Merge release-22.05 into staging-next-22.05

This commit is contained in:
github-actions[bot]
2022-05-30 00:17:24 +00:00
committed by GitHub
26 changed files with 170 additions and 71 deletions

View File

@@ -714,6 +714,13 @@
<literal>services.openldap.settings</literal>, which
represents your <literal>cn=config</literal>.
</para>
<para>
Additionally with 2.5 the argon2 module was included in the
standard distrubtion and renamed from
<literal>pw-argon2</literal> to <literal>argon2</literal>.
Remember to update your <literal>olcModuleLoad</literal> entry
in <literal>cn=config</literal>.
</para>
</listitem>
<listitem>
<para>

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@@ -250,6 +250,8 @@ In addition to numerous new and upgraded packages, this release has the followin
- `openldap` (and therefore the slapd LDAP server) were updated to version 2.6.2. The project introduced backwards-incompatible changes, namely the removal of the bdb, hdb, ndb, and shell backends in slapd. Therefore before updating, dump your database `slapcat -n 1` in LDIF format, and reimport it after updating your `services.openldap.settings`, which represents your `cn=config`.
Additionally with 2.5 the argon2 module was included in the standard distrubtion and renamed from `pw-argon2` to `argon2`. Remember to update your `olcModuleLoad` entry in `cn=config`.
- `openssh` has been update to 8.9p1, changing the FIDO security key middleware interface.
- `git` no longer hardcodes the path to openssh' ssh binary to reduce the amount of rebuilds. If you are using git with ssh remotes and do not have a ssh binary in your enviroment consider adding `openssh` to it or switching to `gitFull`.

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@@ -13,7 +13,7 @@ let
attrsToText = attrs:
concatStringsSep "\n" (
mapAttrsToList (n: v: ''${n}=${escapeIfNeccessary (toString v)}'') attrs
);
) + "\n";
osReleaseContents = {
NAME = "NixOS";

View File

@@ -2,16 +2,16 @@
buildGoModule rec {
pname = "argocd-autopilot";
version = "0.3.5";
version = "0.3.7";
src = fetchFromGitHub {
owner = "argoproj-labs";
repo = "argocd-autopilot";
rev = "v${version}";
sha256 = "sha256-YqnmtDVtprQQFbL++X9rUJFGj+fMD+fvDRWsQ+uOxxo=";
sha256 = "sha256-dLmJQCASdWkzWOPQ0bdJLe2AD06+L2ghP2yWry1XL1k=";
};
vendorSha256 = "sha256-r8RTwMzFS/BkxW08+wfAovuFLpIOReDsuHi/Hx9cVPc=";
vendorSha256 = "sha256-0v/HTiQf/mZUU1b55jAnSj86NEFOUaiM+/MrVvwJYBM=";
proxyVendor = true;
@@ -24,7 +24,7 @@ buildGoModule rec {
"-X ${package_url}.version=${src.rev}"
"-X ${package_url}.buildDate=unknown"
"-X ${package_url}.gitCommit=${src.rev}"
"-X ${package_url}.installationManifestURL=github.com/argoproj-labs/argocd-autopilot/manifests/base?ref=${src.rev}"
"-X ${package_url}.installationManifestsURL=github.com/argoproj-labs/argocd-autopilot/manifests/base?ref=${src.rev}"
"-X ${package_url}.installationManifestsNamespacedURL=github.com/argoproj-labs/argocd-autopilot/manifests/insecure?ref=${src.rev}"
];

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@@ -2,13 +2,13 @@
stdenvNoCC.mkDerivation rec {
pname = "distrobox";
version = "1.2.15";
version = "1.3.0";
src = fetchFromGitHub {
owner = "89luca89";
repo = pname;
rev = version;
sha256 = "sha256-9rivXnHyEE1MoGY+CwUeDStLGPVq+4FvwPjV7Nblk60=";
sha256 = "sha256-31SDi9B6Ug6lRDMgaMp6lwdSsmQ7ywEwjG1Ez/jXjBc=";
};
dontConfigure = true;

