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github-actions[bot] 2023-04-08 00:02:03 +00:00 committed by GitHub
parent 5c10f407bc 2e7d54cfde
commit 75e19b98bb
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74 changed files with 9135 additions and 5336 deletions
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12
maintainers/maintainer-list.nix
View file

@ -9449,6 +9449,12 @@
githubId = 43853194;
name = "Matheus Vieira";
};
mathiassven = {
email = "github@mathiassven.com";
github = "MathiasSven";
githubId = 24759037;
name = "Mathias Sven";
};
mathnerd314 = {
email = "mathnerd314.gph+hs@gmail.com";
github = "Mathnerd314";
@ -17119,6 +17125,12 @@
githubId = 20029431;
name = "Zyansheep";
};
zygot = {
email = "stefan.bordei13@gmail.com";
github = "stefan-bordei";
githubId = 71881325;
name = "Stefan Bordei";
};
zzamboni = {
email = "diego@zzamboni.org";
github = "zzamboni";

1
maintainers/scripts/haskell/update-stackage.sh
View file

@ -40,6 +40,7 @@ sed -r \
-e 's|^constraints:||' \
-e 's|^ +| - |' \
-e 's|,$||' \
-e '/^with-compiler:/d' \
-e '/installed$/d' \
-e '/^$/d' \
< "${tmpfile}" | sort --ignore-case >"${tmpfile_new}"

2
nixos/tests/libreswan.nix
View file

@ -107,6 +107,8 @@ in
with subtest("Network is up"):
alice.wait_until_succeeds("ping -c1 bob")
alice.succeed("systemctl restart ipsec")
bob.succeed("systemctl restart ipsec")
with subtest("Eve can eavesdrop cleartext traffic"):
eavesdrop()

1
pkgs/applications/editors/android-studio/common.nix
View file

@ -227,6 +227,7 @@ in runCommand
canary = [ alapshin ];
dev = canary;
}."${channel}";
mainProgram = pname;
};
}
''

2
pkgs/applications/misc/blender/default.nix
View file

@ -73,6 +73,8 @@ stdenv.mkDerivation rec {
pythonPath = with python310Packages; [ numpy requests ];
postPatch = ''
# allow usage of dynamically linked embree
rm build_files/cmake/Modules/FindEmbree.cmake
'' +
(if stdenv.isDarwin then ''
: > build_files/cmake/platform/platform_apple_xcode.cmake

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

@ -34,6 +34,10 @@ stdenv.mkDerivation rec {
hash = "sha256-Va/Rm35jqxDlIfQdrpZ41qrW8YzWmm1LWra76AW1xUw=";
};
depsBuildBuild = [
pkg-config
];
nativeBuildInputs = [
pkg-config
wayland-scanner

4
pkgs/applications/networking/browsers/lagrange/default.nix
View file

@ -17,13 +17,13 @@
stdenv.mkDerivation (finalAttrs: {
pname = "lagrange";
version = "1.15.7";
version = "1.15.8";
src = fetchFromGitHub {
owner = "skyjake";
repo = "lagrange";
rev = "v${finalAttrs.version}";
hash = "sha256-p6L2Ak8QaRsSs2/Xjbbod9UFy79vjO5C+YcArofe2Ck=";
hash = "sha256-zfwuFa309JysFMueFbtnt/7LyCCoXKhIIiFwJY/lIZc=";
};
nativeBuildInputs = [ cmake pkg-config zip ];

6
pkgs/applications/networking/browsers/librewolf/default.nix
View file

@ -3,7 +3,7 @@
let
librewolf-src = callPackage ./librewolf.nix { };
in
(buildMozillaMach rec {
((buildMozillaMach rec {
pname = "librewolf";
applicationName = "LibreWolf";
binaryName = "librewolf";
@ -30,4 +30,6 @@ in
crashreporterSupport = false;
enableOfficialBranding = false;
pgoSupport = false; # Profiling gets stuck and doesn't terminate.
}
}).overrideAttrs (prev: {
MOZ_REQUIRE_SIGNING = "";
})

4
pkgs/applications/networking/browsers/tor-browser-bundle-bin/default.nix
View file

@ -375,7 +375,11 @@ stdenv.mkDerivation rec {
APULSE_PLAYBACK_DEVICE="\''${APULSE_PLAYBACK_DEVICE:-plug:dmix}" \
\
TOR_SKIP_LAUNCH="\''${TOR_SKIP_LAUNCH:-}" \
TOR_CONTROL_HOST="\''${TOR_CONTROL_HOST:-}" \
TOR_CONTROL_PORT="\''${TOR_CONTROL_PORT:-}" \
TOR_CONTROL_COOKIE_AUTH_FILE="\''${TOR_CONTROL_COOKIE_AUTH_FILE:-}" \
TOR_CONTROL_PASSWD="\''${TOR_CONTROL_PASSWD:-}" \
TOR_SOCKS_HOST="\''${TOR_SOCKS_HOST:-}" \
TOR_SOCKS_PORT="\''${TOR_SOCKS_PORT:-}" \
\
FONTCONFIG_FILE="$FONTCONFIG_FILE" \

27
pkgs/applications/networking/cluster/rke2/default.nix Normal file
View file

@ -0,0 +1,27 @@
{ lib, buildGoModule, fetchFromGitHub }:
buildGoModule rec {
pname = "rke2";
version = "1.26.3+rke2r1";
src = fetchFromGitHub {
owner = "rancher";
repo = pname;
rev = "v${version}";
hash = "sha256-MC3INsuXV2JmazdXOAAslFlApvql6uOnOkWV8u0diOw=";
};
vendorHash = "sha256-W9Phc1JYa3APAKvI34RWqMy4xfmwgX3BaOh4bQYFEnU=";
subPackages = [ "." ];
ldflags = [ "-s" "-w" "-X github.com/k3s-io/k3s/pkg/version.Version=v${version}" ];
meta = with lib; {
homepage = "https://github.com/rancher/rke2";
description = "RKE2, also known as RKE Government, is Rancher's next-generation Kubernetes distribution.";
changelog = "https://github.com/rancher/rke2/releases/tag/v${version}";
license = licenses.asl20;
maintainers = with maintainers; [ zygot ];
};
}

1
pkgs/applications/networking/syncplay/default.nix
View file

@ -13,6 +13,7 @@ buildPythonApplication rec {
sha256 = "0qm3qn4a1nahhs7q81liz514n9blsi107g9s9xfw2i8pzi7v9v0v";
};
buildInputs = lib.optionals enableGUI [ qt5.qtbase ];
propagatedBuildInputs = [ twisted certifi ]
++ twisted.optional-dependencies.tls
++ lib.optional enableGUI pyside2;

10
pkgs/applications/science/logic/tamarin-prover/default.nix
View file

@ -1,4 +1,4 @@
{ haskellPackages, mkDerivation, fetchFromGitHub, lib, stdenv
{ haskellPackages, mkDerivation, fetchFromGitHub, fetchpatch, lib, stdenv
# the following are non-haskell dependencies
, makeWrapper, which, maude, graphviz, glibcLocales
}:
@ -67,6 +67,14 @@ mkDerivation (common "tamarin-prover" src // {
isLibrary = false;
isExecutable = true;
patches = [
# Backport of https://github.com/tamarin-prover/tamarin-prover/pull/536 to 1.6.1
(fetchpatch {
url = "https://github.com/tamarin-prover/tamarin-prover/commit/95fbace0c5cbea57b5f320f6bb4d0387a4beab8d.patch";
sha256 = "sha256-Wjf7C208kcskEN1op//HQZnhoZopKQS42JvE8kV5NhI=";
})
];
# strip out unneeded deps manually
doHaddock = false;
enableSharedExecutables = false;

4
pkgs/applications/version-management/gh/default.nix
View file

@ -2,13 +2,13 @@
buildGoModule rec {
pname = "gh";
version = "2.26.1";
version = "2.27.0";
src = fetchFromGitHub {
owner = "cli";
repo = "cli";
rev = "v${version}";
hash = "sha256-ECYUpbzZXEJv0r9q66kLpUtp1gbgSeXdb3p4vHWIIk4=";
hash = "sha256-WjKHV/GfoPFRTKUJy7ht1H6zbt+EqJk6e9ysjaAkelw=";
};
vendorHash = "sha256-+8/cA0UxyVu7nyLhHYBWmn8Vs0O/EYepqTAOVU4gwt4=";

28
pkgs/applications/version-management/mercurial/default.nix
View file

@ -1,4 +1,4 @@
{ lib, stdenv, fetchurl, python3Packages, makeWrapper, gettext, installShellFiles
{ lib, stdenv, fetchurl, fetchpatch, python3Packages, makeWrapper, gettext, installShellFiles
, re2Support ? true
, rustSupport ? stdenv.hostPlatform.isLinux, rustPlatform
, fullBuild ? false
@ -21,11 +21,11 @@ let
self = python3Packages.buildPythonApplication rec {
pname = "mercurial${lib.optionalString fullBuild "-full"}";
version = "6.3.3";
version = "6.4";
src = fetchurl {
url = "https://mercurial-scm.org/release/mercurial-${version}.tar.gz";
sha256 = "sha256-E8l/9YnHYF6ApIjzNoUs4dU4xdQUPPszvmm9rd2RV70=";
sha256 = "sha256-6Iv7y5kR52kEoxuXLlf4bajmzliSuYw53VHTuVmcE0c=";
};
format = "other";
@ -35,7 +35,7 @@ let
cargoDeps = if rustSupport then rustPlatform.fetchCargoTarball {
inherit src;
name = "mercurial-${version}";
sha256 = "sha256-ZQYNFEbvSwiJ/BSQ0ZxpjFrmyXkKjVJciwz45Br7Rl8=";
sha256 = "sha256-jgB9UMuZ9v+euGN2LPzg0vNK0KeEa8GpQxLJYgQzzbw=";
sourceRoot = "mercurial-${version}/rust";
} else null;
cargoRoot = if rustSupport then "rust" else null;
@ -110,6 +110,22 @@ let
gnupg
];
patches = [
# remove dependency over packaging for test runner
# https://bz.mercurial-scm.org/show_bug.cgi?id=6805
(fetchpatch {
url = "https://foss.heptapod.net/mercurial/mercurial-devel/-/commit/5e5e3733082a25856038f0fde66d4e08d8881539.patch";
hash = "sha256-JNxESWpWZW3AENz57tNJTV/ALnJjkmG1ZnTWSvTr4qY=";
})
# sligthly different test output matching
# https://bz.mercurial-scm.org/show_bug.cgi?id=6807
(fetchpatch {
url = "https://foss.heptapod.net/mercurial/mercurial-devel/-/commit/2231f7d8a60266bb6907b1708400c970ed799017.patch";
hash = "sha256-Lm5qXvM9nbmTpuMuvDoWhY4cQQQN7PFZtmu5e7mQVw4=";
})
];
postPatch = ''
patchShebangs .
@ -149,10 +165,6 @@ let
# doesn't like the extra setlocale warnings emitted by our bash wrappers
test-locale.t
# Python 3.10-3.12 deprecation warning: distutils
# https://bz.mercurial-scm.org/show_bug.cgi?id=6729
test-hghave.t
# Python 3.10-3.12 deprecation warning: asyncore
# https://bz.mercurial-scm.org/show_bug.cgi?id=6727
test-patchbomb-tls.t

4
pkgs/applications/video/mkvtoolnix/default.nix
View file

@ -47,13 +47,13 @@ let
in
stdenv.mkDerivation rec {
pname = "mkvtoolnix";
version = "74.0.0";
version = "75.0.0";
src = fetchFromGitLab {
owner = "mbunkus";
repo = "mkvtoolnix";
rev = "release-${version}";
sha256 = "sha256-p8rIAHSqYCOlNbuxisQlIkMh2OArc+MOYn1kgC5kJsc=";
sha256 = "c3I2ULSvKBTYIm1chVHPkaV0TxblLglBjzeUJ5TRmGw=";
};
nativeBuildInputs = [

5
pkgs/build-support/fetchurl/mirrors.nix
View file

@ -43,6 +43,11 @@
"http://bioconductor.jp/packages/"
];
# CRAN mirrors
cran = [
"https://cran.r-project.org/src/contrib/"
];
# BitlBee mirrors, see https://www.bitlbee.org/main.php/mirrors.html
bitlbee = [
"https://get.bitlbee.org/"

8
pkgs/data/misc/hackage/pin.json
View file

@ -1,6 +1,6 @@
{
"commit": "4a67d2eace63deeaec7dd3553d04e892b39b63a7",
"url": "https://github.com/commercialhaskell/all-cabal-hashes/archive/4a67d2eace63deeaec7dd3553d04e892b39b63a7.tar.gz",
"sha256": "12y659k8qs0rnajcfdwwwwz5ywcnf3ygxi2kmv8b31x4znll1gfs",
"msg": "Update from Hackage at 2023-03-13T08:59:39Z"
"commit": "cf82f82661a5662581a4385c693552b18009b7e2",
"url": "https://github.com/commercialhaskell/all-cabal-hashes/archive/cf82f82661a5662581a4385c693552b18009b7e2.tar.gz",
"sha256": "0wwyikl44dg5x6hirxxqdzbh4ixkpxknd4c0nacsc2mqpjm1wrwq",
"msg": "Update from Hackage at 2023-04-03T07:13:26Z"
}

51
pkgs/development/compilers/abcl/default.nix
View file

@ -1,38 +1,67 @@
{lib, stdenv, fetchurl, ant, jre, jdk}:
{ stdenv
, lib
, fetchurl
, ant
, jre
, jdk
, makeWrapper
}:
stdenv.mkDerivation rec {
pname = "abcl";
version = "1.9.1";
# or fetchFromGitHub(owner,repo,rev) or fetchgit(rev)
src = fetchurl {
url = "https://common-lisp.net/project/armedbear/releases/${version}/${pname}-src-${version}.tar.gz";
sha256 = "sha256-pbxnfJRB9KgzwgpUG93Rb/+SZIRmkd6aHa9mmfj/EeI=";
};
configurePhase = ''
runHook preConfigure
mkdir nix-tools
export PATH="$PWD/nix-tools:$PATH"
echo "echo nix-builder.localdomain" > nix-tools/hostname
chmod a+x nix-tools/*
hostname
runHook postConfigure
'';
buildInputs = [ jre ant jdk jre ];
nativeBuildInputs = [ makeWrapper ];
buildPhase = ''
runHook preBuild
ant
runHook postBuild
'';
# Fix for https://github.com/armedbear/abcl/issues/484
javaOpts =
lib.optionalString
(lib.versionAtLeast jre.version "17")
"--add-opens=java.base/java.util.jar=ALL-UNNAMED";
installPhase = ''
runHook preInstall
mkdir -p "$out"/{bin,share/doc/abcl,lib/abcl}
cp -r README COPYING CHANGES examples/ "$out/share/doc/abcl/"
cp -r dist/*.jar contrib/ "$out/lib/abcl/"
echo "#! ${stdenv.shell}" >> "$out/bin/abcl"
echo "${jre}/bin/java $javaOpts -cp \"$out/lib/abcl/abcl.jar:$out/lib/abcl/abcl-contrib.jar:\$CLASSPATH\" org.armedbear.lisp.Main \"\$@\"" >> "$out/bin/abcl"
chmod a+x "$out"/bin/*
makeWrapper ${jre}/bin/java $out/bin/abcl \
--prefix CLASSPATH : $out/lib/abcl/abcl.jar \
--prefix CLASSPATH : $out/lib/abcl/abcl-contrib.jar \
${lib.optionalString (lib.versionAtLeast jre.version "17")
# Fix for https://github.com/armedbear/abcl/issues/484
"--add-flags --add-opens=java.base/java.util.jar=ALL-UNNAMED \\"
}
--add-flags org.armedbear.lisp.Main
runHook postInstall
'';
buildInputs = [jre ant jdk jre];
passthru.updateScript = ./update.sh;
meta = {
description = "A JVM-based Common Lisp implementation";
license = lib.licenses.gpl3 ;

5
pkgs/development/compilers/abcl/update.sh Executable file
View file

@ -0,0 +1,5 @@
#!/usr/bin/env nix-shell
#!nix-shell -i bash -p nix-update curl
new_version=$(curl https://armedbear.common-lisp.dev/ | grep abcl-src | sed 's;[^>]*>abcl-src-\(.*\).tar[^$]*;\1;' | head -n 1)
nix-update abcl --version "$new_version"

6
pkgs/development/compilers/ghc/head.nix
View file

@ -1,5 +1,5 @@
import ./common-hadrian.nix {
version = "9.7.20230217";
rev = "a203ad854ffee802e6bf0aca26e6c9a99bec3865";
sha256 = "06q6l7svdynvdv90yz6dxbsk3j5c8gh5ghwfl02rdwamcrzw7zic";
version = "9.7.20230406";
rev = "04b80850c535fa8c11f435711577296a99499105";
sha256 = "190fpgg8sbcfp2l62vaqhk3wddkbz8vf5ivd7hw5gkcyyn5px3q9";
}

191
pkgs/development/haskell-modules/configuration-common.nix
View file

@ -13,7 +13,7 @@
let
inherit (pkgs) fetchpatch fetchpatch2 lib;
inherit (lib) throwIfNot versionOlder;
inherit (lib) throwIfNot versionOlder versions;
in
with haskellLib;
@ -100,6 +100,111 @@ self: super: {
guardian
;
#######################################
### HASKELL-LANGUAGE-SERVER SECTION ###
#######################################
haskell-language-server = (lib.pipe super.haskell-language-server [
dontCheck
(disableCabalFlag "stan") # Sorry stan is totally unmaintained and terrible to get to run. It only works on ghc 8.8 or 8.10 anyways …
]).overrideScope (lself: lsuper: {
# For most ghc versions, we overrideScope Cabal in the configuration-ghc-???.nix,
# because some packages, like ormolu, need a newer Cabal version.
# ghc-paths is special because it depends on Cabal for building
# its Setup.hs, and therefor declares a Cabal dependency, but does
# not actually use it as a build dependency.
# That means ghc-paths can just use the ghc included Cabal version,
# without causing package-db incoherence and we should do that because
# otherwise we have different versions of ghc-paths
# around which have the same abi-hash, which can lead to confusions and conflicts.
ghc-paths = lsuper.ghc-paths.override { Cabal = null; };
});
# 2023-04-03: https://github.com/haskell/haskell-language-server/issues/3546#issuecomment-1494139751
# There will probably be a new revision soon.
hls-tactics-plugin = assert super.hls-tactics-plugin.version == "1.8.0.0"; doJailbreak super.hls-tactics-plugin;
hls-brittany-plugin = assert super.hls-brittany-plugin.version == "1.1.0.0"; doJailbreak super.hls-brittany-plugin;
hls-hlint-plugin = super.hls-hlint-plugin.override {
# For "ghc-lib" flag see https://github.com/haskell/haskell-language-server/issues/3185#issuecomment-1250264515
hlint = enableCabalFlag "ghc-lib" super.hlint;
apply-refact = self.apply-refact_0_11_0_0;
};
hls-test-utils = appendPatch (fetchpatch {
name = "hls-test-utils-ghcide-1.10-compat.patch";
url = "https://github.com/haskell/haskell-language-server/commit/014c8f90249f11a8dfa1286e67d452ccfb42b2d0.patch";
relative = "hls-test-utils";
hash = "sha256-sBuqSmgCQSgbXV6KPEZcIP09wbx81q5xjSg7/slH2HQ=";
}) super.hls-test-utils;
hls-rename-plugin = if lib.versionAtLeast super.ghc.version "9.4" then overrideCabal
(drv: {
prePatch = drv.prePatch or "" + ''
"${pkgs.buildPackages.dos2unix}/bin/dos2unix" *.cabal
'';
})
(appendPatch (fetchpatch {
name = "hls-rename-ghc-9.4-compat.patch";
url = "https://github.com/haskell/haskell-language-server/commit/472947cdb9e711f6ef889bba3b83b0dd44a1b6bc.patch";
relative = "plugins/hls-rename-plugin";
hash = "sha256-WPhCQmn3rjCOiQFJz23QQ84zfm43FNll0BfsNK5pkG0=";
}) super.hls-rename-plugin) else super.hls-rename-plugin;
hls-floskell-plugin = if lib.versionAtLeast super.ghc.version "9.4" then overrideCabal
(drv: {
prePatch = drv.prePatch or "" + ''
"${pkgs.buildPackages.dos2unix}/bin/dos2unix" *.cabal
'';
})
(appendPatch (fetchpatch {
name = "hls-floskell-ghc-9.4-compat.patch";
url = "https://github.com/haskell/haskell-language-server/commit/ddc67b2d4d719623b657aa54db20bf58c58a5d4a.patch";
relative = "plugins/hls-floskell-plugin";
hash = "sha256-n2vuzGbdvhW6I8c7Q22SuNIKSX2LwGNBTVyLLHJIsiU=";
}) super.hls-floskell-plugin) else super.hls-floskell-plugin;
hls-stylish-haskell-plugin = if lib.versionAtLeast super.ghc.version "9.4" then overrideCabal
(drv: {
prePatch = drv.prePatch or "" + ''
"${pkgs.buildPackages.dos2unix}/bin/dos2unix" *.cabal
'';
})
(appendPatch (fetchpatch {
name = "hls-stylish-haskell-ghc-9.4-compat.patch";
url = "https://github.com/haskell/haskell-language-server/commit/ddc67b2d4d719623b657aa54db20bf58c58a5d4a.patch";
relative = "plugins/hls-stylish-haskell-plugin";
hash = "sha256-GtN9t5zMOROCDSLiscLZ5GmqDV+ql9R2z/+W++C2h2Q=";
}) super.hls-stylish-haskell-plugin) else super.hls-stylish-haskell-plugin;
hie-compat = if lib.versionAtLeast super.ghc.version "9.6" then overrideCabal
(drv: {
prePatch = drv.prePatch or "" + ''
"${pkgs.buildPackages.dos2unix}/bin/dos2unix" *.cabal
'';
})
(appendPatch (fetchpatch {
name = "hie-compat-9.6-compat.patch";
url = "https://github.com/haskell/haskell-language-server/commit/191bda61fef34696a793503e639a53003ff70660.patch";
relative = "hie-compat";
hash = "sha256-z81+fwxwZ8BQWGRqTnh3XlQ6AG7EiaahdKjT+0lFu1Q=";
}) super.hie-compat) else super.hie-compat;
# For -f-auto see cabal.project in haskell-language-server.
ghc-lib-parser-ex = addBuildDepend self.ghc-lib-parser (disableCabalFlag "auto" super.ghc-lib-parser-ex);
# For -fghc-lib see cabal.project in haskell-language-server.
stylish-haskell = if lib.versionAtLeast super.ghc.version "9.2"
then enableCabalFlag "ghc-lib"
(if lib.versionAtLeast super.ghc.version "9.4"
then super.stylish-haskell_0_14_4_0
else super.stylish-haskell)
else super.stylish-haskell;
###########################################
### END HASKELL-LANGUAGE-SERVER SECTION ###
###########################################
vector = overrideCabal (old: {
# Too strict bounds on doctest which isn't used, but is part of the configuration
jailbreak = true;
@ -179,7 +284,7 @@ self: super: {
name = "git-annex-${super.git-annex.version}-src";
url = "git://git-annex.branchable.com/";
rev = "refs/tags/" + super.git-annex.version;
sha256 = "0ngvdcvskrhdq4m19h4b1cq3jhbzx0bqay6hvsppk6cb2y4wkfd9";
sha256 = "sha256-fZUQ/3q8w6BkFZRaezT7rpKQtAEGBR5qEc4rMm9I36c=";
# delete android and Android directories which cause issues on
# darwin (case insensitive directory). Since we don't need them
# during the build process, we can delete it to prevent a hash
@ -1052,7 +1157,18 @@ self: super: {
jailbreak = assert drv.version == "1.0.9" && drv.revision == "1"; true;
}) super.dhall-nixpkgs);
stack = self.generateOptparseApplicativeCompletions [ "stack" ] super.stack;
stack =
self.generateOptparseApplicativeCompletions
[ "stack" ]
(super.stack.override {
# stack needs to use an exact hpack version. When changing or removing
# this override, double-check the upstream stack release to confirm
# that we are using the correct hpack version. See
# https://github.com/NixOS/nixpkgs/issues/223390 for more information.
#
# hpack tests fail because of https://github.com/sol/hpack/issues/528
hpack = dontCheck self.hpack_0_35_0;
});
# Too strict version bound on hashable-time.
# Tests require newer package version.
@ -1164,6 +1280,7 @@ self: super: {
# Requires API keys to run tests
algolia = dontCheck super.algolia;
openai-hs = dontCheck super.openai-hs;
# antiope-s3's latest stackage version has a hspec < 2.6 requirement, but
# hspec which isn't in stackage is already past that
@ -1512,56 +1629,6 @@ self: super: {
})
] super.binary-strict;
haskell-language-server = (lib.pipe super.haskell-language-server [
dontCheck
(disableCabalFlag "stan") # Sorry stan is totally unmaintained and terrible to get to run. It only works on ghc 8.8 or 8.10 anyways …
# Allow hls-call-hierarchy >= 1.2 which requires only a bound adjustment
(appendPatch (fetchpatch {
name = "hls-allow-hls-call-hierarchy-1.2.patch";
url = "https://github.com/haskell/haskell-language-server/commit/05b248dfacc307c3397b334635cb38298aee9563.patch";
includes = [ "haskell-language-server.cabal" ];
sha256 = "1v0zi1lv92p6xq54yw9swzaf24dxsi9lpk10sngg3ka654ikm7j5";
}))
]).overrideScope (lself: lsuper: {
# For most ghc versions, we overrideScope Cabal in the configuration-ghc-???.nix,
# because some packages, like ormolu, need a newer Cabal version.
# ghc-paths is special because it depends on Cabal for building
# its Setup.hs, and therefor declares a Cabal dependency, but does
# not actually use it as a build dependency.
# That means ghc-paths can just use the ghc included Cabal version,
# without causing package-db incoherence and we should do that because
# otherwise we have different versions of ghc-paths
# around with have the same abi-hash, which can lead to confusions and conflicts.
ghc-paths = lsuper.ghc-paths.override { Cabal = null; };
});
hls-hlint-plugin = super.hls-hlint-plugin.override {
# For "ghc-lib" flag see https://github.com/haskell/haskell-language-server/issues/3185#issuecomment-1250264515
hlint = enableCabalFlag "ghc-lib" super.hlint;
apply-refact = self.apply-refact_0_11_0_0;
};
# For -f-auto see cabal.project in haskell-language-server.
ghc-lib-parser-ex = addBuildDepend self.ghc-lib-parser (disableCabalFlag "auto" super.ghc-lib-parser-ex);
# 2021-05-08: Tests fail: https://github.com/haskell/haskell-language-server/issues/1809
hls-eval-plugin = dontCheck super.hls-eval-plugin;
# 2021-06-20: Tests fail: https://github.com/haskell/haskell-language-server/issues/1949
hls-refine-imports-plugin = dontCheck super.hls-refine-imports-plugin;
# 2021-11-20: https://github.com/haskell/haskell-language-server/pull/2373
hls-explicit-imports-plugin = dontCheck super.hls-explicit-imports-plugin;
# 2021-11-20: https://github.com/haskell/haskell-language-server/pull/2374
hls-module-name-plugin = dontCheck super.hls-module-name-plugin;
# 2022-09-19: https://github.com/haskell/haskell-language-server/issues/3200
hls-refactor-plugin = dontCheck super.hls-refactor-plugin;
# tests require network
ghcide = dontCheck super.ghcide;
# 2020-11-15: nettle tests are pre MonadFail change
# https://github.com/stbuehler/haskell-nettle/issues/10
nettle = dontCheck super.nettle;
@ -1621,6 +1688,9 @@ self: super: {
servant-swagger-ui-core = doJailbreak super.servant-swagger-ui-core;
hercules-ci-agent = lib.pipe super.hercules-ci-agent [
(pkg: pkg.override (_: {
cachix = super.cachix_1_3_3;
}))
(self.generateOptparseApplicativeCompletions [ "hercules-ci-agent" ])
];
@ -2088,16 +2158,6 @@ self: super: {
# 2021-08-18: streamly-posix was released with hspec 2.8.2, but it works with older versions too.
streamly-posix = doJailbreak super.streamly-posix;
# 2021-09-14: Tests are flaky.
hls-splice-plugin = dontCheck super.hls-splice-plugin;
# 2021-09-18: https://github.com/haskell/haskell-language-server/issues/2205
hls-stylish-haskell-plugin = doJailbreak super.hls-stylish-haskell-plugin;
# Necesssary .txt files are not included in sdist.
# https://github.com/haskell/haskell-language-server/pull/2887
hls-change-type-signature-plugin = dontCheck super.hls-change-type-signature-plugin;
# 2022-12-30: Restrictive upper bound on optparse-applicative
retrie = doJailbreak super.retrie;
@ -2547,4 +2607,9 @@ self: super: {
# 2023-03-13: restrictive bounds on validation-selective (>=0.1.0 && <0.2).
# Get rid of this in the next release: https://github.com/kowainik/tomland/commit/37f16460a6dfe4606d48b8b86c13635d409442cd
tomland = doJailbreak super.tomland;
# 2023-04-05: The last version to support libsoup-2.4, required for
# compatability with other gi- packages.
# Take another look when gi-webkit2 updates as it may have become compatible with libsoup-3
gi-soup = assert versions.major self.gi-webkit2.version == "4"; self.gi-soup_2_4_28;
} // import ./configuration-tensorflow.nix {inherit pkgs haskellLib;} self super

3
pkgs/development/haskell-modules/configuration-ghc-9.2.x.nix
View file

@ -69,9 +69,6 @@ self: super: {
# Tests depend on `parseTime` which is no longer available
hourglass = dontCheck super.hourglass;
# For -fghc-lib see cabal.project in haskell-language-server.
stylish-haskell = enableCabalFlag "ghc-lib" super.stylish-haskell;
# Needs to match ghc version
ghc-tags = doDistribute self.ghc-tags_1_5;

18
pkgs/development/haskell-modules/configuration-ghc-9.4.x.nix
View file

@ -125,7 +125,7 @@ in {
hedgehog = doDistribute (dontHaddock super.hedgehog_1_2);
# tasty-hedgehog > 1.3 necessary to work with hedgehog 1.2:
# https://github.com/qfpl/tasty-hedgehog/pull/63
tasty-hedgehog = self.tasty-hedgehog_1_4_0_0;
tasty-hedgehog = self.tasty-hedgehog_1_4_0_1;
# https://github.com/dreixel/syb/issues/38
syb = dontCheck super.syb;
@ -147,7 +147,7 @@ in {
] ++ drv.testFlags or [];
}) (doJailbreak super.hpack);
lens = doDistribute self.lens_5_2_1;
lens = doDistribute self.lens_5_2_2;
# Apply patches from head.hackage.
language-haskell-extract = appendPatch (pkgs.fetchpatch {
@ -184,18 +184,8 @@ in {
})
self.ghc-exactprint_1_6_1_1;
# 2023-02-01: plugins disabled for hls 1.9.0.0 based on
# https://haskell-language-server.readthedocs.io/en/latest/support/plugin-support.html#current-plugin-support-tiers
haskell-language-server = super.haskell-language-server.override {
hls-eval-plugin = null;
hls-ormolu-plugin = null; # This plugin is supposed to work, but fails to compile.
hls-floskell-plugin = null; # This plugin is supposed to work, but fails to compile.
hls-rename-plugin = null; # This plugin is supposed to work, but fails to compile.
hls-stylish-haskell-plugin = null;
};
# needed to build servant
http-api-data = super.http-api-data_0_5;
http-api-data = super.http-api-data_0_5_1;
attoparsec-iso8601 = super.attoparsec-iso8601_1_1_0_0;
# requires newer versions to work with GHC 9.4
@ -221,7 +211,7 @@ in {
ormolu = doDistribute self.ormolu_0_5_3_0;
fourmolu = overrideCabal (drv: {
libraryHaskellDepends = drv.libraryHaskellDepends ++ [ self.file-embed ];
}) (disableCabalFlag "fixity-th" super.fourmolu_0_10_1_0);
}) (disableCabalFlag "fixity-th" super.fourmolu_0_10_0_0);
# Apply workaround for Cabal 3.8 bug https://github.com/haskell/cabal/issues/8455
# by making `pkg-config --static` happy. Note: Cabal 3.9 is also affected, so

