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synced 2024-09-11 15:08:33 +01:00
Merge master into staging-next
This commit is contained in:
github-actions[bot]
GitHub
commit
46a57b6e9d
1
.github/CODEOWNERS
vendored
1
.github/CODEOWNERS
vendored
|
|
@ -254,6 +254,7 @@ pkgs/development/python-modules/buildcatrust/ @ajs124 @lukegb @mweinelt
|
|||
|
||||
# Idris
|
||||
/pkgs/development/idris-modules @Infinisil
|
||||
/pkgs/development/compilers/idris2 @mattpolzin
|
||||
|
||||
# Bazel
|
||||
/pkgs/development/tools/build-managers/bazel @Profpatsch
|
||||
|
|
|
|||
|
|
@ -1,5 +1,5 @@
|
|||
{ lib, stdenv, fetchurl, fetchpatch, pkg-config, file, zip, wxGTK32, gtk3
|
||||
, contribPlugins ? false, hunspell, gamin, boost, wrapGAppsHook3
|
||||
, contribPlugins ? false, hunspell, boost, wrapGAppsHook3
|
||||
}:
|
||||
|
||||
stdenv.mkDerivation rec {
|
||||
|
|
@ -14,7 +14,7 @@ stdenv.mkDerivation rec {
|
|||
|
||||
nativeBuildInputs = [ pkg-config file zip wrapGAppsHook3 ];
|
||||
buildInputs = [ wxGTK32 gtk3 ]
|
||||
++ lib.optionals contribPlugins [ hunspell gamin boost ];
|
||||
++ lib.optionals contribPlugins [ hunspell boost ];
|
||||
enableParallelBuilding = true;
|
||||
patches = [
|
||||
./writable-projects.patch
|
||||
|
|
@ -119,7 +119,7 @@ stdenv.mkDerivation rec {
|
|||
preConfigure = "substituteInPlace ./configure --replace /usr/bin/file ${file}/bin/file";
|
||||
postConfigure = lib.optionalString stdenv.isLinux "substituteInPlace libtool --replace ldconfig ${stdenv.cc.libc.bin}/bin/ldconfig";
|
||||
configureFlags = [ "--enable-pch=no" ] ++ lib.optionals contribPlugins [
|
||||
("--with-contrib-plugins" + lib.optionalString stdenv.isDarwin "=all,-FileManager,-NassiShneiderman")
|
||||
("--with-contrib-plugins=all,-FileManager" + lib.optionalString stdenv.isDarwin ",-NassiShneiderman")
|
||||
"--with-boost-libdir=${boost}/lib"
|
||||
];
|
||||
postInstall = lib.optionalString stdenv.isDarwin ''
|
||||
|
|
|
|||
|
|
@ -21,13 +21,13 @@ assert withMpv || withVlc || withIina;
|
|||
|
||||
stdenvNoCC.mkDerivation rec {
|
||||
pname = "ani-cli";
|
||||
version = "4.8";
|
||||
version = "4.9";
|
||||
|
||||
src = fetchFromGitHub {
|
||||
owner = "pystardust";
|
||||
repo = "ani-cli";
|
||||
rev = "v${version}";
|
||||
hash = "sha256-vntCiWaONndjU622c1BoCoASQxQf/i7yO0x+70OxzPU=";
|
||||
hash = "sha256-7zuepWTtrFp9RW3zTSjPzyJ9e+09PdKgwcnV+DqPEUY=";
|
||||
};
|
||||
|
||||
nativeBuildInputs = [ makeWrapper ];
|
||||
|
|
|
|||
|
|
@ -11,13 +11,13 @@
|
|||
|
||||
buildGoModule rec {
|
||||
pname = "containerd";
|
||||
version = "1.7.20";
|
||||
version = "1.7.21";
|
||||
|
||||
src = fetchFromGitHub {
|
||||
owner = "containerd";
|
||||
repo = "containerd";
|
||||
rev = "v${version}";
|
||||
hash = "sha256-Q9lTzz+G5PSoChy8MZtbOpO81AyNWXC+CgGkdOg14uY=";
|
||||
hash = "sha256-cL1RKFg+B2gTPMg963DKup5BCLLgF9t9VZn2WlmmWPI=";
|
||||
};
|
||||
|
||||
vendorHash = null;
|
||||
|
|
|
|||
|
|
@ -36,6 +36,29 @@ stdenv.mkDerivation (finalAttrs: {
|
|||
hash = "sha256-cyyxu/oj4QEFp3CVx2WeXa9T4OAUyynuBJHGkBZSxJI=";
|
||||
};
|
||||
|
||||
patches = [
|
||||
# CMake formatting, required for the next two commits to cleanly apply
|
||||
(fetchpatch {
|
||||
url = "https://github.com/hyprwm/xdg-desktop-portal-hyprland/commit/5555f467f68ce7cdf1060991c24263073b95e9da.patch";
|
||||
hash = "sha256-yNkg7GCXDPJdsE7M6J98YylnRxQWpcM5N3olix7Oc1A=";
|
||||
})
|
||||
# removes wayland-scanner from deps, as it includes a pkg-config that
|
||||
# defines that it has a non-existent include directory which trips up CMake
|
||||
(fetchpatch {
|
||||
url = "https://github.com/hyprwm/xdg-desktop-portal-hyprland/commit/0dd9af698b9386bcf25d3ea9f5017eca721831c1.patch";
|
||||
hash = "sha256-Y6eWASHoMXVN2rYJ1rs0jy2qP81/qbHsZU+6b7XNBBg=";
|
||||
})
|
||||
# handle finding wayland-scanner more nicely
|
||||
(fetchpatch {
|
||||
url = "https://github.com/hyprwm/xdg-desktop-portal-hyprland/commit/2425e8f541525fa7409d9f26a8ffaf92a3767251.patch";
|
||||
hash = "sha256-6dCg/U/SIjtvo07Z3tn0Hn8Xwx72nwVz6Q2cFnObonU=";
|
||||
})
|
||||
];
|
||||
|
||||
depsBuildBuild = [
|
||||
pkg-config
|
||||
];
|
||||
|
||||
nativeBuildInputs = [
|
||||
cmake
|
||||
pkg-config
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@
|
|||
|
||||
buildDotnetGlobalTool {
|
||||
pname = "csharpier";
|
||||
version = "0.28.2";
|
||||
version = "0.29.1";
|
||||
executables = "dotnet-csharpier";
|
||||
|
||||
nugetHash = "sha256-fXyE25niM80pPXCLC80Hm9XEHGUMx0XZOMxdVoA0h18=";
|
||||
nugetHash = "sha256-VW9QzbQfbY3Tz+Gz3hQ7VC4wOtwfIYV1Yq2WJz6bL04=";
|
||||
|
||||
meta = with lib; {
|
||||
description = "Opinionated code formatter for C#";
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@
|
|||
|
||||
let
|
||||
pname = "gate";
|
||||
version = "0.39.2";
|
||||
version = "0.39.3";
|
||||
in
|
||||
buildGoModule {
|
||||
inherit pname version;
|
||||
|
|
@ -14,10 +14,10 @@ buildGoModule {
|
|||
owner = "minekube";
|
||||
repo = "gate";
|
||||
rev = "refs/tags/v${version}";
|
||||
hash = "sha256-ocstveux4nSev6jUx0niGxjKk0ljEhhagmHpUKncrQY=";
|
||||
hash = "sha256-K2xpRljlKO9DAlXqnmlWsY67ysv449o2vb+OuSXcvnY=";
|
||||
};
|
||||
|
||||
vendorHash = "sha256-e+XIftRRP0Dig6nIRdxE1x60RU8oXChTyyLIEGOQ5Yc=";
|
||||
vendorHash = "sha256-GatbReuW6azrxHnGuW1omR3HRntLBp0J8in4sRc7sJc=";
|
||||
|
||||
ldflags = [ "-s" "-w" ];
|
||||
|
||||
|
|
|
|||
|
|
@ -7,16 +7,16 @@
|
|||
|
||||
buildGoModule rec {
|
||||
pname = "gickup";
|
||||
version = "0.10.31";
|
||||
version = "0.10.34";
|
||||
|
||||
src = fetchFromGitHub {
|
||||
owner = "cooperspencer";
|
||||
repo = "gickup";
|
||||
rev = "refs/tags/v${version}";
|
||||
hash = "sha256-6du9x5QQN1VJzAABJ+8Fm3YscfoRwKVYZO9tTMz22AQ=";
|
||||
hash = "sha256-cdYQU5pQj+vypFtvPxN1Vg4ckui+vcYUmOJQ9d3XTK4=";
|
||||
};
|
||||
|
||||
vendorHash = "sha256-Nmt7T6sDWVHQZuINvON24Mq638Q04r5bpOBnz2vp4vM=";
|
||||
vendorHash = "sha256-x+K3qXV0F4OKsldsnNcR5w4fmwYyt7V7IDrcHBNPttI=";
|
||||
|
||||
ldflags = [ "-X main.version=${version}" ];
|
||||
|
||||
|
|
|
|||
|
|
@ -6,16 +6,16 @@
|
|||
|
||||
rustPlatform.buildRustPackage rec {
|
||||
pname = "harper";
|
||||
version = "0.9.5";
|
||||
version = "0.10.0";
|
||||
|
||||
src = fetchFromGitHub {
|
||||
owner = "elijah-potter";
|
||||
repo = "harper";
|
||||
rev = "v${version}";
|
||||
hash = "sha256-Tk2YOY9myAGHrNTpgwyqo+P6gGQ+2cpKAJbsA3ZfhUA=";
|
||||
hash = "sha256-DpBCTljIigpyZdiFm8x/bqDn+kzK8ILHpzGqX0d1mI8=";
|
||||
};
|
||||
|
||||
cargoHash = "sha256-9ITfjrtc8LPQ3u3G59xESzqky/PCiea5mJiTIiEAmSA=";
|
||||
cargoHash = "sha256-ZMZq/HRvr+JO/fHBJcyRtKXSzCabxkJRBe6OQjij77g=";
|
||||
|
||||
meta = {
|
||||
description = "Grammar Checker for Developers";
|
||||
|
|
|
|||
|
|
@ -14,13 +14,13 @@
|
|||
|
||||
stdenv.mkDerivation rec {
|
||||
pname = "oidc-agent";
|
||||
version = "5.1.0";
|
||||
version = "5.2.0";
|
||||
|
||||
src = fetchFromGitHub {
|
||||
owner = "indigo-dc";
|
||||
repo = pname;
|
||||
rev = "v${version}";
|
||||
sha256 = "sha256-cOK/rZ/jnyALLuhDM3+qvwwe4Fjkv8diQBkw7NfVo0c=";
|
||||
sha256 = "sha256-Nwna8VbhhXtmEbAxgo/E9QgfuglGuyFK2DwHOZL4WXQ=";
|
||||
};
|
||||
|
||||
nativeBuildInputs = [
|
||||
|
|
|
|||
|
|
@ -5,16 +5,16 @@
|
|||
}:
|
||||
buildGoModule rec {
|
||||
pname = "sesh";
|
||||
version = "1.2.0";
|
||||
version = "2.0.2";
|
||||
|
||||
src = fetchFromGitHub {
|
||||
owner = "joshmedeski";
|
||||
repo = "sesh";
|
||||
rev = "v${version}";
|
||||
hash = "sha256-nihyctFnDRLiDgHeXfn/q4G5IVEAOxh9MqFcsInK9UI=";
|
||||
hash = "sha256-oOr2jJAJuddyIPp9z7ottHFUDSpSyc5+PiNYyVD6Alg=";
|
||||
};
|
||||
|
||||
vendorHash = "sha256-zt1/gE4bVj+3yr9n0kT2FMYMEmiooy3k1lQ77rN6sTk=";
|
||||
vendorHash = "sha256-a45P6yt93l0CnL5mrOotQmE/1r0unjoToXqSJ+spimg=";
|
||||
|
||||
ldflags = [ "-s" "-w" ];
|
||||
|
||||
|
|
|
|||
102
pkgs/by-name/ze/zenn-cli/package.nix
Normal file
102
