lzma: deprecate alias

10 files changed, 21 insertions, 20 deletions

diff --git a/pkgs/applications/science/biology/bcftools/default.nix b/pkgs/applications/science/biology/bcftools/default.nix
index 80506bb79b6c6..46d39c1a7ba3d 100644
--- a/pkgs/applications/science/biology/bcftools/default.nix
+++ b/pkgs/applications/science/biology/bcftools/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchurl, htslib, zlib, bzip2, lzma, curl, perl, python3, bash }:
+{ lib, stdenv, fetchurl, htslib, zlib, bzip2, xz, curl, perl, python3, bash }:
 
 stdenv.mkDerivation rec {
   pname = "bcftools";
@@ -14,7 +14,7 @@ stdenv.mkDerivation rec {
     python3
   ];
 
-  buildInputs = [ htslib zlib bzip2 lzma curl ];
+  buildInputs = [ htslib zlib bzip2 xz curl ];
 
   strictDeps = true;
 
diff --git a/pkgs/applications/science/biology/bedtools/default.nix b/pkgs/applications/science/biology/bedtools/default.nix
index f5aad5d055437..aac36d2af3100 100644
--- a/pkgs/applications/science/biology/bedtools/default.nix
+++ b/pkgs/applications/science/biology/bedtools/default.nix
@@ -1,4 +1,4 @@
-{lib, stdenv, fetchFromGitHub, zlib, python3, bzip2, lzma}:
+{lib, stdenv, fetchFromGitHub, zlib, python3, bzip2, xz}:
 
 stdenv.mkDerivation rec {
   pname = "bedtools";
@@ -17,7 +17,8 @@ stdenv.mkDerivation rec {
     python3
   ];
 
-  buildInputs = [ zlib bzip2 lzma ];
+  buildInputs = [ zlib bzip2 xz ];
+
   cxx = if stdenv.cc.isClang then "clang++" else "g++";
   cc = if stdenv.cc.isClang then "clang" else "gcc";
   buildPhase = "make prefix=$out SHELL=${stdenv.shell} CXX=${cxx} CC=${cc} -j $NIX_BUILD_CORES";
diff --git a/pkgs/applications/science/biology/delly/default.nix b/pkgs/applications/science/biology/delly/default.nix
index efaa4403f41d3..fe81ff44d2456 100644
--- a/pkgs/applications/science/biology/delly/default.nix
+++ b/pkgs/applications/science/biology/delly/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchpatch, fetchFromGitHub, htslib, zlib, bzip2, lzma, ncurses, boost }:
+{ lib, stdenv, fetchpatch, fetchFromGitHub, htslib, zlib, bzip2, xz, ncurses, boost }:
 
 stdenv.mkDerivation rec {
   pname = "delly";
@@ -11,7 +11,7 @@ stdenv.mkDerivation rec {
       sha256 = "sha256-DWwC35r8cQbePUzppkFQlev0YZdxk2+BSrNTW/DOY3M=";
   };
 
-  buildInputs = [ zlib htslib bzip2 lzma ncurses boost ];
+  buildInputs = [ zlib htslib bzip2 xz ncurses boost ];
 
   EBROOTHTSLIB = htslib;
 
diff --git a/pkgs/applications/science/biology/freebayes/default.nix b/pkgs/applications/science/biology/freebayes/default.nix
index 32ab614b9682e..8646b8ca54a8c 100644
--- a/pkgs/applications/science/biology/freebayes/default.nix
+++ b/pkgs/applications/science/biology/freebayes/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchFromGitHub, zlib, bzip2, lzma }:
+{ lib, stdenv, fetchFromGitHub, zlib, bzip2, xz }:
 
 stdenv.mkDerivation rec {
   pname = "freebayes";
@@ -13,7 +13,7 @@ stdenv.mkDerivation rec {
     fetchSubmodules = true;
   };
 
-  buildInputs = [ zlib bzip2 lzma ];
+  buildInputs = [ zlib bzip2 xz ];
 
   installPhase = ''
     install -vD bin/freebayes bin/bamleftalign scripts/* -t $out/bin
diff --git a/pkgs/applications/science/biology/kent/default.nix b/pkgs/applications/science/biology/kent/default.nix
index 26c55d3dc383a..12bbfa09c2514 100644
--- a/pkgs/applications/science/biology/kent/default.nix
+++ b/pkgs/applications/science/biology/kent/default.nix
@@ -3,7 +3,7 @@
 , libuuid
 , zlib
 , bzip2
-, lzma
+, xz
 , openssl
 , curl
 , libmysqlclient
@@ -22,7 +22,7 @@ stdenv.mkDerivation rec {
     sha256 = "0l5lmqqc6sqkf4hyk3z4825ly0vdlj5xdfad6zd0708cb1v81nbx";
   };
 
-  buildInputs = [ libpng libuuid zlib bzip2 lzma openssl curl libmysqlclient ];
+  buildInputs = [ libpng libuuid zlib bzip2 xz openssl curl libmysqlclient ];
 
   patchPhase = ''
     substituteInPlace ./src/checkUmask.sh \
diff --git a/pkgs/applications/science/biology/octopus/default.nix b/pkgs/applications/science/biology/octopus/default.nix
index fa88e5c47b471..0ef48ec6413b0 100644
--- a/pkgs/applications/science/biology/octopus/default.nix
+++ b/pkgs/applications/science/biology/octopus/default.nix
@@ -1,4 +1,4 @@
-{lib, stdenv, fetchpatch, fetchFromGitHub, cmake, boost, gmp, htslib, zlib, lzma, pkg-config}:
+{lib, stdenv, fetchpatch, fetchFromGitHub, cmake, boost, gmp, htslib, zlib, xz, pkg-config}:
 
