diff --git a/.gitignore b/.gitignore
index 1c6ca4c99e..8146921fd8 100644
--- a/.gitignore
+++ b/.gitignore
@@ -8,3 +8,4 @@
 /etc/spackconfig
 /share/spack/dotkit
 /share/spack/modules
+*.ropeproject
diff --git a/.gitmodules b/.gitmodules
index a097fcd8cf..1d770f415b 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,3 +1,3 @@
-[submodule "utils/python_recipe_parser"]
-	path = utils/python_recipe_parser
+[submodule "/lib/spack/spack/util/python_recipe_parser"]
+	path = /lib/spack/spack/util/python_recipe_parser
 	url = https://github.com/karenyyng/spack_python_package_parser
diff --git a/utils/python_recipe_parser b/utils/python_recipe_parser
deleted file mode 160000
index 3158074a2d..0000000000
--- a/utils/python_recipe_parser
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 3158074a2d74f99aa72289dfcf093b1b0ba4474e
diff --git a/var/spack/packages/ImageMagick/package.py b/var/spack/packages/ImageMagick/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/Mitos/package.py b/var/spack/packages/Mitos/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/R/package.py b/var/spack/packages/R/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/SAMRAI/no-tool-build.patch b/var/spack/packages/SAMRAI/no-tool-build.patch
old mode 100644
new mode 100755
diff --git a/var/spack/packages/SAMRAI/package.py b/var/spack/packages/SAMRAI/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/adept-utils/package.py b/var/spack/packages/adept-utils/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/arpack/package.py b/var/spack/packages/arpack/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/asciidoc/package.py b/var/spack/packages/asciidoc/package.py
deleted file mode 100644
index 828f3b3f4f..0000000000
--- a/var/spack/packages/asciidoc/package.py
+++ /dev/null
@@ -1,18 +0,0 @@
-from spack import *
-
-class Asciidoc(Package):
-    """ A presentable text document format for writing articles, UNIX man
-    pages and other small to medium sized documents."""
-    homepage = "http://asciidoc.org"
-    url      = "http://downloads.sourceforge.net/project/asciidoc/asciidoc/8.6.9/asciidoc-8.6.9.tar.gz"
-
-    version('8.6.9', 'c59018f105be8d022714b826b0be130a')
-
-    depends_on('libxml2')
-    depends_on('libxslt')
-
-    def install(self, spec, prefix):
-        configure('--prefix=%s' % prefix)
-
-        make()
-        make("install")
diff --git a/var/spack/packages/atk/package.py b/var/spack/packages/atk/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/atlas/package.py b/var/spack/packages/atlas/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/autoconf/package.py b/var/spack/packages/autoconf/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/automaded/package.py b/var/spack/packages/automaded/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/automake/package.py b/var/spack/packages/automake/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/bear/package.py b/var/spack/packages/bear/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/bib2xhtml/package.py b/var/spack/packages/bib2xhtml/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/binutils/package.py b/var/spack/packages/binutils/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/bison/package.py b/var/spack/packages/bison/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/boost/package.py b/var/spack/packages/boost/package.py
old mode 100644
new mode 100755
index 35824d53a2..254d1afda1
--- a/var/spack/packages/boost/package.py
+++ b/var/spack/packages/boost/package.py
@@ -14,10 +14,6 @@ class Boost(Package):
     list_url = "http://sourceforge.net/projects/boost/files/boost/"
     list_depth = 2
 
