Merge branch 'master' into staging

More mass rebuilds from master.

pkgs/development/compilers/tinycc/default.nix

@@ -2,10 +2,10 @@
 with stdenv.lib;
 
 let
-  date = "20170225";
+  date = "20170527";
   version = "0.9.27pre-${date}";
-  rev = "bb93064d7857d887b674999c9b4152b44a628f9a";
-  sha256 = "12wcahj1x4qy9ia931i23lvwkqjmyhaks3wipnzvbnlnc2b03kpr";
+  rev = "53c5fc2246270e0242903de0152a9a5d40f3d679";
+  sha256 = "0z5ayz0kdn5xqm84k730hmd7r9cq0zxxf45g5phgqppdfajrmswz";
 in
 
 stdenv.mkDerivation rec {

pkgs/development/haskell-modules/generic-builder.nix

@@ -197,13 +197,11 @@ stdenv.mkDerivation ({
     ${jailbreak-cabal}/bin/jailbreak-cabal ${pname}.cabal
   '' + postPatch;
 
-  # for ghcjs, we want to put ghcEnv on PATH so compiler plugins will be available.
-  # TODO(cstrahan): would the same be of benefit to native ghc?
   setupCompilerEnvironmentPhase = ''
     runHook preSetupCompilerEnvironment
 
     echo "Build with ${ghc}."
-    export PATH="${if ghc.isGhcjs or false then ghcEnv else ghc}/bin:$PATH"
+    export PATH="${ghc}/bin:$PATH"
     ${optionalString (hasActiveLibrary && hyperlinkSource) "export PATH=${hscolour}/bin:$PATH"}
 
     packageConfDir="$TMPDIR/package.conf.d"

pkgs/development/libraries/physics/cernlib/default.nix

@@ -0,0 +1,63 @@
+{ stdenv, fetchurl, gfortran, gnumake, imake, makedepend, motif, xorg }:
+
+stdenv.mkDerivation rec {
+  version = "2006";
+  name = "cernlib-${version}";
+
+  src = fetchurl {
+    url = "http://cernlib.web.cern.ch/cernlib/download/${version}_source/tar/${version}_src.tar.gz";
+    sha256 = "0awla1rl96z82br7slcmg8ks1d2a7slk6dj79ywb871j2ksi3fky";
+  };
+
+  buildInputs = with xorg; [ gfortran motif libX11 libXft libXt ];
+  nativeBuildInputs = [ gnumake imake makedepend ];
+  sourceRoot = ".";
+
+  patches = [ ./patch ];
+
+  postPatch = ''
+    substituteInPlace 2006/src/config/site.def \
+      --replace "# define MakeCmd gmake" "# define MakeCmd make"
+  '';
+
+  configurePhase = ''
+    export CERN=`pwd`
+    export CERN_LEVEL=${version}
+    export CERN_ROOT=$CERN/$CERN_LEVEL
+    export CVSCOSRC=`pwd`/$CERN_LEVEL/src
+    export PATH=$PATH:$CERN_ROOT/bin
+  '';
+
+  buildPhase = ''
+    cd $CERN_ROOT
+    mkdir -p build bin lib
+
+    cd $CERN_ROOT/build
+    $CVSCOSRC/config/imake_boot
+    make bin/kuipc
+    make scripts/Makefile
+    pushd scripts
+    make install.bin
+    popd
+    make
+  '';
+
+  installPhase = ''
+    mkdir "$out"
+    cp -r "$CERN_ROOT/bin" "$out"
+    cp -r "$CERN_ROOT/lib" "$out"
+    mkdir "$out/$CERN_LEVEL"
+    ln -s "$out/bin" "$out/$CERN_LEVEL/bin"
+    ln -s "$out/lib" "$out/$CERN_LEVEL/lib"
+  '';
+
+  setupHook = ./setup-hook.sh;
+
+  meta = {
+    homepage = http://cernlib.web.cern.ch;
+    description = "Legacy collection of libraries and modules for data analysis in high energy physics";
+    platforms = stdenv.lib.platforms.unix;
+    maintainers = with stdenv.lib.maintainers; [ veprbl ];
+    license = stdenv.lib.licenses.gpl2;
+  };
+}

