1.74.0"; sha256="17n30c0nybsqvmm920zfxfx82yz0afnv1p14jcrnhf3qi9ipdjna"; depends=[affy Biobase genefilter pixmap RColorBrewer strucchange vsn]; };
timeOmics = derive2 { name="timeOmics"; version="1.7.1"; sha256="0s3h8rk7k2s6fnac3v5m8hc2mmdnb4dvbld6ad1as9ac0nvz3521"; depends=[dplyr ggplot2 ggrepel lmtest magrittr mixOmics plyr propr purrr stringr tibble tidyr]; };
@ -2078,7 +2080,7 @@ in with self; {
traviz = derive2 { name="traviz"; version="1.2.0"; sha256="1y2gckk7nm1yb8qv1llkal3mzmdk11kgmdagflymhla4nx2gdgay"; depends=[Biobase ggplot2 mgcv princurve RColorBrewer rgl SingleCellExperiment slingshot SummarizedExperiment viridis]; };
treeio = derive2 { name="treeio"; version="1.20.2"; sha256="1jymbyl82n88ckw0nkbj72rvlxbk5m7xmcmq3fyi885z7aasc0x1"; depends=[ape dplyr jsonlite magrittr rlang tibble tidytree]; };
treekoR = derive2 { name="treekoR"; version="1.4.0"; sha256="0sd1vk1hzvma0644p8wz4037gmm5wpf1d8n22fa0d5m7c97qijrl"; depends=[ape data_table diffcyt dplyr edgeR ggiraph ggplot2 ggtree hopach lme4 multcomp patchwork SingleCellExperiment tidyr]; };
trena = derive2 { name="trena"; version="1.18.0"; sha256="02xhjy1nzjd7lgawqkn3vj3llg1fwl0nisapxmai7yl2lfajhia6"; depends=[AnnotationDbi biomaRt Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 BSgenome_Hsapiens_UCSC_hg38 BSgenome_Mmusculus_UCSC_mm10 DBI GenomicRanges glmnet lassopv MotifDb org_Hs_eg_db randomForest RMySQL RPostgreSQL RSQLite SNPlocs_Hsapiens_dbSNP150_GRCh38 WGCNA xgboost]; };
trena = derive2 { name="trena"; version="1.18.1"; sha256="1d8rf8403by7bfqckhv25qz8bhx4ph0hq48w17d255awb1i8z6ly"; depends=[AnnotationDbi biomaRt Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 BSgenome_Hsapiens_UCSC_hg38 BSgenome_Mmusculus_UCSC_mm10 DBI GenomicRanges glmnet lassopv MotifDb org_Hs_eg_db randomForest RMySQL RPostgreSQL RSQLite SNPlocs_Hsapiens_dbSNP150_GRCh38 WGCNA xgboost]; };
tricycle = derive2 { name="tricycle"; version="1.4.0"; sha256="0bjkajcz6xcfak6071d0ihakrvgf7s0pmkn6vqkjd6yxbfld7zln"; depends=[AnnotationDbi circular dplyr GenomicRanges ggnewscale ggplot2 IRanges RColorBrewer S4Vectors scater scattermore SingleCellExperiment SummarizedExperiment]; };
trigger = derive2 { name="trigger"; version="1.42.0"; sha256="09gbchwpifx5dkmw3irshb63jl22fn2sxsj450krqjjq1gjq1xhx"; depends=[corpcor qtl qvalue sva]; };
trio = derive2 { name="trio"; version="3.34.0"; sha256="1d6gwzx99np8yrsmqnn23s94ib6k41290sv2h4nmzblsidsimlbs"; depends=[LogicReg siggenes survival]; };
@ -2101,7 +2103,7 @@ in with self; {