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@@ -1,7 +1,10 @@
{ lib
, stdenv
, fetchFromGitHub
, fetchpatch
, scfbuild
, fontforge
, libuninameslist
, nodejs
, nodePackages
, python3Packages
@@ -14,6 +17,34 @@ let
[ "OpenMoji-Color.ttf" "OpenMoji-Black.ttf" ]
variant;
# With newer fontforge the build hangs, see
# https://github.com/NixOS/nixpkgs/issues/167869
# Patches etc taken from
# https://github.com/NixOS/nixpkgs/commit/69da642a5a9bb433138ba1b13c8d56fb5bb6ec05
fontforge-20201107 = fontforge.overrideAttrs (old: rec {
version = "20201107";
src = fetchFromGitHub {
owner = "fontforge";
repo = "fontforge";
rev = version;
sha256 = "sha256-Rl/5lbXaPgIndANaD0IakaDus6T53FjiBb45FIuGrvc=";
};
patches = [
(fetchpatch {
url = "https://salsa.debian.org/fonts-team/fontforge/raw/76bffe6ccf8ab20a0c81476a80a87ad245e2fd1c/debian/patches/0001-add-extra-cmake-install-rules.patch";
sha256 = "u3D9od2xLECNEHhZ+8dkuv9818tPkdP6y/Tvd9CADJg=";
})
(fetchpatch {
url = "https://github.com/fontforge/fontforge/commit/69e263b2aff29ad22f97f13935cfa97a1eabf207.patch";
sha256 = "06yyf90605aq6ppfiz83mqkdmnaq5418axp9jgsjyjq78b00xb29";
})
];
buildInputs = old.buildInputs ++ [ libuninameslist ];
});
scfbuild-with-fontforge-20201107 = scfbuild.override (old: {
fontforge = fontforge-20201107;
});
in stdenv.mkDerivation rec {
pname = "openmoji";
version = "13.1.0";
@@ -26,7 +57,7 @@ in stdenv.mkDerivation rec {
};
nativeBuildInputs = [
scfbuild
scfbuild-with-fontforge-20201107
nodejs
nodePackages.glob
nodePackages.lodash

View File

@@ -30,11 +30,11 @@
stdenv.mkDerivation rec {
pname = "gnome-maps";
version = "42.1";
version = "42.2";
src = fetchurl {
url = "mirror://gnome/sources/${pname}/${lib.versions.major version}/${pname}-${version}.tar.xz";
sha256 = "sha256-CC+ElBAf080xvU8a6YgXEOMqUz+y3belcSJ5bJRm0q4=";
sha256 = "sha256-Xm0bDKfMk56pGq39pWM6hl6oX6VlADaGGyv+8L/QabE=";
};
doCheck = true;

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@@ -29,13 +29,13 @@
stdenv.mkDerivation rec {
pname = "eog";
version = "42.1";
version = "42.2";
outputs = [ "out" "dev" "devdoc" ];
src = fetchurl {
url = "mirror://gnome/sources/${pname}/${lib.versions.major version}/${pname}-${version}.tar.xz";
sha256 = "sha256-/LEtXbyFYY3xSzDmMB5eHO+Dgq4nItL1WmQ1Adx8n60=";
sha256 = "sha256-Dk1Kai7hokCui1hEnwK6LGS3+ZSQ0LiRXX9SyQpYBF4=";
};
patches = [

View File

@@ -28,11 +28,11 @@
stdenv.mkDerivation rec {
pname = "gnome-terminal";
version = "3.44.0";
version = "3.44.1";
src = fetchurl {
url = "mirror://gnome/sources/gnome-terminal/${lib.versions.majorMinor version}/${pname}-${version}.tar.xz";
sha256 = "qpZxie62CUWebApGigHqcMuMRTDaHVALLT9PxDi4/io=";
sha256 = "+28g7h/yMamq7asT1dxuWmTJVXESJISLeQCG6IlZ03s=";
};
nativeBuildInputs = [