-    version('1.59.0', '6aa9a5c6a4ca1016edd0ed1178e3cb87')
-    version('1.58.0', 'b8839650e61e9c1c0a89f371dd475546')
-    version('1.57.0', '1be49befbdd9a5ce9def2983ba3e7b76')
-    version('1.56.0', 'a744cf167b05d72335f27c88115f211d')
     version('1.55.0', 'd6eef4b4cacb2183f2bf265a5a03a354')
     version('1.54.0', '15cb8c0803064faef0c4ddf5bc5ca279')
     version('1.53.0', 'a00d22605d5dbcfb4c9936a9b35bc4c2')
diff --git a/var/spack/packages/bowtie2/bowtie2-2.5.patch b/var/spack/packages/bowtie2/bowtie2-2.5.patch
deleted file mode 100644
index 290be39c73..0000000000
--- a/var/spack/packages/bowtie2/bowtie2-2.5.patch
+++ /dev/null
@@ -1,16 +0,0 @@
---- Makefile	2015-02-26 10:50:00.000000000 -0800
-+++ Makefile.new	2015-07-29 18:03:59.891357399 -0700
-@@ -22,10 +22,10 @@
- #
- 
- INC =
--GCC_PREFIX = $(shell dirname `which gcc`)
-+GCC_PREFIX =
- GCC_SUFFIX =
--CC = $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
--CPP = $(GCC_PREFIX)/g++$(GCC_SUFFIX)
-+CC = cc 
-+CPP = c++
- CXX = $(CPP)
- HEADERS = $(wildcard *.h)
- BOWTIE_MM = 1
diff --git a/var/spack/packages/bowtie2/package.py b/var/spack/packages/bowtie2/package.py
deleted file mode 100644
index 339aab6598..0000000000
--- a/var/spack/packages/bowtie2/package.py
+++ /dev/null
@@ -1,24 +0,0 @@
-from spack import *
-from glob import glob
-class Bowtie2(Package):
-    """Description"""
-    homepage = "bowtie-bio.sourceforge.net/bowtie2/index.shtml"
-    version('2.2.5','51fa97a862d248d7ee660efc1147c75f', url = "http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.5/bowtie2-2.2.5-source.zip")
-
-    patch('bowtie2-2.5.patch',when='@2.2.5', level=0)
-
-    def install(self, spec, prefix):
-        make()
-        mkdirp(prefix.bin)
-        for bow in glob("bowtie2*"):
-            install(bow, prefix.bin)
-        # install('bowtie2',prefix.bin)
-        # install('bowtie2-align-l',prefix.bin)
-        # install('bowtie2-align-s',prefix.bin)
-        # install('bowtie2-build',prefix.bin)
-        # install('bowtie2-build-l',prefix.bin)
-        # install('bowtie2-build-s',prefix.bin)
-        # install('bowtie2-inspect',prefix.bin)
-        # install('bowtie2-inspect-l',prefix.bin)
-        # install('bowtie2-inspect-s',prefix.bin)
-
diff --git a/var/spack/packages/boxlib/package.py b/var/spack/packages/boxlib/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/bzip2/package.py b/var/spack/packages/bzip2/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/cairo/package.py b/var/spack/packages/cairo/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/callpath/package.py b/var/spack/packages/callpath/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/cblas/package.py b/var/spack/packages/cblas/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/cgm/package.py b/var/spack/packages/cgm/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/clang/package.py b/var/spack/packages/clang/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/cloog/package.py b/var/spack/packages/cloog/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/cmake/package.py b/var/spack/packages/cmake/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/coreutils/package.py b/var/spack/packages/coreutils/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/cppcheck/package.py b/var/spack/packages/cppcheck/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/cram/package.py b/var/spack/packages/cram/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/cscope/package.py b/var/spack/packages/cscope/package.py
deleted file mode 100644
index 9aac0f7304..0000000000
--- a/var/spack/packages/cscope/package.py
+++ /dev/null
@@ -1,17 +0,0 @@
-from spack import *
-
-class Cscope(Package):
-    """Cscope is a developer's tool for browsing source code."""
-    homepage = "http://http://cscope.sourceforge.net/"
-    url      = "http://downloads.sourceforge.net/project/cscope/cscope/15.8b/cscope-15.8b.tar.gz"
-
-    version('15.8b', '8f9409a238ee313a96f9f87fe0f3b176')
-
-    # Can be configured to use flex (not necessary)
-    # ./configure --with-flex
-
-    def install(self, spec, prefix):
-        configure('--prefix=%s' % prefix)
-
-        make()
-        make("install")
diff --git a/var/spack/packages/cube/package.py b/var/spack/packages/cube/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/czmq/package.py b/var/spack/packages/czmq/package.py
deleted file mode 100644
index a2f1947554..0000000000
--- a/var/spack/packages/czmq/package.py
+++ /dev/null
@@ -1,19 +0,0 @@
-from spack import *
-
-class Czmq(Package):
-    """ A C interface to the ZMQ library """
-    homepage = "http://czmq.zeromq.org"
-    url      = "https://github.com/zeromq/czmq/archive/v3.0.2.tar.gz"
-
-    version('3.0.2', '23e9885f7ee3ce88d99d0425f52e9be1', url='https://github.com/zeromq/czmq/archive/v3.0.2.tar.gz')
-
-    depends_on('zeromq')
-
-    def install(self, spec, prefix):
-        bash = which("bash")
-        bash("./autogen.sh")
-        configure("--prefix=%s" % prefix)
-
-        make()
-        make("install")
-
diff --git a/var/spack/packages/dbus/package.py b/var/spack/packages/dbus/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/docbook-xml/package.py b/var/spack/packages/docbook-xml/package.py
deleted file mode 100644
index fce1de7deb..0000000000
--- a/var/spack/packages/docbook-xml/package.py
+++ /dev/null
@@ -1,19 +0,0 @@
-import os
-import glob
-from spack import *
-
-
-class DocbookXml(Package):
-    """Docbook DTD XML files."""
-    homepage = "http://www.oasis-open.org/docbook"
-    url = "http://www.oasis-open.org/docbook/xml/4.5/docbook-xml-4.5.zip"
-
-    version('4.5', '03083e288e87a7e829e437358da7ef9e')
-
-    def install(self, spec, prefix):
-        cp = which('cp')
-
-        install_args = ['-a', '-t', prefix]
-        install_args.extend(glob.glob('*'))
-
-        cp(*install_args)
diff --git a/var/spack/packages/doxygen/package.py b/var/spack/packages/doxygen/package.py
deleted file mode 100644
index 3d4a4e47a7..0000000000
--- a/var/spack/packages/doxygen/package.py
+++ /dev/null
@@ -1,25 +0,0 @@
-#------------------------------------------------------------------------------
-# Author: Justin Too <justin@doubleotoo.com>
-# Date: September 11, 2015
-#------------------------------------------------------------------------------
-
-from spack import *
-
-class Doxygen(Package):
-    """Doxygen is the de facto standard tool for generating documentation
-    from annotated C++ sources, but it also supports other popular programming
-    languages such as C, Objective-C, C#, PHP, Java, Python, IDL (Corba,
-    Microsoft, and UNO/OpenOffice flavors), Fortran, VHDL, Tcl, and to some extent D..
-    """
-    homepage = "http://www.stack.nl/~dimitri/doxygen/"
-    url      = "http://ftp.stack.nl/pub/users/dimitri/doxygen-1.8.10.src.tar.gz"
-
-    version('1.8.10', '79767ccd986f12a0f949015efb5f058f')
-
-    depends_on("cmake@2.8.12:")
-
-    def install(self, spec, prefix):
-        cmake('.', *std_cmake_args)
-
-        make()
-        make("install")
diff --git a/var/spack/packages/dri2proto/package.py b/var/spack/packages/dri2proto/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/dtcmp/package.py b/var/spack/packages/dtcmp/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/dyninst/package.py b/var/spack/packages/dyninst/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/eigen/package.py b/var/spack/packages/eigen/package.py
new file mode 100644
index 0000000000..b4d89ea3a0
--- /dev/null
+++ b/var/spack/packages/eigen/package.py
@@ -0,0 +1,17 @@
+from spack import *
+
+class Eigen(Package):
+    """Eigen is a C++ template library for linear algebra: matrices, vectors,
+    numerical solvers, and related algorithms.."""
+    homepage = "http://eigen.tuxfamily.org/"
+    url      = "http://bitbucket.org/eigen/eigen/get/3.2.5.tar.gz"
+
+    version('3.2.5', '8cc513ac6ec687117acadddfcacf551b')
+
+    def install(self, spec, prefix):
+        import os 
+        os.system("mkdir ./build_dir && cd ./build_dir")
+        cmake('../', *std_cmake_args)
+
+        make()
+        make("install")
diff --git a/var/spack/packages/elfutils/package.py b/var/spack/packages/elfutils/package.py
deleted file mode 100644
index 926d234584..0000000000
--- a/var/spack/packages/elfutils/package.py
+++ /dev/null
@@ -1,26 +0,0 @@
-from spack import *
-
-class Elfutils(Package):
-    """elfutils is a collection of various binary tools such as
-    eu-objdump, eu-readelf, and other utilities that allow you to
-    inspect and manipulate ELF files. Refer to Table 5.Tools Included
-    in elfutils for Red Hat Developer for a complete list of binary
-    tools that are distributed with the Red Hat Developer Toolset
-    version of elfutils."""
-
-    homepage = "https://fedorahosted.org/elfutils/"
-
-    version('0.163',
-            git='git://git.fedorahosted.org/git/elfutils.git',
-            tag='elfutils-0.163')
-
-    provides('elf')
-
-    def install(self, spec, prefix):
-        autoreconf = which('autoreconf')
-        autoreconf('-if')
-
-        configure('--prefix=%s' % prefix, '--enable-maintainer-mode')
-        make()
-        make("install")
-
diff --git a/var/spack/packages/extrae/package.py b/var/spack/packages/extrae/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/exuberant-ctags/package.py b/var/spack/packages/exuberant-ctags/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/fish/package.py b/var/spack/packages/fish/package.py
deleted file mode 100644
index 1225558705..0000000000
--- a/var/spack/packages/fish/package.py
+++ /dev/null
@@ -1,18 +0,0 @@
-from spack import *
-
-class Fish(Package):
-    """fish is a smart and user-friendly command line shell for OS X, Linux, and
-    the rest of the family.
-    """
-
-    homepage = "http://fishshell.com/"
-    url      = "http://fishshell.com/files/2.2.0/fish-2.2.0.tar.gz"
-    list_url = homepage
-
-    version('2.2.0', 'a76339fd14ce2ec229283c53e805faac48c3e99d9e3ede9d82c0554acfc7b77a')
-
-    def install(self, spec, prefix):
-        configure('--prefix=%s' % prefix)
-
-        make()
-        make("install")
diff --git a/var/spack/packages/flex/package.py b/var/spack/packages/flex/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/flux/package.py b/var/spack/packages/flux/package.py
deleted file mode 100644
index c128f46be8..0000000000
--- a/var/spack/packages/flux/package.py
+++ /dev/null
@@ -1,36 +0,0 @@
-from spack import *
-import os
-
-class Flux(Package):
-    """ A next-generation resource manager (pre-alpha) """
-
-    homepage = "https://github.com/flux-framework/flux-core"
-    url      = "https://github.com/flux-framework/flux-core"
-
-    version('master', branch='master', git='https://github.com/flux-framework/flux-core')
-
-    # Also needs autotools, but should use the system version if available
-    depends_on("zeromq@4.0.4:")
-    depends_on("czmq@2.2:")
-    depends_on("lua@5.1:5.1.99")
-    depends_on("munge")
-    depends_on("libjson-c")
-    depends_on("libxslt")
-    # TODO: This provides a catalog, hacked with environment below for now
-    depends_on("docbook-xml")
-    depends_on("asciidoc")
-    depends_on("python")
-    depends_on("py-cffi")
-
-    def install(self, spec, prefix):
-        # Bootstrap with autotools
-        bash = which('bash')
-        bash('./autogen.sh')
-
-        # Fix asciidoc dependency on xml style sheets and whatnot
-        os.environ['XML_CATALOG_FILES'] = os.path.join(spec['docbook-xml'].prefix,
-                                                       'catalog.xml')
-        # Configure, compile & install
-        configure("--prefix=" + prefix)
-        make("install", "V=1")
-
diff --git a/var/spack/packages/fontconfig/package.py b/var/spack/packages/fontconfig/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/freetype/package.py b/var/spack/packages/freetype/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/gasnet/package.py b/var/spack/packages/gasnet/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/gcc/package.py b/var/spack/packages/gcc/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/gdk-pixbuf/package.py b/var/spack/packages/gdk-pixbuf/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/geos/package.py b/var/spack/packages/geos/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/gflags/package.py b/var/spack/packages/gflags/package.py
deleted file mode 100644
index 62dd80a094..0000000000
--- a/var/spack/packages/gflags/package.py
+++ /dev/null
@@ -1,21 +0,0 @@
-import os
-from spack import *
-
-class Gflags(Package):
-    """The gflags package contains a C++ library that implements
-    commandline flags processing. It includes built-in support for
-    standard types such as string and the ability to define flags
-    in the source file in which they are used. Online documentation
-    available at: https://gflags.github.io/gflags/"""
-
-    homepage = "https://gflags.github.io/gflags"
-    url      = "https://github.com/gflags/gflags/archive/v2.1.2.tar.gz"
-
-    version('2.1.2', 'ac432de923f9de1e9780b5254884599f')
-
-    def install(self, spec, prefix):
-        cmake("-DCMAKE_INSTALL_PREFIX=" + prefix,
-              "-DBUILD_SHARED_LIBS=ON")
-        make()
-        make("test")
-        make("install")
diff --git a/var/spack/packages/ghostscript/package.py b/var/spack/packages/ghostscript/package.py
deleted file mode 100644
index 0ab49d425f..0000000000
--- a/var/spack/packages/ghostscript/package.py
+++ /dev/null
@@ -1,17 +0,0 @@
-from spack import *
-
-class Ghostscript(Package):
-    """an interpreter for the PostScript language and for PDF. """
-    homepage = "http://ghostscript.com/"
-    url      = "http://downloads.ghostscript.com/public/ghostscript-9.16.tar.gz"
-
-    version('9.16', '829319325bbdb83f5c81379a8f86f38f')
-
-    parallel = False
-
-    def install(self, spec, prefix):
-        configure("--prefix=%s" %prefix, "--enable-shared")
-
-        make()
-        make("install")
-
diff --git a/var/spack/packages/git/package.py b/var/spack/packages/git/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/glib/package.py b/var/spack/packages/glib/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/global/package.py b/var/spack/packages/global/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/glog/package.py b/var/spack/packages/glog/package.py
deleted file mode 100644
index d73386b394..0000000000
--- a/var/spack/packages/glog/package.py
+++ /dev/null
@@ -1,15 +0,0 @@
-import os
-from spack import *
-
-class Glog(Package):
-    """C++ implementation of the Google logging module."""
-
-    homepage = "https://github.com/google/glog"
-    url      = "https://github.com/google/glog/archive/v0.3.3.tar.gz"
-
-    version('0.3.3', 'c1f86af27bd9c73186730aa957607ed0')
-
-    def install(self, spec, prefix):
-        configure("--prefix=" + prefix)
-        make()
-        make("install")
diff --git a/var/spack/packages/gmp/package.py b/var/spack/packages/gmp/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/gnutls/package.py b/var/spack/packages/gnutls/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/gperf/package.py b/var/spack/packages/gperf/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/gperftools/package.py b/var/spack/packages/gperftools/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/graphlib/package.py b/var/spack/packages/graphlib/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/graphviz/package.py b/var/spack/packages/graphviz/package.py
index 7af7da1881..8244feccfd 100644
--- a/var/spack/packages/graphviz/package.py
+++ b/var/spack/packages/graphviz/package.py
@@ -1,21 +1,24 @@
 from spack import *
 