87
pkgs/development/haskell-modules/configuration-ghc-9.6.x.nix
View file

@ -57,14 +57,15 @@ self: super: {
# Version deviations from Stackage LTS
#
th-desugar = doDistribute self.th-desugar_1_15;
th-abstraction = doDistribute self.th-abstraction_0_5_0_0;
tagged = doDistribute self.tagged_0_8_7; # allows template-haskell-2.20
primitive = doDistribute (dontCheck self.primitive_0_7_4_0); # allows base >= 4.18
indexed-traversable = doDistribute super.indexed-traversable_0_1_2_1; # allows base >= 4.18
OneTuple = doDistribute (dontCheck super.OneTuple_0_4_1_1); # allows base >= 4.18
doctest = doDistribute super.doctest_0_21_1;
inspection-testing = doDistribute self.inspection-testing_0_5_0_1; # allows base >= 4.18
OneTuple = doDistribute (dontCheck super.OneTuple_0_4_1_1); # allows base >= 4.18
primitive = doDistribute (dontCheck self.primitive_0_7_4_0); # allows base >= 4.18
tagged = doDistribute self.tagged_0_8_7; # allows template-haskell-2.20
some = doDistribute self.some_1_0_5;
tasty-inspection-testing = doDistribute self.tasty-inspection-testing_0_2;
th-abstraction = doDistribute self.th-abstraction_0_5_0_0;
th-desugar = doDistribute self.th-desugar_1_15;
# Too strict bounds on ghc-prim and template-haskell
aeson = doDistribute (doJailbreak self.aeson_2_1_2_1);
# Too strict bounds on ghc-prim
@ -98,45 +99,13 @@ self: super: {
# base >= 4.18 is allowed in those newer versions
boring = assert !(self ? boring_0_2_1); doJailbreak super.boring;
some = assert !(self ? some_1_0_5); doJailbreak super.some;
assoc = assert !(self ? assoc_1_1); doJailbreak super.assoc;
these = assert !(self ? assoc_1_2); doJailbreak super.these;
# Temporarily upgrade manually until the attribute is available
doctest = doDistribute (overrideCabal {
version = "0.21.1";
sha256 = "0vgl89p6iaj2mwnd1gkpq86q1g18shdcws0p3can25algi2sldk3";
} super.doctest_0_21_0);
# XXX: We probably should be using semigroupoids 6.0.1 which is intended for 9.6
semigroupoids = doJailbreak super.semigroupoids;
# XXX: 1.3 supports 9.6 properly, but is intended for bifunctors >= 5.6
semialign = doJailbreak super.semialign;
#
# Too strict bounds, waiting on Revision in nixpkgs
#
# Revision 7 lifts the offending bound on ghc-prim
ed25519 = jailbreakWhileRevision 6 super.ed25519;
# Revision 6 lifts the offending bound on base
tar = jailbreakWhileRevision 5 super.tar;
# Revision 2 lifts the offending bound on base
HTTP = jailbreakWhileRevision 1 super.HTTP;
# Revision 1 lifts the offending bound on base
dec = jailbreakWhileRevision 0 super.dec;
# Revision 2 lifts the offending bound on base
cryptohash-sha256 = jailbreakWhileRevision 1 super.cryptohash-sha256;
# Revision 4 lifts offending template-haskell bound
uuid-types = jailbreakWhileRevision 3 super.uuid-types;
# Revision 1 lifts offending base bound
quickcheck-instances = jailbreakWhileRevision 0 super.quickcheck-instances;
# Revision 1 lifts offending base bound
generically = jailbreakWhileRevision 0 super.generically;
# Revision 3 lifts offending template-haskell bound
hackage-security = jailbreakWhileRevision 2 super.hackage-security;
# Revision 6 lifts offending base bound
parallel = jailbreakWhileRevision 5 super.parallel;
#
# Compilation failure workarounds
#
@ -156,4 +125,46 @@ self: super: {
# Test suite doesn't compile with base-4.18 / GHC 9.6
# https://github.com/dreixel/syb/issues/40
syb = dontCheck super.syb;
# 2023-04-03: plugins disabled for hls 1.10.0.0 based on
#
haskell-language-server = super.haskell-language-server.override {
hls-ormolu-plugin = null;
hls-floskell-plugin = null;
hls-fourmolu-plugin = null;
hls-hlint-plugin = null;
hls-stylish-haskell-plugin = null;
};
MonadRandom = super.MonadRandom_0_6;
unix-compat = super.unix-compat_0_7;
lifted-base = dontCheck super.lifted-base;
hw-fingertree = dontCheck super.hw-fingertree;
hw-prim = dontCheck (doJailbreak super.hw-prim);
stm-containers = dontCheck super.stm-containers;
regex-tdfa = dontCheck super.regex-tdfa;
rebase = doJailbreak super.rebase_1_20;
rerebase = doJailbreak super.rerebase_1_20;
hiedb = dontCheck super.hiedb;
lucid = doJailbreak (dontCheck super.lucid);
retrie = dontCheck (super.retrie);
ghc-exactprint = unmarkBroken (addBuildDepends (with self.ghc-exactprint.scope; [
HUnit Diff data-default extra fail free ghc-paths ordered-containers silently syb
]) super.ghc-exactprint_1_7_0_0);
inherit (pkgs.lib.mapAttrs (_: doJailbreak ) super)
hls-cabal-plugin
algebraic-graphs
co-log-core
lens
cryptohash-sha1
cryptohash-md5
ghc-trace-events
tasty-hspec
constraints-extras
tree-diff
implicit-hie-cradle
focus
hie-compat;
}

20
pkgs/development/haskell-modules/configuration-hackage2nix/broken.yaml
View file

@ -715,6 +715,7 @@ broken-packages:
- cld2
- Clean
- clean-unions
- clerk # failure building library in job https://hydra.nixos.org/build/214864491 at 2023-04-07
- clevercss
- clexer
- CLI
@ -928,6 +929,7 @@ broken-packages:
- crdt
- crdt-event-fold
- credential-store
- crem # test failure in job https://hydra.nixos.org/build/214604824 at 2023-04-07
- critbit
- criterion-cmp
- criterion-compare
@ -973,6 +975,7 @@ broken-packages:
- currency-convert
- curry-base
- CurryDB
- curryer-rpc # dependency missing in job https://hydra.nixos.org/build/214772339 at 2023-04-07
- curry-frontend
- curryrs
- curves
@ -1401,6 +1404,7 @@ broken-packages:
- eved
- event
- event-driven
- eventlog2html # failure in job https://hydra.nixos.org/build/214597490 at 2023-04-07
- eventsource-api
- eventsourced
- eventstore
@ -1446,6 +1450,7 @@ broken-packages:
- ez-couch
- Facebook-Password-Hacker-Online-Latest-Version
- faceted
- factory # test failure in job https://hydra.nixos.org/build/214600338 at 2023-04-07
- facts
- fadno-braids
- fadno-xml
@ -1810,6 +1815,7 @@ broken-packages:
- git-repair
- gitter
- git-vogue
- gi-webkitwebprocessextension # failure in compileBuildDriverPhase in job https://hydra.nixos.org/build/215220491 at 2023-04-07
- glade
- glapp
- glaze
@ -2413,6 +2419,7 @@ broken-packages:
- hpapi
- hpasteit
- HPath
- hpath-directory # failure building library in job https://hydra.nixos.org/build/214497909 at 2023-04-07
- hpc-coveralls
- hpg
- HPi
@ -2491,6 +2498,8 @@ broken-packages:
- hslogger-template
- hs-logo
- hslua-examples
- hslua-repl # dependency missing in job https://hydra.nixos.org/build/214605872 at 2023-04-07
- hslua-typing # dependency missing in job https://hydra.nixos.org/build/214600262 at 2023-04-07
- hsluv-haskell
- hsmagick
- hsmodetweaks
@ -2571,6 +2580,7 @@ broken-packages:
- htssets
- http2-client-exe
- http2-grpc-types
- http3 # dependency missing in job https://hydra.nixos.org/build/214603147 at 2023-04-07
- http-attoparsec
- http-client-lens
- http-client-request-modifiers
@ -2867,6 +2877,7 @@ broken-packages:
- jsonresume
- json-rpc-generic
- json-rpc-server
- json-rpc # test failure in job https://hydra.nixos.org/build/214602304 at 2023-04-07
- jsonrpc-tinyclient
- json-schema
- jsonschema-gen
@ -2930,6 +2941,7 @@ broken-packages:
- kickass-torrents-dump-parser
- kickchan
- kind-generics-deriving
- kind-integer # failure building library in job https://hydra.nixos.org/build/214501345 at 2023-04-07
- kleene-list
- kmn-programming
- kmonad
@ -3076,6 +3088,7 @@ broken-packages:
- liboath-hs
- liboleg
- libpafe
- libphonenumber # dependency missing in job https://hydra.nixos.org/build/214497968 at 2023-04-07
- libpq
- librandomorg
- libsecp256k1
@ -3341,6 +3354,7 @@ broken-packages:
- mida
- midi-simple
- midi-utils
- mighty-metropolis # test failure in job https://hydra.nixos.org/build/214599789 at 2023-04-07
- migrant-postgresql-simple
- mikmod
- mikrokosmos
@ -3726,7 +3740,6 @@ broken-packages:
- opaleye-trans
- open-adt
- OpenAFP
- openai-hs
- openapi3
- openapi3-code-generator
- openapi-petstore
@ -4015,6 +4028,7 @@ broken-packages:
- pipes-errors
- pipes-interleave
- pipes-io
- pipes-network-ws # failure building library in job https://hydra.nixos.org/build/214504366 at 2023-04-07
- pipes-protolude
- pipes-rt
- pipes-s3
@ -4674,6 +4688,7 @@ broken-packages:
- selenium
- selinux
- Semantique
- semaphore-compat # dependency missing in job https://hydra.nixos.org/build/214509429 at 2023-04-07
- semdoc
- semialign-extras
- semibounded-lattices
@ -5577,6 +5592,7 @@ broken-packages:
- unicode-prelude
- unicode-symbols
- unicode-tricks
- uniform-json # failure building test suite 'json-test' in job https://hydra.nixos.org/build/214602707 at 2023-04-07
- union-map
- uniprot-kb
- uniqueid
@ -5839,6 +5855,7 @@ broken-packages:
- wordchoice
- wordify
- Wordlint
- wordlist # dependency missing in job https://hydra.nixos.org/build/214500004 at 2023-04-07
- wordn
- WordNet
- WordNet-ghc74
@ -5944,6 +5961,7 @@ broken-packages:
- yampa-glut
- yampa-sdl2
- YampaSynth
- yampa-test # dependency missing in job https://hydra.nixos.org/build/214864510 at 2023-04-07
- yandex-translate
- yaop
- yapb

4
pkgs/development/haskell-modules/configuration-hackage2nix/main.yaml
View file

@ -55,6 +55,7 @@ extra-packages:
- Cabal == 3.6.*
- Cabal-syntax == 3.8.* # required for cabal-install{,-parsers}
- Cabal == 3.8.* # required for cabal-install{,-parsers}
- cachix < 1.4 # 2023-04-02: cachix 1.4{,.1} have known on multi-user Nix systems
- directory == 1.3.7.* # required to build cabal-install 3.10.* with GHC 9.2
- Diff < 0.4 # required by liquidhaskell-0.8.10.2: https://github.com/ucsd-progsys/liquidhaskell/issues/1729
- aeson < 2 # required by pantry-0.5.2
@ -79,6 +80,7 @@ extra-packages:
- ghc-api-compat == 8.10.7 # 2022-02-17: preserve for GHC 8.10.7
- ghc-api-compat == 8.6 # 2021-09-07: preserve for GHC 8.8.4
- ghc-exactprint == 0.6.* # 2022-12-12: needed for GHC < 9.2
- ghc-exactprint == 1.6.* # 2023-03-30: needed for GHC == 9.4
- ghc-lib == 8.10.7.* # 2022-02-17: preserve for GHC 8.10.7
- ghc-lib == 9.2.* # 2022-02-17: preserve for GHC 9.2
- ghc-lib == 9.4.* # 2023-03-17: preserve for GHC 9.4
@ -88,6 +90,7 @@ extra-packages:
- ghc-lib-parser-ex == 8.10.* # 2022-02-17: preserve for GHC 8.10.7
- ghc-lib-parser-ex == 9.2.* # 2022-07-13: preserve for GHC 9.2
- ghc-lib-parser-ex == 9.4.* # 2023-03-17: preserve for GHC 9.4
- gi-soup == 2.4.28 # 2023-04-05: the last version to support libsoup-2.4 (and thus be compatible with our other gi- packages)
- haddock == 2.23.* # required on GHC < 8.10.x
- haddock-api == 2.23.* # required on GHC < 8.10.x
- haddock-library ==1.7.* # required by stylish-cabal-0.5.0.0
@ -129,6 +132,7 @@ extra-packages:
- retrie < 1.2.0.0 # 2022-12-30: required for hls on ghc < 9.2
- ghc-tags == 1.5.* # 2023-02-18: preserve for ghc-lib == 9.2.*
- primitive == 0.7.4.0 # 2023-03-04: primitive 0.8 is not compatible with too many packages on ghc 9.4 as of now
- fourmolu == 0.10.0.0 # 2023-04-03: for hls-fourmolu-plugin 1.1.1.0
package-maintainers:
abbradar:

149
pkgs/development/haskell-modules/configuration-hackage2nix/stackage.yaml
View file

@ -1,4 +1,4 @@
# Stackage LTS 20.14
# Stackage LTS 20.16
# This file is auto-generated by
# maintainers/scripts/haskell/update-stackage.sh
default-package-overrides:
@ -26,7 +26,7 @@ default-package-overrides:
- aeson-commit ==1.6.0
- aeson-compat ==0.3.10
- aeson-diff ==1.1.0.13
- aeson-extra ==0.5.1.1
- aeson-extra ==0.5.1.2
- aeson-generic-compat ==0.0.1.3
- aeson-iproute ==0.3.0
- aeson-optics ==1.2.0.1
@ -200,7 +200,7 @@ default-package-overrides:
- bits ==0.6
- bitset-word8 ==0.1.1.2
- bits-extra ==0.0.2.3
- bitvec ==1.1.3.0
- bitvec ==1.1.4.0
- bitwise-enum ==1.0.1.0
- blake2 ==0.3.0
- Blammo ==1.1.1.1
@ -230,14 +230,14 @@ default-package-overrides:
- boomerang ==1.4.8.1
- boots ==0.2.0.1
- bordacount ==0.1.0.0
- boring ==0.2
- boring ==0.2.1
- bound ==2.0.6
- BoundedChan ==1.0.3.0
- bounded-queue ==1.0.0
- boundingboxes ==0.2.3
- bower-json ==1.1.0.0
- boxes ==0.1.5
- breakpoint ==0.1.2.0
- breakpoint ==0.1.2.1
- brick ==1.4
- broadcast-chan ==0.2.1.2
- brotli ==0.0.0.1
@ -253,7 +253,7 @@ default-package-overrides:
- bugsnag-wai ==1.0.0.1
- bugsnag-yesod ==1.0.0.1
- bugzilla-redhat ==1.0.1
- burrito ==2.0.1.3
- burrito ==2.0.1.5
- butcher ==1.3.3.2
- bv ==0.5
- byteable ==0.1.1
@ -269,13 +269,13 @@ default-package-overrides:
- bytesmith ==0.3.9.1
- bytestring-builder ==0.10.8.2.0
- bytestring-conversion ==0.3.2
- bytestring-lexing ==0.5.0.9
- bytestring-lexing ==0.5.0.10
- bytestring-mmap ==0.2.2
- bytestring-progress ==1.4
- bytestring-strict-builder ==0.4.5.6
- bytestring-to-vector ==0.3.0.1
- bytestring-tree-builder ==0.2.7.10
- bytestring-trie ==0.2.7
- bytestring-trie ==0.2.7.2
- bz2 ==1.0.1.0
- bzlib-conduit ==0.3.0.2
- c14n ==0.1.0.2
@ -287,7 +287,7 @@ default-package-overrides:
- cabal-doctest ==1.0.9
- cabal-file ==0.1.1
- cabal-file-th ==0.2.7
- cabal-flatpak ==0.1.0.3
- cabal-flatpak ==0.1.0.4
- cabal-plan ==0.7.2.3
- cabal-rpm ==2.0.11.1
- Cabal-syntax ==3.6.0.0
@ -296,7 +296,7 @@ default-package-overrides:
- cacophony ==0.10.1
- cairo ==0.13.8.2
- calendar-recycling ==0.0.0.1
- call-alloy ==0.4.0.2
- call-alloy ==0.4.0.3
- calligraphy ==0.1.4
- call-plantuml ==0.0.1.1
- call-stack ==0.4.0
@ -365,7 +365,7 @@ default-package-overrides:
- cmark ==0.6
- cmark-gfm ==0.2.5
- cmark-lucid ==0.1.0.0
- cmdargs ==0.10.21
- cmdargs ==0.10.22
- codec-beam ==0.2.0
- code-conjure ==0.5.2
- code-page ==0.2.1
@ -502,7 +502,7 @@ default-package-overrides:
- cursor-brick ==0.1.0.1
- cursor-fuzzy-time ==0.0.0.0
- cursor-gen ==0.4.0.0
- cyclotomic ==1.1.1
- cyclotomic ==1.1.2
- czipwith ==1.0.1.4
- d10 ==1.0.1.2
- data-accessor ==0.2.3.1
@ -597,7 +597,7 @@ default-package-overrides:
- dictionary-sharing ==0.1.0.0
- di-df1 ==1.2.1
- Diff ==0.4.1
- digest ==0.0.1.6
- digest ==0.0.1.7
- digits ==0.3.1
- di-handle ==1.0.1
- dimensional ==1.5
@ -613,14 +613,14 @@ default-package-overrides:
- distributive ==0.6.2.1
- diversity ==0.8.1.0
- djinn-lib ==0.0.1.4
- dl-fedora ==0.9.3
- dl-fedora ==0.9.4
- dlist ==1.0
- dlist-instances ==0.1.1.1
- dlist-nonempty ==0.1.2
- dns ==4.1.0
- docker ==0.7.0.1
- dockerfile ==0.2.0
- doclayout ==0.4
- doclayout ==0.4.0.1
- doctemplates ==0.10.0.2
- doctest ==0.20.1
- doctest-discover ==0.2.0.0
@ -658,7 +658,7 @@ default-package-overrides:
- dyre ==0.9.1
- eap ==0.9.0.2
- Earley ==0.13.0.1
- easy-file ==0.2.2
- easy-file ==0.2.3
- easy-logger ==0.1.0.7
- Ebnf2ps ==1.0.15
- echo ==0.1.4
@ -669,7 +669,7 @@ default-package-overrides:
- edit-distance-vector ==1.0.0.4
- editor-open ==0.6.0.0
- effectful ==2.2.2.0
- effectful-core ==2.2.2.1
- effectful-core ==2.2.2.2
- effectful-plugin ==1.0.0.0
- effectful-th ==1.0.0.1
- either ==5.0.2
@ -726,7 +726,7 @@ default-package-overrides:
- exact-combinatorics ==0.2.0.11
- exact-pi ==0.5.0.2
- exception-hierarchy ==0.1.0.8
- exception-mtl ==0.4.0.1
- exception-mtl ==0.4.0.2
- exception-transformers ==0.4.0.11
- executable-hash ==0.2.0.4
- executable-path ==0.0.3.1
@ -801,7 +801,7 @@ default-package-overrides:
- flexible-defaults ==0.0.3
- FloatingHex ==0.5
- floatshow ==0.2.4
- flow ==2.0.0.2
- flow ==2.0.0.3
- flush-queue ==1.0.0
- fmlist ==0.9.4
- fmt ==0.6.3.0
@ -841,7 +841,7 @@ default-package-overrides:
- function-builder ==0.3.0.1
- functor-classes-compat ==2.0.0.2
- fused-effects ==1.1.2.1
- fusion-plugin ==0.2.5
- fusion-plugin ==0.2.6
- fusion-plugin-types ==0.1.0
- fuzzcheck ==0.1.1
- fuzzy ==0.1.0.1
@ -953,7 +953,7 @@ default-package-overrides:
- gi-pango ==1.0.27
- githash ==0.1.6.3
- github ==0.28.0.1
- github-release ==2.0.0.3
- github-release ==2.0.0.5
- github-rest ==1.1.2
- github-types ==0.2.1
- github-webhooks ==0.16.0
@ -1028,7 +1028,7 @@ default-package-overrides:
- hashmap ==1.3.3
- hashtables ==1.3.1
- haskeline ==0.8.2.1
- haskell-gi ==0.26.3
- haskell-gi ==0.26.4
- haskell-gi-base ==0.26.3
- haskell-gi-overloading ==1.0
- haskell-lexer ==1.1.1
@ -1038,7 +1038,7 @@ default-package-overrides:
- haskell-src-exts ==1.23.1
- haskell-src-exts-simple ==1.23.0.0
- haskell-src-exts-util ==0.2.5
- haskell-src-meta ==0.8.11
- haskell-src-meta ==0.8.12
- haskey-btree ==0.3.0.1
- haskintex ==0.8.0.1
- haskoin-core ==0.21.2
@ -1058,7 +1058,7 @@ default-package-overrides:
- hasty-hamiltonian ==1.3.4
- HaTeX ==3.22.3.2
- HaXml ==1.25.12
- haxr ==3000.11.4.1
- haxr ==3000.11.5
- HCodecs ==0.5.2
- hdaemonize ==0.5.6
- HDBC ==2.4.0.4
@ -1135,7 +1135,7 @@ default-package-overrides:
- hpack-dhall ==0.5.7
- hpc-codecov ==0.3.0.0
- hpc-lcov ==1.1.0
- HPDF ==1.6.0
- HPDF ==1.6.1
- hpp ==0.6.5
- hpqtypes ==1.9.4.0
- hreader ==1.1.0
@ -1308,14 +1308,14 @@ default-package-overrides:
- indexed-containers ==0.1.0.2
- indexed-list-literals ==0.2.1.3
- indexed-profunctors ==0.1.1
- indexed-traversable ==0.1.2
- indexed-traversable ==0.1.2.1
- indexed-traversable-instances ==0.1.1.2
- infer-license ==0.2.0
- inflections ==0.4.0.6
- influxdb ==1.9.2.2
- ini ==0.4.2
- inj ==1.0
- inline-c ==0.9.1.6
- inline-c ==0.9.1.7
- inline-c-cpp ==0.5.0.0
- inliterate ==0.1.0
- input-parsers ==0.2.3.2
@ -1335,7 +1335,7 @@ default-package-overrides:
- intset-imperative ==0.1.0.0
- invariant ==0.6.1
- invert ==1.0.0.2
- invertible-grammar ==0.1.3.3
- invertible-grammar ==0.1.3.4
- io-machine ==0.2.0.0
- io-manager ==0.1.0.4
- io-memoize ==1.1.1.0
@ -1369,7 +1369,7 @@ default-package-overrides:
- java-adt ==0.2018.11.4
- jira-wiki-markup ==1.4.0
- jl ==0.1.0
- jmacro ==0.6.17.1
- jmacro ==0.6.18
- jose ==0.9
- jose-jwt ==0.9.4
- js-chart ==2.9.4.1
@ -1377,7 +1377,7 @@ default-package-overrides:
- js-flot ==0.8.3
- js-jquery ==3.3.1
- json ==0.10
- json-feed ==2.0.0.5
- json-feed ==2.0.0.7
- jsonifier ==0.2.1.2
- jsonpath ==0.3.0.0
- json-rpc ==1.0.4
@ -1391,7 +1391,7 @@ default-package-overrides:
- kan-extensions ==5.2.5
- kanji ==3.5.0
- kansas-comet ==0.4.1
- katip ==0.8.7.2
- katip ==0.8.7.3
- katip-logstash ==0.1.0.2
- katip-wai ==0.1.2.1
- kazura-queue ==0.1.0.4
@ -1410,13 +1410,13 @@ default-package-overrides:
- koji ==0.0.2
- l10n ==0.1.0.1
- labels ==0.3.3
- lackey ==2.0.0.4
- lackey ==2.0.0.5
- LambdaHack ==0.11.0.0
- lame ==0.2.0
- language-avro ==0.1.4.0
- language-bash ==0.9.2
- language-c ==0.9.2
- language-c-quote ==0.13
- language-c-quote ==0.13.0.1
- language-docker ==12.0.0
- language-dot ==0.1.1
- language-glsl ==0.3.0
@ -1453,7 +1453,7 @@ default-package-overrides:
- lens-properties ==4.11.1
- lens-regex ==0.1.3
- lens-regex-pcre ==1.1.0.0
- lentil ==1.5.5.0
- lentil ==1.5.5.1
- LetsBeRational ==1.0.0.0
- leveldb-haskell ==0.6.5
- lexer-applicative ==2.1.0.2
@ -1464,15 +1464,15 @@ default-package-overrides:
- libmpd ==0.10.0.0
- liboath-hs ==0.0.1.2
- libyaml ==0.1.2
- lifted-async ==0.10.2.3
- lifted-async ==0.10.2.4
- lifted-base ==0.2.3.12
- lift-generics ==0.2.1
- lift-type ==0.1.1.1
- line ==4.0.1
- linear ==1.21.10
- linear-base ==0.3.0
- linear-base ==0.3.1
- linear-generics ==0.2.1
- linebreak ==1.1.0.2
- linebreak ==1.1.0.3
- linenoise ==0.3.2
- linux-capabilities ==0.1.1.0
- linux-file-extents ==0.2.0.0
@ -1485,7 +1485,7 @@ default-package-overrides:
- list-transformer ==1.0.9
- ListTree ==0.2.3
- ListZipper ==1.2.0.2
- literatex ==0.2.0.2
- literatex ==0.2.1.0
- little-logger ==1.0.1
- little-rio ==1.0.1
- lmdb ==0.2.5
@ -1504,11 +1504,11 @@ default-package-overrides:
- logict ==0.8.0.0
- logstash ==0.1.0.3
- loop ==0.3.0
- lpeg ==1.0.3
- lpeg ==1.0.4
- lrucache ==1.2.0.1
- lrucaching ==0.3.3
- lua ==2.2.1
- lua-arbitrary ==1.0.1
- lua-arbitrary ==1.0.1.1
- lucid2 ==0.0.20221012
- lucid ==2.11.1
- lucid-cdn ==0.2.2.0
@ -1556,7 +1556,7 @@ default-package-overrides:
- mega-sdist ==0.4.2.1
- membership ==0.0.1
- memcache ==0.3.0.1
- memfd ==1.0.1.1
- memfd ==1.0.1.3
- memory ==0.17.0
- MemoTrie ==0.6.10
- mergeful ==0.3.0.0
@ -1669,7 +1669,7 @@ default-package-overrides:
- mpi-hs-cereal ==0.1.0.0
- mstate ==0.2.8
- mtl-compat ==0.2.2
- mtl-prelude ==2.0.3.1
- mtl-prelude ==2.0.3.2
- multiarg ==0.30.0.10
- multi-containers ==0.2
- multimap ==1.2.1
@ -1725,7 +1725,7 @@ default-package-overrides:
- Network-NineP ==0.4.7.2
- network-run ==0.2.4
- network-simple ==0.4.5
- network-simple-tls ==0.4
- network-simple-tls ==0.4.1
- network-transport ==0.5.6
- network-uri ==2.6.4.2
- network-wait ==0.2.0.0
@ -2033,11 +2033,11 @@ default-package-overrides:
- pusher-http-haskell ==2.1.0.12
- pvar ==1.0.0.0
- pwstore-fast ==2.4.4
- PyF ==0.11.1.0
- PyF ==0.11.1.1
- qchas ==1.1.0.1
- qm-interpolated-string ==0.3.1.0
- qrcode-core ==0.9.5
- qrcode-juicypixels ==0.8.3
- qrcode-core ==0.9.6
- qrcode-juicypixels ==0.8.4
- quadratic-irrational ==0.1.1
- QuasiText ==0.1.2.6
- QuickCheck ==2.14.2
@ -2061,7 +2061,7 @@ default-package-overrides:
- rainbow ==0.34.2.2
- rainbox ==0.26.0.0
- ral ==0.2.1
- rampart ==2.0.0.4
- rampart ==2.0.0.5
- ramus ==0.1.2
- rando ==0.0.0.4
- random ==1.2.1.1
@ -2078,12 +2078,12 @@ default-package-overrides:
- rank2classes ==1.4.6
- Rasterific ==0.7.5.4
- rasterific-svg ==0.3.3.2
- ratel ==2.0.0.5
- ratel-wai ==2.0.0.2
- ratel ==2.0.0.7
- ratel-wai ==2.0.0.4
- ratio-int ==0.1.2
- rattle ==0.2
- rattletrap ==11.2.14
- Rattus ==0.5.0.1
- Rattus ==0.5.1
- rawfilepath ==1.0.1
- rawstring-qm ==0.2.3.0
- raw-strings-qq ==1.1
@ -2199,12 +2199,12 @@ default-package-overrides:
- safe-json ==1.1.3.1
- safe-money ==0.9.1
- SafeSemaphore ==0.10.1
- salve ==2.0.0.2
- salve ==2.0.0.3
- sample-frame ==0.0.4
- sample-frame-np ==0.0.5
- sampling ==0.3.5
- sandi ==0.5
- sandwich ==0.1.2.0
- sandwich ==0.1.3.0
- sandwich-hedgehog ==0.1.1.0
- sandwich-quickcheck ==0.1.0.6
- sandwich-slack ==0.1.1.0
@ -2305,7 +2305,7 @@ default-package-overrides:
- setlocale ==1.0.0.10
- set-monad ==0.3.0.0
- sets ==0.0.6.2
- sexp-grammar ==2.3.4.0
- sexp-grammar ==2.3.4.1
- sexpr-parser ==0.2.2.0
- SHA ==1.6.4.4
- shake ==0.19.7
@ -2314,7 +2314,7 @@ default-package-overrides:
- shake-plus-extended ==0.4.1.0
- shakespeare ==2.0.30
- shakespeare-text ==1.1.0
- shared-memory ==0.2.0.0
- shared-memory ==0.2.0.1
- shell-conduit ==5.0.0
- shell-escape ==0.2.0
- shellmet ==0.0.4.1
@ -2417,14 +2417,14 @@ default-package-overrides:
- statistics ==0.16.1.2
- status-notifier-item ==0.3.1.0
- stb-image-redux ==0.2.1.2
- step-function ==0.2
- step-function ==0.2.0.1
- stitch ==0.6.0.0
- stm-chans ==3.0.0.6
- stm-chans ==3.0.0.9
- stm-conduit ==4.0.1
- stm-containers ==1.2.0.2
- stm-delay ==0.1.1.1
- stm-extras ==0.1.0.3
- stm-hamt ==1.2.0.9
- stm-hamt ==1.2.0.10
- stm-lifted ==2.5.0.0
- STMonadTrans ==0.4.6
- stm-split ==0.0.2.1
@ -2446,7 +2446,7 @@ default-package-overrides:
- streaming-commons ==0.2.2.5
- streaming-wai ==0.1.1
- streamly ==0.8.1.1
- streams ==3.3.1
- streams ==3.3.2
- streamt ==0.5.0.1
- strict ==0.4.0.1
- strict-base-types ==0.7
@ -2471,23 +2471,23 @@ default-package-overrides:
- stripe-scotty ==1.1.0.3
- stripe-signature ==1.0.0.15
- stripe-wreq ==1.0.1.15
- strive ==6.0.0.5
- strive ==6.0.0.7
- strongweak ==0.3.2
- structs ==0.1.8
- structured ==0.1.1
- structured-cli ==2.7.0.1
- stylish-haskell ==0.14.3.0
- subcategories ==0.2.0.0
- subcategories ==0.2.0.1
- sundown ==0.6
- superbuffer ==0.3.1.2
- svg-builder ==0.1.1
- SVGFonts ==1.8.0.1
- svg-tree ==0.6.2.4
- swagger2 ==2.8.6
- swish ==0.10.3.0
- syb ==0.7.2.2
- swish ==0.10.4.0
- syb ==0.7.2.3
- syb-with-class ==0.6.1.14
- sydtest ==0.13.0.1
- sydtest ==0.13.0.2
- sydtest-aeson ==0.1.0.0
- sydtest-amqp ==0.1.0.0
- sydtest-autodocodec ==0.0.0.0
@ -2575,7 +2575,7 @@ default-package-overrides:
- termbox-bindings-hs ==0.1.0
- termbox-tea ==0.1.0
- terminal-progress-bar ==0.4.1
- terminal-size ==0.3.3
- terminal-size ==0.3.4
- termonad ==4.4.0.0
- test-framework ==0.8.2.0
- test-framework-hunit ==0.3.0.2
@ -2650,7 +2650,7 @@ default-package-overrides:
- time-manager ==0.0.0
- time-parsers ==0.1.2.1
- timerep ==2.1.0.0
- timers-tick ==0.5.0.2
- timers-tick ==0.5.0.3
- timer-wheel ==0.4.0.1
- timespan ==0.4.0.0
- time-units ==1.0.0
@ -2674,7 +2674,7 @@ default-package-overrides:
- toml-reader ==0.2.0.0
- tophat ==1.0.5.1
- topograph ==1.0.0.2
- torrent ==10000.1.1
- torrent ==10000.1.3
- torsor ==0.1
- tostring ==0.2.1.1
- tracing ==0.0.7.3
@ -2694,7 +2694,7 @@ default-package-overrides:
- triplesec ==0.2.2.1
- trivial-constraint ==0.7.0.0
- tsv2csv ==0.1.0.2
- ttc ==1.2.0.0
- ttc ==1.2.1.0
- ttrie ==0.1.2.2
- tuple ==0.3.0.2
- tuples ==0.1.0.0
@ -2726,7 +2726,7 @@ default-package-overrides:
- type-spec ==0.4.0.0
- typography-geometry ==1.0.1.0
- tz ==0.1.3.6
- tzdata ==0.2.20221129.0
- tzdata ==0.2.20230322.0
- tztime ==0.1.0.0
- ua-parser ==0.7.7.0
- uglymemo ==0.1.0.1
@ -2742,7 +2742,7 @@ default-package-overrides:
- unexceptionalio-trans ==0.5.1
- unfork ==1.0.0.1
- unicode ==0.0.1.1
- unicode-collation ==0.1.3.3
- unicode-collation ==0.1.3.4
- unicode-data ==0.3.1
- unicode-show ==0.1.1.1
- unicode-transforms ==0.4.0.1
@ -2759,7 +2759,7 @@ default-package-overrides:
- unit-constraint ==0.0.0
- units-parser ==0.1.1.4
- universe ==1.2.2
- universe-base ==1.1.3
- universe-base ==1.1.3.1
- universe-dependent-sum ==1.3
- universe-instances-extended ==1.1.3
- universe-reverse-instances ==1.1.1
@ -2767,7 +2767,7 @@ default-package-overrides:
- universum ==1.8.1.1
- unix-bytestring ==0.3.7.8
- unix-compat ==0.5.4
- unix-time ==0.4.8
- unix-time ==0.4.9
- unjson ==0.15.4
- unliftio ==0.2.24.0
- unliftio-core ==0.2.1.0
@ -2834,7 +2834,7 @@ default-package-overrides:
- vector-stream ==0.1.0.0
- vector-th-unbox ==0.2.2
- verbosity ==0.4.0.0
- versions ==5.0.4
- versions ==5.0.5
- vformat ==0.14.1.0
- vformat-time ==0.1.0.0
- ViennaRNAParser ==1.3.3
@ -2902,7 +2902,6 @@ default-package-overrides:
- Win32-notify ==0.3.0.3
- windns ==0.1.0.1
- witch ==1.1.6.1
with-compiler: ghc-9.2.7
- withdependencies ==0.3.0
- witherable ==0.4.2
- within ==0.2.0.1
@ -2926,7 +2925,7 @@ with-compiler: ghc-9.2.7
- writer-cps-mtl ==0.1.1.6
- writer-cps-transformers ==0.5.6.1
- wss-client ==0.3.0.0
- wuss ==2.0.1.1
- wuss ==2.0.1.3
- X11 ==1.10.3
- X11-xft ==0.3.4
- x11-xim ==0.0.9.0
@ -2946,7 +2945,7 @@ with-compiler: ghc-9.2.7
- xmlbf ==0.6.2
- xmlbf-xeno ==0.2.1
- xmlbf-xmlhtml ==0.2
- xml-conduit ==1.9.1.1
- xml-conduit ==1.9.1.2
- xml-conduit-writer ==0.1.1.2
- xmlgen ==0.6.2.2
- xml-hamlet ==0.5.0.2

26
pkgs/development/haskell-modules/configuration-hackage2nix/transitive-broken.yaml
View file