pkgs/development/libraries/physics/cernlib/patch

@@ -0,0 +1,186 @@
+diff --git a/2006/src/config/Imake.tmpl b/2006/src/config/Imake.tmpl
+index 054fb04..a3b3828 100644
+--- a/2006/src/config/Imake.tmpl
++++ b/2006/src/config/Imake.tmpl
+@@ -455,7 +455,7 @@ XCOMM the platform-specific parameters - edit site.def to change
+ #define NoRConst NO /* YES if const for structs of funcs is bad */
+ #endif
+ #ifndef InstPgmFlags
+-#define InstPgmFlags -s
++#define InstPgmFlags
+ #endif
+ #ifndef InstBinFlags
+ #define InstBinFlags -m 0755
+diff --git a/2006/src/config/biglib.rules b/2006/src/config/biglib.rules
+index c90e58a..9173bdc 100644
+--- a/2006/src/config/biglib.rules
++++ b/2006/src/config/biglib.rules
+@@ -368,7 +368,7 @@ define build-object-list						@@\
+ @ (set -e;\							@@\
+ 	 case '${MFLAGS}' in *[i]*) set +e;; esac; \		@@\
+ 	 subdirs=Quote(dirs);\					@@\
+-	 list=`/bin/pwd`/$@;\					@@\
++	 list=`pwd`/$@;\					@@\
+ 	 for dir in $$subdirs; do \				@@\
+ 	  (set -e;cd $$dir;SedCmd -e "\=^[^/]=s=^.=$$dir/&=" $@ >> $$list);\@@\
+ 	 done) || (rm $@; exit 1)				@@\
+diff --git a/2006/src/config/imake_boot b/2006/src/config/imake_boot
+index b52d0d3..69cf1b3 100755
+--- a/2006/src/config/imake_boot
++++ b/2006/src/config/imake_boot
+@@ -10,8 +10,8 @@ if [ "$CVSCOSRC" = "" ] ; then
+ fi
+ if [ -f Imakefile ] ; then
+ 	imake -DUseInstalled -I$CVSCOSRC/config \
+-		-DTOPDIR=`/bin/pwd` -DCURDIR= -fImakefile
++		-DTOPDIR=`pwd` -DCURDIR= -fImakefile
+ else
+ 	imake -DUseInstalled -I$CVSCOSRC/config \
+-		-DTOPDIR=`/bin/pwd` -DCURDIR= -f$CVSCOSRC/Imakefile
++		-DTOPDIR=`pwd` -DCURDIR= -f$CVSCOSRC/Imakefile
+ fi
+diff --git a/2006/src/config/linux-lp64.cf b/2006/src/config/linux-lp64.cf
+index e071b2f..3cc5c3b 100644
+--- a/2006/src/config/linux-lp64.cf
++++ b/2006/src/config/linux-lp64.cf
+@@ -173,7 +173,7 @@
+ #define FortranCmd		g77
+ #define XargsCmd		xargs
+ #define FortranSaveFlags	/* */ /* Everything static !? */
+-#define DefaultFCOptions	-fno-automatic -fno-second-underscore -fugly-complex
++#define DefaultFCOptions	-fno-automatic -fno-second-underscore
+ #define CernlibSystem	        -DCERNLIB_LINUX -DCERNLIB_UNIX -DCERNLIB_LNX -DCERNLIB_QMGLIBC -DCERNLIB_QMLXIA64
+ 
+ # endif
+diff --git a/2006/src/config/linux.cf b/2006/src/config/linux.cf
+index cc0bee5..a8dd954 100644
+--- a/2006/src/config/linux.cf
++++ b/2006/src/config/linux.cf
+@@ -258,7 +258,7 @@ endif									@@\
+ #define FortranCmd		g77
+ #define XargsCmd		xargs
+ #define FortranSaveFlags	/* */ /* Everything static !? */
+-#define DefaultFCOptions	-fno-automatic -fno-second-underscore -fugly-complex
++#define DefaultFCOptions	-fno-automatic -fno-second-underscore
+ #define CernlibSystem	        -DCERNLIB_LINUX -DCERNLIB_UNIX -DCERNLIB_LNX -DCERNLIB_QMGLIBC
+ 
+ # endif
+diff --git a/2006/src/packlib/kuip/code_kuip/kkern.c b/2006/src/packlib/kuip/code_kuip/kkern.c
+index 3a5579f..5f3c352 100644
+--- a/2006/src/packlib/kuip/code_kuip/kkern.c
++++ b/2006/src/packlib/kuip/code_kuip/kkern.c
+@@ -543,24 +543,6 @@ char *str0dup( const char *str )
+ 
+ 
+ /*
+- * like strdup() but string is n characters long and not terminated
+- */
+-char *strndup( const char *str,
+-              size_t len )
+-{
+-  size_t bytes = len + 1;
+-  char *p;
+-
+-  if( bytes < ALLOC_MIN_BYTES )
+-    bytes = ALLOC_MIN_BYTES;
+-
+-  p = strncpy( malloc( bytes ), str, len );