 class Graphviz(Package):
-    """Graph Visualization Software"""
+    """graph visualization software."""
     homepage = "http://www.graphviz.org"
     url      = "http://www.graphviz.org/pub/graphviz/stable/SOURCES/graphviz-2.38.0.tar.gz"
 
     version('2.38.0', '5b6a829b2ac94efcd5fa3c223ed6d3ae')
+    version('2.36.0', '1f41664dba0c93109ac8b71216bf2b57')
 
-    parallel = False
-
-    depends_on("swig")
-    depends_on("python")
-    depends_on("ghostscript")
+    depends_on("cairo@1.1.10")
+    depends_on("freetype@2.1.10")
+    depends_on("fontconfig")
+    depends_on("zlib@1.2.3")
+    # depends_on("libpng@1.2.10")
+    # depends_on("expat@2.0.0")
+    # depends_on("gd@2.0.34")
 
     def install(self, spec, prefix):
-        configure("--prefix=%s" %prefix)
+        configure('--prefix=%s' % prefix)
 
+        # FIXME: Add logic to build and install here
         make()
         make("install")
-
diff --git a/var/spack/packages/gtkplus/package.py b/var/spack/packages/gtkplus/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/harfbuzz/package.py b/var/spack/packages/harfbuzz/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/hdf5/package.py b/var/spack/packages/hdf5/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/hwloc/package.py b/var/spack/packages/hwloc/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/hypre/package.py b/var/spack/packages/hypre/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/icu/package.py b/var/spack/packages/icu/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/icu4c/package.py b/var/spack/packages/icu4c/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/isl/package.py b/var/spack/packages/isl/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/jdk/package.py b/var/spack/packages/jdk/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/jpeg/package.py b/var/spack/packages/jpeg/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/netlib-lapack/package.py b/var/spack/packages/lapack/package.py
old mode 100644
new mode 100755
similarity index 77%
rename from var/spack/packages/netlib-lapack/package.py
rename to var/spack/packages/lapack/package.py
index fb6b99e27c..d9d37e3e4a
--- a/var/spack/packages/netlib-lapack/package.py
+++ b/var/spack/packages/lapack/package.py
@@ -1,6 +1,6 @@
 from spack import *
 
-class NetlibLapack(Package):
+class Lapack(Package):
     """
     LAPACK version 3.X is a comprehensive FORTRAN library that does
     linear algebra operations including matrix inversions, least
@@ -18,16 +18,9 @@ class NetlibLapack(Package):
     version('3.4.0', '02d5706ec03ba885fc246e5fa10d8c70')
     version('3.3.1', 'd0d533ec9a5b74933c2a1e84eedc58b4')
 
-    variant('shared', default=False, description="Build shared library version")
-
-    # virtual dependency
-    provides('lapack')
-
     # blas is a virtual dependency.
     depends_on('blas')
 
-    depends_on('cmake')
-
     # Doesn't always build correctly in parallel
     parallel = False
 