variancePartition = derive2 { name="variancePartition"; version="1.26.0"; sha256="0wk1xql8b0gxyrqz9hs54xvmp7qdw9b8jnv88p4vgv061iwyk7wv"; depends=[aod Biobase BiocParallel doParallel foreach ggplot2 gplots iterators limma lme4 lmerTest MASS Matrix pbkrtest progress Rdpack reshape2 RhpcBLASctl rlang scales]; };
vbmp = derive2 { name="vbmp"; version="1.64.0"; sha256="02xxvam2dmhhqvm30gxh2v16894qbqha1mc7bl78gq5sc067yr0n"; depends=[]; };
velociraptor = derive2 { name="velociraptor"; version="1.6.0"; sha256="07hbrjqwlxpjrznd9jbv3psqgrsadpa626acgzc02wkl9vfgg5bc"; depends=[basilisk BiocGenerics BiocParallel BiocSingular DelayedArray Matrix reticulate S4Vectors scuttle SingleCellExperiment SummarizedExperiment zellkonverter]; };
veloviz = derive2 { name="veloviz"; version="1.2.0"; sha256="0m9vhfqa9vv97ip7h1g0sv90127yhq7bp3rmdd753di66q2p0qd1"; depends=[igraph Matrix mgcv Rcpp RSpectra]; };
veloviz = derive2 { name="veloviz"; version="1.2.1"; sha256="0k84ghg5c0qlkmd1ck3k1gly8gyd7l1qysm2jmw60nf1b8w8lxxz"; depends=[igraph Matrix mgcv Rcpp RSpectra]; };
vidger = derive2 { name="vidger"; version="1.16.0"; sha256="0kn06i2kb6drq4g5y1xx8wrw4fp5q9147d5mnfj0jvi5db7cmsav"; depends=[Biobase DESeq2 edgeR GGally ggplot2 ggrepel knitr RColorBrewer rmarkdown scales SummarizedExperiment tidyr]; };
viper = derive2 { name="viper"; version="1.30.0"; sha256="0ii6fg0bzgnwfrhlvkh34c17xg2wpyqvb1hg1qsh7prv8dij4q0x"; depends=[Biobase e1071 KernSmooth mixtools]; };
vissE = derive2 { name="vissE"; version="1.4.0"; sha256="01gw1cjm9nz804hw64vsk2jicb86p0dl1qrgkadnixxzcksgb3gz"; depends=[ggforce ggplot2 ggraph ggrepel ggwordcloud GSEABase igraph msigdb plyr RColorBrewer reshape2 scales scico textstem tidygraph tm]; };
@ -2124,7 +2126,7 @@ in with self; {
yamss = derive2 { name="yamss"; version="1.22.0"; sha256="1lcfxw73cxvpy3bnq28pxdy5128mpq5xklsa0mzxdjyqc4g55hy8"; depends=[BiocGenerics data_table EBImage IRanges limma Matrix mzR S4Vectors SummarizedExperiment]; };
yarn = derive2 { name="yarn"; version="1.22.0"; sha256="0z5202pqq02fwm8qf1g36004k7sv668s1xacbpr1cvw5sl452lbg"; depends=[Biobase biomaRt downloader edgeR gplots limma matrixStats preprocessCore quantro RColorBrewer readr]; };
zFPKM = derive2 { name="zFPKM"; version="1.18.0"; sha256="1h7g553rgb5mkmmsp8dyqqs9n9x17xmmcg3iijhb54nyrr2j1mji"; depends=[checkmate dplyr ggplot2 SummarizedExperiment tidyr]; };
zellkonverter = derive2 { name="zellkonverter"; version="1.6.3"; sha256="0l6v7a2zyxpq2w3vm85z439ldi3ld3pkc3wx95a1vxzbr31cpdzz"; depends=[basilisk cli DelayedArray Matrix reticulate S4Vectors SingleCellExperiment SummarizedExperiment]; };