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@@ -19,14 +19,14 @@
stdenv.mkDerivation rec {
pname = "aisleriot";
version = "3.22.22";
version = "3.22.23";
src = fetchFromGitLab {
domain = "gitlab.gnome.org";
owner = "GNOME";
repo = pname;
rev = version;
sha256 = "sha256-Jr4XEj6h+gI1gNqoJ/cJ3cDBB4mSbpzvOUQkwGxkLPs=";
sha256 = "sha256-s7z1bR2ZG3YxJcqNrhH+O5PfGeFoPWeWSI26VCCe33Y=";
};
nativeBuildInputs = [

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@@ -20,14 +20,14 @@ in
stdenv.mkDerivation rec {
pname = "fcft";
version = "3.1.1";
version = "3.1.2";
src = fetchFromGitea {
domain = "codeberg.org";
owner = "dnkl";
repo = "fcft";
rev = version;
sha256 = "1b43sqp5hah374ns62pcrmbiriqsdisb60hp1nwqz3ny3rfjvn15";
sha256 = "1m7prc792dsd4mg6iqqwbfbmvs3a2yw2zmj0cd3qrf7h672b8snq";
};
depsBuildBuild = [ pkg-config ];

View File

@@ -21,22 +21,23 @@
buildPythonPackage rec {
pname = "CNVkit";
version = "0.9.7";
version = "0.9.9";
src = fetchFromGitHub {
owner = "etal";
repo = "cnvkit";
rev = "v${version}";
sha256 = "022zplgqil5l76vri647cyjx427vnbg5r2gw6lw712d2janvdjm7";
sha256 = "1q4l7jhr1k135an3n9aa9wsid5lk6fwxb0hcldrr6v6y76zi4gj1";
};
patches = [
# Fix: AttributeError: module 'pandas.io.common' has no attribute 'EmptyDataError'
(fetchpatch {
url = "https://github.com/etal/cnvkit/commit/392adfffedfa0415e635b72c5027835b0a8d7ab5.patch";
sha256 = "0s0gwyy0hybmhc3jij2v9l44b6lkcmclii8bkwsazzj2kc24m2rh";
})
];
postPatch = ''
# see https://github.com/etal/cnvkit/issues/589
substituteInPlace setup.py \
--replace 'joblib < 1.0' 'joblib'
# see https://github.com/etal/cnvkit/issues/680
substituteInPlace test/test_io.py \
--replace 'test_read_vcf' 'dont_test_read_vcf'
'';
propagatedBuildInputs = [
biopython
@@ -63,8 +64,13 @@ buildPythonPackage rec {
${python.interpreter} test_cnvlib.py
${python.interpreter} test_commands.py
${python.interpreter} test_r.py
popd # test/
'';
pythonImportsCheck = [
"cnvlib"
];
meta = with lib; {
homepage = "https://cnvkit.readthedocs.io";
description = "A Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data";

View File

@@ -45,5 +45,7 @@ buildPythonPackage rec {
description = "A package for graph statistical algorithms";
license = licenses.asl20; # changing to `licenses.mit` in next release
maintainers = with maintainers; [ bcdarwin ];
# graspologic-native is not available
broken = true;
};
}

View File

@@ -1,9 +1,12 @@
{ lib
, stdenv
, buildPythonPackage
, pythonOlder
, fetchFromGitHub
, cffi
, pytestCheckHook
, AudioToolbox
, CoreAudio
}:
buildPythonPackage rec {
@@ -19,6 +22,11 @@ buildPythonPackage rec {
sha256 = "16llwmbbd9445rwhl4v66kf5zd7yl3a94zm9xyllq6ij7vnhg5jb";
};
buildInputs = lib.optionals stdenv.isDarwin [
AudioToolbox
CoreAudio
];
propagatedNativeBuildInputs = [ cffi ];
propagatedBuildInputs = [ cffi ];

View File

@@ -2,6 +2,7 @@
, buildPythonPackage
, coloredlogs
, fetchFromGitHub
, fetchpatch
, ghostscript
, img2pdf
, importlib-metadata
@@ -53,6 +54,11 @@ buildPythonPackage rec {
tesseract = "${lib.getBin tesseract4}/bin/tesseract";
unpaper = "${lib.getBin unpaper}/bin/unpaper";
})
# https://github.com/ocrmypdf/OCRmyPDF/pull/973
(fetchpatch {
url = "https://github.com/ocrmypdf/OCRmyPDF/commit/808b24d59f5b541a335006aa6ea7cdc3c991adc0.patch";
hash = "sha256-khsH70fWk5fStf94wcRKKX7cCbgD69LtKkngJIqA3+w=";
})
];
nativeBuildInputs = [