@@ -46,14 +39,7 @@ def get_blas_libs(self):
 
     def install(self, spec, prefix):
         blas_libs = ";".join(self.get_blas_libs())
-        cmake_args = [".", '-DBLAS_LIBRARIES=' + blas_libs]
-
-        if '+shared' in spec:
-            cmake_args.append('-DBUILD_SHARED_LIBS=ON')
-
-        cmake_args += std_cmake_args
-
-        cmake(*cmake_args)
+        cmake(".", '-DBLAS_LIBRARIES=' + blas_libs, *std_cmake_args)
         make()
         make("install")
 
diff --git a/var/spack/packages/launchmon/package.py b/var/spack/packages/launchmon/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/launchmon/patch.lmon_install_dir b/var/spack/packages/launchmon/patch.lmon_install_dir
old mode 100644
new mode 100755
diff --git a/var/spack/packages/lcms/package.py b/var/spack/packages/lcms/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/leveldb/package.py b/var/spack/packages/leveldb/package.py
deleted file mode 100644
index da68a9cbcb..0000000000
--- a/var/spack/packages/leveldb/package.py
+++ /dev/null
@@ -1,29 +0,0 @@
-import os
-import glob
-from spack import *
-
-class Leveldb(Package):
-    """LevelDB is a fast key-value storage library written at Google
-    that provides an ordered mapping from string keys to string values."""
-
-    homepage = "https://github.com/google/leveldb"
-    url      = "https://github.com/google/leveldb/archive/v1.18.tar.gz"
-
-    version('1.18', '73770de34a2a5ab34498d2e05b2b7fa0')
-
-    depends_on("snappy")
-
-    def install(self, spec, prefix):
-        make()
-
-        mkdirp(prefix.include)
-        mkdirp(prefix.lib)
-
-        cp = which('cp')
-
-        # cp --preserve=links libleveldb.* prefix/lib
-        args = glob.glob('libleveldb.*')
-        args.append(prefix + '/lib')
-        cp('--preserve=links', *args)
-
-        cp('-r', 'include/leveldb', prefix + '/include')
diff --git a/var/spack/packages/libNBC/package.py b/var/spack/packages/libNBC/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/libarchive/package.py b/var/spack/packages/libarchive/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/libcircle/package.py b/var/spack/packages/libcircle/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/libdrm/package.py b/var/spack/packages/libdrm/package.py
old mode 100644
new mode 100755
index 00736b7811..1cab5372be
--- a/var/spack/packages/libdrm/package.py
+++ b/var/spack/packages/libdrm/package.py
@@ -2,7 +2,7 @@
 
 class Libdrm(Package):
     """A userspace  library for  accessing the  DRM, direct
-    rendering  manager, on  Linux,  BSD and  other  operating 
+    rendering  manager, on  Linux,  BSD and  other  operating
     systems that support the  ioctl interface."""
 
     homepage = "http://dri.freedesktop.org/libdrm/" # no real website...
@@ -11,8 +11,11 @@ class Libdrm(Package):
     version('2.4.59', '105ac7af1afcd742d402ca7b4eb168b6')
     version('2.4.33', '86e4e3debe7087d5404461e0032231c8')
 
+    depends_on("libpciaccess")
+
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
 
+        make("clean")
         make()
         make("install")
diff --git a/var/spack/packages/libdwarf/package.py b/var/spack/packages/libdwarf/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/libelf/package.py b/var/spack/packages/libelf/package.py
old mode 100644
new mode 100755
index 9338b8f393..bf2fefabd5
--- a/var/spack/packages/libelf/package.py
+++ b/var/spack/packages/libelf/package.py
@@ -36,8 +36,6 @@ class Libelf(Package):
     version('0.8.13', '4136d7b4c04df68b686570afa26988ac')
     version('0.8.12', 'e21f8273d9f5f6d43a59878dc274fec7')
 
-    provides('elf')
-
     def install(self, spec, prefix):
         configure("--prefix=" + prefix,
                   "--enable-shared",
diff --git a/var/spack/packages/libevent/package.py b/var/spack/packages/libevent/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/libffi/package.py b/var/spack/packages/libffi/package.py
old mode 100644
new mode 100755
index 18acabb00c..2c1c4eed4d
--- a/var/spack/packages/libffi/package.py
+++ b/var/spack/packages/libffi/package.py
@@ -6,9 +6,9 @@ class Libffi(Package):
     to call any function specified by a call interface description at
     run time."""
     homepage = "https://sourceware.org/libffi/"
-    
-    version('3.2.1','83b89587607e3eb65c70d361f13bab43',url = "ftp://sourceware.org/pub/libffi/libffi-3.2.1.tar.gz")
-    #version('3.1', 'f5898b29bbfd70502831a212d9249d10',url = "ftp://sourceware.org/pub/libffi/libffi-3.1.tar.gz") # Has a bug $(lib64) instead of ${lib64} in libffi.pc
+    url      = "ftp://sourceware.org/pub/libffi/libffi-3.1.tar.gz"
+
+    version('3.1', 'f5898b29bbfd70502831a212d9249d10')
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
diff --git a/var/spack/packages/libgcrypt/package.py b/var/spack/packages/libgcrypt/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/libgpg-error/package.py b/var/spack/packages/libgpg-error/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/libjpeg-turbo/package.py b/var/spack/packages/libjpeg-turbo/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/libjson-c/package.py b/var/spack/packages/libjson-c/package.py
deleted file mode 100644
index c0801cce9c..0000000000
--- a/var/spack/packages/libjson-c/package.py
+++ /dev/null
@@ -1,14 +0,0 @@
-from spack import *
-
-class LibjsonC(Package):
-    """ A JSON implementation in C """
-    homepage = "https://github.com/json-c/json-c/wiki"
-    url      = "https://s3.amazonaws.com/json-c_releases/releases/json-c-0.11.tar.gz"
-
-    version('0.11', 'aa02367d2f7a830bf1e3376f77881e98')
-
-    def install(self, spec, prefix):
-        configure('--prefix=%s' % prefix)
-
-        make()
-        make("install")
diff --git a/var/spack/packages/libmng/package.py b/var/spack/packages/libmng/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/libmonitor/package.py b/var/spack/packages/libmonitor/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/libpciaccess/package.py b/var/spack/packages/libpciaccess/package.py
old mode 100644
new mode 100755
index 6022fc34a3..371fbb6685
--- a/var/spack/packages/libpciaccess/package.py
+++ b/var/spack/packages/libpciaccess/package.py
@@ -1,21 +1,16 @@
 from spack import *
 
 class Libpciaccess(Package):
-    """Generic PCI access library."""
-
+    """Generic PCI access library"""
     homepage = "http://cgit.freedesktop.org/xorg/lib/libpciaccess/"
-    url      = "http://cgit.freedesktop.org/xorg/lib/libpciaccess/"
+    url      = "http://pkgs.fedoraproject.org/repo/pkgs/libpciaccess/libpciaccess-0.13.2.tar.bz2/b7c0d3afce14eedca57312a3141ec13a/libpciaccess-0.13.2.tar.bz2"
 
