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Daiderd Jordan 2018-04-24 20:22:01 +02:00
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4
.editorconfig
View file

@ -26,3 +26,7 @@ indent_size = 4
# Match diffs, avoid to trim trailing whitespace
[*.{diff,patch}]
trim_trailing_whitespace = false
# https://github.com/NixOS/nixpkgs/pull/39336#discussion_r183387754
[.version]
insert_final_newline = false

2
.version
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@ -1 +1 @@
18.09
18.09

50
doc/languages-frameworks/haskell.section.md
View file

@ -666,6 +666,56 @@ prefer one built with GHC 7.8.x in the first place. However, for users who
cannot use GHC 7.10.x at all for some reason, the approach of downgrading to an
older version might be useful.
### How to override packages in all compiler-specific package sets
In the previous section we learned how to override a package in a single
compiler-specific package set. You may have some overrides defined that you want
to use across multiple package sets. To accomplish this you could use the
technique that we learned in the previous section by repeating the overrides for
all the compiler-specific package sets. For example:
```nix
{
packageOverrides = super: let self = super.pkgs; in
{
haskell = super.haskell // {
packages = super.haskell.packages // {
ghc784 = super.haskell.packages.ghc784.override {
overrides = self: super: {
my-package = ...;
my-other-package = ...;
};
};
ghc822 = super.haskell.packages.ghc784.override {
overrides = self: super: {
my-package = ...;
my-other-package = ...;
};
};
...
};
};
};
}
```
However there's a more convenient way to override all compiler-specific package
sets at once:
```nix
{
packageOverrides = super: let self = super.pkgs; in
{
haskell = super.haskell // {
packageOverrides = self: super: {
my-package = ...;
my-other-package = ...;
};
};
};
}
```
### How to recover from GHC's infamous non-deterministic library ID bug
GHC and distributed build farms don't get along well:

4
doc/reviewing-contributions.xml
View file

@ -23,7 +23,9 @@
xlink:href="https://github.com/NixOS/nixpkgs/pulls?q=is%3Apr+is%3Aopen+sort%3Aupdated-desc">most
recently</link> and the <link
xlink:href="https://github.com/NixOS/nixpkgs/pulls?q=is%3Apr+is%3Aopen+sort%3Aupdated-asc">least
recently</link> updated pull-requests.</para>
recently</link> updated pull-requests.
We highly encourage looking at <link xlink:href="https://github.com/NixOS/nixpkgs/pulls?q=is%3Apr+is%3Aopen+review%3Anone+status%3Asuccess+-label%3A%222.status%3A+work-in-progress%22+no%3Aproject+no%3Aassignee+no%3Amilestone">
this list of ready to merge, unreviewed pull requests</link>.</para>
<para>When reviewing a pull request, please always be nice and polite.
Controversial changes can lead to controversial opinions, but it is important

22
maintainers/maintainer-list.nix
View file

@ -28,6 +28,11 @@
github = "AndersonTorres";
name = "Anderson Torres";
};
Anton-Latukha = {
email = "anton.latuka+nixpkgs@gmail.com";
github = "Anton-Latukha";
name = "Anton Latukha";
};
Baughn = {
email = "sveina@gmail.com";
github = "Baughn";
@ -310,6 +315,11 @@
email = "alex@farfromthere.net";
github = "AJChapman";
};
alexfmpe = {
email = "alexandre.fmp.esteves@gmail.com";
github = "alexfmpe";
name = "Alexandre Esteves";
};
alexvorobiev = {
email = "alexander.vorobiev@gmail.com";
github = "alexvorobiev";
@ -710,6 +720,11 @@
github = "canndrew";
name = "Andrew Cann";
};
carlosdagos = {
email = "m@cdagostino.io";
github = "carlosdagos";
name = "Carlos D'Agostino";
};
carlsverre = {
email = "accounts@carlsverre.com";
github = "carlsverre";
@ -1726,7 +1741,7 @@
name = "Jeffrey David Johnson";
};
jensbin = {
email = "jensbin@protonmail.com";
email = "jensbin+git@pm.me";
github = "jensbin";
name = "Jens Binkert";
};
@ -2660,6 +2675,11 @@
github = "nmattia";
name = "Nicolas Mattia";
};
nocent = {
email = "nocent@protonmail.ch";
github = "nocent";
name = "nocent";
};
nocoolnametom = {
email = "nocoolnametom@gmail.com";
github = "nocoolnametom";

8
nixos/modules/config/zram.nix
View file

@ -25,16 +25,16 @@ in
type = types.bool;
description = ''
Enable in-memory compressed swap space provided by the zram kernel
module. It is recommended to enable only for kernel 3.14 or higher.
module.
See https://www.kernel.org/doc/Documentation/blockdev/zram.txt
'';
};
numDevices = mkOption {
default = 4;
default = 1;
type = types.int;
description = ''
Number of zram swap devices to create. It should be equal to the
number of CPU cores your system has.
Number of zram swap devices to create.
'';
};

3
nixos/modules/installer/tools/nixos-enter.sh
View file

@ -51,8 +51,9 @@ if [[ ! -e $mountPoint/etc/NIXOS ]]; then
exit 126
fi
mkdir -m 0755 -p "$mountPoint/dev"
mkdir -m 0755 -p "$mountPoint/dev" "$mountPoint/sys"
mount --rbind /dev "$mountPoint/dev"
mount --rbind /sys "$mountPoint/sys"
# Run the activation script. Set $LOCALE_ARCHIVE to supress some Perl locale warnings.
LOCALE_ARCHIVE=$system/sw/lib/locale/locale-archive chroot "$mountPoint" "$system/activate" >&2 || true

43
nixos/modules/misc/documentation.nix
View file

@ -16,7 +16,10 @@ let cfg = config.documentation; in
description = ''
Whether to install documentation of packages from
<option>environment.systemPackages</option> into the generated system path.
See "Multiple-output packages" chapter in the nixpkgs manual for more info.
'';
# which is at ../../../doc/multiple-output.xml
};
man.enable = mkOption {
@ -28,6 +31,15 @@ let cfg = config.documentation; in
'';
};
info.enable = mkOption {
type = types.bool;
default = true;
description = ''
Whether to install info pages and the <command>info</command> command.
This also includes "info" outputs.
'';
};
doc.enable = mkOption {
type = types.bool;
default = true;
@ -38,12 +50,19 @@ let cfg = config.documentation; in
'';
};
info.enable = mkOption {
dev.enable = mkOption {
type = types.bool;
default = true;
default = false;
description = ''
Whether to install info pages and the <command>info</command> command.
This also includes "info" outputs.
Whether to install documentation targeted at developers.
<itemizedlist>
<listitem><para>This includes man pages targeted at developers if <option>man.enable</option> is
set (this also includes "devman" outputs).</para></listitem>
<listitem><para>This includes info pages targeted at developers if <option>info.enable</option>
is set (this also includes "devinfo" outputs).</para></listitem>
<listitem><para>This includes other pages targeted at developers if <option>doc.enable</option>
is set (this also includes "devdoc" outputs).</para></listitem>
</itemizedlist>
'';
};
@ -56,20 +75,20 @@ let cfg = config.documentation; in
(mkIf cfg.man.enable {
environment.systemPackages = [ pkgs.man-db ];
environment.pathsToLink = [ "/share/man" ];
environment.extraOutputsToInstall = [ "man" ];
environment.extraOutputsToInstall = [ "man" ] ++ optional cfg.dev.enable [ "devman" ];
})
(mkIf cfg.info.enable {
environment.systemPackages = [ pkgs.texinfoInteractive ];
environment.pathsToLink = [ "/share/info" ];
environment.extraOutputsToInstall = [ "info" ] ++ optional cfg.dev.enable [ "devinfo" ];
})
(mkIf cfg.doc.enable {
# TODO(@oxij): put it here and remove from profiles?
# environment.systemPackages = [ pkgs.w3m ]; # w3m-nox?
environment.pathsToLink = [ "/share/doc" ];
environment.extraOutputsToInstall = [ "doc" ];
})
(mkIf cfg.info.enable {
environment.systemPackages = [ pkgs.texinfoInteractive ];
environment.pathsToLink = [ "/share/info" ];
environment.extraOutputsToInstall = [ "info" ];
environment.extraOutputsToInstall = [ "doc" ] ++ optional cfg.dev.enable [ "devdoc" ];
})
]);

2
nixos/modules/module-list.nix
View file

@ -195,6 +195,7 @@
./services/databases/clickhouse.nix
./services/databases/couchdb.nix
./services/databases/firebird.nix
./services/databases/foundationdb.nix
./services/databases/hbase.nix
./services/databases/influxdb.nix
./services/databases/memcached.nix
@ -481,6 +482,7 @@
./services/networking/gnunet.nix
./services/networking/gogoclient.nix
./services/networking/gvpe.nix
./services/networking/hans.nix
./services/networking/haproxy.nix
./services/networking/heyefi.nix
./services/networking/hostapd.nix

66
nixos/modules/security/acme.nix
View file

@ -58,9 +58,11 @@ let
default = "";
example = "systemctl reload nginx.service";
description = ''
Commands to run after certificates are re-issued. Typically
Commands to run after new certificates go live. Typically
the web server and other servers using certificates need to
be reloaded.
Executed in the same directory with the new certificate.
'';
};
@ -78,6 +80,27 @@ let
'';
};
activationDelay = mkOption {
type = types.nullOr types.str;
default = null;
description = ''
Systemd time span expression to delay copying new certificates to main
state directory. See <citerefentry><refentrytitle>systemd.time</refentrytitle>
<manvolnum>7</manvolnum></citerefentry>.
'';
};
preDelay = mkOption {
type = types.lines;
default = "";
description = ''
Commands to run after certificates are re-issued but before they are
activated. Typically the new certificate is published to DNS.
Executed in the same directory with the new certificate.
'';
};
extraDomains = mkOption {
type = types.attrsOf (types.nullOr types.str);
default = {};
@ -186,14 +209,15 @@ in
servicesLists = mapAttrsToList certToServices cfg.certs;
certToServices = cert: data:
let
cpath = "${cfg.directory}/${cert}";
domain = if data.domain != null then data.domain else cert;
cpath = lpath + optionalString (data.activationDelay != null) ".staging";
lpath = "${cfg.directory}/${cert}";
rights = if data.allowKeysForGroup then "750" else "700";
cmdline = [ "-v" "-d" data.domain "--default_root" data.webroot "--valid_min" cfg.validMin ]
++ optionals (data.email != null) [ "--email" data.email ]
++ concatMap (p: [ "-f" p ]) data.plugins
++ concatLists (mapAttrsToList (name: root: [ "-d" (if root == null then name else "${name}:${root}")]) data.extraDomains)
++ (if cfg.production then []
else ["--server" "https://acme-staging.api.letsencrypt.org/directory"]);
++ optionals (!cfg.production) ["--server" "https://acme-staging.api.letsencrypt.org/directory"];
acmeService = {
description = "Renew ACME Certificate for ${cert}";
after = [ "network.target" "network-online.target" ];
@ -206,7 +230,7 @@ in
Group = data.group;
PrivateTmp = true;
};
path = [ pkgs.simp_le ];
path = with pkgs; [ simp_le systemd ];
preStart = ''
mkdir -p '${cfg.directory}'
chown 'root:root' '${cfg.directory}'
@ -229,15 +253,36 @@ in
exit "$EXITCODE"
'';
postStop = ''
cd '${cpath}'
if [ -e /tmp/lastExitCode ] && [ "$(cat /tmp/lastExitCode)" = "0" ]; then
echo "Executing postRun hook..."
${data.postRun}
${if data.activationDelay != null then ''
${data.preDelay}
if [ -d '${lpath}' ]; then
systemd-run --no-block --on-active='${data.activationDelay}' --unit acme-setlive-${cert}.service
else
systemctl --wait start acme-setlive-${cert}.service
fi
'' else data.postRun}
fi
'';
before = [ "acme-certificates.target" ];
wantedBy = [ "acme-certificates.target" ];
};
delayService = {
description = "Set certificate for ${cert} live";
path = with pkgs; [ rsync ];
serviceConfig = {
Type = "oneshot";
};
script = ''
rsync -a --delete-after '${cpath}/' '${lpath}'
'';
postStop = data.postRun;
};
selfsignedService = {
description = "Create preliminary self-signed certificate for ${cert}";
path = [ pkgs.openssl ];
@ -302,11 +347,8 @@ in
};
in (
[ { name = "acme-${cert}"; value = acmeService; } ]
++
(if cfg.preliminarySelfsigned
then [ { name = "acme-selfsigned-${cert}"; value = selfsignedService; } ]
else []
)
++ optional cfg.preliminarySelfsigned { name = "acme-selfsigned-${cert}"; value = selfsignedService; }
++ optional (data.activationDelay != null) { name = "acme-setlive-${cert}"; value = delayService; }
);
servicesAttr = listToAttrs services;
injectServiceDep = {

360
nixos/modules/services/databases/foundationdb.nix Normal file
View file

@ -0,0 +1,360 @@
{ config, lib, pkgs, ... }:
with lib;
let
cfg = config.services.foundationdb;
# used for initial cluster configuration
initialIpAddr = if (cfg.publicAddress != "auto") then cfg.publicAddress else "127.0.0.1";
fdbServers = n:
concatStringsSep "\n" (map (x: "[fdbserver.${toString (x+cfg.listenPortStart)}]") (range 0 (n - 1)));
backupAgents = n:
concatStringsSep "\n" (map (x: "[backup_agent.${toString x}]") (range 1 n));
configFile = pkgs.writeText "foundationdb.conf" ''
[general]
cluster_file = /etc/foundationdb/fdb.cluster
[fdbmonitor]
restart_delay = ${toString cfg.restartDelay}
user = ${cfg.user}
group = ${cfg.group}
[fdbserver]
command = ${pkgs.foundationdb}/bin/fdbserver
public_address = ${cfg.publicAddress}:$ID
listen_address = ${cfg.listenAddress}
datadir = ${cfg.dataDir}/$ID
logdir = ${cfg.logDir}
logsize = ${cfg.logSize}
maxlogssize = ${cfg.maxLogSize}
${optionalString (cfg.class != null) "class = ${cfg.class}"}
memory = ${cfg.memory}
storage_memory = ${cfg.storageMemory}
${optionalString (cfg.locality.machineId != null) "locality_machineid=${cfg.locality.machineId}"}
${optionalString (cfg.locality.zoneId != null) "locality_zoneid=${cfg.locality.zoneId}"}
${optionalString (cfg.locality.datacenterId != null) "locality_dcid=${cfg.locality.datacenterId}"}
${optionalString (cfg.locality.dataHall != null) "locality_data_hall=${cfg.locality.dataHall}"}
${fdbServers cfg.serverProcesses}
[backup_agent]
command = ${pkgs.foundationdb}/libexec/backup_agent
${backupAgents cfg.backupProcesses}
'';
in
{
options.services.foundationdb = {
enable = mkEnableOption "FoundationDB Server";
publicAddress = mkOption {
type = types.str;
default = "auto";
description = "Publicly visible IP address of the process. Port is determined by process ID";
};
listenAddress = mkOption {
type = types.str;
default = "public";
description = "Publicly visible IP address of the process. Port is determined by process ID";
};
listenPortStart = mkOption {
type = types.int;
default = 4500;
description = ''
Starting port number for database listening sockets. Every FDB process binds to a
subsequent port, to this number reflects the start of the overall range. e.g. having
8 server processes will use all ports between 4500 and 4507.
'';
};
openFirewall = mkOption {
type = types.bool;
default = false;
description = ''
Open the firewall ports corresponding to FoundationDB processes and coordinators
using <option>config.networking.firewall.*</option>.
'';
};
dataDir = mkOption {
type = types.path;
default = "/var/lib/foundationdb";
description = "Data directory. All cluster data will be put under here.";
};
logDir = mkOption {
type = types.path;
default = "/var/log/foundationdb";
description = "Log directory.";
};
user = mkOption {
type = types.str;
default = "foundationdb";
description = "User account under which FoundationDB runs.";
};
group = mkOption {
type = types.str;
default = "foundationdb";
description = "Group account under which FoundationDB runs.";
};
class = mkOption {
type = types.nullOr (types.enum [ "storage" "transaction" "stateless" ]);
default = null;
description = "Process class";
};
restartDelay = mkOption {
type = types.int;
default = 10;
description = "Number of seconds to wait before restarting servers.";
};
logSize = mkOption {
type = types.string;
default = "10MiB";
description = ''
Roll over to a new log file after the current log file
reaches the specified size.
'';
};
maxLogSize = mkOption {
type = types.string;
default = "100MiB";
description = ''
Delete the oldest log file when the total size of all log
files exceeds the specified size. If set to 0, old log files
will not be deleted.
'';
};
serverProcesses = mkOption {
type = types.int;
default = 1;
description = "Number of fdbserver processes to run.";
};
backupProcesses = mkOption {
type = types.int;
default = 1;
description = "Number of backup_agent processes to run for snapshots.";
};
memory = mkOption {
type = types.string;
default = "8GiB";
description = ''
Maximum memory used by the process. The default value is
<literal>8GiB</literal>. When specified without a unit,
<literal>MiB</literal> is assumed. This parameter does not
change the memory allocation of the program. Rather, it sets
a hard limit beyond which the process will kill itself and
be restarted. The default value of <literal>8GiB</literal>
is double the intended memory usage in the default
configuration (providing an emergency buffer to deal with
memory leaks or similar problems). It is not recommended to
decrease the value of this parameter below its default
value. It may be increased if you wish to allocate a very
large amount of storage engine memory or cache. In
particular, when the <literal>storageMemory</literal>
parameter is increased, the <literal>memory</literal>
parameter should be increased by an equal amount.
'';
};
storageMemory = mkOption {
type = types.string;
default = "1GiB";
description = ''
Maximum memory used for data storage. The default value is
<literal>1GiB</literal>. When specified without a unit,
<literal>MB</literal> is assumed. Clusters using the memory
storage engine will be restricted to using this amount of
memory per process for purposes of data storage. Memory
overhead associated with storing the data is counted against
this total. If you increase the
<literal>storageMemory</literal>, you should also increase
the <literal>memory</literal> parameter by the same amount.
'';
};
locality = mkOption {
default = {
machineId = null;
zoneId = null;
datacenterId = null;
dataHall = null;
};
description = ''
FoundationDB locality settings.
'';
type = types.submodule ({
options = {
machineId = mkOption {
default = null;
type = types.nullOr types.str;
description = ''
Machine identifier key. All processes on a machine should share a
unique id. By default, processes on a machine determine a unique id to share.
This does not generally need to be set.
'';
};
zoneId = mkOption {
default = null;
type = types.nullOr types.str;
description = ''
Zone identifier key. Processes that share a zone id are
considered non-unique for the purposes of data replication.
If unset, defaults to machine id.
'';
};
datacenterId = mkOption {
default = null;
type = types.nullOr types.str;
description = ''
Data center identifier key. All processes physically located in a
data center should share the id. If you are depending on data
center based replication this must be set on all processes.
'';
};
dataHall = mkOption {
default = null;
type = types.nullOr types.str;
description = ''
Data hall identifier key. All processes physically located in a
data hall should share the id. If you are depending on data
hall based replication this must be set on all processes.
'';
};
};
});
};
extraReadWritePaths = mkOption {
default = [ ];
type = types.listOf types.path;
description = ''
An extra set of filesystem paths that FoundationDB can read to
and write from. By default, FoundationDB runs under a heavily
namespaced systemd environment without write access to most of
the filesystem outside of its data and log directories. By
adding paths to this list, the set of writeable paths will be
expanded. This is useful for allowing e.g. backups to local files,
which must be performed on behalf of the foundationdb service.
'';
};
pidfile = mkOption {
type = types.path;
default = "/run/foundationdb.pid";
description = "Path to pidfile for fdbmonitor.";
};
};
config = mkIf cfg.enable {
meta.doc = ./foundationdb.xml;
meta.maintainers = with lib.maintainers; [ thoughtpolice ];
environment.systemPackages = [ pkgs.foundationdb ];
users.extraUsers = optionalAttrs (cfg.user == "foundationdb") (singleton
{ name = "foundationdb";
description = "FoundationDB User";
uid = config.ids.uids.foundationdb;
group = cfg.group;
});
users.extraGroups = optionalAttrs (cfg.group == "foundationdb") (singleton
{ name = "foundationdb";
gid = config.ids.gids.foundationdb;
});
networking.firewall.allowedTCPPortRanges = mkIf cfg.openFirewall
[ { from = cfg.listenPortStart;
to = (cfg.listenPortStart + cfg.serverProcesses) - 1;
}
];
systemd.services.foundationdb = {
description = "FoundationDB Service";
after = [ "network.target" ];
wantedBy = [ "multi-user.target" ];
unitConfig =
{ RequiresMountsFor = "${cfg.dataDir} ${cfg.logDir}";
};
serviceConfig =
let rwpaths = [ cfg.dataDir cfg.logDir cfg.pidfile "/etc/foundationdb" ]
++ cfg.extraReadWritePaths;
in
{ Type = "simple";
Restart = "always";
RestartSec = 5;
User = cfg.user;
Group = cfg.group;
PIDFile = "${cfg.pidfile}";
PermissionsStartOnly = true; # setup needs root perms
TimeoutSec = 120; # give reasonable time to shut down
# Security options
NoNewPrivileges = true;
ProtectHome = true;
ProtectSystem = "strict";
ProtectKernelTunables = true;
ProtectControlGroups = true;
PrivateTmp = true;
PrivateDevices = true;
ReadWritePaths = lib.concatStringsSep " " (map (x: "-" + x) rwpaths);
};
path = [ pkgs.foundationdb pkgs.coreutils ];
preStart = ''
rm -f ${cfg.pidfile} && \
touch ${cfg.pidfile} && \
chown -R ${cfg.user}:${cfg.group} ${cfg.pidfile}
for x in "${cfg.logDir}" "${cfg.dataDir}" /etc/foundationdb; do
[ ! -d "$x" ] && mkdir -m 0700 -vp "$x" && chown -R ${cfg.user}:${cfg.group} "$x";
done
if [ ! -f /etc/foundationdb/fdb.cluster ]; then
cf=/etc/foundationdb/fdb.cluster
desc=$(tr -dc A-Za-z0-9 </dev/urandom 2>/dev/null | head -c8)
rand=$(tr -dc A-Za-z0-9 </dev/urandom 2>/dev/null | head -c8)
echo ''${desc}:''${rand}@${initialIpAddr}:${builtins.toString cfg.listenPortStart} > $cf
chmod 0660 $cf && chown -R ${cfg.user}:${cfg.group} $cf
touch "${cfg.dataDir}/.first_startup"
fi
'';
script = ''
exec fdbmonitor --lockfile ${cfg.pidfile} --conffile ${configFile};
'';
postStart = ''
if [ -e "${cfg.dataDir}/.first_startup" ]; then
fdbcli --exec "configure new single ssd"
rm -f "${cfg.dataDir}/.first_startup";
fi
'';
};
};
}

279
nixos/modules/services/databases/foundationdb.xml Normal file
View file

@ -0,0 +1,279 @@
<chapter xmlns="http://docbook.org/ns/docbook"
xmlns:xlink="http://www.w3.org/1999/xlink"
xmlns:xi="http://www.w3.org/2001/XInclude"
version="5.0"
xml:id="module-foundationdb">
<title>FoundationDB</title>
<para><emphasis>Source:</emphasis> <filename>modules/services/databases/foundationdb.nix</filename></para>
<para><emphasis>Upstream documentation:</emphasis> <link xlink:href="https://apple.github.io/foundationdb/"/></para>
<para><emphasis>Maintainer:</emphasis> Austin Seipp</para>
<para><emphasis>Default version:</emphasis> 5.1.x</para>
<para>FoundationDB (or "FDB") is a distributed, open source, high performance,
transactional key-value store. It can store petabytes of data and deliver
exceptional performance while maintaining consistency and ACID semantics over a
large cluster.</para>
<section><title>Configuring and basic setup</title>
<para>To enable FoundationDB, add the following to your
<filename>configuration.nix</filename>:
<programlisting>
services.foundationdb.enable = true;
</programlisting>
</para>
<para>After running <command>nixos-rebuild</command>, you can verify whether
FoundationDB is running by executing <command>fdbcli</command> (which is added
to <option>environment.systemPackages</option>):
<programlisting>
$ sudo -u foundationdb fdbcli
Using cluster file `/etc/foundationdb/fdb.cluster'.
The database is available.
Welcome to the fdbcli. For help, type `help'.
fdb> status
Using cluster file `/etc/foundationdb/fdb.cluster'.
Configuration:
Redundancy mode - single
Storage engine - memory
Coordinators - 1
Cluster:
FoundationDB processes - 1
Machines - 1
Memory availability - 5.4 GB per process on machine with least available
Fault Tolerance - 0 machines
Server time - 04/20/18 15:21:14
...
fdb>
</programlisting>
</para>
<para>FoundationDB is run under the <command>foundationdb</command> user and
group by default, but this may be changed in the NixOS configuration. The
systemd unit <command>foundationdb.service</command> controls the
<command>fdbmonitor</command> process.</para>
<para>By default, the NixOS module for FoundationDB creates a single
SSD-storage based database for development and basic usage. This storage engine
is designed for SSDs and will perform poorly on HDDs; however it can handle far
more data than the alternative "memory" engine and is a better default choice
for most deployments. (Note that you can change the storage backend on-the-fly
for a given FoundationDB cluster using <command>fdbcli</command>.)</para>
<para>Furthermore, only 1 server process and 1 backup agent are started in the
default configuration. See below for more on scaling to increase this.</para>
<para>FoundationDB stores all data for all server processes under
<filename>/var/lib/foundationdb</filename>. You can override this using
<option>services.foundationdb.dataDir</option>, e.g.
<programlisting>
services.foundationdb.dataDir = "/data/fdb";
</programlisting>
</para>
<para>Similarly, logs are stored under
<filename>/var/log/foundationdb</filename> by default, and there is a
corresponding <option>services.foundationdb.logDir</option> as well.</para>
</section>
<section><title>Scaling processes and backup agents</title>
<para>Scaling the number of server processes is quite easy; simply specify
<option>services.foundationdb.serverProcesses</option> to be the number of
FoundationDB worker processes that should be started on the machine.</para>
<para>FoundationDB worker processes typically require 4GB of RAM per-process at
minimum for good performance, so this option is set to 1 by default since the
maximum aount of RAM is unknown. You're advised to abide by this restriction,
so pick a number of processes so that each has 4GB or more.</para>
<para>A similar option exists in order to scale backup agent processes,
<option>services.foundationdb.backupProcesses</option>. Backup agents are not
as performance/RAM sensitive, so feel free to experiment with the number of
available backup processes.</para>
</section>
<section><title>Clustering</title>
<para>FoundationDB on NixOS works similarly to other Linux systems, so this
section will be brief. Please refer to the full FoundationDB documentation for
more on clustering.</para>
<para>FoundationDB organizes clusters using a set of
<emphasis>coordinators</emphasis>, which are just specially-designated worker
processes. By default, every installation of FoundationDB on NixOS will start
as its own individual cluster, with a single coordinator: the first worker
process on <command>localhost</command>.</para>
<para>Coordinators are specified globally using the
<command>/etc/foundationdb/fdb.cluster</command> file, which all servers and
client applications will use to find and join coordinators. Note that this file
<emphasis>can not</emphasis> be managed by NixOS so easily: FoundationDB is
designed so that it will rewrite the file at runtime for all clients and nodes
when cluster coordinators change, with clients transparently handling this
without intervention.</para>
<para>When dealing with a cluster, there are two main things you want to
do:</para>
<itemizedlist>
<listitem><para>Add a node to the cluster for storage/compute.</para></listitem>
<listitem><para>Promote an ordinary worker to a coordinator.</para></listitem>
</itemizedlist>
<para>A node must already be a member of the cluster in order to properly be
promoted to a coordinator, so you must always add it first if you wish to
promote it.</para>
<para>To add a machine to a FoundationDB cluster:</para>
<itemizedlist>
<listitem><para>Choose one of the servers to start as the initial coordinator.
</para></listitem>
<listitem><para>Copy the <command>/etc/foundationdb/fdb.cluster</command> file
from this server to all the other servers. Restart FoundationDB on all of
these other servers, so they join the cluster.</para></listitem>
<listitem><para>All of these servers are now connected and working together
in the cluster, under the chosen coordinator.</para></listitem>
</itemizedlist>
<para>At this point, you can add as many nodes as you want by just repeating
the above steps. By default there will still be a single coordinator: you can
use <command>fdbcli</command> to change this and add new coordinators.</para>
<para>As a convenience, FoundationDB can automatically assign coordinators
based on the redundancy mode you wish to achieve for the cluster. Once all the
nodes have been joined, simply set the replication policy, and then issue the
<command>coordinators auto</command> command</para>
<para>For example, assuming we have 3 nodes available, we can enable double
redundancy mode, then auto-select coordinators. For double redundancy, 3
coordinators is ideal: therefore FoundationDB will make
<emphasis>every</emphasis> node a coordinator automatically:</para>
<programlisting>
fdbcli> configure double ssd
fdbcli> coordinators auto
</programlisting>
<para>This will transparently update all the servers within seconds, and
appropriately rewrite the <command>fdb.cluster</command> file, as well as
informing all client processes to do the same.</para>
</section>
<section><title>Client connectivity</title>
<para>By default, all clients must use the current
<command>fdb.cluster</command> file to access a given FoundationDB cluster.
This file is located by default in
<command>/etc/foundationdb/fdb.cluster</command> on all machines with the
FoundationDB service enabled, so you may copy the active one from your cluster
to a new node in order to connect, if it is not part of the cluster.</para>
</section>
<section><title>Backups and Disaster Recovery</title>
<para>The usual rules for doing FoundationDB backups apply on NixOS as written
in the FoundationDB manual. However, one important difference is the security
profile for NixOS: by default, the <command>foundationdb</command> systemd unit
uses <emphasis>Linux namespaces</emphasis> to restrict write access to the
system, except for the log directory, data directory, and the
<command>/etc/foundationdb/</command> directory. This is enforced by default
and cannot be disabled.</para>
<para>However, a side effect of this is that the <command>fdbbackup</command>
command doesn't work properly for local filesystem backups: FoundationDB uses a
server process alongside the database processes to perform backups and copy the
backups to the filesystem. As a result, this process is put under the
restricted namespaces above: the backup process can only write to a limited
number of paths.</para>
<para>In order to allow flexible backup locations on local disks, the
FoundationDB NixOS module supports a
<option>services.foundationdb.extraReadWritePaths</option> option. This option
takes a list of paths, and adds them to the systemd unit, allowing the
processes inside the service to write (and read) the specified
directories.</para>
<para>For example, to create backups in <command>/opt/fdb-backups</command>,
first set up the paths in the module options:</para>
<programlisting>
services.foundationdb.extraReadWritePaths = [ "/opt/fdb-backups" ];
</programlisting>
<para>Restart the FoundationDB service, and it will now be able to write to
this directory (even if it does not yet exist.) Note: this path
<emphasis>must</emphasis> exist before restarting the unit. Otherwise, systemd
will not include it in the private FoundationDB namespace (and it will not add
it dynamically at runtime).</para>
<para>You can now perform a backup:</para>
<programlisting>
$ sudo -u foundationdb fdbbackup start -t default -d file:///opt/fdb-backups
$ sudo -u foundationdb fdbbackup status -t default
</programlisting>
</section>
<section><title>Known limitations</title>
<para>The FoundationDB setup for NixOS should currently be considered beta.
FoundationDB is not new software, but the NixOS compilation and integration has
only undergone fairly basic testing of all the available functionality.</para>
<itemizedlist>
<listitem><para>TLS plugin support is compiled in, but it's currently not
possible to specify the set of TLS certificate options in
<command>services.foundationdb</command></para></listitem>
<listitem><para>There is no way to specify individual parameters for
individual <command>fdbserver</command> processes. Currently, all server
processes inherit all the global <command>fdbmonitor</command> settings.
</para></listitem>
<listitem><para>Python bindings are not currently installed.</para></listitem>
<listitem><para>Ruby bindings are not currently installed.</para></listitem>
<listitem><para>Java bindings are not currently installed.</para></listitem>
<listitem><para>Go bindings are not currently installed.</para></listitem>
</itemizedlist>
</section>
<section><title>Options</title>
<para>NixOS's FoundationDB module allows you to configure all of the most
relevant configuration options for <command>fdbmonitor</command>, matching it
quite closely. For a complete list of all options, check <command>man
configuration.nix</command>.</para>
</section>
<section><title>Full documentation</title>
<para>FoundationDB is a complex piece of software, and requires careful
administration to properly use. Full documentation for administration can be
found here: <link xlink:href="https://apple.github.io/foundationdb/"/>.</para>
</section>
</chapter>

11
nixos/modules/services/hardware/trezord.nix
View file

@ -26,8 +26,15 @@ in {
name = "trezord-udev-rules";
destination = "/etc/udev/rules.d/51-trezor.rules";
text = ''
SUBSYSTEM=="usb", ATTR{idVendor}=="534c", ATTR{idProduct}=="0001", MODE="0666", GROUP="dialout", SYMLINK+="trezor%n"
KERNEL=="hidraw*", ATTRS{idVendor}=="534c", ATTRS{idProduct}=="0001", MODE="0666", GROUP="dialout"
# Trezor 1
SUBSYSTEM=="usb", ATTR{idVendor}=="534c", ATTR{idProduct}=="0001", MODE="0666", GROUP="dialout", SYMLINK+="trezor%n"
KERNEL=="hidraw*", ATTRS{idVendor}=="534c", ATTRS{idProduct}=="0001", MODE="0666", GROUP="dialout"
# Trezor 2 (Model-T)
SUBSYSTEM=="usb", ATTR{idVendor}=="1209", ATTR{idProduct}=="53c0", MODE="0661", GROUP="dialout", TAG+="uaccess", TAG+="udev-acl", SYMLINK+="trezor%n"
SUBSYSTEM=="usb", ATTR{idVendor}=="1209", ATTR{idProduct}=="53c1", MODE="0660", GROUP="dialout", TAG+="uaccess", TAG+="udev-acl", SYMLINK+="trezor%n"
KERNEL=="hidraw*", ATTRS{idVendor}=="1209", ATTRS{idProduct}=="53c1", MODE="0660", GROUP="dialout", TAG+="uaccess", TAG+="udev-acl"
];
'';
});