+-  p[len] = '\0';
+-  return p;
+-}
+-
+-
+-/*
+  * strdup() of character representation of integer n
+  */
+ char *stridup( int n )
+diff --git a/2006/src/packlib/kuip/code_kuip/kmenu.c b/2006/src/packlib/kuip/code_kuip/kmenu.c
+index f135b07..23007a8 100644
+--- a/2006/src/packlib/kuip/code_kuip/kmenu.c
++++ b/2006/src/packlib/kuip/code_kuip/kmenu.c
+@@ -1404,7 +1404,7 @@ void interactive_find( char *expr, int keym )
+          printf ("See also:\n    ");
+          for (i = 0; i < nval; i++) {
+              if (i == ncmd) continue;
+-             printf (flis_name[i]);
++             printf ("%s", flis_name[i]);
+              if (i < nval-1)
+                 printf (", ");
+              else
+diff --git a/2006/src/packlib/kuip/kuip/kstring.h b/2006/src/packlib/kuip/kuip/kstring.h
+index 7811f15..12a1344 100644
+--- a/2006/src/packlib/kuip/kuip/kstring.h
++++ b/2006/src/packlib/kuip/kuip/kstring.h
+@@ -21,7 +21,6 @@ extern "C" {
+  */
+ 
+ #ifndef WIN32
+-extern void* memmove( void* dst, const void* src, size_t n );
+ #endif
+ 
+ /* GF. make conform to kkern.c#if !defined(__convexc__)*/
+@@ -46,7 +45,6 @@ extern char* str4dup( const char* str1, const char* str2, const char* str3,
+                      const char* str4 );
+ extern char* str5dup( const char* str1, const char* str2, const char* str3,
+                      const char* str4, const char* str5 );
+-extern char* strndup( const char* buf, size_t n );
+ extern char* stridup( int i );
+ 
+ extern char* mstrcat( char* ptr, const char* str );
+diff --git a/2006/src/pawlib/paw/cpaw/bugrep.c b/2006/src/pawlib/paw/cpaw/bugrep.c
+index d503a45..d26e30f 100644
+--- a/2006/src/pawlib/paw/cpaw/bugrep.c
++++ b/2006/src/pawlib/paw/cpaw/bugrep.c
+@@ -432,51 +432,7 @@ br_add_config( char * tmp_file )
+ 
+ static int
+ br_mail_file( char *addr, char *subj, char *file )
+-#if (defined(CERNLIB_UNIX))&&(!defined(CERNLIB_WINNT))&&(!defined(CERNLIB_MACOSX))
+-{
+-        FILE            *mfp, *fp;
+-        char            line[1024], my_addr[L_cuserid];
+-        time_t          clock;
+-        struct tm       *ts;
+-
+-        fp = fopen( file, "r" );
+-        if ( fp == NULL ) {
+-                printf( "BUGREPORT: cannot (re)open temporary file\n" );
+-                return MAIL_ERROR;
+-        }
+-
+-        cuserid( my_addr );
+-
+-        sprintf( line, "/usr/lib/sendmail -t" );
+-        mfp = popen( line, "w" );
+-
+-        if ( mfp == NULL ) {
+-                printf( "BUGREPORT: cannot run sendmail\n" );
+-                return MAIL_ERROR;
+-        }
+-
+-
+-        clock = time( (time_t *) 0 );
+-        ts = localtime( &clock );
+-        strftime( line, sizeof( line ),
+-                "%a, %d %h %y %H:%M:%S", ts );
+-        fprintf ( mfp, "To: %s\n", addr );
+-        fprintf ( mfp, "Bcc: %s\n", my_addr );
+-        fprintf ( mfp, "Date: %s\n", line );
+-        fprintf ( mfp, "Subject: %s\n", subj );
+-        fprintf ( mfp, "\n" );
+-
+-        while( fgets( line, sizeof( line ), fp ) != NULL ) {
+-                fputs( line, mfp );
+-        }
+-        fclose( fp );
+-
+-        pclose( mfp );
+-
+-        return MAIL_OK;
+-}
+-#endif
+-#if defined(CERNLIB_MACOSX)
++#if (defined(CERNLIB_UNIX))&&(!defined(CERNLIB_WINNT))
+ {
+         FILE            *mfp, *fp;
+         char            line[1024], *my_addr;