pkgs/by-name/ze/zenn-cli/package.nix
Normal file
|
|
@ -0,0 +1,102 @@
|
|||
{
|
||||
lib,
|
||||
stdenv,
|
||||
fetchFromGitHub,
|
||||
fetchurl,
|
||||
autoPatchelfHook,
|
||||
makeWrapper,
|
||||
nodejs,
|
||||
pnpm_9,
|
||||
testers,
|
||||
}:
|
||||
let
|
||||
go-turbo-version = "1.7.4";
|
||||
go-turbo-srcs = {
|
||||
x86_64-linux = fetchurl {
|
||||
url = "https://registry.npmjs.org/turbo-linux-64/-/turbo-linux-64-${go-turbo-version}.tgz";
|
||||
hash = "sha256-bwi+jthoDe+SEvCPPNNNv9AR8n5IA1fc4I8cnfC095Y=";
|
||||
};
|
||||
aarch64-linux = fetchurl {
|
||||
url = "https://registry.npmjs.org/turbo-linux-arm64/-/turbo-linux-arm64-${go-turbo-version}.tgz";
|
||||
hash = "sha256-j3mUd3x16tYR3QQweIB07IbCKYuKPeEkKkUHhrpHzyc=";
|
||||
};
|
||||
};
|
||||
go-turbo = stdenv.mkDerivation {
|
||||
pname = "go-turbo";
|
||||
version = go-turbo-version;
|
||||
src = go-turbo-srcs.${stdenv.hostPlatform.system};
|
||||
nativeBuildInputs = [ autoPatchelfHook ];
|
||||
dontBuild = true;
|
||||
installPhase = ''
|
||||
install -Dm755 bin/go-turbo -t $out/bin
|
||||
'';
|
||||
};
|
||||
in
|
||||
|
||||
stdenv.mkDerivation (finalAttrs: {
|
||||
pname = "zenn-cli";
|
||||
version = "0.1.155";
|
||||
|
||||
src = fetchFromGitHub {
|
||||
owner = "zenn-dev";
|
||||
repo = "zenn-editor";
|
||||
rev = "refs/tags/${finalAttrs.version}";
|
||||
hash = "sha256-3SM57DRCz8VuizyUrW6sI9FuBq4NrjoCqriEYUQg27M=";
|
||||
# turborepo requires .git directory
|
||||
leaveDotGit = true;
|
||||
};
|
||||
|
||||
nativeBuildInputs = [
|
||||
nodejs
|
||||
pnpm_9.configHook
|
||||
makeWrapper
|
||||
];
|
||||
|
||||
pnpmDeps = pnpm_9.fetchDeps {
|
||||
inherit (finalAttrs) pname version src;
|
||||
hash = "sha256-FfqBe1WQc6ditizjxYLmjb8mvCjQJMpvyUDdaW29sXY=";
|
||||
};
|
||||
|
||||
preBuild =
|
||||
''
|
||||
echo VITE_EMBED_SERVER_ORIGIN="https://embed.zenn.studio" > packages/zenn-cli/.env
|
||||
''
|
||||
# replace go-turbo since the existing one can't be executed
|
||||
+ lib.optionalString stdenv.hostPlatform.isLinux ''
|
||||
cp ${go-turbo}/bin/go-turbo node_modules/.pnpm/turbo-linux-*/node_modules/turbo-linux*/bin/go-turbo
|
||||
'';
|
||||
|
||||
buildPhase = ''
|
||||
runHook preBuild
|
||||
|
||||
pnpm build --no-daemon
|
||||
|
||||
runHook postBuild
|
||||
'';
|
||||
|
||||
installPhase = ''
|
||||
runHook preInstall
|
||||
|
||||
mkdir -p $out/{bin,lib/node_modules/zenn-cli}
|
||||
cp -r packages/zenn-cli/{dist,LICENSE,package.json,README.md} $out/lib/node_modules/zenn-cli
|
||||
|
||||
makeWrapper "${lib.getExe nodejs}" "$out/bin/zenn" \
|
||||
--add-flags "$out/lib/node_modules/zenn-cli/dist/server/zenn.js"
|
||||
|
||||
runHook postInstall
|
||||
'';
|
||||
|
||||
passthru = {
|
||||
tests.version = testers.testVersion { package = finalAttrs.finalPackage; };
|
||||
};
|
||||
|
||||
meta = {
|
||||
description = "Preview Zenn content locally";
|
||||
homepage = "https://github.com/zenn-dev/zenn-editor";
|
||||
changelog = "https://github.com/zenn-dev/zenn-editor/releases/tag/${finalAttrs.version}";
|
||||
license = lib.licenses.mit;
|
||||
maintainers = with lib.maintainers; [ natsukium ];
|
||||
mainProgram = "zenn";
|
||||
platforms = nodejs.meta.platforms;
|
||||
};
|
||||
})
|
||||
|
|
@ -9,16 +9,16 @@
|
|||
|
||||
rustPlatform.buildRustPackage rec {
|
||||
pname = "erg";
|
||||
version = "0.6.41";
|
||||
version = "0.6.42";
|
||||
|
||||
src = fetchFromGitHub {
|
||||
owner = "erg-lang";
|
||||
repo = "erg";
|
||||
rev = "v${version}";
|
||||
hash = "sha256-CXaHiyPZy454HJfmXnNsUNo30v4PdhupgGz0a8y/q0Y=";
|
||||
hash = "sha256-2tq5bKOUfbRZc0reU6EDk6ZnHn3ZGuNVN37+ZCHfC+M=";
|
||||
};
|
||||
|
||||
cargoHash = "sha256-D3RixepsH6WR7W1REbFLuIzn1eoAacqw0Ripp9lgnpE=";
|
||||
cargoHash = "sha256-71AtzKSCStzWn3ihX4t9JJN8MH1YgPJ+DKgY79Rz0I0=";
|
||||
|
||||
nativeBuildInputs = [
|
||||
makeWrapper
|
||||
|
|
|
|||
|
|
@ -1,73 +0,0 @@
|
|||
From 737452159d521aef2041a2767f3ebf9f68f4b6a9 Mon Sep 17 00:00:00 2001
|
||||
From: Christian Kampka <christian@kampka.net>
|
||||
Date: Tue, 1 Sep 2020 13:54:35 +0200
|
||||
Subject: [PATCH] Pin abstract namespace sockets to host_os
|
||||
|
||||
Running programs with AC_RUN_IFELSE fails when cross-compiling.
|
||||
Since abstract namespace sockets are linux feature, we can easily
|
||||
assume it is available for linux and not for darwin.
|
||||
---
|
||||
configure.in | 47 ++++++-----------------------------------------
|
||||
1 file changed, 6 insertions(+), 41 deletions(-)
|
||||
|
||||
diff --git a/configure.in b/configure.in
|
||||
index eb129db..0ed82ba 100644
|
||||
--- a/configure.in
|
||||
+++ b/configure.in
|
||||
@@ -387,47 +387,12 @@ fi
|
||||
|
||||
#### Abstract sockets
|
||||
|
||||
-AC_MSG_CHECKING(abstract socket namespace)
|
||||
-AC_LANG_PUSH(C)
|
||||
-AC_RUN_IFELSE([AC_LANG_PROGRAM(
|
||||
-[[
|
||||
-#include <sys/types.h>
|
||||
-#include <stdlib.h>
|
||||
-#include <string.h>
|
||||
-#include <stdio.h>
|
||||
-#include <sys/socket.h>
|
||||
-#include <sys/un.h>
|
||||
-#include <errno.h>
|
||||
-]],
|
||||
-[[
|
||||
- int listen_fd;
|
||||
- struct sockaddr_un addr;
|
||||
-
|
||||
- listen_fd = socket (PF_UNIX, SOCK_STREAM, 0);
|
||||
-
|
||||
- if (listen_fd < 0)
|
||||
- {
|
||||
- fprintf (stderr, "socket() failed: %s\n", strerror (errno));
|
||||
- exit (1);
|
||||
- }
|
||||
-
|
||||
- memset (&addr, '\0', sizeof (addr));
|
||||
- addr.sun_family = AF_UNIX;
|
||||
- strcpy (addr.sun_path, "X/tmp/dbus-fake-socket-path-used-in-configure-test");
|
||||
- addr.sun_path[0] = '\0'; /* this is what makes it abstract */
|
||||
-
|
||||
- if (bind (listen_fd, (struct sockaddr*) &addr, SUN_LEN (&addr)) < 0)
|
||||
- {
|
||||
- fprintf (stderr, "Abstract socket namespace bind() failed: %s\n",
|
||||
- strerror (errno));
|
||||
- exit (1);
|
||||
- }
|
||||
- else
|
||||
- exit (0);
|
||||
-]])],
|
||||
- [have_abstract_sockets=yes],
|
||||
- [have_abstract_sockets=no])
|
||||
-AC_LANG_POP(C)
|
||||
+AC_MSG_CHECKING([whether target os has abstract socket namespace])
|
||||
+if test x$target_os = xlinux-gnu ; then
|
||||
+ have_abstract_sockets=yes
|
||||
+else
|
||||
+ have_abstract_sockets=no
|
||||
+fi
|
||||
AC_MSG_RESULT($have_abstract_sockets)
|
||||
|
||||
if test x$enable_abstract_sockets = xyes; then
|
||||
--
|
||||
2.25.4
|
||||
|
||||
|
|
@ -1,68 +0,0 @@
|
|||
Fix for a deadlock:
|
||||
https://bugzilla.gnome.org/show_bug.cgi?id=667230
|
||||
|
||||
From cc14440eface093548cb3bc7814da11d9a99d283 Mon Sep 17 00:00:00 2001
|
||||
From: Anssi Hannula <anssi@mageia.org>
|
||||
Date: Wed, 4 Jan 2012 00:23:55 +0200
|
||||
Subject: [PATCH] fix possible server deadlock in ih_sub_cancel
|
||||
|
||||
ih_sub_foreach() calls ih_sub_cancel() while inotify_lock is locked.
|
||||
However, ih_sub_cancel() locks it again, and locking GMutex recursively
|
||||
causes undefined behaviour.
|
||||
|
||||
Fix that by removing locking from ih_sub_cancel() as ih_sub_foreach()
|
||||
is its only user. Also make the function static so that it won't
|
||||
accidentally get used by other files without locking (inotify-helper.h
|
||||
is an internal server header).
|
||||
|
||||
This should fix the intermittent deadlocks I've been experiencing
|
||||
causing KDE applications to no longer start, and probably also
|
||||
http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=542361
|
||||
---
|
||||
server/inotify-helper.c | 7 ++-----
|
||||
server/inotify-helper.h | 1 -
|
||||
2 files changed, 2 insertions(+), 6 deletions(-)
|
||||
|
||||
diff --git a/server/inotify-helper.c b/server/inotify-helper.c
|
||||
index d77203e..0789fa4 100644
|
||||
--- a/server/inotify-helper.c
|
||||
+++ b/server/inotify-helper.c
|
||||
@@ -123,13 +123,11 @@ ih_sub_add (ih_sub_t * sub)
|
||||
|
||||
/**
|
||||
* Cancels a subscription which was being monitored.
|
||||
+ * inotify_lock must be held when calling.