145
nixos/modules/services/networking/hans.nix Normal file
View file

@ -0,0 +1,145 @@
# NixOS module for hans, ip over icmp daemon
{ config, lib, pkgs, ... }:
with lib;
let
cfg = config.services.hans;
hansUser = "hans";
in
{
### configuration
options = {
services.hans = {
clients = mkOption {
default = {};
description = ''
Each attribute of this option defines a systemd service that
runs hans. Many or none may be defined.
The name of each service is
<literal>hans-<replaceable>name</replaceable></literal>
where <replaceable>name</replaceable> is the name of the
corresponding attribute name.
'';
example = literalExample ''
{
foo = {
server = "192.0.2.1";
extraConfig = "-v";
}
}
'';
type = types.attrsOf (types.submodule (
{
options = {
server = mkOption {
type = types.str;
default = "";
description = "IP address of server running hans";
example = "192.0.2.1";
};
extraConfig = mkOption {
type = types.str;
default = "";
description = "Additional command line parameters";
example = "-v";
};
passwordFile = mkOption {
type = types.str;
default = "";
description = "File that containts password";
};
};
}));
};
server = {
enable = mkOption {
type = types.bool;
default = false;
description = "enable hans server";
};
ip = mkOption {
type = types.str;
default = "";
description = "The assigned ip range";
example = "198.51.100.0";
};
respondToSystemPings = mkOption {
type = types.bool;
default = false;
description = "Force hans respond to ordinary pings";
};
extraConfig = mkOption {
type = types.str;
default = "";
description = "Additional command line parameters";
example = "-v";
};
passwordFile = mkOption {
type = types.str;
default = "";
description = "File that containts password";
};
};
};
};
### implementation
config = mkIf (cfg.server.enable || cfg.clients != {}) {
boot.kernel.sysctl = optionalAttrs cfg.server.respondToSystemPings {
"net.ipv4.icmp_echo_ignore_all" = 1;
};
boot.kernelModules = [ "tun" ];
systemd.services =
let
createHansClientService = name: cfg:
{
description = "hans client - ${name}";
after = [ "network.target" ];
wantedBy = [ "multi-user.target" ];
script = "${pkgs.hans}/bin/hans -f -u ${hansUser} ${cfg.extraConfig} -c ${cfg.server} ${optionalString (cfg.passwordFile != "") "-p $(cat \"${cfg.passwordFile}\")"}";
serviceConfig = {
RestartSec = "30s";
Restart = "always";
};
};
in
listToAttrs (
mapAttrsToList
(name: value: nameValuePair "hans-${name}" (createHansClientService name value))
cfg.clients
) // {
hans = mkIf (cfg.server.enable) {
description = "hans, ip over icmp server daemon";
after = [ "network.target" ];
wantedBy = [ "multi-user.target" ];
script = "${pkgs.hans}/bin/hans -f -u ${hansUser} ${cfg.server.extraConfig} -s ${cfg.server.ip} ${optionalString cfg.server.respondToSystemPings "-r"} ${optionalString (cfg.server.passwordFile != "") "-p $(cat \"${cfg.server.passwordFile}\")"}";
};
};
users.extraUsers = singleton {
name = hansUser;
description = "Hans daemon user";
};
};
meta.maintainers = with maintainers; [ gnidorah ];
}

22
nixos/modules/services/networking/iodine.nix
View file

@ -32,7 +32,7 @@ in
foo = {
server = "tunnel.mdomain.com";
relay = "8.8.8.8";
extraConfig = "-P mysecurepassword";
extraConfig = "-v";
}
}
'';
@ -57,7 +57,13 @@ in
type = types.str;
default = "";
description = "Additional command line parameters";
example = "-P mysecurepassword -l 192.168.1.10 -p 23";
example = "-l 192.168.1.10 -p 23";
};
passwordFile = mkOption {
type = types.str;
default = "";
description = "File that containts password";
};
};
}));
@ -88,7 +94,13 @@ in
type = types.str;
default = "";
description = "Additional command line parameters";
example = "-P mysecurepassword -l 192.168.1.10 -p 23";
example = "-l 192.168.1.10 -p 23";
};
passwordFile = mkOption {
type = types.str;
default = "";
description = "File that containts password";
};
};
@ -108,10 +120,10 @@ in
description = "iodine client - ${name}";
after = [ "network.target" ];
wantedBy = [ "multi-user.target" ];
script = "${pkgs.iodine}/bin/iodine -f -u ${iodinedUser} ${cfg.extraConfig} ${optionalString (cfg.passwordFile != "") "-P $(cat \"${cfg.passwordFile}\")"} ${cfg.relay} ${cfg.server}";
serviceConfig = {
RestartSec = "30s";
Restart = "always";
ExecStart = "${pkgs.iodine}/bin/iodine -f -u ${iodinedUser} ${cfg.extraConfig} ${cfg.relay} ${cfg.server}";
};
};
in
@ -124,7 +136,7 @@ in
description = "iodine, ip over dns server daemon";
after = [ "network.target" ];
wantedBy = [ "multi-user.target" ];
serviceConfig.ExecStart = "${pkgs.iodine}/bin/iodined -f -u ${iodinedUser} ${cfg.server.extraConfig} ${cfg.server.ip} ${cfg.server.domain}";
script = "${pkgs.iodine}/bin/iodined -f -u ${iodinedUser} ${cfg.server.extraConfig} ${optionalString (cfg.server.passwordFile != "") "-P $(cat \"${cfg.server.passwordFile}\")"} ${cfg.server.ip} ${cfg.server.domain}";
};
};

94
nixos/tests/keymap.nix
View file

@ -3,46 +3,34 @@
with import ../lib/testing.nix { inherit system; };
let
readyFile = "/tmp/readerReady";
resultFile = "/tmp/readerResult";
testReader = pkgs.writeScript "test-input-reader" ''
#!${pkgs.stdenv.shell}
readInput() {
touch /tmp/reader.ready
echo "Waiting for '$1' to be typed"
read -r -n1 c
if [ "$c" = "$2" ]; then
echo "SUCCESS: Got back '$c' as expected."
echo 0 >&2
else
echo "FAIL: Expected '$2' but got '$c' instead."
echo 1 >&2
fi
}
rm -f ${resultFile}
logger "testReader: START: Waiting for $1 characters, expecting '$2'."
touch ${readyFile}
read -r -N $1 chars
rm -f ${readyFile}
main() {
error=0
while [ $# -gt 0 ]; do
ret="$((readInput "$2" "$3" | systemd-cat -t "$1") 2>&1)"
if [ $ret -ne 0 ]; then error=1; fi
shift 3
done
return $error
}
main "$@"; echo -n $? > /tmp/reader.exit
if [ "$chars" == "$2" ]; then
logger -s "testReader: PASS: Got '$2' as expected." 2>${resultFile}
else
logger -s "testReader: FAIL: Expected '$2' but got '$chars'." 2>${resultFile}
fi
'';
mkReaderInput = testname: { qwerty, expect }: with pkgs.lib; let
lq = length qwerty;
le = length expect;
msg = "`qwerty' (${lq}) and `expect' (${le}) lists"
+ " need to be of the same length!";
result = flatten (zipListsWith (a: b: [testname a b]) qwerty expect);
in if lq != le then throw msg else result;
mkKeyboardTest = layout: { extraConfig ? {}, tests }: with pkgs.lib; let
readerInput = flatten (mapAttrsToList mkReaderInput tests);
combinedTests = foldAttrs (acc: val: acc ++ val) [] (builtins.attrValues tests);
perlStr = val: "'${escape ["'" "\\"] val}'";
perlReaderInput = concatMapStringsSep ", " perlStr readerInput;
lq = length combinedTests.qwerty;
le = length combinedTests.expect;
msg = "length mismatch between qwerty (${toString lq}) and expect (${toString le}) lists!";
send = concatMapStringsSep ", " perlStr combinedTests.qwerty;
expect = if (lq == le) then concatStrings combinedTests.expect else throw msg;
in makeTest {
name = "keymap-${layout}";
@ -50,38 +38,40 @@ let
machine.i18n.consoleKeyMap = mkOverride 900 layout;
machine.services.xserver.layout = mkOverride 900 layout;
machine.imports = [ ./common/x11.nix extraConfig ];
machine.services.xserver.displayManager.slim.enable = true;
testScript = ''
sub waitCatAndDelete ($) {
return $machine->succeed(
"for i in \$(seq 600); do if [ -e '$_[0]' ]; then ".
"cat '$_[0]' && rm -f '$_[0]' && exit 0; ".
"fi; sleep 0.1; done; echo timed out after 60 seconds >&2; exit 1"
);
};
sub mkTest ($$) {
my ($desc, $cmd) = @_;
my @testdata = (${perlReaderInput});
my $shellTestdata = join ' ', map { "'".s/'/'\\'''/gr."'" } @testdata;
subtest $desc, sub {
$machine->succeed("$cmd ${testReader} $shellTestdata &");
while (my ($testname, $qwerty, $expect) = splice(@testdata, 0, 3)) {
waitCatAndDelete "/tmp/reader.ready";
$machine->sendKeys($qwerty);
};
my $exitcode = waitCatAndDelete "/tmp/reader.exit";
die "tests for $desc failed" if $exitcode ne 0;
# prepare and start testReader
$machine->execute("rm -f ${readyFile} ${resultFile}");
$machine->succeed("$cmd ${testReader} ${toString le} ".q(${escapeShellArg expect} & ));
if ($desc eq "Xorg keymap") {
# make sure the xterm window is open and has focus
$machine->waitForWindow(qr/testterm/);
$machine->succeed("${pkgs.xdotool}/bin/xdotool search --name testterm windowactivate --sync");
}
# wait for reader to be ready
$machine->waitForFile("${readyFile}");
$machine->sleep(1);
# send all keys
foreach ((${send})) { $machine->sendKeys($_); };
# wait for result and check
$machine->waitForFile("${resultFile}");
$machine->succeed("grep -q 'PASS:' ${resultFile}");
};
}
};
$machine->waitForX;
mkTest "VT keymap", "openvt -sw --";
mkTest "Xorg keymap", "DISPLAY=:0 xterm -fullscreen -e";
mkTest "Xorg keymap", "DISPLAY=:0 xterm -title testterm -fullscreen -e";
'';
};

10
pkgs/applications/altcoins/bitcoin-unlimited.nix
View file

@ -1,6 +1,7 @@
{ stdenv, fetchFromGitHub, pkgconfig, autoreconfHook, openssl, db48, boost
, zlib, miniupnpc, qt4, utillinux, protobuf, qrencode, libevent
, withGui }:
, withGui
, Foundation, ApplicationServices, AppKit }:
with stdenv.lib;
@ -19,7 +20,8 @@ stdenv.mkDerivation rec {
nativeBuildInputs = [ pkgconfig autoreconfHook ];
buildInputs = [ openssl db48 boost zlib
miniupnpc utillinux protobuf libevent ]
++ optionals withGui [ qt4 qrencode ];
++ optionals withGui [ qt4 qrencode ]
++ optionals stdenv.isDarwin [ Foundation ApplicationServices AppKit ];
patches = [
./bitcoin-unlimited-const-comparators.patch
@ -36,7 +38,7 @@ stdenv.mkDerivation rec {
completely decentralized, without the need for a central server or trusted
parties. Users hold the crypto keys to their own money and transact directly
with each other, with the help of a P2P network to check for double-spending.
The Bitcoin Unlimited (BU) project seeks to provide a voice to all
stakeholders in the Bitcoin ecosystem.
@ -55,7 +57,7 @@ stdenv.mkDerivation rec {
If you support an increase in the blocksize limit by any means - or just
support Bitcoin conflict resolution as originally envisioned by its founder -
consider running a Bitcoin Unlimited client.
consider running a Bitcoin Unlimited client.
'';
homepage = https://www.bitcoinunlimited.info/;
maintainers = with maintainers; [ DmitryTsygankov ];

8
pkgs/applications/altcoins/bitcoin-xt.nix
View file

@ -1,6 +1,7 @@
{ stdenv, fetchFromGitHub, pkgconfig, autoreconfHook, openssl, db48, boost
, zlib, miniupnpc, qt4, utillinux, protobuf, qrencode, curl, libevent
, withGui }:
, withGui
, Foundation, ApplicationServices, AppKit }:
with stdenv.lib;
stdenv.mkDerivation rec{
@ -18,7 +19,8 @@ stdenv.mkDerivation rec{
nativeBuildInputs = [ pkgconfig autoreconfHook ];
buildInputs = [ openssl db48 boost zlib libevent
miniupnpc utillinux protobuf curl ]
++ optionals withGui [ qt4 qrencode ];
++ optionals withGui [ qt4 qrencode ]
++ optionals stdenv.isDarwin [ Foundation ApplicationServices AppKit ];
configureFlags = [
"--with-boost-libdir=${boost.out}/lib"
@ -36,7 +38,7 @@ stdenv.mkDerivation rec{
Bitcoin XT is an implementation of a Bitcoin full node, based upon the
source code of Bitcoin Core. It is built by taking the latest stable
Core release, applying a series of patches, and then doing deterministic
builds so anyone can check the downloads correspond to the source code.
builds so anyone can check the downloads correspond to the source code.
'';
homepage = https://bitcoinxt.software/;
maintainers = with maintainers; [ jefdaj ];

20
pkgs/applications/altcoins/default.nix
View file

@ -10,14 +10,26 @@ rec {
bitcoin-abc = libsForQt5.callPackage ./bitcoin-abc.nix { boost = boost165; withGui = true; };
bitcoind-abc = callPackage ./bitcoin-abc.nix { boost = boost165; withGui = false; };
bitcoin-unlimited = callPackage ./bitcoin-unlimited.nix { withGui = true; };
bitcoind-unlimited = callPackage ./bitcoin-unlimited.nix { withGui = false; };
bitcoin-unlimited = callPackage ./bitcoin-unlimited.nix {
inherit (darwin.apple_sdk.frameworks) Foundation ApplicationServices AppKit;
withGui = true;
};
bitcoind-unlimited = callPackage ./bitcoin-unlimited.nix {
inherit (darwin.apple_sdk.frameworks) Foundation ApplicationServices AppKit;
withGui = false;
};
bitcoin-classic = libsForQt5.callPackage ./bitcoin-classic.nix { boost = boost165; withGui = true; };
bitcoind-classic = callPackage ./bitcoin-classic.nix { boost = boost165; withGui = false; };
bitcoin-xt = callPackage ./bitcoin-xt.nix { boost = boost165; withGui = true; };
bitcoind-xt = callPackage ./bitcoin-xt.nix { boost = boost165; withGui = false; };
bitcoin-xt = callPackage ./bitcoin-xt.nix {
inherit (darwin.apple_sdk.frameworks) Foundation ApplicationServices AppKit;
boost = boost165; withGui = true;
};
bitcoind-xt = callPackage ./bitcoin-xt.nix {
inherit (darwin.apple_sdk.frameworks) Foundation ApplicationServices AppKit;
boost = boost165; withGui = false;
};
btc1 = callPackage ./btc1.nix { boost = boost165; withGui = true; };
btc1d = callPackage ./btc1.nix { boost = boost165; withGui = false; };

3
pkgs/applications/audio/cdparanoia/default.nix
View file

@ -17,7 +17,8 @@ stdenv.mkDerivation rec {
url = "https://trac.macports.org/export/70964/trunk/dports/audio/cdparanoia/files/patch-paranoia_paranoia.c.10.4.diff";
sha256 = "17l2qhn8sh4jy6ryy5si6ll6dndcm0r537rlmk4a6a8vkn852vad";
})
] ++ stdenv.lib.optional stdenv.hostPlatform.isMusl ./utils.patch;
] ++ stdenv.lib.optional stdenv.hostPlatform.isMusl ./utils.patch
++ [./fix_private_keyword.patch];
buildInputs = stdenv.lib.optional stdenv.isAarch64 autoreconfHook;

468
pkgs/applications/audio/cdparanoia/fix_private_keyword.patch Normal file
View file

@ -0,0 +1,468 @@
--- cdparanoia-III-10.2/interface/cdda_interface.h (revision 15337)
+++ cdparanoia-III-10.2/interface/cdda_interface.h (revision 15338)
@@ -85,5 +85,5 @@
int is_mmc;
- cdda_private_data_t *private;
+ cdda_private_data_t *private_data;
void *reserved;
unsigned char inqbytes[4];
--- cdparanoia-III-10.2/interface/cooked_interface.c (revision 15337)
+++ cdparanoia-III-10.2/interface/cooked_interface.c (revision 15338)
@@ -14,11 +14,11 @@
struct timespec tv1;
struct timespec tv2;
- int ret1=clock_gettime(d->private->clock,&tv1);
+ int ret1=clock_gettime(d->private_data->clock,&tv1);
int ret2=ioctl(fd, command,arg);
- int ret3=clock_gettime(d->private->clock,&tv2);
+ int ret3=clock_gettime(d->private_data->clock,&tv2);
if(ret1<0 || ret3<0){
- d->private->last_milliseconds=-1;
+ d->private_data->last_milliseconds=-1;
}else{
- d->private->last_milliseconds = (tv2.tv_sec-tv1.tv_sec)*1000. + (tv2.tv_nsec-tv1.tv_nsec)/1000000.;
+ d->private_data->last_milliseconds = (tv2.tv_sec-tv1.tv_sec)*1000. + (tv2.tv_nsec-tv1.tv_nsec)/1000000.;
}
return ret2;
--- cdparanoia-III-10.2/interface/interface.c (revision 15337)
+++ cdparanoia-III-10.2/interface/interface.c (revision 15338)
@@ -40,7 +40,7 @@
if(d->cdda_fd!=-1)close(d->cdda_fd);
if(d->ioctl_fd!=-1 && d->ioctl_fd!=d->cdda_fd)close(d->ioctl_fd);
- if(d->private){
- if(d->private->sg_hd)free(d->private->sg_hd);
- free(d->private);
+ if(d->private_data){
+ if(d->private_data->sg_hd)free(d->private_data->sg_hd);
+ free(d->private_data);
}
@@ -128,5 +128,5 @@
}
}
- if(ms)*ms=d->private->last_milliseconds;
+ if(ms)*ms=d->private_data->last_milliseconds;
return(sectors);
}
--- cdparanoia-III-10.2/interface/scan_devices.c (revision 15337)
+++ cdparanoia-III-10.2/interface/scan_devices.c (revision 15338)
@@ -265,9 +265,9 @@
d->bigendianp=-1; /* We don't know yet... */
d->nsectors=-1;
- d->private=calloc(1,sizeof(*d->private));
+ d->private_data=calloc(1,sizeof(*d->private_data));
{
/* goddamnit */
struct timespec tv;
- d->private->clock=(clock_gettime(CLOCK_MONOTONIC,&tv)<0?CLOCK_REALTIME:CLOCK_MONOTONIC);
+ d->private_data->clock=(clock_gettime(CLOCK_MONOTONIC,&tv)<0?CLOCK_REALTIME:CLOCK_MONOTONIC);
}
idmessage(messagedest,messages,"\t\tCDROM sensed: %s\n",description);
@@ -675,13 +675,13 @@
d->nsectors=-1;
d->messagedest = messagedest;
- d->private=calloc(1,sizeof(*d->private));
+ d->private_data=calloc(1,sizeof(*d->private_data));
{
/* goddamnit */
struct timespec tv;
- d->private->clock=(clock_gettime(CLOCK_MONOTONIC,&tv)<0?CLOCK_REALTIME:CLOCK_MONOTONIC);
+ d->private_data->clock=(clock_gettime(CLOCK_MONOTONIC,&tv)<0?CLOCK_REALTIME:CLOCK_MONOTONIC);
}
if(use_sgio){
d->interface=SGIO_SCSI;
- d->private->sg_buffer=(unsigned char *)(d->private->sg_hd=malloc(MAX_BIG_BUFF_SIZE));
+ d->private_data->sg_buffer=(unsigned char *)(d->private_data->sg_hd=malloc(MAX_BIG_BUFF_SIZE));
g_fd=d->cdda_fd=dup(d->ioctl_fd);
}else{
@@ -697,6 +697,6 @@
/* malloc our big buffer for scsi commands */
- d->private->sg_hd=malloc(MAX_BIG_BUFF_SIZE);
- d->private->sg_buffer=((unsigned char *)d->private->sg_hd)+SG_OFF;
+ d->private_data->sg_hd=malloc(MAX_BIG_BUFF_SIZE);
+ d->private_data->sg_buffer=((unsigned char *)d->private_data->sg_hd)+SG_OFF;
}
@@ -773,7 +773,7 @@
if(g_fd!=-1)close(g_fd);
if(d){
- if(d->private){
- if(d->private->sg_hd)free(d->private->sg_hd);
- free(d->private);
+ if(d->private_data){
+ if(d->private_data->sg_hd)free(d->private_data->sg_hd);
+ free(d->private_data);
}
free(d);
@@ -822,5 +822,5 @@
d->bigendianp=-1; /* We don't know yet... */
d->nsectors=-1;
- d->private=calloc(1,sizeof(*d->private));
+ d->private_data=calloc(1,sizeof(*d->private_data));
d->drive_model=copystring("File based test interface");
idmessage(messagedest,messages,"\t\tCDROM sensed: %s\n",d->drive_model);
--- cdparanoia-III-10.2/interface/scsi_interface.c (revision 15337)
+++ cdparanoia-III-10.2/interface/scsi_interface.c (revision 15338)
@@ -16,11 +16,11 @@
struct timespec tv1;
struct timespec tv2;
- int ret1=clock_gettime(d->private->clock,&tv1);
+ int ret1=clock_gettime(d->private_data->clock,&tv1);
int ret2=ioctl(fd, command,arg);
- int ret3=clock_gettime(d->private->clock,&tv2);
+ int ret3=clock_gettime(d->private_data->clock,&tv2);
if(ret1<0 || ret3<0){
- d->private->last_milliseconds=-1;
+ d->private_data->last_milliseconds=-1;
}else{
- d->private->last_milliseconds = (tv2.tv_sec-tv1.tv_sec)*1000. + (tv2.tv_nsec-tv1.tv_nsec)/1000000.;
+ d->private_data->last_milliseconds = (tv2.tv_sec-tv1.tv_sec)*1000. + (tv2.tv_nsec-tv1.tv_nsec)/1000000.;
}
return ret2;
@@ -97,5 +97,5 @@
fd_set fdset;
struct timeval tv;
- struct sg_header *sg_hd=d->private->sg_hd;
+ struct sg_header *sg_hd=d->private_data->sg_hd;
int flag=0;
@@ -186,5 +186,5 @@
int tret1,tret2;
int status = 0;
- struct sg_header *sg_hd=d->private->sg_hd;
+ struct sg_header *sg_hd=d->private_data->sg_hd;
long writebytes=SG_OFF+cmd_len+in_size;
@@ -196,5 +196,5 @@
memset(sg_hd,0,sizeof(sg_hd));
memset(sense_buffer,0,SG_MAX_SENSE);
- memcpy(d->private->sg_buffer,cmd,cmd_len+in_size);
+ memcpy(d->private_data->sg_buffer,cmd,cmd_len+in_size);
sg_hd->twelve_byte = cmd_len == 12;
sg_hd->result = 0;
@@ -210,5 +210,5 @@
if(bytecheck && out_size>in_size){
- memset(d->private->sg_buffer+cmd_len+in_size,bytefill,out_size-in_size);
+ memset(d->private_data->sg_buffer+cmd_len+in_size,bytefill,out_size-in_size);
/* the size does not remove cmd_len due to the way the kernel
driver copies buffers */
@@ -244,5 +244,5 @@
sigprocmask (SIG_BLOCK, &(d->sigset), NULL );
- tret1=clock_gettime(d->private->clock,&tv1);
+ tret1=clock_gettime(d->private_data->clock,&tv1);
errno=0;
status = write(d->cdda_fd, sg_hd, writebytes );
@@ -290,5 +290,5 @@
}
- tret2=clock_gettime(d->private->clock,&tv2);
+ tret2=clock_gettime(d->private_data->clock,&tv2);
errno=0;
status = read(d->cdda_fd, sg_hd, SG_OFF + out_size);
@@ -314,5 +314,5 @@
long i,flag=0;
for(i=in_size;i<out_size;i++)
- if(d->private->sg_buffer[i]!=bytefill){
+ if(d->private_data->sg_buffer[i]!=bytefill){
flag=1;
break;
@@ -327,7 +327,7 @@
errno=0;
if(tret1<0 || tret2<0){
- d->private->last_milliseconds=-1;
+ d->private_data->last_milliseconds=-1;
}else{
- d->private->last_milliseconds = (tv2.tv_sec-tv1.tv_sec)*1000 + (tv2.tv_nsec-tv1.tv_nsec)/1000000;
+ d->private_data->last_milliseconds = (tv2.tv_sec-tv1.tv_sec)*1000 + (tv2.tv_nsec-tv1.tv_nsec)/1000000;
}
return(0);
@@ -348,5 +348,5 @@
memset(&hdr,0,sizeof(hdr));
memset(sense,0,sizeof(sense));
- memcpy(d->private->sg_buffer,cmd+cmd_len,in_size);
+ memcpy(d->private_data->sg_buffer,cmd+cmd_len,in_size);
hdr.cmdp = cmd;
@@ -356,5 +356,5 @@
hdr.timeout = 50000;
hdr.interface_id = 'S';
- hdr.dxferp = d->private->sg_buffer;
+ hdr.dxferp = d->private_data->sg_buffer;
hdr.flags = SG_FLAG_DIRECT_IO; /* direct IO if we can get it */
@@ -401,5 +401,5 @@
long i,flag=0;
for(i=in_size;i<out_size;i++)
- if(d->private->sg_buffer[i]!=bytefill){
+ if(d->private_data->sg_buffer[i]!=bytefill){
flag=1;
break;
@@ -413,5 +413,5 @@
/* Can't rely on .duration because we can't be certain kernel has HZ set to something useful */
- /* d->private->last_milliseconds = hdr.duration; */
+ /* d->private_data->last_milliseconds = hdr.duration; */
errno = 0;
@@ -446,7 +446,7 @@
handle_scsi_cmd(d, cmd, 6, 0, 56, 0,0, sense);
- key = d->private->sg_buffer[2] & 0xf;
- ASC = d->private->sg_buffer[12];
- ASCQ = d->private->sg_buffer[13];
+ key = d->private_data->sg_buffer[2] & 0xf;
+ ASC = d->private_data->sg_buffer[12];
+ ASCQ = d->private_data->sg_buffer[13];
if(key == 2 && ASC == 4 && ASCQ == 1) return 0;
@@ -493,5 +493,5 @@
{
- unsigned char *b=d->private->sg_buffer;
+ unsigned char *b=d->private_data->sg_buffer;
if(b[0])return(1); /* Handles only up to 256 bytes */
if(b[6])return(1); /* Handles only up to 256 bytes */
@@ -605,6 +605,6 @@
if(mode_sense(d,12,0x01))return(-1);
- d->orgdens = d->private->sg_buffer[4];
- return(d->orgsize = ((int)(d->private->sg_buffer[10])<<8)+d->private->sg_buffer[11]);
+ d->orgdens = d->private_data->sg_buffer[4];
+ return(d->orgsize = ((int)(d->private_data->sg_buffer[10])<<8)+d->private_data->sg_buffer[11]);
}
@@ -665,6 +665,6 @@
}
- first=d->private->sg_buffer[2];
- last=d->private->sg_buffer[3];
+ first=d->private_data->sg_buffer[2];
+ last=d->private_data->sg_buffer[3];
tracks=last-first+1;
@@ -684,5 +684,5 @@
}
{
- scsi_TOC *toc=(scsi_TOC *)(d->private->sg_buffer+4);
+ scsi_TOC *toc=(scsi_TOC *)(d->private_data->sg_buffer+4);
d->disc_toc[i-first].bFlags=toc->bFlags;
@@ -705,5 +705,5 @@
}
{
- scsi_TOC *toc=(scsi_TOC *)(d->private->sg_buffer+4);
+ scsi_TOC *toc=(scsi_TOC *)(d->private_data->sg_buffer+4);
d->disc_toc[i-first].bFlags=toc->bFlags;
@@ -739,5 +739,5 @@
/* copy to our structure and convert start sector */
- tracks = d->private->sg_buffer[1];
+ tracks = d->private_data->sg_buffer[1];
if (tracks > MAXTRK) {
cderror(d,"003: CDROM reporting illegal number of tracks\n");
@@ -755,31 +755,31 @@
}
- d->disc_toc[i].bFlags = d->private->sg_buffer[10];
+ d->disc_toc[i].bFlags = d->private_data->sg_buffer[10];
d->disc_toc[i].bTrack = i + 1;
d->disc_toc[i].dwStartSector= d->adjust_ssize *
- (((signed char)(d->private->sg_buffer[2])<<24) |
- (d->private->sg_buffer[3]<<16)|
- (d->private->sg_buffer[4]<<8)|
- (d->private->sg_buffer[5]));
+ (((signed char)(d->private_data->sg_buffer[2])<<24) |
+ (d->private_data->sg_buffer[3]<<16)|
+ (d->private_data->sg_buffer[4]<<8)|
+ (d->private_data->sg_buffer[5]));
}
d->disc_toc[i].bFlags = 0;
d->disc_toc[i].bTrack = i + 1;
- memcpy (&foo, d->private->sg_buffer+2, 4);
- memcpy (&bar, d->private->sg_buffer+6, 4);
+ memcpy (&foo, d->private_data->sg_buffer+2, 4);
+ memcpy (&bar, d->private_data->sg_buffer+6, 4);
d->disc_toc[i].dwStartSector = d->adjust_ssize * (be32_to_cpu(foo) +
be32_to_cpu(bar));
d->disc_toc[i].dwStartSector= d->adjust_ssize *
- ((((signed char)(d->private->sg_buffer[2])<<24) |
- (d->private->sg_buffer[3]<<16)|
- (d->private->sg_buffer[4]<<8)|
- (d->private->sg_buffer[5]))+
+ ((((signed char)(d->private_data->sg_buffer[2])<<24) |
+ (d->private_data->sg_buffer[3]<<16)|
+ (d->private_data->sg_buffer[4]<<8)|
+ (d->private_data->sg_buffer[5]))+
- ((((signed char)(d->private->sg_buffer[6])<<24) |
- (d->private->sg_buffer[7]<<16)|
- (d->private->sg_buffer[8]<<8)|
- (d->private->sg_buffer[9]))));
+ ((((signed char)(d->private_data->sg_buffer[6])<<24) |
+ (d->private_data->sg_buffer[7]<<16)|
+ (d->private_data->sg_buffer[8]<<8)|
+ (d->private_data->sg_buffer[9]))));
@@ -818,5 +818,5 @@
if((ret=handle_scsi_cmd(d,cmd,10,0,sectors * CD_FRAMESIZE_RAW,'\177',1,sense)))
return(ret);
- if(p)memcpy(p,d->private->sg_buffer,sectors*CD_FRAMESIZE_RAW);
+ if(p)memcpy(p,d->private_data->sg_buffer,sectors*CD_FRAMESIZE_RAW);
return(0);
}
@@ -837,5 +837,5 @@
if((ret=handle_scsi_cmd(d,cmd,12,0,sectors * CD_FRAMESIZE_RAW,'\177',1,sense)))
return(ret);
- if(p)memcpy(p,d->private->sg_buffer,sectors*CD_FRAMESIZE_RAW);
+ if(p)memcpy(p,d->private_data->sg_buffer,sectors*CD_FRAMESIZE_RAW);
return(0);
}
@@ -855,5 +855,5 @@
if((ret=handle_scsi_cmd(d,cmd,10,0,sectors * CD_FRAMESIZE_RAW,'\177',1,sense)))
return(ret);
- if(p)memcpy(p,d->private->sg_buffer,sectors*CD_FRAMESIZE_RAW);
+ if(p)memcpy(p,d->private_data->sg_buffer,sectors*CD_FRAMESIZE_RAW);
return(0);
}
@@ -873,5 +873,5 @@
if((ret=handle_scsi_cmd(d,cmd,12,0,sectors * CD_FRAMESIZE_RAW,'\177',1,sense)))
return(ret);
- if(p)memcpy(p,d->private->sg_buffer,sectors*CD_FRAMESIZE_RAW);
+ if(p)memcpy(p,d->private_data->sg_buffer,sectors*CD_FRAMESIZE_RAW);
return(0);
}
@@ -891,5 +891,5 @@
if((ret=handle_scsi_cmd(d,cmd,10,0,sectors * CD_FRAMESIZE_RAW,'\177',1,sense)))
return(ret);
- if(p)memcpy(p,d->private->sg_buffer,sectors*CD_FRAMESIZE_RAW);
+ if(p)memcpy(p,d->private_data->sg_buffer,sectors*CD_FRAMESIZE_RAW);
return(0);
}
@@ -909,5 +909,5 @@
if((ret=handle_scsi_cmd(d,cmd,12,0,sectors * CD_FRAMESIZE_RAW,'\177',1,sense)))
return(ret);
- if(p)memcpy(p,d->private->sg_buffer,sectors*CD_FRAMESIZE_RAW);
+ if(p)memcpy(p,d->private_data->sg_buffer,sectors*CD_FRAMESIZE_RAW);
return(0);
}
@@ -923,5 +923,5 @@
if((ret=handle_scsi_cmd(d,cmd,12,0,sectors * CD_FRAMESIZE_RAW,'\177',1,sense)))
return(ret);
- if(p)memcpy(p,d->private->sg_buffer,sectors*CD_FRAMESIZE_RAW);
+ if(p)memcpy(p,d->private_data->sg_buffer,sectors*CD_FRAMESIZE_RAW);
return(0);
}
@@ -937,5 +937,5 @@
if((ret=handle_scsi_cmd(d,cmd,12,0,sectors * CD_FRAMESIZE_RAW,'\177',1,sense)))
return(ret);
- if(p)memcpy(p,d->private->sg_buffer,sectors*CD_FRAMESIZE_RAW);
+ if(p)memcpy(p,d->private_data->sg_buffer,sectors*CD_FRAMESIZE_RAW);
return(0);
}
@@ -951,5 +951,5 @@
if((ret=handle_scsi_cmd(d,cmd,12,0,sectors * CD_FRAMESIZE_RAW,'\177',1,sense)))
return(ret);
- if(p)memcpy(p,d->private->sg_buffer,sectors*CD_FRAMESIZE_RAW);
+ if(p)memcpy(p,d->private_data->sg_buffer,sectors*CD_FRAMESIZE_RAW);
return(0);
}
@@ -965,5 +965,5 @@
if((ret=handle_scsi_cmd(d,cmd,12,0,sectors * CD_FRAMESIZE_RAW,'\177',1,sense)))
return(ret);
- if(p)memcpy(p,d->private->sg_buffer,sectors*CD_FRAMESIZE_RAW);
+ if(p)memcpy(p,d->private_data->sg_buffer,sectors*CD_FRAMESIZE_RAW);
return(0);
}
@@ -979,5 +979,5 @@
if((ret=handle_scsi_cmd(d,cmd,12,0,sectors * CD_FRAMESIZE_RAW,'\177',1,sense)))
return(ret);
- if(p)memcpy(p,d->private->sg_buffer,sectors*CD_FRAMESIZE_RAW);
+ if(p)memcpy(p,d->private_data->sg_buffer,sectors*CD_FRAMESIZE_RAW);
return(0);
}
@@ -993,5 +993,5 @@
if((ret=handle_scsi_cmd(d,cmd,12,0,sectors * CD_FRAMESIZE_RAW,'\177',1,sense)))
return(ret);
- if(p)memcpy(p,d->private->sg_buffer,sectors*CD_FRAMESIZE_RAW);
+ if(p)memcpy(p,d->private_data->sg_buffer,sectors*CD_FRAMESIZE_RAW);
return(0);
}
@@ -1027,5 +1027,5 @@
if((ret=handle_scsi_cmd(d,cmd,12,0,sectors * CD_FRAMESIZE_RAW,'\177',1,sense)))
return(ret);
- if(p)memcpy(p,d->private->sg_buffer,sectors*CD_FRAMESIZE_RAW);
+ if(p)memcpy(p,d->private_data->sg_buffer,sectors*CD_FRAMESIZE_RAW);
return(0);
}
@@ -1040,5 +1040,5 @@
if((ret=handle_scsi_cmd(d,cmd,12,0,sectors * CD_FRAMESIZE_RAW,'\177',1,sense)))
return(ret);
- if(p)memcpy(p,d->private->sg_buffer,sectors*CD_FRAMESIZE_RAW);
+ if(p)memcpy(p,d->private_data->sg_buffer,sectors*CD_FRAMESIZE_RAW);
return(0);
}
@@ -1053,5 +1053,5 @@
if((ret=handle_scsi_cmd(d,cmd,12,0,sectors * CD_FRAMESIZE_RAW,'\177',1,sense)))
return(ret);
- if(p)memcpy(p,d->private->sg_buffer,sectors*CD_FRAMESIZE_RAW);
+ if(p)memcpy(p,d->private_data->sg_buffer,sectors*CD_FRAMESIZE_RAW);
return(0);
}
@@ -1276,5 +1276,5 @@
long i;
for(i=2351;i>=0;i--)
- if(d->private->sg_buffer[i]!=(unsigned char)'\177')
+ if(d->private_data->sg_buffer[i]!=(unsigned char)'\177')
return(((i+3)>>2)<<2);
@@ -1285,5 +1285,5 @@
long i,flag=0;
for(i=0;i<2352;i++)
- if(d->private->sg_buffer[i]!=0){
+ if(d->private_data->sg_buffer[i]!=0){
flag=1;
break;
@@ -1622,5 +1622,5 @@
if(mode_sense(d,22,0x2A)==0){
- b=d->private->sg_buffer;
+ b=d->private_data->sg_buffer;
b+=b[3]+4;
@@ -1670,5 +1670,5 @@
return(NULL);
}
- return (d->private->sg_buffer);
+ return (d->private_data->sg_buffer);
}
@@ -1726,6 +1726,6 @@
d->error_retry=1;
- d->private->sg_hd=realloc(d->private->sg_hd,d->nsectors*CD_FRAMESIZE_RAW + SG_OFF + 128);
- d->private->sg_buffer=((unsigned char *)d->private->sg_hd)+SG_OFF;
+ d->private_data->sg_hd=realloc(d->private_data->sg_hd,d->nsectors*CD_FRAMESIZE_RAW + SG_OFF + 128);
+ d->private_data->sg_buffer=((unsigned char *)d->private_data->sg_hd)+SG_OFF;
d->report_all=1;
return(0);
--- cdparanoia-III-10.2/interface/test_interface.c (revision 15337)
+++ cdparanoia-III-10.2/interface/test_interface.c (revision 15338)
@@ -67,7 +67,7 @@
if(begin<lastread)
- d->private->last_milliseconds=20;
+ d->private_data->last_milliseconds=20;
else
- d->private->last_milliseconds=sectors;
+ d->private_data->last_milliseconds=sectors;
#ifdef CDDA_TEST_UNDERRUN