-    version('0.13.4', git='http://anongit.freedesktop.org/git/xorg/lib/libpciaccess.git',
-            tag='libpciaccess-0.13.4')
-
-    depends_on('autoconf')
-    depends_on('libtool')
+    version('0.13.2', 'b7c0d3afce14eedca57312a3141ec13a')
 
     def install(self, spec, prefix):
-        from subprocess import call
-        call(["./autogen.sh"])
-        configure("--prefix=%s" % prefix)
+        import os
+        os.system("autoconf")
+        configure('--prefix=%s' % prefix)
 
         make()
         make("install")
diff --git a/var/spack/packages/libpng/package.py b/var/spack/packages/libpng/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/libsodium/package.py b/var/spack/packages/libsodium/package.py
deleted file mode 100644
index 1c8a16d998..0000000000
--- a/var/spack/packages/libsodium/package.py
+++ /dev/null
@@ -1,19 +0,0 @@
-from spack import *
-
-class Libsodium(Package):
-    """Sodium is a modern, easy-to-use software library for encryption,
-    decryption, signatures, password hashing and more."""
-    homepage = "https://download.libsodium.org/doc/"
-    url      = "https://download.libsodium.org/libsodium/releases/libsodium-1.0.3.tar.gz"
-
-    version('1.0.3', 'b3bcc98e34d3250f55ae196822307fab')
-    version('1.0.2', 'dc40eb23e293448c6fc908757738003f')
-    version('1.0.1', '9a221b49fba7281ceaaf5e278d0f4430')
-    version('1.0.0', '3093dabe4e038d09f0d150cef064b2f7')
-    version('0.7.1', 'c224fe3923d1dcfe418c65c8a7246316')
-
-    def install(self, spec, prefix):
-        configure("--prefix=%s" % prefix)
-
-        make()
-        make("install")
diff --git a/var/spack/packages/libtiff/package.py b/var/spack/packages/libtiff/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/libtool/package.py b/var/spack/packages/libtool/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/libunwind/package.py b/var/spack/packages/libunwind/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/libuuid/package.py b/var/spack/packages/libuuid/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/libxcb/package.py b/var/spack/packages/libxcb/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/libxml2/package.py b/var/spack/packages/libxml2/package.py
old mode 100644
new mode 100755
index 3a0af6b368..72199d8def
--- a/var/spack/packages/libxml2/package.py
+++ b/var/spack/packages/libxml2/package.py
@@ -9,12 +9,11 @@ class Libxml2(Package):
 
     version('2.9.2', '9e6a9aca9d155737868b3dc5fd82f788')
 
-    extends('python')
     depends_on('zlib')
     depends_on('xz')
 
     def install(self, spec, prefix):
-        configure("--prefix=%s" % prefix)
-
+        configure("--prefix=%s" % prefix,
+                  "--without-python")
         make()
         make("install")
diff --git a/var/spack/packages/libxshmfence/package.py b/var/spack/packages/libxshmfence/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/libxslt/package.py b/var/spack/packages/libxslt/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/llvm-lld/package.py b/var/spack/packages/llvm-lld/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/llvm/package.py b/var/spack/packages/llvm/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/lmdb/package.py b/var/spack/packages/lmdb/package.py
deleted file mode 100644
index 875b8100c5..0000000000
--- a/var/spack/packages/lmdb/package.py
+++ /dev/null
@@ -1,39 +0,0 @@
-import os
-from spack import *
-
-class Lmdb(Package):
-    """Read-only mirror of official repo on openldap.org. Issues and
-    pull requests here are ignored. Use OpenLDAP ITS for issues.
-    http://www.openldap.org/software/repo.html"""
-
-
-    homepage = "http://www.openldap.org/software/repo.html"
-    url      = "https://github.com/LMDB/lmdb/archive/LMDB_0.9.16.tar.gz"
-
-    version('0.9.16', '0de89730b8f3f5711c2b3a4ba517b648')
-
-    def install(self, spec, prefix):
-        os.chdir('libraries/liblmdb')
-
-        make()
-
-        mkdirp(prefix.bin)
-        mkdirp(prefix + '/man/man1')
-        mkdirp(prefix.lib)
-        mkdirp(prefix.include)
-
-        bins = ['mdb_stat', 'mdb_copy', 'mdb_dump', 'mdb_load']
-        for f in bins:
-            install(f, prefix.bin)
-
-        mans = ['mdb_stat.1', 'mdb_copy.1', 'mdb_dump.1', 'mdb_load.1']
-        for f in mans:
-            install(f, prefix + '/man/man1')
-
-        libs = ['liblmdb.a', 'liblmdb.so']
-        for f in libs:
-            install(f, prefix.lib)
-
-        includes = ['lmdb.h']
-        for f in includes:
-            install(f, prefix.include)
diff --git a/var/spack/packages/lua/package.py b/var/spack/packages/lua/package.py
deleted file mode 100644
index 57c443cc2d..0000000000
--- a/var/spack/packages/lua/package.py
+++ /dev/null
@@ -1,26 +0,0 @@
-from spack import *
-import os
-
-class Lua(Package):
-    """ The Lua programming language interpreter and library """
-    homepage = "http://www.lua.org"
-    url      = "http://www.lua.org/ftp/lua-5.1.5.tar.gz"
-
-    version('5.3.1', '797adacada8d85761c079390ff1d9961')
-    version('5.3.0', 'a1b0a7e92d0c85bbff7a8d27bf29f8af')
-    version('5.2.4', '913fdb32207046b273fdb17aad70be13')
-    version('5.2.3', 'dc7f94ec6ff15c985d2d6ad0f1b35654')
-    version('5.2.2', 'efbb645e897eae37cad4344ce8b0a614')
-    version('5.2.1', 'ae08f641b45d737d12d30291a5e5f6e3')
-    version('5.2.0', 'f1ea831f397214bae8a265995ab1a93e')
-    version('5.1.5', '2e115fe26e435e33b0d5c022e4490567')
-    version('5.1.4', 'd0870f2de55d59c1c8419f36e8fac150')
-    version('5.1.3', 'a70a8dfaa150e047866dc01a46272599')
-
-    depends_on('ncurses')
-
-    def install(self, spec, prefix):
-        make('INSTALL_TOP=%s' % prefix,
-             'MYLDFLAGS=-L%s/lib' % spec['ncurses'].prefix,
-             'linux',
-             'install')
diff --git a/var/spack/packages/lwgrp/package.py b/var/spack/packages/lwgrp/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/lwm2/package.py b/var/spack/packages/lwm2/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/memaxes/package.py b/var/spack/packages/memaxes/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/mesa/package.py b/var/spack/packages/mesa/package.py
old mode 100644
new mode 100755
index 2a04a8fd51..2dba878a77
--- a/var/spack/packages/mesa/package.py
+++ b/var/spack/packages/mesa/package.py
@@ -1,7 +1,7 @@
 from spack import *
 
 class Mesa(Package):
-    """Mesa is an open-source implementation of the OpenGL
+    """Mesa is an open-source implementation of the OpenGL 
     specification - a system for rendering interactive 3D graphics."""
 
     homepage = "http://www.mesa3d.org"
@@ -11,10 +11,9 @@ class Mesa(Package):
     # version('10.4.4', '8d863a3c209bf5116b2babfccccc68ce')
     version('8.0.5', 'cda5d101f43b8784fa60bdeaca4056f2')
 
-    # mesa 7.x, 8.x, 9.x
+    # mesa 7.x, 8.x, 9.x 
     depends_on("libdrm@2.4.33")
     depends_on("llvm@3.0")
-    depends_on("libxml2")
 
