Merge remote-tracking branch 'origin/staging-next' into staging

Conflicts:
	pkgs/applications/radio/soapysdr/default.nix

7 files changed, 37 insertions, 15 deletions

diff --git a/pkgs/applications/science/biology/angsd/default.nix b/pkgs/applications/science/biology/angsd/default.nix
index 035cb2ca2b275..71366dc0d3648 100644
--- a/pkgs/applications/science/biology/angsd/default.nix
+++ b/pkgs/applications/science/biology/angsd/default.nix
@@ -1,4 +1,14 @@
-{ lib, stdenv, fetchFromGitHub, htslib, zlib, bzip2, xz, curl, openssl }:
+{ lib
+, stdenv
+, fetchFromGitHub
+, fetchpatch
+, htslib
+, zlib
+, bzip2
+, xz
+, curl
+, openssl
+}:
 
 stdenv.mkDerivation rec {
   pname = "angsd";
@@ -11,8 +21,20 @@ stdenv.mkDerivation rec {
     rev = version;
   };
 
+  patches = [
+    # Pull pending inclusion upstream patch for parallel buil fixes:
+    #   https://github.com/ANGSD/angsd/pull/590
+    (fetchpatch {
+      name = "parallel-make.patch";
+      url = "https://github.com/ANGSD/angsd/commit/89fd1d898078016df390e07e25b8a3eeadcedf43.patch";
+      hash = "sha256-KQgUfr3v8xc+opAm4qcSV2eaupztv4gzJJHyzJBCxqA=";
+    })
+  ];
+
   buildInputs = [ htslib zlib bzip2 xz curl openssl ];
 
+  enableParallelBuilding = true;
+
   makeFlags = [ "HTSSRC=systemwide" "prefix=$(out)" ];
 
   meta = with lib; {
diff --git a/pkgs/applications/science/chemistry/element/default.nix b/pkgs/applications/science/chemistry/element/default.nix
index f0865b503deaf..c18fc9a563b93 100644
--- a/pkgs/applications/science/chemistry/element/default.nix
+++ b/pkgs/applications/science/chemistry/element/default.nix
@@ -11,7 +11,7 @@ buildGoModule rec {
     sha256 = "sha256-06RDZnie0Lv7i95AwnBGl6PPucuj8pIT6DHW3e3mu1o=";
   };
 
-  vendorSha256 = "sha256-A4g2rQTaYrA4/0rqldUv7iuibzNINEvx9StUnaN2/Yg=";
+  vendorHash = "sha256-A4g2rQTaYrA4/0rqldUv7iuibzNINEvx9StUnaN2/Yg=";
 
   meta = with lib; {
     description = "The periodic table on the command line";
diff --git a/pkgs/applications/science/logic/cbmc/default.nix b/pkgs/applications/science/logic/cbmc/default.nix
index 9cc88ca7081d3..6a878735bb3d9 100644
--- a/pkgs/applications/science/logic/cbmc/default.nix
+++ b/pkgs/applications/science/logic/cbmc/default.nix
@@ -13,13 +13,13 @@
 
 stdenv.mkDerivation rec {
   pname = "cbmc";
-  version = "5.90.0";
+  version = "5.91.0";
 
   src = fetchFromGitHub {
     owner = "diffblue";
     repo = pname;
     rev = "${pname}-${version}";
-    sha256 = "sha256-c6Ms/IStmKug5nz37TzjeexkY3YfWaUqEKIC2viMK9g=";
+    sha256 = "sha256-7DzhGEDS9T6WIjGoxOw9Gf/q+tYNFJDPbQUBV3tbn/I=";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/applications/science/logic/drat-trim/default.nix b/pkgs/applications/science/logic/drat-trim/default.nix
index c58a29dc28944..78d810e19be23 100644
--- a/pkgs/applications/science/logic/drat-trim/default.nix
+++ b/pkgs/applications/science/logic/drat-trim/default.nix
@@ -1,14 +1,14 @@
 { lib, stdenv, fetchFromGitHub }:
 