|
||||
*/
|
||||
-gboolean
|
||||
+static gboolean
|
||||
ih_sub_cancel (ih_sub_t * sub)
|
||||
{
|
||||
- G_LOCK(inotify_lock);
|
||||
-
|
||||
-
|
||||
if (!sub->cancelled)
|
||||
{
|
||||
IH_W("cancelling %s\n", sub->pathname);
|
||||
@@ -140,7 +138,6 @@ ih_sub_cancel (ih_sub_t * sub)
|
||||
sub_list = g_list_remove (sub_list, sub);
|
||||
}
|
||||
|
||||
- G_UNLOCK(inotify_lock);
|
||||
return TRUE;
|
||||
}
|
||||
|
||||
diff --git a/server/inotify-helper.h b/server/inotify-helper.h
|
||||
index 5d3b6d0..d36b5fd 100644
|
||||
--- a/server/inotify-helper.h
|
||||
+++ b/server/inotify-helper.h
|
||||
@@ -34,7 +34,6 @@ gboolean ih_startup (event_callback_t ecb,
|
||||
found_callback_t fcb);
|
||||
gboolean ih_running (void);
|
||||
gboolean ih_sub_add (ih_sub_t *sub);
|
||||
-gboolean ih_sub_cancel (ih_sub_t *sub);
|
||||
|
||||
/* Return FALSE from 'f' if the subscription should be cancelled */
|
||||
void ih_sub_foreach (void *callerdata, gboolean (*f)(ih_sub_t *sub, void *callerdata));
|
||||
--
|
||||
1.7.7.2
|
||||
|
||||
|
|
@ -1,10 +0,0 @@
|
|||
# Generated by debian-patches.sh from debian-patches.txt
|
||||
let
|
||||
prefix = "https://sources.debian.org/data/main/g/gamin/0.1.10-4.1/debian/patches";
|
||||
in
|
||||
[
|
||||
{
|
||||
url = "${prefix}/17_deprecated_const_return.patch";
|
||||
sha256 = "0bssrqcmyivlpk2g0q71d1yavd4wv1lw34l8qipm0ndljjd6rbrk";
|
||||
}
|
||||
]
|
||||
|
|
@ -1,2 +0,0 @@
|
|||
gamin/0.1.10-4.1
|
||||
17_deprecated_const_return.patch
|
||||
|
|
@ -1,50 +0,0 @@
|
|||
{ lib, stdenv, fetchurl, fetchpatch, pkg-config, glib, autoreconfHook }:
|
||||
|
||||
stdenv.mkDerivation rec {
|
||||
pname = "gamin";
|
||||
version = "0.1.10";
|
||||
|
||||
src = fetchurl {
|
||||
url = "https://www.gnome.org/~veillard/gamin/sources/gamin-${version}.tar.gz";
|
||||
sha256 = "18cr51y5qacvs2fc2p1bqv32rs8bzgs6l67zhasyl45yx055y218";
|
||||
};
|
||||
|
||||
nativeBuildInputs = [ pkg-config autoreconfHook ];
|
||||
|
||||
buildInputs = [ glib ];
|
||||
|
||||
# `_GNU_SOURCE' is needed, e.g., to get `struct ucred' from
|
||||
# <sys/socket.h> with Glibc 2.9.
|
||||
configureFlags = [
|
||||
"--disable-debug"
|
||||
"--without-python" # python3 not supported
|
||||
"CPPFLAGS=-D_GNU_SOURCE"
|
||||
];
|
||||
|
||||
preBuild = lib.optionalString stdenv.isDarwin ''
|
||||
sed -i 's/,--version-script=.*$/\\/' libgamin/Makefile
|
||||
'';
|
||||
|
||||
env = lib.optionalAttrs stdenv.cc.isClang {
|
||||
NIX_CFLAGS_COMPILE = "-Wno-error=implicit-function-declaration";
|
||||
};
|
||||
|
||||
patches = [ ./deadlock.patch ]
|
||||
++ map fetchurl (import ./debian-patches.nix)
|
||||
++ lib.optional stdenv.cc.isClang ./returnval.patch
|
||||
++ lib.optional stdenv.hostPlatform.isMusl (fetchpatch {
|
||||
name = "fix-pthread-mutex.patch";
|
||||
url = "https://git.alpinelinux.org/aports/plain/main/gamin/fix-pthread-mutex.patch?h=3.4-stable&id=a1a836b089573752c1b0da7d144c0948b04e8ea8";
|
||||
sha256 = "13igdbqsxb3sz0h417k6ifmq2n4siwqspj6slhc7fdl5wd1fxmdz";
|
||||
}) ++ lib.optional (stdenv.hostPlatform != stdenv.buildPlatform) ./abstract-socket-namespace.patch;
|
||||
|
||||
|
||||
meta = with lib; {
|
||||
homepage = "https://people.gnome.org/~veillard/gamin/";
|
||||
description = "File and directory monitoring system";
|
||||
maintainers = with maintainers; [ lovek323 ];
|
||||
license = licenses.gpl2;
|
||||
platforms = platforms.unix;
|
||||
};
|
||||
}
|
||||
|
||||
|
|
@ -1,12 +0,0 @@
|
|||
diff -rupN gamin-0.1.10-orig/server/gam_eq.c gamin-0.1.10/server/gam_eq.c
|
||||
--- gamin-0.1.10-orig/server/gam_eq.c 2015-04-05 19:25:54.000000000 -0400
|
||||
+++ gamin-0.1.10/server/gam_eq.c 2015-04-05 19:26:00.000000000 -0400
|
||||
@@ -124,7 +124,7 @@ gam_eq_flush (gam_eq_t *eq, GamConnDataP
|
||||
{
|
||||
gboolean done_work = FALSE;
|
||||
if (!eq)
|
||||
- return;
|
||||
+ return done_work;
|
||||
|
||||
#ifdef GAM_EQ_VERBOSE
|
||||
GAM_DEBUG(DEBUG_INFO, "gam_eq: Flushing event queue for %s\n", gam_connection_get_pidname (conn));
|
||||
|
|
@ -21,13 +21,13 @@
|
|||
|
||||
stdenv.mkDerivation rec {
|
||||
pname = "opendht";
|
||||
version = "3.1.11";
|
||||
version = "3.2.0";
|
||||
|
||||
src = fetchFromGitHub {
|
||||
owner = "savoirfairelinux";
|
||||
repo = "opendht";
|
||||
rev = "v${version}";
|
||||
hash = "sha256-lJaQGkhpKfSSNVbP+NqommagtoWyi8CdauVxEhiI9Bc=";
|
||||
hash = "sha256-s172Sj1EvV7Lmnmd+xyKmYF2cDEa8Bot10ovggEsOFg=";
|
||||
};
|
||||
|
||||
nativeBuildInputs = [
|
||||
|
|
|
|||
|
|
@ -11,13 +11,13 @@
|
|||
|
||||
stdenv.mkDerivation rec {
|
||||
pname = "mctc-lib";
|
||||
version = "0.3.1";
|
||||
version = "0.3.2";
|
||||
|
||||
src = fetchFromGitHub {
|
||||
owner = "grimme-lab";
|
||||
repo = pname;
|
||||
rev = "v${version}";
|
||||
hash = "sha256-AXjg/ZsitdDf9fNoGVmVal1iZ4/sxjJb7A9W4yye/rg=";
|
||||
hash = "sha256-dJYKnGlcc4N40h1RnP6MJyBj70/8kb1q4OyKTmlvS70=";
|
||||
};
|
||||
|
||||
nativeBuildInputs = [ gfortran meson ninja pkg-config python3 ];
|
||||
|
|
|
|||
|
|
@ -3,8 +3,14 @@
|
|||
buildPythonPackage,
|
||||
pythonOlder,
|
||||
fetchFromGitHub,
|
||||
|
||||
# build-system
|
||||
hatchling,
|
||||
|
||||
# dependencies
|
||||
typeguard,
|
||||
|
||||
# tests
|
||||
cloudpickle,
|
||||
equinox,
|
||||
ipython,
|
||||
|
|
@ -18,7 +24,7 @@
|
|||
let
|
||||
self = buildPythonPackage rec {
|
||||
pname = "jaxtyping";
|
||||
version = "0.2.33";
|
||||
version = "0.2.34";
|
||||
pyproject = true;
|
||||
|
||||
disabled = pythonOlder "3.9";
|
||||
|
|
@ -27,16 +33,12 @@ let
|
|||
owner = "google";
|
||||
repo = "jaxtyping";
|
||||
rev = "refs/tags/v${version}";
|
||||
hash = "sha256-CL1EONbjjT3SCAn2o1x+1cgfuYWMEgQwbX9j34t+HGs=";
|
||||
hash = "sha256-zkB8/+0PmBKDFhj9dd8QZ5Euglm+W3BBUM4dwFUYYW8=";
|
||||
};
|
||||
|
||||
build-system = [
|
||||
hatchling
|
||||
];
|
||||
build-system = [ hatchling ];
|
||||
|
||||
dependencies = [
|
||||
typeguard
|
||||
];
|
||||
dependencies = [ typeguard ];
|
||||
|
||||
pythonRelaxDeps = [ "typeguard" ];
|
||||
|
||||
|
|
|
|||
|
|
@ -9,14 +9,14 @@
|
|||
|
||||
buildPythonPackage rec {
|
||||
pname = "parse-type";
|
||||
version = "0.6.2";
|
||||
version = "0.6.3";
|
||||
format = "setuptools";
|
||||
|
||||
src = fetchFromGitHub {
|
||||
owner = "jenisys";
|
||||
repo = "parse_type";
|
||||
rev = "refs/tags/v${version}";
|
||||
hash = "sha256-dunvcSi+nN5VruvRUPIEpkyUsmeS+kIYDfS8ibDR96s=";
|
||||
hash = "sha256-oKPyzEKrP9umnDzPC3HwSgWmWkCg/h0ChYVrpseklf8=";
|
||||
};
|
||||
|
||||
propagatedBuildInputs = [
|
||||
|
|
|
|||
|
|
@ -12,7 +12,7 @@
|
|||
|
||||
buildPythonPackage rec {
|
||||
pname = "pipenv-poetry-migrate";
|
||||
version = "0.5.8";
|
||||
version = "0.5.9";
|
||||
format = "pyproject";
|
||||
|
||||
disabled = pythonOlder "3.8";
|
||||
|
|
@ -21,7 +21,7 @@ buildPythonPackage rec {
|
|||
owner = "yhino";
|
||||
repo = "pipenv-poetry-migrate";
|
||||
rev = "refs/tags/v${version}";
|
||||
hash = "sha256-/wWAkO2WKn6o9JClkcxoGfHKZNI3GW9hSXmxmoUJpUM=";
|
||||
hash = "sha256-oV3HdqDuC0t6manVlBqf4cxAWx6U6CbNpCUsBwfAn+o=";
|
||||
};
|
||||
|
||||
nativeBuildInputs = [ poetry-core ];
|
||||
|
|
|
|||
|
|
@ -24,7 +24,7 @@
|
|||
|
||||
buildPythonPackage rec {
|
||||
pname = "python-telegram-bot";
|
||||
version = "21.4";
|
||||
version = "21.5";
|
||||
pyproject = true;
|
||||
|
||||
disabled = pythonOlder "3.8";
|
||||
|
|
@ -33,7 +33,7 @@ buildPythonPackage rec {
|
|||
owner = "python-telegram-bot";
|
||||
repo = "python-telegram-bot";
|
||||
rev = "refs/tags/v${version}";
|
||||
hash = "sha256-5raEejd8WH9JrFvMIy2AuMGK9O/FJ2rq9PeVqK+IMOU=";
|
||||
hash = "sha256-i1YEcN615xeI4HcygXV9kzuXpT2yDSnlNU6bZqu1dPM=";
|
||||
};
|
||||
|
||||
build-system = [ setuptools hatchling ];
|
||||
|
|
|
|||
File diff suppressed because it is too large
Load diff
|
|
@ -85,7 +85,7 @@
|
|||
"name": "BeadArrayUseCases",
|
||||
"version": "1.42.0",
|
||||
"sha256": "1s62vqvl3zxf97syp5lymacah594m8szk23skl4bk88jkzkkx6a5",
|
||||
"depends": ["beadarray", "GEOquery", "limma"]
|
||||
"depends": ["GEOquery", "beadarray", "limma"]
|
||||
},
|
||||
"BeadSorted_Saliva_EPIC": {
|
||||
"name": "BeadSorted.Saliva.EPIC",
|
||||
|
|
@ -97,19 +97,19 @@
|
|||
"name": "BioImageDbs",
|
||||
"version": "1.12.0",
|
||||
"sha256": "1cs6c80h34xbzpsgrpy5aj1f0nlxmy713jj1q5g156z5kiz3mzwc",
