Merge remote-tracking branch 'upstream/master' into staging

pkgs/applications/misc/mdp/default.nix

@@ -1,14 +1,14 @@
 { stdenv, fetchFromGitHub, ncurses }:
 
 stdenv.mkDerivation rec {
-  version = "1.0.10";
+  version = "1.0.12";
   name = "mdp-${version}";
 
   src = fetchFromGitHub {
     owner = "visit1985";
     repo = "mdp";
     rev = version;
-    sha256 = "1swp1hqryai84c8dpzsvjpgg5rz2vnn2vrp0dhwy8r0qgpmby2nn";
+    sha256 = "04izj9i9rxmgswjh2iawqs6qglfv44zfv042smmcvfh1pm43361i";
   };
 
   makeFlags = [ "PREFIX=$(out)" ];

pkgs/applications/science/biology/star/default.nix

@@ -0,0 +1,34 @@
+{ stdenv, fetchFromGitHub, zlib }:
+
+stdenv.mkDerivation rec {
+  name = "star-${version}";
+  version = "2.5.3a";
+
+  src = fetchFromGitHub {
+    repo = "STAR";
+    owner = "alexdobin";
+    rev = version;
+    sha256 = "1fd9xl7i1zxgsxn2qf6gz8s42g2djm29qmp6qb35d8nnxh8ns54x";
+  };
+
+  sourceRoot = "source/source";
+  
+  postPatch = "sed 's:/bin/rm:rm:g' -i Makefile";
+  
+  buildInputs = [ zlib ];
+  
+  buildPhase = "make STAR STARlong";
+
+  installPhase = ''
+    mkdir -p $out/bin
+    cp STAR STARlong $out/bin
+  '';
+  
+  meta = with stdenv.lib; {
+    description = "Spliced Transcripts Alignment to a Reference";
+    homepage = https://github.com/alexdobin/STAR;
+    license = licenses.gpl3Plus;
+    platforms = platforms.linux;
+    maintainers = [ maintainers.arcadio ];
+  };
+}

pkgs/applications/video/streamlink/default.nix

@@ -1,17 +1,17 @@
 { stdenv, pythonPackages, fetchFromGitHub, rtmpdump, ffmpeg }:
 
 pythonPackages.buildPythonApplication rec {
-  version = "0.9.0";
+  version = "0.10.0";
   name = "streamlink-${version}";
 
   src = fetchFromGitHub {
     owner = "streamlink";
     repo = "streamlink";
     rev = "${version}";
-    sha256 = "11jczkar3aqsbl5amkm7lsv4fz6xdaydd5izn222wjzsbvnzrcgd";
+    sha256 = "1p9gkwcvqlnv09ihqh71nh82nnmq9ybp1v8d8kd2vhkg1vm5ximn";
   };
 
-  buildInputs = with pythonPackages; [ pytest mock ];
+  checkInputs = with pythonPackages; [ pytest mock requests-mock ];
 
   propagatedBuildInputs = (with pythonPackages; [ pycryptodome requests iso-639 iso3166 websocket_client ]) ++ [ rtmpdump ffmpeg ];
 

pkgs/development/compilers/rust/rustc.nix

@@ -37,6 +37,12 @@ stdenv.mkDerivation {
   # The build will fail at the very end on AArch64 without this.
   dontUpdateAutotoolsGnuConfigScripts = if stdenv.isAarch64 then true else null;
 
+  # Running the default `strip -S` command on Darwin corrupts the
+  # .rlib files in "lib/".
+  #
+  # See https://github.com/NixOS/nixpkgs/pull/34227
+  stripDebugList = if stdenv.isDarwin then [ "bin" ] else null;
+
   NIX_LDFLAGS = optionalString stdenv.isDarwin "-rpath ${llvmShared}/lib";
 
   # Enable nightly features in stable compiles (used for
@@ -78,8 +84,9 @@ stdenv.mkDerivation {
     #[ -f src/liballoc_jemalloc/lib.rs ] && sed -i 's,je_,,g' src/liballoc_jemalloc/lib.rs
     #[ -f src/liballoc/heap.rs ] && sed -i 's,je_,,g' src/liballoc/heap.rs # Remove for 1.4.0+
 