zellkonverter = derive2 { name="zellkonverter"; version="1.6.5"; sha256="0rxpjkisjj1xjchjjm72k8za5hn48wbdahmbllljvxm5ii6k36k6"; depends=[basilisk cli DelayedArray Matrix reticulate S4Vectors SingleCellExperiment SummarizedExperiment]; };
zinbwave = derive2 { name="zinbwave"; version="1.18.0"; sha256="0vpz721sciw5b4ypxj5lj8p53gwkpfwlwkn6k3y8i65zg80p1g6i"; depends=[BiocParallel edgeR genefilter Matrix SingleCellExperiment softImpute SummarizedExperiment]; };
zlibbioc = derive2 { name="zlibbioc"; version="1.42.0"; sha256="0w0y9jixdk6akmasn55g9g0nhlh93hbca5bwx5w1fypnvqrqpxzv"; depends=[]; };
ABAEnrichment = derive2 { name="ABAEnrichment"; version="1.24.0"; sha256="1sp3f72rzlr822dxx42bswynrwwfx6f520hdhfdikqp13p2y4044"; depends=[ABAData data_table GOfuncR gplots gtools Rcpp]; broken = true; };
@ -2159,7 +2161,6 @@ in with self; {
dualKS = derive2 { name="dualKS"; version="1.53.0"; sha256="16cfcylmmcj8x2808529lbpm7qbbrxygic0jkaglhqcdxgrqw3rw"; depends=[affy Biobase]; broken = true; };
methyAnalysis = derive2 { name="methyAnalysis"; version="1.34.0"; sha256="05k3n7iy5ijidbnblbqqas8dsj8drwzbhyrbs8wl1ypkg51havi0"; depends=[annotate AnnotationDbi Biobase BiocGenerics biomaRt genefilter GenomeInfoDb GenomicFeatures GenomicRanges Gviz IRanges lumi methylumi org_Hs_eg_db rtracklayer SummarizedExperiment VariantAnnotation]; broken = true; };
perturbatr = derive2 { name="perturbatr"; version="1.13.0"; sha256="0ssk8cr42hibn917s2z2nzcdan54c7xiydypbi8f3g4w68q4ly31"; depends=[assertthat diffusr doParallel dplyr foreach formula_tools ggplot2 igraph lazyeval lme4 magrittr rlang scales tibble tidyr]; broken = true; };
phemd = derive2 { name="phemd"; version="1.10.0"; sha256="1n3xvw9x3600pwv2wk7mbgal0lr6zpkwziy0whlkdkxzbgy9xzaw"; depends=[Biobase BiocGenerics cluster cowplot destiny ggplot2 igraph maptree monocle phateR pheatmap pracma RANN RColorBrewer reticulate Rtsne S4Vectors scatterplot3d Seurat SingleCellExperiment SummarizedExperiment transport VGAM]; broken = true; };
predictionet = derive2 { name="predictionet"; version="1.40.0"; sha256="1f3ghlcfnls9mx2hbs923rdz7kn0wdhy2csp1y1286c5q5dybrgh"; depends=[catnet igraph MASS penalized RBGL]; broken = true; };
scClassifR = derive2 { name="scClassifR"; version="1.2.0"; sha256="0p9l9q5ina0axrqvqn1y5wkfqi0nacxm3nm6ny34j53znv07b2zz"; depends=[ape caret data_tree dplyr e1071 ggplot2 kernlab pROC ROCR Seurat SingleCellExperiment SummarizedExperiment]; broken = true; };
slinky = derive2 { name="slinky"; version="1.12.0"; sha256="05ywydvyz3jnzbhabhz1sd61hpy9nb22512zpbi48mv5wic1sv3v"; depends=[curl dplyr foreach httr jsonlite readr rhdf5 SummarizedExperiment tidyr]; broken = true; };