@ -900,6 +900,7 @@ dont-distribute-packages:
- call
- camfort
- campfire
- canadian-income-tax
- canteven-http
- cao
- cap
@ -1193,6 +1194,7 @@ dont-distribute-packages:
- debug
- decidable
- decimal-arithmetic
- declarative
- dedukti
- deeplearning-hs
- deepzoom
@ -1478,6 +1480,7 @@ dont-distribute-packages:
- finite-table
- firestore
- firstify
- fishfood
- fix-parser-simple
- fixed-point-vector
- fixed-point-vector-space
@ -1505,6 +1508,7 @@ dont-distribute-packages:
- format-status
- formlets
- formlets-hsp
- forms-data-format
- forsyde-deep
- forth-hll
- fortran-vars
@ -1515,7 +1519,7 @@ dont-distribute-packages:
- fpnla-examples
- frame-markdown
- freckle-app
- freckle-app_1_8_1_0
- freckle-app_1_9_0_0
- free-functors
- free-game
- free-theorems-counterexamples
@ -1614,7 +1618,7 @@ dont-distribute-packages:
- gi-gsk
- gi-gstpbutils
- gi-gtk-declarative-app-simple
- gi-gtk_4_0_6
- gi-gtk_4_0_8
- git-config
- git-fmt
- git-gpush
@ -2211,6 +2215,7 @@ dont-distribute-packages:
- hpaco-lib
- hpage
- hpaste
- hpath-io
- hpc-tracer
- hplayground
- hpqtypes-effectful
@ -2260,6 +2265,11 @@ dont-distribute-packages:
- hsfacter
- hsinspect-lsp
- hslogstash
- hslua-cli
- hslua-module-zip
- hslua-objectorientation_2_3_0
- hslua-packaging_2_3_0
- hslua_2_3_0
- hsndfile-storablevector
- hspec-expectations-pretty
- hspec-pg-transact
@ -2335,6 +2345,7 @@ dont-distribute-packages:
- hyper-extra
- hyper-haskell-server
- hyperpublic
- i
- iException
- ice40-prim
- ide-backend
@ -2505,6 +2516,7 @@ dont-distribute-packages:
- keyword-args
- kicad-data
- kif-parser
- kind-rational
- kit
- kmeans-par
- kmeans-vector
@ -3007,7 +3019,7 @@ dont-distribute-packages:
- padKONTROL
- pairing
- panda
- pandoc-crossref_0_3_15_1
- pandoc-crossref_0_3_15_2
- pandoc-highlighting-extensions
- pandoc-japanese-filters
- pandora-io
@ -3336,6 +3348,7 @@ dont-distribute-packages:
- reflex-localize
- reflex-localize-dom
- reflex-monad-auth
- reflex-potatoes
- reflex-process
- refractor
- reg-alloc-graph-color
@ -3724,6 +3737,7 @@ dont-distribute-packages:
- squeal-postgresql
- squeal-postgresql-ltree
- squeal-postgresql-uuid-ossp
- squeeze
- sr-extra
- sscgi
- sshd-lint
@ -3912,6 +3926,7 @@ dont-distribute-packages:
- timezone-unix
- tinkoff-invest-sdk
- tintin
- tinytools
- tip-haskell-frontend
- tip-lib
- titan
@ -4024,7 +4039,11 @@ dont-distribute-packages:
- uni-reactor
- uni-uDrawGraph
- unicode-normalization
- uniform-http
- uniform-io
- uniform-latex2pdf
- uniform-pandoc
- uniform-shake
- uniqueness-periods
- uniqueness-periods-vector-examples
- uniqueness-periods-vector-filters
@ -4133,6 +4152,7 @@ dont-distribute-packages:
- wai-transformers
- waldo
- warp-grpc
- warp-quic
- warped
- wavesurfer
- wavy

245
pkgs/development/haskell-modules/configuration-nix.nix
View file

@ -49,6 +49,134 @@ self: super: builtins.intersectAttrs super {
# Apply NixOS-specific patches.
ghc-paths = appendPatch ./patches/ghc-paths-nix.patch super.ghc-paths;
#######################################
### HASKELL-LANGUAGE-SERVER SECTION ###
#######################################
haskell-language-server = overrideCabal (drv: {
# starting with 1.6.1.1 haskell-language-server wants to be linked dynamically
# by default. Unless we reflect this in the generic builder, GHC is going to
# produce some illegal references to /build/.
enableSharedExecutables = true;
# The shell script wrapper checks that the runtime ghc and its boot packages match the ghc hls was compiled with.
# This prevents linking issues when running TH splices.
postInstall = ''
mv "$out/bin/haskell-language-server" "$out/bin/.haskell-language-server-${self.ghc.version}-unwrapped"
BOOT_PKGS=`ghc-pkg-${self.ghc.version} --global list --simple-output`
${pkgs.buildPackages.gnused}/bin/sed \
-e "s!@@EXE_DIR@@!$out/bin!" \
-e "s/@@EXE_NAME@@/.haskell-language-server-${self.ghc.version}-unwrapped/" \
-e "s/@@GHC_VERSION@@/${self.ghc.version}/" \
-e "s/@@BOOT_PKGS@@/$BOOT_PKGS/" \
-e "s/@@ABI_HASHES@@/$(for dep in $BOOT_PKGS; do printf "%s:" "$dep" && ghc-pkg-${self.ghc.version} field $dep abi --simple-output ; done | tr '\n' ' ' | xargs)/" \
-e "s!Consider installing ghc.* via ghcup or build HLS from source.!Visit https://haskell4nix.readthedocs.io/nixpkgs-users-guide.html#how-to-install-haskell-language-server to learn how to correctly install a matching hls for your ghc with nix.!" \
bindist/wrapper.in > "$out/bin/haskell-language-server"
ln -s "$out/bin/haskell-language-server" "$out/bin/haskell-language-server-${self.ghc.version}"
chmod +x "$out/bin/haskell-language-server"
'';
testToolDepends = [ self.cabal-install pkgs.git ];
testTarget = "func-test"; # wrapper test accesses internet
preCheck = ''
export PATH=$PATH:$PWD/dist/build/haskell-language-server:$PWD/dist/build/haskell-language-server-wrapper
export HOME=$TMPDIR
'';
}) super.haskell-language-server;
# ghcide-bench tests need network
ghcide-bench = dontCheck super.ghcide-bench;
# 2023-04-01: TODO: Either reenable at least some tests or remove the preCheck override
ghcide = overrideCabal (drv: {
# tests depend on executable
preCheck = ''export PATH="$PWD/dist/build/ghcide:$PATH"'';
# tests disabled because they require network
doCheck = false;
}) super.ghcide;
hiedb = overrideCabal (drv: {
preCheck = ''
export PATH=$PWD/dist/build/hiedb:$PATH
'';
}) super.hiedb;
# Tests access homeless-shelter.
hie-bios = dontCheck super.hie-bios;
# PLUGINS WITH ENABLED TESTS
# haskell-language-server plugins all use the same test harness so we give them what they want in this loop.
# Every hls plugin should either be in the test disabled list below, or up here in the list fixing it’s tests.
inherit (pkgs.lib.mapAttrs
(_: overrideCabal (drv: {
testToolDepends = (drv.testToolDepends or [ ]) ++ [ pkgs.git ];
preCheck = ''
export HOME=$TMPDIR/home
'' + (drv.preCheck or "");
}))
super)
hls-brittany-plugin
hls-floskell-plugin
hls-fourmolu-plugin
hls-cabal-plugin
;
# PLUGINS WITH DISABLED TESTS
# 2023-04-01: TODO: We should reenable all these tests to figure if they are still broken.
inherit (pkgs.lib.mapAttrs (_: dontCheck) super)
# Tests have file permissions expections that don’t work with the nix store.
hls-gadt-plugin
# https://github.com/haskell/haskell-language-server/pull/3431
hls-cabal-fmt-plugin
hls-code-range-plugin
hls-explicit-record-fields-plugin
# Flaky tests
hls-explicit-fixity-plugin
hls-hlint-plugin
hls-pragmas-plugin
hls-class-plugin
hls-rename-plugin
hls-alternate-number-format-plugin
hls-qualify-imported-names-plugin
hls-haddock-comments-plugin
hls-tactics-plugin
hls-call-hierarchy-plugin
hls-selection-range-plugin
hls-ormolu-plugin
# 2021-05-08: Tests fail: https://github.com/haskell/haskell-language-server/issues/1809
hls-eval-plugin
# 2021-06-20: Tests fail: https://github.com/haskell/haskell-language-server/issues/1949
hls-refine-imports-plugin
# 2021-11-20: https://github.com/haskell/haskell-language-server/pull/2373
hls-explicit-imports-plugin
# 2021-11-20: https://github.com/haskell/haskell-language-server/pull/2374
hls-module-name-plugin
# 2022-09-19: https://github.com/haskell/haskell-language-server/issues/3200
hls-refactor-plugin
# 2021-09-14: Tests are flaky.
hls-splice-plugin
# 2021-09-18: https://github.com/haskell/haskell-language-server/issues/2205
hls-stylish-haskell-plugin
# Necesssary .txt files are not included in sdist.
# https://github.com/haskell/haskell-language-server/pull/2887
hls-change-type-signature-plugin
# 2023-04-03: https://github.com/haskell/haskell-language-server/issues/3549
hls-retrie-plugin
;
###########################################
### END HASKELL-LANGUAGE-SERVER SECTION ###
###########################################
# fix errors caused by hardening flags
epanet-haskell = disableHardening ["format"] super.epanet-haskell;
@ -354,11 +482,6 @@ self: super: builtins.intersectAttrs super {
# Looks like Avahi provides the missing library
dnssd = super.dnssd.override { dns_sd = pkgs.avahi.override { withLibdnssdCompat = true; }; };
# tests depend on executable
ghcide = overrideCabal (drv: {
preCheck = ''export PATH="$PWD/dist/build/ghcide:$PATH"'';
}) super.ghcide;
# Tests execute goldplate
goldplate = overrideCabal (drv: {
preCheck = drv.preCheck or "" + ''
@ -685,9 +808,6 @@ self: super: builtins.intersectAttrs super {
'';
}) (addBuildTool pkgs.buildPackages.makeWrapper super.cut-the-crap);
# Tests access homeless-shelter.
hie-bios = dontCheck super.hie-bios;
# Compiling the readme throws errors and has no purpose in nixpkgs
aeson-gadt-th =
disableCabalFlag "build-readme" (doJailbreak super.aeson-gadt-th);
@ -712,34 +832,6 @@ self: super: builtins.intersectAttrs super {
retrie_1_2_0_0 = addTestToolDepends [pkgs.git pkgs.mercurial] super.retrie_1_2_0_0;
retrie_1_2_1_1 = addTestToolDepends [pkgs.git pkgs.mercurial] super.retrie_1_2_1_1;
haskell-language-server = overrideCabal (drv: {
# starting with 1.6.1.1 haskell-language-server wants to be linked dynamically
# by default. Unless we reflect this in the generic builder, GHC is going to
# produce some illegal references to /build/.
enableSharedExecutables = true;
# The shell script wrapper checks that the runtime ghc and its boot packages match the ghc hls was compiled with.
# This prevents linking issues when running TH splices.
postInstall = ''
mv "$out/bin/haskell-language-server" "$out/bin/.haskell-language-server-${self.ghc.version}-unwrapped"
BOOT_PKGS=`ghc-pkg-${self.ghc.version} --global list --simple-output`
${pkgs.buildPackages.gnused}/bin/sed \
-e "s!@@EXE_DIR@@!$out/bin!" \
-e "s/@@EXE_NAME@@/.haskell-language-server-${self.ghc.version}-unwrapped/" \
-e "s/@@GHC_VERSION@@/${self.ghc.version}/" \
-e "s/@@BOOT_PKGS@@/$BOOT_PKGS/" \
-e "s/@@ABI_HASHES@@/$(for dep in $BOOT_PKGS; do printf "%s:" "$dep" && ghc-pkg-${self.ghc.version} field $dep abi --simple-output ; done | tr '\n' ' ' | xargs)/" \
-e "s!Consider installing ghc.* via ghcup or build HLS from source.!Visit https://haskell4nix.readthedocs.io/nixpkgs-users-guide.html#how-to-install-haskell-language-server to learn how to correctly install a matching hls for your ghc with nix.!" \
bindist/wrapper.in > "$out/bin/haskell-language-server"
ln -s "$out/bin/haskell-language-server" "$out/bin/haskell-language-server-${self.ghc.version}"
chmod +x "$out/bin/haskell-language-server"
'';
testToolDepends = [ self.cabal-install pkgs.git ];
testTarget = "func-test"; # wrapper test accesses internet
preCheck = ''
export PATH=$PATH:$PWD/dist/build/haskell-language-server:$PWD/dist/build/haskell-language-server-wrapper
export HOME=$TMPDIR
'';
}) super.haskell-language-server;
# there are three very heavy test suites that need external repos, one requires network access
hevm = dontCheck super.hevm;
@ -801,12 +893,6 @@ self: super: builtins.intersectAttrs super {
'' + drv.postInstall or "";
}) super.hlint;
hiedb = overrideCabal (drv: {
preCheck = ''
export PATH=$PWD/dist/build/hiedb:$PATH
'';
}) super.hiedb;
taglib = overrideCabal (drv: {
librarySystemDepends = [
pkgs.zlib
@ -885,34 +971,28 @@ self: super: builtins.intersectAttrs super {
# won't work (or would need to patch test suite).
domaindriven-core = dontCheck super.domaindriven-core;
cachix = overrideCabal (drv: {
version = "1.3.3";
cachix = overrideCabal (drv: {
version = "1.4.2";
src = pkgs.fetchFromGitHub {
owner = "cachix";
repo = "cachix";
rev = "v1.3.3";
sha256 = "sha256-xhLCsAkz5c+XIqQ4eGY9bSp3zBgCDCaHXZ2HLk8vqmE=";
rev = "v1.4.2";
sha256 = "sha256-EjfBM5O+wXJhthRU/Nd9VFue7xo5O93nx0pMt3jx0Ow=";
};
buildDepends = [ self.conduit-concurrent-map ];
postUnpack = "sourceRoot=$sourceRoot/cachix";
postPatch = ''
sed -i 's/1.3.2/1.3.3/' cachix.cabal
sed -i 's/1.4.1/1.4.2/' cachix.cabal
'';
}) (super.cachix.override {
nix = self.hercules-ci-cnix-store.passthru.nixPackage;
fsnotify = dontCheck super.fsnotify_0_4_1_0;
hnix-store-core = super.hnix-store-core_0_6_1_0;
});
cachix-api = overrideCabal (drv: {
version = "1.3.3";
src = pkgs.fetchFromGitHub {
owner = "cachix";
repo = "cachix";
rev = "v1.3.3";
sha256 = "sha256-xhLCsAkz5c+XIqQ4eGY9bSp3zBgCDCaHXZ2HLk8vqmE=";
};
postUnpack = "sourceRoot=$sourceRoot/cachix-api";
}) super.cachix-api;
cachix_1_3_3 = super.cachix_1_3_3.override {
nix = self.hercules-ci-cnix-store.nixPackage;
fsnotify = dontCheck super.fsnotify_0_4_1_0;
hnix-store-core = super.hnix-store-core_0_6_1_0;
};
hercules-ci-agent = super.hercules-ci-agent.override { nix = self.hercules-ci-cnix-store.passthru.nixPackage; };
hercules-ci-cnix-expr = addTestToolDepend pkgs.git (super.hercules-ci-cnix-expr.override { nix = self.hercules-ci-cnix-store.passthru.nixPackage; });
@ -1003,11 +1083,11 @@ self: super: builtins.intersectAttrs super {
}) super.fourmolu;
# Test suite wants to run main executable
fourmolu_0_10_1_0 = overrideCabal (drv: {
fourmolu_0_10_0_0 = overrideCabal (drv: {
preCheck = drv.preCheck or "" + ''
export PATH="$PWD/dist/build/fourmolu:$PATH"
'';
}) super.fourmolu_0_10_1_0;
}) super.fourmolu_0_10_0_0;
# Test suite needs to execute 'disco' binary
disco = overrideCabal (drv: {
@ -1125,47 +1205,4 @@ self: super: builtins.intersectAttrs super {
keid-render-basic = addBuildTool pkgs.glslang super.keid-render-basic;
# ghcide-bench tests need network
ghcide-bench = dontCheck super.ghcide-bench;
# haskell-language-server plugins all use the same test harness so we give them what we want in this loop.
} // pkgs.lib.mapAttrs
(_: overrideCabal (drv: {
testToolDepends = (drv.testToolDepends or [ ]) ++ [ pkgs.git ];
preCheck = ''
export HOME=$TMPDIR/home
'' + (drv.preCheck or "");
}))
{
inherit (super)
hls-brittany-plugin
hls-eval-plugin
hls-floskell-plugin
hls-fourmolu-plugin
hls-module-name-plugin
hls-splice-plugin
hls-refactor-plugin
hls-cabal-plugin;
# Tests have file permissions expections that don’t work with the nix store.
hls-stylish-haskell-plugin = dontCheck super.hls-stylish-haskell-plugin;
hls-gadt-plugin = dontCheck super.hls-gadt-plugin;
# https://github.com/haskell/haskell-language-server/pull/3431
hls-cabal-fmt-plugin = dontCheck super.hls-cabal-fmt-plugin;
hls-code-range-plugin = dontCheck super.hls-code-range-plugin;
hls-explicit-record-fields-plugin = dontCheck super.hls-explicit-record-fields-plugin;
# Flaky tests
hls-explicit-fixity-plugin = dontCheck super.hls-explicit-fixity-plugin;
hls-hlint-plugin = dontCheck super.hls-hlint-plugin;
hls-pragmas-plugin = dontCheck super.hls-pragmas-plugin;
hls-class-plugin = dontCheck super.hls-class-plugin;
hls-rename-plugin = dontCheck super.hls-rename-plugin;
hls-alternate-number-format-plugin = dontCheck super.hls-alternate-number-format-plugin;
hls-qualify-imported-names-plugin = dontCheck super.hls-qualify-imported-names-plugin;
hls-haddock-comments-plugin = dontCheck super.hls-haddock-comments-plugin;
hls-tactics-plugin = dontCheck super.hls-tactics-plugin;
hls-call-hierarchy-plugin = dontCheck super.hls-call-hierarchy-plugin;
hls-selection-range-plugin = dontCheck super.hls-selection-range-plugin;
hls-ormolu-plugin = dontCheck super.hls-ormolu-plugin;
}

5140
pkgs/development/haskell-modules/hackage-packages.nix generated
View file

File diff suppressed because it is too large Load diff

22
pkgs/development/libraries/gstreamer/default.nix
View file

@ -1,4 +1,19 @@
{ callPackage, AudioToolbox, AVFoundation, Cocoa, CoreFoundation, CoreMedia, CoreServices, CoreVideo, DiskArbitration, Foundation, IOKit, MediaToolbox, OpenGL, VideoToolbox }:
{ callPackage
, AVFoundation
, AudioToolbox
, Cocoa
, CoreFoundation
, CoreMedia
, CoreServices
, CoreVideo
, DiskArbitration
, Foundation
, IOKit
, MediaToolbox
, OpenGL
, VideoToolbox
, ipu6ep-camera-hal
}:
{
gstreamer = callPackage ./core { inherit CoreServices; };
@ -25,7 +40,10 @@
gst-vaapi = callPackage ./vaapi { };
icamerasrc = callPackage ./icamerasrc { };
icamerasrc-ipu6 = callPackage ./icamerasrc { };
icamerasrc-ipu6ep = callPackage ./icamerasrc {
ipu6-camera-hal = ipu6ep-camera-hal;
};
# note: gst-python is in ./python/default.nix - called under pythonPackages
}

12
pkgs/development/libraries/gstreamer/icamerasrc/default.nix
View file

@ -9,14 +9,14 @@
}:
stdenv.mkDerivation rec {
pname = "icamerasrc";
version = "20221209";
pname = "icamerasrc-${ipu6-camera-hal.ipuVersion}";
version = "unstable-2023-03-09";
src = fetchFromGitHub {
owner = "intel";
repo = "icamerasrc";
rev = "refs/tags/rpl_plat_${version}_pv";
hash = "sha256-qlV363l4tUjUAa1LiZQq55byKpz1tLESKAXEmgiYHVo=";
rev = "17841ab6249aaa69bd9b3959262bf182dee74111";
hash = "sha256-j8ZYe4nyy5yfo10CGeXDwbAaAPvdr0ptMWB8hQDyESQ=";
};
nativeBuildInputs = [
@ -45,6 +45,10 @@ stdenv.mkDerivation rec {
enableParallelBuilding = true;
passthru = {
inherit (ipu6-camera-hal) ipuVersion;
};
meta = with lib; {
description = "GStreamer Plugin for MIPI camera support through the IPU6/IPU6EP/IPU6SE on Intel Tigerlake/Alderlake/Jasperlake platforms";
homepage = "https://github.com/intel/icamerasrc/tree/icamerasrc_slim_api";

9
pkgs/development/libraries/howard-hinnant-date/default.nix
View file

@ -35,6 +35,15 @@ stdenv.mkDerivation rec {
})
];
# Tweaks to fix undefined variable substitutions
# https://github.com/HowardHinnant/date/pull/538#pullrequestreview-1373268697
postPatch = ''
substituteInPlace date.pc.in \
--replace '@CMAKE_INSTALL_LIB@' '@CMAKE_INSTALL_FULL_LIBDIR@' \
--replace '@CMAKE_INSTALL_INCLUDE@' '@CMAKE_INSTALL_FULL_INCLUDEDIR@' \
--replace '@PACKAGE_VERSION@' '${version}'
'';
nativeBuildInputs = [ cmake ];
cmakeFlags = [

28
pkgs/development/libraries/ipu6-camera-hal/default.nix
View file

@ -14,14 +14,14 @@
}:
stdenv.mkDerivation {
pname = "ipu6-camera-hal";
version = "unstable-2023-01-09";
pname = "${ipu6-camera-bin.ipuVersion}-camera-hal";
version = "unstable-2023-02-08";
src = fetchFromGitHub {
owner = "intel";
repo = "ipu6-camera-hal";
rev = "37292891c73367d22ba1fc96ea9b6e4546903037";
hash = "sha256-dJvTZt85rt5/v2JXOsfbSY933qffyXW74L0nWdIlqug=";
rev = "884b81aae0ea19a974eb8ccdaeef93038136bdd4";
hash = "sha256-AePL7IqoOhlxhfPRLpCman5DNh3wYS4MUcLgmgBUcCM=";
};
nativeBuildInputs = [
@ -52,16 +52,20 @@ stdenv.mkDerivation {
gst_all_1.gst-plugins-base
];
preFixup = ''
ls -lah $out/lib/pkgconfig/
sed -Ei \
-e "s,^prefix=.*,prefix=$out," \
-e "s,^exec_prefix=.*,exec_prefix=''${prefix}," \
-e "s,^libdir=.*,libdir=''${prefix}/lib," \
-e "s,^includedir=.*,includedir=''${prefix}/include/libcamhal," \
$out/lib/pkgconfig/libcamhal.pc
postPatch = ''
substituteInPlace src/platformdata/PlatformData.h \
--replace '/usr/share/' "${placeholder "out"}/share/"
'';
postFixup = ''
substituteInPlace $out/lib/pkgconfig/libcamhal.pc \
--replace 'prefix=/usr' "prefix=$out"
'';
passthru = {
inherit (ipu6-camera-bin) ipuVersion;
};
meta = with lib; {
description = "HAL for processing of images in userspace";
homepage = "https://github.com/intel/ipu6-camera-hal";

5
pkgs/development/libraries/libHX/default.nix
View file

@ -11,12 +11,11 @@ stdenv.mkDerivation rec {
patches = [];
nativeBuildInputs = [ autoconf automake ];
buildInputs = [ libtool ];
nativeBuildInputs = [ autoconf automake libtool ];
preConfigure = ''
sh autogen.sh
'';
'';
meta = with lib; {
homepage = "https://libhx.sourceforge.net/";

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

@ -24,7 +24,8 @@ stdenv.mkDerivation rec {
pname = "libchamplain";
version = "0.12.21";
outputs = [ "out" "dev" "devdoc" ];
outputs = [ "out" "dev" ]
++ lib.optionals (stdenv.buildPlatform == stdenv.hostPlatform) [ "devdoc" ];
src = fetchurl {
url = "mirror://gnome/sources/${pname}/${lib.versions.majorMinor version}/${pname}-${version}.tar.xz";
@ -37,6 +38,7 @@ stdenv.mkDerivation rec {
pkg-config
gobject-introspection
vala
] ++ lib.optionals (stdenv.buildPlatform == stdenv.hostPlatform) [
gtk-doc
docbook_xsl
docbook_xml_dtd_412
@ -55,7 +57,7 @@ stdenv.mkDerivation rec {
];
mesonFlags = [
"-Dgtk_doc=true"
(lib.mesonBool "gtk_doc" (stdenv.buildPlatform == stdenv.hostPlatform))
"-Dvapi=true"
(lib.mesonBool "libsoup3" withLibsoup3)
];

1
pkgs/development/libraries/libjcat/default.nix
View file

@ -43,6 +43,7 @@ stdenv.mkDerivation rec {
docbook-xsl-nons
gobject-introspection
vala
gnutls
gtk-doc
python3
];

3
pkgs/development/libraries/librest/default.nix
View file

@ -26,6 +26,7 @@ stdenv.mkDerivation rec {
nativeBuildInputs = [
pkg-config
gobject-introspection
] ++ lib.optionals (stdenv.hostPlatform == stdenv.buildPlatform) [
gtk-doc
docbook-xsl-nons
docbook_xml_dtd_412
@ -38,7 +39,7 @@ stdenv.mkDerivation rec {
];
configureFlags = [
"--enable-gtk-doc"
(lib.enableFeature (stdenv.hostPlatform == stdenv.buildPlatform) "gtk-doc")
# Remove when https://gitlab.gnome.org/GNOME/librest/merge_requests/2 is merged.
"--with-ca-certificates=/etc/ssl/certs/ca-certificates.crt"
];

2
pkgs/development/libraries/rapidfuzz-cpp/default.nix
View file

@ -33,7 +33,7 @@ stdenv.mkDerivation rec {
catch2_3
];
doCheck = true;
doCheck = stdenv.buildPlatform.canExecute stdenv.hostPlatform;
meta = {
description = "Rapid fuzzy string matching in C++ using the Levenshtein Distance";

32
pkgs/development/python-modules/calysto-scheme/default.nix Normal file
View file

@ -0,0 +1,32 @@
{ lib
, python3
, fetchFromGitHub
}:
python3.pkgs.buildPythonPackage rec {
pname = "calysto-scheme";
version = "1.4.7";
format = "setuptools";
src = fetchFromGitHub {
owner = "Calysto";
repo = "calysto_scheme";
rev = "v${version}";
hash = "sha256-5InImTbucggjf/tl8K31ZtLrwu5hqvggl7sYb0eqIEg=";
};
propagatedBuildInputs = with python3.pkgs; [
yasi
metakernel
];
pythonImportsCheck = [ "calysto_scheme" ];
meta = with lib; {
description = "A Scheme kernel for Jupyter that can use Python libraries";
homepage = "https://github.com/Calysto/calysto_scheme";
changelog = "https://github.com/Calysto/calysto_scheme/blob/${src.rev}/ChangeLog.md";
license = licenses.bsd3;
maintainers = with maintainers; [ kranzes ];
};
}

37
pkgs/development/python-modules/calysto/default.nix Normal file
View file

@ -0,0 +1,37 @@
{ lib
, python3
, fetchFromGitHub
}:
python3.pkgs.buildPythonPackage rec {
pname = "calysto";
version = "1.0.6";
format = "setuptools";
src = fetchFromGitHub {
owner = "Calysto";
repo = "calysto";
rev = "v${version}";
hash = "sha256-lr/cHFshpFs/PGMCsa3FKMRPTP+eE9ziH5XCpV+KzO8=";
};
propagatedBuildInputs = with python3.pkgs; [
metakernel
svgwrite
ipywidgets
cairosvg
numpy
];
# Tests are failing not because of Nix.
doCheck = false;
pythonImportsCheck = [ "calysto" ];
meta = with lib; {
description = "Tools for Jupyter and Python";
homepage = "https://github.com/Calysto/calysto";
license = licenses.bsd2;
maintainers = with maintainers; [ kranzes ];
};
}

10
pkgs/development/python-modules/chacha20poly1305-reuseable/default.nix
View file

@ -3,8 +3,10 @@
, fetchFromGitHub
, pythonOlder
# build
# build-system
, cython
, poetry-core
, setuptools
# propagates
, cryptography
@ -15,7 +17,7 @@
let
pname = "chacha20poly1305-reuseable";
version = "0.0.4";
version = "0.2.2";
in
buildPythonPackage {
@ -28,11 +30,13 @@ buildPythonPackage {
owner = "bdraco";
repo = pname;
rev = "v${version}";
hash = "sha256-iOGDTQyiznjYblT/NfHxewIwEZsPnp7bdNVD1p9/H1M=";
hash = "sha256-vMc5fgFYS06m01WDLRyna3T1uuR+JinqM6huXAQ34rI=";
};
nativeBuildInputs = [
cython
poetry-core
setuptools
];
propagatedBuildInputs = [

31
pkgs/development/python-modules/functiontrace/default.nix Normal file
View file

@ -0,0 +1,31 @@
{ lib
, buildPythonPackage
, fetchPypi
, setuptools
, toml
}:
buildPythonPackage rec {
pname = "functiontrace";
version = "0.3.7";
format = "pyproject";
src = fetchPypi {
inherit pname version;
hash = "sha256-3bnxZFq1/D9ntwfv7O2YU6MnKEDWWIG4zX0e3cgCleg=";
};
nativeBuildInputs = [
setuptools
toml
];
pythonImportsCheck = [ "functiontrace" ];
meta = with lib; {
homepage = "https://functiontrace.com";
description = "The Python module for Functiontrace";
license = licenses.prosperity30;
maintainers = with maintainers; [ mathiassven ];
};
}

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

@ -16,12 +16,12 @@
buildPythonPackage rec {
pname = "imageio";
version = "2.26.0";
version = "2.27.0";
disabled = pythonOlder "3.7";
src = fetchPypi {
inherit pname version;
hash = "sha256-Fp8WQs23IxM/6P6QGIf08bObwDZFjEZk8fnSViJs7TU=";
hash = "sha256-7iaclXeF7wNzzHpzIxhZVtg+wF5s3yC0KgO6e3SsWMY=";
};
patches = [

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

@ -16,7 +16,7 @@
buildPythonPackage rec {
pname = "slowapi";
version = "0.1.7";
version = "0.1.8";
format = "pyproject";
disabled = pythonOlder "3.7";
@ -25,7 +25,7 @@ buildPythonPackage rec {
owner = "laurentS";
repo = pname;
rev = "refs/tags/v${version}";
hash = "sha256-IAB7JW8iVb5M610GVK0POXlSiya22KzNgr26BNvPC4Q=";
hash = "sha256-xgHz8b95SXf/GwzKPfQ/RHbUNJfCx6+7a2HB8+6hjsw=";
};
pythonRelaxDeps = [

63
pkgs/development/python-modules/torchaudio/default.nix Normal file
View file

@ -0,0 +1,63 @@
{ lib
, buildPythonPackage
, fetchFromGitHub
, cmake
, pkg-config
, ninja
, pybind11
, torch
, cudaSupport ? false
, cudaPackages
}:
buildPythonPackage rec {
pname = "torchaudio";
version = "2.0.1";
src = fetchFromGitHub {
owner = "pytorch";
repo = "audio";
rev = "v${version}";
hash = "sha256-qrDWFY+6eVV9prUzUzb5yzyFYtEvaSyEW0zeKqAg2Vk=";
};
postPatch = ''
substituteInPlace setup.py \
--replace 'print(" --- Initializing submodules")' "return" \
--replace "_fetch_archives(_parse_sources())" "pass"
'';
nativeBuildInputs = [
cmake
pkg-config
ninja
] ++ lib.optionals cudaSupport [
cudaPackages.cudatoolkit
];
buildInputs = [
pybind11
] ++ lib.optionals cudaSupport [
cudaPackages.cudnn
];
propagatedBuildInputs = [
torch
];
BUILD_SOX=0;
BUILD_KALDI=0;
BUILD_RNNT=0;
BUILD_CTC_DECODER=0;
dontUseCmakeConfigure = true;
doCheck = false; # requires sox backend
meta = with lib; {
description = "PyTorch audio library";
homepage = "https://pytorch.org/";
changelog = "https://github.com/pytorch/audio/releases/tag/v${version}";
license = licenses.bsd2;
platforms = platforms.unix;
maintainers = with maintainers; [ junjihashimoto ];
};
}

36
pkgs/development/python-modules/yasi/default.nix Normal file
View file

@ -0,0 +1,36 @@
{ lib
, python3
, fetchFromGitHub
}:
python3.pkgs.buildPythonApplication rec {
pname = "yasi";
version = "2.1.2";
format = "setuptools";
src = fetchFromGitHub {
owner = "nkmathew";
repo = "yasi-sexp-indenter";
rev = "v${version}";
hash = "sha256-xKhVTmh/vrtBkatxtk8R4yqbGroH0I+xTKNYUpuikt4=";
};
propagatedBuildInputs = with python3.pkgs; [
colorama
];
postPatch = ''
substituteInPlace setup.py \
--replace "test.test_yasi" "tests.test_yasi"
'';
pythonImportsCheck = [ "yasi" ];
meta = with lib; {
description = "A dialect-aware s-expression indenter written in Python and newLISP";
homepage = "https://github.com/nkmathew/yasi-sexp-indenter";
changelog = "https://github.com/nkmathew/yasi-sexp-indenter/blob/${src.rev}/CHANGELOG.md";
license = licenses.mit;
maintainers = with maintainers; [ kranzes ];
};
}