     # patch("llvm-fixes.patch") # using newer llvm
 
diff --git a/var/spack/packages/metis/package.py b/var/spack/packages/metis/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/mpc/package.py b/var/spack/packages/mpc/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/mpe2/mpe2.patch b/var/spack/packages/mpe2/mpe2.patch
old mode 100644
new mode 100755
diff --git a/var/spack/packages/mpe2/package.py b/var/spack/packages/mpe2/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/mpfr/package.py b/var/spack/packages/mpfr/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/mpibash/mpibash-4.3.patch b/var/spack/packages/mpibash/mpibash-4.3.patch
old mode 100644
new mode 100755
diff --git a/var/spack/packages/mpibash/package.py b/var/spack/packages/mpibash/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/mpich/package.py b/var/spack/packages/mpich/package.py
old mode 100644
new mode 100755
index b6b2dfde21..6aa8f2eca4
--- a/var/spack/packages/mpich/package.py
+++ b/var/spack/packages/mpich/package.py
@@ -38,6 +38,7 @@ class Mpich(Package):
     provides('mpi@:3', when='@3:')
     provides('mpi@:1', when='@1:')
 
+
     def setup_dependent_environment(self, module, spec, dep_spec):
         """For dependencies, make mpicc's use spack wrapper."""
         os.environ['MPICH_CC']  = 'cc'
diff --git a/var/spack/packages/mpileaks/package.py b/var/spack/packages/mpileaks/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/mrnet/package.py b/var/spack/packages/mrnet/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/munge/package.py b/var/spack/packages/munge/package.py
deleted file mode 100644
index c737ca0354..0000000000
--- a/var/spack/packages/munge/package.py
+++ /dev/null
@@ -1,20 +0,0 @@
-from spack import *
-import os
-
-class Munge(Package):
-    """ MUNGE Uid 'N' Gid Emporium """
-    homepage = "https://code.google.com/p/munge/"
-    url      = "https://github.com/dun/munge/releases/download/munge-0.5.11/munge-0.5.11.tar.bz2"
-
-    version('0.5.11', 'bd8fca8d5f4c1fcbef1816482d49ee01', url='https://github.com/dun/munge/releases/download/munge-0.5.11/munge-0.5.11.tar.bz2')
-
-    depends_on('openssl')
-    depends_on('libgcrypt')
-
-    def install(self, spec, prefix):
-        os.makedirs(os.path.join(prefix, "lib/systemd/system"))
-        configure("--prefix=%s" % prefix)
-
-        make()
-        make("install")
-
diff --git a/var/spack/packages/muster/package.py b/var/spack/packages/muster/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/mvapich2/ad_lustre_rwcontig_open_source.patch b/var/spack/packages/mvapich2/ad_lustre_rwcontig_open_source.patch
old mode 100644
new mode 100755
diff --git a/var/spack/packages/mvapich2/package.py b/var/spack/packages/mvapich2/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/nasm/package.py b/var/spack/packages/nasm/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/ncurses/package.py b/var/spack/packages/ncurses/package.py
old mode 100644
new mode 100755
index 8f5763bfdd..a22e83503f
--- a/var/spack/packages/ncurses/package.py
+++ b/var/spack/packages/ncurses/package.py
@@ -21,11 +21,3 @@ def install(self, spec, prefix):
         make()
         make("install")
 
-        configure("--prefix=%s" % prefix,
-                  "--with-shared",
-                  "--disable-widec",
-                  "--disable-pc-files",
-                  "--without-ada")
-        make()
-        make("install")
-
diff --git a/var/spack/packages/netcdf/package.py b/var/spack/packages/netcdf/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/netgauge/package.py b/var/spack/packages/netgauge/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/netlib-blas/package.py b/var/spack/packages/netlib-blas/package.py
old mode 100644
new mode 100755
index 85e97323d3..0a6cdb0442
--- a/var/spack/packages/netlib-blas/package.py
+++ b/var/spack/packages/netlib-blas/package.py
@@ -9,8 +9,6 @@ class NetlibBlas(Package):
 
     version('3.5.0', 'b1d3e3e425b2e44a06760ff173104bdf')
 
-    variant('fpic', default=False, description="Build with -fpic compiler option")
-
     # virtual dependency
     provides('blas')
 
@@ -25,10 +23,6 @@ def patch(self):
         mf.filter('^LOADER.*',  'LOADER = f90')
         mf.filter('^CC =.*',  'CC = cc')
 
-        if '+fpic' in self.spec:
-            mf.filter('^OPTS.*=.*',  'OPTS = -O2 -frecursive -fpic')
-            mf.filter('^CFLAGS =.*',  'CFLAGS = -O3 -fpic')
-
 