5625
pkgs/development/r-modules/cran-packages.nix generated
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File diff suppressed because it is too large Load Diff

5
pkgs/development/r-modules/default.nix
View File

@ -511,6 +511,7 @@ let
nat = [ pkgs.which ];
nat_templatebrains = [ pkgs.which ];
pbdZMQ = lib.optionals stdenv.isDarwin [ pkgs.darwin.binutils ];
bigmemory = [ pkgs.libuuid.dev ];
clustermq = [ pkgs.pkg-config ];
RMark = [ pkgs.which ];
RPushbullet = [ pkgs.which ];
@ -1323,10 +1324,6 @@ let
Rhdf5lib = old.Rhdf5lib.overrideDerivation (attrs: {
propagatedBuildInputs = attrs.propagatedBuildInputs ++ [ pkgs.hdf5.dev ];
});
RNifti = old.RNifti.overrideDerivation (attrs: {
patches = [ ./patches/RNifti.patch ];
});
};
in
self

33
pkgs/development/r-modules/patches/RNifti.patch
View File

@ -1,33 +0,0 @@
diff --git a/configure.ac b/configure.ac
index 05e8a1e..2dcde81 100644
--- a/configure.ac
+++ b/configure.ac
@@ -17,16 +17,5 @@ CXXFLAGS=`"${R_HOME}/bin/R" CMD config CXXFLAGS`
CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS`
LDFLAGS=`"${R_HOME}/bin/R" CMD config LDFLAGS`
-# Checks for libraries.
-ZLIB_FLAGS="-Izlib"
-ZLIB_OBJECTS=`ls -1 src/zlib/*.c | sed 's/^src\///' | sed 's/\\.c$/\\.o/'`
-AC_SEARCH_LIBS([inflate], [z], [
- ZLIB_FLAGS=""
- ZLIB_OBJECTS=""
-])
-
-AC_SUBST(ZLIB_FLAGS)
-AC_SUBST(ZLIB_OBJECTS)
-
AC_CONFIG_FILES([src/Makevars])
AC_OUTPUT
diff --git a/src/Makevars.in b/src/Makevars.in
index 77da572..358cc1d 100644
--- a/src/Makevars.in
+++ b/src/Makevars.in
@@ -1,5 +1,5 @@
-PKG_CPPFLAGS = -DNDEBUG -DHAVE_ZLIB -DUSING_R -DRNIFTI_NIFTILIB_DEDUPLICATE -I../inst/include @ZLIB_FLAGS@
+PKG_CPPFLAGS = -DNDEBUG -DHAVE_ZLIB -DUSING_R -DRNIFTI_NIFTILIB_DEDUPLICATE -I../inst/include
PKG_LIBS = @LIBS@
NIFTI_OBJECTS = znzlib/znzlib.o niftilib/nifti1_io.o niftilib/nifti2_io.o
-OBJECTS = main.o zzz.o @ZLIB_OBJECTS@ $(NIFTI_OBJECTS)
+OBJECTS = main.o zzz.o $(NIFTI_OBJECTS)

51
pkgs/development/tools/buf/buf-tests-dont-use-file-transport.patch Normal file
View File

@ -0,0 +1,51 @@
commit e9219b88de5ed37af337ee2d2e71e7ec7c0aad1b
Author: Robbert van Ginkel <rvanginkel@buf.build>
Date: Thu Oct 20 16:43:28 2022 -0400
Fix git unit test by using fake git server rather than file:// (#1518)
More recent versions of git fix a CVE by disabling some usage of the
`file://` transport, see
https://github.blog/2022-10-18-git-security-vulnerabilities-announced/#cve-2022-39253.
We were using this transport in tests.
Instead, use https://git-scm.com/docs/git-http-backend to serve up this
repository locally so we don't have to use the file protocol. This
should be a more accurate tests, since we mostly expect submodules to
come from servers.
diff --git a/private/pkg/git/git_test.go b/private/pkg/git/git_test.go
index 7b77b6cd..7132054e 100644
--- a/private/pkg/git/git_test.go
+++ b/private/pkg/git/git_test.go
@@ -17,6 +17,8 @@ package git
import (
"context"
"errors"
+ "net/http/cgi"
+ "net/http/httptest"
"os"
"os/exec"
"path/filepath"
@@ -213,6 +215,21 @@ func createGitDirs(
runCommand(ctx, t, container, runner, "git", "-C", submodulePath, "add", "test.proto")
runCommand(ctx, t, container, runner, "git", "-C", submodulePath, "commit", "-m", "commit 0")
+ gitExecPath, err := command.RunStdout(ctx, container, runner, "git", "--exec-path")
+ require.NoError(t, err)
+ t.Log(filepath.Join(string(gitExecPath), "git-http-backend"))
+ // https://git-scm.com/docs/git-http-backend#_description
+ f, err := os.Create(filepath.Join(submodulePath, ".git", "git-daemon-export-ok"))
+ require.NoError(t, err)
+ require.NoError(t, f.Close())
+ server := httptest.NewServer(&cgi.Handler{
+ Path: filepath.Join(strings.TrimSpace(string(gitExecPath)), "git-http-backend"),
+ Dir: submodulePath,
+ Env: []string{"GIT_PROJECT_ROOT=" + submodulePath},
+ })
+ t.Cleanup(server.Close)
+ submodulePath = server.URL
+
originPath := filepath.Join(tmpDir, "origin")
require.NoError(t, os.MkdirAll(originPath, 0777))
runCommand(ctx, t, container, runner, "git", "-C", originPath, "init")