View File

@@ -51,6 +51,10 @@ buildPythonPackage rec {
})
];
postPatch = ''
sed -i 's|\S*/opt/homebrew.*|pass|' setup.py
'';
SETUPTOOLS_SCM_PRETEND_VERSION = version;
buildInputs = [

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@@ -15,28 +15,16 @@
buildPythonPackage rec {
pname = "pomegranate";
version = "0.13.5";
version = "0.14.8";
src = fetchFromGitHub {
repo = pname;
owner = "jmschrei";
rev = "v${version}";
sha256 = "1hbxchp3daykkf1fa79a9mh34p78bygqcf1nv4qwkql3gw0pd6l7";
# no tags for recent versions: https://github.com/jmschrei/pomegranate/issues/974
rev = "0652e955c400bc56df5661db3298a06854c7cce8";
sha256 = "16g49nl2bgnh6nh7bd21s393zbksdvgp9l13ww2diwhplj6hlly3";
};
patches = lib.optionals (lib.versionOlder version "13.6") [
# Fix compatibility with recent joblib release, will be part of the next
# pomegranate release after 0.13.5
(fetchpatch {
url = "https://github.com/jmschrei/pomegranate/commit/42d14bebc44ffd4a778b2a6430aa845591b7c3b7.patch";
sha256 = "0f9cx0fj9xkr3hch7jyrn76zjypilh5bqw734caaw6g2m49lvbff";
})
] ++ [
# Likely an upstream test bug and not a real problem:
# https://github.com/jmschrei/pomegranate/issues/939
./disable-failed-on-nextworkx-2.6.patch
] ;
propagatedBuildInputs = [ numpy scipy cython networkx joblib pyyaml ];
checkInputs = [ pandas nose ]; # as of 0.13.5, it depends explicitly on nose, rather than pytest.

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@@ -17,12 +17,12 @@ index 834f1cd..10ab1e7 100644
* parameter given to the kernel. So reserving memory from low to high
- * satisfies this constraint again. Reserving 1M at 0x02600000-0x02700000 for
- * the DTB leaves rest of the free RAM to the initrd starting at 0x02700000.
+ * satisfies this constraint again. Reserving 1M at 0x03700000-0x03800000 for
+ * the DTB leaves rest of the free RAM to the initrd starting at 0x03800000.
+ * satisfies this constraint again. Reserving 1M at 0x04700000-0x04800000 for
+ * the DTB leaves rest of the free RAM to the initrd starting at 0x04800000.
* Even with the smallest possible CPU-GPU memory split of the CPU getting
- * only 64M, the remaining 25M starting at 0x02700000 should allow quite
- * large initrds before they start colliding with U-Boot.
+ * only 64M, the remaining 9M starting at 0x03800000 should allow reasonably
+ * only 64M, the remaining 8M starting at 0x04800000 should allow reasonably
+ * sized initrds before they start colliding with U-Boot.
*/
#define ENV_MEM_LAYOUT_SETTINGS \
@@ -33,10 +33,10 @@ index 834f1cd..10ab1e7 100644
- "pxefile_addr_r=0x02500000\0" \
- "fdt_addr_r=0x02600000\0" \
- "ramdisk_addr_r=0x02700000\0"
+ "scriptaddr=0x03500000\0" \
+ "pxefile_addr_r=0x03600000\0" \
+ "fdt_addr_r=0x03700000\0" \
+ "ramdisk_addr_r=0x03800000\0"
+ "scriptaddr=0x04500000\0" \
+ "pxefile_addr_r=0x04600000\0" \
+ "fdt_addr_r=0x04700000\0" \
+ "ramdisk_addr_r=0x04800000\0"
#if CONFIG_IS_ENABLED(CMD_MMC)
#define BOOT_TARGET_MMC(func) \