33
pkgs/applications/audio/dragonfly-reverb/default.nix Normal file
View file

@ -0,0 +1,33 @@
{ stdenv, fetchgit, libjack2, libGL, pkgconfig, xorg }:
stdenv.mkDerivation rec {
name = "dragonfly-reverb-${src.rev}";
src = fetchgit {
url = "https://github.com/michaelwillis/dragonfly-reverb";
rev = "0.9.1";
sha256 = "1dbykx044h768bbzabdagl4jh65gqgfsxsrarjrkp07sqnhlnhpd";
};
patchPhase = ''
patchShebangs dpf/utils/generate-ttl.sh
'';
nativeBuildInputs = [ pkgconfig ];
buildInputs = [
libjack2 xorg.libX11 libGL
];
installPhase = ''
mkdir -p $out/lib/lv2/
cp -a bin/DragonflyReverb.lv2/ $out/lib/lv2/
'';
meta = with stdenv.lib; {
homepage = https://github.com/michaelwillis/dragonfly-reverb;
description = "A hall-style reverb based on freeverb3 algorithms";
maintainers = [ maintainers.magnetophon ];
license = licenses.gpl2;
platforms = ["x86_64-linux"];
};
}

12
pkgs/applications/editors/android-studio/default.nix
View file

@ -8,14 +8,14 @@ let
inherit (gnome2) GConf gnome_vfs;
};
stableVersion = {
version = "3.1.1.0"; # "Android Studio 3.1.1"
build = "173.4697961";
sha256Hash = "0xn02miq2hz7666mziza56pfqw9sjflgvn88ds7j5yd4rlcr0lq8";
version = "3.1.2.0"; # "Android Studio 3.1.2"
build = "173.4720617";
sha256Hash = "1h9f4pkyqxkqxampi8v035czg5d4g6lp4bsrnq5mgpwhjwkr1whk";
};
latestVersion = {
version = "3.2.0.10"; # "Android Studio 3.2 Canary 11"
build = "181.4720098";
sha256Hash = "00cd7qdznspi69cgs1a13a3fnkvsc7zjfl517jgp32vdygkb0qxw";
version = "3.2.0.11"; # "Android Studio 3.2 Canary 12"
build = "181.4729833";
sha256Hash = "1b976m59d230pl35ajhdic46cw8qmnykkbrg3l7am7zmih0zk64c";
};
in rec {
# Old alias

30
pkgs/applications/editors/bonzomatic/default.nix Normal file
View file

@ -0,0 +1,30 @@
{ stdenv, makeWrapper, fetchFromGitHub, cmake, alsaLib, mesa_glu, libXcursor, libXinerama, libXrandr, xorgserver }:
stdenv.mkDerivation rec {
name = "${pname}-${version}";
pname = "bonzomatic";
version = "2018-03-29";
src = fetchFromGitHub {
owner = "Gargaj";
repo = pname;
rev = version;
sha256 = "12mdfjvbhdqz1585772rj4cap8m4ijfci6ib62jysxjf747k41fg";
};
buildInputs = [ cmake makeWrapper alsaLib mesa_glu libXcursor libXinerama libXrandr xorgserver ];
postFixup = ''
wrapProgram $out/bin/Bonzomatic --prefix LD_LIBRARY_PATH : "${alsaLib}/lib"
'';
meta = with stdenv.lib; {
description = "A live-coding tool for writing 2D fragment/pixel shaders";
license = with licenses; [
unlicense
unfreeRedistributable # contains libbass.so in repository
];
maintainers = [ maintainers.nocent ];
platforms = [ "i686-linux" "x86_64-linux" ];
};
}

41
pkgs/applications/misc/coursera-dl/default.nix Normal file
View file

@ -0,0 +1,41 @@
{ stdenv, fetchFromGitHub, glibcLocales, pandoc, python3 }:
let
pythonPackages = python3.pkgs;
in pythonPackages.buildPythonApplication rec {
name = "coursera-dl-${version}";
version = "0.10.0";
src = fetchFromGitHub {
owner = "coursera-dl";
repo = "coursera-dl";
rev = version;
sha256 = "0m3f6ly8c3mkb8yy2y398afswqgy17rz159s1054wzxpb4f85zlb";
};
nativeBuildInputs = with pythonPackages; [ pandoc ];
buildInputs = with pythonPackages; [ glibcLocales ];
propagatedBuildInputs = with pythonPackages; [ beautifulsoup4 ConfigArgParse keyring pyasn1 requests six urllib3 ];
checkInputs = with pythonPackages; [ pytest mock ];
preConfigure = ''
export LC_ALL=en_US.utf-8
'';
checkPhase = ''
# requires dbus service
py.test -k 'not test_get_credentials_with_keyring' .
'';
meta = with stdenv.lib; {
description = "CLI for downloading Coursera.org videos and naming them";
homepage = https://github.com/coursera-dl/coursera-dl;
license = licenses.lgpl3Plus;
maintainers = with maintainers; [ alexfmpe ];
platforms = platforms.darwin ++ platforms.linux;
};
}

22
pkgs/applications/misc/go-jira/default.nix Normal file
View file

@ -0,0 +1,22 @@
# This file was generated by https://github.com/kamilchm/go2nix v1.2.1
{ stdenv, buildGoPackage, fetchgit }:
buildGoPackage rec {
name = "go-jira-${version}";
version = "1.0.17";
goPackagePath = "gopkg.in/Netflix-Skunkworks/go-jira.v1";
src = fetchgit {
rev = "v${version}";
url = "https://gopkg.in/Netflix-Skunkworks/go-jira.v1";
sha256 = "0ap5dzikp934mawigmv7ighajr5yxpck2gpnb2cmkc1p6qa6gn4v";
};
meta = with stdenv.lib; {
description = "Simple command line client for Atlassian's Jira service written in Go";
homepage = "https://github.com/Netflix-Skunkworks/go-jira";
license = licenses.asl20;
maintainers = [ maintainers.carlosdagos ];
};
}

4
pkgs/applications/misc/gphoto2/default.nix
View file

@ -3,11 +3,11 @@
}:
stdenv.mkDerivation rec {
name = "gphoto2-2.5.15";
name = "gphoto2-2.5.17";
src = fetchurl {
url = "mirror://sourceforge/gphoto/${name}.tar.bz2";
sha256 = "0xsa12k5fz49v8y4h3zahzr427a3ylxaf0k7hybrkp43g4i1lmxf";
sha256 = "0kslwclyyzvnxjw3gdzhlagj7l5f8lba833ipr9s0s0c4hwi0mxa";
};
nativeBuildInputs = [ pkgconfig gettext libtool ];

4
pkgs/applications/misc/orca/default.nix
View file

@ -10,7 +10,7 @@
with lib;
let
pname = "orca";
version = "3.28.0";
version = "3.28.1";
in buildPythonApplication rec {
name = "${pname}-${version}";
@ -18,7 +18,7 @@ in buildPythonApplication rec {
src = fetchurl {
url = "mirror://gnome/sources/${pname}/${gnome3.versionBranch version}/${name}.tar.xz";
sha256 = "1jy2zxs50ah1rg4zgiaj2l2sm1zyyvs37phws0hwmy3xd90ljfc2";
sha256 = "04l5ccn7wf175gyq3blfpx0yh70ny06n161297jwc9idf951852g";
};
patches = [

4
pkgs/applications/misc/qlcplus/default.nix
View file

@ -5,13 +5,13 @@
mkDerivation rec {
name = "qlcplus-${version}";
version = "4.11.1";
version = "4.11.2";
src = fetchFromGitHub {
owner = "mcallegari";
repo = "qlcplus";
rev = "QLC+_${version}";
sha256 = "0lb1mdp7kbnkja14phgyknr65irwkxcmzk96rqacysvwrvzvfzyd";
sha256 = "0ry7j8d5mm3h3mzd49xqlagnldmfhfr6plwk73pz62hxr4j58s6w";
};
nativeBuildInputs = [ qmake pkgconfig ];

22
pkgs/applications/misc/teseq/default.nix Normal file
View file

@ -0,0 +1,22 @@
{ stdenv, fetchurl }:
let
version = "1.1.1";
in
stdenv.mkDerivation {
name = "teseq-${version}";
src = fetchurl {
url = "mirror://gnu/teseq/teseq-${version}.tar.gz";
sha256 = "08ln005qciy7f3jhv980kfhhfmh155naq59r5ah9crz1q4mx5yrj";
};
meta = {
homepage = https://www.gnu.org/software/teseq/;
description = "Escape sequence illuminator";
license = stdenv.lib.licenses.gpl3;
platforms = stdenv.lib.platforms.unix;
maintainers = [ stdenv.lib.maintainers.vaibhavsagar ];
};
}

4
pkgs/applications/misc/urh/default.nix
View file

@ -2,13 +2,13 @@
python3Packages.buildPythonApplication rec {
name = "urh-${version}";
version = "2.0.1";
version = "2.0.2";
src = fetchFromGitHub {
owner = "jopohl";
repo = "urh";
rev = "v${version}";
sha256 = "0mnnrxm49s77s1qg7zbfciw0525ipsl010sciqdw8a22jg1rfjh8";
sha256 = "1qqb31y65rd85rf3gvxxxy06hm89ary00km1ac84qz5bwm6n5fyb";
};
buildInputs = [ hackrf rtl-sdr ];

9
pkgs/applications/misc/xmr-stak/default.nix
View file

@ -1,11 +1,16 @@
{ stdenv, lib, fetchFromGitHub, cmake, libuv, libmicrohttpd, openssl
{ stdenv, stdenvGcc6, lib
, fetchFromGitHub, cmake, libuv, libmicrohttpd, openssl
, opencl-headers, ocl-icd, hwloc, cudatoolkit
, devDonationLevel ? "0.0"
, cudaSupport ? false
, openclSupport ? true
}:
stdenv.mkDerivation rec {
let
stdenv' = if cudaSupport then stdenvGcc6 else stdenv;
in
stdenv'.mkDerivation rec {
name = "xmr-stak-${version}";
version = "2.4.3";

4
pkgs/applications/networking/browsers/firefox/wrapper.nix
View file

@ -132,8 +132,10 @@ let
else
for res in 16 32 48 64 128; do
mkdir -p "$out/share/icons/hicolor/''${res}x''${res}/apps"
ln -s "${browser}/lib/"*"/browser/chrome/icons/default/default''${res}.png" \
icon=( "${browser}/lib/"*"/browser/chrome/icons/default/default''${res}.png" )
if [ -e "$icon" ]; then ln -s "$icon" \
"$out/share/icons/hicolor/''${res}x''${res}/apps/${browserName}.png"
fi
done
fi

23
pkgs/applications/networking/cluster/spark/default.nix
View file

@ -1,20 +1,16 @@
{ stdenv, fetchzip, makeWrapper, jre, pythonPackages, coreutils
{ stdenv, fetchzip, makeWrapper, jre, pythonPackages, coreutils, hadoop
, RSupport? true, R
, mesosSupport ? true, mesos
, version
}:
let
versionMap = {
"2.2.1" = {
hadoopVersion = "hadoop2.7";
sparkSha256 = "10nxsf9a6hj1263sxv0cbdqxdb8mb4cl6iqq32ljq9ydvk32s99c";
};
};
sha256 = {
"1.6.3" = "142hw73wf20d846l83ydx0yg7qj5qxywm4h7qrhwnd7lsy2sbnjf";
"2.2.1" = "10nxsf9a6hj1263sxv0cbdqxdb8mb4cl6iqq32ljq9ydvk32s99c";
}.${version};
in
with versionMap.${version};
with stdenv.lib;
stdenv.mkDerivation rec {
@ -22,15 +18,15 @@ stdenv.mkDerivation rec {
name = "spark-${version}";
src = fetchzip {
url = "mirror://apache/spark/${name}/${name}-bin-${hadoopVersion}.tgz";
sha256 = sparkSha256;
inherit sha256;
url = "mirror://apache/spark/${name}/${name}-bin-without-hadoop.tgz";
};
buildInputs = [ makeWrapper jre pythonPackages.python pythonPackages.numpy ]
++ optional RSupport R
++ optional mesosSupport mesos;
untarDir = "${name}-bin-${hadoopVersion}";
untarDir = "${name}-bin-without-hadoop";
installPhase = ''
mkdir -p $out/{lib/${untarDir}/conf,bin,/share/java}
mv * $out/lib/${untarDir}
@ -42,6 +38,7 @@ stdenv.mkDerivation rec {
cat > $out/lib/${untarDir}/conf/spark-env.sh <<- EOF
export JAVA_HOME="${jre}"
export SPARK_HOME="$out/lib/${untarDir}"
export SPARK_DIST_CLASSPATH=$(${hadoop}/bin/hadoop classpath)
export PYSPARK_PYTHON="${pythonPackages.python}/bin/${pythonPackages.python.executable}"
export PYTHONPATH="\$PYTHONPATH:$PYTHONPATH"
${optionalString RSupport
@ -63,7 +60,7 @@ stdenv.mkDerivation rec {
homepage = "http://spark.apache.org";
license = stdenv.lib.licenses.asl20;
platforms = stdenv.lib.platforms.all;
maintainers = with maintainers; [ thoughtpolice offline ];
maintainers = with maintainers; [ thoughtpolice offline kamilchm ];
repositories.git = git://git.apache.org/spark.git;
};
}

15
pkgs/applications/networking/enhanced-ctorrent/default.nix
View file

@ -1,13 +1,26 @@
{ stdenv, fetchurl }:
{ stdenv, fetchurl, fetchpatch }:
stdenv.mkDerivation rec {
version = "dnh3.3.2";
name = "enhanced-ctorrent";
src = fetchurl {
url = "http://www.rahul.net/dholmes/ctorrent/ctorrent-dnh3.3.2.tar.gz";
sha256 = "0qs8waqwllk56i3yy3zhncy7nsnhmf09a494p5siz4vm2k4ncwy8";
};
# These patches come from Debian and fix CVE-2009-1759.
patches = [
(fetchpatch {
url = "https://sources.debian.org/data/main/c/ctorrent/1.3.4.dnh3.3.2-5/debian/patches/cve-security-fix.diff";
sha256 = "1qkzzm8sfspbcs10azmmif4qcr7pr8r38dsa2py84lsjm1yi3kls";
})
(fetchpatch {
url = "https://sources.debian.org/data/main/c/ctorrent/1.3.4.dnh3.3.2-5/debian/patches/FTBFS-fix.diff";
sha256 = "1m3zh96xwqjjzsbg62f7kx0miams58nys1f484qhdn870b5x9p06";
})
];
meta = {
description = "BitTorrent client written in C++";
longDescription = ''

6
pkgs/applications/office/mendeley/default.nix
View file

@ -44,14 +44,14 @@ let
then "i386"
else "amd64";
shortVersion = "1.17.13-stable";
shortVersion = "1.18-stable";
version = "${shortVersion}_${arch}";
url = "http://desktop-download.mendeley.com/download/apt/pool/main/m/mendeleydesktop/mendeleydesktop_${version}.deb";
sha256 = if stdenv.system == arch32
then "0q4x62k00whmq8lskphpcxc610cvclxzcr5k0v7pxjxs9sx5yx43"
else "01ylyily1hip35z0d4qkdpbzp5yn4r015psc5773xsqlgrnlwjm3";
then "046v1j4sc6m0bf89f52zsg8riygrhldplyih5p0cjhcsd45q6fx8"
else "072fppgxhiryb6m1fb4qvq8nbblx88xpknnklygch1sw0lyks69h";
deps = [
qtbase

4
pkgs/applications/office/mendeley/update.nix
View file

@ -15,9 +15,9 @@ writeScript "update-mendeley" ''
}
amd64URL=$(follow https://www.mendeley.com/repositories/ubuntu/stable/amd64/mendeleydesktop-latest)
amd64V=$(basename $amd64URL|grep -m1 -o "[0-9]\+\.[0-9]\+\.[0-9]\+")
amd64V=$(basename $amd64URL|grep -m1 -o "[0-9]\+\.[0-9]\+\(\.[0-9]\+\)\?")
i386URL=$(follow https://www.mendeley.com/repositories/ubuntu/stable/i386/mendeleydesktop-latest)
i386V=$(basename $i386URL|grep -m1 -o "[0-9]\+\.[0-9]\+\.[0-9]\+")
i386V=$(basename $i386URL|grep -m1 -o "[0-9]\+\.[0-9]\+\(\.[0-9]\+\)\?")
echo "amd64 version: $amd64V"
echo "i386 version: $i386V"

4
pkgs/applications/office/todo.txt-cli/default.nix
View file

@ -1,12 +1,12 @@
{ stdenv, fetchurl }:
let
version = "2.10";
version = "2.11.0";
in stdenv.mkDerivation {
name = "todo.txt-cli-${version}";
src = fetchurl {
url = "https://github.com/ginatrapani/todo.txt-cli/releases/download/v${version}/todo.txt_cli-${version}.tar.gz";
sha256 = "1agn4zzbizrrylvbfi053b5mpb39bvl1gzziw08xibzfdyi1g55m";
sha256 = "0majx8lcvhh8ji54qi0sxr833wchdss95fjc92byd8g3lfz27rsz";
};
installPhase = ''

7
pkgs/applications/science/math/R/default.nix
View file

@ -7,11 +7,11 @@
}:
stdenv.mkDerivation rec {
name = "R-3.4.4";
name = "R-3.5.0";
src = fetchurl {
url = "http://cran.r-project.org/src/base/R-3/${name}.tar.gz";
sha256 = "0dq3jsnwsb5j3fhl0wi3p5ycv8avf8s5j1y4ap3d2mkjmcppvsdk";
sha256 = "0w38865laqg28cdhikxdxhx4rfp0kgcn72gakwypsy91br9ja5zx";
};
buildInputs = [
@ -65,7 +65,8 @@ stdenv.mkDerivation rec {
installTargets = [ "install" "install-info" "install-pdf" ];
doCheck = true;
doCheck = withRecommendedPackages; # R 3.5.0 fails the test suite if the
# recommended packages are not built
preCheck = "export TZ=CET; bin/Rscript -e 'sessionInfo()'";
enableParallelBuilding = true;

56
pkgs/applications/science/math/calc/default.nix
View file

@ -1,47 +1,49 @@
{ stdenv, fetchurl, makeWrapper, glibc, readline, ncurses, utillinux }:
{ stdenv, lib, fetchurl, utillinux, makeWrapper
, enableReadline ? true, readline, ncurses }:
with stdenv.lib;
let
makeFlags = ''
INCDIR=${glibc.dev}/include \
BINDIR=$out/bin LIBDIR=$out/lib CALC_INCDIR=$out/include/calc CALC_SHAREDIR=$out/share/calc MANDIR=$out/share/man/man1 \
USE_READLINE=-DUSE_READLINE READLINE_LIB=-lreadline READLINE_EXTRAS='-lhistory -lncurses' \
TERMCONTROL=-DUSE_TERMIOS \
'';
in
stdenv.mkDerivation rec {
name = "calc-${version}";
version = "2.12.6.6";
src = fetchurl {
url = "https://github.com/lcn2/calc/releases/download/${version}/${name}.tar.bz2";
urls = [
"https://github.com/lcn2/calc/releases/download/${version}/${name}.tar.bz2"
"http://www.isthe.com/chongo/src/calc/${name}.tar.bz2"
];
sha256 = "03sg1xhin6qsrz82scf96mmzw8lz1yj68rhj4p4npp4s0fawc9d5";
};
buildInputs = [ makeWrapper readline ncurses utillinux ];
configurePhase = ''
sed -i 's/all: check_include/all:/' Makefile
patchPhase = ''
substituteInPlace Makefile \
--replace 'all: check_include' 'all:' \
--replace '-install_name ''${LIBDIR}/libcalc''${LIB_EXT_VERSION}' '-install_name ''${T}''${LIBDIR}/libcalc''${LIB_EXT_VERSION}' \
--replace '-install_name ''${LIBDIR}/libcustcalc''${LIB_EXT_VERSION}' '-install_name ''${T}''${LIBDIR}/libcustcalc''${LIB_EXT_VERSION}'
'';
buildPhase = ''
make ${makeFlags}
'';
buildInputs = [ utillinux makeWrapper ]
++ lib.optionals enableReadline [ readline ncurses ];
installPhase = ''
make install ${makeFlags}
wrapProgram $out/bin/calc --prefix LD_LIBRARY_PATH : $out/lib
'';
makeFlags = [
"T=$(out)"
"INCDIR=${lib.getDev stdenv.cc.libc}/include"
"BINDIR=/bin"
"LIBDIR=/lib"
"CALC_SHAREDIR=/share/calc"
"CALC_INCDIR=/include"
"MANDIR=/share/man/man1"
# Hack to avoid TMPDIR in RPATHs.
preFixup = ''rm -rf "$(pwd)" '';
# Handle LDFLAGS defaults in calc
"DEFAULT_LIB_INSTALL_PATH=$(out)/lib"
] ++ lib.optionals enableReadline [
"READLINE_LIB=-lreadline"
"USE_READLINE=-DUSE_READLINE"
];
meta = {
meta = with lib; {
description = "C-style arbitrary precision calculator";
homepage = http://www.isthe.com/chongo/tech/comp/calc/;
license = licenses.lgpl21;
maintainers = [ ];
maintainers = with maintainers; [ matthewbauer ];
platforms = platforms.all;
};
}

23
pkgs/applications/science/math/mathematica/default.nix
View file

@ -1,7 +1,7 @@
{ stdenv
, coreutils
, patchelf
, requireFile
, callPackage
, alsaLib
, dbus
, fontconfig
@ -18,6 +18,7 @@
, zlib
, libxml2
, libuuid
, lang ? "en"
}:
let
@ -26,21 +27,15 @@ let
"Linux"
else
throw "Mathematica requires i686-linux or x86_64 linux";
l10n =
with stdenv.lib;
with callPackage ./l10ns.nix {};
flip (findFirst (l: l.lang == lang)) l10ns
(throw "Language '${lang}' not supported");
in
stdenv.mkDerivation rec {
version = "11.2.0";
name = "mathematica-${version}";
src = requireFile rec {
name = "Mathematica_${version}_LINUX.sh";
message = ''
This nix expression requires that ${name} is
already part of the store. Find the file on your Mathematica CD
and add it to the nix store with nix-store --add-fixed sha256 <FILE>.
'';
sha256 = "4a1293cc1c404303aa1cab1bd273c7be151d37ac5ed928fbbb18e9c5ab2d8df9";
};
inherit (l10n) version name src;
buildInputs = [
coreutils

33
pkgs/applications/science/math/mathematica/l10ns.nix Normal file
View file

@ -0,0 +1,33 @@
{ lib, requireFile }:
with lib;
{
l10ns = flip map
[
{
version = "11.2.0";
lang = "en";
language = "English";
sha256 = "4a1293cc1c404303aa1cab1bd273c7be151d37ac5ed928fbbb18e9c5ab2d8df9";
}
{
version = "11.2.0";
lang = "ja";
language = "Japanese";
sha256 = "916392edd32bed8622238df435dd8e86426bb043038a3336f30df10d819b49b1";
}
]
({ version, lang, language, sha256 }: {
inherit version lang;
name = "mathematica-${version}" + optionalString (lang != "en") "-${lang}";
src = requireFile rec {
name = "Mathematica_${version}" + optionalString (lang != "en") "_${language}" + "_LINUX.sh";
message = ''
This nix expression requires that ${name} is
already part of the store. Find the file on your Mathematica CD
and add it to the nix store with nix-store --add-fixed sha256 <FILE>.
'';
inherit sha256;
};
});
}

4
pkgs/applications/science/math/maxima/default.nix
View file

@ -69,6 +69,10 @@ stdenv.mkDerivation ({
url = "https://git.sagemath.org/sage.git/plain/build/pkgs/maxima/patches/maxima.system.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba";
sha256 = "18zafig8vflhkr80jq2ivk46k92dkszqlyq8cfmj0b2vcfjwwbar";
})
# There are some transient test failures. I hope this disables all those tests.
# If those test failures ever happen in the non-ecl version, that should be
# reportetd upstream.
./known-ecl-failures.patch
];
# Failures in the regression test suite won't abort the build process. We run

21
pkgs/applications/science/math/maxima/known-ecl-failures.patch Normal file
View file

@ -0,0 +1,21 @@
diff --git a/tests/testsuite.lisp b/tests/testsuite.lisp
index 45a81f4..36c35b8 100644
--- a/tests/testsuite.lisp
+++ b/tests/testsuite.lisp
@@ -25,13 +25,14 @@
((mlist simp) "rtest10" 24 25)
((mlist) "rtest11" #+(or gcl cmucl ccl64) 158 #+(or gcl cmucl ccl64) 174 #+gcl 175)
"rtest13" "rtest13s"
- "rtest14"
+ ;; "rtest14" ;; some tests sometimes fail with ecl, hard to reproduce. Observed failing: 250, 267, 297, 307, 310, 312, 315, 319
"rtest15"
;; ccl versions 1.11 and earlier fail test 50. Mark it as a
;; known failure. Presumably 1.12 will have this fixed.
((mlist simp) "rtest16" #+ccl 50)
"rtestode" "rtestode_zp"
- "rtest3" "rtest8"
+ "rtest3"
+ ((mlist simp) "rtest8" 104) ;; fails with ecl
((mlist simp) "rtest12" 76 78)
"rexamples"
((mlist simp) "rtesthyp" 105 112 113 123 124 128)

20
pkgs/applications/science/math/pari/default.nix
View file

@ -1,5 +1,9 @@
{ stdenv, fetchurl
, gmp, readline, libX11, libpthreadstubs, tex, perl }:
, gmp, readline, libX11, tex, perl
, withThread ? true, libpthreadstubs
}:
assert withThread -> libpthreadstubs != null;
stdenv.mkDerivation rec {
@ -11,14 +15,22 @@ stdenv.mkDerivation rec {
sha256 = "0ir6m3a8r46md5x6zk4xf159qra7aqparby9zk03k81hjrrxr72g";
};
buildInputs = [ gmp readline libX11 libpthreadstubs tex perl ];
buildInputs = [
gmp
readline
libX11
tex
perl
] ++ stdenv.lib.optionals withThread [
libpthreadstubs
];
configureScript = "./Configure";
configureFlags = [
"--mt=pthread"
"--with-gmp=${gmp.dev}"
"--with-readline=${readline.dev}"
] ++ stdenv.lib.optional stdenv.isDarwin "--host=x86_64-darwin";
] ++ stdenv.lib.optional stdenv.isDarwin "--host=x86_64-darwin"
++ stdenv.lib.optional withThread "--mt=pthread";
preConfigure = ''
export LD=$CC

31
pkgs/applications/science/math/pari/unstable.nix
View file

@ -1,31 +0,0 @@
{ stdenv, fetchurl, gmp, readline, perl }:
stdenv.mkDerivation rec {
version = "2.9.3";
name = "pari-unstable-${version}";
src = fetchurl {
url = "http://pari.math.u-bordeaux.fr/pub/pari/unstable/pari-${version}.tar.gz";
sha256 = "0qqal1lpggd6dvs19svnz0dil86xk0xkcj5s3b7104ibkmvjfsp7";
};
buildInputs = [gmp readline];
nativeBuildInputs = [perl];
configureScript = "./Configure";
configureFlags =
"--with-gmp=${gmp.dev} " +
"--with-readline=${readline.dev}";
meta = with stdenv.lib; {
description = "Computer algebra system for high-performance number theory computations";
homepage = "http://pari.math.u-bordeaux.fr/";
license = licenses.gpl2Plus;
maintainers = with maintainers; [ ertes raskin ];
platforms = platforms.linux;
inherit version;
downloadPage = "http://pari.math.u-bordeaux.fr/download.html";
updateWalker = true;
};
}

21
pkgs/applications/science/math/singular/default.nix
View file

@ -1,5 +1,6 @@
{ stdenv, fetchurl, gmp, bison, perl, autoconf, ncurses, readline, coreutils, pkgconfig
, autoreconfHook
, file
, flint
, ntl
, cddlib
@ -18,7 +19,9 @@ stdenv.mkDerivation rec {
sha256 = "0wvgz7l1b7zkpmim0r3mvv4fp8xnhlbz4c7hc90rn30snlansnf1";
};
configureFlags = stdenv.lib.optionals enableFactory [
configureFlags = [
"--with-ntl=${ntl}"
] ++stdenv.lib.optionals enableFactory [
"--enable-factory"
] ++ stdenv.lib.optionals enableGfanlib [
"--enable-gfanlib"
@ -42,11 +45,19 @@ stdenv.mkDerivation rec {
] ++ stdenv.lib.optionals enableGfanlib [
cddlib
];
nativeBuildInputs = [ autoconf bison perl pkgconfig autoreconfHook ];
nativeBuildInputs = [
bison
perl
pkgconfig
autoreconfHook
];
preConfigure = ''
find . -type f -exec sed -e 's@/bin/rm@${coreutils}&@g' -i '{}' ';'
find . -type f -exec sed -e 's@/bin/uname@${coreutils}&@g' -i '{}' ';'
preAutoreconf = ''
find . -type f -readable -writable -exec sed \
-e 's@/bin/rm@${coreutils}&@g' \
-e 's@/bin/uname@${coreutils}&@g' \
-e 's@/usr/bin/file@${file}/bin/file@g' \
-i '{}' ';'
'';
hardeningDisable = stdenv.lib.optional stdenv.isi686 "stackprotector";

20
pkgs/applications/video/handbrake/default.nix
View file

@ -37,15 +37,13 @@ stdenv.mkDerivation rec {
nativeBuildInputs = [
cmake python2 pkgconfig yasm autoconf automake libtool m4
] ++ lib.optionals useGtk [
intltool wrapGAppsHook
];
] ++ lib.optionals useGtk [ intltool wrapGAppsHook ];
buildInputs = [
fribidi fontconfig freetype jansson zlib
libass libiconv libsamplerate libxml2 bzip2
libogg libopus libtheora libvorbis libdvdcss a52dec libmkv
lame ffmpeg libdvdread libdvdnav libbluray mp4v2 mpeg2dec x264 x265 libvpx
lame libdvdread libdvdnav libbluray mp4v2 mpeg2dec x264 x265 libvpx
] ++ lib.optionals useGtk [
glib gtk3 libappindicator-gtk3 libnotify
gst_all_1.gstreamer gst_all_1.gst-plugins-base dbus-glib udev
@ -60,8 +58,6 @@ stdenv.mkDerivation rec {
preConfigure = ''
patchShebangs scripts
echo 'TAG=${version}' > version.txt
# `configure` errors out when trying to read the current year which is too low
substituteInPlace make/configure.py \
--replace developer release \
@ -97,13 +93,17 @@ stdenv.mkDerivation rec {
meta = with stdenv.lib; {
homepage = http://handbrake.fr/;
description = "A tool for ripping DVDs into video files";
description = "A tool for converting video files and ripping DVDs";
longDescription = ''
Handbrake is a versatile transcoding DVD ripper. This package
provides the cli HandbrakeCLI and the GTK+ version ghb.
Tool for converting and remuxing video files
into selection of modern and widely supported codecs
and containers. Very versatile and customizable.
Package provides:
CLI - `HandbrakeCLI`
GTK+ GUI - `ghb`
'';
license = licenses.gpl2;
maintainers = with maintainers; [ wmertens ];
maintainers = with maintainers; [ Anton-Latukha wmertens ];
# Not tested on anything else
platforms = platforms.linux;
};

4
pkgs/applications/virtualization/qemu/default.nix
View file

@ -8,7 +8,7 @@
, seccompSupport ? stdenv.isLinux, libseccomp
, pulseSupport ? !stdenv.isDarwin, libpulseaudio
, sdlSupport ? !stdenv.isDarwin, SDL2
, gtkSupport ? !xenSupport, gtk3, gettext, gnome3
, gtkSupport ? !stdenv.isDarwin && !xenSupport, gtk3, gettext, gnome3
, vncSupport ? true, libjpeg, libpng
, spiceSupport ? !stdenv.isDarwin, spice, spice-protocol
, usbredirSupport ? spiceSupport, usbredir
@ -107,6 +107,8 @@ stdenv.mkDerivation rec {
"--sysconfdir=/etc"
"--localstatedir=/var"
]
# disable sysctl check on darwin.
++ optional stdenv.isDarwin "--cpu=x86_64"
++ optional numaSupport "--enable-numa"
++ optional seccompSupport "--enable-seccomp"
++ optional spiceSupport "--enable-spice"

12
pkgs/build-support/vm/default.nix
View file

@ -997,22 +997,22 @@ rec {
};
debian9i386 = {
name = "debian-9.3-stretch-i386";
fullName = "Debian 9.3 Stretch (i386)";
name = "debian-9.4-stretch-i386";
fullName = "Debian 9.4 Stretch (i386)";
packagesList = fetchurl {
url = mirror://debian/dists/stretch/main/binary-i386/Packages.xz;
sha256 = "1rpv0r92pkr9dmjvpffvgmq3an1s83npfmq870h67jqag3qpwj9l";
sha256 = "05z5ccg4ysbrgallhai53sh83i0364w7a3fdq84dpv1li059jf10";
};
urlPrefix = mirror://debian;
packages = commonDebianPackages;
};
debian9x86_64 = {
name = "debian-9.3-stretch-amd64";
fullName = "Debian 9.3 Stretch (amd64)";
name = "debian-9.4-stretch-amd64";
fullName = "Debian 9.4 Stretch (amd64)";
packagesList = fetchurl {
url = mirror://debian/dists/stretch/main/binary-amd64/Packages.xz;
sha256 = "1gnkvh7wc5yp0rw8kq8p8rlskvl0lc4cv3gdylw8qpqzy75xqlig";
sha256 = "19j0c54b1b9lbk9fv2c2aswdh0s2c3klf97zrlmsz4hs8wm9jylq";
};
urlPrefix = mirror://debian;
packages = commonDebianPackages;