-    # Disable fragile linker-output-non-utf8 test
+    # Disable fragile tests.
     rm -vr src/test/run-make/linker-output-non-utf8 || true
+    rm -vr src/test/run-make/issue-26092.rs || true
 
     # Remove test targeted at LLVM 3.9 - https://github.com/rust-lang/rust/issues/36835
     rm -vr src/test/run-pass/issue-36023.rs || true

pkgs/development/libraries/ldb/default.nix

@@ -3,11 +3,11 @@
 }:
 
 stdenv.mkDerivation rec {
-  name = "ldb-1.3.1";
+  name = "ldb-1.1.27";
 
   src = fetchurl {
     url = "mirror://samba/ldb/${name}.tar.gz";
-    sha256 = "1b1mkggp8swb67s9aswavhzswlib34hpgsv66zgns009paf2df6d";
+    sha256 = "1b1mkl5p8swb67s9aswavhzswlib34hpgsv66zgns009paf2df6d";
   };
 
   outputs = [ "out" "dev" ];

pkgs/development/libraries/libbsd/default.nix

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "libbsd-${version}";
-  version = "0.8.6";
+  version = "0.8.7";
 
   src = fetchurl {
     url = "http://libbsd.freedesktop.org/releases/${name}.tar.xz";
-    sha256 = "11wnkzims5grprvhb1ssmq9pc2lcgh2r2rk8gwgz36ply6fvyzs6";
+    sha256 = "0c9bl49zs0xdddcwj5dh0lay9sxi2m1yi74848g8p87mb87g2j7m";
   };
 
   # darwin changes configure.ac which means we need to regenerate

pkgs/development/tools/fac/default.nix

@@ -1,8 +1,14 @@
-{ stdenv, buildGoPackage, fetchFromGitHub, makeWrapper, git }:
+{ stdenv, buildGoPackage, fetchFromGitHub, fetchurl, makeWrapper, git }:
 
-buildGoPackage rec {
+let
+  # TODO: Remove this on next update, should be included
+  fac_1 = fetchurl {
+    url = https://raw.githubusercontent.com/mkchoi212/fac/0a500c2a2dba9017fe7c2a45f15c328755f561a6/doc/fac.1;
+    sha256 = "1fsyx9i20ryhpihdpvs2z7vccl13b9bnh5hcdxn7bvqjz78mbqhw";
+  };
+in buildGoPackage rec {
   name = "fac-${version}";
-  version = "1.0.1";
+  version = "1.0.4";
 
   goPackagePath = "github.com/mkchoi212/fac";
 
@@ -10,7 +16,7 @@ buildGoPackage rec {
     owner = "mkchoi212";
     repo = "fac";
     rev = "v${version}";
-    sha256 = "1j5kip3l3p9qlly03pih905sdz3ncvpj7135jpnfhckbk1s5x9dc";
+    sha256 = "0jhx80jbkxfxj95hmdpb9wwwya064xpfkaa218l1lwm3qwfbpk95";
   };
 
   nativeBuildInputs = [ makeWrapper ];
@@ -18,6 +24,8 @@ buildGoPackage rec {
   postInstall = ''
     wrapProgram $bin/bin/fac \
       --prefix PATH : ${git}/bin
+
+    install -D ${fac_1} $out/share/man/man1/fac.1
   '';
 
   meta = with stdenv.lib; {

pkgs/development/tools/packer/default.nix

@@ -1,7 +1,7 @@
 { stdenv, buildGoPackage, fetchFromGitHub }:
 buildGoPackage rec {
   name = "packer-${version}";
-  version = "1.1.0";
+  version = "1.1.3";
 
   goPackagePath = "github.com/hashicorp/packer";
 
@@ -11,7 +11,7 @@ buildGoPackage rec {
     owner = "hashicorp";
     repo = "packer";
     rev = "v${version}";
-    sha256 = "09hwq6dxyzhpl97akwbb02bjrisz9rf296avg5zj2p5qdsf4y777";
+    sha256 = "0bfjv4sqci10jzy11qg6q1xyik36v98vd6ck91sarawvgbaprsp2";
   };
 
   meta = with stdenv.lib; {

pkgs/development/tools/yq/default.nix

@@ -2,9 +2,8 @@
 
 buildPythonApplication rec {
 
-  name = "${pname}-${version}";
   pname = "yq";
-  version = "2.3.3";
+  version = "2.3.4";
 
   propagatedBuildInputs = [ pyyaml jq ];
 