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@@ -6,11 +6,11 @@
let
self = stdenv.mkDerivation rec {
pname = "mysql";
version = "8.0.28";
version = "8.0.29";
src = fetchurl {
url = "https://dev.mysql.com/get/Downloads/MySQL-${self.mysqlVersion}/${pname}-${version}.tar.gz";
sha256 = "sha256-2Gk2nrbeTyuy2407Mbe3OWjjVuX/xDVPS5ZlirHkiyI=";
sha256 = "sha256-USFw+m94ppTW8Y0ZfpmdJxbuaNxUHXZE3ZIqNmNAcmY=";
};
nativeBuildInputs = [ bison cmake pkg-config ]
@@ -20,8 +20,6 @@ self = stdenv.mkDerivation rec {
postPatch = ''
substituteInPlace cmake/libutils.cmake --replace /usr/bin/libtool libtool
substituteInPlace cmake/os/Darwin.cmake --replace /usr/bin/libtool libtool
substituteInPlace cmake/fido2.cmake \
--replace ''$\{MY_PKG_CONFIG_EXECUTABLE\} "${pkg-config}/bin/pkg-config"
'';
buildInputs = [

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@@ -22,15 +22,13 @@ stdenv.mkDerivation rec {
buildInputs = [ libuuid gettext ]
++ lib.optionals stdenv.isLinux [ fuse ];
# Only use glibc's __GNUC_PREREQ(X,Y) (checks if compiler is gcc version >= X.Y) when using glibc
patches = [
(fetchpatch {
name = "CVE-2022-1304.patch";
url = "https://git.kernel.org/pub/scm/fs/ext2/e2fsprogs.git/patch/?id=ab51d587bb9b229b1fade1afd02e1574c1ba5c76";
sha256 = "sha256-YEEow34/81NBOc6F6FS6i505FCQ7GHeIz0a0qWNs7Fg=";
})
] ++ lib.optionals (stdenv.hostPlatform.libc == "glibc") [
(fetchpatch {
(fetchpatch { # avoid using missing __GNUC_PREREQ(X,Y)
url = "https://raw.githubusercontent.com/void-linux/void-packages/9583597eb3e6e6b33f61dbc615d511ce030bc443/srcpkgs/e2fsprogs/patches/fix-glibcism.patch";
sha256 = "1gfcsr0i3q8q2f0lqza8na0iy4l4p3cbii51ds6zmj0y4hz2dwhb";
excludes = [ "lib/ext2fs/hashmap.h" ];

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@@ -2,11 +2,11 @@
stdenv.mkDerivation rec {
pname = "genimage";
version = "9";
version = "15";
src = fetchurl {
url = "https://public.pengutronix.de/software/genimage/genimage-${version}.tar.xz";
sha256 = "0y4h8x8lqxam8m90rdfq8cg5137kvilxr3d1qzddpx7nxpvmmwv9";
sha256 = "0gh05pkmqn9ck79mwvl2812ssh0fb0xbq72iwh7b641ki2zj9jlv";
};
nativeBuildInputs = [ pkg-config ];
@@ -17,7 +17,7 @@ stdenv.mkDerivation rec {
# documentation.
docdir="$out/share/doc/genimage"
mkdir -p "$docdir"
cp -v README "$docdir"
cp -v README.rst "$docdir"
'';
meta = with lib; {

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@@ -0,0 +1,48 @@
{ lib
, stdenv
, meson
, ninja
, vulkan-loader
, vulkan-headers
, fetchFromGitHub
}:
stdenv.mkDerivation rec {
pname = "vkdisplayinfo";
version = "0.1";
src = fetchFromGitHub {
owner = "ChristophHaag";
repo = "vkdisplayinfo";
rev = version;
hash = "sha256-n6U7T5aOYTpgWE2WGPBPHtQKzitf9PxAoXJNWyz4rYw=";
};
postInstall = ''
install vkdisplayinfo -Dm755 -t $out/bin
'';
doInstallCheck = true;
installCheckPhase = ''
runHook preInstallCheck
($out/bin/vkdisplayinfo 2>&1 || true) | grep -q vkdisplayinfo
runHook postInstallCheck
'';
nativeBuildInputs = [
meson
ninja
];
buildInputs = [
vulkan-loader
vulkan-headers
];
meta = with lib; {
description = "Print displays and modes enumerated with the Vulkan function vkGetPhysicalDeviceDisplayPropertiesKHR";
homepage = "https://github.com/ChristophHaag/vkdisplayinfo";
platforms = platforms.linux;
license = licenses.boost;
maintainers = [ maintainers.LunNova ];
};
}