4
pkgs/data/fonts/dejavu-fonts/default.nix
View file

@ -1,4 +1,4 @@
{fetchFromGitHub, stdenv, fontforge, perl, FontTTF}:
{ fetchFromGitHub, stdenv, fontforge, perl, perlPackages }:
let
version = "2.37";
@ -25,7 +25,7 @@ let
full-ttf = stdenv.mkDerivation {
name = "dejavu-fonts-full-${version}";
nativeBuildInputs = [fontforge perl FontTTF];
nativeBuildInputs = [fontforge perl perlPackages.IOString perlPackages.FontTTF];
src = fetchFromGitHub {
owner = "dejavu-fonts";

4
pkgs/desktops/gnome-3/core/epiphany/default.nix
View file

@ -6,11 +6,11 @@
stdenv.mkDerivation rec {
name = "epiphany-${version}";
version = "3.28.1";
version = "3.28.1.1";
src = fetchurl {
url = "mirror://gnome/sources/epiphany/${gnome3.versionBranch version}/${name}.tar.xz";
sha256 = "0zvxrwlswxadq4zbr4f73ms141d08j0lhi6rzmj83j1s3gan88md";
sha256 = "15d4dr4dwb1dyw3mvs7wp5gik57kdg0rxdc49n92wx46wfh6lhlr";
};
# Tests need an X display

4
pkgs/desktops/gnome-3/core/gjs/default.nix
View file

@ -4,11 +4,11 @@
stdenv.mkDerivation rec {
name = "gjs-${version}";
version = "1.52.1";
version = "1.52.2";
src = fetchurl {
url = "mirror://gnome/sources/gjs/${gnome3.versionBranch version}/${name}.tar.xz";
sha256 = "1s1m8xv3ixgl0hah3r364ws249d6w8yn56q2ahfn3dg2j54rmz58";
sha256 = "00x08ypx61i3k84bmvkhdj37q81g79lzm5sxqm1lz4xzzad9rg98";
};
passthru = {

4
pkgs/desktops/gnome-3/core/sushi/default.nix
View file

@ -5,11 +5,11 @@
stdenv.mkDerivation rec {
name = "sushi-${version}";
version = "3.24.0";
version = "3.28.3";
src = fetchurl {
url = "mirror://gnome/sources/sushi/${gnome3.versionBranch version}/${name}.tar.xz";
sha256 = "f90bb95172664486f8d529995007fd12f0df9d0c998e20658b6203f46ce70d48";
sha256 = "1yydd34q7r05z0jdgym3r4f8jv8snrcvvhxw0vxn6damlvj5lbiw";
};
passthru = {

4
pkgs/desktops/gnome-3/misc/geary/default.nix
View file

@ -6,14 +6,14 @@
let
pname = "geary";
version = "0.12.1";
version = "0.12.2";
in
stdenv.mkDerivation rec {
name = "${pname}-${version}";
src = fetchurl {
url = "mirror://gnome/sources/${pname}/${stdenv.lib.versions.majorMinor version}/${name}.tar.xz";
sha256 = "12hbpd5j3rb122nrsqmgsg31x82xl0ksm0nmsl614v1dd7crqnh6";
sha256 = "09j5gh4zm49fcg2ycvy00dkkw69rfppqwc3lqdi4994hry4jivx9";
};
nativeBuildInputs = [ vala_0_40 intltool pkgconfig wrapGAppsHook cmake ninja desktop-file-utils gnome-doc-utils gobjectIntrospection ];

20
pkgs/development/compilers/ecl/16.1.2.nix
View file

@ -1,10 +1,14 @@
{stdenv, fetchurl
{ stdenv, fetchurl, fetchpatch
, libtool, autoconf, automake
, gmp, mpfr, libffi, makeWrapper
, noUnicode ? false
, gcc
, threadSupport ? true
, threadSupport ? false
, useBoehmgc ? true, boehmgc
}:
assert useBoehmgc -> boehmgc != null;
let
s = # Generated upstream information
rec {
@ -19,6 +23,9 @@ let
];
propagatedBuildInputs = [
libffi gmp mpfr gcc
] ++ stdenv.lib.optionals useBoehmgc [
# replaces ecl's own gc which other packages can depend on, thus propagated
boehmgc
];
in
stdenv.mkDerivation {
@ -39,6 +46,15 @@ stdenv.mkDerivation {
"--enable-unicode")
;
patches = [
(fetchpatch {
# Avoid infinite loop, see https://gitlab.com/embeddable-common-lisp/ecl/issues/43 (fixed upstream)
name = "avoid-infinite-loop.patch";
url = "https://gitlab.com/embeddable-common-lisp/ecl/commit/caba1989f40ef917e7486f41b9cd5c7e3c5c2d79.patch";
sha256 = "07vw91psbc9gdn8grql46ra8lq3bgkzg5v480chnbryna4sv6lbb";
})
];
hardeningDisable = [ "format" ];
postInstall = ''

6
pkgs/development/compilers/ecl/default.nix
View file

@ -4,6 +4,7 @@
, noUnicode ? false
, gcc
, threadSupport ? true
, useBoehmgc ? false, boehmgc
}:
let
s = # Generated upstream information
@ -20,6 +21,10 @@ let
];
propagatedBuildInputs = [
libffi gmp mpfr gcc
# replaces ecl's own gc which other packages can depend on, thus propagated
] ++ stdenv.lib.optionals useBoehmgc [
# replaces ecl's own gc which other packages can depend on, thus propagated
boehmgc
];
in
stdenv.mkDerivation {
@ -53,6 +58,7 @@ stdenv.mkDerivation {
meta = {
inherit (s) version;
description = "Lisp implementation aiming to be small, fast and easy to embed";
homepage = https://common-lisp.net/project/ecl/;
license = stdenv.lib.licenses.mit ;
maintainers = [stdenv.lib.maintainers.raskin];
platforms = stdenv.lib.platforms.linux;

3
pkgs/development/compilers/mono/4.0.nix
View file

@ -3,4 +3,7 @@ callPackage ./generic.nix (rec {
inherit Foundation libobjc;
version = "4.0.4.1";
sha256 = "1ydw9l89apc9p7xr5mdzy0h97g2q6v243g82mxswfc2rrqhfs4gd";
meta = {
knownVulnerabilities = [ "CVE-2009-0689" ];
};
})

8
pkgs/development/compilers/mono/generic.nix
View file

@ -5,13 +5,15 @@
, version, sha256
, withLLVM ? false
, enableParallelBuilding ? true
, meta ? {}
}:
let
llvm = callPackage ./llvm.nix { };
in
stdenv.mkDerivation rec {
name = "mono-${version}";
in
stdenv.mkDerivation {
inherit name;
src = fetchurl {
inherit sha256;
@ -91,5 +93,5 @@ stdenv.mkDerivation rec {
platforms = stdenv.lib.platforms.x86;
maintainers = with stdenv.lib.maintainers; [ viric thoughtpolice obadz vrthra ];
license = stdenv.lib.licenses.free; # Combination of LGPL/X11/GPL ?
};
} // meta;
}

23
pkgs/development/interpreters/eff/default.nix
View file

@ -1,20 +1,21 @@
{ stdenv, fetchgit, ocaml, findlib, ocamlbuild, menhir, which }:
{ stdenv, fetchFromGitHub, which, ocamlPackages }:
let inherit (stdenv.lib) getVersion versionAtLeast; in
assert versionAtLeast (getVersion ocaml) "3.12";
let version = "5.0"; in
stdenv.mkDerivation {
name = "eff-20140928";
name = "eff-${version}";
src = fetchgit {
url = "https://github.com/matijapretnar/eff.git";
rev = "90f884a790fddddb51d4d1d3b7c2edf1e8aabb64";
sha256 = "0cqqrpvfw0nrk5d28mkzfvc8yzqxcss0k46bkmqhqjkqq886n2mm";
src = fetchFromGitHub {
owner = "matijapretnar";
repo = "eff";
rev = "v${version}";
sha256 = "1fslfj5d7fhj3f7kh558b8mk5wllwyq4rnhfkyd96fpy144sdcka";
};
buildInputs = [ ocaml findlib ocamlbuild menhir which ];
buildInputs = [ which ] ++ (with ocamlPackages; [
ocaml findlib ocamlbuild menhir js_of_ocaml js_of_ocaml-ocamlbuild
]);
doCheck = true;
checkTarget = "test";
@ -29,7 +30,7 @@ stdenv.mkDerivation {
backtracking, multi-threading, and much more...
'';
license = licenses.bsd2;
platforms = ocaml.meta.platforms or [];
inherit (ocamlPackages.ocaml.meta) platforms;
maintainers = [ maintainers.jirkamarsik ];
};
}

4
pkgs/development/interpreters/supercollider/default.nix
View file

@ -9,12 +9,12 @@ in
stdenv.mkDerivation rec {
name = "supercollider-${version}";
version = "3.9.2";
version = "3.9.3";
src = fetchurl {
url = "https://github.com/supercollider/supercollider/releases/download/Version-${version}/SuperCollider-${version}-Source-linux.tar.bz2";
sha256 = "0d3cb6dw8jz7ijriqn3rlwin24gffczp69hl17pzxj1d5w57yj44";
sha256 = "1d8ixfl100jvlialxdizp8wqsl1mp5pi2bam25vp97bhjd59cfdr";
};
hardeningDisable = [ "stackprotector" ];

12
pkgs/development/libraries/arb/default.nix
View file

@ -2,15 +2,21 @@
stdenv.mkDerivation rec {
name = "${pname}-${version}";
pname = "arb";
version = "2.8.1";
version = "2.13.0";
src = fetchFromGitHub {
owner = "fredrik-johansson";
repo = "${pname}";
rev = "${version}";
sha256 = "15phk71ci9rr32aqznpkd2b993wjahsgliilkg4mnxsr86nwdf6x";
sha256 = "1fl9gmxf6c1cphk5r8jbys5pywj2rfm705kv0055i0aqc6hrv303";
};
buildInputs = [mpir gmp mpfr flint];
configureFlags = "--with-gmp=${gmp} --with-mpir=${mpir} --with-mpfr=${mpfr} --with-flint=${flint}";
configureFlags = [
"--with-gmp=${gmp}"
"--with-mpir=${mpir}"
"--with-mpfr=${mpfr}"
"--with-flint=${flint}"
];
doCheck = true;
meta = {
inherit version;
description = ''A library for arbitrary-precision interval arithmetic'';

39
pkgs/development/libraries/eclib/default.nix
View file

@ -1,21 +1,44 @@
{stdenv, fetchFromGitHub, autoconf, automake, libtool, gettext, autoreconfHook
, pari, ntl, gmp}:
{ stdenv
, fetchFromGitHub
, autoreconfHook
, libtool
, gettext
, pari
, ntl
, gmp
# "FLINT is optional and only used for one part of sparse matrix reduction,
# which is used in the modular symbol code but not mwrank or other elliptic
# curve programs." -- https://github.com/JohnCremona/eclib/blob/master/README
, withFlint ? false, flint ? null
}:
assert withFlint -> flint != null;
stdenv.mkDerivation rec {
name = "${pname}-${version}";
pname = "eclib";
version = "20160720";
# or fetchFromGitHub(owner,repo,rev) or fetchgit(rev)
version = "20171002";
src = fetchFromGitHub {
owner = "JohnCremona";
repo = "${pname}";
rev = "${version}";
sha256 = "0qrcd5c8cqhw9f14my6k6013w8li5vdigrjvchkr19n2l8g75j0h";
rev = "v${version}";
sha256 = "092an90405q9da0k0z5jfp5rng9jl0mqbvsbv4fx6jc9ykfcahsj";
};
buildInputs = [pari ntl gmp];
nativeBuildInputs = [autoconf automake libtool gettext autoreconfHook];
buildInputs = [
pari
ntl
gmp
] ++ stdenv.lib.optionals withFlint [
flint
];
nativeBuildInputs = [
autoreconfHook
];
doCheck = true;
meta = {
inherit version;
description = ''Elliptic curve tools'';
homepage = https://github.com/JohnCremona/eclib;
license = stdenv.lib.licenses.gpl2Plus;
maintainers = [stdenv.lib.maintainers.raskin];
platforms = stdenv.lib.platforms.linux;

33
pkgs/development/libraries/fflas-ffpack/default.nix
View file

@ -1,4 +1,7 @@
{stdenv, fetchFromGitHub, autoreconfHook, givaro, pkgconfig, openblas, liblapack}:
{ stdenv, fetchFromGitHub, autoreconfHook, givaro, pkgconfig, openblas
, gmpxx
, optimize ? false # impure
}:
stdenv.mkDerivation rec {
name = "${pname}-${version}";
pname = "fflas-ffpack";
@ -9,9 +12,31 @@ stdenv.mkDerivation rec {
rev = "v${version}";
sha256 = "1cqhassj2dny3gx0iywvmnpq8ca0d6m82xl5rz4mb8gaxr2kwddl";
};
nativeBuildInputs = [ autoreconfHook pkgconfig ];
buildInputs = [ givaro (liblapack.override {shared = true;}) openblas];
configureFlags = "--with-blas-libs=-lopenblas --with-lapack-libs=-llapack";
checkInputs = [
gmpxx
];
nativeBuildInputs = [
autoreconfHook
pkgconfig
] ++ stdenv.lib.optionals doCheck checkInputs;
buildInputs = [ givaro openblas];
configureFlags = [
"--with-blas-libs=-lopenblas"
"--with-lapack-libs=-lopenblas"
] ++ stdenv.lib.optionals (!optimize) [
# disable SIMD instructions (which are enabled *when available* by default)
"--disable-sse"
"--disable-sse2"
"--disable-sse3"
"--disable-ssse3"
"--disable-sse41"
"--disable-sse42"
"--disable-avx"
"--disable-avx2"
"--disable-fma"
"--disable-fma4"
];
doCheck = true;
meta = {
inherit version;
description = ''Finite Field Linear Algebra Subroutines'';

26
pkgs/development/libraries/glpk/default.nix
View file

@ -1,13 +1,33 @@
{ fetchurl, stdenv }:
{ stdenv
, fetchurl
# Excerpt from glpk's INSTALL file:
# This feature allows the exact simplex solver to use the GNU MP
# bignum library. If it is disabled, the exact simplex solver uses the
# GLPK bignum module, which provides the same functionality as GNU MP,
# however, it is much less efficient.
, withGmp ? true
, gmp
}:
assert withGmp -> gmp != null;
stdenv.mkDerivation rec {
name = "glpk-4.65";
version = "4.65";
name = "glpk-${version}";
src = fetchurl {
url = "mirror://gnu/glpk/${name}.tar.gz";
sha256 = "040sfaa9jclg2nqdh83w71sv9rc1sznpnfiripjdyr48cady50a2";
};
buildInputs = stdenv.lib.optionals withGmp [
gmp
];
configureFlags = stdenv.lib.optionals withGmp [
"--with-gmp"
];
doCheck = true;
meta = {
@ -23,7 +43,7 @@ stdenv.mkDerivation rec {
homepage = http://www.gnu.org/software/glpk/;
license = stdenv.lib.licenses.gpl3Plus;
maintainers = [ stdenv.lib.maintainers.bjg ];
maintainers = with stdenv.lib.maintainers; [ bjg ];
platforms = stdenv.lib.platforms.all;
};
}

6
pkgs/development/libraries/gmime/3.nix
View file

@ -1,12 +1,12 @@
{ stdenv, fetchurl, pkgconfig, glib, zlib, gpgme, libidn, gobjectIntrospection }:
stdenv.mkDerivation rec {
version = "3.0.5";
version = "3.2.0";
name = "gmime-${version}";
src = fetchurl {
url = "mirror://gnome/sources/gmime/3.0/${name}.tar.xz";
sha256 = "1q45gd1ahnz9q1milc2lqqwl7j3q0wd6kiswhp25iak222n56lrg";
url = "mirror://gnome/sources/gmime/3.2/${name}.tar.xz";
sha256 = "1q6palbpf6lh6bvy9ly26q5apl5k0z0r4mvl6zzqh90rz4rn1v3m";
};
outputs = [ "out" "dev" ];

50
pkgs/development/libraries/gstreamer/base/default.nix
View file

@ -1,17 +1,22 @@
{ stdenv, fetchurl, fetchpatch, pkgconfig, meson
, ninja, gettext, gobjectIntrospection, python
, gstreamer, orc, alsaLib, libXv, pango, libtheora
, wayland, cdparanoia, libvisual, libintl
}:
{ stdenv, fetchurl, fetchpatch, lib
, pkgconfig, meson, ninja, gettext, gobjectIntrospection
, python, gstreamer, orc, pango, libtheora, libvisual
, libintl
, enableX11 ? stdenv.isLinux, libXv
, enableWayland ? stdenv.isLinux, wayland
, enableAlsa ? stdenv.isLinux, alsaLib
, enableCocoa ? false, darwin
, enableCdparanoia ? (!stdenv.isDarwin), cdparanoia }:
stdenv.mkDerivation rec {
name = "gst-plugins-base-1.14.0";
meta = {
meta = with lib; {
description = "Base plugins and helper libraries";
homepage = https://gstreamer.freedesktop.org;
license = stdenv.lib.licenses.lgpl2Plus;
platforms = stdenv.lib.platforms.unix;
license = licenses.lgpl2Plus;
platforms = platforms.unix;
maintainers = with maintainers; [ matthewbauer ];
};
src = fetchurl {
@ -21,19 +26,32 @@ stdenv.mkDerivation rec {
outputs = [ "out" "dev" ];
nativeBuildInputs = [
pkgconfig python meson ninja gettext gobjectIntrospection
];
nativeBuildInputs = [ pkgconfig python gettext gobjectIntrospection ]
buildInputs = [
orc libXv pango libtheora cdparanoia libintl wayland
# Broken meson with Darwin. Should hopefully be fixed soon. Tracking
# in https://bugzilla.gnome.org/show_bug.cgi?id=781148.
++ lib.optionals (!stdenv.isDarwin) [ meson ninja ];
# TODO How to pass these to Meson?
configureFlags = [
"--enable-x11=${if enableX11 then "yes" else "no"}"
"--enable-wayland=${if enableWayland then "yes" else "no"}"
"--enable-cocoa=${if enableCocoa then "yes" else "no"}"
]
++ stdenv.lib.optional stdenv.isLinux alsaLib
++ stdenv.lib.optional (!stdenv.isDarwin) libvisual;
# Introspection fails on my MacBook currently
++ lib.optional stdenv.isDarwin "--disable-introspection";
buildInputs = [ orc libtheora libintl ]
++ lib.optional enableAlsa alsaLib
++ lib.optionals enableX11 [ libXv pango ]
++ lib.optional enableWayland wayland
++ lib.optional enableCocoa darwin.apple_sdk.frameworks.Cocoa
++ lib.optional enableCdparanoia cdparanoia;
propagatedBuildInputs = [ gstreamer ];
preConfigure = ''
postPatch = ''
patchShebangs .
'';

15
pkgs/development/libraries/gstreamer/core/default.nix
View file

@ -2,17 +2,18 @@
, pkgconfig, gettext, gobjectIntrospection
, bison, flex, python3, glib, makeWrapper
, libcap,libunwind, darwin
, lib
}:
stdenv.mkDerivation rec {
name = "gstreamer-1.14.0";
meta = {
meta = with lib ;{
description = "Open source multimedia framework";
homepage = https://gstreamer.freedesktop.org;
license = stdenv.lib.licenses.lgpl2Plus;
platforms = stdenv.lib.platforms.unix;
maintainers = [ stdenv.lib.maintainers.ttuegel ];
license = licenses.lgpl2Plus;
platforms = platforms.unix;
maintainers = with maintainers; [ ttuegel matthewbauer ];
};
src = fetchurl {
@ -20,7 +21,7 @@ stdenv.mkDerivation rec {
sha256 = "0vj6k01lp2yva6rfd95fkyng9jdr62gkz0x8d2l81dyly1ki6dpw";
};
patches = [
patches = [
(fetchpatch {
url = "https://bug794856.bugzilla-attachments.gnome.org/attachment.cgi?id=370411";
sha256 = "16plzzmkk906k4892zq68j3c9z8vdma5nxzlviq20jfv04ykhmk2";
@ -34,7 +35,9 @@ stdenv.mkDerivation rec {
nativeBuildInputs = [
meson ninja pkgconfig gettext bison flex python3 makeWrapper gobjectIntrospection
];
buildInputs = [ libcap libunwind ] ++ stdenv.lib.optional stdenv.isDarwin darwin.apple_sdk.frameworks.CoreServices;
buildInputs =
lib.optionals stdenv.isLinux [ libcap libunwind ]
++ lib.optional stdenv.isDarwin darwin.apple_sdk.frameworks.CoreServices;
propagatedBuildInputs = [ glib ];

6
pkgs/development/libraries/libgphoto2/default.nix
View file

@ -7,7 +7,7 @@ stdenv.mkDerivation rec {
owner = "gphoto";
repo = "libgphoto2";
rev = "${meta.tag}";
sha256 = "1svbpmxqm56pqkv0rxhlyk4vw7mjgjz8zz4p669qvmw630082yj9";
sha256 = "0pbfg89817qkb35mmajsw2iz6j9nhkkj67m419f8x8yxpqkaa0wb";
};
patches = [];
@ -33,8 +33,8 @@ stdenv.mkDerivation rec {
MTP, and other vendor specific protocols for controlling and transferring data
from digital cameras.
'';
version = "2.5.16";
tag = "libgphoto2-2_5_16-release";
version = "2.5.17";
tag = "libgphoto2-2_5_17-release";
# XXX: the homepage claims LGPL, but several src files are lgpl21Plus
license = stdenv.lib.licenses.lgpl21Plus;
platforms = with stdenv.lib.platforms; unix;

4
pkgs/development/libraries/libhttpseverywhere/default.nix
View file

@ -3,13 +3,13 @@
let
pname = "libhttpseverywhere";
version = "0.8.2";
version = "0.8.3";
in stdenv.mkDerivation rec {
name = "${pname}-${version}";
src = fetchurl {
url = "mirror://gnome/sources/${pname}/${gnome3.versionBranch version}/${name}.tar.xz";
sha256 = "0vcnimlfcscyvjbh845xbnjb9qc8x0mliaqz2gczxxpakxrbl3gh";
sha256 = "1jmn6i4vsm89q1axlq4ajqkzqmlmjaml9xhw3h9jnal46db6y00w";
};
nativeBuildInputs = [ gnome3.vala gobjectIntrospection meson ninja pkgconfig ];

79
pkgs/development/libraries/linbox/default.nix Normal file
View file

@ -0,0 +1,79 @@
{ stdenv
, fetchFromGitHub
, fetchpatch
, autoreconfHook
, givaro
, pkgconfig
, openblas
, liblapack
, fflas-ffpack
, gmpxx
, optimize ? false # impure
, withSage ? false # sage support
}:
stdenv.mkDerivation rec {
name = "${pname}-${version}";
pname = "linbox";
version = "1.5.2";
src = fetchFromGitHub {
owner = "linbox-team";
repo = "${pname}";
rev = "v${version}";
sha256 = "1wfivlwp30mzdy1697w7rzb8caajim50mc8h27k82yipn2qc5n4i";
};
nativeBuildInputs = [
autoreconfHook
pkgconfig
];
buildInputs = [
givaro
(liblapack.override {shared = true;})
openblas
gmpxx
fflas-ffpack
];
configureFlags = [
"--with-blas-libs=-lopenblas"
"--with-lapack-libs=-llapack"
"--disable-optimization"
] ++ stdenv.lib.optionals (!optimize) [
# disable SIMD instructions (which are enabled *when available* by default)
"--disable-sse"
"--disable-sse2"
"--disable-sse3"
"--disable-ssse3"
"--disable-sse41"
"--disable-sse42"
"--disable-avx"
"--disable-avx2"
"--disable-fma"
"--disable-fma4"
] ++ stdenv.lib.optionals withSage [
"--enable-sage"
];
patches = stdenv.lib.optionals withSage [
# https://trac.sagemath.org/ticket/24214#comment:39
# Will be resolved by
# https://github.com/linbox-team/linbox/issues/69
(fetchpatch {
url = "https://raw.githubusercontent.com/sagemath/sage/a843f48b7a4267e44895a3dfa892c89c85b85611/build/pkgs/linbox/patches/linbox_charpoly_fullCRA.patch";
sha256 = "16nxfzfknra3k2yk3xy0k8cq9rmnmsch3dnkb03kx15h0y0jmibk";
})
];
doCheck = true;
meta = {
inherit version;
description = "C++ library for exact, high-performance linear algebra";
license = stdenv.lib.licenses.lgpl21Plus;
maintainers = [stdenv.lib.maintainers.timokau];
platforms = stdenv.lib.platforms.linux;
homepage = http://linalg.org/;
};
}

13
pkgs/development/libraries/oniguruma/default.nix
View file

@ -13,16 +13,11 @@ stdenv.mkDerivation rec {
nativeBuildInputs = [ cmake ];
prePatch = stdenv.lib.optional stdenv.isDarwin ''
substituteInPlace cmake/dist.cmake \
--replace '@executable_path/''${UP_DIR}/''${INSTALL_LIB}' $out'/''${INSTALL_LIB}'
'';
meta = {
meta = with stdenv.lib; {
homepage = https://github.com/kkos/oniguruma;
description = "Regular expressions library";
license = stdenv.lib.licenses.bsd2;
maintainers = with stdenv.lib.maintainers; [ fuuzetsu ];
platforms = with stdenv.lib.platforms; unix;
license = licenses.bsd2;
maintainers = with maintainers; [ fuuzetsu ];
platforms = platforms.unix;
};
}

4
pkgs/development/libraries/openmpi/default.nix
View file

@ -9,14 +9,14 @@
let
majorVersion = "3.0";
minorVersion = "0";
minorVersion = "1";
in stdenv.mkDerivation rec {
name = "openmpi-${majorVersion}.${minorVersion}";
src = fetchurl {
url = "http://www.open-mpi.org/software/ompi/v${majorVersion}/downloads/${name}.tar.bz2";
sha256 = "1mw2d94k6mp4scg1wnkj50vdh734fy5m2ygyrj65s4mh3prbz6gn";
sha256 = "0pbqrm5faf57nasy1s81wqivl7zvxmv8lzjh8hvb0f3qxv8m0d36";
};
postPatch = ''

4
pkgs/development/libraries/rocksdb/default.nix
View file

@ -19,7 +19,7 @@ let
in
stdenv.mkDerivation rec {
name = "rocksdb-${version}";
version = "5.10.3";
version = "5.11.3";
outputs = [ "dev" "out" "static" "bin" ];
@ -27,7 +27,7 @@ stdenv.mkDerivation rec {
owner = "facebook";
repo = "rocksdb";
rev = "v${version}";
sha256 = "19d8i8map8qz639mhflmxc0w9gp78fvkq1l46y5s6b5imwh0w7xq";
sha256 = "15x2r7aib1xinwcchl32wghs8g96k4q5xgv6z97mxgp35475x01p";
};
nativeBuildInputs = [ which perl ];

28
pkgs/development/libraries/science/math/rankwidth/default.nix Normal file
View file

@ -0,0 +1,28 @@
{ stdenv
, fetchurl
}:
stdenv.mkDerivation rec {
pname = "rankwidth";
version = "0.7";
name = "${pname}-${version}";
src = fetchurl {
url = "http://mirrors.mit.edu/sage/spkg/upstream/rw/rw-${version}.tar.gz";
sha256 = "1rv2v42x2506x7f10349m1wpmmfxrv9l032bkminni2gbip9cjg0";
};
configureFlags = [
"--enable-executable=no" # no igraph dependency
];
# check phase is empty for now (as of version 0.7)
doCheck = true;
meta = with stdenv.lib; {
description = "Calculates rank-width and rank-decompositions";
license = with licenses; [ gpl2Plus ];
maintainers = with maintainers; [ timokau ];
platforms = platforms.linux;
};
}

50
pkgs/development/libraries/science/math/zn_poly/default.nix Normal file
View file

@ -0,0 +1,50 @@
{ stdenv
, fetchurl
, gmp
, python2
}:
stdenv.mkDerivation rec {
version = "0.9";
pname = "zn_poly";
name = "${pname}-${version}";
src = fetchurl {
url = "http://web.maths.unsw.edu.au/~davidharvey/code/zn_poly/releases/zn_poly-${version}.tar.gz";
sha256 = "1kxl25av7i3v68k32hw5bayrfcvmahmqvs97mlh9g238gj4qb851";
};
buildInputs = [
gmp
];
nativeBuildInputs = [
python2 # needed by ./configure to create the makefile
];
libname = "libzn_poly${stdenv.targetPlatform.extensions.sharedLibrary}";
# Tuning (either autotuning or with hand-written paramters) is possible
# but not implemented here.
# It seems buggy anyways (see homepage).
buildFlags = [ "all" libname ];
# `make install` fails to install some header files and the lib file.
installPhase = ''
mkdir -p "$out/include/zn_poly"
mkdir -p "$out/lib"
cp "${libname}" "$out/lib"
cp include/*.h "$out/include/zn_poly"
'';
doCheck = true;
meta = with stdenv.lib; {
homepage = http://web.maths.unsw.edu.au/~davidharvey/code/zn_poly/;
description = "Polynomial arithmetic over Z/nZ";
license = with licenses; [ gpl3 ];
maintainers = with maintainers; [ timokau ];
platforms = platforms.linux;
};
}

15
pkgs/development/python-modules/faulthandler/default.nix
View file

@ -2,24 +2,13 @@
buildPythonPackage rec {
pname = "faulthandler";
version = "3.0";
version = "3.1";
src = fetchPypi {
inherit pname version;
sha256 = "acc10e10909f0f956ba1b42b6c450ea0bdaaa27b3942899f65931396cfcdd36a";
sha256 = "83301ffab03c86b291677b64b5cec7026f412cbda5ebd27e4cb3338452c40021";
};
patches = [
(fetchpatch {
url = https://github.com/vstinner/faulthandler/commit/67b661e.patch;
sha256 = "1nn8c9nq5qypja949hzz0n4yprsyr63wihf5g3gwrinm2nkjnnv7";
})
(fetchpatch {
url = https://github.com/vstinner/faulthandler/commit/07cbb7b.patch;
sha256 = "0fh6rjyjw7z1hsiy3sgdc8j9mncg1vlv3y0h4bplqyw18vq3srb3";
})
];
meta = {
description = "Dump the Python traceback";
license = stdenv.lib.licenses.bsd2;

44
pkgs/development/python-modules/flask-autoindex/default.nix Normal file
View file

@ -0,0 +1,44 @@
{ stdenv
, buildPythonPackage
, fetchpatch
, fetchPypi
, flask
, flask-silk
, future
}:
buildPythonPackage rec {
pname = "Flask-AutoIndex";
version = "0.6";
src = fetchPypi {
inherit pname version;
sha256 = "19b10mb1nrqfjyafki6wnrbn8mqi30bbyyiyvp5xssc74pciyfqs";
};
propagatedBuildInputs = [
flask
flask-silk
future
];
patches = [
# fix generated binary, see https://github.com/sublee/flask-autoindex/pull/32
(fetchpatch {
name = "fix_binary.patch";
url = "https://github.com/sublee/flask-autoindex/pull/32.patch";
sha256 = "1v2r0wvi7prhipjq89774svv6aqj0a13mdfj07pdlkpzfbf029dn";
})
];
meta = with stdenv.lib; {
description = "The mod_autoindex for Flask";
longDescription = ''
Flask-AutoIndex generates an index page for your Flask application automatically.
The result is just like mod_autoindex, but the look is more awesome!
'';
license = licenses.bsd2;
maintainers = with maintainers; [ timokau ];
homepage = http://pythonhosted.org/Flask-AutoIndex/;
};
}

4
pkgs/development/python-modules/html5-parser/default.nix
View file

@ -2,12 +2,12 @@
buildPythonPackage rec {
pname = "html5-parser";
version = "0.4.4";
version = "0.4.5";
name = "${pname}-${version}";
src = fetchPypi {
inherit pname version;
sha256 = "b9f3a1d4cdb8742e8e4ecafab04bff541bde4ff09af233293ed0b94028ec1ab5";
sha256 = "01mx33sx4dhl4kj6wc48nj6jz7ry60rkhjv0s6k8h5xmjf5yy0x9";
};
nativeBuildInputs = [ pkgconfig ];

26
pkgs/development/python-modules/milksnake/default.nix Normal file
View file

@ -0,0 +1,26 @@
{ lib, buildPythonPackage, fetchPypi, cffi }:
buildPythonPackage rec {
pname = "milksnake";
version = "0.1.5";
src = fetchPypi {
inherit pname version;
extension = "zip";
sha256 = "120nprd8lqis7x7zy72536gk2j68f7gxm8gffmx8k4ygifvl7kfz";
};
propagatedBuildInputs = [
cffi
];
# tests rely on pip/venv
doCheck = false;
meta = with lib; {
description = "A python library that extends setuptools for binary extensions";
homepage = https://github.com/getsentry/milksnake;
license = licenses.asl20;
maintainers = with maintainers; [ matthiasbeyer ];
};
}