@@ -13,7 +12,7 @@ buildPythonApplication rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "14ywdi464z68qclsqzb8r50rzmypknaz74zmpppkahjigfcfppm3";
+    sha256 = "04ckrlmin8m176iicyfhddp4r0yry5hx306vhfglf8mcp1jkga78";
   };
 
   meta = with lib; {

pkgs/tools/audio/beets/default.nix

@@ -195,7 +195,7 @@ in pythonPackages.buildPythonApplication rec {
     BASH_COMPLETION_SCRIPT="${completion}" \
     HOME="$(mktemp -d)" \
       # Exclude failing test https://github.com/beetbox/beets/issues/2652
-      nosetests -v --exclude="test_single_month_nonmatch_"
+      nosetests -v --exclude=test_single_month_nonmatch_ --exclude=test_asciify_variable --exclude=test_asciify_character_expanding_to_slash
 
     runHook postCheck
   '';

pkgs/tools/misc/diffoscope/default.nix

@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchgit, python3Packages, docutils
+{ lib, stdenv, fetchgit, python3Packages, docutils, help2man
 , acl, apktool, libbfd, bzip2, cbfstool, cdrkit, colord, colordiff, coreutils, cpio, diffutils, dtc
 , e2fsprogs, file, findutils, fontforge-fonttools, fpc, gettext, ghc, ghostscriptX, giflib, gnupg1, gnutar
 , gzip, imagemagick, jdk, libarchive, libcaca, llvm, mono, openssh, pdftk, pgpdump, poppler_utils, sng, sqlite
@@ -8,12 +8,12 @@
 
 python3Packages.buildPythonApplication rec {
   name = "diffoscope-${version}";
-  version = "87";
+  version = "90";
 
   src = fetchgit {
     url    = "git://anonscm.debian.org/reproducible/diffoscope.git";
     rev    = "refs/tags/${version}";
-    sha256 = "0j3pljwmggrpaghbamvr24x4cg5yj7hl2ll27405p7970scnpngv";
+    sha256 = "1w16667j6ag2iim1xcy8y9v9965mq50k64wnf693mivddll62704";
   };
 
   patches = [
@@ -25,6 +25,8 @@ python3Packages.buildPythonApplication rec {
     sed -i setup.py -e "/'rpm-python',/d"
   '';
 
+  nativeBuildInputs = [ docutils help2man ];
+
   # Still missing these tools: docx2txt enjarify js-beautify oggDump Rscript
   # Also these libraries: python3-guestfs
   pythonPath = with python3Packages; [ debian libarchive-c python_magic tlsh rpm ] ++ [
@@ -37,10 +39,12 @@ python3Packages.buildPythonApplication rec {
     ];
 
   doCheck = false; # Calls 'mknod' in squashfs tests, which needs root
+  checkInputs = with python3Packages; [ pytest ];
 
   postInstall = ''
+    make -C doc
     mkdir -p $out/share/man/man1
-    ${docutils}/bin/rst2man.py debian/diffoscope.1.rst $out/share/man/man1/diffoscope.1
+    cp doc/diffoscope.1 $out/share/man/man1/diffoscope.1
   '';
 
   meta = with stdenv.lib; {

pkgs/tools/security/spectre-meltdown-checker/default.nix

@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   name = "spectre-meltdown-checker-${version}";
-  version = "0.32";
+  version = "0.33";
 
   src = fetchFromGitHub {
     owner = "speed47";
     repo = "spectre-meltdown-checker";
     rev = "v${version}";
-    sha256 = "1qd3cwmg3p309czmghczlacygiyngp2wcwdghacg0y4l9vrndg8c";
+    sha256 = "0a0vbzjfmvcvak804y2s0301f9bcnr0nwg2piafx6i6ibisp917y";
   };
 
   prePatch = ''

pkgs/top-level/all-packages.nix

@@ -18995,6 +18995,8 @@ with pkgs;
 
   snpeff = callPackage ../applications/science/biology/snpeff/default.nix { };
 
+  star = callPackage ../applications/science/biology/star { };
+
   varscan = callPackage ../applications/science/biology/varscan/default.nix { };
 
   bwa = callPackage ../applications/science/biology/bwa/default.nix { };