3
pkgs/development/tools/buf/default.nix
View File

@ -26,6 +26,9 @@ buildGoModule rec {
./skip_test_requiring_network.patch
# Skip TestWorkspaceGit which requires .git and commits.
./skip_test_requiring_dotgit.patch
# Remove reliance of tests on file protocol which is disabled in git by default now
# Rebased upstream change https://github.com/bufbuild/buf/commit/bcaa77f8bbb8f6c198154c7c8d53596da4506dab
./buf-tests-dont-use-file-transport.patch
];
nativeBuildInputs = [ installShellFiles ];

2
pkgs/development/tools/electron/generic.nix
View File

@ -31,7 +31,7 @@ let
++ optionals (versionAtLeast version "11.0.0") [ "aarch64-darwin" ]
++ optionals (versionOlder version "19.0.0") [ "i686-linux" ];
sourceProvenance = with sourceTypes; [ binaryNativeCode ];
knownVulnerabilities = optional (versionOlder version "15.0.0") "Electron version ${version} is EOL";
knownVulnerabilities = optional (versionOlder version "18.0.0") "Electron version ${version} is EOL";
};
fetcher = vers: tag: hash: fetchurl {

27
pkgs/development/tools/esbuild/netlify.nix
View File

@ -1,4 +1,9 @@
{ buildGoModule, fetchFromGitHub, lib }:
{ lib
, buildGoModule
, fetchFromGitHub
, fetchpatch
, netlify-cli
}:
buildGoModule rec {
pname = "esbuild";
@ -11,7 +16,25 @@ buildGoModule rec {
sha256 = "0asjmqfzdrpfx2hd5hkac1swp52qknyqavsm59j8xr4c1ixhc6n9";
};
vendorSha256 = "sha256-2ABWPqhK2Cf4ipQH7XvRrd+ZscJhYPc3SV2cGT0apdg=";
vendorSha256 = "sha256-+BfxCyg0KkDQpHt/wycy/8CTG6YBA/VJvJFhhzUnSiQ=";
patches = [
# Both upstream patches update the same dependency "x/sys". It's required for darwin compatibility.
(fetchpatch {
url = "https://github.com/evanw/esbuild/commit/2567e099fcc6959e630f100b2c737ca80e88ba82.patch";
hash = "sha256-KdX/Ru9TBX0mSDaS1ijxgzDI+2AoCvt6Wilhpca3VC0=";
})
(fetchpatch {
url = "https://github.com/evanw/esbuild/commit/fd13718c6195afb9e63682476a774fa6d4483be0.patch";
hash = "sha256-va/bXRBQf9qgE9LZXcKKAa0ZpMt/QG7BFClJ8bPWG1Y=";
})
];
passthru = {
tests = {
inherit netlify-cli;
};
};
meta = with lib; {
description = "A fork of esbuild maintained by netlify";

17
pkgs/development/tools/gllvm/default.nix
View File

@ -1,18 +1,23 @@
{ lib, buildGoPackage, fetchFromGitHub }:
{ lib, buildGoModule, fetchFromGitHub, llvmPackages, getconf }:
buildGoPackage rec {
buildGoModule rec {
pname = "gllvm";
version = "1.3.0";
goPackagePath = "github.com/SRI-CSL/gllvm";
version = "1.3.1";
src = fetchFromGitHub {
owner = "SRI-CSL";
repo = "gllvm";
rev = "v${version}";
sha256 = "sha256-nu6PRFk+GoN1gT1RTbX6mTPZByAGf0bSsj2C5YriGp8=";
sha256 = "sha256-CoreqnMRuPuv+Ci1uyF3HJCJFwK2jwB79okynv6AHTA=";
};
vendorSha256 = "sha256-pQpattmS9VmO3ZIQUFn66az8GSmB4IvYhTTCFn6SUmo=";
checkInputs = with llvmPackages; [
clang
llvm
] ++ lib.optionals stdenv.isDarwin [ getconf ];
meta = with lib; {
homepage = "https://github.com/SRI-CSL/gllvm";
description = "Whole Program LLVM: wllvm ported to go";

24
pkgs/development/tools/misc/aviator/bump-golang-x-sys.patch Normal file
View File