pkgs/development/libraries/physics/cernlib/setup-hook.sh

@@ -0,0 +1,3 @@
+export CERN_LEVEL=@version@
+export CERN=@out@
+export CERN_ROOT=$CERN/$CERN_LEVEL

pkgs/development/ocaml-modules/cmdliner/default.nix

@@ -1,31 +1,34 @@
-{ stdenv, fetchurl, ocaml, findlib, ocamlbuild, opam }:
+{ stdenv, fetchurl, ocaml, findlib, ocamlbuild, opam, topkg, result }:
 
 let
   pname = "cmdliner";
 in
 
-assert stdenv.lib.versionAtLeast ocaml.version "3.12";
+assert stdenv.lib.versionAtLeast ocaml.version "4.01.0";
 
 stdenv.mkDerivation rec {
-
   name = "ocaml-${pname}-${version}";
-  version = "0.9.8";
+  version = "1.0.0";
 
   src = fetchurl {
     url = "http://erratique.ch/software/${pname}/releases/${pname}-${version}.tbz";
-    sha256 = "0hdxlkgiwjml9dpaa80282a8350if7mc1m6yz2mrd7gci3fszykx";
+    sha256 = "1ryn7qis0izg0wcal8zdlikzzl689l75y6f4zc6blrm93y5agy9x";
   };
 
   unpackCmd = "tar xjf $src";
-  buildInputs = [ ocaml findlib ocamlbuild opam ];
+
+  nativeBuildInputs = [ ocamlbuild opam topkg ];
+  buildInputs = [ ocaml findlib ];
+  propagatedBuildInputs = [ result ];
 
   createFindlibDestdir = true;
 
-  configurePhase = "ocaml pkg/git.ml";
-  buildPhase     = "ocaml pkg/build.ml native=true native-dynlink=true";
-  installPhase   = ''
-    opam-installer --script --prefix=$out ${pname}.install > install.sh
-    sh install.sh
+  buildPhase = ''
+    ocaml -I ${findlib}/lib/ocaml/${ocaml.version}/site-lib pkg/pkg.ml build
+  '';
+
+  installPhase = ''
+    opam-installer --script --prefix=$out | sh
     ln -s $out/lib/${pname} $out/lib/ocaml/${ocaml.version}/site-lib/
   '';
 