     def install(self, spec, prefix):
         make('blaslib')
diff --git a/var/spack/packages/nettle/package.py b/var/spack/packages/nettle/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/ompss/package.py b/var/spack/packages/ompss/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/opari2/package.py b/var/spack/packages/opari2/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/openmpi/ad_lustre_rwcontig_open_source.patch b/var/spack/packages/openmpi/ad_lustre_rwcontig_open_source.patch
old mode 100644
new mode 100755
diff --git a/var/spack/packages/openmpi/llnl-platforms.patch b/var/spack/packages/openmpi/llnl-platforms.patch
old mode 100644
new mode 100755
diff --git a/var/spack/packages/openmpi/package.py b/var/spack/packages/openmpi/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/openssl/package.py b/var/spack/packages/openssl/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/otf/package.py b/var/spack/packages/otf/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/otf2/package.py b/var/spack/packages/otf2/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/pango/package.py b/var/spack/packages/pango/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/papi/package.py b/var/spack/packages/papi/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/paraver/package.py b/var/spack/packages/paraver/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/parmetis/package.py b/var/spack/packages/parmetis/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/parpack/package.py b/var/spack/packages/parpack/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/pcre/package.py b/var/spack/packages/pcre/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/petsc/package.py b/var/spack/packages/petsc/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/pidx/package.py b/var/spack/packages/pidx/package.py
deleted file mode 100644
index 81aed62fb1..0000000000
--- a/var/spack/packages/pidx/package.py
+++ /dev/null
@@ -1,21 +0,0 @@
-from spack import *
-
-class Pidx(Package):
-    """PIDX Parallel I/O Library.
-
-    PIDX is an efficient parallel I/O library that reads and writes
-    multiresolution IDX data files.
-    """
-
-    homepage = "http://www.cedmav.com/pidx"
-
-    version('1.0', git='https://github.com/sci-visus/PIDX.git',
-            commit='6afa1cf71d1c41263296dc049c8fabaf73c296da')
-
-    depends_on("mpi")
-
-    def install(self, spec, prefix):
-        with working_dir('spack-build', create=True):
-            cmake('..', *std_cmake_args)
-            make()
-            make("install")
diff --git a/var/spack/packages/pixman/package.py b/var/spack/packages/pixman/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/pkg-config/package.py b/var/spack/packages/pkg-config/package.py
deleted file mode 100644
index 9964c6ce34..0000000000
--- a/var/spack/packages/pkg-config/package.py
+++ /dev/null
@@ -1,17 +0,0 @@
-from spack import *
-
-class PkgConfig(Package):
-    """pkg-config is a helper tool used when compiling applications and libraries"""
-    homepage = "http://www.freedesktop.org/wiki/Software/pkg-config/"
-    url      = "http://pkgconfig.freedesktop.org/releases/pkg-config-0.28.tar.gz"
-
-    version('0.28', 'aa3c86e67551adc3ac865160e34a2a0d')
-
-    parallel = False
-
-    def install(self, spec, prefix):
-        configure("--prefix=%s" %prefix, "--enable-shared")
-
-        make()
-        make("install")
-
diff --git a/var/spack/packages/pmgr_collective/package.py b/var/spack/packages/pmgr_collective/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/postgresql/package.py b/var/spack/packages/postgresql/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/ppl/package.py b/var/spack/packages/ppl/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/protobuf/package.py b/var/spack/packages/protobuf/package.py
deleted file mode 100644
index 34085c7ce9..0000000000
--- a/var/spack/packages/protobuf/package.py
+++ /dev/null
@@ -1,16 +0,0 @@
-import os
-from spack import *
-
-class Protobuf(Package):
-    """Google's data interchange format."""
-
-    homepage = "https://developers.google.com/protocol-buffers"
-    url      = "https://github.com/google/protobuf/releases/download/v2.5.0/protobuf-2.5.0.tar.bz2"
-
-    version('2.5.0', 'a72001a9067a4c2c4e0e836d0f92ece4')
-
-    def install(self, spec, prefix):
-        configure("--prefix=" + prefix)
-        make()
-        make("check")
-        make("install")
diff --git a/var/spack/packages/py-Cython/package.py b/var/spack/packages/py-Cython/package.py
new file mode 100644
index 0000000000..c250139114
--- /dev/null
+++ b/var/spack/packages/py-Cython/package.py
@@ -0,0 +1,12 @@
+from spack import *
+
+class PyCython(Package):
+    """The Cython compiler for writing C extensions for the Python language."""
+    homepage = "http://www.cython.org"
+    version("0.21.2", "d21adb870c75680dc857cd05d41046a4",
+            url="https://pypi.python.org/packages/source/C/Cython/Cython-0.21.2.tar.gz")
+
+    extends("python")
+
+    def install(self, spec, prefix):
+        python("setup.py", "install", "--prefix=%s" % prefix)
diff --git a/var/spack/packages/py-Distutils2/package.py b/var/spack/packages/py-Distutils2/package.py
new file mode 100644
index 0000000000..8690f569fe
--- /dev/null
+++ b/var/spack/packages/py-Distutils2/package.py
@@ -0,0 +1,15 @@
+from spack import *
+
+class PyDistutils2(Package):
+    """Python Packaging Library."""
+    
+    homepage = "https://hg.python.org/distutils2"
+    url      = "https://pypi.python.org/packages/source/D/Distutils2/Distutils2-1.0a4.tar.gz"
+
+    version('1.0a4', '52bc9dffb394970c27e02853ae3a3241')
+
+    depends_on("python")
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
+
diff --git a/var/spack/packages/py-astroML/package.py b/var/spack/packages/py-astroML/package.py
new file mode 100644
index 0000000000..1583e249d2
--- /dev/null
+++ b/var/spack/packages/py-astroML/package.py
@@ -0,0 +1,12 @@
+from spack import *
+
+class PyAstroml(Package):
+    """tools for machine learning and data mining in Astronomy"""
+    homepage = "http://astroML.github.com"
+    version("0.2", "85f558368546660564f20b30efafb024",
+            url="https://pypi.python.org/packages/source/a/astroML/astroML-0.2.tar.gz")
+
+    extends("python")
+
+    def install(self, spec, prefix):
+        python("setup.py", "install", "--prefix=%s" % prefix)
diff --git a/var/spack/packages/py-astropy/package.py b/var/spack/packages/py-astropy/package.py
new file mode 100644
index 0000000000..5d2d0619cc
--- /dev/null
+++ b/var/spack/packages/py-astropy/package.py
@@ -0,0 +1,12 @@
+from spack import *
+
+class PyAstropy(Package):
+    """Community-developed python astronomy tools"""
+    homepage = "http://astropy.org"
+    version("0.4.2", "6dc4f643cde37ba0a8b4967dc8becee8",
+            url="https://pypi.python.org/packages/source/a/astropy/astropy-0.4.2.tar.gz")
+
+    extends("python")
+
+    def install(self, spec, prefix):
+        python("setup.py", "install", "--prefix=%s" % prefix)
diff --git a/var/spack/packages/py-autopep8/package.py b/var/spack/packages/py-autopep8/package.py
new file mode 100644
index 0000000000..39a2288ea0
--- /dev/null
+++ b/var/spack/packages/py-autopep8/package.py
@@ -0,0 +1,12 @@
+from spack import *
+
+class PyAutopep8(Package):
+    """A tool that automatically formats Python code to conform to the PEP 8 style guide"""
+    homepage = "https://github.com/hhatto/autopep8"
+    version("1.1", "7998358d8f0efd77dcb2cc8e34e3cb5c",
+            url="https://pypi.python.org/packages/source/a/autopep8/autopep8-1.1.tar.gz")
+
+    extends("python")
+
+    def install(self, spec, prefix):
+        python("setup.py", "install", "--prefix=%s" % prefix)
diff --git a/var/spack/packages/py-basemap/package.py b/var/spack/packages/py-basemap/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/py-biopython/package.py b/var/spack/packages/py-biopython/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/py-certifi/package.py b/var/spack/packages/py-certifi/package.py
new file mode 100644
index 0000000000..442903e6a0
--- /dev/null
+++ b/var/spack/packages/py-certifi/package.py
@@ -0,0 +1,12 @@
+from spack import *
+
+class PyCertifi(Package):
+    """Python package for providing Mozilla's CA Bundle."""
+    homepage = "http://python-requests.org"
+    version("14.05.14", "315ea4e50673a16ab047099f816fd32a",
+            url="https://pypi.python.org/packages/source/c/certifi/certifi-14.05.14.tar.gz")
+
+    extends("python")
+
+    def install(self, spec, prefix):
+        python("setup.py", "install", "--prefix=%s" % prefix)
diff --git a/var/spack/packages/py-cffi/package.py b/var/spack/packages/py-cffi/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/py-cython/package.py b/var/spack/packages/py-cython/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/py-dateutil/package.py b/var/spack/packages/py-dateutil/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/py-decorator/package.py b/var/spack/packages/py-decorator/package.py
new file mode 100644
index 0000000000..00c1c541d4
--- /dev/null
+++ b/var/spack/packages/py-decorator/package.py
@@ -0,0 +1,12 @@
+from spack import *
+
+class PyDecorator(Package):
+    """Better living through Python with decorators"""
+    homepage = "https://github.com/micheles/decorator"
+    version("4.0.4", "dd3a0669e1e6f09699eefa2c7fbd9756",
+            url="https://pypi.python.org/packages/source/d/decorator/decorator-4.0.4.tar.gz")
+
+    extends("python")
+
+    def install(self, spec, prefix):
+        python("setup.py", "install", "--prefix=%s" % prefix)
diff --git a/var/spack/packages/py-emcee/package.py b/var/spack/packages/py-emcee/package.py
new file mode 100644
index 0000000000..544066b92d
--- /dev/null
+++ b/var/spack/packages/py-emcee/package.py
@@ -0,0 +1,12 @@
+from spack import *
+
+class PyEmcee(Package):
+    """Kick ass affine-invariant ensemble MCMC sampling"""
+    homepage = "http://dan.iel.fm/emcee/"
+    version("2.1.0", "c6b6fad05c824d40671d4a4fc58dfff7",
+            url="https://pypi.python.org/packages/source/e/emcee/emcee-2.1.0.tar.gz")
+
+    extends("python")
+
+    def install(self, spec, prefix):
+        python("setup.py", "install", "--prefix=%s" % prefix)
diff --git a/var/spack/packages/py-epydoc/package.py b/var/spack/packages/py-epydoc/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/py-fitsio/package.py b/var/spack/packages/py-fitsio/package.py
new file mode 100644
index 0000000000..046bc386d5
--- /dev/null
+++ b/var/spack/packages/py-fitsio/package.py
@@ -0,0 +1,13 @@
+from spack import *
+
+class PyFitsio(Package):
+    """A full featured python library to read from and write to FITS files."""
+    homepage = "https://github.com/esheldon/fitsio"
+    version("0.9.7", "75fa05f999ae8f55c8290bd78ada49e7",
+            url="https://pypi.python.org/packages/source/f/fitsio/fitsio-0.9.7.tar.gz")
+
+    extends("python")
+    depends_on("py-numpy")
+
+    def install(self, spec, prefix):
+        python("setup.py", "install", "--prefix=%s" % prefix)
diff --git a/var/spack/packages/py-genders/package.py b/var/spack/packages/py-genders/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/py-gnuplot/package.py b/var/spack/packages/py-gnuplot/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/py-gnureadline/package.py b/var/spack/packages/py-gnureadline/package.py
new file mode 100644
index 0000000000..51d1c6227e
--- /dev/null
+++ b/var/spack/packages/py-gnureadline/package.py
@@ -0,0 +1,12 @@
+from spack import *
+
+class PyGnureadline(Package):
+    """The standard Python readline extension statically linked against the GNU readline library."""
+    homepage = "http://github.com/ludwigschwardt/python-gnureadline"
+    version("6.3.3", "c4af83c9a3fbeac8f2da9b5a7c60e51c",
+            url="https://pypi.python.org/packages/source/g/gnureadline/gnureadline-6.3.3.tar.gz")
+
+    extends("python")
+
+    def install(self, spec, prefix):
+        python("setup.py", "install", "--prefix=%s" % prefix)
diff --git a/var/spack/packages/py-h5py/package.py b/var/spack/packages/py-h5py/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/py-ipython/package.py b/var/spack/packages/py-ipython/package.py
old mode 100644
new mode 100755
index 8d0e64a07f..3b94b71f29
--- a/var/spack/packages/py-ipython/package.py
+++ b/var/spack/packages/py-ipython/package.py
@@ -3,14 +3,29 @@
 class PyIpython(Package):
     """IPython provides a rich toolkit to help you make the most out of using Python interactively."""
     homepage = "https://pypi.python.org/pypi/ipython"
-    url      = "https://pypi.python.org/packages/source/i/ipython/ipython-2.3.1.tar.gz"
 