|
||||
"depends": ["animation", "AnnotationHub", "EBImage", "einsum", "ExperimentHub", "filesstrings", "magick", "magrittr", "markdown", "rmarkdown"]
|
||||
"depends": ["AnnotationHub", "EBImage", "ExperimentHub", "animation", "einsum", "filesstrings", "magick", "magrittr", "markdown", "rmarkdown"]
|
||||
},
|
||||
"BioPlex": {
|
||||
"name": "BioPlex",
|
||||
"version": "1.10.0",
|
||||
"sha256": "1bkakf7yi1lhwc48pmwifk7qdnc9hzaqnlcni7sy0ypwgb1mfsh7",
|
||||
"depends": ["BiocFileCache", "GenomeInfoDb", "GenomicRanges", "GEOquery", "graph", "SummarizedExperiment"]
|
||||
"depends": ["BiocFileCache", "GEOquery", "GenomeInfoDb", "GenomicRanges", "SummarizedExperiment", "graph"]
|
||||
},
|
||||
"BloodCancerMultiOmics2017": {
|
||||
"name": "BloodCancerMultiOmics2017",
|
||||
"version": "1.24.0",
|
||||
"sha256": "16c6nirflpj0zf2wrj0hb5xcq2168si95np3sm76r3kvwlr48zm7",
|
||||
"depends": ["beeswarm", "Biobase", "DESeq2", "devtools", "dplyr", "ggdendro", "ggplot2", "glmnet", "gtable", "ipflasso", "RColorBrewer", "reshape2", "scales", "SummarizedExperiment", "survival", "tibble"]
|
||||
"depends": ["Biobase", "DESeq2", "RColorBrewer", "SummarizedExperiment", "beeswarm", "devtools", "dplyr", "ggdendro", "ggplot2", "glmnet", "gtable", "ipflasso", "reshape2", "scales", "survival", "tibble"]
|
||||
},
|
||||
"CCl4": {
|
||||
"name": "CCl4",
|
||||
|
|
@ -121,7 +121,7 @@
|
|||
"name": "CLL",
|
||||
"version": "1.44.0",
|
||||
"sha256": "18bjaqf6cjvjfcp80b5zmb48qbywacqs6aiarsh6ksq2yj4np4zs",
|
||||
"depends": ["affy", "Biobase"]
|
||||
"depends": ["Biobase", "affy"]
|
||||
},
|
||||
"CLLmethylation": {
|
||||
"name": "CLLmethylation",
|
||||
|
|
@ -259,19 +259,19 @@
|
|||
"name": "DNAZooData",
|
||||
"version": "1.4.0",
|
||||
"sha256": "1bs2pnak2v2szp7zly8ysf8pqh7f70w70cbqqzvnxlf35npv7cxd",
|
||||
"depends": ["BiocFileCache", "HiCExperiment", "rjson", "S4Vectors"]
|
||||
"depends": ["BiocFileCache", "HiCExperiment", "S4Vectors", "rjson"]
|
||||
},
|
||||
"DeSousa2013": {
|
||||
"name": "DeSousa2013",
|
||||
"version": "1.40.0",
|
||||
"sha256": "1icjl4rr8jk16hs8ri925v3gf9lasi4x39yf5a7av39byb2zwqif",
|
||||
"depends": ["affy", "AnnotationDbi", "Biobase", "cluster", "ConsensusClusterPlus", "frma", "frmaTools", "gplots", "hgu133plus2_db", "hgu133plus2frmavecs", "pamr", "rgl", "ROCR", "siggenes", "survival", "sva"]
|
||||
"depends": ["AnnotationDbi", "Biobase", "ConsensusClusterPlus", "ROCR", "affy", "cluster", "frma", "frmaTools", "gplots", "hgu133plus2_db", "hgu133plus2frmavecs", "pamr", "rgl", "siggenes", "survival", "sva"]
|
||||
},
|
||||
"DmelSGI": {
|
||||
"name": "DmelSGI",
|
||||
"version": "1.36.0",
|
||||
"sha256": "0xjj2ky0k8vazw97qsaf79c6cc3whxg0n5v6lrj6slk4hyfcmbw4",
|
||||
"depends": ["abind", "gplots", "igraph", "knitr", "limma", "rhdf5", "TSP"]
|
||||
"depends": ["TSP", "abind", "gplots", "igraph", "knitr", "limma", "rhdf5"]
|
||||
},
|
||||
"DonaPLLP2013": {
|
||||
"name": "DonaPLLP2013",
|
||||
|
|
@ -295,7 +295,7 @@
|
|||
"name": "DuoClustering2018",
|
||||
"version": "1.22.0",
|
||||
"sha256": "042v3dpirp68qsdbhygvx3apx94xxdmzpm0swii30kzkw1r1xfck",
|
||||
"depends": ["dplyr", "ExperimentHub", "ggplot2", "ggthemes", "magrittr", "mclust", "purrr", "reshape2", "tidyr", "viridis"]
|
||||
"depends": ["ExperimentHub", "dplyr", "ggplot2", "ggthemes", "magrittr", "mclust", "purrr", "reshape2", "tidyr", "viridis"]
|
||||
},
|
||||
"DvDdata": {
|
||||
"name": "DvDdata",
|
||||
|
|
@ -319,7 +319,7 @@
|
|||
"name": "EatonEtAlChIPseq",
|
||||
"version": "0.42.0",
|
||||
"sha256": "109law5cc64xipwqyanw71h8v5nx08s1iaskh05hm1w18dsjxff1",
|
||||
"depends": ["GenomicRanges", "rtracklayer", "ShortRead"]
|
||||
"depends": ["GenomicRanges", "ShortRead", "rtracklayer"]
|
||||
},
|
||||
"EpiMix_data": {
|
||||
"name": "EpiMix.data",
|
||||
|
|
@ -349,13 +349,13 @@
|
|||
"name": "Fletcher2013a",
|
||||
"version": "1.40.0",
|
||||
"sha256": "0l839hd76xr94qjcnscr9c40nvsx99ir6vsy1zx6dn7cha52mpar",
|
||||
"depends": ["Biobase", "gplots", "limma", "VennDiagram"]
|
||||
"depends": ["Biobase", "VennDiagram", "gplots", "limma"]
|
||||
},
|
||||
"Fletcher2013b": {
|
||||
"name": "Fletcher2013b",
|
||||
"version": "1.40.0",
|
||||
"sha256": "0agnkc207bma3h89xxrzcywny664f42vfd63qnmyda4kvdvvk0km",
|
||||
"depends": ["Fletcher2013a", "igraph", "RColorBrewer", "RedeR", "RTN"]
|
||||
"depends": ["Fletcher2013a", "RColorBrewer", "RTN", "RedeR", "igraph"]
|
||||
},
|
||||
"FlowSorted_Blood_450k": {
|
||||
"name": "FlowSorted.Blood.450k",
|
||||
|
|
@ -367,7 +367,7 @@
|
|||
"name": "FlowSorted.Blood.EPIC",
|
||||
"version": "2.8.0",
|
||||
"sha256": "1b0azyslk2g08i6v1vv2niw32f0zqasw85b9klw83zdy2f5dcdvh",
|
||||
"depends": ["AnnotationHub", "ExperimentHub", "genefilter", "minfi", "nlme", "quadprog", "S4Vectors", "SummarizedExperiment"]
|
||||
"depends": ["AnnotationHub", "ExperimentHub", "S4Vectors", "SummarizedExperiment", "genefilter", "minfi", "nlme", "quadprog"]
|
||||
},
|
||||
"FlowSorted_CordBlood_450k": {
|
||||
"name": "FlowSorted.CordBlood.450k",
|
||||
|
|
@ -379,7 +379,7 @@
|
|||
"name": "FlowSorted.CordBloodCombined.450k",
|
||||
"version": "1.20.0",
|
||||
"sha256": "14486v4cs3j1jmifsgy3ihpm5x7i9581yz4bwsl3h2a7p86cdsbv",
|
||||
"depends": ["AnnotationHub", "ExperimentHub", "IlluminaHumanMethylation450kanno_ilmn12_hg19", "IlluminaHumanMethylationEPICanno_ilm10b4_hg19", "minfi", "SummarizedExperiment"]
|
||||
"depends": ["AnnotationHub", "ExperimentHub", "IlluminaHumanMethylation450kanno_ilmn12_hg19", "IlluminaHumanMethylationEPICanno_ilm10b4_hg19", "SummarizedExperiment", "minfi"]
|
||||
},
|
||||
"FlowSorted_CordBloodNorway_450k": {
|
||||
"name": "FlowSorted.CordBloodNorway.450k",
|
||||
|
|
@ -415,7 +415,7 @@
|
|||
"name": "GSE13015",
|
||||
"version": "1.12.0",
|
||||
"sha256": "0l1v30g1g93wk5bnhkw52pwypby6n0rxpp11aw93j733whn9j2y4",
|
||||
"depends": ["Biobase", "GEOquery", "preprocessCore", "SummarizedExperiment"]
|
||||
"depends": ["Biobase", "GEOquery", "SummarizedExperiment", "preprocessCore"]
|
||||
},
|
||||
"GSE159526": {
|
||||
"name": "GSE159526",
|
||||
|
|
@ -445,7 +445,7 @@
|
|||
"name": "GenomicDistributionsData",
|
||||
"version": "1.12.0",
|
||||
"sha256": "16cj8w6n053aciz9wclppmc22b9s4a9lh58r6wi2lhs0sp7iirzn",
|
||||
"depends": ["AnnotationFilter", "AnnotationHub", "BSgenome", "data_table", "ensembldb", "ExperimentHub", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges"]
|
||||
"depends": ["AnnotationFilter", "AnnotationHub", "BSgenome", "ExperimentHub", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "data_table", "ensembldb"]
|
||||
},
|
||||
"GeuvadisTranscriptExpr": {
|
||||
"name": "GeuvadisTranscriptExpr",
|
||||
|
|
@ -463,19 +463,19 @@
|
|||
"name": "HCATonsilData",
|
||||
"version": "1.2.0",
|
||||
"sha256": "1wg0mvc3gwf80bgsfkvdcnnzy7qbnffbbrcy3f87jyw4a20irpp1",
|
||||
"depends": ["base64enc", "ExperimentHub", "HDF5Array", "htmltools", "rmarkdown", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment"]
|
||||
"depends": ["ExperimentHub", "HDF5Array", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "base64enc", "htmltools", "rmarkdown"]
|
||||
},
|
||||
"HD2013SGI": {
|
||||
"name": "HD2013SGI",
|
||||
"version": "1.44.0",
|
||||
"sha256": "0r4nlbz7b70z1ii9wisk8nj218m2j5qmpfj8k2sp8k723gmsg4x0",
|
||||
"depends": ["EBImage", "geneplotter", "gplots", "limma", "LSD", "RColorBrewer", "splots", "vcd"]
|
||||
"depends": ["EBImage", "LSD", "RColorBrewer", "geneplotter", "gplots", "limma", "splots", "vcd"]
|
||||
},
|
||||
"HDCytoData": {
|
||||
"name": "HDCytoData",
|
||||
"version": "1.24.0",
|
||||
"sha256": "0pmzgp7x1zam3b7agi8mdq14qmx8nln9lnhiglax2pvg2a5n4ii4",
|
||||
"depends": ["ExperimentHub", "flowCore", "SummarizedExperiment"]
|
||||
"depends": ["ExperimentHub", "SummarizedExperiment", "flowCore"]
|
||||
},
|
||||
"HEEBOdata": {
|
||||
"name": "HEEBOdata",
|
||||
|
|
@ -493,13 +493,13 @@
|
|||
"name": "HMP16SData",
|
||||
"version": "1.24.0",
|
||||
"sha256": "16x7mw5bdsyda1qv0v739pkr8lxq8hga84vhmaa8qnx45pwqyyh0",
|
||||
"depends": ["AnnotationHub", "assertthat", "dplyr", "ExperimentHub", "kableExtra", "knitr", "magrittr", "readr", "S4Vectors", "stringr", "SummarizedExperiment", "tibble"]
|
||||