 stdenv.mkDerivation rec {
   pname = "octopus";
@@ -24,7 +24,7 @@ stdenv.mkDerivation rec {
   ];
 
   nativeBuildInputs = [ cmake pkg-config ];
-  buildInputs = [ boost gmp htslib zlib lzma ];
+  buildInputs = [ boost gmp htslib zlib xz ];
 
   postInstall = ''
     mkdir $out/bin
diff --git a/pkgs/applications/science/biology/svaba/default.nix b/pkgs/applications/science/biology/svaba/default.nix
index 87b77f6ac0456..1aed501919f9b 100644
--- a/pkgs/applications/science/biology/svaba/default.nix
+++ b/pkgs/applications/science/biology/svaba/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, zlib, bzip2, lzma, fetchFromGitHub } :
+{ lib, stdenv, zlib, bzip2, xz, fetchFromGitHub } :
 
 stdenv.mkDerivation rec {
   version = "1.1.0";
@@ -12,7 +12,7 @@ stdenv.mkDerivation rec {
     fetchSubmodules = true;
   };
 
-  buildInputs = [ zlib bzip2 lzma ];
+  buildInputs = [ zlib bzip2 xz ];
 
   installPhase = ''
     runHook preInstall
diff --git a/pkgs/applications/science/machine-learning/shogun/default.nix b/pkgs/applications/science/machine-learning/shogun/default.nix
index 7d052c6c5e9ec..47b826078f24d 100644
--- a/pkgs/applications/science/machine-learning/shogun/default.nix
+++ b/pkgs/applications/science/machine-learning/shogun/default.nix
@@ -1,6 +1,6 @@
 { stdenv, lib, fetchFromGitHub, fetchpatch, fetchurl, cmake, ctags, swig
 # data, compression
-, bzip2, curl, hdf5, json_c, lzma, lzo, protobuf, snappy
+, bzip2, curl, hdf5, json_c, xz, lzo, protobuf, snappy
 # maths
 , blas, lapack, eigen, nlopt, lp_solve, colpack, glpk
 # libraries
@@ -67,7 +67,7 @@ stdenv.mkDerivation rec {
 
   nativeBuildInputs = [ cmake ];
   buildInputs = with lib; [
-      blas lapack bzip2 colpack curl ctags eigen hdf5 json_c lp_solve lzma lzo
+      blas lapack bzip2 colpack curl ctags eigen hdf5 json_c lp_solve xz lzo
       protobuf nlopt snappy swig (libarchive.dev) libxml2 lapack glpk
     ]
     ++ optionals (pythonSupport) (with pythonPackages; [ python ply numpy ])
diff --git a/pkgs/applications/science/misc/root/5.nix b/pkgs/applications/science/misc/root/5.nix
index 144827413b5e4..75607fdda348d 100644
--- a/pkgs/applications/science/misc/root/5.nix
+++ b/pkgs/applications/science/misc/root/5.nix
@@ -1,5 +1,5 @@
 { lib, stdenv, fetchurl, fetchpatch, cmake, pcre, pkg-config, python2
-, libX11, libXpm, libXft, libXext, libGLU, libGL, zlib, libxml2, lz4, lzma, gsl_1, xxHash
+, libX11, libXpm, libXft, libXext, libGLU, libGL, zlib, libxml2, lz4, xz, gsl_1, xxHash
 , Cocoa, OpenGL, noSplash ? false }:
 
 stdenv.mkDerivation rec {
@@ -12,7 +12,7 @@ stdenv.mkDerivation rec {
   };
 
   nativeBuildInputs = [ cmake pkg-config ];
-  buildInputs = [ pcre python2 zlib libxml2 lz4 lzma gsl_1 xxHash ]
+  buildInputs = [ pcre python2 zlib libxml2 lz4 xz gsl_1 xxHash ]
     ++ lib.optionals (!stdenv.isDarwin) [ libX11 libXpm libXft libXext libGLU libGL ]
     ++ lib.optionals (stdenv.isDarwin) [ Cocoa OpenGL ]
     ;
diff --git a/pkgs/applications/science/misc/root/default.nix b/pkgs/applications/science/misc/root/default.nix
index 2f3d57c31e7bf..9df3b0020a01e 100644
--- a/pkgs/applications/science/misc/root/default.nix
+++ b/pkgs/applications/science/misc/root/default.nix
@@ -1,5 +1,5 @@
 { stdenv, lib, fetchurl, makeWrapper, cmake, ftgl, gl2ps, glew, gsl, llvm_5
-, libX11, libXpm, libXft, libXext, libGLU, libGL, libxml2, lz4, lzma, pcre
+, libX11, libXpm, libXft, libXext, libGLU, libGL, libxml2, lz4, xz, pcre
 , pkg-config, python, xxHash, zlib, zstd
 , libAfterImage, giflib, libjpeg, libtiff, libpng
 , Cocoa, OpenGL, noSplash ? false }:
@@ -14,7 +14,7 @@ stdenv.mkDerivation rec {
   };
 
   nativeBuildInputs = [ makeWrapper cmake pkg-config ];
-  buildInputs = [ ftgl gl2ps glew pcre zlib zstd llvm_5 libxml2 lz4 lzma gsl xxHash libAfterImage giflib libjpeg libtiff libpng python.pkgs.numpy ]
+  buildInputs = [ ftgl gl2ps glew pcre zlib zstd llvm_5 libxml2 lz4 xz gsl xxHash libAfterImage giflib libjpeg libtiff libpng python.pkgs.numpy ]
     ++ lib.optionals (!stdenv.isDarwin) [ libX11 libXpm libXft libXext libGLU libGL ]
     ++ lib.optionals (stdenv.isDarwin) [ Cocoa OpenGL ]
     ;