6
pkgs/development/r-modules/bioc-experiment-packages.nix generated
View file

@ -70,7 +70,7 @@ in with self; {
HelloRangesData = derive2 { name="HelloRangesData"; version="1.4.0"; sha256="1c7gfhwr9g6hv0p3s4yd8v9rhjp3jmrnzsqsqq4ysc2i24nf7drr"; depends=[]; };
HiCDataHumanIMR90 = derive2 { name="HiCDataHumanIMR90"; version="0.112.0"; sha256="1qxg7650lbfbjl9p75clrybsdbzd0yzpi8pi2biv83jgqkkjrd0b"; depends=[]; };
HiCDataLymphoblast = derive2 { name="HiCDataLymphoblast"; version="1.14.0"; sha256="0708xgm495a330h70yi2qd494h6gf0n46j016mw9bc4gzbb7aq9p"; depends=[]; };
Hiiragi2013 = derive2 { name="Hiiragi2013"; version="1.14.0"; sha256="0lah9l8gd5gs1wj68l9hqakcwha0rl88dg2p0zk92nff64jxn3pj"; depends=[affy Biobase boot clue cluster genefilter geneplotter gplots gtools KEGGREST lattice latticeExtra MASS mouse4302_db RColorBrewer xtable]; };
Hiiragi2013 = derive2 { name="Hiiragi2013"; version="1.14.1"; sha256="0b47hi6di0gy4f8bzhsjm5ag5jhqqsgh5h19h4lwr5jcg2710ang"; depends=[affy Biobase boot clue cluster genefilter geneplotter gplots gtools KEGGREST lattice latticeExtra MASS mouse4302_db RColorBrewer xtable]; };
HumanAffyData = derive2 { name="HumanAffyData"; version="1.4.0"; sha256="0xgb3rrvgrx6sdwbb8gb1q8mgf0s2giih8l8d3hzvnxazh80qs8b"; depends=[Biobase ExperimentHub]; };
IHWpaper = derive2 { name="IHWpaper"; version="1.6.0"; sha256="08gkdi1lra9mn1cbsqddqn3pwj3pfy2yfgzay5igr7n1akfmgh7k"; depends=[Biobase BiocGenerics BiocParallel cowplot DESeq2 dplyr fdrtool genefilter ggplot2 IHW qvalue Rcpp SummarizedExperiment]; };
ITALICSData = derive2 { name="ITALICSData"; version="2.16.0"; sha256="1rrfxc3hzlq2i0z5j432w3s33ln56i91a06q49piisz06vviz6yv"; depends=[]; };
@ -260,7 +260,7 @@ in with self; {
lungExpression = derive2 { name="lungExpression"; version="0.16.0"; sha256="09v9r6rmfcqprqd1rx53sa4dhjjmg6d9649vlhfhzkyc73yknwmb"; depends=[Biobase]; };
lydata = derive2 { name="lydata"; version="1.4.0"; sha256="0dflfp14gdjgy7qf3my0vas5zbg77l16li7xgv1924cry11w2dxx"; depends=[]; };
mAPKLData = derive2 { name="mAPKLData"; version="1.10.0"; sha256="1bfx4imb5yg17n0g1ag436zlks4jcp8ga0xj9wyh9bhx4miwyay4"; depends=[]; };
mammaPrintData = derive2 { name="mammaPrintData"; version="1.14.0"; sha256="0ks72wnagdvnbilqcsvl5lbhgh64fhbfys0da03336f1z16f5lv9"; depends=[]; };
mammaPrintData = derive2 { name="mammaPrintData"; version="1.14.2"; sha256="04ymimgj8ng5qgvq0cglmhcxv7a3jqx9a2zyg8lwiwzpyip18inx"; depends=[]; };
maqcExpression4plex = derive2 { name="maqcExpression4plex"; version="1.22.0"; sha256="0hn20i11vl9x23mx283aki097r1a8rspagac821kmlwghyab1mxq"; depends=[]; };
metaMSdata = derive2 { name="metaMSdata"; version="1.14.0"; sha256="1iygqxymvb98cm325bmdqb34n9b4k1vdzdyzcq8a0gh1dvs2m0iw"; depends=[]; };
methyvimData = derive2 { name="methyvimData"; version="1.0.0"; sha256="1b2mvcawafkr15py8h9j10w5givifi99h9clbdmkgfyixbbh0m94"; depends=[minfi]; };
@ -287,7 +287,7 @@ in with self; {
pcaGoPromoter_Hs_hg19 = derive2 { name="pcaGoPromoter.Hs.hg19"; version="1.14.0"; sha256="137lj4j0hlz3mkwyf334xr3bpm9j2jg1cd2sw9203kx6hvk92i2z"; depends=[]; };
pcaGoPromoter_Mm_mm9 = derive2 { name="pcaGoPromoter.Mm.mm9"; version="1.14.0"; sha256="0kb62bm1a8m88g59v6553qg69rmv0gh0wy4yfkqvn2sgz51zk4r4"; depends=[]; };
pcaGoPromoter_Rn_rn4 = derive2 { name="pcaGoPromoter.Rn.rn4"; version="1.14.0"; sha256="0b3cak7nzd6qxr7gnly4246gjdhxyp8h0w5dr1xsgwd9zy1k0psw"; depends=[]; };
pcxnData = derive2 { name="pcxnData"; version="1.0.0"; sha256="0bkzqac0b2x1f398bflv077dp6nb3ysdf75jcwxpj4nwyhcb7n4f"; depends=[]; };
pcxnData = derive2 { name="pcxnData"; version="2.0.0"; sha256="10qhw7v1nzf4y9xhd34jiimcyi6lgjy6y9zc6kzk80hm6qiry8j2"; depends=[]; };
pd_atdschip_tiling = derive2 { name="pd.atdschip.tiling"; version="0.16.0"; sha256="1ilwm4nx232dll01xqqvagq3qi6qa060v84y20ihxhfwdm46z0ci"; depends=[Biostrings DBI IRanges oligo oligoClasses RSQLite S4Vectors]; };
pepDat = derive2 { name="pepDat"; version="0.112.0"; sha256="15v4yk9cpnz2k16ka4iyc61ji5ck9mlkabgzxalwfnz77ri23mk0"; depends=[GenomicRanges]; };
plasFIA = derive2 { name="plasFIA"; version="1.6.0"; sha256="0p3pbjm5ww24ax7h72m38l0rcm01w5a4h8j5rsgynczvfv9jlwjq"; depends=[proFIA]; };