@@ -33,7 +36,7 @@ stdenv.mkDerivation rec {
     homepage = http://erratique.ch/software/cmdliner;
     description = "An OCaml module for the declarative definition of command line interfaces";
     license = licenses.bsd3;
-    maintainers = [ maintainers.vbgl ];
     platforms = ocaml.meta.platforms or [];
+    maintainers = [ maintainers.vbgl ];
   };
 }

pkgs/development/python-modules/hypothesis.nix

@@ -1,6 +1,6 @@
 { stdenv, buildPythonPackage, fetchFromGitHub, python
 , pythonOlder, pythonAtLeast, enum34
-, doCheck ? true, pytest, flake8, flaky
+, doCheck ? true, pytest, pytest_xdist, flake8, flaky
 }:
 buildPythonPackage rec {
   # http://hypothesis.readthedocs.org/en/latest/packaging.html
@@ -21,13 +21,14 @@ buildPythonPackage rec {
     sha256 = "1s911pd3y9hvk0hq2fr6i68dqv1ciagryhgp13wgyfqh8hz8j6zv";
   };
 
-  checkInputs = stdenv.lib.optionals doCheck [ pytest flake8 flaky ];
+  checkInputs = stdenv.lib.optionals doCheck [ pytest pytest_xdist flake8 flaky ];
   propagatedBuildInputs = stdenv.lib.optionals (pythonOlder "3.4") [ enum34 ];
 
   inherit doCheck;
 
   # https://github.com/DRMacIver/hypothesis/issues/300
   checkPhase = ''
+    rm tox.ini # This file changes how py.test runs and breaks it
     py.test tests/cover
   '';
 

pkgs/development/python-modules/ldap.nix

@@ -1,4 +1,4 @@
-{ buildPythonPackage, isPy3k, fetchurl
+{ buildPythonPackage, isPy3k, fetchPypi
 , openldap, cyrus_sasl, openssl }:
 
 buildPythonPackage rec {
@@ -7,8 +7,8 @@ buildPythonPackage rec {
   name = "${pname}-${version}";
   disabled = isPy3k;
 
-  src = fetchurl {
-    url = "mirror://pypi/p/python-ldap/${name}.tar.gz";
+  src = fetchPypi {
+    inherit pname version;
     sha256 = "88bab69e519dd8bd83becbe36bd141c174b0fe309e84936cf1bae685b31be779";
   };
 

pkgs/development/python-modules/pylibmc/default.nix

@@ -1,11 +1,11 @@
-{ buildPythonPackage, fetchurl, stdenv, libmemcached, zlib }:
+{ buildPythonPackage, fetchPypi, stdenv, libmemcached, zlib }:
 buildPythonPackage rec {
   version = "1.5.2";
   pname = "pylibmc";
   name = "${pname}-${version}";
 
-  src = fetchurl {
-    url = "https://pypi.python.org/packages/source/p/pylibmc/${name}.tar.gz";
+  src = fetchPypi {
+    inherit pname version;
     sha256 = "fc54e28a9f1b5b2ec0c030da29c7ad8a15c2755bd98aaa4142eaf419d5fabb33";
   };
 

pkgs/development/python-modules/pylint/default.nix

@@ -1,5 +1,5 @@
 { stdenv, fetchurl, buildPythonPackage, python, astroid, isort,
-  pytest,  mccabe, configparser, backports_functools_lru_cache }:
+  pytest, pytestrunner,  mccabe, configparser, backports_functools_lru_cache }:
 
   buildPythonPackage rec {
     name = "${pname}-${version}";
@@ -11,7 +11,7 @@
       sha256 = "8b4a7ab6cf5062e40e2763c0b4a596020abada1d7304e369578b522e46a6264a";
     };
 
