Merge master into staging-next

3 files changed, 50 insertions, 27 deletions

diff --git a/pkgs/applications/misc/remnote/default.nix b/pkgs/applications/misc/remnote/default.nix
index d9028d8876db1..198922f1876c8 100644
--- a/pkgs/applications/misc/remnote/default.nix
+++ b/pkgs/applications/misc/remnote/default.nix
@@ -6,11 +6,11 @@ stdenv.mkDerivation (finalAttrs: let
 in
 {
   pname = "remnote";
-  version = "1.15.4";
+  version = "1.16.4";
 
   src = fetchurl {
     url = "https://download.remnote.io/remnote-desktop/RemNote-${version}.AppImage";
-    hash = "sha256-6WBdTOj/seinx1wJGb/4if3PzCPmtzHyNAFmQwmsrvE=";
+    hash = "sha256-dgbQ0cbPq7BSQ9VwwH6+GoAxb85HDxRixfjeDJBtOrg=";
   };
 
   appexec = appimageTools.wrapType2 {
diff --git a/pkgs/applications/networking/browsers/firefox/common.nix b/pkgs/applications/networking/browsers/firefox/common.nix
index 988cc5481c32b..56dda27e54c92 100644
--- a/pkgs/applications/networking/browsers/firefox/common.nix
+++ b/pkgs/applications/networking/browsers/firefox/common.nix
@@ -298,9 +298,6 @@ buildStdenv.mkDerivation {
   setOutputFlags = false; # `./mach configure` doesn't understand `--*dir=` flags.
 
   preConfigure = ''
-    # remove distributed configuration files
-    rm -f configure js/src/configure .mozconfig*
-
     # Runs autoconf through ./mach configure in configurePhase
     configureScript="$(realpath ./mach) configure"
 
@@ -308,8 +305,8 @@ buildStdenv.mkDerivation {
     export MOZ_BUILD_DATE=$(head -n1 sourcestamp.txt)
 
     # Set predictable directories for build and state
-    export MOZ_OBJDIR=$(pwd)/mozobj
-    export MOZBUILD_STATE_PATH=$(pwd)/mozbuild
+    export MOZ_OBJDIR=$(pwd)/objdir
+    export MOZBUILD_STATE_PATH=$TMPDIR/mozbuild
 
     # Don't try to send libnotify notifications during build
     export MOZ_NOSPAM=1
@@ -353,7 +350,7 @@ buildStdenv.mkDerivation {
       # since the profiling build has not been installed to $out
       ''
         OLD_LDFLAGS="$LDFLAGS"
-        LDFLAGS="-Wl,-rpath,$(pwd)/mozobj/dist/${binaryName}"
+        LDFLAGS="-Wl,-rpath,$(pwd)/objdir/dist/${binaryName}"
       ''}
     fi
   '' + lib.optionalString googleAPISupport ''
@@ -510,7 +507,7 @@ buildStdenv.mkDerivation {
   '';
 
   preBuild = ''
-    cd mozobj
+    cd objdir
   '';
 
   postBuild = ''
@@ -535,9 +532,9 @@ buildStdenv.mkDerivation {
   preInstall = lib.optionalString crashreporterSupport ''
     ./mach buildsymbols
     mkdir -p $symbols/
-    cp mozobj/dist/*.crashreporter-symbols.zip $symbols/
+    cp objdir/dist/*.crashreporter-symbols.zip $symbols/
   '' + ''
-    cd mozobj
+    cd objdir
   '';
 
   postInstall = ''
diff --git a/pkgs/applications/science/biology/mafft/default.nix b/pkgs/applications/science/biology/mafft/default.nix
index f2e3ead2e913c..ca1f89388a442 100644
--- a/pkgs/applications/science/biology/mafft/default.nix
+++ b/pkgs/applications/science/biology/mafft/default.nix
@@ -1,14 +1,20 @@
-{ lib, stdenv, fetchFromGitLab }:
+{
+  lib,
+  stdenv,
+  fetchFromGitLab,
+  runCommand,
+  mafft,
+}:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation (finalAttrs: {
   pname = "mafft";
-  version = "7.525";
+  version = "7.526";
 
   src = fetchFromGitLab {
     owner = "sysimm";
-    repo = pname;
-    rev = "v${version}";
-    sha256 = "sha256-ckBmvFssYAmYcBHAEftjQqBV0MB0theGfemaPx3XUws=";
+    repo = "mafft";
+    rev = "v${finalAttrs.version}";
+    hash = "sha256-VNe00r12qEkLEbpZdJCe5xZ73JA3uAmuAeG+eSeRDI0=";
   };
 
   preBuild = ''
@@ -16,14 +22,34 @@ stdenv.mkDerivation rec {
     make clean
   '';
 
-  makeFlags = [ "CC=${stdenv.cc.targetPrefix}cc" "PREFIX=$(out)" ];
+  makeFlags = [
+    "CC=${stdenv.cc.targetPrefix}cc"
+    "PREFIX=$(out)"
+  ];
 
-  meta = with lib;
-    {
-      description = "Multiple alignment program for amino acid or nucleotide sequences";
-      homepage = "https://mafft.cbrc.jp/alignment/software/";
-      license = licenses.bsd3;
-      maintainers = with maintainers; [ natsukium ];
-      platforms = platforms.unix;
-    };
-}
+  passthru.tests = {
+    simple = runCommand "${finalAttrs.pname}-test" { } ''
+      mkdir $out
+      cd ${finalAttrs.src}/test
+      ${lib.getExe mafft} sample > $out/test.fftns2
+      ${lib.getExe mafft} --maxiterate 100  sample > $out/test.fftnsi
+      ${lib.getExe mafft} --globalpair sample > $out/test.gins1
+      ${lib.getExe mafft} --globalpair --maxiterate 100  sample > $out/test.ginsi
+      ${lib.getExe mafft} --localpair sample > $out/test.lins1
+      ${lib.getExe mafft} --localpair --maxiterate 100  sample > $out/test.linsi
+      diff $out/test.fftns2 sample.fftns2
+      diff $out/test.fftnsi sample.fftnsi
+      diff $out/test.gins1 sample.gins1
+      diff $out/test.ginsi sample.ginsi
+      diff $out/test.lins1 sample.lins1
+    '';
+  };
+
+  meta = with lib; {
+    description = "Multiple alignment program for amino acid or nucleotide sequences";
+    homepage = "https://mafft.cbrc.jp/alignment/software/";
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ natsukium ];
+    platforms = platforms.unix;
+  };
+})