108
pkgs/development/r-modules/bioc-packages.nix generated
View file

@ -38,7 +38,7 @@ in with self; {
AnnotationForge = derive2 { name="AnnotationForge"; version="1.20.0"; sha256="01vbrf76vqfvxh6vpfxkjwccxggnha3byqzj333glqz2b6kwx5q1"; depends=[AnnotationDbi Biobase BiocGenerics DBI RCurl RSQLite S4Vectors XML]; };
AnnotationFuncs = derive2 { name="AnnotationFuncs"; version="1.28.0"; sha256="1g6y7bwk573yaays0fmlicxq2452sli0kv41bq8sh4ja2l5jh5i6"; depends=[AnnotationDbi DBI]; };
AnnotationHub = derive2 { name="AnnotationHub"; version="2.10.1"; sha256="14v8g44a6zg9j2rwn9x9y8509k0wr2cw8yccliz24glplb40wva4"; depends=[AnnotationDbi BiocGenerics BiocInstaller curl httr interactiveDisplayBase RSQLite S4Vectors yaml]; };
AnnotationHubData = derive2 { name="AnnotationHubData"; version="1.8.0"; sha256="1nsai8a2vf5jwczd4k3vbdd9xbn6dfg6dydvf4byklxj6pk6vi97"; depends=[AnnotationDbi AnnotationForge AnnotationHub Biobase BiocGenerics BiocInstaller biocViews Biostrings DBI futile_logger GenomeInfoDb GenomicFeatures GenomicRanges GEOquery IRanges jsonlite OrganismDbi rBiopaxParser RCurl Rsamtools RSQLite rtracklayer S4Vectors XML]; };
AnnotationHubData = derive2 { name="AnnotationHubData"; version="1.8.1"; sha256="08pvswszxnbr6b3amg2g2353iil2bm9bs571c6lf4v8z0z1by8g5"; depends=[AnnotationDbi AnnotationForge AnnotationHub Biobase BiocGenerics BiocInstaller biocViews Biostrings DBI futile_logger GenomeInfoDb GenomicFeatures GenomicRanges GEOquery IRanges jsonlite OrganismDbi rBiopaxParser RCurl Rsamtools RSQLite rtracklayer S4Vectors XML]; };
ArrayExpress = derive2 { name="ArrayExpress"; version="1.38.0"; sha256="01kb4322pfl9w6za6glb777hdyc8j36xs6flz3b11n1mjryipz7c"; depends=[Biobase limma oligo XML]; };
ArrayExpressHTS = derive2 { name="ArrayExpressHTS"; version="1.28.0"; sha256="04qnxgywyxww8xd6r8vgy8sglbixd25749dmbsw0wgqk6zcgysim"; depends=[Biobase BiocGenerics biomaRt Biostrings bitops DESeq edgeR GenomicRanges Hmisc IRanges R2HTML RColorBrewer rJava Rsamtools sampling sendmailR ShortRead snow svMisc XML]; };
ArrayTV = derive2 { name="ArrayTV"; version="1.16.0"; sha256="1hn5dngk4civwzx1w2py1n9g1k1jv3kwrj6z6ysvfsfi4q668341"; depends=[DNAcopy foreach oligoClasses S4Vectors]; };
@ -47,7 +47,7 @@ in with self; {
BAC = derive2 { name="BAC"; version="1.38.0"; sha256="04s7fbb8b4is97alj64p86jnh1lgf4a0n02wg3g9rvd75jxmzbai"; depends=[]; };
BADER = derive2 { name="BADER"; version="1.16.0"; sha256="05p006rqydnvz5a8gdbara9fsyn51b5flc05j593bvvlmkc6anl5"; depends=[]; };
BAGS = derive2 { name="BAGS"; version="2.18.0"; sha256="1qhmrz6ffhhsbnmcc0xmb64psv50b1jd1gxkjhhv479mcfl6mk06"; depends=[Biobase breastCancerVDX]; };
BASiCS = derive2 { name="BASiCS"; version="1.0.0"; sha256="15yby5dz0hizr76bpa5clrpfh1ycvpkk11i7y7ak164ikzxvvmd9"; depends=[BiocGenerics coda data_table KernSmooth matrixStats Rcpp RcppArmadillo S4Vectors scran SingleCellExperiment SummarizedExperiment testthat]; };
BASiCS = derive2 { name="BASiCS"; version="1.0.1"; sha256="02acpq0mrdr8l3xa3k32k2mq8k96c95gm9603m5z5z3x3npjdzq7"; depends=[BiocGenerics coda data_table KernSmooth matrixStats Rcpp RcppArmadillo S4Vectors scran SingleCellExperiment SummarizedExperiment testthat]; };
BBCAnalyzer = derive2 { name="BBCAnalyzer"; version="1.8.0"; sha256="0fv5gyzfv0093dlyrlci9d88fcb0ifgljxwivrxpkbbsll5vrpxh"; depends=[Biostrings GenomicRanges IRanges Rsamtools SummarizedExperiment VariantAnnotation]; };
BCRANK = derive2 { name="BCRANK"; version="1.40.0"; sha256="0vbjskazhm5v4lmwdc456r5vl2v848ldqrzbdjrdxjlvd72wfprw"; depends=[Biostrings]; };
BEAT = derive2 { name="BEAT"; version="1.16.0"; sha256="0x4k45qgzwv6m00zq1jhbhc2aa5slgg5p4g8g909vajc75fpp6g7"; depends=[Biostrings BSgenome GenomicRanges ShortRead]; };
@ -83,13 +83,13 @@ in with self; {
Biobase = derive2 { name="Biobase"; version="2.38.0"; sha256="1cgm1ja1kp56zdlzyy9ggbkfn8r2vbsd4hncmz8g4hjd47fg18kg"; depends=[BiocGenerics]; };
BiocCaseStudies = derive2 { name="BiocCaseStudies"; version="1.40.0"; sha256="0hwmqv8nimc8gl1c5a72ckmgag5j8886ab62i1irlkfis5x2rj8m"; depends=[Biobase]; };
BiocCheck = derive2 { name="BiocCheck"; version="1.14.0"; sha256="1nzp8kgw13z9pgf885rplj6k37jcldfhbz0adqclxr2gq0yalmyx"; depends=[BiocInstaller biocViews codetools graph httr optparse stringdist]; };
BiocFileCache = derive2 { name="BiocFileCache"; version="1.2.2"; sha256="111rrzz366kmqs1v8jx5ck0kb0xs42f250m5i0sn65ypvg9ag504"; depends=[DBI dbplyr dplyr httr rappdirs RSQLite]; };
BiocFileCache = derive2 { name="BiocFileCache"; version="1.2.3"; sha256="0fam0j8kwf9kfbvh4h7q4m53via75c5wnbn2g55cv3d37hikbpsm"; depends=[DBI dbplyr dplyr httr rappdirs RSQLite]; };
BiocGenerics = derive2 { name="BiocGenerics"; version="0.24.0"; sha256="03wxvhxyrhipbgcg83lqlfn7p9gbzzrnl48y0dq7303xgp232zai"; depends=[]; };
BiocInstaller = derive2 { name="BiocInstaller"; version="1.28.0"; sha256="19fga27bv6q9v5mpil74y76lahmnwvpg2h33rdx1r79nvljkd19d"; depends=[]; };
BiocParallel = derive2 { name="BiocParallel"; version="1.12.0"; sha256="13ng3n2wsgl3fh0v6jnz3vg51k5c1sh44pqdvblcrcd1qyjmmqhd"; depends=[BH futile_logger snow]; };
BiocSklearn = derive2 { name="BiocSklearn"; version="1.0.2"; sha256="1zpfb7g353c01ffldrx7251919r6giy58s19w78jf0bslagblv4y"; depends=[BBmisc knitr reticulate SummarizedExperiment]; };
BiocStyle = derive2 { name="BiocStyle"; version="2.6.1"; sha256="03pp04pkcq99kdv2spzr995h2cxsza7l6w3d4gp4112m06prcybm"; depends=[bookdown knitr rmarkdown yaml]; };
BiocWorkflowTools = derive2 { name="BiocWorkflowTools"; version="1.4.1"; sha256="13xcsd4c2l9jrcbl8axrragk4g2x6sp6xrk5r4gcligdicgxpq9l"; depends=[BiocStyle bookdown git2r httr knitr rmarkdown stringr]; };
BiocWorkflowTools = derive2 { name="BiocWorkflowTools"; version="1.4.2"; sha256="1nfph17y36vkji7yyvmkry134s4naml256p6687ag53klqxvvz7x"; depends=[BiocStyle bookdown git2r httr knitr rmarkdown stringr]; };
Biostrings = derive2 { name="Biostrings"; version="2.46.0"; sha256="0vg50qdlxqcm2d6axjnzg8wh8pr4c5gz03l8bdl0llmwzp0zclzk"; depends=[BiocGenerics IRanges S4Vectors XVector]; };
BitSeq = derive2 { name="BitSeq"; version="1.22.0"; sha256="1xkmvzv2kdla3mrarlw21w1hz788w71443jbn36a8dc4p6wrnxhy"; depends=[IRanges Rsamtools S4Vectors zlibbioc]; };
BrainStars = derive2 { name="BrainStars"; version="1.22.0"; sha256="0fipnpjpsp462dsfsvcrnysca4vsq2k6z15a6mxfxvqs1gybhvvj"; depends=[Biobase RCurl RJSONIO]; };
@ -129,7 +129,7 @@ in with self; {
CNVtools = derive2 { name="CNVtools"; version="1.72.0"; sha256="0ihmgg5f0p7yhg0273jb785fcrhcw704vz8r6ban8c63wk0qbqb5"; depends=[survival]; };
CODEX = derive2 { name="CODEX"; version="1.10.0"; sha256="1knfgii0n8grn4436aksk7f2xkk93ih2snvrp7p8pkr206kqadnq"; depends=[Biostrings BSgenome_Hsapiens_UCSC_hg19 GenomeInfoDb IRanges Rsamtools S4Vectors]; };
COHCAP = derive2 { name="COHCAP"; version="1.24.0"; sha256="1ggxn35hif4x4k1rbnxinf0pdqbg1n53wym9rm5zs6cnya4aimgj"; depends=[COHCAPanno gplots RColorBrewer WriteXLS]; };
COMPASS = derive2 { name="COMPASS"; version="1.16.0"; sha256="1x1vcn37nr4mcx5q8zahyg654gbx0srxckxvz6shvprpdvgs83sn"; depends=[abind clue data_table dplyr knitr magrittr pdist plyr RColorBrewer Rcpp reshape2 rlang scales tidyr]; };
COMPASS = derive2 { name="COMPASS"; version="1.16.2"; sha256="1g9y5gryy1r8sg75008v3b2a1l2wkxvf8h5bnljnkc0wsd4f4nvb"; depends=[abind clue data_table dplyr knitr magrittr pdist plyr RColorBrewer Rcpp reshape2 rlang scales tidyr]; };
CONFESS = derive2 { name="CONFESS"; version="1.6.0"; sha256="0kmvhwyzxz9ahvvzicigxal3r4ya8y5i090m7pi7d1p5arir7djl"; depends=[changepoint cluster contrast data_table EBImage ecp flexmix flowClust flowCore flowMeans flowMerge flowPeaks foreach ggplot2 limma MASS moments outliers plotrix raster readbitmap reshape2 SamSPECTRAL waveslim wavethresh zoo]; };
CORREP = derive2 { name="CORREP"; version="1.44.0"; sha256="10bjv02x2xzanajfbsvbxd7s2s07z0gydx1ypmbfym41jjwac9ra"; depends=[e1071]; };
COSNet = derive2 { name="COSNet"; version="1.12.0"; sha256="0x5kg4c5ml7ndqq81k5jy07fyra4q6nhhly6v7qd98gpmvrj6gnk"; depends=[]; };
@ -193,7 +193,7 @@ in with self; {
DEP = derive2 { name="DEP"; version="1.0.1"; sha256="0glkq6xlhcsr364zl4nkc7g3gnscv0yb3kcyvhzgm3bbfvd9q7ac"; depends=[assertthat Biobase broom circlize ComplexHeatmap dplyr DT fdrtool ggplot2 ggrepel gridExtra imputeLCMD limma MSnbase purrr RColorBrewer readr rmarkdown shiny shinydashboard SummarizedExperiment tibble tidyr vsn]; };
DESeq = derive2 { name="DESeq"; version="1.30.0"; sha256="0mn5w3cy16iwwk8zxs7za6aa6cnrca75z0g45zd5zh1py5d7nfv9"; depends=[Biobase BiocGenerics genefilter geneplotter lattice locfit MASS RColorBrewer]; };
DESeq2 = derive2 { name="DESeq2"; version="1.18.1"; sha256="1iyimg1s0x5pdmvl8x08s8h0v019y0nhjzs50chagbpk2x91fsmv"; depends=[Biobase BiocGenerics BiocParallel genefilter geneplotter GenomicRanges ggplot2 Hmisc IRanges locfit Rcpp RcppArmadillo S4Vectors SummarizedExperiment]; };
DEXSeq = derive2 { name="DEXSeq"; version="1.24.3"; sha256="0xip73hlbr3zry9d7ly9vvvsbb3xjcmfa09lr9fdy528dwjrf084"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel biomaRt DESeq2 genefilter geneplotter GenomicRanges hwriter IRanges RColorBrewer Rsamtools S4Vectors statmod stringr SummarizedExperiment]; };
DEXSeq = derive2 { name="DEXSeq"; version="1.24.4"; sha256="1a80yv742fx5c7qav7imsdybphf0d5bixsqyf8w5zng7fk8j16d5"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel biomaRt DESeq2 genefilter geneplotter GenomicRanges hwriter IRanges RColorBrewer Rsamtools S4Vectors statmod stringr SummarizedExperiment]; };
DEsubs = derive2 { name="DEsubs"; version="1.4.0"; sha256="1i9blymzj18r9646vac9grrjxw6xar8m6chn1dgdila17jag1wlp"; depends=[circlize DESeq DESeq2 EBSeq edgeR ggplot2 graph igraph jsonlite limma locfit Matrix NBPSeq pheatmap RBGL samr]; };
DFP = derive2 { name="DFP"; version="1.36.0"; sha256="117gmzcgr9wr9wb7g0rm7wlrakd76ys1frhmhx1k6ps97ibxlz1k"; depends=[Biobase]; };
DMCHMM = derive2 { name="DMCHMM"; version="1.0.0"; sha256="1y0wmxks51h0d21v8g4mryq7kzq49khhpa88fbhza9xp2bmwk358"; depends=[BiocParallel calibrate fdrtool GenomicRanges IRanges multcomp rtracklayer S4Vectors SummarizedExperiment]; };
@ -242,8 +242,8 @@ in with self; {
ENmix = derive2 { name="ENmix"; version="1.14.0"; sha256="117jp47hpm276x4q25jwqfagymvay0qk3ji5l9xvrj74piwqpgwh"; depends=[doParallel foreach geneplotter impute MASS minfi preprocessCore SummarizedExperiment sva wateRmelon]; };
EasyqpcR = derive2 { name="EasyqpcR"; version="1.20.0"; sha256="06lmq3pp0j86rv9bgs809r30qscgpxv5vjbkccf32q9wv82vd7hw"; depends=[gWidgetsRGtk2 matrixStats plotrix plyr]; };
EmpiricalBrownsMethod = derive2 { name="EmpiricalBrownsMethod"; version="1.6.0"; sha256="1wv1anm4bwm2kqi9lqn06bl1w17q6wvc1v2amrifbqjbmi5k7g8y"; depends=[]; };
EnrichedHeatmap = derive2 { name="EnrichedHeatmap"; version="1.9.2"; sha256="0ffyb40qcvpjqval78146w8wvk3ng7v1ipdwnqkzj705gqkwbw9y"; depends=[ComplexHeatmap GenomicRanges GetoptLong IRanges locfit matrixStats Rcpp]; };
EnrichmentBrowser = derive2 { name="EnrichmentBrowser"; version="2.8.6"; sha256="1vxnl0n34ygl4fx28s8zmp71b8hidlp4sn34k1cfkw7hiaf2gg9n"; depends=[AnnotationDbi BiocFileCache biocGraph ComplexHeatmap DESeq2 EDASeq edgeR geneplotter GO_db graph GSEABase hwriter KEGGgraph KEGGREST limma MASS pathview rappdirs ReportingTools Rgraphviz S4Vectors safe SPIA SummarizedExperiment topGO]; };
EnrichedHeatmap = derive2 { name="EnrichedHeatmap"; version="1.9.4"; sha256="03n7w56r14y3jrrsdl2awcan5d0hsn3kd8900lrj015pmgf2r9d0"; depends=[circlize ComplexHeatmap GenomicRanges GetoptLong IRanges locfit matrixStats Rcpp]; };
EnrichmentBrowser = derive2 { name="EnrichmentBrowser"; version="2.8.7"; sha256="12wrxbp14ahjjph85g040f72yk4j47svsyyv7b9s56mkc513vd6v"; depends=[AnnotationDbi BiocFileCache biocGraph ComplexHeatmap DESeq2 EDASeq edgeR geneplotter GO_db graph GSEABase hwriter KEGGgraph KEGGREST limma MASS pathview rappdirs ReportingTools Rgraphviz S4Vectors safe SPIA SummarizedExperiment topGO]; };
EpiDISH = derive2 { name="EpiDISH"; version="1.0.0"; sha256="065bvrfsssf5y4j9axqdcybqb5i8y2hnl09f9jr44bpbay34ay5f"; depends=[e1071 MASS quadprog]; };
EventPointer = derive2 { name="EventPointer"; version="1.2.0"; sha256="1yh6yhaf8c2rp8f4ipsk014552pplb28cl5z7wjwvarjb21waj05"; depends=[affxparser doParallel foreach GenomeInfoDb GenomicFeatures GenomicRanges graph igraph limma MASS Matrix matrixStats nnls prodlim RBGL S4Vectors SGSeq stringr SummarizedExperiment]; };
ExiMiR = derive2 { name="ExiMiR"; version="2.20.0"; sha256="0saxway680972dmn6q1gbbmkxcwv08hl2bq973qbyrv5drg6g4vv"; depends=[affy affyio Biobase limma preprocessCore]; };
@ -298,10 +298,10 @@ in with self; {
GSRI = derive2 { name="GSRI"; version="2.26.0"; sha256="12silcf67r3ni40g7vsc7iv15arzy7w12abpj2xcjfd9nr4d84js"; depends=[Biobase fdrtool genefilter GSEABase les]; };
GSReg = derive2 { name="GSReg"; version="1.12.0"; sha256="1rdzkv6kf14shfddvrz3pssjgr6pvg6is4lzcvjzrxai4y34n0y6"; depends=[AnnotationDbi GenomicFeatures Homo_sapiens org_Hs_eg_db]; };
GSVA = derive2 { name="GSVA"; version="1.26.0"; sha256="1zvi0w7clm5qg6fv6akqw4cx84kswcgzfzjdkhxsrid0l4hwmw09"; depends=[Biobase BiocGenerics geneplotter GSEABase shiny shinythemes]; };
GUIDEseq = derive2 { name="GUIDEseq"; version="1.8.0"; sha256="1xsjz3mq6iawspdz1rif3fb8j2h92ykfrjj3lzlcsnvg92bnlczq"; depends=[BiocGenerics BiocParallel Biostrings BSgenome ChIPpeakAnno CRISPRseek data_table GenomeInfoDb GenomicAlignments GenomicRanges hash IRanges limma matrixStats Rsamtools S4Vectors]; };
GUIDEseq = derive2 { name="GUIDEseq"; version="1.8.1"; sha256="1vx24scbwr4xqhza4q90jpw3xv1pyd7afbqlxijy2fv4p1fzwi4h"; depends=[BiocGenerics BiocParallel Biostrings BSgenome ChIPpeakAnno CRISPRseek data_table GenomeInfoDb GenomicAlignments GenomicRanges hash IRanges limma matrixStats Rsamtools S4Vectors]; };
GWASTools = derive2 { name="GWASTools"; version="1.24.1"; sha256="1x8p32f47fki2kl0pkjv4v7az8s1b6zwqjnxywfxy0drs9g6lky4"; depends=[Biobase DBI DNAcopy gdsfmt GWASExactHW lmtest logistf quantsmooth RSQLite sandwich survival]; };
GenRank = derive2 { name="GenRank"; version="1.6.0"; sha256="071k23qknpd46x22bj2cmp07mmxj22higw8ma4b0a8w0wmd05bwz"; depends=[matrixStats reshape2 survcomp]; };
GenVisR = derive2 { name="GenVisR"; version="1.8.0"; sha256="03jc5qz1xfqpbll8qbs5ib7g70s21crmggc9a6xi9nvjq8ky05r6"; depends=[AnnotationDbi BiocGenerics biomaRt Biostrings DBI FField GenomicFeatures GenomicRanges ggplot2 gridExtra gtable gtools IRanges plyr reshape2 Rsamtools scales viridis]; };
GenVisR = derive2 { name="GenVisR"; version="1.8.1"; sha256="0c8dm4k2fn4g7vpjvd452vx0a1xb4rp5w1ii1h4q96957s8s52hj"; depends=[AnnotationDbi BiocGenerics biomaRt Biostrings DBI FField GenomicFeatures GenomicRanges ggplot2 gridExtra gtable gtools IRanges plyr reshape2 Rsamtools scales viridis]; };
GeneAnswers = derive2 { name="GeneAnswers"; version="2.20.0"; sha256="11bdc59ybi1kck3jkzilf0vmql6a3k97b1f9h940h28mhgn5x9w6"; depends=[annotate Biobase downloader Heatplus igraph MASS RBGL RColorBrewer RCurl RSQLite XML]; };
GeneBreak = derive2 { name="GeneBreak"; version="1.8.0"; sha256="1157crj12c3girr6973a24ph15rfjw0vcakr42fpx7yhhirs89lb"; depends=[CGHbase CGHcall GenomicRanges QDNAseq]; };
GeneExpressionSignature = derive2 { name="GeneExpressionSignature"; version="1.24.0"; sha256="1l8829axy6fp29bkqlwbjcsajq99yb86yp5cc8211zprlhlxb30i"; depends=[Biobase PGSEA]; };
@ -318,7 +318,7 @@ in with self; {
GenoGAM = derive2 { name="GenoGAM"; version="1.6.0"; sha256="1dvaapinarpgn3i63iqhdbjh9mc5h7sgdxwlv9d55l42d1jyj6h3"; depends=[BiocParallel Biostrings data_table DESeq2 futile_logger GenomeInfoDb GenomicAlignments GenomicRanges IRanges mgcv reshape2 Rsamtools S4Vectors SummarizedExperiment]; };
GenomeGraphs = derive2 { name="GenomeGraphs"; version="1.38.0"; sha256="15p75cbbgwgcc3awyvawkah491yim0rp73af815pfiai11a51i4m"; depends=[biomaRt]; };
GenomeInfoDb = derive2 { name="GenomeInfoDb"; version="1.14.0"; sha256="1jhm0imkac4gvchbjxj408aakk39xdv2fyh818d3lk295bz6bnyp"; depends=[BiocGenerics GenomeInfoDbData IRanges RCurl S4Vectors]; };
GenomicAlignments = derive2 { name="GenomicAlignments"; version="1.14.1"; sha256="033p6fw46sn7w2yyn14nb9qcnkf30cl0nv6zh014ixflm3iifz39"; depends=[BiocGenerics BiocParallel Biostrings GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors SummarizedExperiment]; };
GenomicAlignments = derive2 { name="GenomicAlignments"; version="1.14.2"; sha256="1659nj1xps7vliy5955i51x6hvrf16n1z0dfh10mmpaaswn2d2mv"; depends=[BiocGenerics BiocParallel Biostrings GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors SummarizedExperiment]; };
GenomicDataCommons = derive2 { name="GenomicDataCommons"; version="1.2.0"; sha256="0ndzpzripibx38nk40xpz4xkghhr4an3skqdhfh8479jk2fnfwjd"; depends=[data_table GenomicRanges httr IRanges jsonlite lazyeval magrittr readr xml2]; };
GenomicFeatures = derive2 { name="GenomicFeatures"; version="1.30.3"; sha256="010vn8hlwbnw12pd1d8pv6m12yp3xwx557gba5rbjq9p4qypnn3z"; depends=[AnnotationDbi Biobase BiocGenerics biomaRt Biostrings DBI GenomeInfoDb GenomicRanges IRanges RCurl RMySQL RSQLite rtracklayer S4Vectors XVector]; };
GenomicFiles = derive2 { name="GenomicFiles"; version="1.14.0"; sha256="0r0wmrs5jycf1kckhnc2sgjmp336srlcjdkpbb1ymm7kazdd0s9n"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation]; };
@ -352,7 +352,7 @@ in with self; {
Heatplus = derive2 { name="Heatplus"; version="2.24.0"; sha256="0lil1yfqqga9l6qrgismngvary4495zmi4yk01izpcx29pk8zn6n"; depends=[RColorBrewer]; };
HelloRanges = derive2 { name="HelloRanges"; version="1.4.0"; sha256="0pbikr79lh6iij044sy6fw6i2bqigmna4hb806kyihclpm0rs3y2"; depends=[BiocGenerics Biostrings BSgenome docopt GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation]; };
HiCcompare = derive2 { name="HiCcompare"; version="1.0.0"; sha256="1r25l4q7rpzjhz02ys78a4p8ga3wrd231znk84pp7xgka3xpprv0"; depends=[BiocParallel data_table dplyr GenomicRanges ggplot2 gridExtra gtools InteractionSet IRanges KernSmooth mgcv pheatmap QDNAseq S4Vectors]; };
HiTC = derive2 { name="HiTC"; version="1.22.0"; sha256="0288xa1jy6nzvz2ha07csmp6dirjw5r7p9vy69q2wsbyzr02ymkp"; depends=[Biostrings GenomeInfoDb GenomicRanges IRanges Matrix RColorBrewer rtracklayer]; };
HiTC = derive2 { name="HiTC"; version="1.22.1"; sha256="0da1jw9my2n2gihs31zyn14wwr23d8v2vij39ll7rm6fma3ydfbl"; depends=[Biostrings GenomeInfoDb GenomicRanges IRanges Matrix RColorBrewer rtracklayer]; };
HilbertCurve = derive2 { name="HilbertCurve"; version="1.9.1"; sha256="1k3l3i8fpfhzsdwrlkyp7k8rpkyg51lx6c776vd8nm4f2nqn7z36"; depends=[circlize GenomicRanges HilbertVis IRanges png]; };
HilbertVis = derive2 { name="HilbertVis"; version="1.36.0"; sha256="1yilvi5pcr0z5h0n0mf7hfrjc7cl44vn6svczlmw57n8pxf8p35g"; depends=[lattice]; };
HilbertVisGUI = derive2 { name="HilbertVisGUI"; version="1.36.0"; sha256="12bwk0lj2s6jgrpwigc4jd80irzxqjwc8smq1dhsm6pj62v0gvlk"; depends=[HilbertVis]; };
@ -420,7 +420,7 @@ in with self; {
MBCB = derive2 { name="MBCB"; version="1.32.0"; sha256="0amqmzi54dvkgzylavy0dbv973s2p02jppd5vzqzkrqs8amb3r4c"; depends=[preprocessCore tcltk2]; };
MBttest = derive2 { name="MBttest"; version="1.5.0"; sha256="0gswdh61mmqn7h4d6vwvis08lxx383ynj6pk2va3z8bn25qki5lz"; depends=[gplots gtools]; };
MCRestimate = derive2 { name="MCRestimate"; version="2.34.0"; sha256="1n4abpm6ld4ap87pgrv3mfr1aycdjb4hjg3fm699rckyl9qynjr3"; depends=[Biobase e1071 golubEsets pamr randomForest RColorBrewer]; };
MCbiclust = derive2 { name="MCbiclust"; version="1.2.1"; sha256="1yqm6fwap4553nmh1dl3vg87hixljzm097wcv4l6sd5sd0sg63c7"; depends=[AnnotationDbi BiocParallel cluster GGally ggplot2 GO_db org_Hs_eg_db scales WGCNA]; };
MCbiclust = derive2 { name="MCbiclust"; version="1.2.2"; sha256="0xll7qdg8cf854yzwxmzvd8xh0pjzkq9x9fskcsv7brm25ar6ghv"; depends=[AnnotationDbi BiocParallel cluster GGally ggplot2 GO_db org_Hs_eg_db scales WGCNA]; };
MEAL = derive2 { name="MEAL"; version="1.8.0"; sha256="0mccjr21jvmwlszhb9qixm7dr83gkhm2hjh9yrn11d22cm9r6g1q"; depends=[Biobase BiocGenerics DMRcate doParallel GenomicRanges ggplot2 Gviz IRanges isva limma matrixStats minfi missMethyl MultiDataSet permute S4Vectors SmartSVA SNPassoc snpStats SummarizedExperiment vegan]; };
MEDIPS = derive2 { name="MEDIPS"; version="1.30.0"; sha256="06mm424g3rc8j64wfyv6w40m106wifzhi91nsbpi317fg98qfd3d"; depends=[biomaRt Biostrings BSgenome DNAcopy edgeR GenomicRanges gtools IRanges preprocessCore Rsamtools rtracklayer]; };
MEDME = derive2 { name="MEDME"; version="1.38.0"; sha256="137p9z1g3z4r7q3nsrpsp2gbm657nrbrrq96ph1mykvv41ylq59p"; depends=[Biostrings drc MASS]; };
@ -428,9 +428,9 @@ in with self; {
MGFM = derive2 { name="MGFM"; version="1.12.0"; sha256="0yjr14anr5rny6g1508nrw905d4b01jh34vpwi8737p1q4d9bzis"; depends=[annotate AnnotationDbi]; };
MGFR = derive2 { name="MGFR"; version="1.4.0"; sha256="04nxg65m1s8qyq8sbs8733d541r0vcmabz27w03vs87f0dbxhg11"; depends=[annotate biomaRt]; };
MIGSA = derive2 { name="MIGSA"; version="1.2.0"; sha256="0ih5i1acb7igbcqk7wykxhncvl5vbgx34gl5nqc65adpqb0199fl"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel data_table edgeR futile_logger ggdendro ggplot2 GO_db GOstats graph GSEABase limma matrixStats mGSZ org_Hs_eg_db RBGL reshape2 Rgraphviz RJSONIO vegan]; };
MIMOSA = derive2 { name="MIMOSA"; version="1.16.0"; sha256="0rnxr7gxcps2raxka8c2x58liwwc75acwpahi2xc1dl8c2z4jpvx"; depends=[Biobase coda data_table Formula ggplot2 MASS MCMCpack modeest plyr pracma Rcpp RcppArmadillo reshape scales testthat]; };
MIMOSA = derive2 { name="MIMOSA"; version="1.16.1"; sha256="1fsjpqpv32ps8pyj1mjkhrpikchhmm3l06yyjqy3bgrfa1ch36vx"; depends=[Biobase coda data_table Formula ggplot2 MASS MCMCpack modeest plyr pracma Rcpp RcppArmadillo reshape scales testthat]; };
MIRA = derive2 { name="MIRA"; version="1.0.1"; sha256="0dapp1q6vrdixz8n2g6ivav4d4si3wg1na7cg5jirb22mwi2rrpk"; depends=[Biobase BiocGenerics bsseq data_table GenomicRanges ggplot2 IRanges S4Vectors]; };
MLInterfaces = derive2 { name="MLInterfaces"; version="1.58.0"; sha256="1py603bykvnzyq15rcqvq1nly3l6chh5zh6x4biwdn0smyjlnkns"; depends=[annotate Biobase BiocGenerics cluster fpc gbm gdata genefilter ggvis hwriter MASS mlbench pls RColorBrewer rda rpart sfsmisc shiny threejs]; };
MLInterfaces = derive2 { name="MLInterfaces"; version="1.58.1"; sha256="0hran4cavh1zlzwjwpmmd13qsx95z7kf8pqmh7w1pb36isj2z3hy"; depends=[annotate Biobase BiocGenerics cluster fpc gbm gdata genefilter ggvis hwriter MASS mlbench pls RColorBrewer rda rpart sfsmisc shiny threejs]; };
MLP = derive2 { name="MLP"; version="1.26.0"; sha256="0mhaw39rbzrnrminvsiq6vrdrmf3zm2zqg3ilnsq1zw8bm2bsbh7"; depends=[affy AnnotationDbi gdata gmodels gplots gtools plotrix]; };
MLSeq = derive2 { name="MLSeq"; version="1.18.0"; sha256="1r6b33ic2lnj3v2qzs7r904rfyibz96yr35mgpiz4zzsax4ar6v4"; depends=[Biobase caret DESeq2 edgeR limma randomForest]; };
MMDiff2 = derive2 { name="MMDiff2"; version="1.6.0"; sha256="13f96dw630hadqa0z83ispdni728g7zl12xj8zxrf5hvw1c1hs2h"; depends=[Biobase Biostrings BSgenome GenomicRanges ggplot2 locfit RColorBrewer Rsamtools S4Vectors shiny]; };
@ -468,7 +468,7 @@ in with self; {
MiRaGE = derive2 { name="MiRaGE"; version="1.20.0"; sha256="1jbs427vpld18l83s5dngijc8rgllqvrili8gv4in20nr6dyk9hi"; depends=[AnnotationDbi Biobase BiocGenerics S4Vectors]; };
MineICA = derive2 { name="MineICA"; version="1.18.0"; sha256="1zdq5i14ksm8rirbry6j1dh56r1bhy5yvfzrxfjkm94lynqcdpdy"; 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="1.22.0"; sha256="1j2g0ji1ac9608b965rr9vvbhlcbvirqypngh11havh3vn54m9rf"; depends=[Biobase BiocGenerics data_table DNAcopy ff foreach GenomeInfoDb GenomicRanges IRanges lattice matrixStats oligoClasses S4Vectors SummarizedExperiment VanillaICE]; };
Mirsynergy = derive2 { name="Mirsynergy"; version="1.14.0"; sha256="1mwcv1fb3vda4ilmvwjrwb2qg65bgdxsvd2jd9ndaccxb7m3c2lk"; depends=[ggplot2 gridExtra igraph Matrix RColorBrewer reshape scales]; };
Mirsynergy = derive2 { name="Mirsynergy"; version="1.14.1"; sha256="09hg5mak0ba0vifix5s0nq7md4hjldmar23jyxz5da1lp22cza9i"; depends=[ggplot2 gridExtra igraph Matrix RColorBrewer reshape scales]; };
MmPalateMiRNA = derive2 { name="MmPalateMiRNA"; version="1.28.0"; sha256="058nvymnnzd61a7x2vpzic1s2nm3q520cnfdhd6i09isg6kqr6c8"; depends=[Biobase lattice limma statmod vsn xtable]; };
MoPS = derive2 { name="MoPS"; version="1.12.0"; sha256="0g4awrm90kjnk66b291y2n5vwwwzpdb3kaq96sxfc5a1af8q5q81"; depends=[Biobase]; };
MoonlightR = derive2 { name="MoonlightR"; version="1.4.0"; sha256="0kisic6bzp2gy1yjg717izbkirlvrwb1wndckd2yvncrjzpidcq6"; depends=[Biobase circlize clusterProfiler doParallel DOSE foreach GEOquery gplots HiveR limma parmigene randomForest RColorBrewer RISmed SummarizedExperiment TCGAbiolinks]; };
@ -478,7 +478,7 @@ in with self; {
MultiAssayExperiment = derive2 { name="MultiAssayExperiment"; version="1.4.9"; sha256="0kbr2nfxkny9y6hgijr2xpzczs0ijv0g7nh37yrzgkh10rwjsflq"; depends=[Biobase BiocGenerics GenomicRanges IRanges reshape2 S4Vectors shiny shinydashboard SummarizedExperiment tidyr]; };
MultiDataSet = derive2 { name="MultiDataSet"; version="1.6.0"; sha256="0h187dkqn63m6askai30x31va24hiv4ig0kxvp9xraz7n9zfr24g"; depends=[Biobase BiocGenerics GenomicRanges ggplot2 ggrepel IRanges limma qqman S4Vectors SummarizedExperiment]; };
MultiMed = derive2 { name="MultiMed"; version="1.12.0"; sha256="1b48iv34bnsbyg7j70kwi8iyikc1hxlcfmaxsc97249dfq71rfab"; depends=[]; };
MutationalPatterns = derive2 { name="MutationalPatterns"; version="1.4.2"; sha256="08ay9h5cqsi8ypb6r0g4rfa5l1g06jgfzl64wmhgz134yqbl7vfv"; depends=[BiocGenerics Biostrings cowplot GenomeInfoDb GenomicRanges ggdendro ggplot2 gridExtra IRanges NMF plyr pracma reshape2 S4Vectors SummarizedExperiment VariantAnnotation]; };
MutationalPatterns = derive2 { name="MutationalPatterns"; version="1.4.3"; sha256="0ml4gsp5dfv23xqrknxh25q8q65hly1xb1215lcwyc8hj9z8f941"; depends=[BiocGenerics Biostrings cowplot GenomeInfoDb GenomicRanges ggdendro ggplot2 IRanges NMF plyr pracma reshape2 S4Vectors SummarizedExperiment VariantAnnotation]; };
NADfinder = derive2 { name="NADfinder"; version="1.2.0"; sha256="0npzbgbpwir4jv8h4giar9w8vjy3rivk55bimqd9bq7m83iwqapq"; depends=[baseline BiocGenerics GenomeInfoDb GenomicAlignments GenomicRanges IRanges limma rtracklayer S4Vectors signal SummarizedExperiment trackViewer]; };
NCIgraph = derive2 { name="NCIgraph"; version="1.26.0"; sha256="094dnqj1gss4dh8hsc8y9k98b0g33n7yy714kjavcd16glp4w7i0"; depends=[graph KEGGgraph R_methodsS3 RBGL RCy3]; };
NGScopy = derive2 { name="NGScopy"; version="1.12.0"; sha256="1aibq3rbs52vyhcx388p7szax7v8ac023pxayqmn2xq3kzj172ah"; depends=[changepoint rbamtools Xmisc]; };
@ -501,7 +501,7 @@ in with self; {
OmicCircos = derive2 { name="OmicCircos"; version="1.16.0"; sha256="13dw36n0lg5cafsrgkgr65al6y7jij2clyf1wzidn05p508i02m3"; depends=[GenomicRanges]; };
OmicsMarkeR = derive2 { name="OmicsMarkeR"; version="1.10.0"; sha256="0s7zyj3xkr74w0jw604hv3v775kqjpdgks4gkkrkfa3a1xj7xa5b"; depends=[assertive assertive_base caret caTools data_table DiscriMiner e1071 foreach gbm glmnet pamr permute plyr randomForest]; };
Onassis = derive2 { name="Onassis"; version="1.0.1"; sha256="11sq6f3qcq37i4blml024kb24ifcq1xplklv2i9c55wg299ni620"; depends=[AnnotationDbi data_table GEOmetadb OnassisJavaLibs rJava RSQLite SRAdb]; };
OncoScore = derive2 { name="OncoScore"; version="1.6.0"; sha256="02vzvvdnisx3xhr7428xdclgx90apa49h64bvp2h3nsa0vnhnj9l"; depends=[biomaRt]; };
OncoScore = derive2 { name="OncoScore"; version="1.6.2"; sha256="0lv3rx92fslikv79cpib839wbhj7v3ad869n50frqylyp6kn5nyg"; depends=[biomaRt]; };
OncoSimulR = derive2 { name="OncoSimulR"; version="2.8.0"; sha256="1b0myymp38j6fbd4y8ppwmsj8v9w96g8wayc20bcygm16i1zjm5k"; depends=[car data_table dplyr ggplot2 ggrepel graph gtools igraph nem RColorBrewer Rcpp Rgraphviz smatr]; };
OperaMate = derive2 { name="OperaMate"; version="1.9.0"; sha256="11ah55sl04gm8hq3gkcz3b4shq4dxdpwlwl0wn4j82ciai0k6wsm"; depends=[fBasics ggplot2 gProfileR gridExtra pheatmap reshape2 stabledist]; };
OrderedList = derive2 { name="OrderedList"; version="1.50.0"; sha256="1sk9ni3vyixb3vwn86vz174lfd7n7rnc8jmm1fx94pjsp9r6sbgr"; depends=[Biobase twilight]; };
@ -538,10 +538,10 @@ in with self; {
PathoStat = derive2 { name="PathoStat"; version="1.4.1"; sha256="1al0h4mw5lsmn4n3d76d8p9px62l4y5c5z78md2zchnam3x9ii78"; depends=[alluvial ape BatchQC BiocStyle corpcor DESeq2 dplyr DT edgeR ggplot2 gtools knitr limma matrixStats MCMCpack pander phyloseq plyr preprocessCore rentrez reshape2 rmarkdown scales shiny tidyr XML]; };
PathwaySplice = derive2 { name="PathwaySplice"; version="1.0.0"; sha256="1yi302xjf355xi14vx5rl6qyrm35qz9llf48fwrj7ycb41vla0fj"; depends=[AnnotationDbi AnnotationHub BiasedUrn Biobase BiocGenerics DOSE dplyr ensembldb gdata geneLenDataBase GO_db goseq gplots gridExtra htmlwidgets igraph JunctionSeq mgcv org_Hs_eg_db org_Mm_eg_db plotly RColorBrewer reshape2 S4Vectors tibble VennDiagram webshot]; };
Pbase = derive2 { name="Pbase"; version="0.18.0"; sha256="17ya1mmz8dqrr81vcfy3ygw490bwg26xkj72mcmba17cyy0nv11x"; depends=[AnnotationFilter Biobase BiocGenerics BiocParallel biomaRt Biostrings cleaver ensembldb GenomicRanges Gviz IRanges MSnbase mzID mzR Pviz Rcpp rtracklayer S4Vectors]; };
PharmacoGx = derive2 { name="PharmacoGx"; version="1.8.2"; sha256="0w77wpvi4qs8ngf5404m2cgac9zfj4jvkh88xcrz7zmmjmg2wvb9"; depends=[Biobase caTools downloader lsa magicaxis piano RColorBrewer reshape2]; };
PharmacoGx = derive2 { name="PharmacoGx"; version="1.8.3"; sha256="1lax2naj6qcjp4fy640m9pflvi2y1aqbsh5m9j2mpphy6a1dlvmh"; depends=[Biobase caTools downloader lsa magicaxis piano RColorBrewer reshape2]; };
PhenStat = derive2 { name="PhenStat"; version="2.14.0"; sha256="1hjj1i083ihi7c1lc1rrh3k7513xcqpybn3aaivdjw66pi1bg7vp"; depends=[car corrplot ggplot2 graph knitr lme4 logistf MASS msgps nlme nortest pingr reshape SmoothWin]; };
Pi = derive2 { name="Pi"; version="1.6.2"; sha256="0x3b5cs7r4cjvjjc2gx7xapzlkvg56784aj04zg6271hldpcd84j"; depends=[caret dnet GenomeInfoDb GenomicRanges ggbio ggplot2 ggrepel glmnet Gviz igraph lattice MASS Matrix plot3D randomForest ROCR scales supraHex XGR]; };
Pigengene = derive2 { name="Pigengene"; version="1.4.2"; sha256="15wnq91k360jblns36dgx4a24jk6a7rwkj342ja0sgfc6kvwvvqb"; depends=[bnlearn C50 GO_db graph impute MASS matrixStats partykit pheatmap preprocessCore Rgraphviz WGCNA]; };
Pigengene = derive2 { name="Pigengene"; version="1.4.20"; sha256="13pzgzls2k48h31h25n2rw028n97xaxfxlb4dq49ndwy5874cbzb"; depends=[bnlearn C50 GO_db graph impute MASS matrixStats partykit pheatmap preprocessCore Rgraphviz WGCNA]; };
Polyfit = derive2 { name="Polyfit"; version="1.12.0"; sha256="1gkn6g5hwa8ss156armxam9ky5fd7dj0k3gh1b0gy5plpzzyzv1h"; depends=[DESeq]; };
Prize = derive2 { name="Prize"; version="1.8.0"; sha256="1vaf4n69pb2sa6fd79988picz08d3c46cjmxfr5qf7hxay9lbwc6"; depends=[diagram ggplot2 gplots matrixcalc reshape2 stringr]; };
ProCoNA = derive2 { name="ProCoNA"; version="1.16.0"; sha256="06jlzcr9b6nfrlgb1wqxp7r2z8042ygjx4d2z7jzg07hqn3gymjz"; depends=[BiocGenerics flashClust GOstats MSnbase WGCNA]; };
@ -562,7 +562,7 @@ in with self; {
RBGL = derive2 { name="RBGL"; version="1.54.0"; sha256="18jad23i3899ypv4bg3l47cvvs3qnj1pqis2p9x0135yv5y6wnv7"; depends=[graph]; };
RBM = derive2 { name="RBM"; version="1.10.0"; sha256="1nqmf9yiaam767f2wkwggnw6v0rymszx7chnkis0xbdsllzqb0j4"; depends=[limma marray]; };
RBioinf = derive2 { name="RBioinf"; version="1.38.0"; sha256="01qk9ddk8bm9sl70rlwgmrkz2y7dnqzrhi13hhh0ii62s0z0gdwh"; depends=[graph]; };
RCAS = derive2 { name="RCAS"; version="1.4.3"; sha256="0ajnhi8i9p755lr0l2j5j52d5j6rsilrjhm3zrjr1zsgwqm2an6z"; depends=[AnnotationDbi BiocGenerics biomaRt Biostrings BSgenome_Hsapiens_UCSC_hg19 cowplot data_table DBI DT genomation GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggseqlogo knitr motifRG org_Hs_eg_db pbapply pheatmap plotly plotrix proxy rmarkdown RSQLite rtracklayer S4Vectors topGO]; };
RCAS = derive2 { name="RCAS"; version="1.4.4"; sha256="0jnrikh0qhpxgjc6rdgfj9d57x4i5b40wxx7lfafrxdxg60qsy1g"; depends=[AnnotationDbi BiocGenerics biomaRt Biostrings BSgenome_Hsapiens_UCSC_hg19 cowplot data_table DBI DT genomation GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggseqlogo knitr motifRG org_Hs_eg_db pbapply pheatmap plotly plotrix proxy rmarkdown RSQLite rtracklayer S4Vectors topGO]; };
RCASPAR = derive2 { name="RCASPAR"; version="1.24.0"; sha256="1v19pv81q0g965mks88ablznzhcdk3kfd7j2dgxx4r12bl1afawg"; depends=[]; };
RCy3 = derive2 { name="RCy3"; version="1.8.0"; sha256="09p66zxh82j5pcjz1zn3cg43rpsp0gnkwja836m6g1i450zrialv"; depends=[graph httr RCurl RJSONIO]; };
RCyjs = derive2 { name="RCyjs"; version="1.10.0"; sha256="0vlyh32byw49j3vfw0avknixflpjs5h599xxlbf2zc6irvncg1wg"; depends=[base64enc BiocGenerics BrowserViz graph httpuv igraph jsonlite Rcpp]; };
@ -577,19 +577,19 @@ in with self; {
RIPSeeker = derive2 { name="RIPSeeker"; version="1.18.0"; sha256="0bqkzwrncww7il36273chkd3gfxmii7p566ycki9qij419pwr35y"; depends=[GenomicAlignments GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment]; };
RITAN = derive2 { name="RITAN"; version="1.2.0"; sha256="199kddc19fwkfgqnbhx7v4sl5h6lj6f3wqs5xy9f9n9bg09f5rrf"; depends=[BgeeDB dynamicTreeCut ggplot2 gplots gridExtra gsubfn hash igraph knitr linkcomm MCL plotrix png ProNet RColorBrewer reshape2 RITANdata sqldf STRINGdb]; };
RIVER = derive2 { name="RIVER"; version="1.2.0"; sha256="00j9i0hrn0j2i5rxgsax3ixj8pwm2ks9fyvp657yd5amm1vackxq"; depends=[Biobase ggplot2 glmnet pROC]; };
RImmPort = derive2 { name="RImmPort"; version="1.6.0"; sha256="1fj69k1mb0gbajsiah23azp0ina3wvc43ghr6866glqcfh4xckj7"; depends=[data_table DBI dplyr plyr reshape2 RSQLite sqldf]; };
RImmPort = derive2 { name="RImmPort"; version="1.7.2"; sha256="0h3r7q7lfl4z7srmallaldljv2231j3zhxy0d4x9q7ghcfglfnbf"; depends=[data_table DBI dplyr plyr reshape2 RSQLite sqldf]; };
RJMCMCNucleosomes = derive2 { name="RJMCMCNucleosomes"; version="1.2.0"; sha256="0xjscfbxrrfnd40dmzhrrly0v3pk1k33jdl4z19bslh89gmrmygr"; depends=[BiocGenerics BiocParallel consensusSeekeR GenomeInfoDb GenomicRanges IRanges Rcpp S4Vectors]; };
RLMM = derive2 { name="RLMM"; version="1.40.0"; sha256="01mbk00fbhzldivxlr5jfy1fgfrdbd657lya3s3p7zxw7z0054a0"; depends=[MASS]; };
RMassBank = derive2 { name="RMassBank"; version="2.6.0"; sha256="1yfnj64ybl95a7bc4980i5h6cvs2hq3nkmj9dklarcp9wfw5p59w"; depends=[Biobase digest MSnbase mzR rcdk Rcpp RCurl rjson S4Vectors XML yaml]; };
RNASeqPower = derive2 { name="RNASeqPower"; version="1.18.0"; sha256="08x58sd6q5xm47ix2f1kkqpgyk10nnbf994i4m1wia8fjhx0hdkm"; depends=[]; };
RNAinteract = derive2 { name="RNAinteract"; version="1.26.0"; sha256="1cscf2izpx924ai0vian9mm528mn1k618zqscss7mry13ik78p3c"; depends=[abind Biobase cellHTS2 geneplotter gplots hwriter ICS ICSNP lattice latticeExtra limma locfit RColorBrewer splots]; };
RNAither = derive2 { name="RNAither"; version="2.26.0"; sha256="1dyxmk0j319822qf0wwd41xw7v9qdahixkhmsbv3qp6203hp49w5"; depends=[biomaRt car geneplotter limma prada RankProd splots topGO]; };
RNAither = derive2 { name="RNAither"; version="2.26.1"; sha256="0fs3kab20h77d00kg48rdgslj3fsmnl73qi740sa7xmwx6ra5lc7"; depends=[biomaRt car geneplotter limma prada RankProd splots topGO]; };
RNAprobR = derive2 { name="RNAprobR"; version="1.10.0"; sha256="0lq0cf5g004w2gi8rs29rhdy3p49njmwnw5jhfijfj4hgkgc6caf"; depends=[BiocGenerics Biostrings GenomicAlignments GenomicFeatures GenomicRanges IRanges plyr Rsamtools rtracklayer S4Vectors]; };
ROC = derive2 { name="ROC"; version="1.54.0"; sha256="0a60k93q0zsmj2s4gy9wgzpd5yl9xdv2g62m18z4s4dmr3ykwsdv"; depends=[]; };
ROTS = derive2 { name="ROTS"; version="1.6.0"; sha256="12dqbwqiiz21im45iqf41nm25anf0fffip86glpydwwc0km054jh"; depends=[Biobase Rcpp]; };
ROntoTools = derive2 { name="ROntoTools"; version="2.6.0"; sha256="0lxxqa8syanb9v4nzc93arlwg65zyf4hkgxgw6q4h62mxkabdp0d"; depends=[boot graph KEGGgraph KEGGREST Rgraphviz]; };
RPA = derive2 { name="RPA"; version="1.34.0"; sha256="1s5d8wpy3n69f9lnsi8avwalbzzvi7v8np6bv3vcnxy3nfx0iqx3"; depends=[affy BiocGenerics phyloseq]; };
RProtoBufLib = derive2 { name="RProtoBufLib"; version="1.0.1"; sha256="1a8psx12hwbzybkd92k9n3351g24fqqxrmq5x3sln62z2f0c7psw"; depends=[]; };
RProtoBufLib = derive2 { name="RProtoBufLib"; version="1.0.2"; sha256="14hs5mam4yjcm00zqz5fgmgxzwhw45fniaihch2mwrb6kbys2y68"; depends=[]; };
RRHO = derive2 { name="RRHO"; version="1.18.0"; sha256="1nz643k6bahg1bizw5bgjkpv2hd7hpi87s4kh1z38jqfpfixw9lk"; depends=[VennDiagram]; };
RSVSim = derive2 { name="RSVSim"; version="1.18.0"; sha256="0f2fv2cxwhsl6gvz3dpgk55faymdwxyry6lr3l6f2s8f6rqpnzgf"; depends=[Biostrings GenomicRanges IRanges ShortRead]; };
RTCA = derive2 { name="RTCA"; version="1.30.0"; sha256="0y2vrqfr4qjgsq8f82a5xnfhm835wi5zqf1xlxrv4mpxm9f9jr38"; depends=[Biobase gtools RColorBrewer]; };
@ -628,7 +628,7 @@ in with self; {
Rhdf5lib = derive2 { name="Rhdf5lib"; version="1.0.0"; sha256="0kkc4rprjbqn2wvbx4d49kk9l91vihccxbl4843qr1wqk6v33r1w"; depends=[]; };
Rhtslib = derive2 { name="Rhtslib"; version="1.10.0"; sha256="1dw3p44bfr0m7w39ckc2k37sjcp1zz0b9g12mr8am15jaj6v0q2j"; depends=[zlibbioc]; };
RiboProfiling = derive2 { name="RiboProfiling"; version="1.7.2"; sha256="0yygf098phiakaj8c74c337gbwpd0dh4haabbg2qq1k0qjw4prmp"; depends=[BiocGenerics Biostrings data_table GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggbio ggplot2 IRanges plyr reshape2 Rsamtools rtracklayer S4Vectors sqldf]; };
Ringo = derive2 { name="Ringo"; version="1.42.0"; sha256="174zcz86x43yrg9wl1wwdhammgyxhfc3aqas3yqgrdq7vdsnxzxq"; depends=[Biobase BiocGenerics genefilter lattice limma Matrix RColorBrewer vsn]; };
Ringo = derive2 { name="Ringo"; version="1.42.1"; sha256="12r4bcn2sivcp68rd7jr4w4a8yz7xdydwx6bv1mi2lp2s2mzf5c5"; depends=[Biobase BiocGenerics genefilter lattice limma Matrix RColorBrewer vsn]; };
Risa = derive2 { name="Risa"; version="1.20.0"; sha256="10ypbd9qwh1rk27fwm8naf3gl05w9zlw79qyr55pk5m6x5lnn9cb"; depends=[affy Biobase biocViews Rcpp xcms]; };
Rmagpie = derive2 { name="Rmagpie"; version="1.34.0"; sha256="1hvv8pps0q7xnsl33rammqvyj191j5gs78r2333jgscxnw4byqb7"; depends=[Biobase e1071 kernlab pamr]; };
RmiR = derive2 { name="RmiR"; version="1.34.0"; sha256="10n8i7qirbd8xrb73ccxyj7c6bi1szx263nwjh8w2j9x4dgzx22x"; depends=[DBI RmiR_Hs_miRNA RSVGTipsDevice]; };
@ -655,7 +655,7 @@ in with self; {
SICtools = derive2 { name="SICtools"; version="1.8.0"; sha256="0n3m3435wa95mld4b57hr31rfhlk41yw1qqi1jdnybkqgdndpqf8"; depends=[Biostrings doParallel GenomicRanges IRanges matrixStats plyr Rsamtools stringr]; };
SIM = derive2 { name="SIM"; version="1.48.0"; sha256="1n207w5idd2v515v8ppsfx7q1wvn2zxy6if7dp2hpr0x2qvxijnf"; depends=[globaltest quantreg quantsmooth]; };
SIMAT = derive2 { name="SIMAT"; version="1.10.0"; sha256="0gd99p8kjf1wn0xygdyppxgddp9bnp3a3grg8za2mmm8xv5r990h"; depends=[ggplot2 mzR Rcpp reshape2]; };
SIMLR = derive2 { name="SIMLR"; version="1.4.0"; sha256="1sfd32qd39wy8a1206xkazbmvkqwhs09p7fhdn8n59xf56914pfa"; depends=[Matrix pracma Rcpp RcppAnnoy RSpectra]; };
SIMLR = derive2 { name="SIMLR"; version="1.4.1"; sha256="09siwqc57f0rfx0297hk2jbpvvayhk47wkvapz2ap621ya203b0z"; depends=[Matrix pracma Rcpp RcppAnnoy RSpectra]; };
SISPA = derive2 { name="SISPA"; version="1.8.0"; sha256="18v8fw3l4pxh4fi18fhnqxbd1hlhp2w36s31vf58ffldq3bz1bpb"; depends=[changepoint data_table genefilter ggplot2 GSVA plyr]; };
SLGI = derive2 { name="SLGI"; version="1.38.0"; sha256="1p0lwzmzz820npnsw9sk6x12innc39qv0ja0di7rplkmsi60z92j"; depends=[AnnotationDbi Biobase BiocGenerics GO_db lattice ScISI]; };
SLqPCR = derive2 { name="SLqPCR"; version="1.44.0"; sha256="16kvssib1j4d5cn3b350ip2m9m7fcsgm1mgq13wbfnwcd6sx52kb"; depends=[]; };
@ -669,7 +669,7 @@ in with self; {
SPEM = derive2 { name="SPEM"; version="1.18.0"; sha256="05gpj1fykiw8xjcbd6splqkb8jsyksnhzl6g6pzinpbczhslq55a"; depends=[Biobase Rsolnp]; };
SPIA = derive2 { name="SPIA"; version="2.30.0"; sha256="0m2vv6zj0vgd98w2jrlbwbyn998ml2i2wr9160gmq5h77rn91xq3"; depends=[KEGGgraph]; };
SPLINTER = derive2 { name="SPLINTER"; version="1.4.0"; sha256="06xamivcwlpwj6n8c3wzgd5ykh21q2mrdl7zz1bnicq5npha99l9"; depends=[biomaRt Biostrings BSgenome_Mmusculus_UCSC_mm9 GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 Gviz IRanges plyr S4Vectors seqLogo]; };
SPONGE = derive2 { name="SPONGE"; version="1.0.2"; sha256="100gbcysmf3fhn22zmvvx2sck6hhfgc7ar782l822vbsig1vnyk9"; depends=[bigmemory Biobase data_table doRNG expm foreach glmnet gRbase igraph iterators logging MASS ppcor]; };
SPONGE = derive2 { name="SPONGE"; version="1.0.3"; sha256="1jb7nwji4j9kvnx40hr26qhcn3pbmjaahl4cpvqbljs9pmi9lfdy"; depends=[bigmemory Biobase data_table doRNG expm foreach glmnet gRbase igraph iterators logging MASS ppcor]; };
SQUADD = derive2 { name="SQUADD"; version="1.28.0"; sha256="1z139p0xbaq4gvd9acxnd8dlapdsiaab1fj10pc7wx2iz4dj9zd6"; depends=[RColorBrewer]; };
SRAdb = derive2 { name="SRAdb"; version="1.40.0"; sha256="18aayqid2fhhkjf7anlk34qw3fj3byxsxcrw2lmq4s4mqq06k5vh"; depends=[GEOquery graph RCurl RSQLite]; };
SRGnet = derive2 { name="SRGnet"; version="1.4.0"; sha256="1a2as38svd6vp6pdllir4gs6jqicg7n7ya42ffjgiy2rpnyijbci"; depends=[DMwR EBcoexpress gbm Hmisc igraph limma MASS matrixStats pvclust]; };
@ -688,7 +688,7 @@ in with self; {
SeqArray = derive2 { name="SeqArray"; version="1.18.2"; sha256="05w051i63af4akr6zna9w14bdyi06bpif0vab9yvf6iwq2ag72kz"; depends=[Biostrings gdsfmt GenomeInfoDb GenomicRanges IRanges S4Vectors]; };
SeqGSEA = derive2 { name="SeqGSEA"; version="1.18.0"; sha256="1vaqa6jkvwxpbqnz9wz3i6p26mky6d7d704cjv5as67j04v99b2a"; depends=[Biobase biomaRt DESeq doParallel]; };
SeqSQC = derive2 { name="SeqSQC"; version="1.0.0"; sha256="0qj1y9zsjxkh08jkw80hl62072viincq1pvcz9r3i0m28nhk7pg5"; depends=[e1071 ExperimentHub gdsfmt GenomicRanges GGally ggplot2 IRanges rbokeh RColorBrewer reshape2 rmarkdown S4Vectors SNPRelate]; };
SeqVarTools = derive2 { name="SeqVarTools"; version="1.16.0"; sha256="14n70xzj91f4rshl0kx549rqzy9rrv5mv0b0xvj891i8anxahb2n"; depends=[Biobase dplyr gdsfmt GenomicRanges GWASExactHW IRanges logistf S4Vectors SeqArray tidyr]; };
SeqVarTools = derive2 { name="SeqVarTools"; version="1.16.1"; sha256="0vjgksqyapvkdbnl3af0sjbbraslyc6m7f63sl05m87zdkav8fzz"; depends=[Biobase dplyr gdsfmt GenomicRanges GWASExactHW IRanges logistf S4Vectors SeqArray tidyr]; };