96
pkgs/development/r-modules/bioc-packages.nix generated
View file

@ -17,7 +17,7 @@ in with self; {
AGDEX = derive2 { name="AGDEX"; version="1.46.0"; sha256="0yvdx32yr4mv7dl5ycpbxhrkm6csrr7k3398ggjavdcfhz54dgr8"; depends=[Biobase GSEABase]; };
AIMS = derive2 { name="AIMS"; version="1.30.0"; sha256="1civ4a14ynccv6xs27fm95fw6254l1z0q37546ivyv2mhbz0d2i1"; depends=[Biobase e1071]; };
ALDEx2 = derive2 { name="ALDEx2"; version="1.30.0"; sha256="0585s5pb8zr9il1vhxw9vjzzajmdcjmf9zz3zlc5vpczd3fnzfkf"; depends=[BiocParallel GenomicRanges IRanges multtest Rfast S4Vectors SummarizedExperiment zCompositions]; };
AMARETTO = derive2 { name="AMARETTO"; version="1.13.0"; sha256="18w65sf3h4yzw9v5xgkalxnkmgzgsx100v7qc7z4ifx10lgpji5n"; depends=[BiocFileCache callr circlize ComplexHeatmap curatedTCGAData doParallel dplyr DT foreach ggplot2 glmnet gridExtra httr impute knitr limma Matrix matrixStats MultiAssayExperiment Rcpp readr reshape2 rmarkdown tibble]; };
AMARETTO = derive2 { name="AMARETTO"; version="1.14.0"; sha256="06j75c4j71fkkw5s52nbzb3k084y2f4v4h3js9dgsxxrd6jkzfz9"; depends=[BiocFileCache callr circlize ComplexHeatmap curatedTCGAData doParallel dplyr DT foreach ggplot2 glmnet gridExtra httr impute knitr limma Matrix matrixStats MultiAssayExperiment Rcpp readr reshape2 rmarkdown tibble]; };
AMOUNTAIN = derive2 { name="AMOUNTAIN"; version="1.24.0"; sha256="0zzl5dv64yhdivsm2pgsfjikygib9pkfiv34h1lnmqrj6yivvvw8"; depends=[]; };
ANCOMBC = derive2 { name="ANCOMBC"; version="2.0.2"; sha256="0dlinv4vhxgni8ygzvfw8pbc6d1v9x5chhrpxblhs2c65bkgyxz5"; depends=[CVXR DescTools doParallel doRNG dplyr emmeans energy foreach Hmisc lme4 lmerTest magrittr MASS mia nloptr Rdpack rlang rngtools S4Vectors SingleCellExperiment SummarizedExperiment tibble tidyr TreeSummarizedExperiment]; };
ANF = derive2 { name="ANF"; version="1.20.0"; sha256="0yfwvgx7144r894fr13sx4gyyq6ljh7y734wx74sb7q80cl2gs1j"; depends=[Biobase igraph MASS RColorBrewer survival]; };
@ -45,14 +45,14 @@ in with self; {
AllelicImbalance = derive2 { name="AllelicImbalance"; version="1.36.0"; sha256="0zn8pp4pl5wr957mf6agjpn61f9qpnjx0nbxb5wnbr40672x0263"; depends=[AnnotationDbi BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges gridExtra Gviz IRanges lattice latticeExtra nlme Rsamtools S4Vectors seqinr SummarizedExperiment VariantAnnotation]; };
AlphaBeta = derive2 { name="AlphaBeta"; version="1.12.0"; sha256="000apg879li9wkbyrl8cm73z6h0xasqp41h9ir9hywy2v38rmc5b"; depends=[BiocParallel data_table dplyr expm ggplot2 gtools igraph optimx plotly stringr]; };
AlpsNMR = derive2 { name="AlpsNMR"; version="4.0.4"; sha256="19j97qsa1vnxw05dlllbwzdap0xgnmgxyqbi5dy8w2ppwdzxgsfv"; depends=[baseline BiocParallel cli dplyr fs future generics ggplot2 glue htmltools magrittr matrixStats mixOmics pcaPP purrr readxl reshape2 rlang rmarkdown scales signal speaq stringr tibble tidyr tidyselect vctrs]; };
AnVIL = derive2 { name="AnVIL"; version="1.10.1"; sha256="0iqsffkrxv28g9cddx2w05f2dbscwxhh6bpizwa8xaxhvn5bcpsv"; depends=[BiocManager dplyr DT futile_logger htmltools httr jsonlite miniUI rapiclient rlang shiny tibble tidyr tidyselect]; };
AnVIL = derive2 { name="AnVIL"; version="1.10.2"; sha256="1j7n8c47j3njd5rnlrj8bkn4q5z7jpm0c9rdq1mlwd2i1yy9fz9b"; depends=[BiocManager dplyr DT futile_logger htmltools httr jsonlite miniUI rapiclient rlang shiny tibble tidyr tidyselect]; };
AnVILBilling = derive2 { name="AnVILBilling"; version="1.8.0"; sha256="13qcp2s012ai44dkddk71ga44y87jnl0vljyd93lj1dlh8nw7c00"; depends=[bigrquery DBI dplyr DT ggplot2 lubridate magrittr plotly shiny shinytoastr]; };
AnVILPublish = derive2 { name="AnVILPublish"; version="1.8.0"; sha256="1i5zf7pyrzi6v13gpscmdb5qdb5gknicc8fk9s9nmsl1wpj6wlsw"; depends=[AnVIL httr jsonlite readr rmarkdown whisker yaml]; };
Anaquin = derive2 { name="Anaquin"; version="2.22.0"; sha256="08y2syaacy15rxcf3x2r3906kfm58fkx7ainaqvy5inlc9f670j5"; depends=[DESeq2 ggplot2 knitr locfit plyr qvalue ROCR]; };
AneuFinder = derive2 { name="AneuFinder"; version="1.26.0"; sha256="154cg63n7h9h5jkj00aqf0hzbmmjg16bzvvk50fyixwq0a4q1j00"; depends=[AneuFinderData bamsignals BiocGenerics Biostrings cowplot DNAcopy doParallel ecp foreach GenomeInfoDb GenomicAlignments GenomicRanges ggdendro ggplot2 ggrepel IRanges mclust reshape2 Rsamtools S4Vectors]; };
AnnotationDbi = derive2 { name="AnnotationDbi"; version="1.60.2"; sha256="1c7f2vgdnh99zp83pvmghb7l0rihdijlhdj6ff992h7wrrha8lhg"; depends=[Biobase BiocGenerics DBI IRanges KEGGREST RSQLite S4Vectors]; };
AnnotationFilter = derive2 { name="AnnotationFilter"; version="1.22.0"; sha256="0m16kfssxbblf03ykawkmqa038cl90prhb23k6y88g2hwm00wynk"; depends=[GenomicRanges lazyeval]; };
AnnotationForge = derive2 { name="AnnotationForge"; version="1.40.1"; sha256="16wdcl56d5i8wrmin610kzs9ldy7h9w5fbnysjb1crkcgbikq1yy"; depends=[AnnotationDbi Biobase BiocGenerics DBI RCurl RSQLite S4Vectors XML]; };
AnnotationForge = derive2 { name="AnnotationForge"; version="1.40.2"; sha256="1ab7nl9zrlhlkwjrjr69zqq5hy9a8rp457hcr075n8qm5r5lf6wd"; depends=[AnnotationDbi Biobase BiocGenerics DBI RCurl RSQLite S4Vectors XML]; };
AnnotationHub = derive2 { name="AnnotationHub"; version="3.6.0"; sha256="1hk02q6mwx49khbhydndfa1qry8ylhmwz2dff8845a510hm0di7n"; depends=[AnnotationDbi BiocFileCache BiocGenerics BiocManager BiocVersion curl dplyr httr interactiveDisplayBase rappdirs RSQLite S4Vectors yaml]; };
AnnotationHubData = derive2 { name="AnnotationHubData"; version="1.28.0"; sha256="0mcx09kcxccw2gkf4c3w7sxgb7v3gwbvahvx9wgq8f93q85yzg95"; depends=[AnnotationDbi AnnotationForge AnnotationHub Biobase BiocCheck BiocGenerics BiocManager biocViews Biostrings DBI futile_logger GenomeInfoDb GenomicFeatures GenomicRanges graph IRanges jsonlite OrganismDbi RCurl Rsamtools RSQLite rtracklayer S4Vectors XML]; };
ArrayExpress = derive2 { name="ArrayExpress"; version="1.57.0"; sha256="1fzi951mjc4kbkkvlfvwlfrpfnjckkmw4xz4m5dapy1z2jkgp8w6"; depends=[Biobase limma oligo XML]; };
@ -104,7 +104,7 @@ in with self; {
BioMM = derive2 { name="BioMM"; version="1.14.0"; sha256="06c36lpbmcz0s8v6dsjbmlmisab3h02jx67ycwlnymfwzw1hq1cb"; depends=[BiocParallel CMplot e1071 ggplot2 glmnet imager lattice nsprcomp precrec ranger rms topGO vioplot xlsx]; };
BioMVCClass = derive2 { name="BioMVCClass"; version="1.66.0"; sha256="1xclmwxps7yvqnaw8kn6z4mlpx6v8xfzyly4cadsjaj2qm535xxk"; depends=[Biobase graph MVCClass Rgraphviz]; };
BioNAR = derive2 { name="BioNAR"; version="1.0.0"; sha256="1z0ln7j4ack0pv8bzxjfrq6ncsnd0jif5s42njm94c7j408fj9kz"; depends=[AnnotationDbi clusterCons dplyr fgsea ggplot2 ggrepel GO_db igraph latex2exp org_Hs_eg_db poweRlaw Rdpack RSpectra rSpectral scales stringr synaptome_db WGCNA]; };
BioNERO = derive2 { name="BioNERO"; version="1.6.0"; sha256="10nwgp8a9chn33p5k7cdp920rraiw187xfrylyd9bq010c7vp7xh"; depends=[BiocParallel ComplexHeatmap dynamicTreeCut GENIE3 ggnetwork ggnewscale ggplot2 ggrepel igraph intergraph matrixStats minet NetRep networkD3 patchwork RColorBrewer reshape2 SummarizedExperiment sva WGCNA]; };
BioNERO = derive2 { name="BioNERO"; version="1.6.1"; sha256="0ijdnl43cgzywgsz80jd6q0irixh6367qm1ll5ww1rcr4xas2nsl"; depends=[BiocParallel ComplexHeatmap dynamicTreeCut GENIE3 ggnetwork ggnewscale ggplot2 ggrepel igraph intergraph matrixStats minet NetRep networkD3 patchwork RColorBrewer reshape2 SummarizedExperiment sva WGCNA]; };
BioNet = derive2 { name="BioNet"; version="1.58.0"; sha256="12c6m7dzwkdh4bk1c5xmzm5ajrsba7v62mag1f3rrpmrapdh6s0j"; depends=[AnnotationDbi Biobase graph igraph RBGL]; };
BioNetStat = derive2 { name="BioNetStat"; version="1.18.0"; sha256="1h99d6gnqw5v9ha2169zfhw9cvxhyjgkf4zm8qj1i03h2cywapgv"; depends=[BiocParallel DT ggplot2 Hmisc igraph knitr markdown pathview pheatmap plyr psych RColorBrewer RJSONIO rmarkdown shiny shinyBS whisker yaml]; };
BioQC = derive2 { name="BioQC"; version="1.26.0"; sha256="1ssxsxdm8vmlrmvvdz5p98apd3xsal1h3ss8556g83kgw830zsxf"; depends=[Biobase edgeR Rcpp]; };
@ -119,7 +119,7 @@ in with self; {
BiocIO = derive2 { name="BiocIO"; version="1.8.0"; sha256="15d4xsn3k32q7lzcyxvs70f0jbh9fgwl3vi7xd6sqpggar12hh9f"; depends=[BiocGenerics S4Vectors]; };
BiocNeighbors = derive2 { name="BiocNeighbors"; version="1.16.0"; sha256="09f00rf5gwwlxxaycsciq4l53gjg5kjayx8xzhns2yf1fv297j9p"; depends=[BiocParallel Matrix Rcpp RcppHNSW S4Vectors]; };
BiocOncoTK = derive2 { name="BiocOncoTK"; version="1.18.0"; sha256="1x4mzzjvjgcxg5xyxjib8r2n55hpf2vzcci0xkb7d8frakfncn9s"; depends=[bigrquery car ComplexHeatmap curatedTCGAData DBI dplyr DT GenomicFeatures GenomicRanges ggplot2 ggpubr graph httr IRanges magrittr plyr Rgraphviz rjson S4Vectors scales shiny SummarizedExperiment]; };
BiocParallel = derive2 { name="BiocParallel"; version="1.32.5"; sha256="1yd6ln9cl3dcvfziar52fkvqi2lzm31l7j21r1rwl1mpkz0xapir"; depends=[BH codetools cpp11 futile_logger snow]; };
BiocParallel = derive2 { name="BiocParallel"; version="1.32.6"; sha256="1aq3b5fjs8j0d6nf3992a6gnzvmmaxbbkrj1im0k6ppsqac6dlj0"; depends=[BH codetools cpp11 futile_logger snow]; };
BiocPkgTools = derive2 { name="BiocPkgTools"; version="1.16.1"; sha256="0cl88adkbxv7sz07b8h5qpwwkwg85jx6xjinkd0yjac4xm7s4lyf"; depends=[BiocFileCache BiocManager biocViews dplyr DT gh graph htmltools htmlwidgets httr igraph jsonlite magrittr RBGL readr rlang rorcid rvest stringr tibble xml2]; };
BiocSet = derive2 { name="BiocSet"; version="1.12.1"; sha256="1cqp5m6yic5vsp8k05r50sx2cmi9cwzxfmlswcjw28nascq3gpv0"; depends=[AnnotationDbi BiocIO dplyr KEGGREST ontologyIndex plyr rlang S4Vectors tibble tidyr]; };
BiocSingular = derive2 { name="BiocSingular"; version="1.14.0"; sha256="041izymcifvi0pa97fh5000bwlyl0mdk9003i5bbvlld6mbbv2kk"; depends=[beachmat BiocGenerics BiocParallel DelayedArray irlba Matrix Rcpp rsvd S4Vectors ScaledMatrix]; };
@ -168,7 +168,7 @@ in with self; {
CNVMetrics = derive2 { name="CNVMetrics"; version="1.2.0"; sha256="11i47ml2y5s8adh3qysasjl8b3w4xhg5h7v9rcdmd1hysjl4d4hi"; depends=[BiocParallel GenomicRanges gridExtra IRanges magrittr pheatmap S4Vectors]; };
CNVPanelizer = derive2 { name="CNVPanelizer"; version="1.30.0"; sha256="02k6bbzaj7q87nsg9zqda8dz44q3wshsps5pzm2764gxcwn4sz0z"; depends=[BiocGenerics exomeCopy foreach GenomeInfoDb GenomicRanges ggplot2 gplots IRanges NOISeq openxlsx plyr reshape2 Rsamtools S4Vectors shiny shinyFiles shinyjs stringr testthat]; };
CNVRanger = derive2 { name="CNVRanger"; version="1.14.0"; sha256="1if6k9iakrvq0fw6j2xpd26l13ikkpni8px3w76c9z0wsvbjf0cc"; depends=[BiocGenerics BiocParallel data_table edgeR GDSArray gdsfmt GenomeInfoDb GenomicRanges IRanges lattice limma plyr qqman RaggedExperiment rappdirs reshape2 S4Vectors SNPRelate SummarizedExperiment]; };
CNVfilteR = derive2 { name="CNVfilteR"; version="1.12.1"; sha256="0jkd65ncsbgwrrg0xs8ycj2lm9ailrayqqd6a453sbhx74gjsnyy"; depends=[assertthat Biostrings CopyNumberPlots GenomeInfoDb GenomicRanges IRanges karyoploteR pracma regioneR Rsamtools SummarizedExperiment VariantAnnotation]; };
CNVfilteR = derive2 { name="CNVfilteR"; version="1.12.2"; sha256="07jjrzkf8bk20wb8wiw155bq0dhgnz24bhwzsdh2dakirmjhfpzb"; depends=[assertthat Biostrings CopyNumberPlots GenomeInfoDb GenomicRanges IRanges karyoploteR pracma regioneR Rsamtools SummarizedExperiment VariantAnnotation]; };
CNVgears = derive2 { name="CNVgears"; version="1.6.0"; sha256="0gqw8l7pswamjm4j1jr8ri1rpf31szlx9ba6b99j3iypisxq1r1r"; depends=[data_table ggplot2]; };
CNViz = derive2 { name="CNViz"; version="1.6.0"; sha256="1nm8k4ry8p6k8cb6bqi6dyffi48fyhv1gq1277cz1nys31y0pdnv"; depends=[CopyNumberPlots dplyr DT GenomicRanges karyoploteR magrittr plotly scales shiny]; };
CNVrd2 = derive2 { name="CNVrd2"; version="1.36.0"; sha256="0jr9m08ip17l9w9i62nqdv13p5f3s7n0zyj4y3vy671s6c1syfiv"; depends=[DNAcopy ggplot2 gridExtra IRanges rjags Rsamtools VariantAnnotation]; };
@ -245,7 +245,7 @@ in with self; {
CrispRVariants = derive2 { name="CrispRVariants"; version="1.26.0"; sha256="184bn5gyjj0s7wpnyrqxrsh47f7f9w020p5fbhbi48nnks38j7ca"; depends=[AnnotationDbi BiocParallel Biostrings GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridExtra IRanges reshape2 Rsamtools S4Vectors]; };
CyTOFpower = derive2 { name="CyTOFpower"; version="1.4.0"; sha256="0g3629xi5hvkds2ixibr9p2ipjyr341nksafh38ap2w870whc31j"; depends=[CytoGLMM diffcyt dplyr DT ggplot2 magrittr rlang shiny shinyFeedback shinyjs shinyMatrix SummarizedExperiment tibble tidyr]; };
CytoDx = derive2 { name="CytoDx"; version="1.18.0"; sha256="1w5xy40wpyw6fj42zj2zf79r0kkdhn6h7wxzilh1dhnqkd0k8ay1"; depends=[doParallel dplyr flowCore glmnet rpart rpart_plot]; };
CytoGLMM = derive2 { name="CytoGLMM"; version="1.6.0"; sha256="1vvzw440blicfmdidr1sh8wiyfwmgrhmvazikm4f7g8jcw0cn9dm"; depends=[BiocParallel caret cowplot doParallel dplyr factoextra flexmix ggplot2 ggrepel logging magrittr MASS Matrix mbest pheatmap RColorBrewer rlang speedglm stringr strucchange tibble tidyr]; };
CytoGLMM = derive2 { name="CytoGLMM"; version="1.6.0"; sha256="1vvzw440blicfmdidr1sh8wiyfwmgrhmvazikm4f7g8jcw0cn9dm"; depends=[BiocParallel caret cowplot doParallel dplyr factoextra flexmix ggplot2 ggrepel logging magrittr MASS Matrix mbest pheatmap RColorBrewer rlang stringr strucchange tibble tidyr]; };
CytoML = derive2 { name="CytoML"; version="2.10.0"; sha256="105vdmwwglknwk7x7cb6b2jf6bngbxsly0ymjf8175p2lfv98jsa"; depends=[BH Biobase cpp11 cytolib data_table dplyr flowCore flowWorkspace ggcyto graph jsonlite openCyto RBGL Rgraphviz Rhdf5lib RProtoBufLib tibble XML yaml]; };
DAMEfinder = derive2 { name="DAMEfinder"; version="1.10.1"; sha256="1cgykb70mxnhilwwp1jr4dr523zvjxpix173s4ldfh49064gzwc1"; depends=[BiocGenerics Biostrings bumphunter cowplot GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges limma plyr readr reshape2 Rsamtools S4Vectors stringr SummarizedExperiment VariantAnnotation]; };
DAPAR = derive2 { name="DAPAR"; version="1.30.6"; sha256="1z0p3aiypi5lpa4nam45klcf9dq8k18aig917w0v73ix3l88bmad"; depends=[Biobase DAPARdata foreach highcharter MSnbase]; };
@ -267,7 +267,7 @@ in with self; {
DExMA = derive2 { name="DExMA"; version="1.6.0"; sha256="04j5h3ijmhzkgs02r0vsq3p00i4ydcnnis4kn1a69bp3x1bnv0n9"; depends=[Biobase bnstruct DExMAdata GEOquery impute limma pheatmap plyr RColorBrewer scales snpStats sva swamp]; };
DFP = derive2 { name="DFP"; version="1.56.0"; sha256="1pkg4461ib1iplcrlwkwrqzdzqixj2rhwwfkhjw87z4rx04hz3gf"; depends=[Biobase]; };
DIAlignR = derive2 { name="DIAlignR"; version="2.6.0"; sha256="04kpdab8h0krxqzsxl3sb1gsxqwrrdpsn7irgdpns8qqjlzcbzv5"; depends=[ape bit64 data_table DBI dplyr ggplot2 magrittr mzR phangorn pracma Rcpp RcppEigen reticulate rlang RMSNumpress RSQLite signal tidyr zoo]; };
DMCFB = derive2 { name="DMCFB"; version="1.12.0"; sha256="00j362frx70vj326xjppkzfd36mvfq3ym58dnckz3c0jb2dxv3wr"; depends=[arm benchmarkme BiocParallel data_table fastDummies GenomicRanges IRanges MASS matrixStats rtracklayer S4Vectors speedglm SummarizedExperiment tibble]; };
DMCFB = derive2 { name="DMCFB"; version="1.12.0"; sha256="00j362frx70vj326xjppkzfd36mvfq3ym58dnckz3c0jb2dxv3wr"; depends=[arm benchmarkme BiocParallel data_table fastDummies GenomicRanges IRanges MASS matrixStats rtracklayer S4Vectors SummarizedExperiment tibble]; };
DMCHMM = derive2 { name="DMCHMM"; version="1.20.0"; sha256="1cf5i3ikn81qw0s3kbx2yl15fmgwal22yqpys8wya8pd2agbi4lj"; depends=[BiocParallel calibrate fdrtool GenomicRanges IRanges multcomp rtracklayer S4Vectors SummarizedExperiment]; };
DMRScan = derive2 { name="DMRScan"; version="1.20.0"; sha256="1mx0kk1rbn0mkk94mm1a7mk64ia315fvwwb34adyslmyq5gq93i5"; depends=[GenomeInfoDb GenomicRanges IRanges MASS Matrix mvtnorm RcppRoll]; };
DMRcaller = derive2 { name="DMRcaller"; version="1.30.0"; sha256="03d7rl5z1pxdwxya53mkf8a8n9jzp8rb8awhfhfd22dgdf2l327h"; depends=[betareg GenomicRanges IRanges Rcpp RcppRoll S4Vectors]; };
@ -327,13 +327,13 @@ in with self; {
EasyCellType = derive2 { name="EasyCellType"; version="1.0.0"; sha256="1xry2kgb7ha2hg82jap88px9xxcq609il85xi0k0gilla1swvjc1"; depends=[AnnotationDbi clusterProfiler dplyr forcats ggplot2 magrittr org_Hs_eg_db org_Mm_eg_db rlang]; };
EmpiricalBrownsMethod = derive2 { name="EmpiricalBrownsMethod"; version="1.26.0"; sha256="1vws49a204xkwixdvp5l62in7vxbpf4qsfcnm34zkc4kx5hval9j"; depends=[]; };
EnhancedVolcano = derive2 { name="EnhancedVolcano"; version="1.16.0"; sha256="1nbg2r097rz24ybzh9ww6myd6kc2rz02vbg6g0rb3dlng0002xsm"; depends=[ggplot2 ggrepel]; };
EnrichedHeatmap = derive2 { name="EnrichedHeatmap"; version="1.27.2"; sha256="1il5cj5zmjwp3drw9psj1nsp94yxd421kd7jqrv34p4r1v0zw5z5"; depends=[circlize ComplexHeatmap GenomicRanges GetoptLong IRanges locfit matrixStats Rcpp]; };
EnrichmentBrowser = derive2 { name="EnrichmentBrowser"; version="2.28.1"; sha256="1phcd2j19a7n2crqdigkh4bf8xn10drvsm1y6ny6hrk7scrnxz4j"; depends=[AnnotationDbi BiocFileCache BiocManager edgeR GO_db graph graphite GSEABase hwriter KEGGgraph KEGGREST limma pathview Rgraphviz S4Vectors safe SPIA SummarizedExperiment]; };
EnrichedHeatmap = derive2 { name="EnrichedHeatmap"; version="1.28.1"; sha256="0ikvs91qfswnyc2p6pn5b0n7rz0szx65pv0ywgzr94arm85gwirc"; depends=[circlize ComplexHeatmap GenomicRanges GetoptLong IRanges locfit matrixStats Rcpp]; };
EnrichmentBrowser = derive2 { name="EnrichmentBrowser"; version="2.28.2"; sha256="03z0ya3qsg4drsjiqb5akbjivbsmqjv8r52y8nhrc5kqa04zffxk"; depends=[AnnotationDbi BiocFileCache BiocManager edgeR GO_db graph graphite GSEABase hwriter KEGGgraph KEGGREST limma pathview Rgraphviz S4Vectors safe SPIA SummarizedExperiment]; };
EpiCompare = derive2 { name="EpiCompare"; version="1.2.0"; sha256="0h0ap1xa0g57zh4djr263d97firklsvb6nwq0dk1h39j8wyp5j54"; depends=[AnnotationHub BiocGenerics BRGenomics ChIPseeker data_table genomation GenomeInfoDb GenomicRanges ggplot2 htmltools IRanges plotly reshape2 rmarkdown rtracklayer stringr]; };
EpiDISH = derive2 { name="EpiDISH"; version="2.14.1"; sha256="02pf0y8sj1j48qfmfjckr4vx9rz3aypb6iydlpfvhcm829jr51cl"; depends=[e1071 locfdr MASS Matrix matrixStats quadprog stringr]; };
EpiMix = derive2 { name="EpiMix"; version="1.0.1"; sha256="1rn6hpxxiw8n7im2dnb2x19ahvahljxac6853qkwxb7a8gwvwlad"; depends=[AnnotationDbi AnnotationHub Biobase biomaRt data_table doParallel doSNOW downloader dplyr ELMER_data EpiMix_data ExperimentHub foreach GenomeInfoDb GenomicFeatures GenomicRanges GEOquery ggplot2 impute IRanges limma plyr progress R_matlab RColorBrewer RCurl rlang RPMM S4Vectors SummarizedExperiment tibble tidyr]; };
EpiTxDb = derive2 { name="EpiTxDb"; version="1.10.0"; sha256="152snn75nixdas9n3g80f32hmdrqdyv71cl8fkax5jl4mqrp6px5"; depends=[AnnotationDbi BiocFileCache BiocGenerics Biostrings curl DBI GenomeInfoDb GenomicFeatures GenomicRanges httr IRanges Modstrings RSQLite S4Vectors tRNAdbImport xml2]; };
EventPointer = derive2 { name="EventPointer"; version="3.6.0"; sha256="0z9bcqfwi8mym1pwywmvdmiszw0whpz4svh7jgwjvza94z5w5ly5"; depends=[abind affxparser Biostrings BSgenome cobs doParallel fgsea foreach GenomeInfoDb GenomicFeatures GenomicRanges glmnet graph igraph IRanges iterators limma lpSolve MASS Matrix matrixStats nnls poibin prodlim qvalue RBGL rhdf5 S4Vectors SGSeq speedglm stringr SummarizedExperiment tximport]; };
EventPointer = derive2 { name="EventPointer"; version="3.6.0"; sha256="0z9bcqfwi8mym1pwywmvdmiszw0whpz4svh7jgwjvza94z5w5ly5"; depends=[abind affxparser Biostrings BSgenome cobs doParallel fgsea foreach GenomeInfoDb GenomicFeatures GenomicRanges glmnet graph igraph IRanges iterators limma lpSolve MASS Matrix matrixStats nnls poibin prodlim qvalue RBGL rhdf5 S4Vectors SGSeq stringr SummarizedExperiment tximport]; };
ExCluster = derive2 { name="ExCluster"; version="1.16.0"; sha256="0m635as5xigkjqlmwh32afbbxffjf6ahrr83gr8z886z365h4m81"; depends=[GenomicRanges IRanges matrixStats Rsubread rtracklayer]; };
ExiMiR = derive2 { name="ExiMiR"; version="2.40.0"; sha256="02aw2kjpg2xfmx0xjphsalw81gixwd2yrw73rcbcxyz7fpq98c5h"; depends=[affy affyio Biobase limma preprocessCore]; };
ExperimentHub = derive2 { name="ExperimentHub"; version="2.6.0"; sha256="1j71zmxwiz82gg6kii2bmynzwll1r6fmsq972kmvxvm6crpvi15s"; depends=[AnnotationHub BiocFileCache BiocGenerics BiocManager curl rappdirs S4Vectors]; };
@ -592,8 +592,8 @@ in with self; {
MSPrep = derive2 { name="MSPrep"; version="1.8.0"; sha256="05bq27v2iwmrf92y6fyzczvnrwmpqy5b7faa3z4si68fhpa81p2s"; depends=[crmn dplyr magrittr missForest pcaMethods preprocessCore rlang S4Vectors stringr SummarizedExperiment sva tibble tidyr VIM]; };
MSnID = derive2 { name="MSnID"; version="1.32.0"; sha256="1ljhxbyq5pa32sh44f06cwcdq79xh5nm51bpx1i8xig3bvwyg7p9"; depends=[AnnotationDbi AnnotationHub Biobase BiocGenerics BiocStyle Biostrings data_table doParallel dplyr foreach ggplot2 iterators msmsTests MSnbase mzID mzR ProtGenerics purrr R_cache Rcpp reshape2 rlang RUnit stringr tibble xtable]; };
MSnbase = derive2 { name="MSnbase"; version="2.24.2"; sha256="0jdq41rhn9qyhxfihvrgim76fzdrycc02wjsjdrff42gmray49w7"; depends=[affy Biobase BiocGenerics BiocParallel digest ggplot2 impute IRanges lattice MALDIquant MASS MsCoreUtils mzID mzR pcaMethods plyr ProtGenerics Rcpp S4Vectors scales vsn XML]; };
MSstats = derive2 { name="MSstats"; version="4.6.3"; sha256="0zivmbkf5k21r0wg2p2gzhhb53qynf5yr2p4rd0dscb60ngsv0y3"; depends=[checkmate data_table ggplot2 ggrepel gplots limma lme4 marray MASS MSstatsConvert preprocessCore Rcpp RcppArmadillo survival]; };
MSstatsConvert = derive2 { name="MSstatsConvert"; version="1.8.2"; sha256="0nvmpjp4bf8gbx3701phfwlc8jjdnxdh9hi6vzsmn8sf0k43l6dk"; depends=[checkmate data_table log4r stringi]; };
MSstats = derive2 { name="MSstats"; version="4.6.5"; sha256="12gxr7615fp4yks0mqs6ikzhalihf0bq7kkc7sflpjqgzdv3jmws"; depends=[checkmate data_table ggplot2 ggrepel gplots limma lme4 marray MASS MSstatsConvert preprocessCore Rcpp RcppArmadillo statmod survival]; };
MSstatsConvert = derive2 { name="MSstatsConvert"; version="1.8.3"; sha256="1488vl6ijnb415510pa381206xjwzn64bjvvz4vm0s80h6bzpsix"; depends=[checkmate data_table log4r stringi]; };
MSstatsLOBD = derive2 { name="MSstatsLOBD"; version="1.6.0"; sha256="1hg9bjx9rwsdpj65mzd931lbyj4gb26x32mly4n1gkk1rf6iplry"; depends=[ggplot2 minpack_lm Rcpp]; };
MSstatsLiP = derive2 { name="MSstatsLiP"; version="1.4.1"; sha256="0hj10r3x1pql0497x3clk9wlv8xvbcvbv35q45x1ki8hfc5b3ifc"; depends=[Biostrings checkmate data_table dplyr factoextra ggplot2 ggpubr gridExtra MSstats MSstatsConvert MSstatsPTM purrr Rcpp scales stringr tibble tidyr tidyverse]; };
MSstatsPTM = derive2 { name="MSstatsPTM"; version="2.0.3"; sha256="1n0hf9xxqpq5yp23hdlv0ki919m69adr6a0m7577zx0icg30c0gy"; depends=[Biostrings checkmate data_table dplyr ggplot2 ggrepel gridExtra MSstats MSstatsConvert MSstatsTMT Rcpp stringr]; };
@ -670,7 +670,7 @@ in with self; {
NBSplice = derive2 { name="NBSplice"; version="1.15.0"; sha256="0yn7s7igshall34cflmdwvmknv8h1zdi6vg8svvcyn9fvzlgjdm8"; depends=[BiocParallel car edgeR ggplot2 MASS reshape2]; };
NCIgraph = derive2 { name="NCIgraph"; version="1.46.0"; sha256="06y04lbp1wn1w9xy3lsqcdsycp4cdlrcyhga5kn1a4skb48bc6rc"; depends=[graph KEGGgraph R_methodsS3 RBGL RCy3]; };
NOISeq = derive2 { name="NOISeq"; version="2.42.0"; sha256="1j0yafl5r1vsn99zkhvaz2mrwv37l4p8ldgiq09d9hxpjq9ls7i2"; depends=[Biobase Matrix]; };
NPARC = derive2 { name="NPARC"; version="1.10.0"; sha256="0zph5lxw7ysra897jkbrmxjvb4zd5q2knl07xw8q5dyphjw8bbr3"; depends=[BiocParallel broom dplyr magrittr MASS rlang tidyr]; };
NPARC = derive2 { name="NPARC"; version="1.10.1"; sha256="09xh883v929zabr6g1prr80885b4q0mhlvlw9mlycprrd8l2qch9"; depends=[BiocParallel broom dplyr magrittr MASS rlang tidyr]; };
NTW = derive2 { name="NTW"; version="1.48.0"; sha256="0vx5swxmw76vba5wwl1qjyyb2dm7vg9wa7jsky93knhdl0s2fli9"; depends=[mvtnorm]; };
NanoMethViz = derive2 { name="NanoMethViz"; version="2.4.2"; sha256="0qfw2smqqv6pj0a34plbxgdk49zh6nbf2r077hldbmp23ml6l6qj"; depends=[AnnotationDbi assertthat BiocSingular bsseq cpp11 data_table dplyr e1071 forcats fs GenomicRanges ggplot2 ggrastr glue limma patchwork purrr R_utils Rcpp readr rlang Rsamtools RSQLite S4Vectors scales scico stringr SummarizedExperiment tibble tidyr withr zlibbioc]; };
NanoStringDiff = derive2 { name="NanoStringDiff"; version="1.28.0"; sha256="1fjmp78q3hsnslarb7w39r3kcvf8m9jrzcw4na6k55dqp5917lys"; depends=[Biobase matrixStats Rcpp]; };
@ -757,7 +757,7 @@ in with self; {
PloGO2 = derive2 { name="PloGO2"; version="1.10.0"; sha256="0sq2x68bcslzldrh367hh9r1vrnk56mkc6iqiq3zy7rzgxhjigpl"; depends=[GO_db GOstats httr lattice openxlsx xtable]; };
PoDCall = derive2 { name="PoDCall"; version="1.6.0"; sha256="1x368wc96nn4k17kbbwavriqfp6qywxivdas6sp069c053xkjxrq"; depends=[diptest DT ggplot2 gridExtra LaplacesDemon mclust purrr readr rlist shiny shinyjs]; };
PoTRA = derive2 { name="PoTRA"; version="1.13.0"; sha256="1a32d1wndb24pxza3h53yddj9z2clff5srny2k00pbbfq1h99mjf"; depends=[BiocGenerics graph graphite igraph org_Hs_eg_db]; };
PrInCE = derive2 { name="PrInCE"; version="1.14.0"; sha256="07q3x6rx3raz187akwfdd01x57hxbf6njbrydnl9r6a8q0b0gb0b"; depends=[Biobase dplyr forecast Hmisc LiblineaR magrittr MSnbase naivebayes progress purrr ranger Rdpack robustbase speedglm tester tidyr]; };
PrInCE = derive2 { name="PrInCE"; version="1.14.0"; sha256="07q3x6rx3raz187akwfdd01x57hxbf6njbrydnl9r6a8q0b0gb0b"; depends=[Biobase dplyr forecast Hmisc LiblineaR magrittr MSnbase naivebayes progress purrr ranger Rdpack robustbase tester tidyr]; };
Prostar = derive2 { name="Prostar"; version="1.30.7"; sha256="10lzh7gib43f8l2a9p2bnvyf23llzm1931kpna1vpf6p1hswsxzv"; depends=[DAPAR DAPARdata data_table future ggplot2 gplots highcharter htmlwidgets later promises rhandsontable shiny shinyAce shinyBS shinycssloaders shinyjqui shinyjs shinythemes tibble vioplot webshot]; };
ProtGenerics = derive2 { name="ProtGenerics"; version="1.30.0"; sha256="1k5pg0zbhz9mjsl5i3j33p7qv2adax2lf7yqv6qz229fxxaxs5li"; depends=[]; };
ProteoDisco = derive2 { name="ProteoDisco"; version="1.4.0"; sha256="0df39hwg5kmc900b57dxw76mz11a7h4nb9kq1z1wl6ampx27w0ks"; depends=[BiocGenerics BiocParallel Biostrings checkmate cleaver dplyr GenomeInfoDb GenomicFeatures GenomicRanges IRanges ParallelLogger plyr rlang S4Vectors tibble tidyr VariantAnnotation XVector]; };
@ -805,7 +805,7 @@ in with self; {
RMassBank = derive2 { name="RMassBank"; version="3.8.0"; sha256="1zlv2vyarj0przwdn39iybk9fkghqbiic5y24i603jzajv9hqxz0"; depends=[assertthat Biobase ChemmineOB ChemmineR data_table digest enviPat httr logger MSnbase mzR R_utils rcdk Rcpp RCurl readJDX rjson S4Vectors webchem XML yaml]; };
RNAAgeCalc = derive2 { name="RNAAgeCalc"; version="1.10.0"; sha256="0zj6ham16bjycdh1qids0pfq6xdbp8y1hdjm966ba6cwl9xxwl5d"; depends=[AnnotationDbi ggplot2 impute org_Hs_eg_db recount SummarizedExperiment]; };
RNASeqPower = derive2 { name="RNASeqPower"; version="1.38.0"; sha256="1f8jiljxacqjj0vf2v01fclhl3i0w7xddxcs6ajxzlmmpqs19b8a"; depends=[]; };
RNASeqR = derive2 { name="RNASeqR"; version="1.15.1"; sha256="0rkn98mp6d9lzm82r37mixfq7vka71c9nwkzkixajpsba2915sh6"; depends=[ballgown Biostrings clusterProfiler corrplot DESeq2 DOSE edgeR factoextra FactoMineR ggplot2 gridExtra org_Hs_eg_db org_Sc_sgd_db pathview PerformanceAnalytics pheatmap rafalib reshape2 reticulate Rsamtools stringr systemPipeR systemPipeRdata]; };
RNASeqR = derive2 { name="RNASeqR"; version="1.16.0"; sha256="0m7d3mm644n81630v2m6vv7798x3rjshb9jcp63xq631j1wmk63i"; depends=[ballgown Biostrings clusterProfiler corrplot DESeq2 DOSE edgeR factoextra FactoMineR ggplot2 gridExtra org_Hs_eg_db org_Sc_sgd_db pathview PerformanceAnalytics pheatmap rafalib reshape2 reticulate Rsamtools stringr systemPipeR systemPipeRdata]; };
RNAdecay = derive2 { name="RNAdecay"; version="1.18.0"; sha256="1zf5gg25lyn4z8yq8mmysxzpm7jkpspawyv7siwzb0m80h59rpiy"; depends=[ggplot2 gplots nloptr scales TMB]; };
RNAinteract = derive2 { name="RNAinteract"; version="1.46.0"; sha256="18yhkkwq4gvwvph8pz53cl7id644vv1n2d3jngwrfk918jay5d0s"; depends=[abind Biobase cellHTS2 geneplotter gplots hwriter ICS ICSNP lattice latticeExtra limma locfit RColorBrewer splots]; };
RNAmodR = derive2 { name="RNAmodR"; version="1.12.0"; sha256="0xhz2fz0lw2yw14cw8fcnghk9y9q0v75b4bkf7bg5v0jrcgg6bc4"; depends=[BiocGenerics BiocParallel Biostrings BSgenome colorRamps GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 Gviz IRanges matrixStats Modstrings RColorBrewer reshape2 ROCR Rsamtools rtracklayer S4Vectors]; };
@ -825,7 +825,7 @@ in with self; {
RSeqAn = derive2 { name="RSeqAn"; version="1.18.0"; sha256="0fjcwm3fw13yv3vdawwdbmbqws3n47f5s10rcvllm3wrbb1zrwb6"; depends=[Rcpp]; };
RTCA = derive2 { name="RTCA"; version="1.50.0"; sha256="1jd5rknlbhdi650xg1isqxmgvi797c4jimn53x4nzaq88b8rabsc"; depends=[Biobase gtools RColorBrewer]; };
RTCGA = derive2 { name="RTCGA"; version="1.28.0"; sha256="1h7x1hb7lnjaq842k72l76j7l4d9130vfh8flvsjvzyc3l98cywq"; depends=[assertthat data_table dplyr ggplot2 ggthemes htmltools knitr purrr RCurl rmarkdown rvest scales stringi survival survminer viridis XML xml2]; };