"depends": ["AnnotationHub", "ExperimentHub", "S4Vectors", "SummarizedExperiment", "assertthat", "dplyr", "kableExtra", "knitr", "magrittr", "readr", "stringr", "tibble"]
|
||||
},
|
||||
"HMP2Data": {
|
||||
"name": "HMP2Data",
|
||||
"version": "1.18.0",
|
||||
"sha256": "014bf29kg9dizi3p0fdxrs42bf9a0dc2f7zd7yxzvzs3jqvniji2",
|
||||
"depends": ["AnnotationHub", "assertthat", "data_table", "dplyr", "ExperimentHub", "kableExtra", "knitr", "magrittr", "MultiAssayExperiment", "phyloseq", "readr", "S4Vectors", "SummarizedExperiment"]
|
||||
"depends": ["AnnotationHub", "ExperimentHub", "MultiAssayExperiment", "S4Vectors", "SummarizedExperiment", "assertthat", "data_table", "dplyr", "kableExtra", "knitr", "magrittr", "phyloseq", "readr"]
|
||||
},
|
||||
"HSMMSingleCell": {
|
||||
"name": "HSMMSingleCell",
|
||||
|
|
@ -529,7 +529,7 @@
|
|||
"name": "HiBED",
|
||||
"version": "1.2.0",
|
||||
"sha256": "0sqxlm2nn8g7qfwhndf79dg7v57ngmznr0b297v59nhhpigs1g2q",
|
||||
"depends": ["AnnotationHub", "dplyr", "FlowSorted_Blood_EPIC", "FlowSorted_DLPFC_450k", "minfi", "SummarizedExperiment", "tibble"]
|
||||
"depends": ["AnnotationHub", "FlowSorted_Blood_EPIC", "FlowSorted_DLPFC_450k", "SummarizedExperiment", "dplyr", "minfi", "tibble"]
|
||||
},
|
||||
"HiCDataHumanIMR90": {
|
||||
"name": "HiCDataHumanIMR90",
|
||||
|
|
@ -559,7 +559,7 @@
|
|||
"name": "Hiiragi2013",
|
||||
"version": "1.40.0",
|
||||
"sha256": "0xn3ayh2x04cvwrr476k8vlp8lhk5lxaqg01a0ynkrrc4scf2f99",
|
||||
"depends": ["affy", "Biobase", "boot", "clue", "cluster", "genefilter", "geneplotter", "gplots", "gtools", "KEGGREST", "lattice", "latticeExtra", "MASS", "mouse4302_db", "RColorBrewer", "xtable"]
|
||||
"depends": ["Biobase", "KEGGREST", "MASS", "RColorBrewer", "affy", "boot", "clue", "cluster", "genefilter", "geneplotter", "gplots", "gtools", "lattice", "latticeExtra", "mouse4302_db", "xtable"]
|
||||
},
|
||||
"HumanAffyData": {
|
||||
"name": "HumanAffyData",
|
||||
|
|
@ -571,7 +571,7 @@
|
|||
"name": "IHWpaper",
|
||||
"version": "1.32.0",
|
||||
"sha256": "0s3x2chbr8ik3rhgzmfhaq8xlsnnkzfhjh4p327sn5aar6xhaj67",
|
||||
"depends": ["Biobase", "BiocGenerics", "BiocParallel", "cowplot", "DESeq2", "dplyr", "fdrtool", "genefilter", "ggplot2", "IHW", "qvalue", "Rcpp", "SummarizedExperiment"]
|
||||
"depends": ["Biobase", "BiocGenerics", "BiocParallel", "DESeq2", "IHW", "Rcpp", "SummarizedExperiment", "cowplot", "dplyr", "fdrtool", "genefilter", "ggplot2", "qvalue"]
|
||||
},
|
||||
"ITALICSData": {
|
||||
"name": "ITALICSData",
|
||||
|
|
@ -613,7 +613,7 @@
|
|||
"name": "JohnsonKinaseData",
|
||||
"version": "1.0.0",
|
||||
"sha256": "1ry5p2zll8hazxil4sa57v50b7xr9bk4p5a509i4mvasb089al3l",
|
||||
"depends": ["BiocParallel", "checkmate", "dplyr", "ExperimentHub", "purrr", "stringr", "tidyr"]
|
||||
"depends": ["BiocParallel", "ExperimentHub", "checkmate", "dplyr", "purrr", "stringr", "tidyr"]
|
||||
},
|
||||
"KEGGandMetacoreDzPathwaysGEO": {
|
||||
"name": "KEGGandMetacoreDzPathwaysGEO",
|
||||
|
|
@ -679,7 +679,7 @@
|
|||
"name": "MAQCsubset",
|
||||
"version": "1.42.0",
|
||||
"sha256": "0x59gbv91d90hasa2gwkv00c06zp8fj4fk18386ajfag0wpvpb2n",
|
||||
"depends": ["affy", "Biobase", "lumi"]
|
||||
"depends": ["Biobase", "affy", "lumi"]
|
||||
},
|
||||
"MEDIPSData": {
|
||||
"name": "MEDIPSData",
|
||||
|
|
@ -733,25 +733,25 @@
|
|||
"name": "MetaGxBreast",
|
||||
"version": "1.24.0",
|
||||
"sha256": "05cz500r6fhlq5pfviiqj8cfv173027dqsdvhvvi57cbbx3qqn6r",
|
||||
"depends": ["AnnotationHub", "Biobase", "ExperimentHub", "impute", "lattice", "SummarizedExperiment"]
|
||||
"depends": ["AnnotationHub", "Biobase", "ExperimentHub", "SummarizedExperiment", "impute", "lattice"]
|
||||
},
|
||||
"MetaGxOvarian": {
|
||||
"name": "MetaGxOvarian",
|
||||
"version": "1.24.0",
|
||||
"sha256": "01cnm2rf6ls1q5plgazxqkrrw3b6mcrxbq0wrmi0ra8daqh6asi7",
|
||||
"depends": ["AnnotationHub", "Biobase", "ExperimentHub", "impute", "lattice", "SummarizedExperiment"]
|
||||
"depends": ["AnnotationHub", "Biobase", "ExperimentHub", "SummarizedExperiment", "impute", "lattice"]
|
||||
},
|
||||
"MetaGxPancreas": {
|
||||
"name": "MetaGxPancreas",
|
||||
"version": "1.24.0",
|
||||
"sha256": "150i72jrq3qshsh0m20kxdcx7zxz1cgvlk0y2nxnacs1xbdnywxv",
|
||||
"depends": ["AnnotationHub", "ExperimentHub", "impute", "S4Vectors", "SummarizedExperiment"]
|
||||
"depends": ["AnnotationHub", "ExperimentHub", "S4Vectors", "SummarizedExperiment", "impute"]
|
||||
},
|
||||
"MetaScope": {
|
||||
"name": "MetaScope",
|
||||
"version": "1.4.0",
|
||||
"sha256": "1kaisvhp66g95w4dycw8jzsxh00f2c193rjcla6l5k2dn5rnsyr9",
|
||||
"depends": ["BiocFileCache", "Biostrings", "data_table", "dplyr", "ggplot2", "magrittr", "Matrix", "MultiAssayExperiment", "Rbowtie2", "readr", "rlang", "Rsamtools", "S4Vectors", "stringr", "SummarizedExperiment", "taxize", "tibble", "tidyr"]
|
||||
"depends": ["BiocFileCache", "Biostrings", "Matrix", "MultiAssayExperiment", "Rbowtie2", "Rsamtools", "S4Vectors", "SummarizedExperiment", "data_table", "dplyr", "ggplot2", "magrittr", "readr", "rlang", "stringr", "taxize", "tibble", "tidyr"]
|
||||
},
|
||||
"MethylAidData": {
|
||||
"name": "MethylAidData",
|
||||
|
|
@ -763,13 +763,13 @@
|
|||
"name": "MethylSeqData",
|
||||
"version": "1.14.0",
|
||||
"sha256": "197347pavq9hjcpwa9lq66lyjr1jb7mymd9pjz01rr9f77d7rqq5",
|
||||
"depends": ["ExperimentHub", "GenomeInfoDb", "GenomicRanges", "HDF5Array", "IRanges", "rhdf5", "S4Vectors", "SummarizedExperiment"]
|
||||
"depends": ["ExperimentHub", "GenomeInfoDb", "GenomicRanges", "HDF5Array", "IRanges", "S4Vectors", "SummarizedExperiment", "rhdf5"]
|
||||
},
|
||||
"MicrobiomeBenchmarkData": {
|
||||
"name": "MicrobiomeBenchmarkData",
|
||||
"version": "1.6.0",
|
||||
"sha256": "00lr183x24yx4xd9cpxvzkcxmqp4dinfi1nz2arqqxnbfcp2s25j",
|
||||
"depends": ["ape", "BiocFileCache", "S4Vectors", "SummarizedExperiment", "TreeSummarizedExperiment"]
|
||||
"depends": ["BiocFileCache", "S4Vectors", "SummarizedExperiment", "TreeSummarizedExperiment", "ape"]
|
||||
},
|
||||
"MouseAgingData": {
|
||||
"name": "MouseAgingData",
|
||||
|
|
@ -811,7 +811,7 @@
|
|||
"name": "NestLink",
|
||||
"version": "1.20.0",
|
||||
"sha256": "1yh1nivipyrx3h0par8cf943licl1rs47jvfwz1392hi09vji15j",
|
||||
"depends": ["AnnotationHub", "Biostrings", "ExperimentHub", "gplots", "protViz", "ShortRead"]
|
||||
"depends": ["AnnotationHub", "Biostrings", "ExperimentHub", "ShortRead", "gplots", "protViz"]
|
||||
},
|
||||
"NetActivityData": {
|
||||
"name": "NetActivityData",
|
||||
|
|
@ -823,7 +823,7 @@
|
|||
"name": "Neve2006",
|
||||
"version": "0.42.0",
|
||||
"sha256": "0w3ph610lhxyg1knhsnnxpw32sw2n5p57svpbhqm3zmphx29nw3h",
|
||||
"depends": ["annotate", "Biobase", "hgu133a_db"]
|
||||
"depends": ["Biobase", "annotate", "hgu133a_db"]
|
||||
},
|
||||
"NxtIRFdata": {
|
||||
"name": "NxtIRFdata",
|
||||
|
|
@ -859,7 +859,7 @@
|
|||
"name": "PREDAsampledata",
|
||||
"version": "0.44.0",
|
||||
"sha256": "0ydb4y2s8kshia7k6mr941f1fc7nsqahm1g86ig3wpcq7al33z1b",
|
||||
"depends": ["affy", "annotate", "Biobase", "PREDA"]
|
||||
"depends": ["Biobase", "PREDA", "affy", "annotate"]
|
||||
},
|
||||
"PWMEnrich_Dmelanogaster_background": {
|
||||
"name": "PWMEnrich.Dmelanogaster.background",
|
||||
|
|
@ -961,7 +961,7 @@
|
|||
"name": "RNAinteractMAPK",
|
||||
"version": "1.42.0",
|
||||
"sha256": "0vm20x1lfgl671rrwvxybcwjgk7falb3d5xi6hiq9jivvbms9120",
|
||||
"depends": ["Biobase", "fields", "gdata", "genefilter", "lattice", "MASS", "RNAinteract", "sparseLDA"]
|
||||
"depends": ["Biobase", "MASS", "RNAinteract", "fields", "gdata", "genefilter", "lattice", "sparseLDA"]
|
||||
},
|
||||
"RNAmodR_Data": {
|
||||
"name": "RNAmodR.Data",
|
||||
|
|
@ -1051,7 +1051,7 @@
|
|||
"name": "ReactomeGSA.data",
|
||||
"version": "1.18.0",
|
||||
"sha256": "1410ks6s7albf6sly8ry0ln58ws9jlfn62amniqqsg46kx4xc4bh",
|
||||
"depends": ["edgeR", "limma", "ReactomeGSA", "Seurat"]
|
||||
"depends": ["ReactomeGSA", "Seurat", "edgeR", "limma"]
|
||||
},
|
||||
"RegParallel": {
|
||||
"name": "RegParallel",
|
||||
|
|
@ -1063,7 +1063,7 @@
|
|||
"name": "RforProteomics",
|
||||
"version": "1.42.0",
|
||||
"sha256": "0irg6wrwy82xhlkgj1vphh6ncp9s6qcpp40mxv1vq969qjjchkk9",
|
||||
"depends": ["BiocManager", "biocViews", "MSnbase", "R_utils"]
|
||||