ShortRead = derive2 { name="ShortRead"; version="1.36.1"; sha256="1cyv47632m9ljkxfsvnvmd19sb607ys5kz8fwh6v39dnw16g0a6m"; depends=[Biobase BiocGenerics BiocParallel Biostrings GenomeInfoDb GenomicAlignments GenomicRanges hwriter IRanges lattice latticeExtra Rsamtools S4Vectors XVector zlibbioc]; };
SigCheck = derive2 { name="SigCheck"; version="2.10.0"; sha256="1k2xmb7jcjbdxafr8fspf9pbc0jwcll914lqc42gvhhjq6rnf8q4"; depends=[Biobase BiocParallel e1071 MLInterfaces survival]; };
SigFuge = derive2 { name="SigFuge"; version="1.16.0"; sha256="0ddy6bayb05gsgh06p5awhjwyx57z0l8fb5x6p0dci2fgzy6gr4f"; depends=[GenomicRanges ggplot2 matlab reshape sigclust]; };
@ -708,7 +708,7 @@ in with self; {
SwimR = derive2 { name="SwimR"; version="1.16.0"; sha256="033hh3bpkn6qladvn7iz0fvrbphffzy1rkvmi0j32v9n9h88lizz"; depends=[gplots heatmap_plus R2HTML signal]; };
TCC = derive2 { name="TCC"; version="1.18.0"; sha256="10nmha786k85jr93vbnlsxkrr2wiykxa5rl2z5ry49w14fis82m5"; depends=[baySeq DESeq DESeq2 edgeR ROC samr]; };
TCGAbiolinks = derive2 { name="TCGAbiolinks"; version="2.6.12"; sha256="0pih8jpzffsjlhamfpvgcapa48dq2m86f4hxqr5m5z4vgjd7j1mv"; depends=[biomaRt circlize ComplexHeatmap ConsensusClusterPlus data_table doParallel downloader dplyr EDASeq edgeR genefilter GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggrepel ggthemes gridExtra httr IRanges jsonlite knitr limma matlab plyr R_utils RColorBrewer readr rvest S4Vectors scales selectr stringr SummarizedExperiment survival survminer sva tibble XML xml2]; };
TCGAbiolinksGUI = derive2 { name="TCGAbiolinksGUI"; version="1.4.2"; sha256="1g81w346lvws8bcm8w94b1r3jjr1zfg5ln80p0rq69gzv9hkdjyw"; depends=[clusterProfiler colourpicker data_table downloader DT ELMER ggplot2 ggrepel maftools pathview plotly readr shiny shinyBS shinydashboard shinyFiles shinyjs stringr SummarizedExperiment TCGAbiolinks]; };
TCGAbiolinksGUI = derive2 { name="TCGAbiolinksGUI"; version="1.4.7"; sha256="1hwq13rsynxv18pzahq54107n2dm0wgbh7a5xizda4zqgf4s50gj"; depends=[clusterProfiler colourpicker data_table downloader DT ELMER ggplot2 ggrepel maftools pathview plotly readr shiny shinyBS shinydashboard shinyFiles shinyjs stringr SummarizedExperiment TCGAbiolinks]; };
TCseq = derive2 { name="TCseq"; version="1.2.0"; sha256="07wbp4caw18g1mf5h40i1c1y7jadfqmx3p7a8zz5rjjibsfa2bw1"; depends=[BiocGenerics cluster e1071 edgeR GenomicAlignments GenomicRanges ggplot2 IRanges locfit reshape2 Rsamtools SummarizedExperiment]; };
TDARACNE = derive2 { name="TDARACNE"; version="1.28.0"; sha256="0agzpgz39ya46kgnz95ff2h0hml2mb14fb3pdj218adas24zq9jf"; depends=[Biobase GenKern Rgraphviz]; };
TEQC = derive2 { name="TEQC"; version="3.18.0"; sha256="0rnqlk677hcf2w3whc9gdqm21gjqf4rsanaw8a847jc7li8isnpj"; depends=[Biobase BiocGenerics hwriter IRanges Rsamtools]; };
@ -718,7 +718,7 @@ in with self; {
TIN = derive2 { name="TIN"; version="1.10.0"; sha256="16lv7k4js3zbak0b1m2mlimd1f56gif3vlm2hpc5vx1y315mz9gd"; depends=[aroma_affymetrix data_table impute squash stringr WGCNA]; };
TMixClust = derive2 { name="TMixClust"; version="1.0.1"; sha256="1mv9hv5hjg55mwbp824n5b74w8zcb9sv8a1wa6hxmfb00n6wcr4h"; depends=[Biobase BiocParallel cluster flexclust gss mvtnorm SPEM zoo]; };
TPP = derive2 { name="TPP"; version="3.6.0"; sha256="1gma7lfnq1ybcqnl9536wv22advjaqxmysfgamrgn38zwbcwhdi9"; 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 sme stringr tidyr VennDiagram VGAM]; };
TRONCO = derive2 { name="TRONCO"; version="2.10.0"; sha256="1lvzfx75z50r8kd3yrcjwzvsg16yi5644rz90bm1l6hpkmw2wcpf"; depends=[bnlearn cgdsr circlize doParallel foreach gridExtra gtable gtools igraph iterators R_matlab RColorBrewer Rgraphviz scales xtable]; };
TRONCO = derive2 { name="TRONCO"; version="2.10.3"; sha256="1kw4j57wri0sm3piinq169pkljfb3ff4vcj1ify2il2pl7va94l4"; depends=[bnlearn cgdsr circlize doParallel foreach gridExtra gtable gtools igraph iterators R_matlab RColorBrewer Rgraphviz scales xtable]; };
TReNA = derive2 { name="TReNA"; version="0.99.10"; sha256="1yiq953w6830v1fba4gglnf485m6lis11qlpp9g1jw0x4s0rpg70"; depends=[DBI doParallel flare foreach GenomicRanges glmnet lassopv randomForest RPostgreSQL RSQLite vbsr]; };
TSCAN = derive2 { name="TSCAN"; version="1.16.0"; sha256="0m88r5yg46ra8k6ymzfrk68fqbg2y47kshzgj5flblbay079hnxg"; depends=[combinat fastICA ggplot2 gplots igraph mclust mgcv plyr shiny]; };
TSRchitect = derive2 { name="TSRchitect"; version="1.4.0"; sha256="0qymyjmzpi1n5fpyzw8riz32kwsc2bi1cw3sx9sxvpvhjk45dmyx"; depends=[AnnotationHub BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicRanges gtools IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment]; };
@ -742,7 +742,7 @@ in with self; {
VariantTools = derive2 { name="VariantTools"; version="1.20.0"; sha256="1ma1qs9n606a5gjcm8l9fna8vfg5f8ixdzriwaalhys22pyjgqsy"; depends=[Biobase BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicFeatures GenomicRanges IRanges Matrix Rsamtools rtracklayer S4Vectors VariantAnnotation]; };
Vega = derive2 { name="Vega"; version="1.26.0"; sha256="1kya7h7xa47d7l3svkpnkwjg49izpjfird5fjja6490ynr1a55yd"; depends=[]; };
VegaMC = derive2 { name="VegaMC"; version="3.16.0"; sha256="1lmgmaf4andfxv2z4h2pahyggnic5wj61llzkm8q4k0q7i50l63i"; depends=[Biobase biomaRt genoset]; };
XBSeq = derive2 { name="XBSeq"; version="1.8.0"; sha256="07123c1wd3l7lj29kaa0d83dlv7zsrx8gk8aag7g0h8k9vlhcni4"; depends=[Biobase DESeq2 dplyr ggplot2 locfit magrittr matrixStats pracma roar]; };
XBSeq = derive2 { name="XBSeq"; version="1.10.0"; sha256="0p2f2wckndgrsf0jjcag22i6bgrn2ky78ngdk9c5cvqnxwjcfagz"; depends=[Biobase DESeq2 dplyr ggplot2 locfit magrittr matrixStats pracma roar]; };
XDE = derive2 { name="XDE"; version="2.24.0"; sha256="11g74znfafp03q710mhmzgxap6f7j04b75jhm7x6lmd6cbwqh25p"; depends=[Biobase BiocGenerics genefilter GeneMeta gtools MergeMaid mvtnorm RColorBrewer siggenes]; };
XVector = derive2 { name="XVector"; version="0.18.0"; sha256="1i4i3kdxr78lr1kcxq657p11ybi7kq10c8kyaqyh6gfc8i9rhvmk"; depends=[BiocGenerics IRanges S4Vectors zlibbioc]; };
YAPSA = derive2 { name="YAPSA"; version="1.4.0"; sha256="0jv940xdqrbb8hw13nm6cky767zn9k8wh6sh5vz5b7hgh7c75kww"; depends=[circlize ComplexHeatmap corrplot dendextend GenomeInfoDb GenomicRanges GetoptLong ggplot2 gridExtra gtrellis KEGGREST lsei PMCMR reshape2 SomaticSignatures VariantAnnotation]; };
@ -776,11 +776,11 @@ in with self; {
anamiR = derive2 { name="anamiR"; version="1.6.1"; sha256="0mxpxangzbvx7rpzm4ak321pcgj6pa0nbslgvh8rplyz4sf6v0z6"; depends=[agricolae DBI DESeq2 gage gplots limma lumi RMySQL S4Vectors SummarizedExperiment]; };
annaffy = derive2 { name="annaffy"; version="1.50.0"; sha256="0qprkcvq56h6dwcylqsa0dq0nmv5bk280j89cwa3brm4jfncs4hm"; depends=[AnnotationDbi Biobase DBI GO_db KEGG_db]; };
annmap = derive2 { name="annmap"; version="1.20.0"; sha256="0q4lcx1j5av5jpn2wmarn7z32clzzdaprvpcagnvv453i11vp5bi"; depends=[Biobase BiocGenerics DBI digest genefilter GenomicRanges IRanges lattice RMySQL Rsamtools]; };
annotate = derive2 { name="annotate"; version="1.56.1"; sha256="14c5xd9kasvcwg5gbjys2c1vizxhlqlzxakqc2kml0kw97hmx0rq"; depends=[AnnotationDbi Biobase BiocGenerics DBI RCurl XML xtable]; };
annotate = derive2 { name="annotate"; version="1.56.2"; sha256="0ybg9k1s289h15nj1kp9821i1rsk1gkn8i8blplmk7gsgpbw1f42"; depends=[AnnotationDbi Biobase BiocGenerics DBI RCurl XML xtable]; };
annotationTools = derive2 { name="annotationTools"; version="1.52.0"; sha256="1kmhgasb26dbq10d4r8wig5pjlbiqcqsa12zpgcsasj8kvpr2gpd"; depends=[Biobase]; };
annotatr = derive2 { name="annotatr"; version="1.4.1"; sha256="10izqb0x92fjpsycsyppvz6yidg8ssix452jfni692na7ih564y9"; depends=[AnnotationDbi AnnotationHub dplyr GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 IRanges org_Dm_eg_db org_Hs_eg_db org_Mm_eg_db org_Rn_eg_db readr regioneR reshape2 rtracklayer S4Vectors TxDb_Dmelanogaster_UCSC_dm3_ensGene TxDb_Dmelanogaster_UCSC_dm6_ensGene TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Hsapiens_UCSC_hg38_knownGene TxDb_Mmusculus_UCSC_mm10_knownGene TxDb_Mmusculus_UCSC_mm9_knownGene TxDb_Rnorvegicus_UCSC_rn4_ensGene TxDb_Rnorvegicus_UCSC_rn5_refGene TxDb_Rnorvegicus_UCSC_rn6_refGene]; };
anota = derive2 { name="anota"; version="1.26.0"; sha256="1fvr9yvyf0m7m5dnfbzbm29kd1yqq78carv9v7xx60szi30w4lvq"; depends=[multtest qvalue]; };
anota2seq = derive2 { name="anota2seq"; version="1.0.0"; sha256="1pcmjlnvx3g2209l54jcbw044k6iz9zch3l01d1vr1cxiqag8smh"; depends=[DESeq2 edgeR limma multtest qvalue RColorBrewer SummarizedExperiment]; };
anota2seq = derive2 { name="anota2seq"; version="1.0.1"; sha256="0fya2plqvpmypm3jf6mwncpi1ngjsprbnadh7j33wdshr4znhyc3"; depends=[DESeq2 edgeR limma multtest qvalue RColorBrewer SummarizedExperiment]; };
antiProfiles = derive2 { name="antiProfiles"; version="1.18.0"; sha256="03y6j3y0qvfzwbwzjgjsl5zlqayqj1400gj278m28l70l43ifnyg"; depends=[locfit matrixStats]; };
apComplex = derive2 { name="apComplex"; version="2.44.0"; sha256="132j6gm70h8sma82jd566hrih7npa217h5r6kqx4lq5yw3dlqcs1"; depends=[graph org_Sc_sgd_db RBGL Rgraphviz]; };
apeglm = derive2 { name="apeglm"; version="1.0.3"; sha256="06j68szmxdr9c8qmmlcx85rv1hjl2rk52lagack83cr3q1gd10bj"; depends=[emdbook GenomicRanges SummarizedExperiment]; };
@ -844,10 +844,10 @@ in with self; {
chipenrich = derive2 { name="chipenrich"; version="2.2.0"; sha256="0q24il68grjqdxpy7qjk6lw6l5zlmw6yybrbrbb8l42gljyi6s74"; depends=[AnnotationDbi BiocGenerics chipenrich_data GenomeInfoDb GenomicRanges IRanges lattice latticeExtra mgcv org_Dm_eg_db org_Dr_eg_db org_Hs_eg_db org_Mm_eg_db org_Rn_eg_db plyr rms rtracklayer S4Vectors stringr]; };
chipseq = derive2 { name="chipseq"; version="1.28.0"; sha256="1ymcq77krwjzrkzzcw7i9909cmkqa7c0675z9wzvrrk81hgdssfq"; depends=[BiocGenerics GenomicRanges IRanges lattice S4Vectors ShortRead]; };
chopsticks = derive2 { name="chopsticks"; version="1.42.0"; sha256="0awwk8k7vnsc0c1ic17m2mhmpin0s0ijd2gn7my9yysqzld9sncd"; depends=[survival]; };
chroGPS = derive2 { name="chroGPS"; version="1.26.0"; sha256="1lx12mlrj1syl2qaibm08b4vq8h2xw609vr6vxynl1wvvf8wdarp"; depends=[Biobase changepoint cluster DPpackage GenomicRanges ICSNP MASS]; };
chroGPS = derive2 { name="chroGPS"; version="1.27.3"; sha256="0glqisz3nzlrcvjryxf406dkiq6sg9bg1g3bcqqnmayirm92w5qv"; depends=[Biobase changepoint cluster DPpackage GenomicRanges ICSNP MASS]; };
chromDraw = derive2 { name="chromDraw"; version="2.8.0"; sha256="1lqrpbf322kxpx5068mw650ibzqksfmxc4j6q1fs4dv0ghpxdcsf"; depends=[GenomicRanges Rcpp]; };
chromPlot = derive2 { name="chromPlot"; version="1.6.0"; sha256="16qy1zqwlxc2pdkdb1jf8rknvr5cz2k4vbg2jybr6ks73pzagb47"; depends=[biomaRt GenomicRanges]; };
chromVAR = derive2 { name="chromVAR"; version="1.0.1"; sha256="0a62gp47ymspn9pbdz7j2vjpd0g7bhl333dicbs468qjjfpm8fbw"; depends=[BiocGenerics BiocParallel Biostrings BSgenome DT GenomeInfoDb GenomicRanges ggplot2 IRanges Matrix miniUI nabor plotly RColorBrewer Rcpp RcppArmadillo Rsamtools Rtsne S4Vectors shiny SummarizedExperiment TFBSTools]; };
chromVAR = derive2 { name="chromVAR"; version="1.0.2"; sha256="08bp5wyxg5s9gjwnpymcahhy5rar64x385msczam62i1h1y95f8b"; depends=[BiocGenerics BiocParallel Biostrings BSgenome DT GenomeInfoDb GenomicRanges ggplot2 IRanges Matrix miniUI nabor plotly RColorBrewer Rcpp RcppArmadillo Rsamtools Rtsne S4Vectors shiny SummarizedExperiment TFBSTools]; };
chromstaR = derive2 { name="chromstaR"; version="1.4.0"; sha256="1ky2z9v6gwwgzvd498ng9ac5s7x8nkgm5170gywr7bgw7lqrycjz"; depends=[bamsignals chromstaRData doParallel foreach GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges mvtnorm reshape2 Rsamtools S4Vectors]; };
chromswitch = derive2 { name="chromswitch"; version="1.0.0"; sha256="1ym7vdj6lfwi4nja38lixm3vsxp296dpb90zwnmabws3dhysxhfy"; depends=[Biobase BiocParallel cluster DescTools dplyr GenomicRanges gplots IRanges lazyeval magrittr matrixStats mclust NMF rtracklayer S4Vectors tidyr]; };
cisPath = derive2 { name="cisPath"; version="1.18.0"; sha256="0ya1kkvghs23c4rqydkas68a7y6z16ihjnv8ljjy9h3i7pdani4h"; depends=[]; };
@ -934,7 +934,7 @@ in with self; {
eegc = derive2 { name="eegc"; version="1.4.0"; sha256="1v3586qddx1l74ha083x36m3lqdblrhmwd63k22jzfpkh30adz09"; 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="1.18.0"; sha256="1ypd7yq9c6mqp7nm984dm60qzvwy4qb81zrp2mvp7g87c5vdj2a3"; depends=[BiocGenerics ChemmineR DBI digest gespeR RcppAnnoy RCurl RUnit snow snowfall]; };
eisa = derive2 { name="eisa"; version="1.30.0"; sha256="11ydmv5kddq75sknbax1aiyxq60rx146qa7pd3m09axjzvk83mq5"; depends=[AnnotationDbi Biobase BiocGenerics Category DBI genefilter isa2]; };
ensemblVEP = derive2 { name="ensemblVEP"; version="1.20.0"; sha256="1xza76fyqp8xikc98ipamsz6175nirdv7aisfvkb9nmzba4q0r62"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicRanges S4Vectors SummarizedExperiment VariantAnnotation]; };
ensemblVEP = derive2 { name="ensemblVEP"; version="1.20.1"; sha256="0785hhfsgmnkangcq6lg48kdr5pifxs6j9v6apv80457k70d7ybv"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicRanges S4Vectors SummarizedExperiment VariantAnnotation]; };
ensembldb = derive2 { name="ensembldb"; version="2.2.2"; sha256="1yngndkf3588z91z0a2fvkg423p26ajm6xv1p27x0l9mzhhaqq3k"; depends=[AnnotationDbi AnnotationFilter AnnotationHub Biobase BiocGenerics Biostrings curl DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges ProtGenerics Rsamtools RSQLite rtracklayer S4Vectors]; };
epiNEM = derive2 { name="epiNEM"; version="1.2.0"; sha256="0d3r4m0q3w2ljf4bm03z1dpiiih9cshzpbi4nnqq3jwls82f7nlq"; depends=[BoolNet e1071 graph gtools igraph lattice latticeExtra minet nem pcalg RColorBrewer]; };
epigenomix = derive2 { name="epigenomix"; version="1.18.0"; sha256="0x567fxak38ngy5hs3x567381aigh1x1fb8ww8xvmpf2wlzrlfwp"; depends=[beadarray Biobase BiocGenerics GenomeInfoDb GenomicRanges IRanges MCMCpack Rsamtools S4Vectors SummarizedExperiment]; };
@ -943,8 +943,8 @@ in with self; {
epivizrData = derive2 { name="epivizrData"; version="1.6.0"; sha256="101ibx9nq17dnn5j8kjy31pm8ly4nyzs1rrlbsvk0140avjhz154"; depends=[Biobase ensembldb epivizrServer GenomeInfoDb GenomicFeatures GenomicRanges IRanges OrganismDbi S4Vectors SummarizedExperiment]; };
epivizrServer = derive2 { name="epivizrServer"; version="1.6.0"; sha256="0qa13yvq9ywa3m1n2vmi60087cgg18rpnqbr1m7f137ivnxyb11b"; depends=[httpuv mime R6 rjson]; };
epivizrStandalone = derive2 { name="epivizrStandalone"; version="1.6.0"; sha256="0rbd2kmdi0y97mx72gkg93s97slfig1k1bgcv5maknsqqqcwzz8j"; depends=[BiocGenerics epivizr epivizrServer GenomeInfoDb GenomicFeatures git2r S4Vectors]; };
erccdashboard = derive2 { name="erccdashboard"; version="1.12.0"; sha256="07dc80l8618rlv3sywr0gp9i49kq66i9glx3md2r0k5c4l67mw37"; depends=[edgeR ggplot2 gplots gridExtra gtools limma locfit MASS plyr qvalue reshape2 ROCR scales stringr]; };
erma = derive2 { name="erma"; version="0.10.0"; sha256="0gcfs9g8vvdv5vmq9b21kd8sq5mizjj49nfzd4in9zvp4b9v7x1g"; depends=[AnnotationDbi Biobase BiocGenerics foreach GenomicFiles GenomicRanges ggplot2 Homo_sapiens rtracklayer S4Vectors shiny SummarizedExperiment]; };
erccdashboard = derive2 { name="erccdashboard"; version="1.12.1"; sha256="19fg4n99w983wp6ffmzadzfp1bzmsn8papb5szbrxz102r2mq6df"; depends=[edgeR ggplot2 gplots gridExtra gtools limma locfit MASS plyr qvalue reshape2 ROCR scales stringr]; };
erma = derive2 { name="erma"; version="0.10.1"; sha256="1fi8nc6fbd7i4p9i9hli31xplmdpsxqcdrb8v3nf8fx9klllbdav"; depends=[AnnotationDbi Biobase BiocGenerics foreach GenomicFiles GenomicRanges ggplot2 Homo_sapiens rtracklayer S4Vectors shiny SummarizedExperiment]; };
esATAC = derive2 { name="esATAC"; version="1.0.23"; sha256="1g2pai0b98dfnng4h7w2xs73qp2dqacmx8x3ackqi6a515x0cyaf"; depends=[AnnotationDbi BiocGenerics BiocInstaller Biostrings BSgenome ChIPseeker clusterProfiler corrplot DiagrammeR digest GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 igraph IRanges JASPAR2016 knitr magrittr R_utils Rbowtie2 Rcpp rJava rmarkdown Rsamtools rtracklayer S4Vectors ShortRead TFBSTools VennDiagram]; };
esetVis = derive2 { name="esetVis"; version="1.4.0"; sha256="1yb238lxy8sqmxim3zd25rp642cpz8p25vdffjlija2wivq8phn1"; depends=[Biobase hexbin MASS MLP mpm Rtsne]; };
eudysbiome = derive2 { name="eudysbiome"; version="1.8.0"; sha256="13ayrigzy55h6an3am9f77r6mzcvyfcpxpby71xilhaf6mjhyj39"; depends=[Biostrings plyr R_utils Rsamtools]; };
@ -992,14 +992,14 @@ in with self; {
flowUtils = derive2 { name="flowUtils"; version="1.42.0"; sha256="0d4ab30xp722h9avi785wj8z1qz7dy65z5faqf3jc6j6v40bzikq"; depends=[Biobase corpcor flowCore graph RUnit XML]; };
flowVS = derive2 { name="flowVS"; version="1.10.0"; sha256="07vcqcxzd9cw4hvc1yld2v05zcxqs5p9spka2l80pmsjr0aij043"; depends=[flowCore flowStats flowViz]; };
flowViz = derive2 { name="flowViz"; version="1.42.0"; sha256="1fbr0snid9vgb133sb5dwkk469n465p8r490r67vsmm8wqsf6iyl"; depends=[Biobase flowCore hexbin IDPmisc KernSmooth lattice latticeExtra MASS RColorBrewer]; };
flowWorkspace = derive2 { name="flowWorkspace"; version="3.26.6"; sha256="11r9c9h1ffp3i1p7gw0f93l5g30waawl7f2vbyh06p5mcr732dmp"; depends=[BH Biobase BiocGenerics cytolib data_table dplyr flowCore flowViz graph gridExtra lattice latticeExtra ncdfFlow RBGL RColorBrewer Rcpp Rgraphviz RProtoBufLib scales stringr XML]; };
flowWorkspace = derive2 { name="flowWorkspace"; version="3.26.9"; sha256="04vs7knal0mrlj0rxpq5p3x1243ji0191zf0xmvk9689m94ib2za"; depends=[BH Biobase BiocGenerics cytolib data_table dplyr flowCore flowViz graph gridExtra lattice latticeExtra ncdfFlow RBGL RColorBrewer Rcpp Rgraphviz RProtoBufLib scales stringr XML]; };
flowcatchR = derive2 { name="flowcatchR"; version="1.12.0"; sha256="0i6r86b1g98kaw8nhbnjjrw8gw6vvhfpr5r7dn4whl4hwlizc5qx"; depends=[abind BiocParallel colorRamps EBImage rgl]; };
fmcsR = derive2 { name="fmcsR"; version="1.20.0"; sha256="0cbbil337zbb968zibkysrmpc8bwlpn7rl908zyvzvj8v11lxzcc"; depends=[BiocGenerics ChemmineR RUnit]; };
focalCall = derive2 { name="focalCall"; version="1.12.0"; sha256="07lb0ijdsryd31dxp5fgp393p9f21b7in3rnf9j43qn8wmz48hnl"; depends=[CGHcall]; };
frma = derive2 { name="frma"; version="1.30.1"; sha256="0319m8l7n2sfp4m6zipm7pkc57xikb735qk605m952m8ra08v8ml"; depends=[affy Biobase BiocGenerics DBI MASS oligo oligoClasses preprocessCore]; };
frmaTools = derive2 { name="frmaTools"; version="1.30.0"; sha256="02z7igfcvhjg9f36snmmif8d7lsca9n9izg8zc543hcy7s704aa2"; depends=[affy Biobase DBI preprocessCore]; };
funtooNorm = derive2 { name="funtooNorm"; version="1.2.0"; sha256="09n7vq5f26px57sy35s29b8pmb9wcx6kii0h0i354sr3yg21ccpc"; depends=[GenomeInfoDb IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest matrixStats minfi pls]; };
gCMAP = derive2 { name="gCMAP"; version="1.22.0"; sha256="1ghaidxm8wpg9jx8s9ymlkciwkxjnlr5g5yfjappj7mf4qaqxvil"; depends=[annotate AnnotationDbi bigmemory bigmemoryExtras Biobase Category DESeq genefilter GSEABase GSEAlm limma Matrix]; };
gCMAP = derive2 { name="gCMAP"; version="1.22.1"; sha256="0va9jixmp3v001gnym3clyjwarxs5d31vnyklzv31n5zffd7dm3l"; depends=[annotate AnnotationDbi bigmemory bigmemoryExtras Biobase Category DESeq genefilter GSEABase GSEAlm limma Matrix]; };
gCMAPWeb = derive2 { name="gCMAPWeb"; version="1.18.0"; sha256="152nd7vxz3cja8xmg5rq4j08lvd7cw1y09a737bfdq1zwrxc22v8"; depends=[annotate AnnotationDbi Biobase BiocGenerics brew gCMAP GSEABase hwriter Rook yaml]; };
gCrisprTools = derive2 { name="gCrisprTools"; version="1.6.0"; sha256="0x7bsnhs3qwimfkkxr8yslawdfy83x5ip8j2wlwq4m9hqwqk060g"; depends=[Biobase ggplot2 limma PANTHER_db rmarkdown RobustRankAggreg]; };
gQTLBase = derive2 { name="gQTLBase"; version="1.10.0"; sha256="1756vfcj2dkkgcmfkkg7qdaig36dv9gfvpypn9rbrky56wm1p035"; depends=[BatchJobs BBmisc BiocGenerics bit doParallel ff ffbase foreach GenomicFiles GenomicRanges rtracklayer S4Vectors SummarizedExperiment]; };
@ -1024,7 +1024,7 @@ in with self; {
geneRxCluster = derive2 { name="geneRxCluster"; version="1.14.0"; sha256="0r0lnhf19qw1d4p87632lz0rgx0d9q3cakpd6qh43b10fil7wjgp"; depends=[GenomicRanges IRanges]; };
geneXtendeR = derive2 { name="geneXtendeR"; version="1.4.0"; sha256="02a3aqn115l85cnvxy16ppri4hwir6mcp1av6s00nj66afxxnzmv"; depends=[AnnotationDbi data_table dplyr GO_db networkD3 org_Ag_eg_db org_Bt_eg_db org_Ce_eg_db org_Cf_eg_db org_Dm_eg_db org_Dr_eg_db org_Gg_eg_db org_Hs_eg_db org_Mm_eg_db org_Mmu_eg_db org_Pt_eg_db org_Rn_eg_db org_Sc_sgd_db org_Ss_eg_db org_Xl_eg_db RColorBrewer rtracklayer SnowballC tm wordcloud]; };
genefilter = derive2 { name="genefilter"; version="1.60.0"; sha256="173swlg6gj4kdllbqvyiw5dggbcxiwlwpqmllsv4dxzn7h25i3g7"; depends=[annotate AnnotationDbi Biobase S4Vectors survival]; };
genefu = derive2 { name="genefu"; version="2.10.0"; sha256="0pg9425z0inlbgvi15d050s6928xyqbxj36kk12z3dh3w2gwkycf"; depends=[AIMS amap biomaRt iC10 limma mclust survcomp]; };
genefu = derive2 { name="genefu"; version="2.11.2"; sha256="1z70pnzgci0sjpr8vsvyg93zrjim7jh9jmba0p3pgqp3qw4gbi34"; depends=[AIMS amap biomaRt iC10 limma mclust survcomp]; };
geneplast = derive2 { name="geneplast"; version="1.4.0"; sha256="12ncf9rpnv1mwmdw4rbzzhggppcnzch764aiipy0jb21ix9xj61q"; depends=[ape snow]; };
geneplotter = derive2 { name="geneplotter"; version="1.56.0"; sha256="1z3g7frc1iviwrsv2dlm4nqvkc0685h4va0388yfxn102ln8wwma"; depends=[annotate AnnotationDbi Biobase BiocGenerics lattice RColorBrewer]; };
genoCN = derive2 { name="genoCN"; version="1.30.0"; sha256="0m4sj2w0zra67d939knzriwda0nwphzspsmnl9jakl0kq8dvhjki"; depends=[]; };
@ -1034,9 +1034,9 @@ in with self; {
genoset = derive2 { name="genoset"; version="1.34.0"; sha256="1cw6g8r3n33xlqmbjsfn6kkdzz19kh71ag529sjbk9wlxi69rrz0"; depends=[BiocGenerics GenomeInfoDb GenomicRanges IRanges S4Vectors SummarizedExperiment]; };
genotypeeval = derive2 { name="genotypeeval"; version="1.10.0"; sha256="1pff2n1s350j6i7klsnwqlizkdvvfpyqqrvc7kq5gj7yh508dxy9"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicRanges ggplot2 IRanges rtracklayer Rtsne VariantAnnotation]; };
genphen = derive2 { name="genphen"; version="1.6.0"; sha256="0m1g1hfhhbq3xjdr2fjf3wbng6d953kci965h298c168dv3864k6"; depends=[Biostrings e1071 effsize ggplot2 randomForest rjags]; };
gespeR = derive2 { name="gespeR"; version="1.10.0"; sha256="09xd080b08bfpqqbha4rxn4vmglv7c5asd4gibfjgjkasd78g40m"; depends=[Biobase biomaRt cellHTS2 doParallel dplyr foreach ggplot2 glmnet Matrix reshape2]; };
gespeR = derive2 { name="gespeR"; version="1.10.1"; sha256="10aw6s5bn5jiw3qlqskcp2ngshgyykslsqlwrdpyahr4rh7z0zyl"; depends=[Biobase biomaRt cellHTS2 doParallel dplyr foreach ggplot2 glmnet Matrix reshape2]; };
ggbio = derive2 { name="ggbio"; version="1.26.1"; sha256="1xlmlngn27iwnr21s9di4059kav1a7c1sajx08wja8yn8f7j06hp"; depends=[AnnotationDbi AnnotationFilter Biobase BiocGenerics Biostrings biovizBase BSgenome ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GGally ggplot2 gridExtra gtable Hmisc IRanges OrganismDbi reshape2 Rsamtools rtracklayer S4Vectors scales SummarizedExperiment VariantAnnotation]; };
ggcyto = derive2 { name="ggcyto"; version="1.6.1"; sha256="07rsg673hnrn1kf82nb59sxa925hjlb3qnjwlxvzlr2lzs958rcd"; depends=[data_table flowCore flowWorkspace ggplot2 gridExtra ncdfFlow plyr RColorBrewer scales]; };
ggcyto = derive2 { name="ggcyto"; version="1.6.2"; sha256="0qg9ivya9c2998hq40c0pvzfilb1q24h13fafymwa8p2lj59jyrg"; depends=[data_table flowCore flowWorkspace ggplot2 gridExtra ncdfFlow plyr RColorBrewer scales]; };
ggtree = derive2 { name="ggtree"; version="1.10.5"; sha256="1gkfjgihykkvqrhvzhr5brwzsgva0mxvfpa664k08jan9brjg22f"; depends=[ape ggplot2 magrittr rvcheck scales tidyr treeio]; };
girafe = derive2 { name="girafe"; version="1.30.0"; sha256="0k8fjn7d1hxwin0vywly7vc570048i7nckhyw9j4cind6fi6f75v"; depends=[Biobase BiocGenerics Biostrings genomeIntervals intervals IRanges Rsamtools S4Vectors ShortRead]; };
globalSeq = derive2 { name="globalSeq"; version="1.6.0"; sha256="19aws180r5gwxrz6xmfgic0mp8piki2qmzrxyy1f75866blk3r4f"; depends=[]; };
@ -1100,7 +1100,7 @@ in with self; {
keggorthology = derive2 { name="keggorthology"; version="2.30.0"; sha256="117s7b32nkv95adh2j91b87r90svhfb91ag28brsq3r333m2q8cn"; depends=[AnnotationDbi DBI graph hgu95av2_db]; };
kimod = derive2 { name="kimod"; version="1.6.0"; sha256="0mb9bv6bz7k27vs8rl26kh2zm8mvpkgzqhgc471lp4qz8f4fsbxc"; depends=[Biobase cluster]; };
lapmix = derive2 { name="lapmix"; version="1.44.0"; sha256="1b7daaqsq3bvb1wbhf99pk8kl4pm4kac7bnx211isr7ica34pxb5"; depends=[Biobase]; };
ldblock = derive2 { name="ldblock"; version="1.8.0"; sha256="18nfsixh6d2wfrb9laqsgly5w1frzihhak683k0p8fdf51h4aqba"; depends=[erma GenomeInfoDb GenomicFiles GO_db Homo_sapiens Matrix Rsamtools snpStats VariantAnnotation]; };
ldblock = derive2 { name="ldblock"; version="1.8.1"; sha256="1q8dz8wcq1r7kr635s9q21g36sxkdybk8khhpa4p57qv8r0gppl0"; depends=[erma GenomeInfoDb GenomicFiles GO_db Homo_sapiens Matrix Rsamtools snpStats VariantAnnotation]; };
les = derive2 { name="les"; version="1.28.0"; sha256="0xy7ggc2b20i1c78mww84xvc0jhbinxn00nbfvnbw997vjqr7r79"; depends=[boot fdrtool gplots RColorBrewer]; };
lfa = derive2 { name="lfa"; version="1.8.0"; sha256="06w0032wwqm2cxid7brb6iq6bkhqc5x3a08wwyjbib6lnj5n7rvh"; depends=[corpcor]; };
limma = derive2 { name="limma"; version="3.34.9"; sha256="1y2fm61g5i0fn0j3l31xvwh9zww9bpkc4nwzb1d0yv1cag20jkdc"; depends=[]; };
@ -1121,7 +1121,7 @@ in with self; {
maanova = derive2 { name="maanova"; version="1.48.0"; sha256="1vvjk6y8mp5h7l8yk4f1y48jx5k9fl9s12x2mgsbap306paw860q"; depends=[Biobase]; };
macat = derive2 { name="macat"; version="1.52.0"; sha256="168jw5bi1nbj2dfhipnvja7w0avmiw6vrvdany73d41fvigmagj5"; depends=[annotate Biobase]; };
made4 = derive2 { name="made4"; version="1.52.0"; sha256="1ns7f47l7ig2fm95l67ppym5gbkbr8lp18vx51pqwjg8r5rvj9sc"; depends=[ade4 gplots RColorBrewer scatterplot3d]; };
maftools = derive2 { name="maftools"; version="1.4.25"; sha256="0k4ry5pnh3lxyzkab094wpjiaqjrymq9hbgpz8xv9g67fhg2g8ah"; depends=[Biostrings changepoint cometExactTest ComplexHeatmap cowplot data_table ggplot2 ggrepel gridExtra mclust NMF RColorBrewer rjson Rsamtools survival VariantAnnotation wordcloud]; };
maftools = derive2 { name="maftools"; version="1.4.28"; sha256="17b3v1v9ipid8gqsq2gy0fpminc58f1mng9i2andswfr5ip38g7s"; depends=[Biostrings changepoint cometExactTest ComplexHeatmap cowplot data_table ggplot2 ggrepel gridExtra mclust NMF RColorBrewer rjson Rsamtools survival VariantAnnotation wordcloud]; };
maigesPack = derive2 { name="maigesPack"; version="1.42.0"; sha256="1c92kkr2rmfydckmbvri8g0lzz1v3hx93zpmb1pwrnlfpm01j95j"; depends=[convert graph limma marray]; };
makecdfenv = derive2 { name="makecdfenv"; version="1.54.0"; sha256="17fmzd12acdpq3vfnqrafmmg5jcmdgkf83mrqjpw92zah2w8490a"; depends=[affy affyio Biobase zlibbioc]; };
manta = derive2 { name="manta"; version="1.24.0"; sha256="060x5rdzkx882pa8x9w7j3sgj0clar6w35yblbcggq579r9jpx06"; depends=[caroline edgeR Hmisc]; };
@ -1177,7 +1177,7 @@ in with self; {
missMethyl = derive2 { name="missMethyl"; version="1.12.0"; sha256="1fvpny7x56l55zhgabm6al2i2n0hix7fp7d01bzirsn7chxpwny3"; depends=[AnnotationDbi BiasedUrn GO_db IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno_ilm10b2_hg19 IlluminaHumanMethylationEPICmanifest limma methylumi minfi org_Hs_eg_db ruv statmod stringr]; };
mitoODE = derive2 { name="mitoODE"; version="1.16.0"; sha256="11kyihynbl3kcrngv8dhiqn3ghpkvv0xi35pf8np2p41zdhbrpyv"; depends=[KernSmooth MASS minpack_lm mitoODEdata]; };
mogsa = derive2 { name="mogsa"; version="1.12.2"; sha256="0a29q9jak4vr05ngh2pcsfifa9i6p086acjk2qrzwnc3lcfm00bm"; depends=[Biobase BiocGenerics cluster corpcor genefilter gplots graphite GSEABase svd]; };
monocle = derive2 { name="monocle"; version="2.6.3"; sha256="1qag8q6wy1wf1zx16h2lwki6rn4nxkjff7yhpn8m30hp3v01fvhn"; depends=[Biobase BiocGenerics biocViews cluster combinat DDRTree densityClust dplyr fastICA ggplot2 HSMMSingleCell igraph irlba limma MASS Matrix matrixStats pheatmap plyr proxy qlcMatrix RANN Rcpp reshape2 Rtsne slam stringr tibble VGAM viridis]; };
monocle = derive2 { name="monocle"; version="2.6.4"; sha256="1x4y02kn8spzz8y4hgmis9h2l494ys2j1vjs0axh32fp1rpc6d8c"; depends=[Biobase BiocGenerics biocViews cluster combinat DDRTree densityClust dplyr fastICA ggplot2 HSMMSingleCell igraph irlba limma MASS Matrix matrixStats pheatmap plyr proxy qlcMatrix RANN Rcpp reshape2 Rtsne slam stringr tibble VGAM viridis]; };
mosaics = derive2 { name="mosaics"; version="2.16.0"; sha256="08q48zakyfydrj8vix3a5w0j4ix5h1hpqccv0jxgj55gpdc062kj"; depends=[GenomeInfoDb GenomicAlignments GenomicRanges IRanges lattice MASS Rcpp Rsamtools S4Vectors]; };
motifRG = derive2 { name="motifRG"; version="1.22.0"; sha256="193zl2rlzwxv9p9q5i7rilj3w05ndqfyp9bdpvagp5s5cin4hf44"; depends=[Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 IRanges seqLogo XVector]; };
motifStack = derive2 { name="motifStack"; version="1.22.4"; sha256="13wrpdgyhzrqdp7k0d7iym2pjjla46rh3i1qwm34j22n7j0pxs8x"; depends=[ade4 Biostrings grImport htmlwidgets MotIV scales XML]; };
@ -1202,7 +1202,7 @@ in with self; {
mzID = derive2 { name="mzID"; version="1.16.0"; sha256="0yk70dka56zd8w62f03ggx3mandj91gfa767h9ajj0sd3mjmfqb9"; depends=[doParallel foreach iterators plyr ProtGenerics XML]; };
mzR = derive2 { name="mzR"; version="2.12.0"; sha256="1x3gp30sfxz2v3k3swih9kff9b2rvk7hzhnlkp6ywlnn2wgb0q8c"; depends=[Biobase BiocGenerics ProtGenerics Rcpp zlibbioc]; };
ncdfFlow = derive2 { name="ncdfFlow"; version="2.24.0"; sha256="1rvqlfzdbqz7a035c2d0rfziail71pvyla6fi3mv1xzrm2vpw0b8"; depends=[BH Biobase BiocGenerics flowCore flowViz Rcpp RcppArmadillo Rhdf5lib zlibbioc]; };
ndexr = derive2 { name="ndexr"; version="1.0.3"; sha256="05wnjya61w0mbskrfs9k5w04pr3hcf4c8w15y85z7j1vxjhpgwjq"; depends=[httr igraph jsonlite plyr tidyr]; };
ndexr = derive2 { name="ndexr"; version="1.0.4"; sha256="1hr49a3svk65d585yix13ggd57zv5zzmavb81c452y2jpay0www0"; depends=[httr igraph jsonlite plyr tidyr]; };
nem = derive2 { name="nem"; version="2.52.0"; sha256="0114b8nzv07gii87rdcvia6n7jn203f5whx6x6x54ijxq8m1fkk8"; depends=[boot e1071 graph limma plotrix RBGL RColorBrewer Rgraphviz statmod]; };
netReg = derive2 { name="netReg"; version="1.2.0"; sha256="1cmh66m5zp1awrg79f8d09b48shq8hyjvkz6mfxrnvqbcj32v8ph"; depends=[Rcpp RcppArmadillo]; };
netbenchmark = derive2 { name="netbenchmark"; version="1.10.0"; sha256="173jmvslg8vj078psnvk6s4sns8n9zv2z8hkq6iq64pavmn9cf91"; depends=[c3net corpcor fdrtool GeneNet grndata Matrix minet PCIT pracma randomForest Rcpp]; };
@ -1231,7 +1231,7 @@ in with self; {
ontoCAT = derive2 { name="ontoCAT"; version="1.29.0"; sha256="057sbc0s08i22gjg886ngz0k59r4v29ssh11qj0wyv4n5g3zs0hg"; depends=[rJava]; };
ontoProc = derive2 { name="ontoProc"; version="1.0.0"; sha256="0la7lcynmdgavvzdz7b5g726pm4205r8194dnsmnhc5h3lryr36k"; depends=[AnnotationDbi Biobase ontologyIndex S4Vectors shiny]; };
openCyto = derive2 { name="openCyto"; version="1.16.1"; sha256="1qzx0qq1d2hi5whqi0kbg8xmjbglv6j2fli3wcx932g66lxwg3sv"; depends=[Biobase clue data_table flowClust flowCore flowStats flowViz flowWorkspace graph gtools ks lattice MASS ncdfFlow plyr R_utils RBGL RColorBrewer Rcpp rrcov]; };
openPrimeR = derive2 { name="openPrimeR"; version="1.0.0"; sha256="0x4h7lcanzclcxnbrj2hii5mpv2b7rm5izm9p51drqylr69gvns2"; depends=[ape BiocGenerics Biostrings DECIPHER digest distr distrEx dplyr fitdistrplus foreach GenomicRanges ggplot2 Hmisc IRanges lpSolveAPI magrittr openxlsx plyr RColorBrewer reshape2 S4Vectors scales seqinr stringdist stringr uniqtag XML]; };
openPrimeR = derive2 { name="openPrimeR"; version="1.0.4"; sha256="1gw4b7df390q40zy0bnv0wlwr9dwji99rhgy678k32nm8r2cdc19"; depends=[ape BiocGenerics Biostrings DECIPHER digest distr distrEx dplyr fitdistrplus foreach GenomicRanges ggplot2 Hmisc IRanges lpSolveAPI magrittr openxlsx plyr RColorBrewer reshape2 S4Vectors scales seqinr stringdist stringr uniqtag XML]; };
openPrimeRui = derive2 { name="openPrimeRui"; version="1.0.0"; sha256="1mchbalmq6mbxp9mdrmndz3pja7j1ffx5xglnzglfdqm2004gdlf"; depends=[DT openPrimeR rmarkdown shiny shinyBS shinyjs]; };
oposSOM = derive2 { name="oposSOM"; version="1.16.0"; sha256="1855wrszaxwc8rghhn1hgj6hrp5mxsyffbs9ccjckq5jl3z7z1mj"; depends=[ape arules Biobase biomaRt fastICA fdrtool igraph pixmap scatterplot3d som tsne]; };
oppar = derive2 { name="oppar"; version="1.6.0"; sha256="0h4wfgjq8xm5f6bcaj5vxy686ymr42r3ig9zw93ayycpfl81p275"; depends=[Biobase GSEABase GSVA]; };
@ -1254,7 +1254,7 @@ in with self; {
pcaGoPromoter = derive2 { name="pcaGoPromoter"; version="1.22.0"; sha256="0371ns6702nk5s3pj59z04i2sjf24sj0wm3m4rj67q4p5v7v1ksz"; depends=[AnnotationDbi Biostrings ellipse]; };
pcaMethods = derive2 { name="pcaMethods"; version="1.70.0"; sha256="0ii235g0x0492kh8cfrf28ni0b6vd6fh7kizkqmczzqggd6b1bk8"; depends=[Biobase BiocGenerics MASS Rcpp]; };
pcot2 = derive2 { name="pcot2"; version="1.46.0"; sha256="1pymhr9ypp5g27bbnayrz4ks8rg5j634bf4l596m2b6c4q9d9rc5"; depends=[amap Biobase]; };
pcxn = derive2 { name="pcxn"; version="1.0.0"; sha256="105mzgy6bcwmk1nsnlr44bik8pazyjc7zcqn56732g1dj5na5v5w"; depends=[pcxnData pheatmap]; };
pcxn = derive2 { name="pcxn"; version="2.0.0"; sha256="1iq3i3cj7zq7xyprgjv4v4whycm67lzcrsz9p08lxyzz7ci2y6xn"; depends=[pcxnData pheatmap]; };
pdInfoBuilder = derive2 { name="pdInfoBuilder"; version="1.42.0"; sha256="0cs47qzkpphixcwn3fl9pfrw1qans8y51y8lb9phikh4s8cdq061"; depends=[affxparser Biobase BiocGenerics Biostrings DBI IRanges oligo oligoClasses RSQLite S4Vectors]; };
pdmclass = derive2 { name="pdmclass"; version="1.47.0"; sha256="1grc1fyn8yhwixi7638bsyb3zc6zhzzrbfh4hcpqk6gf653dls63"; depends=[Biobase fibroEset mda]; };
pepStat = derive2 { name="pepStat"; version="1.12.0"; sha256="0bnak90zfycd5a9qkz4lhwk4h61pr0pwn3hzaksxcv6c025h0mwm"; depends=[Biobase data_table fields GenomicRanges ggplot2 IRanges limma plyr]; };
@ -1293,7 +1293,7 @@ in with self; {
prot2D = derive2 { name="prot2D"; version="1.16.0"; sha256="1fp530fammi9xifx5g72jz8k7y3chjfg3mpybsbf5pzvva1429sj"; depends=[Biobase fdrtool impute limma MASS Mulcom qvalue samr st]; };
proteinProfiles = derive2 { name="proteinProfiles"; version="1.18.0"; sha256="069ksj5md9m7zylqwy6pyj3p9pa4j04vn4ss4d2r8n7a5z8f7d1g"; depends=[]; };
proteoQC = derive2 { name="proteoQC"; version="1.14.0"; sha256="1kv8ah7pbfl1gbb1pnjlmdw5bskfyh0hsn0nxraz0ybvwzn3kdsl"; depends=[dplyr ggplot2 MSnbase Nozzle_R1 plotly plyr reshape2 rmarkdown rpx rTANDEM seqinr tidyr VennDiagram XML]; };
psichomics = derive2 { name="psichomics"; version="1.4.4"; sha256="1h8vg90nlvjmpz8ific6n41xqc3fzs1133hvbyrjzqbwqy0cgqzp"; depends=[AnnotationHub cluster colourpicker data_table digest dplyr DT edgeR fastICA fastmatch ggplot2 ggrepel highcharter htmltools httr jsonlite limma miscTools pairsD3 plyr R_utils Rcpp shiny shinyBS shinyjs stringr survival XML xtable]; };
psichomics = derive2 { name="psichomics"; version="1.4.5"; sha256="0lvkbjkdg5m1ni6rrnzzq2d2p5j0156vp2q9i3c8ji40fp7rx0vv"; depends=[AnnotationHub cluster colourpicker data_table digest dplyr DT edgeR fastICA fastmatch ggplot2 ggrepel highcharter htmltools httr jsonlite limma miscTools pairsD3 plyr R_utils Rcpp shiny shinyBS shinyjs stringr survival XML xtable]; };
psygenet2r = derive2 { name="psygenet2r"; version="1.10.0"; sha256="0xf03vjyjiz4093cqnvi3dm532scx3f17mcf0av96h052vy10qb7"; depends=[BgeeDB Biobase BiocInstaller biomaRt ggplot2 GO_db igraph labeling RCurl reshape2 stringr topGO]; };
puma = derive2 { name="puma"; version="3.20.0"; sha256="0pcwppa2zlzpfl5fafl4h5xcf0pnyvz3hkykl192hzp26wcjsc1i"; depends=[affy affyio Biobase mclust oligo oligoClasses]; };
pvac = derive2 { name="pvac"; version="1.26.0"; sha256="0lmwy5a74ikq0sl6zqw69kag6q3p092qwh1lzvv7rl2j9wm2yl46"; depends=[affy Biobase]; };
@ -1382,7 +1382,7 @@ in with self; {
seqbias = derive2 { name="seqbias"; version="1.26.0"; sha256="1i1zqslv0qws12x45c37h7fkgpz5wv3v87h72n4pw8gh80bgcafl"; depends=[Biostrings GenomicRanges Rsamtools zlibbioc]; };
seqcombo = derive2 { name="seqcombo"; version="1.0.0"; sha256="0bkap2c1061yg2ws2m1fafxi37pqzkg9mzim5sqiq8sgcfmk6na6"; depends=[Biostrings cowplot dplyr ggplot2 igraph magrittr rvcheck]; };
seqplots = derive2 { name="seqplots"; version="1.16.0"; sha256="1plwmdq2hjcqs94l7s03h9amcxdimwdrmi11z03xn10dfn1xig70"; depends=[Biostrings BSgenome class DBI digest DT fields GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridExtra IRanges jsonlite kohonen plotrix RColorBrewer reshape2 Rsamtools RSQLite rtracklayer S4Vectors shiny]; };
sevenbridges = derive2 { name="sevenbridges"; version="1.8.0"; sha256="1jlw69yxh697q3bwd54mvzfiqskg469jyyh97sqnlizjmm5hiw11"; depends=[curl docopt dplyr httr jsonlite liftr miniUI objectProperties rstudioapi S4Vectors shiny stringr uuid yaml]; };
sevenbridges = derive2 { name="sevenbridges"; version="1.8.1"; sha256="0v22pwyrgxh6mjqqcxz9ix7ripl5xds0l8p38w0w08ynbdns1w5b"; depends=[curl docopt dplyr httr jsonlite liftr miniUI objectProperties rstudioapi S4Vectors shiny stringr uuid yaml]; };
shinyMethyl = derive2 { name="shinyMethyl"; version="1.14.0"; sha256="17w7shgr4s5w3y1ik8zgr9brv7q87dx9l6dfqywsyvfmmkddimwa"; depends=[BiocGenerics IlluminaHumanMethylation450kmanifest matrixStats minfi RColorBrewer shiny]; };
shinyTANDEM = derive2 { name="shinyTANDEM"; version="1.16.0"; sha256="17x0bq1kzvmqqf30y0dmmp9777i62525mp4ysyv2m6vb9bgrbc4y"; depends=[mixtools rTANDEM shiny xtable]; };
sigPathway = derive2 { name="sigPathway"; version="1.46.0"; sha256="18nn7rpg67dz30v1drm0lnsb1wnww7maxdg4gk960wayasp8hk2z"; depends=[]; };
@ -1406,7 +1406,7 @@ in with self; {
specL = derive2 { name="specL"; version="1.12.0"; sha256="03bkh0z3pd6jl47wq2h6zd73fvaggwnaj2b4ibijwkg1643mfiip"; depends=[DBI protViz Rcpp RSQLite seqinr]; };
spikeLI = derive2 { name="spikeLI"; version="2.38.0"; sha256="00fixl9jpjfm0qgsg1lwi0315sa53j1j9fbrl69j8y2gbr8kgg28"; depends=[]; };
spkTools = derive2 { name="spkTools"; version="1.34.0"; sha256="0vpyv78c6c58qrcz91mir7jh9gx2j2l48bclabvgi0k2156wpwn7"; depends=[Biobase gtools RColorBrewer]; };
splatter = derive2 { name="splatter"; version="1.2.1"; sha256="0iap91mmfan5p8wcpkxmqrrlk4zhgcigl08js5k1kcizmqkiar5g"; depends=[akima BiocGenerics BiocParallel checkmate edgeR fitdistrplus ggplot2 locfit matrixStats scales scater SingleCellExperiment SummarizedExperiment]; };
splatter = derive2 { name="splatter"; version="1.2.2"; sha256="05bqmck2hszxlvj0vb1j7fbyv4fp2q7bjv7ywlg6hs9bx7zk1iaj"; depends=[akima BiocGenerics BiocParallel checkmate edgeR fitdistrplus ggplot2 locfit matrixStats scales scater SingleCellExperiment SummarizedExperiment]; };
spliceR = derive2 { name="spliceR"; version="1.20.0"; sha256="1skwj4cqf4s14df42jgy5b9fxrb5c5np9khc0wkg732qddbdlagd"; depends=[cummeRbund GenomicRanges IRanges plyr RColorBrewer rtracklayer VennDiagram]; };
spliceSites = derive2 { name="spliceSites"; version="1.26.0"; sha256="19av0wkdvy4x4p0nkhy9ca450d6j0s68m2lp26116ydh4lzv4p8x"; depends=[Biobase BiocGenerics Biostrings doBy IRanges rbamtools refGenome seqLogo]; };
splicegear = derive2 { name="splicegear"; version="1.50.0"; sha256="0i47l91p77s4acgrx9c8ll2va7amysw1g2acs36mn99hpz86v4m4"; depends=[annotate Biobase XML]; };
@ -1423,7 +1423,7 @@ in with self; {
stepNorm = derive2 { name="stepNorm"; version="1.50.0"; sha256="10fd623pqy944q9l913bv1a3dh7wk4i0r211hvvzdr39kfhjl6mf"; depends=[marray MASS]; };
subSeq = derive2 { name="subSeq"; version="1.8.0"; sha256="1z9qwfclhnnvcp4r4zfi201rmgd0hj47rd77x958m1d6d3z65m34"; depends=[Biobase data_table digest dplyr ggplot2 magrittr qvalue tidyr]; };
supraHex = derive2 { name="supraHex"; version="1.16.0"; sha256="10lhdhlb33p91np6ldmxc8yqgxwly7p37nlacm77q35dp05a453n"; depends=[ape hexbin MASS]; };
survcomp = derive2 { name="survcomp"; version="1.28.4"; sha256="185k9srpfzvr51xfbgq1xy39x40cxgcvvq772y9gdk1702fxvyw0"; depends=[bootstrap ipred KernSmooth prodlim rmeta SuppDists survival survivalROC]; };
survcomp = derive2 { name="survcomp"; version="1.28.5"; sha256="09winy33410hw6srybaw49m2nb5cyp3fx0ww9gyhhkh73cvb6xwb"; depends=[bootstrap ipred KernSmooth prodlim rmeta SuppDists survival survivalROC]; };
sva = derive2 { name="sva"; version="3.26.0"; sha256="0q5xb68wfcnchy8rkv5ma67pmz1i91lsnvmwmj8f1c3w4xan3pgw"; depends=[BiocParallel genefilter limma matrixStats mgcv]; };
swfdr = derive2 { name="swfdr"; version="1.4.0"; sha256="0ls0w09bkxxqv1y50d5c1s0qpxb1xdyall8ypvky8awi7v6jlrcg"; depends=[dplyr ggplot2 reshape2]; };
switchBox = derive2 { name="switchBox"; version="1.14.0"; sha256="0mhkf4wwd3v3s1148nafbd6x6ys8j933glh4gp3wj24ddmmpxvb2"; depends=[gplots pROC]; };
@ -1468,7 +1468,7 @@ in with self; {
vtpnet = derive2 { name="vtpnet"; version="0.18.0"; sha256="02nws97nmlrpzwb5jqm3fmg38mp1qdf41hzwmmprhfhsymnmc4ch"; depends=[doParallel foreach GenomicRanges graph gwascat]; };
vulcan = derive2 { name="vulcan"; version="1.0.0"; sha256="1yxm6yg7d65wh9rl6k5b6831y4hr5l9nnmfi0azxz1h4x1ghqbdj"; depends=[Biobase caTools ChIPpeakAnno csaw DESeq DiffBind GenomicRanges gplots locfit S4Vectors TxDb_Hsapiens_UCSC_hg19_knownGene viper wordcloud zoo]; };
wateRmelon = derive2 { name="wateRmelon"; version="1.22.1"; sha256="08imbxhs4ikm6panz3y64b24d2ghy1s2ksgd8siff53hg2v59rqr"; depends=[Biobase IlluminaHumanMethylation450kanno_ilmn12_hg19 illuminaio limma lumi matrixStats methylumi ROC]; };
wavClusteR = derive2 { name="wavClusteR"; version="2.11.0"; sha256="0f1lk45a9yqr0ysjq8kjpqys8qln2b8ix03nywcqnkl1lk2b5ymi"; depends=[BiocGenerics Biostrings foreach GenomicFeatures GenomicRanges ggplot2 Hmisc IRanges mclust Rsamtools rtracklayer S4Vectors seqinr stringr wmtsa]; };
wavClusteR = derive2 { name="wavClusteR"; version="2.12.1"; sha256="01b8aqwi7nd8l7mkiqgg9skvl0r6y1vwslwchyk95a9l4hkhxrz9"; depends=[BiocGenerics Biostrings foreach GenomicFeatures GenomicRanges ggplot2 Hmisc IRanges mclust Rsamtools rtracklayer S4Vectors seqinr stringr wmtsa]; };
waveTiling = derive2 { name="waveTiling"; version="1.20.0"; sha256="1dlz548vjnarz15mscmj56jp2hn810w0dy7xprxx22n51h7kb7jg"; depends=[affy Biobase Biostrings GenomeGraphs GenomicRanges IRanges oligo oligoClasses preprocessCore waveslim]; };
weaver = derive2 { name="weaver"; version="1.44.0"; sha256="06fg8z4gp2mabiy9jrfwkrrz1r4qzzgjk3lxj6d53ii2xhq95vy6"; depends=[codetools digest]; };
webbioc = derive2 { name="webbioc"; version="1.50.0"; sha256="1kg6apnhq97ypmpx6qm2f7wip81f910mjlg9kmd9zzmhnkrhqamd"; depends=[affy annaffy Biobase BiocInstaller gcrma multtest qvalue vsn]; };