-    buildInputs = [ pytest mccabe configparser backports_functools_lru_cache ];
+    buildInputs = [ pytest pytestrunner mccabe configparser backports_functools_lru_cache ];
 
     propagatedBuildInputs = [ astroid isort ];
 

pkgs/development/python-modules/simplejson/default.nix

@@ -0,0 +1,28 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+}:
+
+buildPythonPackage rec {
+  pname = "simplejson";
+  version = "3.10.0";
+  name = "${pname}-${version}";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "953be622e88323c6f43fad61ffd05bebe73b9fd9863a46d68b052d2aa7d71ce2";
+  };
+
+  meta = {
+    description = "A simple, fast, extensible JSON encoder/decoder for Python";
+    longDescription = ''
+      simplejson is compatible with Python 2.4 and later with no
+      external dependencies.  It covers the full JSON specification
+      for both encoding and decoding, with unicode support.  By
+      default, encoding is done in an encoding neutral fashion (plain
+      ASCII with \uXXXX escapes for unicode characters).
+    '';
+    homepage = http://code.google.com/p/simplejson/;
+    license = lib.licenses.mit;
+  };
+}

pkgs/development/tools/analysis/cppcheck/default.nix

@@ -2,12 +2,12 @@
 
 stdenv.mkDerivation rec {
   pname = "cppcheck";
-  version = "1.78";
+  version = "1.79";
   name = "${pname}-${version}";
 
   src = fetchurl {
     url = "mirror://sourceforge/${pname}/${name}.tar.bz2";
-    sha256 = "1cc60y2vjq4g88183jkan91ybzqy0n6p5ncs8z5rh6rjsvvrc9p4";
+    sha256 = "0vgh4zx191d7mcmiilkhcbd9jkspfkppl7l4y5451walvs9vd19b";
   };
 
   buildInputs = [ pcre ];

pkgs/development/tools/ocaml/merlin/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchzip, ocaml, findlib, yojson, menhir, lib
+{ stdenv, fetchzip, ocaml, findlib, yojson, lib
 , withEmacsMode ? false, emacs }:
 
 assert stdenv.lib.versionAtLeast (stdenv.lib.getVersion ocaml) "4.00";
@@ -8,10 +8,10 @@ let
   then
     "2.3.1"
   else
-    "2.5.3";
+    "2.5.4";
   hashes = {
     "2.3.1" = "192jamcc7rmvadlqqsjkzsl6hlgwhg9my1qc89fxh1lmd4qdsrpn";
-    "2.5.3" = "0qljklgcrpqdxzvcqj7b4785zcz322pjvw9cddbmzla33hagglha";
+    "2.5.4" = "101vk16c5wayd51s8w0mvy99bk7q3gm2gz8i8616wa1lmyszjknh";
   };
 in
 
@@ -24,7 +24,7 @@ stdenv.mkDerivation {
     sha256 = hashes."${version}";
   };
 
-  buildInputs = [ ocaml findlib yojson menhir ]
+  buildInputs = [ ocaml findlib yojson ]
     ++ stdenv.lib.optional withEmacsMode emacs;
 
   preConfigure = "mkdir -p $out/bin";

pkgs/development/tools/ocaml/ocp-indent/default.nix

@@ -3,18 +3,21 @@
 let inherit (stdenv.lib) getVersion versionAtLeast; in
 
 assert versionAtLeast (getVersion ocaml) "3.12.1";
+assert versionAtLeast (getVersion cmdliner) "1.0.0";
 assert versionAtLeast (getVersion ocpBuild) "1.99.6-beta";
 
-stdenv.mkDerivation {
+stdenv.mkDerivation rec {
 
-  name = "ocp-indent-1.5.2";
+  name = "ocp-indent-${version}";
+  version = "1.6.0";
 
   src = fetchzip {
-    url = "https://github.com/OCamlPro/ocp-indent/archive/1.5.2.tar.gz";
-    sha256 = "0ynv2yhm7akpvqp72pdabhddwr352s1k85q8m1khsvspgg1mkiqz";
+    url = "https://github.com/OCamlPro/ocp-indent/archive/${version}.tar.gz";
+    sha256 = "1h9y597s3ag8w1z32zzv4dfk3ppq557s55bnlfw5a5wqwvia911f";
   };
 
-  buildInputs = [ ocaml findlib ocpBuild opam cmdliner ];
+  nativeBuildInputs = [ ocpBuild opam ];
+  buildInputs = [ ocaml findlib cmdliner ];
 
   createFindlibDestdir = true;