RTCGAToolbox = derive2 { name="RTCGAToolbox"; version="2.28.0"; sha256="0w02191nj94wapywy43r33f04ck92mww49lg1gik38pbafaahv68"; depends=[BiocGenerics data_table DelayedArray GenomeInfoDb GenomicRanges httr limma RaggedExperiment RCircos RCurl RJSONIO rvest S4Vectors stringr SummarizedExperiment survival TCGAutils XML]; };
RTCGAToolbox = derive2 { name="RTCGAToolbox"; version="2.28.4"; sha256="14pw75cy4y5s6y2szdy8hwf8q1cysxiln6z45yn5lgdha96c6zdp"; depends=[BiocGenerics data_table DelayedArray GenomeInfoDb GenomicRanges httr limma RaggedExperiment RCircos RCurl RJSONIO rvest S4Vectors stringr SummarizedExperiment survival TCGAutils XML]; };
RTN = derive2 { name="RTN"; version="2.22.1"; sha256="0ga96f1qmbq5a8nxb94b60ml2fwynnz590xjbzcx1g5vhrblkj42"; depends=[car data_table igraph IRanges limma minet mixtools pheatmap pwr RedeR S4Vectors snow SummarizedExperiment viper]; };
RTNduals = derive2 { name="RTNduals"; version="1.22.0"; sha256="0m3h0rkix48pr4jywvm0h1pbqlv62gdzq3safwgqpgb7m0pg6d08"; depends=[RTN]; };
RTNsurvival = derive2 { name="RTNsurvival"; version="1.22.0"; sha256="00naywzamklldsvipyg3q2c16s84y8cw1bngdw2l1d8yra4qpq9r"; depends=[data_table dunn_test egg ggplot2 pheatmap RColorBrewer RTN RTNduals scales survival]; };
@ -886,7 +886,7 @@ in with self; {
Rtpca = derive2 { name="Rtpca"; version="1.8.0"; sha256="0n2k1pqba4fnf0mpkxywd93yzv9dk37c134pna3f25mgzgd84qj3"; depends=[Biobase dplyr fdrtool ggplot2 pROC tibble tidyr]; };
Rtreemix = derive2 { name="Rtreemix"; version="1.60.0"; sha256="0pkc4xsqqfdvszbb0xwx3hbxl1f7kcx3vm9bhjd7zkwls1jvv2n8"; depends=[Biobase graph Hmisc]; };
S4Vectors = derive2 { name="S4Vectors"; version="0.36.2"; sha256="131cg5fzrqgyp4kv260yn8hpr0zv5mxjhdnpl50ydgc2k0l43d38"; depends=[BiocGenerics]; };
SAIGEgds = derive2 { name="SAIGEgds"; version="1.12.4"; sha256="12cxrl47ka1h3b31f0i145shhxbiss976vzp78iw1ldh032sbdyh"; depends=[gdsfmt Rcpp RcppArmadillo RcppParallel SeqArray SPAtest]; };
SAIGEgds = derive2 { name="SAIGEgds"; version="1.12.5"; sha256="10cck00fc4wmj7iwzm0s5ddgm32rpw8f32fawqaigxxrb3r9yn20"; depends=[gdsfmt Rcpp RcppArmadillo RcppParallel SeqArray SPAtest]; };
SANTA = derive2 { name="SANTA"; version="2.34.0"; sha256="1i99s33id75srjr0x3yfz1gdyxw6766pr9w4afs8varfq8gxyc48"; depends=[igraph Matrix]; };
SBGNview = derive2 { name="SBGNview"; version="1.12.0"; sha256="0644hd9m4d1s9y000yh831pwyx7q1dzr69fjqf15bby78xkn70yn"; depends=[AnnotationDbi bookdown httr igraph KEGGREST knitr pathview Rdpack rmarkdown rsvg SBGNview_data SummarizedExperiment xml2]; };
SBMLR = derive2 { name="SBMLR"; version="1.94.0"; sha256="1x7p27abv9yc9mxbnprlwh5ph50jkycmlb90qib0mj361g4sr72d"; depends=[deSolve XML]; };
@ -896,7 +896,7 @@ in with self; {
SCATE = derive2 { name="SCATE"; version="1.8.0"; sha256="1zxliw0q979jps5lrmwks5m39qjd827jbvax1ndkd8p6lp1pcm2h"; depends=[GenomicAlignments GenomicRanges mclust preprocessCore Rtsne SCATEData splines2 xgboost]; };
SCArray = derive2 { name="SCArray"; version="1.6.0"; sha256="0crh2ddh87j5qbxnslr1f94nsf24rzqz61ng6v3g8zpsldkrw09b"; depends=[BiocGenerics DelayedArray DelayedMatrixStats gdsfmt IRanges S4Vectors SingleCellExperiment SummarizedExperiment]; };
SCBN = derive2 { name="SCBN"; version="1.16.0"; sha256="1lan5anf451dmb19sra79d4w2qi9kk7xw3zijswlbhfnd4fv9kgz"; depends=[]; };
SCFA = derive2 { name="SCFA"; version="1.8.0"; sha256="02g7hzgg68y8ckwhdwlp86574x0ffjp86nwg11whyira80v5y97y"; depends=[BiocParallel cluster coro glmnet igraph Matrix matrixStats psych RhpcBLASctl survival torch]; };
SCFA = derive2 { name="SCFA"; version="1.8.1"; sha256="1839mh15wxn07nh2zx7ahs2nimgxczpvn11dcr113zimxibm1r5z"; depends=[BiocParallel cluster coro glmnet igraph Matrix matrixStats psych RhpcBLASctl survival torch]; };
SCOPE = derive2 { name="SCOPE"; version="1.10.0"; sha256="1z9v27l8bs7gkbgp1kd1q9nyq77x46anc0x0c1as0m04qq7c5xbj"; depends=[BiocGenerics Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 DescTools DNAcopy doParallel foreach GenomeInfoDb GenomicRanges gplots IRanges RColorBrewer Rsamtools S4Vectors]; };
SCnorm = derive2 { name="SCnorm"; version="1.20.0"; sha256="0zv4pf650crwliby34cjv7kxkrbqhc7xvz15n39hz5d0fk7ablgd"; depends=[BiocGenerics BiocParallel cluster data_table forcats ggplot2 moments quantreg S4Vectors SingleCellExperiment SummarizedExperiment]; };
SDAMS = derive2 { name="SDAMS"; version="1.18.0"; sha256="0i9i9w24qb66rbvkpjn2fin8x0mxd7g767i4ly0s75v9kbbp3ca6"; depends=[qvalue SummarizedExperiment trust]; };
@ -956,7 +956,7 @@ in with self; {
SimBindProfiles = derive2 { name="SimBindProfiles"; version="1.36.0"; sha256="12383rvcq7l2b3ik2gi741d33shrijj09gqpkbvbksj046j90swm"; depends=[Biobase limma mclust Ringo]; };
SimBu = derive2 { name="SimBu"; version="1.0.2"; sha256="0w8aksmcs16d6zmczarni8vrkw5b5kmv7n495w0qhmy6ync197bx"; depends=[basilisk BiocParallel data_table dplyr ggplot2 Matrix phyloseq proxyC RColorBrewer RCurl reticulate sparseMatrixStats SummarizedExperiment tidyr]; };
SimFFPE = derive2 { name="SimFFPE"; version="1.10.0"; sha256="1mlmlbnqqzxmjmir9lnqnqqb6hmj6wfxhy6wpmf6sv9y2vi2cvjz"; depends=[Biostrings doParallel dplyr foreach GenomicRanges IRanges Rsamtools truncnorm]; };
SingleCellExperiment = derive2 { name="SingleCellExperiment"; version="1.20.0"; sha256="1y9c9wf3009w4qh03zpsmc0ff0nkzal673a4nql5c11cn55sza2g"; depends=[BiocGenerics DelayedArray GenomicRanges S4Vectors SummarizedExperiment]; };
SingleCellExperiment = derive2 { name="SingleCellExperiment"; version="1.20.1"; sha256="1xwa6ncmqp21a4zx1dbs9p9b9rqbxhdgq2279mj4yl0gnpyqr9d7"; depends=[BiocGenerics DelayedArray GenomicRanges S4Vectors SummarizedExperiment]; };
SingleCellSignalR = derive2 { name="SingleCellSignalR"; version="1.10.0"; sha256="194gnss397wv3pxh1vf8gfikbz519l8hx3w4fm2hxvjs6q8k2234"; depends=[BiocManager circlize data_table edgeR foreach gplots igraph limma multtest pheatmap Rtsne scran SIMLR stringr]; };
SingleMoleculeFootprinting = derive2 { name="SingleMoleculeFootprinting"; version="1.6.0"; sha256="0dqyx3w8mxhf04xczzdv49lc2jkyamv1vlbdvfj0556y54z45cgg"; depends=[BiocGenerics Biostrings BSgenome data_table GenomeInfoDb GenomicRanges IRanges plyr QuasR RColorBrewer]; };
SingleR = derive2 { name="SingleR"; version="2.0.0"; sha256="05rw6l0d4n9m1dd7dp55zfripx036x1riwy83sx3aj5mw4r1awb6"; depends=[beachmat BiocNeighbors BiocParallel BiocSingular DelayedArray DelayedMatrixStats Matrix Rcpp S4Vectors SummarizedExperiment]; };
@ -969,10 +969,10 @@ in with self; {
SpatialExperiment = derive2 { name="SpatialExperiment"; version="1.8.1"; sha256="1kdsdk6n81n83bbbk4k8wqyj441d3xjbc4hqv1rpn8ny5mjcbpqg"; depends=[BiocFileCache BiocGenerics DropletUtils magick rjson S4Vectors SingleCellExperiment SummarizedExperiment]; };
SpatialFeatureExperiment = derive2 { name="SpatialFeatureExperiment"; version="1.0.3"; sha256="1616qpg31cnahj42s4gz435jj4j3d4rprr3bzxy58bdi7l2f8gv6"; depends=[BiocGenerics BiocParallel rjson S4Vectors sf SingleCellExperiment SpatialExperiment spdep SummarizedExperiment]; };
SpeCond = derive2 { name="SpeCond"; version="1.52.0"; sha256="09f5nz799ai7y4ig6y24xnldd37qvv7yd1k258z3s9ckc76cdgd4"; depends=[Biobase fields hwriter mclust RColorBrewer]; };
Spectra = derive2 { name="Spectra"; version="1.8.2"; sha256="0aj04f7lfs6fv34crxq49p98hvzvpggx3xlwic4s2227hswysfc0"; depends=[BiocGenerics BiocParallel fs IRanges MsCoreUtils ProtGenerics S4Vectors]; };
Spectra = derive2 { name="Spectra"; version="1.8.3"; sha256="1qib5rdyhgcs657hjnvp9zfhj05z3lpd3ngybqw3pikmc93ssf0h"; depends=[BiocGenerics BiocParallel fs IRanges MsCoreUtils ProtGenerics S4Vectors]; };
SpectralTAD = derive2 { name="SpectralTAD"; version="1.14.1"; sha256="1iml0by529cxhj6v82046l86affipar143ddk627b3p6a2sg35zr"; depends=[BiocParallel cluster dplyr GenomicRanges HiCcompare magrittr Matrix PRIMME]; };
SpidermiR = derive2 { name="SpidermiR"; version="1.28.0"; sha256="13dbz24g7l25d26piq00cpyll4cf8ss5l1kih7nvp8lrb540h6df"; depends=[AnnotationDbi gdata httr igraph miRNAtap miRNAtap_db org_Hs_eg_db]; };
SpliceWiz = derive2 { name="SpliceWiz"; version="1.0.2"; sha256="0d3d95pkk75pd076i275azhd1s0r8hrhki9xr9s4biihfa3f86ws"; depends=[AnnotationHub BiocFileCache BiocGenerics BiocParallel Biostrings BSgenome data_table DelayedArray DelayedMatrixStats DT fst genefilter GenomeInfoDb GenomicRanges ggplot2 HDF5Array heatmaply IRanges magrittr matrixStats NxtIRFdata ompBAM pheatmap plotly progress R_utils RColorBrewer Rcpp RcppProgress rhandsontable rhdf5 rtracklayer S4Vectors shiny shinydashboard shinyFiles shinyWidgets SummarizedExperiment XML zlibbioc]; };
SpliceWiz = derive2 { name="SpliceWiz"; version="1.0.4"; sha256="1lf9rcqplp6zzq11zvd1barcr0a99hfw0rgxlc93sg9gi8vm5xbn"; depends=[AnnotationHub BiocFileCache BiocGenerics BiocParallel Biostrings BSgenome data_table DelayedArray DelayedMatrixStats DT fst genefilter GenomeInfoDb GenomicRanges ggplot2 HDF5Array heatmaply IRanges magrittr matrixStats NxtIRFdata ompBAM pheatmap plotly progress R_utils RColorBrewer Rcpp RcppProgress rhandsontable rhdf5 rtracklayer S4Vectors shiny shinydashboard shinyFiles shinyWidgets SummarizedExperiment XML zlibbioc]; };
SplicingFactory = derive2 { name="SplicingFactory"; version="1.6.0"; sha256="1l92i96n7pgwrrl4ywwmbpl1al5x3lamn9wrplclkh0l8yx8c033"; depends=[SummarizedExperiment]; };
SplicingGraphs = derive2 { name="SplicingGraphs"; version="1.38.0"; sha256="0bqgn2lcmf6n188mj70cczwaps97dghmsililviq9sll91dj1gn8"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph igraph IRanges Rgraphviz Rsamtools S4Vectors]; };
SpotClean = derive2 { name="SpotClean"; version="1.0.1"; sha256="1sxmj1zgx7xf3f29l9qws4sf9k6v1wwh94brawqd6qq1plv79g51"; depends=[dplyr ggplot2 Matrix RColorBrewer readbitmap rhdf5 rjson rlang S4Vectors Seurat SpatialExperiment SummarizedExperiment tibble viridis]; };
@ -1017,7 +1017,7 @@ in with self; {
TSCAN = derive2 { name="TSCAN"; version="1.36.0"; sha256="0aqn1rxzbil9m9mpcdfc0k75s5k6ljy0k4bjrn0zq3492zz4x1qi"; depends=[combinat DelayedArray fastICA ggplot2 gplots igraph Matrix mclust mgcv plyr S4Vectors shiny SingleCellExperiment SummarizedExperiment TrajectoryUtils]; };
TTMap = derive2 { name="TTMap"; version="1.20.0"; sha256="1vfj2zq4k4fzjnq48pckxkl3bwxwghhfwq8cz14hhwf10f735pq7"; depends=[Biobase colorRamps rgl SummarizedExperiment]; };
TVTB = derive2 { name="TVTB"; version="1.24.0"; sha256="16lhbbisgxmvp86qfkp0cdd8akjld0ryklw41hi3k4ndimzax6hf"; depends=[AnnotationFilter BiocGenerics BiocParallel Biostrings ensembldb ensemblVEP GenomeInfoDb GenomicRanges GGally ggplot2 Gviz IRanges limma reshape2 Rsamtools S4Vectors SummarizedExperiment VariantAnnotation]; };
TarSeqQC = derive2 { name="TarSeqQC"; version="1.27.0"; sha256="0iiv7c3jd1iw7i5nn65370zbvi11s9qn72zig9rw1gz8nvnmdgpq"; depends=[BiocGenerics BiocParallel Biostrings cowplot GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 Hmisc IRanges openxlsx plyr reshape2 Rsamtools S4Vectors]; };
TarSeqQC = derive2 { name="TarSeqQC"; version="1.28.0"; sha256="14ima8ymdb91lpkhdnsg6q7ajxs5p1xzzcsjfhixxkm341k45j35"; depends=[BiocGenerics BiocParallel Biostrings cowplot GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 Hmisc IRanges openxlsx plyr reshape2 Rsamtools S4Vectors]; };
TargetDecoy = derive2 { name="TargetDecoy"; version="1.4.0"; sha256="1xx9y5faf5ic14h7cnxpb83nr34mqzz0c846g1z28f3x9d0kg9kz"; depends=[ggplot2 ggpubr miniUI mzID mzR shiny]; };
TargetScore = derive2 { name="TargetScore"; version="1.36.0"; sha256="00z2zv5yhxriagvcz3bwkpr9ii0r9lw4vcf7kjp7x5pjzcc6q6wq"; depends=[Matrix pracma]; };
TargetSearch = derive2 { name="TargetSearch"; version="2.0.0"; sha256="1m5v2d67w0hi3x1b6nlsq97z197djnr23d6lj9krib1im70cclwy"; depends=[assertthat ncdf4]; };
@ -1090,7 +1090,7 @@ in with self; {
agilp = derive2 { name="agilp"; version="3.30.0"; sha256="15cw004g1vxfwvf939018vmlv9gym4r473jissamkygqdv78hcr0"; depends=[]; };
airpart = derive2 { name="airpart"; version="1.6.0"; sha256="07zxv0sjhlajaw4gxpjni14qyyqn70ar8ph5cpibzcky1lx6pmkl"; depends=[apeglm clue ComplexHeatmap dplyr dynamicTreeCut emdbook forestplot ggplot2 lpSolve matrixStats mclust pbapply plyr RColorBrewer rlang S4Vectors scater SingleCellExperiment smurf SummarizedExperiment]; };
alevinQC = derive2 { name="alevinQC"; version="1.14.0"; sha256="0rd64j4hkdk2d6mlld6qkv2m96lqc93807xjdf05xm8qkyx8g8y2"; depends=[cowplot dplyr DT GGally ggplot2 Rcpp rjson rlang rmarkdown shiny shinydashboard tximport]; };
alpine = derive2 { name="alpine"; version="1.24.0"; sha256="0rjnwljh4c2f7ml0m14pllns4pvyjwwf23qsn6zjygm5x04bapf0"; depends=[Biostrings GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph IRanges RBGL Rsamtools S4Vectors speedglm stringr SummarizedExperiment]; };
alpine = derive2 { name="alpine"; version="1.24.0"; sha256="0rjnwljh4c2f7ml0m14pllns4pvyjwwf23qsn6zjygm5x04bapf0"; depends=[Biostrings GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph IRanges RBGL Rsamtools S4Vectors stringr SummarizedExperiment]; };
altcdfenvs = derive2 { name="altcdfenvs"; version="2.60.0"; sha256="0fm4l93j6nm1w1w57zzryc1hkzapp8l16pkwjzdzllvwvsnsg8r0"; depends=[affy Biobase BiocGenerics Biostrings hypergraph makecdfenv S4Vectors]; };
amplican = derive2 { name="amplican"; version="1.20.0"; sha256="1c990i6gxbarcpbdpkz017x94spwzap95l95synlizbkyif4z8ij"; depends=[BiocGenerics BiocParallel Biostrings data_table dplyr GenomeInfoDb GenomicRanges ggplot2 ggthemes gridExtra gtable IRanges knitr Matrix matrixStats Rcpp rmarkdown S4Vectors ShortRead stringr waffle]; };
animalcules = derive2 { name="animalcules"; version="1.14.0"; sha256="1alpsamrglgvzhcibkaf7m3gyiv61wbj1gvsq4lw6vjka100j9qr"; depends=[ape assertthat biomformat caret covr DESeq2 dplyr DT forcats ggplot2 glmnet GUniFrac lattice limma magrittr Matrix MultiAssayExperiment plotly plotROC rentrez reshape2 S4Vectors scales shiny shinyjs SummarizedExperiment tibble tsne umap vegan XML]; };
@ -1155,7 +1155,7 @@ in with self; {
biodbNcbi = derive2 { name="biodbNcbi"; version="1.2.0"; sha256="0bjw5q9ls7p5pi13rzmax4iqfi5l7b0inga9b96bz18mcq071pqp"; depends=[biodb chk R6 XML]; };
biodbNci = derive2 { name="biodbNci"; version="1.2.0"; sha256="18kjpc71gis82hkg6h7jn0qqwc3m2dlc6ddmyr9cfmm1wvr3fdc6"; depends=[biodb chk R6 Rcpp testthat]; };
biodbUniprot = derive2 { name="biodbUniprot"; version="1.4.0"; sha256="1xg4f72maczqm2srscnzj3fhibnsya49d9a00d5r6qg1avc3g33v"; depends=[biodb R6]; };
biomaRt = derive2 { name="biomaRt"; version="2.54.0"; sha256="0c6agi652kbffqwd1r3c22ncisqaiy3gqbc9fz13767rr71im6lq"; depends=[AnnotationDbi BiocFileCache digest httr progress rappdirs stringr XML xml2]; };
biomaRt = derive2 { name="biomaRt"; version="2.54.1"; sha256="13nhp97cklaimc3cd931hz584nc58szk2gyxrkfhp7knfli6jbpi"; depends=[AnnotationDbi BiocFileCache digest httr progress rappdirs stringr XML xml2]; };
biomformat = derive2 { name="biomformat"; version="1.26.0"; sha256="0728fpj05bvna5lpm29pdbn4slfmq16nz35as086ddbl2hhc9ni1"; depends=[jsonlite Matrix plyr rhdf5]; };
biomvRCNS = derive2 { name="biomvRCNS"; version="1.38.0"; sha256="0n026b744ah5kcnipsyiqqs7vlz5n5im1kgv35i2pgxyzvf7a8sn"; depends=[GenomicRanges Gviz IRanges mvtnorm]; };
biosigner = derive2 { name="biosigner"; version="1.26.0"; sha256="11ncmxy4wqdg30w8a6dgcsywyzda49f9al435fz3pfj5rmlbbrlj"; depends=[Biobase e1071 MultiAssayExperiment MultiDataSet randomForest ropls SummarizedExperiment]; };
@ -1333,7 +1333,7 @@ in with self; {
dittoSeq = derive2 { name="dittoSeq"; version="1.10.0"; sha256="0sxpwg2cjw70pzdxbdw68nic521w65ryn83mj0pb2m1ncpimin4b"; depends=[colorspace cowplot ggplot2 ggrepel ggridges gridExtra pheatmap reshape2 S4Vectors SingleCellExperiment SummarizedExperiment]; };
divergence = derive2 { name="divergence"; version="1.14.0"; sha256="1khxmngdqsvn77hfiyz732q4z268qwk0r9ydmipz25lnddb25p7m"; depends=[SummarizedExperiment]; };
dks = derive2 { name="dks"; version="1.44.0"; sha256="1vg6xlw5ia6r1xycd5hrh6s2nxrkrgi34dsd1kfzhkf11d40ydfh"; depends=[cubature]; };
dmrseq = derive2 { name="dmrseq"; version="1.18.0"; sha256="1zx62lbj0am85p0c1vk06s7qf8294vk8yyh67nkiqc7xgqqwybyk"; depends=[AnnotationHub annotatr BiocParallel bsseq bumphunter DelayedMatrixStats GenomeInfoDb GenomicRanges ggplot2 IRanges locfit matrixStats nlme outliers RColorBrewer rtracklayer S4Vectors]; };
dmrseq = derive2 { name="dmrseq"; version="1.18.1"; sha256="0djd2r0xzjcyw496wdw2gwzk4wjf3jp639b198x4pc0g0mmgw245"; depends=[AnnotationHub annotatr BiocParallel bsseq bumphunter DelayedMatrixStats GenomeInfoDb GenomicRanges ggplot2 IRanges locfit matrixStats nlme outliers RColorBrewer rtracklayer S4Vectors]; };
doppelgangR = derive2 { name="doppelgangR"; version="1.26.0"; sha256="1qfgfvxj44zyqfcj57lphrqgh7yb3lv807bl9xhg7k2gc3rmy5n1"; depends=[Biobase BiocParallel digest impute mnormt SummarizedExperiment sva]; };
doseR = derive2 { name="doseR"; version="1.14.0"; sha256="0cpjy8whi7nhpyhyz8k2g70l7rhfpg2xcgclxdasbrj695qy79f0"; depends=[digest edgeR lme4 matrixStats mclust RUnit S4Vectors SummarizedExperiment]; };
dpeak = derive2 { name="dpeak"; version="1.10.0"; sha256="1cnbvi8x3zjfvbsc71gz8pk7x7fglydhnc8msp6c10sd06blpibs"; depends=[BSgenome IRanges MASS Rcpp]; };
@ -1360,7 +1360,7 @@ in with self; {
epialleleR = derive2 { name="epialleleR"; version="1.6.1"; sha256="0b416ibi9y81h7xycj1sxmq344ami3a5mcqac3rzbn3l380kl5ms"; depends=[BH BiocGenerics data_table GenomeInfoDb GenomicRanges Rcpp Rhtslib stringi SummarizedExperiment VariantAnnotation zlibbioc]; };
epidecodeR = derive2 { name="epidecodeR"; version="1.6.0"; sha256="0qfb912xsyp4cvblhpwpa22iziwqz39hfnf8x68d23pnfwnb1v74"; depends=[dplyr EnvStats GenomicRanges ggplot2 ggpubr IRanges rstatix rtracklayer]; };
epigenomix = derive2 { name="epigenomix"; version="1.38.0"; sha256="0vdrnn2qmcy3znz534m5iynvzw208whcyypw7mhdqvrfzkzb4m4a"; depends=[beadarray Biobase BiocGenerics GenomeInfoDb GenomicRanges IRanges MCMCpack Rsamtools S4Vectors SummarizedExperiment]; };
epigraHMM = derive2 { name="epigraHMM"; version="1.6.3"; sha256="1qnh135gzz7fq73ryqg3bax0bw6krghpyf05b9xp5py1fk9ic9d3"; depends=[bamsignals csaw data_table GenomeInfoDb GenomicRanges ggplot2 ggpubr GreyListChIP IRanges limma magrittr MASS Matrix pheatmap Rcpp RcppArmadillo rhdf5 Rhdf5lib Rsamtools rtracklayer S4Vectors scales SummarizedExperiment]; };
epigraHMM = derive2 { name="epigraHMM"; version="1.6.4"; sha256="137qs09idwrc40379dvl3gmy2dcfhmp2x09rzzslkzkh0nj4ikcn"; depends=[bamsignals csaw data_table GenomeInfoDb GenomicRanges ggplot2 ggpubr GreyListChIP IRanges limma magrittr MASS Matrix pheatmap Rcpp RcppArmadillo rhdf5 Rhdf5lib Rsamtools rtracklayer S4Vectors scales SummarizedExperiment]; };
epihet = derive2 { name="epihet"; version="1.13.0"; sha256="1p5sgb438yj6h0fv0v17dhz1pl32vai5zcbmgpgagrd5829a6a7r"; depends=[data_table doParallel foreach GenomicRanges ggplot2 igraph IRanges pheatmap qvalue ReactomePA Rtsne S4Vectors WGCNA]; };
epimutacions = derive2 { name="epimutacions"; version="1.2.0"; sha256="1anpx122fcrwldkv5bz5c1cmf6a7y1ai8pc5wjpch7c0nim4a8xg"; depends=[AnnotationDbi AnnotationHub BiocGenerics BiocParallel biomaRt bumphunter ensembldb epimutacionsData ExperimentHub GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggrepel gridExtra Gviz Homo_sapiens IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno_ilm10b2_hg19 IlluminaHumanMethylationEPICmanifest IRanges isotree matrixStats minfi purrr reshape2 robustbase rtracklayer S4Vectors SummarizedExperiment tibble TxDb_Hsapiens_UCSC_hg18_knownGene TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Hsapiens_UCSC_hg38_knownGene]; };
epistack = derive2 { name="epistack"; version="1.4.0"; sha256="06z380js0hgnps8nkfrk2ay7s8fyqbndipavk5ipihbp80yzmgpx"; depends=[BiocGenerics GenomicRanges IRanges plotrix S4Vectors SummarizedExperiment viridisLite]; };
@ -1378,7 +1378,7 @@ in with self; {
eudysbiome = derive2 { name="eudysbiome"; version="1.28.0"; sha256="0q6x3nlvarhgc1fq5j4h7hxq5dcmfm0fgm3lmgz63bcbpsf60n5g"; depends=[Biostrings plyr R_utils Rsamtools]; };
evaluomeR = derive2 { name="evaluomeR"; version="1.14.0"; sha256="0wjmm2wzqprn0v0vn90cc3b3wsa274b305p661fdpsql4714jmrq"; depends=[class cluster corrplot flexmix fpc ggdendro ggplot2 kableExtra MASS matrixStats mclust MultiAssayExperiment plotrix prabclus randomForest Rdpack reshape2 SummarizedExperiment]; };
exomeCopy = derive2 { name="exomeCopy"; version="1.44.0"; sha256="11a95rpqzc5502s75ar703bv9hisgfx7yqdf03n0q1qh6ykil35g"; depends=[GenomeInfoDb GenomicRanges IRanges Rsamtools]; };
exomePeak2 = derive2 { name="exomePeak2"; version="1.10.0"; sha256="1j8l3q5bq3yb1889vjpk8l9qzrmg7lv38m7jb57cb9q67sflqjzs"; depends=[BiocGenerics BiocParallel Biostrings BSgenome DESeq2 GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges magrittr mclust Rsamtools rtracklayer S4Vectors speedglm SummarizedExperiment]; };
exomePeak2 = derive2 { name="exomePeak2"; version="1.10.0"; sha256="1j8l3q5bq3yb1889vjpk8l9qzrmg7lv38m7jb57cb9q67sflqjzs"; depends=[BiocGenerics BiocParallel Biostrings BSgenome DESeq2 GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges magrittr mclust Rsamtools rtracklayer S4Vectors SummarizedExperiment]; };
extraChIPs = derive2 { name="extraChIPs"; version="1.2.4"; sha256="1jhpzw7ps8bknf3b1pjcpsf5kncm3ia7q5niygvrw3idkbszz2c2"; depends=[BiocIO BiocParallel broom ComplexUpset csaw dplyr edgeR EnrichedHeatmap forcats GenomeInfoDb GenomicInteractions GenomicRanges ggforce ggplot2 ggrepel ggside glue Gviz InteractionSet IRanges limma patchwork RColorBrewer rlang Rsamtools rtracklayer S4Vectors scales stringr SummarizedExperiment tibble tidyr tidyselect vctrs VennDiagram]; };
fCCAC = derive2 { name="fCCAC"; version="1.24.0"; sha256="1r4rdbv1xv8rwsna8w89fzd76hzspf825fxzcn475ll31gmsxsrv"; depends=[ComplexHeatmap fda genomation GenomicRanges ggplot2 IRanges RColorBrewer S4Vectors]; };
fCI = derive2 { name="fCI"; version="1.28.0"; sha256="1jiws5q3ppq0z0s71nhb6fs63470v2di45y0gdf7anjnpxgjcjq9"; depends=[FNN gtools psych rgl VennDiagram zoo]; };
@ -1405,7 +1405,7 @@ in with self; {
flowCHIC = derive2 { name="flowCHIC"; version="1.32.0"; sha256="18mcywl4857wmka63rcnvp2xvh8wj5r8gvbsri9a3f4190wg8yn9"; depends=[EBImage flowCore ggplot2 hexbin vegan]; };
flowCL = derive2 { name="flowCL"; version="1.35.0"; sha256="1jxr0zn3fgm5nqishssxh332mmxfz3fc9zgshn0lbq4avxc2x128"; depends=[graph Rgraphviz]; };
flowClean = derive2 { name="flowClean"; version="1.36.0"; sha256="1wqwq8fw0dk78l43p4cjzll3psc0d4mg7gjckddvpmzlg6w4ha3k"; depends=[bit changepoint flowCore sfsmisc]; };
flowClust = derive2 { name="flowClust"; version="3.36.0"; sha256="1l1lfgm6x06gyzda36m6gvqmb91zbrz8m83b1fnfzpxkhqha20yq"; depends=[Biobase BiocGenerics flowCore graph]; };
flowClust = derive2 { name="flowClust"; version="3.36.1"; sha256="1r27nm5dxlhl5rk96dkjfx8326bvdgx55xg4w2zji3m49x9db2gs"; depends=[Biobase BiocGenerics flowCore graph]; };
flowCore = derive2 { name="flowCore"; version="2.10.0"; sha256="0j0ryyz3vcih964is5gdm2jp39ssdli9q6r03q6rj9nwzplq5asj"; depends=[BH Biobase BiocGenerics cpp11 cytolib matrixStats Rcpp RProtoBufLib S4Vectors]; };
flowCut = derive2 { name="flowCut"; version="1.8.0"; sha256="0p66wcr940m5nvl024izqn3w0x6zmp0n7j43xj70arfcxrxp9gxd"; depends=[Cairo e1071 flowCore flowDensity]; };
flowCyBar = derive2 { name="flowCyBar"; version="1.34.0"; sha256="1nbg49s18mxvr5pzv4lx4hvdrwxn5spagxn71zid5kgk13f142a6"; depends=[gplots vegan]; };
@ -1442,7 +1442,7 @@ in with self; {
gcapc = derive2 { name="gcapc"; version="1.22.0"; sha256="1n3g6fvj86q9n6q3ccmj6ns0gdd4sqfdm43sh1hpxkid9v88209y"; depends=[BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicRanges IRanges MASS matrixStats Rsamtools S4Vectors]; };
gcatest = derive2 { name="gcatest"; version="1.28.2"; sha256="1f2bp16x7ji9sh5kk150w57gqpbrisrb0xlkjv8wnd63j0vnng3l"; depends=[lfa]; };
gcrma = derive2 { name="gcrma"; version="2.70.0"; sha256="0a3wjwjgjkpmfvgg0b4jc1rkwzsqrjbaziydjfnkll4rw9xcavy1"; depends=[affy affyio Biobase BiocManager Biostrings XVector]; };
gdsfmt = derive2 { name="gdsfmt"; version="1.34.0"; sha256="1ck3qq4vhjp6vvicpldr7d2rkpspp5albjkbqjbshnbq11fhrk06"; depends=[]; };
gdsfmt = derive2 { name="gdsfmt"; version="1.34.1"; sha256="1sx7yw44djrnc6km8fip3w3vclkgz5s0w6ibp8lpvmjcay8nv2sx"; depends=[]; };
geNetClassifier = derive2 { name="geNetClassifier"; version="1.38.0"; sha256="1ahlml1ssjmg126ki1phdprq4v0nawzbbfq8jray5ypaj32qx3r2"; depends=[Biobase e1071 EBarrays minet]; };
gemini = derive2 { name="gemini"; version="1.12.0"; sha256="12p44p3nzn32am2m609k64iy4lfj42dygdxmb770ld8lpihhrkmz"; depends=[dplyr ggplot2 magrittr mixtools pbmcapply scales]; };
gemma_R = derive2 { name="gemma.R"; version="1.0.1"; sha256="0m6mmv55ghvwqw462ym335bcng61c52d84irkn5xwq6yzr2dgxsa"; depends=[Biobase bit64 data_table glue httr jsonlite lubridate magrittr memoise rappdirs rlang S4Vectors stringr SummarizedExperiment tibble tidyr]; };
@ -1479,7 +1479,7 @@ in with self; {
glmGamPoi = derive2 { name="glmGamPoi"; version="1.10.2"; sha256="1ihjqzdhx6k99gdd4556xxn9822sblg6vmblcmbzml01bhv6xzar"; depends=[beachmat BiocGenerics DelayedArray DelayedMatrixStats HDF5Array MatrixGenerics matrixStats Rcpp RcppArmadillo rlang SingleCellExperiment SummarizedExperiment]; };
glmSparseNet = derive2 { name="glmSparseNet"; version="1.16.0"; sha256="1573cclc2qn4mhw24k7ab75a9inc7z205b0j85favmvv1zcyqal4"; depends=[biomaRt digest dplyr forcats futile_logger futile_options ggplot2 glmnet glue httr Matrix MultiAssayExperiment readr reshape2 stringr SummarizedExperiment survminer]; };
globalSeq = derive2 { name="globalSeq"; version="1.26.0"; sha256="0l4n755v8gxxrxqgzhks4yz06rr3m703zaaavh0fyryk2mnijpip"; depends=[]; };
globaltest = derive2 { name="globaltest"; version="5.52.0"; sha256="1qcrs7dasb1aaws3zkiipznlc1z6i7zijhcsfv6hw3d9wpb0np9k"; depends=[annotate AnnotationDbi Biobase survival]; };
globaltest = derive2 { name="globaltest"; version="5.52.1"; sha256="1g5dv3bw0fj8sq0hsr8c7nh6n1rzvx1bisqlyqjqq3f8lsyb51kb"; depends=[annotate AnnotationDbi Biobase survival]; };
gmapR = derive2 { name="gmapR"; version="1.40.0"; sha256="03fi4ld4f102xch75z6s67kb27mvyg5zik5n59ni4zdiipi9i2cl"; depends=[Biobase BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rsamtools rtracklayer S4Vectors VariantAnnotation]; };
gmoviz = derive2 { name="gmoviz"; version="1.10.0"; sha256="0vafsa3i8z08bfl4x0adlg3bf0jdw4a7zb459cw7bfdkkw8g4850"; depends=[BiocGenerics Biostrings circlize colorspace ComplexHeatmap GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges gridBase IRanges pracma Rsamtools rtracklayer S4Vectors]; };
goProfiles = derive2 { name="goProfiles"; version="1.60.0"; sha256="0wkvb79lb309ff6iv8p23z9rwrrv7qha86ngs0ag670mpm9yra5j"; depends=[AnnotationDbi Biobase CompQuadForm GO_db stringr]; };
@ -1531,7 +1531,7 @@ in with self; {
iSEE = derive2 { name="iSEE"; version="2.10.0"; sha256="1l2bwqk7ivj79xxjzc0hc3x5v5h19zpk9pa0vbpb5p64z1pshnjn"; depends=[BiocGenerics circlize colourpicker ComplexHeatmap DT ggplot2 ggrepel igraph mgcv rintrojs S4Vectors shiny shinyAce shinydashboard shinyjs shinyWidgets SingleCellExperiment SummarizedExperiment vipor viridisLite]; };
iSEEhex = derive2 { name="iSEEhex"; version="1.0.0"; sha256="06n9ls71rg2kilr3kjlwwk5rnj8v68svjmzcr2hg0gwwyaxcyk9w"; depends=[ggplot2 hexbin iSEE shiny SummarizedExperiment]; };
iSEEhub = derive2 { name="iSEEhub"; version="1.0.0"; sha256="1ggkm7931axcl0464h0d5cnf5lbd6nx3fbac1zrlkwyb2lym7wi8"; depends=[AnnotationHub BiocManager DT ExperimentHub iSEE rintrojs S4Vectors shiny shinydashboard shinyjs SingleCellExperiment SummarizedExperiment]; };
iSEEu = derive2 { name="iSEEu"; version="1.10.0"; sha256="0040k9p1bmlg2065s3a124qvx5qgqqs4kgbkkz0k9vsdvr3z87zs"; depends=[colourpicker DT ggplot2 IRanges iSEE iSEEhex S4Vectors shiny shinyAce SingleCellExperiment SummarizedExperiment]; };
iSEEu = derive2 { name="iSEEu"; version="1.10.1"; sha256="04c2ha4s4fvk30qm65shzzvymiilj0y85qdjc3lw4c90jfvnf44q"; depends=[colourpicker DT ggplot2 IRanges iSEE iSEEhex S4Vectors shiny shinyAce SingleCellExperiment SummarizedExperiment]; };
iSeq = derive2 { name="iSeq"; version="1.50.0"; sha256="1h0da0298g2lvvqbys3jh2acjjzh1dvivfpl07g319nafxkfsi1q"; depends=[]; };
iasva = derive2 { name="iasva"; version="1.16.0"; sha256="192cpnpyyjf16pqnzj70nsqkzv6wp4acia7fciz1zvz5jhncrsva"; depends=[BiocParallel cluster irlba SummarizedExperiment]; };
ibh = derive2 { name="ibh"; version="1.46.0"; sha256="0kxqpb9711yxg5xz2mhpwjw9nwixmfzzy6qql1sifi4mp6bh2fzf"; depends=[simpIntLists]; };
@ -1672,7 +1672,7 @@ in with self; {
minfi = derive2 { name="minfi"; version="1.44.0"; sha256="15989zilgy2j4k4nw046qg8wli7ynjh2b1yzfv7cwgn87mp618lc"; depends=[beanplot Biobase BiocGenerics BiocParallel Biostrings bumphunter data_table DelayedArray DelayedMatrixStats genefilter GenomeInfoDb GenomicRanges GEOquery HDF5Array illuminaio IRanges lattice limma MASS mclust nlme nor1mix preprocessCore quadprog RColorBrewer reshape S4Vectors siggenes SummarizedExperiment]; };
mirIntegrator = derive2 { name="mirIntegrator"; version="1.28.0"; sha256="0662jsrw745973kf3f95l3n6i5s9h2nk2ap6alv8sb5rkykva2in"; depends=[AnnotationDbi ggplot2 graph org_Hs_eg_db Rgraphviz ROntoTools]; };