"depends": ["BiocManager", "MSnbase", "R_utils", "biocViews"]
|
||||
},
|
||||
"RnBeads_hg19": {
|
||||
"name": "RnBeads.hg19",
|
||||
|
|
@ -1201,13 +1201,13 @@
|
|||
"name": "SpikeInSubset",
|
||||
"version": "1.44.0",
|
||||
"sha256": "118v972wwq4h2ww2nlb7mzva3d38c4hzmbq0v28500q2zc1ykv4l",
|
||||
"depends": ["affy", "Biobase"]
|
||||
"depends": ["Biobase", "affy"]
|
||||
},
|
||||
"SubcellularSpatialData": {
|
||||
"name": "SubcellularSpatialData",
|
||||
"version": "1.0.0",
|
||||
"sha256": "0lyg6hiv8ch7c8a7zzi02c9fmq2zqif88khhslj15gvg5dznw79v",
|
||||
"depends": ["dplyr", "hexbin", "Matrix", "SpatialExperiment"]
|
||||
"depends": ["Matrix", "SpatialExperiment", "dplyr", "hexbin"]
|
||||
},
|
||||
"TBX20BamSubset": {
|
||||
"name": "TBX20BamSubset",
|
||||
|
|
@ -1291,7 +1291,7 @@
|
|||
"name": "TabulaMurisSenisData",
|
||||
"version": "1.10.0",
|
||||
"sha256": "1b1aj06qacvzpabz8r0vkqpm0pp48vx26xx84h5ihzg9232wrqmy",
|
||||
"depends": ["AnnotationHub", "ExperimentHub", "gdata", "HDF5Array", "SingleCellExperiment", "SummarizedExperiment"]
|
||||
"depends": ["AnnotationHub", "ExperimentHub", "HDF5Array", "SingleCellExperiment", "SummarizedExperiment", "gdata"]
|
||||
},
|
||||
"TargetScoreData": {
|
||||
"name": "TargetScoreData",
|
||||
|
|
@ -1321,7 +1321,7 @@
|
|||
"name": "TumourMethData",
|
||||
"version": "1.2.0",
|
||||
"sha256": "1xwm2amlb1vrf3hpdw9387nglc6pbxxdxik56byr5p8856fkjdav",
|
||||
"depends": ["ExperimentHub", "GenomicRanges", "HDF5Array", "R_utils", "rhdf5", "SummarizedExperiment"]
|
||||
"depends": ["ExperimentHub", "GenomicRanges", "HDF5Array", "R_utils", "SummarizedExperiment", "rhdf5"]
|
||||
},
|
||||
"VariantToolsData": {
|
||||
"name": "VariantToolsData",
|
||||
|
|
@ -1357,7 +1357,7 @@
|
|||
"name": "XhybCasneuf",
|
||||
"version": "1.42.0",
|
||||
"sha256": "0n0k6h9b9gkywy6cmlx15g09287aqzvc228j3jgjkv0ljbwsq756",
|
||||
"depends": ["affy", "ath1121501cdf", "RColorBrewer", "tinesath1cdf"]
|
||||
"depends": ["RColorBrewer", "affy", "ath1121501cdf", "tinesath1cdf"]
|
||||
},
|
||||
"adductData": {
|
||||
"name": "adductData",
|
||||
|
|
@ -1369,7 +1369,7 @@
|
|||
"name": "affycompData",
|
||||
"version": "1.42.0",
|
||||
"sha256": "16fri51jhp0lm3aj9hw2s6jzxjlxz2qbd36j9zcbcs7sb6jh42jy",
|
||||
"depends": ["affycomp", "Biobase"]
|
||||
"depends": ["Biobase", "affycomp"]
|
||||
},
|
||||
"affydata": {
|
||||
"name": "affydata",
|
||||
|
|
@ -1405,7 +1405,7 @@
|
|||
"name": "beadarrayExampleData",
|
||||
"version": "1.42.0",
|
||||
"sha256": "0l5n1d7x4gc3w2kc6vq0gqxp1wdpa2sn5k75yf5fc802m11nrkd1",
|
||||
"depends": ["beadarray", "Biobase"]
|
||||
"depends": ["Biobase", "beadarray"]
|
||||
},
|
||||
"benchmarkfdrData2019": {
|
||||
"name": "benchmarkfdrData2019",
|
||||
|
|
@ -1429,7 +1429,7 @@
|
|||
"name": "biscuiteerData",
|
||||
"version": "1.18.0",
|
||||
"sha256": "1qv2ajy312diacb3mihc3q7hrrlq48k5vd9v0g6w38cqz6gnz0as",
|
||||
"depends": ["AnnotationHub", "curl", "ExperimentHub", "GenomicRanges"]
|
||||
"depends": ["AnnotationHub", "ExperimentHub", "GenomicRanges", "curl"]
|
||||
},
|
||||
"bladderbatch": {
|
||||
"name": "bladderbatch",
|
||||
|
|
@ -1537,7 +1537,7 @@
|
|||
"name": "celldex",
|
||||
"version": "1.14.0",
|
||||
"sha256": "155hnh62ra06b52xk78f111b10gm34d1djvl5w5mabvrk4vknwj6",
|
||||
"depends": ["alabaster_base", "alabaster_matrix", "alabaster_se", "AnnotationDbi", "AnnotationHub", "DBI", "DelayedArray", "DelayedMatrixStats", "ExperimentHub", "gypsum", "jsonlite", "Matrix", "RSQLite", "S4Vectors", "SummarizedExperiment"]
|
||||
"depends": ["AnnotationDbi", "AnnotationHub", "DBI", "DelayedArray", "DelayedMatrixStats", "ExperimentHub", "Matrix", "RSQLite", "S4Vectors", "SummarizedExperiment", "alabaster_base", "alabaster_matrix", "alabaster_se", "gypsum", "jsonlite"]
|
||||
},
|
||||
"cfToolsData": {
|
||||
"name": "cfToolsData",
|
||||
|
|
@ -1549,7 +1549,7 @@
|
|||
"name": "chipenrich.data",
|
||||
"version": "2.28.0",
|
||||
"sha256": "1kpc3ljayxycadshdgyzkbagh4vd7cmyqqccy61269skpasdnwbv",
|
||||
"depends": ["AnnotationDbi", "BiocGenerics", "GenomeInfoDb", "GenomicRanges", "IRanges", "readr", "rtracklayer", "S4Vectors"]
|
||||
"depends": ["AnnotationDbi", "BiocGenerics", "GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "readr", "rtracklayer"]
|
||||
},
|
||||
"chipseqDBData": {
|
||||
"name": "chipseqDBData",
|
||||
|
|
@ -1615,7 +1615,7 @@
|
|||
"name": "curatedBreastData",
|
||||
"version": "2.32.0",
|
||||
"sha256": "0zglh1h9hw6rnpdl4v5v7cmzgcvxa0phfixfwwmi8il0rn40jd68",
|
||||
"depends": ["Biobase", "BiocStyle", "ggplot2", "impute", "XML"]
|
||||
"depends": ["Biobase", "BiocStyle", "XML", "ggplot2", "impute"]
|
||||
},
|
||||
"curatedCRCData": {
|
||||
"name": "curatedCRCData",
|
||||
|
|
@ -1627,7 +1627,7 @@
|
|||
"name": "curatedMetagenomicData",
|
||||
"version": "3.12.0",
|
||||
"sha256": "1hp1s5v567xidmmpn6jv7i3fid5hwg3i43y9471aabq00nsg67b1",
|
||||
"depends": ["AnnotationHub", "dplyr", "ExperimentHub", "magrittr", "mia", "purrr", "rlang", "S4Vectors", "stringr", "SummarizedExperiment", "tibble", "tidyr", "tidyselect", "TreeSummarizedExperiment"]
|
||||
"depends": ["AnnotationHub", "ExperimentHub", "S4Vectors", "SummarizedExperiment", "TreeSummarizedExperiment", "dplyr", "magrittr", "mia", "purrr", "rlang", "stringr", "tibble", "tidyr", "tidyselect"]
|
||||
},
|
||||
"curatedOvarianData": {
|
||||
"name": "curatedOvarianData",
|
||||
|
|
@ -1639,7 +1639,7 @@
|
|||
"name": "curatedPCaData",
|
||||
"version": "1.0.0",
|
||||
"sha256": "0wqvg0z19lxyqbbsl7fbq12jgycpqycx45vy24z4sph48kz2ag3w",
|
||||
"depends": ["AnnotationHub", "ExperimentHub", "MultiAssayExperiment", "RaggedExperiment", "rlang", "S4Vectors"]
|
||||
"depends": ["AnnotationHub", "ExperimentHub", "MultiAssayExperiment", "RaggedExperiment", "S4Vectors", "rlang"]
|
||||
},
|
||||
"curatedTBData": {
|
||||
"name": "curatedTBData",
|
||||
|
|
@ -1663,7 +1663,7 @@
|
|||
"name": "depmap",
|
||||
"version": "1.18.0",
|
||||
"sha256": "0imajc5kiqf45sjwxagvg5bjvmnrzrk3ls4bflwxj9rnd84v2r62",
|
||||
"depends": ["AnnotationHub", "BiocFileCache", "curl", "dplyr", "ExperimentHub", "httr2", "tibble"]
|
||||
"depends": ["AnnotationHub", "BiocFileCache", "ExperimentHub", "curl", "dplyr", "httr2", "tibble"]
|
||||
},
|
||||
"derfinderData": {
|
||||
"name": "derfinderData",
|
||||
|
|
@ -1717,7 +1717,7 @@
|
|||
"name": "emtdata",
|
||||
"version": "1.12.0",
|
||||
"sha256": "0b3hvggndw3bzddk0vflbn0wx8fr08b6nphjhil1wqlyp3535xk4",
|
||||
"depends": ["edgeR", "ExperimentHub", "SummarizedExperiment"]
|
||||
"depends": ["ExperimentHub", "SummarizedExperiment", "edgeR"]
|
||||
},
|
||||
"epimutacionsData": {
|
||||
"name": "epimutacionsData",
|
||||
|
|
@ -1801,7 +1801,7 @@
|
|||
"name": "furrowSeg",
|
||||
"version": "1.32.0",
|
||||
"sha256": "125wyqi4h7kkrhbcn4gknwlw6panian2hfsapwyqfxz0mg6ssg5z",
|
||||
"depends": ["abind", "dplyr", "EBImage", "locfit", "tiff"]
|
||||
"depends": ["EBImage", "abind", "dplyr", "locfit", "tiff"]
|
||||
},
|
||||
"gDNAinRNAseqData": {
|
||||
"name": "gDNAinRNAseqData",
|
||||
|
|
@ -1915,7 +1915,7 @@
|
|||
"name": "healthyControlsPresenceChecker",
|
||||
"version": "1.8.0",
|
||||
"sha256": "14gq24z99l04kcn13414zjn17184l3p5l6draxwy3820m9sijzgq",
|
||||
"depends": ["geneExpressionFromGEO", "GEOquery", "magrittr", "xml2"]
|
||||
"depends": ["GEOquery", "geneExpressionFromGEO", "magrittr", "xml2"]
|
||||
},
|
||||
"healthyFlowData": {
|
||||
"name": "healthyFlowData",
|
||||
|
|
@ -1951,7 +1951,7 @@
|
|||
"name": "homosapienDEE2CellScore",
|
||||
"version": "1.0.0",
|
||||
"sha256": "1vwasylfqv4xgmhkzykdwhlxh0kk4pl4bcndx5dpn7i386zp6chs",
|
||||
"depends": ["BiocGenerics", "DESeq2", "ExperimentHub", "getDEE2", "MatrixGenerics", "Rtsne", "S4Vectors", "SummarizedExperiment"]
|
||||
"depends": ["BiocGenerics", "DESeq2", "ExperimentHub", "MatrixGenerics", "Rtsne", "S4Vectors", "SummarizedExperiment", "getDEE2"]
|
||||
},
|
||||
"humanStemCell": {
|
||||
"name": "humanStemCell",
|
||||
|
|
@ -1963,7 +1963,7 @@
|
|||
"name": "imcdatasets",
|
||||
"version": "1.12.0",
|
||||
"sha256": "135sffkn322g6zp6wz6ri2cg4wj9pwadmv4b6zaaxwximpx5xy04",
|
||||
"depends": ["cytomapper", "DelayedArray", "ExperimentHub", "HDF5Array", "S4Vectors", "SingleCellExperiment", "SpatialExperiment"]
|
||||