2314
pkgs/development/r-modules/cran-packages.nix generated
View file

File diff suppressed because it is too large Load diff

2
pkgs/development/r-modules/default.nix
View file

@ -438,7 +438,6 @@ let
packagesRequireingX = [
"accrual"
"ade4TkGUI"
"adehabitat"
"analogue"
"analogueExtra"
"AnalyzeFMRI"
@ -585,7 +584,6 @@ let
"ProbForecastGOP"
"qtbase"
"qtpaint"
"R2STATS"
"r4ss"
"RandomFields"
"rareNMtests"

4
pkgs/development/tools/build-managers/buildbot/default.nix
View file

@ -14,11 +14,11 @@ let
package = pythonPackages.buildPythonApplication rec {
name = "${pname}-${version}";
pname = "buildbot";
version = "1.0.0";
version = "1.1.0";
src = pythonPackages.fetchPypi {
inherit pname version;
sha256 = "0y7gpymxl09gd9dyqj7zqhaihpl9da1v8ppxi4r161ywd8jv9b1g";
sha256 = "1rhmlcvw0dsr4f37sb3xmb9xcn76lsrsw2g1z611g339nmxzi0sc";
};
buildInputs = with pythonPackages; [

22
pkgs/development/tools/database/sqldeveloper/default.nix
View file

@ -1,7 +1,21 @@
{ stdenv, makeWrapper, requireFile, unzip, openjdk }:
{ stdenv, makeDesktopItem, makeWrapper, requireFile, unzip, openjdk }:
stdenv.mkDerivation rec {
let
version = "17.4.1.054.0712";
desktopItem = makeDesktopItem {
name = "sqldeveloper";
exec = "sqldeveloper";
icon = "sqldeveloper";
desktopName = "Oracle SQL Developer";
genericName = "Oracle SQL Developer";
comment = "Oracle's Oracle DB GUI client";
categories = "Application;Development;";
};
in
stdenv.mkDerivation rec {
inherit version;
name = "sqldeveloper-${version}";
src = requireFile rec {
@ -51,6 +65,10 @@ stdenv.mkDerivation rec {
cd $out
unzip ${src}
mv sqldeveloper $out/lib/${name}
install -D -m 444 $out/lib/$name/icon.png $out/share/pixmaps/sqldeveloper.png
mkdir -p $out/share/applications
cp ${desktopItem}/share/applications/* $out/share/applications
'';
meta = with stdenv.lib; {

2
pkgs/development/tools/misc/hydra/default.nix
View file

@ -27,6 +27,7 @@ let
CatalystViewDownload
CatalystViewJSON
CatalystViewTT
CatalystXRoleApplicator
CatalystXScriptServerStarman
CryptRandPasswd
DBDPg
@ -39,6 +40,7 @@ let
FileSlurp
IOCompress
IPCRun
JSONAny
JSONXS
LWP
LWPProtocolHttps

4
pkgs/games/openarena/default.nix
View file

@ -1,4 +1,4 @@
{ fetchurl, makeWrapper, patchelf, pkgs, stdenv, SDL, libogg, libvorbis }:
{ fetchurl, makeWrapper, patchelf, pkgs, stdenv, SDL, libogg, libvorbis, curl }:
stdenv.mkDerivation rec {
name = "openarena-${version}";
@ -15,7 +15,7 @@ stdenv.mkDerivation rec {
installPhase = let
gameDir = "$out/openarena-$version";
interpreter = "$(< \"$NIX_CC/nix-support/dynamic-linker\")";
libPath = stdenv.lib.makeLibraryPath [ SDL libogg libvorbis ];
libPath = stdenv.lib.makeLibraryPath [ SDL libogg libvorbis curl ];
in ''
mkdir -pv $out/bin
cd $out

4
pkgs/misc/drivers/sc-controller/default.nix
View file

@ -7,13 +7,13 @@
buildPythonApplication rec {
pname = "sc-controller";
version = "0.4.1";
version = "0.4.2";
src = fetchFromGitHub {
owner = "kozec";
repo = pname;
rev = "v${version}";
sha256 = "0zal8sl3j17gqmynig8jhqrhj7zfqql8vci4whn19gymchwjalzi";
sha256 = "19i9z5cjjgi3a94hrz5g3a6m4vj71p1gs6mhklc6dq8ydwsadwzz";
};
nativeBuildInputs = [ wrapGAppsHook ];

4
pkgs/os-specific/linux/kernel/linux-4.14.nix
View file

@ -3,13 +3,13 @@
with stdenv.lib;
buildLinux (args // rec {
version = "4.14.35";
version = "4.14.36";
# branchVersion needs to be x.y
extraMeta.branch = concatStrings (intersperse "." (take 2 (splitString "." version)));
src = fetchurl {
url = "mirror://kernel/linux/kernel/v4.x/linux-${version}.tar.xz";
sha256 = "01zfbd766y8hfsd248lffaj6d4ghl4j918m3yvl892p84xsp5aq2";
sha256 = "0hxwd3kl5g7zrcl3b00nxdv0zjkmmfrk1i5v3hrjm0dmsw249qna";
};
} // (args.argsOverride or {}))

18
pkgs/os-specific/linux/kernel/linux-4.15.nix
View file

@ -1,18 +0,0 @@
{ stdenv, buildPackages, hostPlatform, fetchurl, perl, buildLinux, ... } @ args:
with stdenv.lib;
buildLinux (args // rec {
version = "4.15.18";
# modDirVersion needs to be x.y.z, will automatically add .0 if needed
modDirVersion = concatStrings (intersperse "." (take 3 (splitString "." "${version}.0")));
# branchVersion needs to be x.y
extraMeta.branch = concatStrings (intersperse "." (take 2 (splitString "." version)));
src = fetchurl {
url = "mirror://kernel/linux/kernel/v4.x/linux-${version}.tar.xz";
sha256 = "0hdg5h91zwypsgb1lp1m5q1iak1g00rml54fh6j7nj8dgrqwv29z";
};
} // (args.argsOverride or {}))

4
pkgs/os-specific/linux/kernel/linux-4.16.nix
View file

@ -3,7 +3,7 @@
with stdenv.lib;
buildLinux (args // rec {
version = "4.16.3";
version = "4.16.4";
# modDirVersion needs to be x.y.z, will automatically add .0 if needed
modDirVersion = concatStrings (intersperse "." (take 3 (splitString "." "${version}.0")));
@ -13,6 +13,6 @@ buildLinux (args // rec {
src = fetchurl {
url = "mirror://kernel/linux/kernel/v4.x/linux-${version}.tar.xz";
sha256 = "18w1dhq5dnmcqc3d8imwm90zwfw0fhda7sy5fjwkhzm93nl72s8d";
sha256 = "0v494vm1vbyfk8xmvgf27chsjpy9x7q0iwdaana8vnih2ai6vdcs";
};
} // (args.argsOverride or {}))

4
pkgs/os-specific/linux/kernel/linux-4.4.nix
View file

@ -1,11 +1,11 @@
{ stdenv, buildPackages, hostPlatform, fetchurl, perl, buildLinux, ... } @ args:
buildLinux (args // rec {
version = "4.4.128";
version = "4.4.129";
extraMeta.branch = "4.4";
src = fetchurl {
url = "mirror://kernel/linux/kernel/v4.x/linux-${version}.tar.xz";
sha256 = "1c5nlxazn2ijfra1bn3x4fdz3fx02j76hg430jgyij61vndgi5ka";
sha256 = "0aviyky8f73l6jpi1d4by947rj78d5vckxkyf9aj73bavaxc8rd1";
};
} // (args.argsOverride or {}))

4
pkgs/os-specific/linux/kernel/linux-4.9.nix
View file

@ -1,11 +1,11 @@
{ stdenv, buildPackages, hostPlatform, fetchurl, perl, buildLinux, ... } @ args:
buildLinux (args // rec {
version = "4.9.95";
version = "4.9.96";
extraMeta.branch = "4.9";
src = fetchurl {
url = "mirror://kernel/linux/kernel/v4.x/linux-${version}.tar.xz";
sha256 = "1x4z66v6zl4q0hzinzb1wvlq9fd3v4sbwj9lay69f3vdq8knsnly";
sha256 = "0zw7x86c8qa2kzkwlxlhqzsnddyp1ncw4ja660bqnzqrnmp5jvw2";
};
} // (args.argsOverride or {}))

6
pkgs/os-specific/linux/kernel/linux-testing.nix
View file

@ -1,13 +1,13 @@
{ stdenv, buildPackages, hostPlatform, fetchurl, perl, buildLinux, libelf, utillinux, ... } @ args:
buildLinux (args // rec {
version = "4.17-rc1";
modDirVersion = "4.17.0-rc1";
version = "4.17-rc2";
modDirVersion = "4.17.0-rc2";
extraMeta.branch = "4.17";
src = fetchurl {
url = "https://git.kernel.org/torvalds/t/linux-${version}.tar.gz";
sha256 = "0a3lrax6f8f98lj65aawpqkzkmxcl2x4h20kr0cr7wf0jvpnn5y3";
sha256 = "1z4kl25x8m498wicbzhx21kvksp63ab8l2s0nfxf7fwj7dd13cld";
};
# Should the testing kernels ever be built on Hydra?

50
pkgs/os-specific/linux/tbs/default.nix
View file

@ -1,50 +0,0 @@
{ stdenv, fetchFromGitHub, kernel, kmod, perl, patchutils, perlPackages }:
let
media = fetchFromGitHub {
owner = "tbsdtv";
repo = "linux_media";
rev = "14ebbec91f2cd0423aaf859fc6e6d5d986397cd4";
sha256 = "1cmqj3kby8sxfcpvslbxywr95529vjxzbn800fdp35lka1fv962h";
};
build = fetchFromGitHub {
owner = "tbsdtv";
repo = "media_build";
rev = "c340e29a4047e43f7ea7ebf19e1e28c1f2112d05";
sha256 = "0hfn1j9qk8lh30z3ywj22qky480nsf8z2iag2bqhrhy4375vjlbl";
};
in stdenv.mkDerivation {
name = "tbs-2017-11-05-${kernel.version}";
srcs = [ media build ];
sourceRoot = "${build.name}";
preConfigure = ''
make dir DIR=../${media.name}
'';
postPatch = ''
patchShebangs .
sed -i v4l/Makefile \
-i v4l/scripts/make_makefile.pl \
-e 's,/sbin/depmod,${kmod}/bin/depmod,g' \
-e 's,/sbin/lsmod,${kmod}/bin/lsmod,g'
sed -i v4l/Makefile \
-e 's,^OUTDIR ?= /lib/modules,OUTDIR ?= ${kernel.dev}/lib/modules,' \
-e 's,^SRCDIR ?= /lib/modules,SRCDIR ?= ${kernel.dev}/lib/modules,'
'';
buildFlags = [ "VER=${kernel.modDirVersion}" ];
installFlags = [ "DESTDIR=$(out)" ];
hardeningDisable = [ "pic" "format" ];
nativeBuildInputs = [ patchutils kmod perl perlPackages.ProcProcessTable ];
meta = with stdenv.lib; {
homepage = https://www.tbsdtv.com/;
license = licenses.gpl2;
maintainers = with maintainers; [ ck3d ];
priority = 20;
};
}

2
pkgs/os-specific/linux/zfs/default.nix
View file

@ -153,7 +153,7 @@ in {
# to be adapted
zfsStable = common {
# comment/uncomment if breaking kernel versions are known
incompatibleKernelVersion = null;
incompatibleKernelVersion = "4.16";
# this package should point to the latest release.
version = "0.7.8";

2
pkgs/servers/dns/knot-dns/default.nix
View file

@ -32,7 +32,7 @@ stdenv.mkDerivation rec {
#doCheck = true; problems in combination with dynamic linking
postInstall = ''rm -r "$out"/var'';
postInstall = ''rm -r "$out"/var "$out"/lib/*.la'';
meta = with stdenv.lib; {
description = "Authoritative-only DNS server from .cz domain registry";

4
pkgs/servers/dns/knot-resolver/default.nix
View file

@ -12,11 +12,11 @@ inherit (stdenv.lib) optional optionals optionalString concatStringsSep;
unwrapped = stdenv.mkDerivation rec {
name = "knot-resolver-${version}";
version = "2.2.0";
version = "2.3.0";
src = fetchurl {
url = "http://secure.nic.cz/files/knot-resolver/${name}.tar.xz";
sha256 = "1yhlwvpl81klyfb8hhvrhii99q7wvydi3vandmq9j7dvig6z1dvv";
sha256 = "2d19c5daf8440bd3d2acd1886b9ede65f04f7753c6fd4618a92a1a4ba3b27a9b";
};
outputs = [ "out" "dev" ];

99
pkgs/servers/foundationdb/default.nix Normal file
View file

@ -0,0 +1,99 @@
{ stdenv, fetchurl, fetchFromGitHub
, which, findutils, m4, gawk, python, openjdk, mono58, libressl_2_6
}:
let
version = "5.1.7";
branch = "release-5.1";
rev = "9ad8d02386d4a6a5efecf898df80f2747695c627";
sha256 = "1rc472ih24f9s5g3xmnlp3v62w206ny0pvvw02bzpix2sdrpbp06";
# hysterical raisins dictate a version of boost this old. however,
# we luckily do not need to build anything, we just need the header
# files.
boost152 = stdenv.mkDerivation rec {
name = "boost-headers-1.52.0";
src = fetchurl {
url = "mirror://sourceforge/boost/boost_1_52_0.tar.bz2";
sha256 = "14mc7gsnnahdjaxbbslzk79rc0d12h1i681cd3srdwr3fzynlar2";
};
buildPhase = ":";
configurePhase = ":";
installPhase = ''
mkdir -p $out/include/
cp -R boost $out/include/
'';
};
in stdenv.mkDerivation rec {
name = "foundationdb-${version}";
inherit version;
src = fetchFromGitHub {
owner = "apple";
repo = "foundationdb";
inherit rev sha256;
};
nativeBuildInputs = [ gawk which m4 findutils boost152 mono58 ];
buildInputs = [ python openjdk libressl_2_6 ];
patches =
[ ./fix-scm-version.patch
./ldflags.patch
];
postPatch = ''
substituteInPlace ./build/scver.mk \
--subst-var-by NIXOS_FDB_VERSION_ID "${rev}" \
--subst-var-by NIXOS_FDB_SCBRANCH "${branch}"
substituteInPlace ./Makefile \
--replace 'shell which ccache' 'shell true' \
--replace -Werror ""
substituteInPlace ./Makefile \
--replace libstdc++_pic libstdc++
substituteInPlace ./build/link-validate.sh \
--replace 'exit 1' '#exit 1'
patchShebangs .
'';
enableParallelBuilding = true;
makeFlags = [ "all" "fdb_c" "KVRELEASE=1" ];
configurePhase = ":";
installPhase = ''
mkdir -vp $out/{bin,libexec/plugins} $lib/lib $dev/include/foundationdb
cp -v ./lib/libfdb_c.so $lib/lib
cp -v ./lib/libFDBLibTLS.so $out/libexec/plugins/FDBLibTLS.so
cp -v ./bindings/c/foundationdb/fdb_c.h $dev/include/foundationdb
cp -v ./bindings/c/foundationdb/fdb_c_options.g.h $dev/include/foundationdb
for x in fdbbackup fdbcli fdbserver fdbmonitor; do
cp -v "./bin/$x" $out/bin;
done
ln -sfv $out/bin/fdbbackup $out/bin/dr_agent
ln -sfv $out/bin/fdbbackup $out/bin/fdbrestore
ln -sfv $out/bin/fdbbackup $out/bin/fdbdr
ln -sfv $out/bin/fdbbackup $out/libexec/backup_agent
'';
outputs = [ "out" "lib" "dev" ];
meta = with stdenv.lib; {
description = "Open source, distributed, transactional key-value store";
homepage = https://www.foundationdb.org;
license = licenses.asl20;
platforms = platforms.linux;
maintainers = with maintainers; [ thoughtpolice ];
};
}

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