@ -0,0 +1,24 @@
diff --git a/go.mod b/go.mod
index 9bc55db..4bddb07 100644
--- a/go.mod
+++ b/go.mod
@@ -19,5 +19,6 @@ require (
github.com/smallfish/simpleyaml v0.0.0-20170527020626-116d8e577389 // indirect
github.com/starkandwayne/goutils v0.0.0-20190115202530-896b8a6904be
github.com/urfave/cli v1.19.1
+ golang.org/x/sys v0.0.0-20220731174439-a90be440212d // indirect
gopkg.in/yaml.v2 v2.3.0
)
diff --git a/go.sum b/go.sum
index 7641199..d983a95 100644
--- a/go.sum
+++ b/go.sum
@@ -138,6 +138,8 @@ golang.org/x/sys v0.0.0-20191120155948-bd437916bb0e/go.mod h1:h1NjWce9XRLGQEsW7w
golang.org/x/sys v0.0.0-20200116001909-b77594299b42/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
golang.org/x/sys v0.0.0-20200523222454-059865788121 h1:rITEj+UZHYC927n8GT97eC3zrpzXdb/voyeOuVKS46o=
golang.org/x/sys v0.0.0-20200523222454-059865788121/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
+golang.org/x/sys v0.0.0-20220731174439-a90be440212d h1:Sv5ogFZatcgIMMtBSTTAgMYsicp25MXBubjXNDKwm80=
+golang.org/x/sys v0.0.0-20220731174439-a90be440212d/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
golang.org/x/text v0.3.0 h1:g61tztE5qeGQ89tm6NTjjM9VPIm088od1l6aSorWRWg=
golang.org/x/text v0.3.0/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ=
golang.org/x/tools v0.0.0-20190328211700-ab21143f2384/go.mod h1:LCzVGOaR6xXOjkQ3onu1FJEFr0SW1gC7cKk1uF8kGRs=

6
pkgs/development/tools/misc/aviator/default.nix
View File

@ -11,8 +11,12 @@ buildGoModule rec {
sha256 = "sha256-Oa4z8n+q7LKWMnwk+xj9UunzOa3ChaPBCTo828yYJGQ=";
};
patches = [
./bump-golang-x-sys.patch
];
deleteVendor = true;
vendorSha256 = "sha256-rYOphvI1ZE8X5UExfgxHnWBn697SDkNnmxeY7ihIZ1s=";
vendorSha256 = "sha256-AJyxCE4DdAXRS+2sY4Zzu8NTEFKJoV1bopfOqOFKZfI=";
meta = with lib; {
description = "Merge YAML/JSON files in a in a convenient fashion";

4
pkgs/development/tools/misc/ccache/default.nix
View File

@ -15,13 +15,13 @@
let ccache = stdenv.mkDerivation rec {
pname = "ccache";
version = "4.7.2";
version = "4.7.3";
src = fetchFromGitHub {
owner = pname;
repo = pname;
rev = "v${version}";
sha256 = "sha256-djqqXw6SSxH0ki1905hvRrCa1vYKDRFIsCvZ2vat/CM=";
sha256 = "sha256-i5VOKBNAzu65Ha3Lj3Hh6k+EMGPRAo5/qnwnJipDnMI=";
};
outputs = [ "out" "man" ];

6
pkgs/development/tools/nil/default.nix
View File

@ -2,16 +2,16 @@
rustPlatform.buildRustPackage rec {
pname = "nil";
version = "2022-10-03";
version = "2022-11-07";
src = fetchFromGitHub {
owner = "oxalica";
repo = pname;
rev = version;
hash = "sha256-Oo0y/333YyeW9zeYQyiUUay7q7GK/Uu/FdEa6+5c4Pk=";
hash = "sha256-ioY9RvKx9DKnNTeMW8mAIEq23w7Y+lAOFWMkgUQ5fu4=";
};
cargoHash = "sha256-z7wjap7IL2OTd2wEUB6EbSbP71dZiqbKDmJ7oUjVi0U=";
cargoHash = "sha256-sL/bnLK3TifmVHy3LOsduETHh9SGz639vgEKkbHE0HQ=";
CFG_DATE = version;
CFG_REV = "release";

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