View File

@@ -2,15 +2,15 @@
buildGoModule rec {
pname = "snowflake";
version = "2.0.1";
version = "2.2.0";
src = fetchgit {
url = "https://git.torproject.org/pluggable-transports/${pname}";
rev = "v${version}";
hash = "sha256-ULkqsh0DeFI1GsaVaHGSjoEY38EktvDVC52Sx6cQLOE=";
sha256 = "0iazamrfixv6yxc5m49adm97biq93pn6hwwpbh8yq558hrc6bh70";
};
vendorSha256 = "D5A19UHL1WEE1ODT80jKT+PJ5CTXPjc9Eg6v2Nfm4aw=";
vendorSha256 = "1v7cpg3kny0vqmdbgcc7i61wi5gx5wvrv0hmjykjrqgrvyq764c1";
meta = with lib; {
description = "System to defeat internet censorship";

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@@ -20957,6 +20957,8 @@ with pkgs;
hdf5 = hdf5.override { usev110Api = true; };
};
vkdisplayinfo = callPackage ../tools/graphics/vkdisplayinfo { };
vlock = callPackage ../misc/screensavers/vlock { };
vmime = callPackage ../development/libraries/vmime { };
@@ -22233,9 +22235,9 @@ with pkgs;
mysql80 = callPackage ../servers/sql/mysql/8.0.x.nix {
inherit (darwin) cctools developer_cmds DarwinTools;
inherit (darwin.apple_sdk.frameworks) CoreServices;
boost = boost173; # Configure checks for specific version.
protobuf = protobuf3_11;
icu = icu67;
boost = boost177; # Configure checks for specific version.
protobuf = protobuf3_19;
icu = icu69;
};
mysql_jdbc = callPackage ../servers/sql/mysql/jdbc { };

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@@ -5294,7 +5294,9 @@ in {
minexr = callPackage ../development/python-modules/minexr { };
miniaudio = callPackage ../development/python-modules/miniaudio { };
miniaudio = callPackage ../development/python-modules/miniaudio {
inherit (pkgs.darwin.apple_sdk.frameworks) AudioToolbox CoreAudio;
};
minidb = callPackage ../development/python-modules/minidb { };

View File

@@ -57,7 +57,6 @@ let
jobs.openssl.x86_64-darwin
jobs.pandoc.x86_64-darwin
jobs.postgresql.x86_64-darwin
jobs.python2.x86_64-darwin
jobs.python3.x86_64-darwin
jobs.ruby.x86_64-darwin
jobs.rustc.x86_64-darwin
@@ -102,7 +101,6 @@ let
jobs.go.x86_64-linux
jobs.linux.x86_64-linux
jobs.pandoc.x86_64-linux
jobs.python2.x86_64-linux
jobs.python3.x86_64-linux
# Needed by contributors to test PRs (by inclusion of the PR template)
jobs.nixpkgs-review.x86_64-linux
@@ -110,7 +108,7 @@ let
jobs.nix-info.x86_64-linux
jobs.nix-info-tested.x86_64-linux
# Ensure that X11/GTK are in order.
jobs.thunderbird-unwrapped.x86_64-linux
jobs.firefox-unwrapped.x86_64-linux
jobs.cachix.x86_64-linux
/*
@@ -138,7 +136,6 @@ let
jobs.cargo.x86_64-darwin
jobs.cachix.x86_64-darwin
jobs.go.x86_64-darwin
jobs.python2.x86_64-darwin
jobs.python3.x86_64-darwin
jobs.nixpkgs-review.x86_64-darwin
jobs.nix-info.x86_64-darwin