mirTarRnaSeq = derive2 { name="mirTarRnaSeq"; version="1.6.0"; sha256="07lfh8c7ks9lbnskvqjhjrssp0wk1kpp7mbh7c7cg6q1kxcxpqyx"; depends=[assertthat caTools corrplot data_table dplyr ggplot2 MASS pheatmap pscl purrr R_utils reshape2]; };
missMethyl = derive2 { name="missMethyl"; version="1.32.0"; sha256="10r3yvamkd1h291lmbas66mshrmy7djkz6pldh8lpqngm0rpgdr6"; depends=[AnnotationDbi BiasedUrn Biobase BiocGenerics GenomicRanges GO_db IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno_ilm10b4_hg19 IlluminaHumanMethylationEPICmanifest IRanges limma methylumi minfi org_Hs_eg_db ruv S4Vectors statmod stringr SummarizedExperiment]; };
missMethyl = derive2 { name="missMethyl"; version="1.32.1"; sha256="1rrm8m68kgjkrw1wdli5lrwqlavhbm490zgnj5vafzpvx7xajfma"; depends=[AnnotationDbi BiasedUrn Biobase BiocGenerics GenomicRanges GO_db IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno_ilm10b4_hg19 IlluminaHumanMethylationEPICmanifest IRanges limma methylumi minfi org_Hs_eg_db ruv S4Vectors statmod stringr SummarizedExperiment]; };
missRows = derive2 { name="missRows"; version="1.18.0"; sha256="0kwbmhz80an07fcp6skv4bik0ncszxcllfi7jv9h0k814qciij0y"; depends=[ggplot2 gtools MultiAssayExperiment plyr S4Vectors]; };
mistyR = derive2 { name="mistyR"; version="1.6.1"; sha256="0kcqcr1bmmhxngmygr64ca5kl8gsc7z9qwq2ivcc97f78xs3p6p8"; depends=[assertthat caret deldir digest distances dplyr filelock furrr ggplot2 purrr R_utils ranger readr ridge rlang rlist stringr tibble tidyr tidyselect withr]; };
mitch = derive2 { name="mitch"; version="1.10.0"; sha256="174hiq8xzbvdkfxdgm742sjs7qcmnkb9shcid1p8x8ci6fk9vs61"; depends=[beeswarm echarts4r GGally ggplot2 gplots gridExtra knitr MASS plyr reshape2 rmarkdown]; };
@ -1694,12 +1694,12 @@ in with self; {
msPurity = derive2 { name="msPurity"; version="1.24.0"; sha256="1w998i5lv1c2485cmdzk31inykhl64s7njaj725cs1r3gzi4l7h4"; depends=[DBI dbplyr doSNOW dplyr fastcluster foreach ggplot2 magrittr mzR plyr Rcpp reshape2 RSQLite stringr]; };
msa = derive2 { name="msa"; version="1.30.1"; sha256="064hmry0zhmpchxgjsw0krsybr9v9gbsz26zmj2a39pg1nggwbq4"; depends=[BiocGenerics Biostrings IRanges Rcpp S4Vectors]; };
msgbsR = derive2 { name="msgbsR"; version="1.22.0"; sha256="0g6d0gx5af61svxjdzx438vz24sd81qml7f755kq8nrr89pacvh0"; depends=[BSgenome easyRNASeq edgeR GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggbio ggplot2 IRanges plyr R_utils Rsamtools S4Vectors SummarizedExperiment]; };
mslp = derive2 { name="mslp"; version="1.0.1"; sha256="01w9lzfl1vci4z63yzcjk9fn7yzkcxiw6ms528qbg3nmfq08kx5a"; depends=[data_table doRNG fmsb foreach magrittr org_Hs_eg_db pROC randomForest RankProd]; };
mslp = derive2 { name="mslp"; version="1.0.2"; sha256="0sv6a9vjrgi4cd2mvb88jvr8wdwf6hr3570zpq3w3072m8m8gj4v"; depends=[data_table doRNG fmsb foreach magrittr org_Hs_eg_db pROC randomForest RankProd]; };
msmsEDA = derive2 { name="msmsEDA"; version="1.36.0"; sha256="17xklsg483zd205q5hyxy6b3cgrb53pplb1wc7pmv5638y7nsq2v"; depends=[gplots MASS MSnbase RColorBrewer]; };
msmsTests = derive2 { name="msmsTests"; version="1.36.0"; sha256="10frsvqhi3i0v2w4q4q9xz1ykyf6s3nrjlmn94x3kd06p3s839k3"; depends=[edgeR msmsEDA MSnbase qvalue]; };
msqrob2 = derive2 { name="msqrob2"; version="1.6.1"; sha256="1cv7i2n8a470jzpldlwyrx12d8my2al2522vilyyfr9j74xgi0ln"; depends=[BiocParallel codetools limma lme4 MASS Matrix MultiAssayExperiment purrr QFeatures SummarizedExperiment]; };
multiClust = derive2 { name="multiClust"; version="1.28.0"; sha256="0mw48jm154c0k9nhal56xc4jv0n3ms0s1770g2i2lxkr37905swq"; depends=[amap cluster ctc dendextend mclust survival]; };
multiGSEA = derive2 { name="multiGSEA"; version="1.8.1"; sha256="1y43nf7c3zyqjsdpx7g5xfdy53qwzzbynb9lhhyj6rbbirrpj48b"; depends=[AnnotationDbi dplyr fgsea graphite magrittr metap rappdirs rlang]; };
multiGSEA = derive2 { name="multiGSEA"; version="1.8.2"; sha256="1s8rdrzpvnscdisv1ld31aiv5vbddvr7f523sc9ngv2nsmisxdq8"; depends=[AnnotationDbi dplyr fgsea graphite magrittr metap rappdirs rlang]; };
multiHiCcompare = derive2 { name="multiHiCcompare"; version="1.16.0"; sha256="0mwb61c6yqq1frnsgp3nafmlrl1zi8sxckp5yw7z083805y3fbyr"; depends=[aggregation BiocParallel data_table dplyr edgeR GenomeInfoDb GenomeInfoDbData GenomicRanges HiCcompare pbapply pheatmap qqman]; };
multiMiR = derive2 { name="multiMiR"; version="1.20.0"; sha256="1zfjr1cw1qpi70wxrkw32y3dmwhbsdzd2522cgkj4x97g4d5cn99"; depends=[AnnotationDbi BiocGenerics dplyr purrr RCurl tibble XML]; };
multiOmicsViz = derive2 { name="multiOmicsViz"; version="1.22.0"; sha256="0g28ksb9vf2lpv15s9s64nnz6smhxrf9cbsw4kba0dlyrrzzha4a"; depends=[doParallel foreach SummarizedExperiment]; };
@ -1742,7 +1742,7 @@ in with self; {
nuCpos = derive2 { name="nuCpos"; version="1.16.3"; sha256="14anlg6a7b3qw2k39q273p5396v3nqlask0gz92h170z24gjyc1s"; depends=[]; };
nucleR = derive2 { name="nucleR"; version="2.30.0"; sha256="0j8g0lf6pzqzak259fp6xckgcjrabqgd28bwy9fbx3pd1qj5yrh0"; depends=[Biobase BiocGenerics Biostrings dplyr GenomeInfoDb GenomicRanges ggplot2 IRanges magrittr Rsamtools S4Vectors ShortRead]; };
nucleoSim = derive2 { name="nucleoSim"; version="1.26.0"; sha256="0cgljwk9car3s5ncslx0j0bya6hchfv1zk09q8r0y6258mim4qy6"; depends=[IRanges S4Vectors]; };
nullranges = derive2 { name="nullranges"; version="1.4.0"; sha256="01f7x99nzgi0si02p5bsjvf0mybl52kxnkm2j1f1s2rai5srkca4"; depends=[data_table GenomeInfoDb GenomicRanges ggplot2 ggridges InteractionSet IRanges ks plyranges progress rlang S4Vectors scales speedglm]; };
nullranges = derive2 { name="nullranges"; version="1.4.0"; sha256="01f7x99nzgi0si02p5bsjvf0mybl52kxnkm2j1f1s2rai5srkca4"; depends=[data_table GenomeInfoDb GenomicRanges ggplot2 ggridges InteractionSet IRanges ks plyranges progress rlang S4Vectors scales]; };
occugene = derive2 { name="occugene"; version="1.58.0"; sha256="13hv71w25jzlf0fs5wx400m1zh4l4vxlvv42vidiyggj894ky5a3"; depends=[]; };
octad = derive2 { name="octad"; version="1.0.0"; sha256="0qa407rhi9z1n2hif40j27vbfsy222wi2hh26qn4s0s7f2fnfyfl"; depends=[AnnotationHub Biobase data_table DESeq2 dplyr EDASeq edgeR ExperimentHub foreach ggplot2 GSVA htmlwidgets httr limma magrittr octad_db plotly reshape2 Rfast rhdf5 RUVSeq S4Vectors]; };
odseq = derive2 { name="odseq"; version="1.26.0"; sha256="0p51lay3xasqg55j99gdx1gpk93p4m2czvbw912h559v2s4hnzqq"; depends=[kebabs mclust msa]; };
@ -1799,6 +1799,7 @@ in with self; {
periodicDNA = derive2 { name="periodicDNA"; version="1.8.0"; sha256="03wdxbgsrj2c7j3fgxigjbq349y5c8cw80xvb5ja7lbi1isfb785"; depends=[BiocParallel Biostrings BSgenome cowplot GenomeInfoDb GenomicRanges ggplot2 IRanges magrittr rtracklayer S4Vectors zoo]; };
pgca = derive2 { name="pgca"; version="1.22.0"; sha256="0bcq1qks87jjgd2bwpds6xvcvidcvl9pq53mi0dafihgd0s2ycfn"; depends=[]; };
phantasus = derive2 { name="phantasus"; version="1.18.4"; sha256="0rjn66xjkr57w4nsjczxrw3hw90r9zfwqbmhs8pw4y1hd7j1alhi"; depends=[AnnotationDbi assertthat Biobase ccaPP curl data_table DESeq2 fgsea GEOquery ggplot2 gtable htmltools httpuv httr jsonlite limma Matrix opencpu pheatmap protolite rhdf5 Rook scales stringr svglite]; };
phemd = derive2 { name="phemd"; version="1.14.1"; sha256="18i2qps2r8h9fqln9gm0wz373xg3lfkgb3my8wk4w944h3an6280"; depends=[Biobase BiocGenerics cluster cowplot destiny ggplot2 igraph maptree monocle phateR pheatmap pracma RANN RColorBrewer reticulate Rtsne S4Vectors scatterplot3d Seurat SingleCellExperiment SummarizedExperiment transport VGAM]; };
phenoTest = derive2 { name="phenoTest"; version="1.46.0"; sha256="0rcgbnqglfs9asyrssnhy7h99kikmnr7s1827y8q2agq3pl96q13"; depends=[annotate AnnotationDbi Biobase biomaRt BMA Category ellipse genefilter ggplot2 gplots GSEABase Heatplus hgu133a_db Hmisc hopach limma mgcv survival xtable]; };
phenomis = derive2 { name="phenomis"; version="1.0.2"; sha256="15lk3wapaaqqrlp02b2cvdlx8dgcvc3vjsfv8i70qh89rljialf8"; depends=[Biobase biodb biodbChebi data_table futile_logger ggplot2 ggrepel htmlwidgets igraph limma MultiAssayExperiment MultiDataSet plotly PMCMRplus ranger RColorBrewer ropls SummarizedExperiment tibble tidyr VennDiagram]; };
phenopath = derive2 { name="phenopath"; version="1.22.0"; sha256="0p2lh858ykhqz0zj4h1vmjd27szwkrlswanapz4shhmvb4plrlbv"; depends=[dplyr ggplot2 Rcpp SummarizedExperiment tibble tidyr]; };
@ -1832,7 +1833,7 @@ in with self; {
primirTSS = derive2 { name="primirTSS"; version="1.16.0"; sha256="00h9m37ga3wsbcafg4c338457xqjlmgmhhkcrvm38x39h20kxrqy"; depends=[BiocGenerics Biostrings BSgenome_Hsapiens_UCSC_hg38 dplyr GenomicRanges GenomicScores Gviz IRanges JASPAR2018 phastCons100way_UCSC_hg38 purrr R_utils rtracklayer S4Vectors shiny stringr TFBSTools tibble tidyr]; };
proActiv = derive2 { name="proActiv"; version="1.8.0"; sha256="150n6nglbji1510g6kkq6b7i0nix70c6zahdrr4a6p1dpg15gfgv"; depends=[AnnotationDbi BiocParallel data_table DESeq2 dplyr GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 gplots IRanges rlang S4Vectors scales SummarizedExperiment tibble]; };
proBAMr = derive2 { name="proBAMr"; version="1.32.0"; sha256="1pn48pmiz6cgc3hjczhpzgld69my7xk37d1k7k37gm0dwzpd85c3"; depends=[AnnotationDbi Biostrings GenomicFeatures GenomicRanges IRanges rtracklayer]; };
proBatch = derive2 { name="proBatch"; version="1.13.0"; sha256="1z55rbgjzxkj0i9gwwbh3wa82w9xflnipkkx58bgnni1nfnbia9k"; depends=[Biobase corrplot data_table dplyr ggfortify ggplot2 lazyeval lubridate magrittr pheatmap preprocessCore purrr pvca RColorBrewer reshape2 rlang scales sva tibble tidyr viridis wesanderson WGCNA]; };
proBatch = derive2 { name="proBatch"; version="1.14.0"; sha256="079dh61v1dmsasrh5sn6sn1rgi34mavxa1sc1y8x6wqjwabm4w1j"; depends=[Biobase corrplot data_table dplyr ggfortify ggplot2 lazyeval lubridate magrittr pheatmap preprocessCore purrr pvca RColorBrewer reshape2 rlang scales sva tibble tidyr viridis wesanderson WGCNA]; };
proDA = derive2 { name="proDA"; version="1.12.0"; sha256="1b1p8sh80x5967rakyq75cj0sz01303w7p05b9irfr69yvfvlj45"; depends=[BiocGenerics extraDistr S4Vectors SummarizedExperiment]; };
proFIA = derive2 { name="proFIA"; version="1.23.0"; sha256="0y08vj401f45dvgxjwjx94hvd0rk1wljk8n1irpkdafg24gv4fvj"; depends=[Biobase BiocParallel minpack_lm missForest pracma ropls xcms]; };
procoil = derive2 { name="procoil"; version="2.26.0"; sha256="1ncls2bgdaaq1kc728p5ay95ypm5byyhpzjck34hfpq867lp7x7m"; depends=[Biostrings kebabs S4Vectors]; };
@ -1851,7 +1852,7 @@ in with self; {
pvca = derive2 { name="pvca"; version="1.38.0"; sha256="1cpyxgw1ynq3dms5yvcwaqd3s55ky80dgy811nl226mji278v9cl"; depends=[Biobase lme4 Matrix vsn]; };
pwOmics = derive2 { name="pwOmics"; version="1.30.0"; sha256="1mklwy9p6miwzvcjzin5q0qcg9625bmbj5hi9dvm6cq48r0x5gwp"; depends=[AnnotationDbi AnnotationHub Biobase BiocGenerics biomaRt data_table GenomicRanges gplots graph igraph rBiopaxParser STRINGdb]; };
pwrEWAS = derive2 { name="pwrEWAS"; version="1.12.0"; sha256="1y8knyl0axnbidkg1z9n1dmchdb79ixr7d6m1g2zhlzp10kmi4pk"; depends=[abind BiocManager CpGassoc doParallel doSNOW foreach genefilter ggplot2 limma pwrEWAS_data shiny shinyBS shinyWidgets truncnorm]; };
qPLEXanalyzer = derive2 { name="qPLEXanalyzer"; version="1.16.0"; sha256="18hswwff9smiz9dr28mmh7fh58wknb8cfzxvg5xdw4fw09cb48m9"; depends=[assertthat Biobase BiocGenerics Biostrings dplyr ggdendro ggplot2 IRanges limma magrittr MSnbase preprocessCore purrr RColorBrewer readr rlang scales stringr tibble tidyr tidyselect]; };
qPLEXanalyzer = derive2 { name="qPLEXanalyzer"; version="1.16.1"; sha256="0jzk0h6lll7yxmiplrk0rhx5pvhq8jjifhi2fj4nyskx1brsnnfh"; depends=[assertthat Biobase BiocGenerics Biostrings dplyr ggdendro ggplot2 IRanges limma magrittr MSnbase preprocessCore purrr RColorBrewer readr rlang scales stringr tibble tidyr tidyselect]; };
qckitfastq = derive2 { name="qckitfastq"; version="1.14.0"; sha256="0220r27adgm8mj348602hzgrbj8f94d0xbcrfg9r5sjaajqbmf8w"; depends=[data_table dplyr ggplot2 magrittr Rcpp reshape2 rlang RSeqAn seqTools zlibbioc]; };
qcmetrics = derive2 { name="qcmetrics"; version="1.36.0"; sha256="1ab6w3ghalgjarkq91ci85dwpwp1dqdsj2m9adlmx05wpljg9qc4"; depends=[Biobase knitr pander S4Vectors xtable]; };
qmtools = derive2 { name="qmtools"; version="1.2.0"; sha256="19zn0q493vn45wllzbzqfgnazr5x6ik2hvh7pay3s95421vls1bd"; depends=[ggplot2 heatmaply igraph MsCoreUtils patchwork rlang scales SummarizedExperiment VIM]; };
@ -1878,7 +1879,7 @@ in with self; {
rScudo = derive2 { name="rScudo"; version="1.14.0"; sha256="1bk7w1rb87j6c3280r6bwnvfhfzdv0ck9g96y0a8k1g297gvyvcc"; depends=[Biobase BiocGenerics igraph S4Vectors stringr SummarizedExperiment]; };
rTRM = derive2 { name="rTRM"; version="1.36.0"; sha256="11dp7vz1343hmaa7lly5m9h9fx94cpqqhsrvbb6vy57bh8nb6v4v"; depends=[AnnotationDbi DBI igraph RSQLite]; };
rTRMui = derive2 { name="rTRMui"; version="1.36.0"; sha256="1gindmnq5vkapmfjpy9hglbk79g0s1sgzdljmhn3m5925h2al4k0"; depends=[MotifDb org_Hs_eg_db org_Mm_eg_db rTRM shiny]; };
rWikiPathways = derive2 { name="rWikiPathways"; version="1.18.0"; sha256="0vk6j07xxkpdaybsiip41xavsiwc8qr165sxab5fy1r13w3ya4d3"; depends=[data_table httr RCurl rjson tidyr XML]; };
rWikiPathways = derive2 { name="rWikiPathways"; version="1.18.1"; sha256="1zh6yz49s4jdpgg17dkkjv32fkp4zvdrcljfpbysbvc9lplrlj65"; depends=[data_table httr RCurl rjson tidyr XML]; };
rain = derive2 { name="rain"; version="1.32.0"; sha256="0zlb52z0wk6057ph12lj7313bfkpbn502568cgdwify8s6q9g8ms"; depends=[gmp multtest]; };
rama = derive2 { name="rama"; version="1.72.0"; sha256="0i6crxnzhwxnc55xh2rv36jfwh4bd30alw1f05ixdrxwqwsslbpy"; depends=[]; };
ramr = derive2 { name="ramr"; version="1.6.0"; sha256="1rn5jvrcl3823124iwwbrjx89yyp3yflhlvjwnf6jldvm5bwqwpz"; depends=[BiocGenerics doParallel doRNG EnvStats ExtDist foreach GenomicRanges ggplot2 IRanges matrixStats reshape2 S4Vectors]; };
@ -1893,7 +1894,7 @@ in with self; {
reconsi = derive2 { name="reconsi"; version="1.10.0"; sha256="1hzwjmnbkdb4v8nvsk06vmyh5hm1snjn1a2q21jingppjs0dzvik"; depends=[ggplot2 ks Matrix matrixStats phyloseq reshape2]; };
recount = derive2 { name="recount"; version="1.24.1"; sha256="0ryxz7kf52rwwri1bbpfpn67ivcx3fxrnym430d4nv6j1qfb1kh4"; depends=[BiocParallel derfinder downloader GenomeInfoDb GenomicRanges GEOquery IRanges RCurl rentrez rtracklayer S4Vectors SummarizedExperiment]; };
recount3 = derive2 { name="recount3"; version="1.8.0"; sha256="1syfy713ybsl8vlvfag6i85icv34k1y0f6g6v168snc2z1xq4yrd"; depends=[BiocFileCache data_table GenomicRanges Matrix R_utils RCurl rtracklayer S4Vectors sessioninfo SummarizedExperiment]; };
recountmethylation = derive2 { name="recountmethylation"; version="1.8.3"; sha256="04xcj58wdsbz4ibx030br2d27lvld4aqvj1j7686r7jcjj2s92kq"; depends=[BiocFileCache HDF5Array IlluminaHumanMethylation450kmanifest minfi R_utils RCurl rhdf5 S4Vectors]; };
recountmethylation = derive2 { name="recountmethylation"; version="1.8.6"; sha256="1nrav24pq3jwi9jmy7b0h799q6bnw1sjd8a0gca3c1pn9zvg8xqn"; depends=[basilisk BiocFileCache DelayedMatrixStats HDF5Array minfi R_utils RCurl reticulate rhdf5 S4Vectors]; };
recoup = derive2 { name="recoup"; version="1.26.0"; sha256="00ia9a9kqmcn329pvipaz15xfci6rw4377hpf7gnxhjkxx4b1rna"; depends=[BiocGenerics biomaRt Biostrings circlize ComplexHeatmap GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 httr IRanges Rsamtools RSQLite rtracklayer S4Vectors stringr]; };
regionReport = derive2 { name="regionReport"; version="1.32.0"; sha256="0ilqm51dnhv5bhda7ljdn1x4hwr4infpngsvwn7wvssvsgp1pcz0"; depends=[BiocStyle DEFormats derfinder DESeq2 GenomeInfoDb GenomicRanges knitr knitrBootstrap RefManageR rmarkdown S4Vectors SummarizedExperiment]; };
regioneR = derive2 { name="regioneR"; version="1.30.0"; sha256="01anwhz0axdl0g2zsaqz1qdxswxrryarbw6pmn5kmlpz4ipiq049"; depends=[Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges memoise rtracklayer S4Vectors]; };
@ -1908,7 +1909,7 @@ in with self; {
rgsepd = derive2 { name="rgsepd"; version="1.30.0"; sha256="1bk6i336x2ng1kvgywcs18v6sn47cndahfbpcagl17x77pcna7by"; depends=[AnnotationDbi biomaRt DESeq2 GO_db goseq gplots org_Hs_eg_db SummarizedExperiment]; };
rhdf5 = derive2 { name="rhdf5"; version="2.42.0"; sha256="1vxs227d1295fz8irr6fsv603cw96a801j8njhblvs0cry38d087"; depends=[rhdf5filters Rhdf5lib]; };
rhdf5client = derive2 { name="rhdf5client"; version="1.20.0"; sha256="0wf0mv1kc3gd7vpazdip9253c1727ns9xysqfipg9lf1ydjny1fq"; depends=[DelayedArray httr R6 rjson S4Vectors]; };
rhdf5filters = derive2 { name="rhdf5filters"; version="1.10.0"; sha256="17x2a3122mm3z9qnalw25am2x08cfpm17nwhigabid3ha3d2mgz1"; depends=[Rhdf5lib]; };
rhdf5filters = derive2 { name="rhdf5filters"; version="1.10.1"; sha256="14rkr0fisy7qrvjikpnwxwag79205hdxy6nkpwz501li4fr1rbnp"; depends=[Rhdf5lib]; };
riboSeqR = derive2 { name="riboSeqR"; version="1.32.0"; sha256="0la8kmxxh5jnqsrmmvyhi313bjdbqkiq16hcxar6mgyjhxlsm610"; depends=[abind baySeq GenomeInfoDb GenomicRanges IRanges Rsamtools seqLogo]; };
ribor = derive2 { name="ribor"; version="1.10.0"; sha256="16ikb3815cmwagjjjcv8rmshybpjl0vfc20mpl5xr92dzbnn7jj2"; depends=[dplyr ggplot2 hash rhdf5 rlang S4Vectors tidyr yaml]; };
ribosomeProfilingQC = derive2 { name="ribosomeProfilingQC"; version="1.10.0"; sha256="04r0nhjfm659i5n2351f67dghjm9jrfvcnzbf7ylqgnhym4ibzrn"; depends=[AnnotationDbi BiocGenerics Biostrings BSgenome cluster EDASeq GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggfittext ggplot2 ggrepel IRanges motifStack Rsamtools Rsubread rtracklayer RUVSeq S4Vectors scales XVector]; };
@ -1930,7 +1931,7 @@ in with self; {
rtracklayer = derive2 { name="rtracklayer"; version="1.58.0"; sha256="1qxr0ffmmkbfkbijz7pbks3kvms9k4a5rmma4j9p7ar477fxvlmk"; depends=[BiocGenerics BiocIO Biostrings GenomeInfoDb GenomicAlignments GenomicRanges IRanges RCurl restfulr Rsamtools S4Vectors XML XVector zlibbioc]; };
runibic = derive2 { name="runibic"; version="1.20.0"; sha256="0g7hqgsq7h0338fmlb4ipv1kwiijcrfajhgwchn5akhspvsch269"; depends=[biclust Rcpp SummarizedExperiment testthat]; };
sRACIPE = derive2 { name="sRACIPE"; version="1.14.0"; sha256="079lmgi6az5ri05lvca58msh678r7k1xwk3xhq8iffqh87wy6cmj"; depends=[BiocGenerics ggplot2 gplots gridExtra htmlwidgets MASS RColorBrewer Rcpp reshape2 S4Vectors SummarizedExperiment umap visNetwork]; };
sSNAPPY = derive2 { name="sSNAPPY"; version="1.2.4"; sha256="0ja3hbsfhmwibc8mj4192kcwcp4bj2lish1nsy7kd6hdv28i5nm8"; depends=[BiocParallel dplyr edgeR ggforce ggnewscale ggplot2 ggraph graphite igraph magrittr org_Hs_eg_db pheatmap purrr Rcpp RcppArmadillo reshape2 rlang SummarizedExperiment tibble]; };
sSNAPPY = derive2 { name="sSNAPPY"; version="1.2.5"; sha256="17z0iz6jr0nx14s4d80j94jdk78af4i1zkin24z56fas28sm2ka8"; depends=[BiocParallel dplyr edgeR ggforce ggnewscale ggplot2 ggraph graphite igraph magrittr org_Hs_eg_db pheatmap purrr Rcpp RcppArmadillo reshape2 rlang SummarizedExperiment tibble]; };
sSeq = derive2 { name="sSeq"; version="1.36.0"; sha256="1w0iq7pih9z8662wj2lj1xbg66n752mx4g2q33ck5vwdxg10ry4c"; depends=[caTools RColorBrewer]; };
safe = derive2 { name="safe"; version="3.38.0"; sha256="1gza1liz0y2i6f5nnnwbwl99fjp3cr1aknxiy3rmbjydfq8yxbrw"; depends=[AnnotationDbi Biobase SparseM]; };
sagenhaft = derive2 { name="sagenhaft"; version="1.68.0"; sha256="0hh9gkv07qrlnarrj7h579dhisyq01c5jjl3rvq5w086wfy9154m"; depends=[SparseM]; };
@ -1940,7 +1941,7 @@ in with self; {
sarks = derive2 { name="sarks"; version="1.10.0"; sha256="1f3yypn7dzjq58jnkv3jc0330mddpapzn1wlvq2crjbh161mxaym"; depends=[binom Biostrings cluster IRanges rJava]; };
satuRn = derive2 { name="satuRn"; version="1.6.0"; sha256="1gldcdnpbxc2bgi5sr3g0cgkfx8gx2jmyadnxzm07zcmi724nsyx"; depends=[BiocParallel boot ggplot2 limma locfdr Matrix pbapply SummarizedExperiment]; };
savR = derive2 { name="savR"; version="1.36.0"; sha256="1b7kjgj2r6lgkdnrq91wcwvwb5an0gfdsbyp7j0pvn2byfm4lply"; depends=[ggplot2 gridExtra reshape2 scales XML]; };
scAlign = derive2 { name="scAlign"; version="1.11.0"; sha256="01gy9p07nyx42i0phgc89yhjavpykzgh1mwr11358ddbwz41hxnr"; depends=[FNN ggplot2 irlba purrr Rtsne Seurat SingleCellExperiment tensorflow]; };
scAlign = derive2 { name="scAlign"; version="1.12.0"; sha256="1mlhxwsfrmhysa5mcyx7vf2jn49snf41yb7xqmyi40wilj9h8qlb"; depends=[FNN ggplot2 irlba purrr Rtsne Seurat SingleCellExperiment tensorflow]; };
scAnnotatR = derive2 { name="scAnnotatR"; version="1.4.0"; sha256="0rc035kzbzrxvlcpphzg0yg7q82jvlxpi9xjq8q59hvbpyg1sz93"; depends=[AnnotationHub ape caret data_tree dplyr e1071 ggplot2 kernlab pROC ROCR Seurat SingleCellExperiment SummarizedExperiment]; };
scBFA = derive2 { name="scBFA"; version="1.12.0"; sha256="0884s9laa63yf2p9wf66a67ipkc2x075c432x8p96vr326p4h8nf"; depends=[copula DESeq2 ggplot2 MASS Matrix Seurat SingleCellExperiment SummarizedExperiment zinbwave]; };
scBubbletree = derive2 { name="scBubbletree"; version="1.0.0"; sha256="0ivyp3zf7clr4zbdv2srjv42dx2zvlaq4yprccxb3yimrnmihks6"; depends=[ape future future_apply ggplot2 ggtree patchwork reshape2 scales Seurat]; };
@ -2096,8 +2097,8 @@ in with self; {
ternarynet = derive2 { name="ternarynet"; version="1.42.0"; sha256="01z262509vka2sfhzccwlmgi5frf56x07gbsan762hgvrcscg8jb"; depends=[BiocParallel igraph]; };
terraTCGAdata = derive2 { name="terraTCGAdata"; version="1.2.0"; sha256="1yfvqdsgd3apan43cbjin95mwnbym1m0f1c8x212k277cc3rm22r"; depends=[AnVIL BiocFileCache dplyr GenomicRanges MultiAssayExperiment RaggedExperiment readr S4Vectors TCGAutils tidyr]; };
tidySingleCellExperiment = derive2 { name="tidySingleCellExperiment"; version="1.8.0"; sha256="0kkxd64rlksw7l0hw53ckc9mhsvsb0yj8w078bh4rd16iqk3jnnc"; depends=[cli dplyr ellipsis fansi ggplot2 lifecycle magrittr pillar plotly purrr rlang S4Vectors SingleCellExperiment stringr SummarizedExperiment tibble tidyr tidyselect ttservice]; };
tidySummarizedExperiment = derive2 { name="tidySummarizedExperiment"; version="1.8.0"; sha256="0y7k0svcjx0lvxn3jw8g7vkrvwhvj9b7mhb0igavad1rc5pc54f3"; depends=[cli dplyr ellipsis fansi ggplot2 lifecycle magrittr pillar plotly purrr rlang S4Vectors stringr SummarizedExperiment tibble tidyr tidyselect vctrs]; };
tidybulk = derive2 { name="tidybulk"; version="1.10.0"; sha256="1n31wqad7wdfyfy1mcjsq68rlyyyd15srcrvz6ylp2pi8nbwxfly"; depends=[crayon dplyr GenomicRanges lifecycle magrittr preprocessCore purrr readr rlang S4Vectors scales stringi stringr SummarizedExperiment tibble tidyr tidyselect]; };
tidySummarizedExperiment = derive2 { name="tidySummarizedExperiment"; version="1.8.1"; sha256="1sry782zf2sisjwlhgdh1vfr0ljbw2rrwwb907jxmafg6jm96rxq"; depends=[cli dplyr ellipsis fansi ggplot2 lifecycle magrittr pillar plotly purrr rlang S4Vectors stringr SummarizedExperiment tibble tidyr tidyselect vctrs]; };
tidybulk = derive2 { name="tidybulk"; version="1.10.1"; sha256="100xnjz73wl48a93gv4361pllyb96nbhg5q8spgq131wp0i0zjzz"; depends=[crayon dplyr GenomicRanges lifecycle magrittr preprocessCore purrr readr rlang S4Vectors scales stringi stringr SummarizedExperiment tibble tidyr tidyselect]; };
tigre = derive2 { name="tigre"; version="1.52.0"; sha256="1cj4yqdad1xs8k682qx92b03nbyx51qdqsf7y90bll3z51xhwvdq"; depends=[annotate AnnotationDbi Biobase BiocGenerics DBI gplots RSQLite]; };
tilingArray = derive2 { name="tilingArray"; version="1.76.0"; sha256="19bkgblpkcp3w3sdyn82c37gkz1sv3r4d546zpbnh36q2pi3l4zd"; depends=[affy Biobase genefilter pixmap RColorBrewer strucchange vsn]; };
timeOmics = derive2 { name="timeOmics"; version="1.10.0"; sha256="1szhdd29gfa7ah7yf683d69s2w0w6r8nh3kc7fii3vnyqspspb19"; depends=[dplyr ggplot2 ggrepel lmtest magrittr mixOmics plyr purrr stringr tibble tidyr]; };
@ -2136,11 +2137,11 @@ in with self; {
tximeta = derive2 { name="tximeta"; version="1.16.1"; sha256="15qf8s9akl5qp5wklph5i61d96d9ifr5ijl796v1vafwrj4f3wpa"; depends=[AnnotationDbi AnnotationHub BiocFileCache Biostrings ensembldb GenomeInfoDb GenomicFeatures GenomicRanges IRanges jsonlite Matrix S4Vectors SummarizedExperiment tibble tximport]; };
tximport = derive2 { name="tximport"; version="1.26.1"; sha256="1r67q4nb2bx9nqycyr2gnfmh4gizl0c7l510vmlcdvplv3yi73yn"; depends=[]; };
uSORT = derive2 { name="uSORT"; version="1.24.0"; sha256="1fhhl00qdj7ihvb3ia2nd215m1ylbaszpyq1w7bmgv89v5ghhsgf"; depends=[Biobase BiocGenerics cluster fpc gplots igraph Matrix monocle plyr RANN RSpectra VGAM]; };
uncoverappLib = derive2 { name="uncoverappLib"; version="1.7.0"; sha256="1fsn5wpknx1f6sj12x9q456iqi68kwgcqzkk3343hfg185rnn8sh"; depends=[BiocFileCache BSgenome_Hsapiens_UCSC_hg19 BSgenome_Hsapiens_UCSC_hg38 condformat DT EnsDb_Hsapiens_v75 EnsDb_Hsapiens_v86 GenomicRanges Gviz Homo_sapiens markdown openxlsx org_Hs_eg_db OrganismDbi processx rappdirs rlist Rsamtools S4Vectors shiny shinyBS shinycssloaders shinyjs shinyWidgets stringr TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Hsapiens_UCSC_hg38_knownGene]; };
uncoverappLib = derive2 { name="uncoverappLib"; version="1.8.1"; sha256="196xw6m69ld6nnbgqyyr7vd9qgqlczybgs7phvm7g36q4rywsnkm"; depends=[BiocFileCache condformat DT EnsDb_Hsapiens_v75 EnsDb_Hsapiens_v86 GenomicRanges Gviz Homo_sapiens markdown openxlsx org_Hs_eg_db OrganismDbi processx rappdirs rlist Rsamtools S4Vectors shiny shinyBS shinycssloaders shinyjs shinyWidgets stringr TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Hsapiens_UCSC_hg38_knownGene]; };
unifiedWMWqPCR = derive2 { name="unifiedWMWqPCR"; version="1.34.0"; sha256="0zkqr1s8gagwsh33kzp0n2n7ff5jhfn6a60gvab5spk7vr76j442"; depends=[BiocGenerics HTqPCR]; };
universalmotif = derive2 { name="universalmotif"; version="1.16.0"; sha256="1vfg703wxbgxw2cwqqz3kfyqj4za5n3skxxzi8c31azamg4hxs18"; depends=[BiocGenerics Biostrings ggplot2 IRanges MASS Rcpp RcppThread rlang S4Vectors yaml]; };
updateObject = derive2 { name="updateObject"; version="1.2.0"; sha256="13rq1hv0rg8cj3z8d2b9mfih5sybicb4razv8vaic1i7c7sbypwf"; depends=[BiocGenerics digest S4Vectors]; };
variancePartition = derive2 { name="variancePartition"; version="1.28.7"; sha256="0iv5c5p0g4axhanc62mmk0c43qcwdsxzslxh5qdck0v1kb7bd1d9"; depends=[aod Biobase BiocParallel doParallel foreach ggplot2 gplots iterators limma lme4 lmerTest MASS Matrix pbkrtest progress Rdpack remaCor reshape2 RhpcBLASctl rlang scales]; };
variancePartition = derive2 { name="variancePartition"; version="1.28.9"; sha256="1al7wkbv26gldba61gq80c3mznsxwr7z5njv2s0lb7hnll9bscar"; depends=[aod Biobase BiocParallel doParallel foreach ggplot2 gplots iterators limma lme4 lmerTest MASS Matrix pbkrtest progress Rdpack remaCor reshape2 RhpcBLASctl rlang scales]; };
vbmp = derive2 { name="vbmp"; version="1.66.0"; sha256="1gfvk1g9q73p9z91zasblya1w218yhzawp6dgyf0lnldx36kpvc9"; depends=[]; };
velociraptor = derive2 { name="velociraptor"; version="1.8.0"; sha256="07nwx9cahia4a6g15xhccdlwxnhvwq46dy2hqcqqzydgpsapa6wv"; depends=[basilisk BiocGenerics BiocParallel BiocSingular DelayedArray Matrix reticulate S4Vectors scuttle SingleCellExperiment SummarizedExperiment zellkonverter]; };
veloviz = derive2 { name="veloviz"; version="1.4.0"; sha256="01f2d28h0gnh38g50yphmg3aqy1ya2ysj1xabs2a6y3wnqzrahzk"; depends=[igraph Matrix mgcv Rcpp RSpectra]; };
@ -2228,7 +2229,6 @@ in with self; {
methyAnalysis = derive2 { name="methyAnalysis"; version="1.34.0"; sha256="05k3n7iy5ijidbnblbqqas8dsj8drwzbhyrbs8wl1ypkg51havi0"; depends=[annotate AnnotationDbi Biobase BiocGenerics biomaRt genefilter GenomeInfoDb GenomicFeatures GenomicRanges Gviz IRanges lumi methylumi org_Hs_eg_db rtracklayer SummarizedExperiment VariantAnnotation]; broken = true; };
networkBMA = derive2 { name="networkBMA"; version="2.35.0"; sha256="0xa0b977apbr6p9kqk38582af635kp99csj32bsn2bf8pjsmd4d2"; depends=[BH BMA leaps Rcpp RcppArmadillo RcppEigen]; broken = true; };
perturbatr = derive2 { name="perturbatr"; version="1.13.0"; sha256="0ssk8cr42hibn917s2z2nzcdan54c7xiydypbi8f3g4w68q4ly31"; depends=[assertthat diffusr doParallel dplyr foreach formula_tools ggplot2 igraph lazyeval lme4 magrittr rlang scales tibble tidyr]; broken = true; };
phemd = derive2 { name="phemd"; version="1.12.0"; sha256="0nn0qgb0rz4j2xsjq0wydjhg5pmf2ra67rm9fdm4m1izmzwa0nhs"; depends=[Biobase BiocGenerics cluster cowplot destiny ggplot2 igraph maptree monocle phateR pheatmap pracma RANN RColorBrewer reticulate Rtsne S4Vectors scatterplot3d Seurat SingleCellExperiment SummarizedExperiment transport VGAM]; broken = true; };
ppiStats = derive2 { name="ppiStats"; version="1.62.0"; sha256="0w5gkfah2y50x4wj5fn8i6ycx1x013mn9w4bs8r2vfqabpws1a81"; depends=[Biobase Category graph lattice RColorBrewer]; broken = true; };
predictionet = derive2 { name="predictionet"; version="1.40.0"; sha256="1f3ghlcfnls9mx2hbs923rdz7kn0wdhy2csp1y1286c5q5dybrgh"; depends=[catnet igraph MASS penalized RBGL]; broken = true; };
pulsedSilac = derive2 { name="pulsedSilac"; version="1.9.1"; sha256="1zb8xzs9h4rcrnmsfvrwb1qixn3jbnzxdwqgdrb82hgmxabmajlb"; depends=[cowplot ggplot2 ggridges MuMIn R_utils robustbase S4Vectors SummarizedExperiment UpSetR]; broken = true; };