 stdenv.mkDerivation {
-  pname = "drat-trim-unstable";
-  version = "2020-06-05";
+  pname = "drat-trim";
+  version = "2023-05-22";
 
   src = fetchFromGitHub {
     owner = "marijnheule";
     repo = "drat-trim";
-    rev = "9afad0f7156a1e9c6ce19dce5d72cf1cb9a3ef27";
-    sha256 = "1zq585igfaknwqbvv2cji744016zxadbvr0ifr5l6yq13m0vvn3b";
+    rev = "refs/tags/v05.22.2023";
+    hash = "sha256-sV3A0f1TLSaTIdAtT6y8rU3ZS2UqEePJYSf3UySOlSA=";
   };
 
   postPatch = ''
diff --git a/pkgs/applications/science/logic/egglog/default.nix b/pkgs/applications/science/logic/egglog/default.nix
index d594034333705..eedd90315db86 100644
--- a/pkgs/applications/science/logic/egglog/default.nix
+++ b/pkgs/applications/science/logic/egglog/default.nix
@@ -5,13 +5,13 @@
 
 rustPlatform.buildRustPackage {
   pname = "egglog";
-  version = "unstable-2023-08-29";
+  version = "unstable-2023-09-12";
 
   src = fetchFromGitHub {
     owner = "egraphs-good";
     repo = "egglog";
-    rev = "c83fc750878755eb610a314da90f9273b3bfe25d";
-    hash = "sha256-bo3LU7WQ7WWnyL4EVOpzxxSFioXTozCSQFIFXyoxKLg=";
+    rev = "4d67f262a6f27aa5cfb62a2cfc7df968959105df";
+    hash = "sha256-1mc7dW2pgaK4D7ZmlSHohb+6lcr7M9SRLUV/Dod8Rv0=";
   };
 
   cargoLock = {
diff --git a/pkgs/applications/science/misc/boinc/default.nix b/pkgs/applications/science/misc/boinc/default.nix
index f806be834bca4..4721e946464e4 100644
--- a/pkgs/applications/science/misc/boinc/default.nix
+++ b/pkgs/applications/science/misc/boinc/default.nix
@@ -27,14 +27,14 @@
 
 stdenv.mkDerivation rec {
   pname = "boinc";
-  version = "7.22.2";
+  version = "7.24.1";
 
   src = fetchFromGitHub {
     name = "${pname}-${version}-src";
     owner = "BOINC";
     repo = "boinc";
     rev = "client_release/${lib.versions.majorMinor version}/${version}";
-    hash = "sha256-9GgvyYiDfppRuDFfxn50e+YZeSX0SLKSfo31lWx2FBs=";
+    hash = "sha256-CAzAKxNHG8ew9v2B1jK7MxfWGwTfdmDncDe7QT+twd8=";
   };
 
   nativeBuildInputs = [ libtool automake autoconf m4 pkg-config ];
diff --git a/pkgs/applications/science/molecular-dynamics/viennarna/default.nix b/pkgs/applications/science/molecular-dynamics/viennarna/default.nix
index 3d20eeabe2685..f292cbb378c9a 100644
--- a/pkgs/applications/science/molecular-dynamics/viennarna/default.nix
+++ b/pkgs/applications/science/molecular-dynamics/viennarna/default.nix
@@ -8,11 +8,11 @@
 }:
 
 stdenv.mkDerivation rec {
-  pname = "ViennaRNA";
+  pname = "viennarna";
   version = "2.5.1";
 
   src = fetchurl {
-    url = "https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_5_x/${pname}-${version}.tar.gz";
+    url = "https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_5_x/ViennaRNA-${version}.tar.gz";
     sha256 = "sha256-BUAEN88VWV4QsaJd9snEiFbzVhMPnR44D6iGa20n9Fc=";
   };