"depends": ["DelayedArray", "ExperimentHub", "HDF5Array", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "cytomapper"]
|
||||
},
|
||||
"kidpack": {
|
||||
"name": "kidpack",
|
||||
|
|
@ -1975,7 +1975,7 @@
|
|||
"name": "leeBamViews",
|
||||
"version": "1.40.0",
|
||||
"sha256": "15prksw8pi302i8qpw3skwljyj3hfm9wld2lzpcgz7nnpzrqm8bc",
|
||||
"depends": ["Biobase", "BSgenome", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors"]
|
||||
"depends": ["BSgenome", "Biobase", "GenomicAlignments", "GenomicRanges", "IRanges", "Rsamtools", "S4Vectors"]
|
||||
},
|
||||
"leukemiasEset": {
|
||||
"name": "leukemiasEset",
|
||||
|
|
@ -2069,9 +2069,9 @@
|
|||
},
|
||||
"microbiomeDataSets": {
|
||||
"name": "microbiomeDataSets",
|
||||
"version": "1.12.0",
|
||||
"sha256": "0ng0sbdn3y2h7dyn42rq5ci12xx5y3hqb87n7xi7lc1gp1pcxcf2",
|
||||
"depends": ["ape", "BiocGenerics", "Biostrings", "ExperimentHub", "MultiAssayExperiment", "SummarizedExperiment", "TreeSummarizedExperiment"]
|
||||
"version": "1.12.1",
|
||||
"sha256": "1jc5xcf48xwa7m1g55z38mjnbsqj7gqzwdb37kg1q60rk6bj4mj2",
|
||||
"depends": ["BiocGenerics", "Biostrings", "ExperimentHub", "MultiAssayExperiment", "SummarizedExperiment", "TreeSummarizedExperiment", "ape"]
|
||||
},
|
||||
"minfiData": {
|
||||
"name": "minfiData",
|
||||
|
|
@ -2161,7 +2161,7 @@
|
|||
"name": "mvoutData",
|
||||
"version": "1.40.0",
|
||||
"sha256": "01rxr4867w2zcy4gmcg868g2xqal5vb4xw2izfmcwplxah5380wv",
|
||||
"depends": ["affy", "Biobase", "lumi"]
|
||||
"depends": ["Biobase", "affy", "lumi"]
|
||||
},
|
||||
"nanotubes": {
|
||||
"name": "nanotubes",
|
||||
|
|
@ -2197,7 +2197,7 @@
|
|||
"name": "orthosData",
|
||||
"version": "1.2.0",
|
||||
"sha256": "000jqijl7mpp0qfgg0aqx7jzn5bviybp2ndxmikyn0rmcvi9057k",
|
||||
"depends": ["AnnotationHub", "BiocFileCache", "ExperimentHub", "HDF5Array", "stringr", "SummarizedExperiment"]
|
||||
"depends": ["AnnotationHub", "BiocFileCache", "ExperimentHub", "HDF5Array", "SummarizedExperiment", "stringr"]
|
||||
},
|
||||
"pRolocdata": {
|
||||
"name": "pRolocdata",
|
||||
|
|
@ -2233,7 +2233,7 @@
|
|||
"name": "pd.atdschip.tiling",
|
||||
"version": "0.42.0",
|
||||
"sha256": "17sf3x7mhkjk605hmc0idx1d3pbx49hyfaxzifkc6bq1mmq5113x",
|
||||
"depends": ["Biostrings", "DBI", "IRanges", "oligo", "oligoClasses", "RSQLite", "S4Vectors"]
|
||||
"depends": ["Biostrings", "DBI", "IRanges", "RSQLite", "S4Vectors", "oligo", "oligoClasses"]
|
||||
},
|
||||
"pepDat": {
|
||||
"name": "pepDat",
|
||||
|
|
@ -2305,7 +2305,7 @@
|
|||
"name": "qPLEXdata",
|
||||
"version": "1.22.0",
|
||||
"sha256": "1a8mzbll0s9w82y4sy153jna6677sdpp3bfzs83qaqpnjymjzfpc",
|
||||
"depends": ["dplyr", "knitr", "MSnbase", "qPLEXanalyzer"]
|
||||
"depends": ["MSnbase", "dplyr", "knitr", "qPLEXanalyzer"]
|
||||
},
|
||||
"rRDPData": {
|
||||
"name": "rRDPData",
|
||||
|
|
@ -2317,7 +2317,7 @@
|
|||
"name": "raerdata",
|
||||
"version": "1.2.0",
|
||||
"sha256": "15j7sw3kvgqqb7m4y4kn40p8g8s1f204lfnb5zskkjfakj6c2j03",
|
||||
"depends": ["BiocGenerics", "ExperimentHub", "Rsamtools", "rtracklayer", "SingleCellExperiment"]
|
||||
"depends": ["BiocGenerics", "ExperimentHub", "Rsamtools", "SingleCellExperiment", "rtracklayer"]
|
||||
},
|
||||
"rcellminerData": {
|
||||
"name": "rcellminerData",
|
||||
|
|
@ -2347,19 +2347,19 @@
|
|||
"name": "scATAC.Explorer",
|
||||
"version": "1.10.0",
|
||||
"sha256": "0s2w9b9bb1bzqnlhlrgvp17bifhryvymzaid02ypkqaql06d6nyx",
|
||||
"depends": ["BiocFileCache", "data_table", "Matrix", "S4Vectors", "SingleCellExperiment"]
|
||||
"depends": ["BiocFileCache", "Matrix", "S4Vectors", "SingleCellExperiment", "data_table"]
|
||||
},
|
||||
"scMultiome": {
|
||||
"name": "scMultiome",
|
||||
"version": "1.4.0",
|
||||
"sha256": "1fiivxs35zanssfkjv83fa898fjr93xgq5g2i9m2qkv2pxqlyan8",
|
||||
"depends": ["AnnotationHub", "AzureStor", "checkmate", "DelayedArray", "ExperimentHub", "GenomicRanges", "HDF5Array", "MultiAssayExperiment", "rhdf5", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment"]
|
||||
"version": "1.4.1",
|
||||
"sha256": "0rgcg8qhpap7wnlndf9bmild55yxv21zdn89hs5h1503rfchlx2d",
|
||||
"depends": ["AnnotationHub", "AzureStor", "DelayedArray", "ExperimentHub", "GenomicRanges", "HDF5Array", "MultiAssayExperiment", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "checkmate", "rhdf5"]
|
||||
},
|
||||
"scRNAseq": {
|
||||
"name": "scRNAseq",
|
||||
"version": "2.18.0",
|
||||
"sha256": "0jsq037ba4xsb3bwwf021jw2hqv30vb5nrjag97xadx75z5fzqlr",
|
||||
"depends": ["alabaster_base", "alabaster_matrix", "alabaster_sce", "AnnotationDbi", "AnnotationHub", "BiocGenerics", "DBI", "DelayedArray", "ensembldb", "ExperimentHub", "GenomicFeatures", "GenomicRanges", "gypsum", "jsonlite", "Matrix", "RSQLite", "S4Vectors", "SingleCellExperiment", "SparseArray", "SummarizedExperiment"]
|
||||
"depends": ["AnnotationDbi", "AnnotationHub", "BiocGenerics", "DBI", "DelayedArray", "ExperimentHub", "GenomicFeatures", "GenomicRanges", "Matrix", "RSQLite", "S4Vectors", "SingleCellExperiment", "SparseArray", "SummarizedExperiment", "alabaster_base", "alabaster_matrix", "alabaster_sce", "ensembldb", "gypsum", "jsonlite"]
|
||||
},
|
||||
"scTHI_data": {
|
||||
"name": "scTHI.data",
|
||||
|
|
@ -2407,7 +2407,7 @@
|
|||
"name": "sesameData",
|
||||
"version": "1.22.0",
|
||||
"sha256": "05k67isysszzfkkbi811dkab0cmxnwz81p2ldcqz3gsq5qin3p1g",
|
||||
"depends": ["AnnotationHub", "ExperimentHub", "GenomeInfoDb", "GenomicRanges", "IRanges", "readr", "S4Vectors", "stringr"]
|
||||
"depends": ["AnnotationHub", "ExperimentHub", "GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors", "readr", "stringr"]
|
||||
},
|
||||
"seventyGeneData": {
|
||||
"name": "seventyGeneData",
|
||||
|
|
@ -2425,7 +2425,7 @@
|
|||
"name": "signatureSearchData",
|
||||
"version": "1.18.0",
|
||||
"sha256": "11y1dbixj9b91whzq4lrmad5f4f6gqdv70ar4rg20ql1699dx5l5",
|
||||
"depends": ["affy", "Biobase", "dplyr", "ExperimentHub", "limma", "magrittr", "R_utils", "rhdf5"]
|
||||
"depends": ["Biobase", "ExperimentHub", "R_utils", "affy", "dplyr", "limma", "magrittr", "rhdf5"]
|
||||
},
|
||||
"simpIntLists": {
|
||||
"name": "simpIntLists",
|
||||
|
|
@ -2449,7 +2449,7 @@
|
|||
"name": "spatialLIBD",
|
||||
"version": "1.16.2",
|
||||
"sha256": "0bbwh9mfz7iscv8a1jlc7g1c452hv4qr95hwv3z6h2mqf8pcr5g8",
|
||||
"depends": ["AnnotationHub", "benchmarkme", "BiocFileCache", "BiocGenerics", "cowplot", "DT", "edgeR", "ExperimentHub", "fields", "GenomicRanges", "ggplot2", "golem", "IRanges", "jsonlite", "limma", "magick", "Matrix", "MatrixGenerics", "paletteer", "plotly", "png", "RColorBrewer", "rlang", "rtracklayer", "S4Vectors", "scater", "scuttle", "sessioninfo", "shiny", "shinyWidgets", "SingleCellExperiment", "SpatialExperiment", "statmod", "SummarizedExperiment", "tibble", "viridisLite"]
|
||||
"depends": ["AnnotationHub", "BiocFileCache", "BiocGenerics", "DT", "ExperimentHub", "GenomicRanges", "IRanges", "Matrix", "MatrixGenerics", "RColorBrewer", "S4Vectors", "SingleCellExperiment", "SpatialExperiment", "SummarizedExperiment", "benchmarkme", "cowplot", "edgeR", "fields", "ggplot2", "golem", "jsonlite", "limma", "magick", "paletteer", "plotly", "png", "rlang", "rtracklayer", "scater", "scuttle", "sessioninfo", "shiny", "shinyWidgets", "statmod", "tibble", "viridisLite"]
|
||||
},
|
||||
"spqnData": {
|
||||
"name": "spqnData",
|
||||
|
|
@ -2521,7 +2521,7 @@
|
|||
"name": "tuberculosis",
|
||||
"version": "1.10.0",
|
||||
"sha256": "1l9gm8jlvall905053mmbn0wd053ssnsxy74gza37w669il85awn",
|
||||
"depends": ["AnnotationHub", "dplyr", "ExperimentHub", "magrittr", "purrr", "rlang", "S4Vectors", "stringr", "SummarizedExperiment", "tibble", "tidyr"]
|
||||
"depends": ["AnnotationHub", "ExperimentHub", "S4Vectors", "SummarizedExperiment", "dplyr", "magrittr", "purrr", "rlang", "stringr", "tibble", "tidyr"]
|
||||
},
|
||||
"tweeDEseqCountData": {
|
||||
"name": "tweeDEseqCountData",
|
||||
|
|
|
|||
File diff suppressed because it is too large
Load diff
File diff suppressed because it is too large
Load diff
|
|
@ -767,6 +767,7 @@ let
|
|||
redux = [ pkgs.hiredis ];
|
||||
RmecabKo = [ pkgs.mecab ];
|
||||
markets = [ pkgs.gsl ];
|
||||
rlas = [ pkgs.boost ];
|
||||
PoissonBinomial = [ pkgs.fftw.dev ];
|