7243
pkgs/development/r-modules/cran-packages.nix generated
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File diff suppressed because it is too large Load diff

7
pkgs/development/r-modules/default.nix
View file

@ -68,9 +68,10 @@ let
hydraPlatforms = [];
};
deriveCran = mkDerive {
mkHomepage = {name, snapshot, ...}: "https://cran.r-project.org/${snapshot}/web/packages/${name}/";
mkUrls = {name, version, snapshot}: [
"https://packagemanager.rstudio.com/cran/${snapshot}/src/contrib/${name}_${version}.tar.gz"
mkHomepage = {name, ...}: "https://cran.r-project.org/web/packages/${name}/";
mkUrls = {name, version}: [
"mirror://cran/${name}_${version}.tar.gz"
"mirror://cran/Archive/${name}/${name}_${version}.tar.gz"
];
};

14
pkgs/development/r-modules/generate-r-packages.R
View file

@ -1,6 +1,5 @@
#!/usr/bin/env Rscript
library(data.table)
library(jsonlite)
library(parallel)
library(BiocManager)
cl <- makeCluster(10)
@ -12,13 +11,11 @@ if ("release" %in% biocVersion$BiocStatus) {
} else {
biocVersion <- max(as.numeric(as.character(biocVersion$Bioc)))
}
dates <- stream_in(url("https://packagemanager.rstudio.com/__api__/repos/2/transaction-dates"), verbose = FALSE)
snapshotDate <- as.Date(dates[nrow(dates), "alias"])
mirrorUrls <- list( bioc=paste0("http://bioconductor.statistik.tu-dortmund.de/packages/", biocVersion, "/bioc/src/contrib/")
, "bioc-annotation"=paste0("http://bioconductor.statistik.tu-dortmund.de/packages/", biocVersion, "/data/annotation/src/contrib/")
, "bioc-experiment"=paste0("http://bioconductor.statistik.tu-dortmund.de/packages/", biocVersion, "/data/experiment/src/contrib/")
, cran=paste0("https://packagemanager.rstudio.com/cran/", snapshotDate, "/src/contrib/")
, cran="https://cran.r-project.org/src/contrib/"
)
mirrorType <- commandArgs(trailingOnly=TRUE)[1]
@ -44,6 +41,10 @@ nixPrefetch <- function(name, version) {
url <- paste0(mirrorUrl, name, "_", version, ".tar.gz")
tmp <- tempfile(pattern=paste0(name, "_", version), fileext=".tar.gz")
cmd <- paste0("wget -q -O '", tmp, "' '", url, "'")
if(mirrorType == "cran"){
archiveUrl <- paste0(mirrorUrl, "Archive/", name, "/", name, "_", version, ".tar.gz")
cmd <- paste0(cmd, " || wget -q -O '", tmp, "' '", archiveUrl, "'")
}
cmd <- paste0(cmd, " && nix-hash --type sha256 --base32 --flat '", tmp, "'")
cmd <- paste0(cmd, " && echo >&2 ' added ", name, " v", version, "'")
cmd <- paste0(cmd, " ; rm -rf '", tmp, "'")
@ -74,9 +75,8 @@ formatPackage <- function(name, version, sha256, depends, imports, linkingTo) {
paste0(" ", attr, " = derive2 { name=\"", name, "\"; version=\"", version, "\"; sha256=\"", sha256, "\"; depends=[", depends, "]; };")
}
clusterExport(cl, c("nixPrefetch","readFormatted", "mirrorUrl", "knownPackages"))
clusterExport(cl, c("nixPrefetch","readFormatted", "mirrorUrl", "mirrorType", "knownPackages"))
pkgs <- as.data.table(available.packages(mirrorUrl, filters=c("R_version", "OS_type", "duplicates"), method="libcurl"))
pkgs <- pkgs[order(Package)]
write(paste("updating", mirrorType, "packages"), stderr())
@ -102,7 +102,7 @@ cat(paste("# Rscript generate-r-packages.R", mirrorType, ">new && mv new", packa
cat("\n\n")
cat("{ self, derive }:\n")
cat("let derive2 = derive ")
if (mirrorType == "cran") { cat("{ snapshot = \"", paste(snapshotDate), "\"; }", sep="")
if (mirrorType == "cran") { cat("{ }")
} else if (mirrorType == "irkernel") { cat("{}")
} else { cat("{ biocVersion = \"", biocVersion, "\"; }", sep="") }
cat(";\n")

1
pkgs/development/r-modules/generate-shell.nix
View file

@ -15,7 +15,6 @@ stdenv.mkDerivation {
(rWrapper.override {
packages = with rPackages; [
data_table
jsonlite
parallel
BiocManager
];

28
pkgs/development/tools/analysis/checkov/default.nix
View file

@ -6,16 +6,15 @@
let
py = python3.override {
packageOverrides = self: super: {
dpath = super.dpath.overridePythonAttrs (oldAttrs: rec {
version = "1.5.0";
src = oldAttrs.src.override {
inherit version;
hash = "sha256-SWYVtOqEI20Y4NKGEi3nSGmmDg+H4sfsZ4f/KGxINhs=";
cyclonedx-python-lib = super.cyclonedx-python-lib.overridePythonAttrs (oldAttrs: rec {
version = "2.7.1";
src = fetchFromGitHub {
owner = "CycloneDX";
repo = "cyclonedx-python-lib";
rev = "v${version}";
hash = "sha256-c/KhoJOa121/h0n0GUazjUFChnUo05ThD+fuZXc5/Pk=";
};
doCheck = false;
});
};
};
in
@ -23,14 +22,14 @@ with py.pkgs;
buildPythonApplication rec {
pname = "checkov";
version = "2.3.96";
version = "2.3.150";
format = "setuptools";
src = fetchFromGitHub {
owner = "bridgecrewio";
repo = pname;
rev = "refs/tags/${version}";
hash = "sha256-jQ5VaOvJkxhZ0fHrNmkuFK+qmRUNdzR5XCWqWv1iBs4=";
hash = "sha256-AgYI3V5xJT6LEZYrJV8nO/86MMp5deuTdLhnUHdrge4=";
};
patches = [
@ -38,17 +37,19 @@ buildPythonApplication rec {
];
pythonRelaxDeps = [
"dpath"
"bc-detect-secrets"
"bc-python-hcl2"
"pycep-parser"
"networkx"
];
nativeBuildInputs = with py.pkgs; [
nativeBuildInputs = [
pythonRelaxDepsHook
setuptools-scm
];
propagatedBuildInputs = with py.pkgs; [
propagatedBuildInputs = [
aiodns
aiohttp
aiomultiprocess
@ -74,6 +75,7 @@ buildPythonApplication rec {
jsonschema
junit-xml
networkx
openai
packaging
policyuniverse
prettytable
@ -87,7 +89,7 @@ buildPythonApplication rec {
update_checker
];
nativeCheckInputs = with py.pkgs; [
nativeCheckInputs = [
aioresponses
mock
pytest-asyncio

55
pkgs/games/openrct2/default.nix
View file

@ -1,4 +1,6 @@
{ lib, stdenv, fetchFromGitHub
{ lib
, stdenv
, fetchFromGitHub
, SDL2
, cmake
@ -26,25 +28,41 @@
}:
let
openrct2-version = "0.4.3";
openrct2-version = "0.4.4";
# Those versions MUST match the pinned versions within the CMakeLists.txt
# file. The REPLAYS repository from the CMakeLists.txt is not necessary.
objects-version = "1.3.7";
objects-version = "1.3.8";
openmsx-version = "1.1.0";
opensfx-version = "1.0.2";
title-sequences-version = "0.4.0";
openrct2-src = fetchFromGitHub {
owner = "OpenRCT2";
repo = "OpenRCT2";
rev = "v${openrct2-version}";
sha256 = "sha256-TAe9b7uqdC8XzwDWZkyYKFV+Rn2AeR3MMBZ1lo9pRis=";
sha256 = "sha256-kCGX+L3bXAG9fUjv04T9wV+R20kmmuREHY8h0w+CESg=";
};
objects-src = fetchFromGitHub {
owner = "OpenRCT2";
repo = "objects";
rev = "v${objects-version}";
sha256 = "sha256-6c6bbXFi6iqmOOfqggXv3DyYgo4+eiPUIDnkKAAhX5s=";
sha256 = "sha256-7fKv2dSsWJ/YIneyVeuPMjdNI/kgJ7zkMoAgV/s240w=";
};
openmsx-src = fetchFromGitHub {
owner = "OpenRCT2";
repo = "OpenMusic";
rev = "v${openmsx-version}";
sha256 = "sha256-SqTYJSst1tgVot/c4seuPQVoxnqWiM2Jb/pP3mHtkKs=";
};
opensfx-src = fetchFromGitHub {
owner = "OpenRCT2";
repo = "OpenSoundEffects";
rev = "v${opensfx-version}";
sha256 = "sha256-AMuCpq1Hszi2Vikto/cX9g81LwBDskaRMTLxNzU0/Gk=";
};
title-sequences-src = fetchFromGitHub {
@ -91,6 +109,8 @@ stdenv.mkDerivation {
cmakeFlags = [
"-DDOWNLOAD_OBJECTS=OFF"
"-DDOWNLOAD_OPENMSX=OFF"
"-DDOWNLOAD_OPENSFX=OFF"
"-DDOWNLOAD_TITLE_SEQUENCES=OFF"
];
@ -100,18 +120,31 @@ stdenv.mkDerivation {
];
postUnpack = ''
mkdir -p $sourceRoot/data/assetpack
cp -r ${objects-src} $sourceRoot/data/object
cp -r ${openmsx-src} $sourceRoot/data/assetpack/openrct2.music.alternative.parkap
cp -r ${opensfx-src} $sourceRoot/data/assetpack/openrct2.sound.parkap
cp -r ${title-sequences-src} $sourceRoot/data/sequence
'';
preConfigure = ''
preConfigure =
# Verify that the correct version of each third party repository is used.
(let
versionCheck = cmakeKey: version: ''
grep -q '^set(${cmakeKey}_VERSION "${version}")$' CMakeLists.txt \
|| (echo "${cmakeKey} differs from expected version!"; exit 1)
'';
in
(versionCheck "OBJECTS" objects-version) +
(versionCheck "OPENMSX" openmsx-version) +
(versionCheck "OPENSFX" opensfx-version) +
(versionCheck "TITLE_SEQUENCE" title-sequences-version)) +
grep -q '^set(OBJECTS_VERSION "${objects-version}")$' CMakeLists.txt \
|| (echo "OBJECTS_VERSION differs!"; exit 1)
grep -q '^set(TITLE_SEQUENCE_VERSION "${title-sequences-version}")$' CMakeLists.txt \
|| (echo "TITLE_SEQUENCE_VERSION differs!"; exit 1)
'';
# Fixup FS rights for the cmake setup-hook in the OPENMSX subsystem
''
chmod -R +w ./data/assetpack/openrct2.music.alternative.parkap/musictools
'';
preFixup = "ln -s $out/share/openrct2 $out/bin/data";

10
pkgs/os-specific/darwin/apple-source-releases/network_cmds/default.nix
View file

@ -1,9 +1,9 @@
{ lib, appleDerivation, xcbuildHook, stdenv
, libressl_3_4, Librpcsvc, xnu, libpcap, developer_cmds }:
, Librpcsvc, xnu, libpcap, developer_cmds }:
appleDerivation {
nativeBuildInputs = [ xcbuildHook ];
buildInputs = [ libressl_3_4 xnu Librpcsvc libpcap developer_cmds ];
buildInputs = [ xnu Librpcsvc libpcap developer_cmds ];
# Work around error from <stdio.h> on aarch64-darwin:
# error: 'TARGET_OS_IPHONE' is not defined, evaluates to 0 [-Werror,-Wundef-prefix=TARGET_OS_]
@ -12,15 +12,13 @@ appleDerivation {
# "spray" requires some files that aren't compiling correctly in xcbuild.
# "rtadvd" seems to fail with some missing constants.
# "traceroute6" and "ping6" require ipsec which doesn't build correctly
# "unbound" doesn’t build against supported versions of OpenSSL or LibreSSL
patchPhase = ''
substituteInPlace network_cmds.xcodeproj/project.pbxproj \
--replace "7294F0EA0EE8BAC80052EC88 /* PBXTargetDependency */," "" \
--replace "7216D34D0EE89FEC00AE70E4 /* PBXTargetDependency */," "" \
--replace "72CD1D9C0EE8C47C005F825D /* PBXTargetDependency */," "" \
--replace "7216D2C20EE89ADF00AE70E4 /* PBXTargetDependency */," ""
'' + lib.optionalString stdenv.isAarch64 ''
# "unbound" does not build on aarch64
substituteInPlace network_cmds.xcodeproj/project.pbxproj \
--replace "7216D2C20EE89ADF00AE70E4 /* PBXTargetDependency */," "" \
--replace "71D958C51A9455A000C9B286 /* PBXTargetDependency */," ""
'';

14
pkgs/os-specific/darwin/utm/default.nix
View file

@ -1,5 +1,6 @@
{ lib
, undmg
, makeWrapper
, fetchurl
, stdenvNoCC
}:
@ -13,12 +14,23 @@ stdenvNoCC.mkDerivation rec {
hash = "sha256-YOmTf50UUvvh4noWnmV6WsoWSua0tpWTgLTg+Cdr3bQ=";
};
nativeBuildInputs = [ undmg ];
nativeBuildInputs = [ undmg makeWrapper ];
sourceRoot = ".";
installPhase = ''
runHook preInstall
mkdir -p $out/Applications
cp -r *.app $out/Applications
mkdir -p $out/bin
for bin in $out/Applications/UTM.app/Contents/MacOS/*; do
# Symlinking `UTM` doesn't work; seems to look for files in the wrong
# place
makeWrapper $bin "$out/bin/$(basename $bin)"
done
runHook postInstall
'';
meta = with lib; {

16
pkgs/os-specific/linux/firmware/ipu6-camera-bins/default.nix
View file

@ -1,6 +1,9 @@
{ lib
, stdenv
, fetchFromGitHub
, autoPatchelfHook
, expat
, zlib
# Pick one of
# - ipu6 (Tiger Lake)
@ -10,17 +13,24 @@
stdenv.mkDerivation {
pname = "${ipuVersion}-camera-bin";
version = "unstable-2022-11-12";
version = "unstable-2023-02-08";
src = fetchFromGitHub {
owner = "intel";
repo = "ipu6-camera-bins";
rev = "4694ba7ee51652d29ef41e7fde846b83a2a1c53b";
hash = "sha256-XPT3dbV6Kl1/TEeiQESF4Q4s95hjtiv4VLlqlahQXqE=";
rev = "276859fc6de83918a32727d676985ec40f31af2b";
hash = "sha256-QnedM2UBbGyd2wIF762Mi+VkDZYtC6MifK4XGGxlUzw=";
};
sourceRoot = "source/${ipuVersion}";
nativeBuildInputs = [
autoPatchelfHook
stdenv.cc.cc.lib
expat
zlib
];
installPhase = ''
runHook preInstall

13
pkgs/os-specific/linux/ipu6-drivers/default.nix
View file

@ -7,15 +7,20 @@
stdenv.mkDerivation rec {
pname = "ipu6-drivers";
version = "unstable-2023-01-17";
version = "unstable-2023-02-20";
src = fetchFromGitHub {
owner = "intel";
repo = pname;
rev = "f83b0747b297cc42325668aaf69471d89253b88e";
hash = "sha256-yl2ZtJUTh1/qmTA8USd+FBCUAY5qNdh4bSvFRPImQNI=";
rev = "dfedab03f3856010d37968cb384696038c73c984";
hash = "sha256-TKo04+fqY64SdDuWApuzRXBnaAW2DReubwFRsdfJMWM=";
};
patches = [
# https://github.com/intel/ipu6-drivers/pull/84
./pr-84-unpatched-upstream-compatiblity.patch
];
postPatch = ''
cp --no-preserve=mode --recursive --verbose \
${ivsc-driver.src}/backport-include \
@ -47,6 +52,6 @@ stdenv.mkDerivation rec {
license = lib.licenses.gpl2;
maintainers = with lib.maintainers; [ hexa ];
platforms = [ "x86_64-linux" ];
broken = kernel.kernelOlder "5.15";
broken = kernel.kernelOlder "6.1.7";
};
}

365
pkgs/os-specific/linux/ipu6-drivers/pr-84-unpatched-upstream-compatiblity.patch Normal file
View file

@ -0,0 +1,365 @@
From 8f4346915bb7e3a3ad3eea2c24b6da09dac257b2 Mon Sep 17 00:00:00 2001
From: Hans de Goede <hdegoede@redhat.com>
Date: Tue, 29 Nov 2022 15:06:23 +0100
Subject: [PATCH 1/4] sensors: Use clk-framework instead of a "clken" GPIO
Use the clk-framework to get a clk-provider reference and use
clk_prepare_enable() / clk_disable_unprepare() to control the clk.
This replace modelling the clock as a "clken" GPIO, which is not a valid
way to model it when the clk is e.g. generated by the clk-generator of
a TPS68470 PMIC.
This relies on the following upstream bugfix for the INT3472 clk provider:
https://git.kernel.org/pub/scm/linux/kernel/git/torvalds/linux.git/commit/?id=cf5ac2d45f6e4d11ad78e7b10ae9a4121ba5e995
"platform/x86: int3472/discrete: Ensure the clk/power enable pins are in output mode"
This patch is available since upstream kernel 6.1.7, so the new
code is only enabled for LINUX_VERSION_CODE >= KERNEL_VERSION(6, 1, 7)
This allow susing the IPU6 sensor drivers with the upstream int3472
driver with unmodified upstream kernels >= 6.1.7 .
Signed-off-by: Hans de Goede <hdegoede@redhat.com>
---
drivers/media/i2c/hm11b1.c | 18 ++++++++++++++++++
drivers/media/i2c/ov01a1s.c | 18 ++++++++++++++++++
2 files changed, 36 insertions(+)
diff --git a/drivers/media/i2c/hm11b1.c b/drivers/media/i2c/hm11b1.c
index 1cc5cd761fbf..e14810bdd612 100644
--- a/drivers/media/i2c/hm11b1.c
+++ b/drivers/media/i2c/hm11b1.c
@@ -468,8 +468,13 @@ struct hm11b1 {
struct gpio_desc *reset_gpio;
/* GPIO for powerdown */
struct gpio_desc *powerdown_gpio;
+#if LINUX_VERSION_CODE < KERNEL_VERSION(6, 1, 7)
/* GPIO for clock enable */
struct gpio_desc *clken_gpio;
+#else
+ /* Clock provider */
+ struct clk *clk;
+#endif
/* GPIO for privacy LED */
struct gpio_desc *pled_gpio;
#endif
@@ -508,7 +513,14 @@ static void hm11b1_set_power(struct hm11b1 *hm11b1, int on)
return;
gpiod_set_value_cansleep(hm11b1->reset_gpio, on);
gpiod_set_value_cansleep(hm11b1->powerdown_gpio, on);
+#if LINUX_VERSION_CODE < KERNEL_VERSION(6, 1, 7)
gpiod_set_value_cansleep(hm11b1->clken_gpio, on);
+#else
+ if (on)
+ clk_prepare_enable(hm11b1->clk);
+ else
+ clk_disable_unprepare(hm11b1->clk);
+#endif
gpiod_set_value_cansleep(hm11b1->pled_gpio, on);
msleep(20);
#elif IS_ENABLED(CONFIG_POWER_CTRL_LOGIC)
@@ -1093,12 +1105,18 @@ static int hm11b1_parse_dt(struct hm11b1 *hm11b1)
return ret;
}
+#if LINUX_VERSION_CODE < KERNEL_VERSION(6, 1, 7)
hm11b1->clken_gpio = devm_gpiod_get(dev, "clken", GPIOD_OUT_HIGH);
ret = PTR_ERR_OR_ZERO(hm11b1->clken_gpio);
if (ret < 0) {
dev_err(dev, "error while getting clken_gpio gpio: %d\n", ret);
return ret;
}
+#else
+ hm11b1->clk = devm_clk_get_optional(dev, "clk");
+ if (IS_ERR(hm11b1->clk))
+ return dev_err_probe(dev, PTR_ERR(hm11b1->clk), "getting clk\n");
+#endif
hm11b1->pled_gpio = devm_gpiod_get(dev, "pled", GPIOD_OUT_HIGH);
ret = PTR_ERR_OR_ZERO(hm11b1->pled_gpio);
diff --git a/drivers/media/i2c/ov01a1s.c b/drivers/media/i2c/ov01a1s.c
index e4477625ce3b..628a1dd83ddf 100644
--- a/drivers/media/i2c/ov01a1s.c
+++ b/drivers/media/i2c/ov01a1s.c
@@ -317,8 +317,13 @@ struct ov01a1s {
struct gpio_desc *reset_gpio;
/* GPIO for powerdown */
struct gpio_desc *powerdown_gpio;
+#if LINUX_VERSION_CODE < KERNEL_VERSION(6, 1, 7)
/* GPIO for clock enable */
struct gpio_desc *clken_gpio;
+#else
+ /* Clock provider */
+ struct clk *clk;
+#endif
/* GPIO for privacy LED */
struct gpio_desc *pled_gpio;
#endif
@@ -339,7 +344,14 @@ static void ov01a1s_set_power(struct ov01a1s *ov01a1s, int on)
return;
gpiod_set_value_cansleep(ov01a1s->reset_gpio, on);
gpiod_set_value_cansleep(ov01a1s->powerdown_gpio, on);
+#if LINUX_VERSION_CODE < KERNEL_VERSION(6, 1, 7)
gpiod_set_value_cansleep(ov01a1s->clken_gpio, on);
+#else
+ if (on)
+ clk_prepare_enable(ov01a1s->clk);
+ else
+ clk_disable_unprepare(ov01a1s->clk);
+#endif
gpiod_set_value_cansleep(ov01a1s->pled_gpio, on);
msleep(20);
#elif IS_ENABLED(CONFIG_POWER_CTRL_LOGIC)
@@ -945,12 +957,18 @@ static int ov01a1s_parse_dt(struct ov01a1s *ov01a1s)
return -EPROBE_DEFER;
}
+#if LINUX_VERSION_CODE < KERNEL_VERSION(6, 1, 7)
ov01a1s->clken_gpio = devm_gpiod_get(dev, "clken", GPIOD_OUT_HIGH);
ret = PTR_ERR_OR_ZERO(ov01a1s->clken_gpio);
if (ret < 0) {
dev_err(dev, "error while getting clken_gpio gpio: %d\n", ret);
return -EPROBE_DEFER;
}
+#else
+ ov01a1s->clk = devm_clk_get_optional(dev, "clk");
+ if (IS_ERR(ov01a1s->clk))
+ return dev_err_probe(dev, PTR_ERR(ov01a1s->clk), "getting clk\n");
+#endif
ov01a1s->pled_gpio = devm_gpiod_get(dev, "pled", GPIOD_OUT_HIGH);
ret = PTR_ERR_OR_ZERO(ov01a1s->pled_gpio);
From b04fdf6433f6b64840d46f92ddf3d6d18e86ede3 Mon Sep 17 00:00:00 2001
From: Hans de Goede <hdegoede@redhat.com>
Date: Tue, 29 Nov 2022 23:37:50 +0100
Subject: [PATCH 2/4] sensors: Make powerdown and reset signals active-low by
default
The powerdown and reset functions should be set to 0, as in
not-powered-down, not-in-reset when the sensor is turned on.
Adjust the gpiod_set() value parameters for the powerdown_gpio
and reset_gpio to !on to properly reflect this.
Typical sensors however have a NRESET aka /RESET pin which needs
to be driven low to put the device in reset and the have
a powerup/enable pin rather then a powerdown pin. So at
the physicical level the pins associated with the reset and
powerdown functions need to be driven low to put the chip
in reset / to power the chip down. Mark the pins as active-low
in the added gpio-lookup table entries for these pin to
reflect this.
This double negation has 0 net effect, but it uses the GPIO
subsystem functionality as intended (setting reset to 0
on poweron makes lot more sense then setting it to 1 on poweron)
and it aligns the use of these GPIOs with that of the mainline
kernel allowing future use of the IPU6 driver with the
mainline INT3472 driver without needing to patch the mainline
kernel.
Signed-off-by: Hans de Goede <hdegoede@redhat.com>
---
drivers/media/i2c/hm11b1.c | 4 ++--
drivers/media/i2c/ov01a1s.c | 4 ++--
drivers/media/i2c/ov2740.c | 2 +-
...nt3472-support-independent-clock-and-LED-gpios-5.17+.patch | 4 ++--
patch/int3472-support-independent-clock-and-LED-gpios.patch | 4 ++--
5 files changed, 9 insertions(+), 9 deletions(-)
diff --git a/drivers/media/i2c/hm11b1.c b/drivers/media/i2c/hm11b1.c
index e14810bdd612..652e8f177044 100644
--- a/drivers/media/i2c/hm11b1.c
+++ b/drivers/media/i2c/hm11b1.c
@@ -511,8 +511,8 @@ static void hm11b1_set_power(struct hm11b1 *hm11b1, int on)
#if IS_ENABLED(CONFIG_INTEL_SKL_INT3472)
if (!(hm11b1->reset_gpio && hm11b1->powerdown_gpio))
return;
- gpiod_set_value_cansleep(hm11b1->reset_gpio, on);
- gpiod_set_value_cansleep(hm11b1->powerdown_gpio, on);
+ gpiod_set_value_cansleep(hm11b1->reset_gpio, !on);
+ gpiod_set_value_cansleep(hm11b1->powerdown_gpio, !on);
#if LINUX_VERSION_CODE < KERNEL_VERSION(6, 1, 7)
gpiod_set_value_cansleep(hm11b1->clken_gpio, on);
#else
diff --git a/drivers/media/i2c/ov01a1s.c b/drivers/media/i2c/ov01a1s.c
index 628a1dd83ddf..2ce81d04abf6 100644
--- a/drivers/media/i2c/ov01a1s.c
+++ b/drivers/media/i2c/ov01a1s.c
@@ -342,8 +342,8 @@ static void ov01a1s_set_power(struct ov01a1s *ov01a1s, int on)
#if IS_ENABLED(CONFIG_INTEL_SKL_INT3472)
if (!(ov01a1s->reset_gpio && ov01a1s->powerdown_gpio))
return;
- gpiod_set_value_cansleep(ov01a1s->reset_gpio, on);
- gpiod_set_value_cansleep(ov01a1s->powerdown_gpio, on);
+ gpiod_set_value_cansleep(ov01a1s->reset_gpio, !on);
+ gpiod_set_value_cansleep(ov01a1s->powerdown_gpio, !on);
#if LINUX_VERSION_CODE < KERNEL_VERSION(6, 1, 7)
gpiod_set_value_cansleep(ov01a1s->clken_gpio, on);
#else
diff --git a/drivers/media/i2c/ov2740.c b/drivers/media/i2c/ov2740.c
index 67fb17e08e36..a8bb101776bd 100644
--- a/drivers/media/i2c/ov2740.c
+++ b/drivers/media/i2c/ov2740.c
@@ -596,7 +596,7 @@ static void ov2740_set_power(struct ov2740 *ov2740, int on)
{
if (!(ov2740->reset_gpio && ov2740->pled_gpio))
return;
- gpiod_set_value_cansleep(ov2740->reset_gpio, on);
+ gpiod_set_value_cansleep(ov2740->reset_gpio, !on);
gpiod_set_value_cansleep(ov2740->pled_gpio, on);
msleep(20);
}
diff --git a/patch/int3472-support-independent-clock-and-LED-gpios-5.17+.patch b/patch/int3472-support-independent-clock-and-LED-gpios-5.17+.patch
index 57373ac85f39..66ed770b68a0 100644
--- a/patch/int3472-support-independent-clock-and-LED-gpios-5.17+.patch
+++ b/patch/int3472-support-independent-clock-and-LED-gpios-5.17+.patch
@@ -65,7 +65,7 @@ index ed4c9d760757..f5857ec334fa 100644
case INT3472_GPIO_TYPE_RESET:
ret = skl_int3472_map_gpio_to_sensor(int3472, agpio, "reset",
- GPIO_ACTIVE_LOW);
-+ polarity);
++ polarity ^ GPIO_ACTIVE_LOW);
if (ret)
err_msg = "Failed to map reset pin to sensor\n";
@@ -73,7 +73,7 @@ index ed4c9d760757..f5857ec334fa 100644
case INT3472_GPIO_TYPE_POWERDOWN:
ret = skl_int3472_map_gpio_to_sensor(int3472, agpio, "powerdown",
- GPIO_ACTIVE_LOW);
-+ polarity);
++ polarity ^ GPIO_ACTIVE_LOW);
if (ret)
err_msg = "Failed to map powerdown pin to sensor\n";
diff --git a/patch/int3472-support-independent-clock-and-LED-gpios.patch b/patch/int3472-support-independent-clock-and-LED-gpios.patch
index a2def0d76852..df70ce4a7117 100644
--- a/patch/int3472-support-independent-clock-and-LED-gpios.patch
+++ b/patch/int3472-support-independent-clock-and-LED-gpios.patch
@@ -65,7 +65,7 @@ index e59d79c7e82f..5cf6dd63d43f 100644
case INT3472_GPIO_TYPE_RESET:
ret = skl_int3472_map_gpio_to_sensor(int3472, agpio, "reset",
- GPIO_ACTIVE_LOW);
-+ polarity);
++ polarity ^ GPIO_ACTIVE_LOW);
if (ret)
err_msg = "Failed to map reset pin to sensor\n";
@@ -73,7 +73,7 @@ index e59d79c7e82f..5cf6dd63d43f 100644
case INT3472_GPIO_TYPE_POWERDOWN:
ret = skl_int3472_map_gpio_to_sensor(int3472, agpio, "powerdown",
- GPIO_ACTIVE_LOW);
-+ polarity);
++ polarity ^ GPIO_ACTIVE_LOW);
if (ret)
err_msg = "Failed to map powerdown pin to sensor\n";
From 90d4b2d9cb07292c6a2580572252938a836f4a86 Mon Sep 17 00:00:00 2001
From: Hans de Goede <hdegoede@redhat.com>
Date: Thu, 15 Dec 2022 16:00:31 +0100
Subject: [PATCH 3/4] sensors: Make "pled" GPIO optional
Starting with kernel 6.3 the mainline int3472 driver models the privacy
LED device as a LED class device rather then as a GPIO.
As part of these changed the v4l2-core subdev code in 6.3 turns
the LED on/off on s_stream() on/off calls on the sensor v4l2-subdev,
so sensor drivers don't have to take care of this themselves.
Change the devm_gpiod_get() calls for the "pled" GPIO into
devm_gpiod_get_optional() calls so that the sensor drivers
can work with both older kernel (controlling the GPIO) and
with newer kernels which don't have a "pled" GPIO.
Signed-off-by: Hans de Goede <hdegoede@redhat.com>
---
drivers/media/i2c/hm11b1.c | 2 +-
drivers/media/i2c/ov01a1s.c | 2 +-
drivers/media/i2c/ov2740.c | 4 +---
3 files changed, 3 insertions(+), 5 deletions(-)
diff --git a/drivers/media/i2c/hm11b1.c b/drivers/media/i2c/hm11b1.c
index 652e8f177044..6257f7987268 100644
--- a/drivers/media/i2c/hm11b1.c
+++ b/drivers/media/i2c/hm11b1.c
@@ -1118,7 +1118,7 @@ static int hm11b1_parse_dt(struct hm11b1 *hm11b1)
return dev_err_probe(dev, PTR_ERR(hm11b1->clk), "getting clk\n");
#endif
- hm11b1->pled_gpio = devm_gpiod_get(dev, "pled", GPIOD_OUT_HIGH);
+ hm11b1->pled_gpio = devm_gpiod_get_optional(dev, "pled", GPIOD_OUT_HIGH);
ret = PTR_ERR_OR_ZERO(hm11b1->pled_gpio);
if (ret < 0) {
dev_err(dev, "error while getting pled gpio: %d\n", ret);
diff --git a/drivers/media/i2c/ov01a1s.c b/drivers/media/i2c/ov01a1s.c
index 2ce81d04abf6..1bc6199713f3 100644
--- a/drivers/media/i2c/ov01a1s.c
+++ b/drivers/media/i2c/ov01a1s.c
@@ -970,7 +970,7 @@ static int ov01a1s_parse_dt(struct ov01a1s *ov01a1s)
return dev_err_probe(dev, PTR_ERR(ov01a1s->clk), "getting clk\n");
#endif
- ov01a1s->pled_gpio = devm_gpiod_get(dev, "pled", GPIOD_OUT_HIGH);
+ ov01a1s->pled_gpio = devm_gpiod_get_optional(dev, "pled", GPIOD_OUT_HIGH);
ret = PTR_ERR_OR_ZERO(ov01a1s->pled_gpio);
if (ret < 0) {
dev_err(dev, "error while getting pled gpio: %d\n", ret);
diff --git a/drivers/media/i2c/ov2740.c b/drivers/media/i2c/ov2740.c
index a8bb101776bd..08f284d4aca1 100644
--- a/drivers/media/i2c/ov2740.c
+++ b/drivers/media/i2c/ov2740.c
@@ -594,8 +594,6 @@ static u64 to_pixels_per_line(u32 hts, u32 f_index)
static void ov2740_set_power(struct ov2740 *ov2740, int on)
{
- if (!(ov2740->reset_gpio && ov2740->pled_gpio))
- return;
gpiod_set_value_cansleep(ov2740->reset_gpio, !on);
gpiod_set_value_cansleep(ov2740->pled_gpio, on);
msleep(20);
@@ -633,7 +631,7 @@ static int ov2740_parse_dt(struct ov2740 *ov2740)
return ret;
}
- ov2740->pled_gpio = devm_gpiod_get(dev, "pled", GPIOD_OUT_HIGH);
+ ov2740->pled_gpio = devm_gpiod_get_optional(dev, "pled", GPIOD_OUT_HIGH);
ret = PTR_ERR_OR_ZERO(ov2740->pled_gpio);
if (ret < 0) {
dev_err(dev, "error while getting pled gpio: %d\n", ret);
From 5ed1980822f0cb4787d1346493d126aad1bf9210 Mon Sep 17 00:00:00 2001
From: Hans de Goede <hdegoede@redhat.com>
Date: Tue, 29 Nov 2022 15:15:15 +0100
Subject: [PATCH 4/4] ov01a1s: Drop unused link_freq variable
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Drop the unused link_freq variable, fixing this compiler warning:
drivers/media/i2c/ov01a1s.c:994:13: warning: unused variable ‘link_freq’ [-Wunused-variable]
994 | s64 link_freq;
| ^~~~~~~~~
Signed-off-by: Hans de Goede <hdegoede@redhat.com>
---
drivers/media/i2c/ov01a1s.c | 1 -
1 file changed, 1 deletion(-)
diff --git a/drivers/media/i2c/ov01a1s.c b/drivers/media/i2c/ov01a1s.c
index 1bc6199713f3..ab4ff255d4c1 100644
--- a/drivers/media/i2c/ov01a1s.c
+++ b/drivers/media/i2c/ov01a1s.c
@@ -988,7 +988,6 @@ static int ov01a1s_probe(struct i2c_client *client)
#if IS_ENABLED(CONFIG_INTEL_VSC)
struct vsc_mipi_config conf;
struct vsc_camera_status status;
- s64 link_freq;
#endif
ov01a1s = devm_kzalloc(&client->dev, sizeof(*ov01a1s), GFP_KERNEL);

81
pkgs/os-specific/linux/v4l2-relayd/default.nix Normal file
View file

@ -0,0 +1,81 @@
{ lib
, stdenv
, fetchgit
, autoreconfHook
, coreutils
, glib
, gnugrep
, gst_all_1
, icamerasrc
, libtool
, makeWrapper
, pkg-config
, which
}:
let
gst = [
gst_all_1.gstreamer.out
gst_all_1.gst-plugins-bad
gst_all_1.gst-plugins-base
gst_all_1.gst-plugins-good
icamerasrc
];
in
stdenv.mkDerivation rec {
pname = "v4l2-relayd-${icamerasrc.ipuVersion}";
version = "0.1.3";
src = fetchgit {
url = "https://git.launchpad.net/v4l2-relayd";
rev = "refs/tags/upstream/${version}";
hash = "sha256-oU6naDFZ0PQVHZ3brANfMULDqYMYxeJN+MCUCvN/DpU=";
};
patches = [
./upstream-v4l2loopback-compatibility.patch
];
nativeBuildInputs = [
autoreconfHook
libtool
makeWrapper
pkg-config
which
];
buildInputs = [
glib
] ++ gst;
preConfigure = "./autogen.sh --prefix=$out";
postInstall = ''
mkdir -p $out/lib/systemd/system $out/etc/default
cp data/systemd/v4l2-relayd.service $out/lib/systemd/system
cp data/etc/default/v4l2-relayd $out/etc/default
substituteInPlace $out/lib/systemd/system/v4l2-relayd.service \
--replace grep ${gnugrep}/bin/grep \
--replace cut ${coreutils}/bin/cut \
--replace /usr/bin/test ${coreutils}/bin/test \
--replace /usr/bin/v4l2-relayd $out/bin/v4l2-relayd \
--replace /etc/default $out/etc/default \
--replace "DeviceAllow=char-video4linux" ""
substituteInPlace $out/etc/default/v4l2-relayd \
--replace 'FORMAT=YUY2' 'FORMAT=NV12' \
--replace 'CARD_LABEL="Virtual Camera"' 'CARD_LABEL="Intel MIPI Camera"' \
--replace 'VIDEOSRC="videotestsrc"' 'VIDEOSRC="icamerasrc"'
wrapProgram $out/bin/v4l2-relayd \
--prefix GST_PLUGIN_PATH : ${lib.makeSearchPathOutput "lib" "lib/gstreamer-1.0" gst}
'';
meta = with lib; {
description = "Streaming relay for v4l2loopback using GStreamer";
homepage = "https://git.launchpad.net/v4l2-relayd";
license = licenses.gpl2;
maintainers = with maintainers; [ betaboon ];
platforms = [ "x86_64-linux" ];
};
}

16
pkgs/os-specific/linux/v4l2-relayd/upstream-v4l2loopback-compatibility.patch Normal file
View file

@ -0,0 +1,16 @@
diff --git a/src/v4l2-relayd.c b/src/v4l2-relayd.c
index 21bb0d5..cfc9e27 100644
--- a/src/v4l2-relayd.c
+++ b/src/v4l2-relayd.c
@@ -27,7 +27,10 @@
#include <gst/app/gstappsrc.h>
#include <gst/video/video-info.h>
-#define V4L2_EVENT_PRI_CLIENT_USAGE V4L2_EVENT_PRIVATE_START
+#define V4L2LOOPBACK_EVENT_BASE (V4L2_EVENT_PRIVATE_START)
+#define V4L2LOOPBACK_EVENT_OFFSET 0x08E00000
+#define V4L2_EVENT_PRI_CLIENT_USAGE \
+ (V4L2LOOPBACK_EVENT_BASE + V4L2LOOPBACK_EVENT_OFFSET + 1)
struct v4l2_event_client_usage {
__u32 count;

11
pkgs/os-specific/linux/v4l2loopback/default.nix
View file

@ -2,15 +2,20 @@
stdenv.mkDerivation rec {
pname = "v4l2loopback";
version = "unstable-2022-08-05-${kernel.version}";
version = "unstable-2023-02-19-${kernel.version}";
src = fetchFromGitHub {
owner = "umlaeute";
repo = "v4l2loopback";
rev = "76434ab6f71d5ecbff8a218ff6bed91ea2bf73b8";
sha256 = "sha256-TdZacRkFAO2HAEbljzXeJ241VcDqSwBECq3bnn7yvBY=";
rev = "fb410fc7af40e972058809a191fae9517b9313af";
hash = "sha256-gLFtR7s+3LUQ0BZxHbmaArHbufuphbtAX99nxJU3c84=";
};
patches = [
# fix bug https://github.com/umlaeute/v4l2loopback/issues/535
./revert-pr518.patch
];
hardeningDisable = [ "format" "pic" ];
preBuild = ''

55
pkgs/os-specific/linux/v4l2loopback/revert-pr518.patch Normal file
View file

@ -0,0 +1,55 @@
diff --git a/v4l2loopback.c b/v4l2loopback.c
index 2ab1f76..2514f09 100644
--- a/v4l2loopback.c
+++ b/v4l2loopback.c
@@ -92,17 +92,6 @@ MODULE_LICENSE("GPL");
} \
} while (0)
-/* TODO: Make sure that function is never interrupted. */
-static inline int mod_inc(int *number, int mod)
-{
- int result;
- result = (*number + 1) % mod;
- if (unlikely(result < 0))
- result += mod;
- *number = result;
- return result;
-}
-
static inline void v4l2l_get_timestamp(struct v4l2_buffer *b)
{
/* ktime_get_ts is considered deprecated, so use ktime_get_ts64 if possible */
@@ -1424,8 +1413,9 @@ static int vidioc_reqbufs(struct file *file, void *fh,
i = dev->write_position;
list_for_each_entry(pos, &dev->outbufs_list,
list_head) {
- dev->bufpos2index[mod_inc(&i, b->count)] =
+ dev->bufpos2index[i % b->count] =
pos->buffer.index;
+ ++i;
}
}
@@ -1489,9 +1479,10 @@ static void buffer_written(struct v4l2_loopback_device *dev,
del_timer_sync(&dev->timeout_timer);
spin_lock_bh(&dev->lock);
- dev->bufpos2index[mod_inc(&dev->write_position, dev->used_buffers)] =
+ dev->bufpos2index[dev->write_position % dev->used_buffers] =
buf->buffer.index;
list_move_tail(&buf->list_head, &dev->outbufs_list);
+ ++dev->write_position;
dev->reread_count = 0;
check_timers(dev);
@@ -1586,7 +1577,8 @@ static int get_capture_buffer(struct file *file)
if (dev->write_position >
opener->read_position + dev->used_buffers)
opener->read_position = dev->write_position - 1;
- pos = mod_inc(&opener->read_position, dev->used_buffers);
+ pos = opener->read_position % dev->used_buffers;
+ ++opener->read_position;
}
timeout_happened = dev->timeout_happened;
dev->timeout_happened = 0;

4
pkgs/servers/dns/pdns-recursor/default.nix
View file

@ -5,11 +5,11 @@
stdenv.mkDerivation rec {
pname = "pdns-recursor";
version = "4.8.3";
version = "4.8.4";
src = fetchurl {
url = "https://downloads.powerdns.com/releases/pdns-recursor-${version}.tar.bz2";
sha256 = "sha256-N7kaVFjFRBH0444tEmPs9B51HkPF/WboExANmXjwJQU=";
sha256 = "sha256-8KY/0I4D2oL6INMz6lF50bkln0JkVGz0mVKGZ32UWMc=";
};
nativeBuildInputs = [ pkg-config ];

4
pkgs/servers/tailscale/default.nix
View file

@ -2,13 +2,13 @@
buildGoModule rec {
pname = "tailscale";
version = "1.38.3";
version = "1.38.4";
src = fetchFromGitHub {
owner = "tailscale";
repo = "tailscale";
rev = "v${version}";
hash = "sha256-UKLneaHGTbGBM3M+GjZbb0mEBkXK3q+ZtTudYh94c0o=";
hash = "sha256-HjN8VzysxQvx5spXgbgbItH3y1bLbfHO+udNQMuyhAk=";
};
vendorHash = "sha256-LIvaxSo+4LuHUk8DIZ27IaRQwaDnjW6Jwm5AEc/V95A=";

6
pkgs/tools/graphics/pfstools/default.nix
View file

@ -18,9 +18,11 @@ mkDerivation rec {
cmakeFlags = [ "-DWITH_MATLAB=false" ];
preConfigure = ''
sed -e 's|#include( ''${PROJECT_SRC_DIR}/cmake/FindNETPBM.cmake )|include( ''${PROJECT_SOURCE_DIR}/cmake/FindNETPBM.cmake )|' -i CMakeLists.txt
rm cmake/FindNETPBM.cmake
echo "SET(NETPBM_LIBRARY `find ${lib.getLib netpbm} -name "*.${stdenv.hostPlatform.extensions.sharedLibrary}*" -type f`)" >> cmake/FindNETPBM.cmake
echo "SET(NETPBM_LIBRARIES `find ${lib.getLib netpbm} -name "*.${stdenv.hostPlatform.extensions.sharedLibrary}*" -type f`)" >> cmake/FindNETPBM.cmake
echo "SET(NETPBM_LIBRARY `find ${lib.getLib netpbm} -name "*${stdenv.hostPlatform.extensions.sharedLibrary}*" -type f`)" >> cmake/FindNETPBM.cmake
echo "SET(NETPBM_LIBRARIES `find ${lib.getLib netpbm} -name "*${stdenv.hostPlatform.extensions.sharedLibrary}*" -type f`)" >> cmake/FindNETPBM.cmake
echo "SET(NETPBM_INCLUDE_DIR ${lib.getDev netpbm}/include/netpbm)" >> cmake/FindNETPBM.cmake
echo "INCLUDE(FindPackageHandleStandardArgs)" >> cmake/FindNETPBM.cmake
echo "FIND_PACKAGE_HANDLE_STANDARD_ARGS(NETPBM DEFAULT_MSG NETPBM_LIBRARY NETPBM_INCLUDE_DIR)" >> cmake/FindNETPBM.cmake

12
pkgs/tools/inputmethods/fcitx5/fcitx5-mozc.nix
View file

@ -84,13 +84,19 @@ in clangStdenv.mkDerivation rec {
'';
buildPhase = ''
runHook preBuild
python build_mozc.py build -c Release \
server/server.gyp:mozc_server \
gui/gui.gyp:mozc_tool \
unix/fcitx5/fcitx5.gyp:fcitx5-mozc
runHook postBuild
'';
installPhase = ''
runHook preInstall
export PREFIX=$out
export _bldtype=Release
../scripts/install_server
@ -101,6 +107,12 @@ in clangStdenv.mkDerivation rec {
install -d $out/share/fcitx5/inputmethod
install -d $out/lib/fcitx5
../scripts/install_fcitx5
runHook postInstall
'';
preFixup = ''
wrapQtApp $out/lib/mozc/mozc_tool
'';
meta = with lib; {

5
pkgs/tools/networking/libreswan/default.nix
View file

@ -89,6 +89,11 @@ stdenv.mkDerivation rec {
-e 's|systemd-tmpfiles|true|g' \
-i initsystems/systemd/Makefile
# Fix systemd detection on NixOS
sed -e 's|\(-a ! -x /bin/journalctl\)|\1 -a ! -x /run/current-system/sw/bin/journalctl|g' \
-e 's|\(-o ! -x /bin/journalctl\)|\1 -o ! -x /run/current-system/sw/bin/journalctl|g' \
-i programs/barf/barf.in
# Fix the ipsec program from crushing the PATH
sed -e 's|\(PATH=".*"\):.*$|\1:$PATH|' -i programs/ipsec/ipsec.in

4
pkgs/tools/package-management/nixpkgs-review/default.nix
View file

@ -14,13 +14,13 @@
python3.pkgs.buildPythonApplication rec {
pname = "nixpkgs-review";
version = "2.9.0";
version = "2.9.1";
src = fetchFromGitHub {
owner = "Mic92";
repo = "nixpkgs-review";
rev = version;
sha256 = "sha256-SNAroKkPXiX5baGPRYnzqiVwPwko/Uari/tvjIU7/4k=";
sha256 = "sha256-9fdoTKaYfqsAXysRwgLq44UrmOGlr5rjF5Ge93PcHDk=";
};
makeWrapperArgs =

6
pkgs/tools/security/cariddi/default.nix
View file

@ -5,16 +5,16 @@
buildGoModule rec {
pname = "cariddi";
version = "1.3.0";
version = "1.3.1";
src = fetchFromGitHub {
owner = "edoardottt";
repo = pname;
rev = "refs/tags/v${version}";
hash = "sha256-pO1FXlkaQveDIfMSWiLB9QvVxmFJixc/HHcEuhg5KmY=";
hash = "sha256-zz9p35Wk5jwp5Cn4+FgJCwG2KKgBuOQsH4lJeAVhpCM=";
};
vendorHash = "sha256-zDKByBISZNRb4sMCrHKGlp4EBtifBfj92tygcaBH/Fc=";
vendorHash = "sha256-s6aEq3LzCj9xzieLD1aC69KV3aeav+bQ5VUZ3TbFetw=";
meta = with lib; {
description = "Crawler for URLs and endpoints";

9
pkgs/tools/security/tpm2-abrmd/default.nix
View file

@ -15,7 +15,14 @@ stdenv.mkDerivation rec {
sha256 = "sha256-l0ncCMsStaeFACRU3Bt6F1zyiOTGY6wOHewA4AD58Ww=";
};
nativeBuildInputs = [ pkg-config makeWrapper autoreconfHook autoconf-archive which ];
nativeBuildInputs = [
autoconf-archive
autoreconfHook
glib
makeWrapper
pkg-config
which
];
buildInputs = [ tpm2-tss glib dbus ];
nativeCheckInputs = [ cmocka ];

4
pkgs/tools/text/ansifilter/default.nix
View file

@ -2,11 +2,11 @@
stdenv.mkDerivation rec {
pname = "ansifilter";
version = "2.18";
version = "2.19";
src = fetchurl {
url = "http://www.andre-simon.de/zip/ansifilter-${version}.tar.bz2";
sha256 = "sha256-Zs8BfTakPV9q4gYJzjtYZHSU7mwOQfxoLFmL/859fTk=";
hash = "sha256-+cJ7GIORShsdSWX0xJsr5QLiqfyd0/YRI6vq6YnDVLw=";
};
nativeBuildInputs = [ pkg-config ];

9
pkgs/top-level/all-packages.nix
View file

@ -27430,6 +27430,13 @@ with pkgs;
v4l-utils = qt5.callPackage ../os-specific/linux/v4l-utils { };
v4l2-relayd-ipu6 = callPackage ../os-specific/linux/v4l2-relayd {
icamerasrc = gst_all_1.icamerasrc-ipu6;
};
v4l2-relayd-ipu6ep = callPackage ../os-specific/linux/v4l2-relayd {
icamerasrc = gst_all_1.icamerasrc-ipu6ep;
};
vendir = callPackage ../development/tools/vendir { };
vndr = callPackage ../development/tools/vndr { };
@ -33371,6 +33378,8 @@ with pkgs;
rke = callPackage ../applications/networking/cluster/rke { };
rke2 = callPackage ../applications/networking/cluster/rke2 { };
rocketchat-desktop = callPackage ../applications/networking/instant-messengers/rocketchat-desktop { };
rofi-unwrapped = callPackage ../applications/misc/rofi { };

10
pkgs/top-level/python-packages.nix
View file

@ -1587,6 +1587,10 @@ self: super: with self; {
calmjs-parse = callPackage ../development/python-modules/calmjs-parse { };
calysto = callPackage ../development/python-modules/calysto { };
calysto-scheme = callPackage ../development/python-modules/calysto-scheme { };
camel-converter = callPackage ../development/python-modules/camel-converter { };
can = callPackage ../development/python-modules/can { };
@ -3731,6 +3735,8 @@ self: super: with self; {
funcsigs = callPackage ../development/python-modules/funcsigs { };
functiontrace = callPackage ../development/python-modules/functiontrace { };
functools32 = callPackage ../development/python-modules/functools32 { };
funcy = callPackage ../development/python-modules/funcy { };
@ -11869,6 +11875,8 @@ self: super: with self; {
torch-tb-profiler = callPackage ../development/python-modules/torch-tb-profiler/default.nix { };
torchaudio = callPackage ../development/python-modules/torchaudio { };
torchaudio-bin = callPackage ../development/python-modules/torchaudio/bin.nix { };
torchgpipe = callPackage ../development/python-modules/torchgpipe { };
@ -12844,6 +12852,8 @@ self: super: with self; {
yarl = callPackage ../development/python-modules/yarl { };
yasi = toPythonModule (callPackage ../development/python-modules/yasi { });
yaspin = callPackage ../development/python-modules/yaspin { };
yaswfp = callPackage ../development/python-modules/yaswfp { };