||||
poisbinom = [ pkgs.fftw.dev ];
|
||||
PoissonMultinomial = [ pkgs.fftw.dev ];
|
||||
|
|
|
|||
|
|
@ -7,13 +7,13 @@
|
|||
|
||||
buildGoModule rec {
|
||||
pname = "clickhouse-backup";
|
||||
version = "2.5.29";
|
||||
version = "2.6.0";
|
||||
|
||||
src = fetchFromGitHub {
|
||||
owner = "Altinity";
|
||||
repo = "clickhouse-backup";
|
||||
rev = "v${version}";
|
||||
hash = "sha256-Ouep7jd3t+5cryINIYV9KvY2j1caW3TxvPitThRU3kE=";
|
||||
hash = "sha256-FlF/XOZS3oaxW+LkWv8K47PVWR1vffkp9YnEH+eKFyA=";
|
||||
};
|
||||
|
||||
vendorHash = "sha256-IEqxC4EzkEZnZru6U9O7U9kf375YKqBeyeJPqzaWbuM=";
|
||||
|
|
|
|||
|
|
@ -2,13 +2,13 @@
|
|||
|
||||
buildGoModule rec {
|
||||
pname = "jd-diff-patch";
|
||||
version = "1.7.1";
|
||||
version = "1.9.1";
|
||||
|
||||
src = fetchFromGitHub {
|
||||
owner = "josephburnett";
|
||||
repo = "jd";
|
||||
rev = "v${version}";
|
||||
sha256 = "sha256-fi+vj1vHhgw2OPQqQ0827P6Axy/cio0UVFLeD/nhFvw=";
|
||||
sha256 = "sha256-qq/Y2/NGK3xsgljT0D9+dD1D1UfjB9Niay81nQJ4gX0=";
|
||||
};
|
||||
|
||||
# not including web ui
|
||||
|
|
|
|||
|
|
@ -2,13 +2,13 @@
|
|||
|
||||
buildGoModule rec {
|
||||
pname = "linuxkit";
|
||||
version = "1.5.0";
|
||||
version = "1.5.1";
|
||||
|
||||
src = fetchFromGitHub {
|
||||
owner = "linuxkit";
|
||||
repo = "linuxkit";
|
||||
rev = "v${version}";
|
||||
sha256 = "sha256-Tcc2FdZ0h97r1C5BMTVb45HB8AuN/wPD+A8samhaJY8=";
|
||||
sha256 = "sha256-Od6ij4RUWWNN3pm6Yt8W7LkeHnrusikJi2pXw6axbhU=";
|
||||
};
|
||||
|
||||
vendorHash = null;
|
||||
|
|
|
|||
|
|
@ -5,12 +5,12 @@
|
|||
|
||||
python3.pkgs.buildPythonApplication rec {
|
||||
pname = "pifpaf";
|
||||
version = "3.1.5";
|
||||
version = "3.2.1";
|
||||
format = "setuptools";
|
||||
|
||||
src = fetchPypi {
|
||||
inherit pname version;
|
||||
hash = "sha256-lmixfUP+pq0RdyXeY6MmUQOx1sMLHqojOKUK1mivbaU=";
|
||||
hash = "sha256-8SSSdXBj9Yd351Iv7TdASLCfYPnkG7h6X8rBLrArgFI=";
|
||||
};
|
||||
|
||||
propagatedBuildInputs = with python3.pkgs; [
|
||||
|
|
|
|||
|
|
@ -14,16 +14,16 @@
|
|||
|
||||
rustPlatform.buildRustPackage rec {
|
||||
pname = "cargo-dist";
|
||||
version = "0.21.1";
|
||||
version = "0.22.0";
|
||||
|
||||
src = fetchFromGitHub {
|
||||
owner = "axodotdev";
|
||||
repo = "cargo-dist";
|
||||
rev = "v${version}";
|
||||
hash = "sha256-0CL/2n1MZJLMdlrtD7IoYBJY0aHtE93Z/gpWnJw1+zQ=";
|
||||
hash = "sha256-h8LiR+eU0d80OdXNi4/jdQocNPHEWP3qHY3hC0bPflw=";
|
||||
};
|
||||
|
||||
cargoHash = "sha256-JJWPFsFQ+2DFyMxscjrzA/nnAAEIM3dnwKAqQPKcLP0=";
|
||||
cargoHash = "sha256-HacPF457CvKo4xsygSVyRNYOb8ToHEG1OFOXbFRhsDs=";
|
||||
|
||||
nativeBuildInputs = [
|
||||
pkg-config
|
||||
|
|
|
|||
|
|
@ -1,34 +0,0 @@
|
|||
{ lib, stdenv, fetchurl, gamin }:
|
||||
|
||||
stdenv.mkDerivation rec {
|
||||
pname = "fileschanged";
|
||||
version = "0.6.9";
|
||||
|
||||
src = fetchurl {
|
||||
url = "mirror://savannah/fileschanged/fileschanged-${version}.tar.gz";
|
||||
sha256 = "0ajc9h023vzpnlqqjli4wbvs0q36nr5p9msc3wzbic8rk687qcxc";
|
||||
};
|
||||
|
||||
buildInputs = [ gamin ];
|
||||
|
||||
patches = [./unused-variables.debian.patch];
|
||||
|
||||
doCheck = true;
|
||||
|
||||
meta = {
|
||||
homepage = "https://www.nongnu.org/fileschanged/";
|
||||
description = "Command-line utility that reports when files have been altered";
|
||||
license = lib.licenses.gpl3Plus;
|
||||
|
||||
longDescription = ''
|
||||
This utility is a client to FAM (File Alteration Monitor) servers
|
||||
like FAM or Gamin. You give it some filenames on the command line
|
||||
and then it monitors those files for changes. When it discovers
|
||||
that a file has been altered, it displays the filename on the
|
||||
standard-output or executes a given command.
|
||||
'';
|
||||
|
||||
platforms = lib.platforms.linux;
|
||||
mainProgram = "fileschanged";
|
||||
};
|
||||
}
|
||||
|
|
@ -1,48 +0,0 @@
|
|||
#! /bin/sh /usr/share/dpatch/dpatch-run
|
||||
## 07_unused_variables.dpatch by Colin Watson <cjwatson@ubuntu.com>
|
||||
##
|
||||
## All lines beginning with `## DP:' are a description of the patch.
|
||||
## DP: GCC 4.6 warns about unused variables, and fileschanged builds with
|
||||
## DP: -Werror, so deal with unused variable warnings.
|
||||
|
||||
@DPATCH@
|
||||
diff -urNad '--exclude=CVS' '--exclude=.svn' '--exclude=.git' '--exclude=.arch' '--exclude=.hg' '--exclude=_darcs' '--exclude=.bzr' fileschanged-0.6.5~/src/monitor.c fileschanged-0.6.5/src/monitor.c
|
||||
--- fileschanged-0.6.5~/src/monitor.c 2006-04-19 20:42:29.000000000 +0100
|
||||
+++ fileschanged-0.6.5/src/monitor.c 2011-09-14 01:17:23.000000000 +0100
|
||||
@@ -84,6 +84,7 @@
|
||||
retval = FAMMonitorDirectory (c, node->filename, &node->request,
|
||||
(void *) node);
|
||||
//printf ("FAMMonitorDirectory returns %d (reqnum %d)\n", retval, node->request.reqnum);
|
||||
+ (void) retval;
|
||||
}
|
||||
else if (S_ISREG (node->statbuf.st_mode))
|
||||
{
|
||||
@@ -91,6 +92,7 @@
|
||||
retval = FAMMonitorFile (c, node->filename, &node->request,
|
||||
(void *) node);
|
||||
//printf ("FAMMonitorFile returns %d (reqnum %d)\n", retval, node->request.reqnum);
|
||||
+ (void) retval;
|
||||
}
|
||||
monitor_handle_events (c, list, 0, 30);
|
||||
}
|
||||
|
||||
diff -r -U3 fileschanged-0.6.9-orig/src/main.c fileschanged-0.6.9/src/main.c
|
||||
--- fileschanged-0.6.9-orig/src/main.c 2012-04-13 01:31:59.160601022 +0400
|
||||
+++ fileschanged-0.6.9/src/main.c 2012-04-13 01:32:47.549599643 +0400
|
||||
@@ -126,6 +126,7 @@
|
||||
{
|
||||
retval = process_file (filelist, filelist_len, arguments.args[i]);
|
||||
}
|
||||
+ (void) retval;
|
||||
return 0;
|
||||
}
|
||||
|
||||
@@ -168,6 +169,7 @@
|
||||
|
||||
if (fileptr != stdin)
|
||||
fclose (fileptr);
|
||||
+ (void) retval;
|
||||
return 0;
|
||||
}
|
||||
int
|
||||
|
||||
|
|
@ -442,6 +442,7 @@ mapAliases ({
|
|||
|
||||
### F ###
|
||||
|
||||
fam = throw "'fam' (aliased to 'gamin') has been removed as it is unmaintained upstream"; # Added 2024-04-19
|
||||
fancypp = throw "'fancypp' was removed because it and its dependants are unmaintained"; # Added 2024-02-14
|
||||
faustStk = faustPhysicalModeling; # Added 2023-05-16
|
||||
fastnlo = fastnlo-toolkit; # Added 2021-04-24
|
||||
|
|
@ -454,6 +455,7 @@ mapAliases ({
|
|||
ffmpeg_5-headless = throw "ffmpeg_5-headless has been removed, please use another version"; # Added 2024-07-12
|
||||
ffmpeg_5-full = throw "ffmpeg_5-full has been removed, please use another version"; # Added 2024-07-12
|
||||
FIL-plugins = fil-plugins; # Added 2024-06-12
|
||||
fileschanged = throw "'fileschanged' has been removed as it is unmaintained upstream"; # Added 2024-04-19
|
||||
findimagedupes = throw "findimagedupes has been removed because the perl bindings are no longer compatible"; # Added 2023-07-10
|
||||
finger_bsd = bsd-finger;
|
||||
fingerd_bsd = bsd-fingerd;
|
||||
|
|
@ -497,6 +499,7 @@ mapAliases ({
|
|||
|
||||
g4music = gapless; # Added 2024-07-26
|
||||
g4py = python3Packages.geant4; # Added 2020-06-06
|
||||
gamin = throw "'gamin' has been removed as it is unmaintained upstream"; # Added 2024-04-19
|
||||
garage_0_7 = throw "garage 0.7.x has been removed as it is EOL. Please upgrade to 0.8 series."; # Added 2023-10-10
|
||||
garage_0_7_3 = throw "garage 0.7.x has been removed as it is EOL. Please upgrade to 0.8 series."; # Added 2023-10-10
|
||||
garmin-plugin = throw "garmin-plugin has been removed, as it is unmaintained upstream and no longer works with modern browsers."; # Added 2024-01-12
|
||||
|
|
|
|||
|
|
@ -7725,8 +7725,6 @@ with pkgs;
|
|||
|
||||
filegive = callPackage ../tools/networking/filegive { };
|
||||
|
||||
fileschanged = callPackage ../tools/misc/fileschanged { };
|
||||
|
||||
filet = callPackage ../applications/misc/filet { };
|
||||
|
||||
findex = callPackage ../applications/misc/findex { };
|
||||
|
|
@ -20119,9 +20117,6 @@ with pkgs;
|
|||
|
||||
game-music-emu = callPackage ../development/libraries/audio/game-music-emu { };
|
||||
|
||||
gamin = callPackage ../development/libraries/gamin { };
|
||||
fam = gamin; # added 2018-04-25
|
||||
|
||||
ganv = callPackage ../development/libraries/ganv { };
|
||||
|
||||
garble = callPackage ../development/tools/garble { };
|
||||
|
|
|
|||
Loading…
Reference in a new issue