-    version('2.3.1', '2b7085525dac11190bfb45bb8ec8dcbf')
+    version('3.0.0','b3f00f3c0be036fafef3b0b9d663f27e',
+           url='https://pypi.python.org/packages/source/i/ipython/ipython-3.0.0.tar.gz')
+    version('4.0.0','c2fecbcf1c0fbdc82625c77a50733dd6',
+           url='https://pypi.python.org/packages/source/i/ipython/ipython-4.0.0.tar.gz')
+    version('2.3.1', '2b7085525dac11190bfb45bb8ec8dcbf',
+            url="https://pypi.python.org/packages/source/i/ipython/ipython-2.3.1.tar.gz")
     version('3.1.0', 'a749d90c16068687b0ec45a27e72ef8f')
+    version('3.2.1', 'f4c93d67ac4b2d4fc69df693b6f3c9e0',
+            url='https://github.com/ipython/ipython/archive/rel-3.2.1.tar.gz')
 
     extends('python')
     depends_on('py-pygments')
-    depends_on('py-setuptools')
+    depends_on('py-setuptools@18.1')
+    depends_on('py-traitlets')
+    depends_on('py-pyzmq')
+    depends_on('py-pexpect')
+    depends_on('py-tornado')
+    depends_on('py-jinja2')
 
     def install(self, spec, prefix):
+        import os
+        # os.system("spack activate py-setuptools@18.1")
+        # os.system("easy_install pip")
+        # os.system("pip install ipython[notebook]")
         python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-ipython/package.py.backup b/var/spack/packages/py-ipython/package.py.backup
new file mode 100755
index 0000000000..1ed8b57e60
--- /dev/null
+++ b/var/spack/packages/py-ipython/package.py.backup
@@ -0,0 +1,27 @@
+from spack import *
+
+class PyIpython(Package):
+    """IPython provides a rich toolkit to help you make the most out of using Python interactively."""
+    homepage = "https://pypi.python.org/pypi/ipython"
+
+    version('2.3.1', '2b7085525dac11190bfb45bb8ec8dcbf',
+            url="https://pypi.python.org/packages/source/i/ipython/ipython-2.3.1.tar.gz")
+    version('3.1.0', 'a749d90c16068687b0ec45a27e72ef8f')
+    version('3.2.1', 'f4c93d67ac4b2d4fc69df693b6f3c9e0',
+            url='https://github.com/ipython/ipython/archive/rel-3.2.1.tar.gz')
+
+    extends('python')
+    depends_on('py-pygments')
+    depends_on('py-setuptools@18.1')
+    depends_on('py-traitlets')
+    depends_on('py-pyzmq')
+    depends_on('py-pexpect')
+    depends_on('py-tornado')
+    depends_on('py-Jinja2')
+
+    def install(self, spec, prefix):
+        import os
+        # os.system("spack activate py-setuptools@18.1")
+        # os.system("easy_install pip")
+        # os.system("pip install ipython[notebook]")
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-ipython_genutils/package.py b/var/spack/packages/py-ipython_genutils/package.py
new file mode 100644
index 0000000000..39b15eec73
--- /dev/null
+++ b/var/spack/packages/py-ipython_genutils/package.py
@@ -0,0 +1,12 @@
+from spack import *
+
+class PyIpythonGenutils(Package):
+    """Vestigial utilities from IPython"""
+    homepage = "http://ipython.org"
+    version("0.1.0", "9a8afbe0978adbcbfcb3b35b2d015a56",
+            url="https://pypi.python.org/packages/source/i/ipython_genutils/ipython_genutils-0.1.0.tar.gz")
+
+    extends("python")
+
+    def install(self, spec, prefix):
+        python("setup.py", "install", "--prefix=%s" % prefix)
diff --git a/var/spack/packages/py-joblib/package.py b/var/spack/packages/py-joblib/package.py
new file mode 100644
index 0000000000..10672314de
--- /dev/null
+++ b/var/spack/packages/py-joblib/package.py
@@ -0,0 +1,12 @@
+from spack import *
+
+class PyJoblib(Package):
+    """Lightweight pipelining: using Python functions as pipeline jobs."""
+    homepage = "http://packages.python.org/joblib/"
+    version("0.8.4", "90a1c25cc4dc4a8e3536093dbc35cff3",
+            url="https://pypi.python.org/packages/source/j/joblib/joblib-0.8.4.tar.gz")
+
+    extends("python")
+
+    def install(self, spec, prefix):
+        python("setup.py", "install", "--prefix=%s" % prefix)
diff --git a/var/spack/packages/py-jsonschema/package.py b/var/spack/packages/py-jsonschema/package.py
new file mode 100755
index 0000000000..9a7fc21862
--- /dev/null
+++ b/var/spack/packages/py-jsonschema/package.py
@@ -0,0 +1,16 @@
+from spack import *
+
+class PyJsonschema(Package):
+    """implementation of JSON Schema validation for Python"""
+    homepage = "https://github.com/Julian/jsonschema"
+    url      = "https://pypi.python.org/packages/source/j/jsonschema/jsonschema-2.5.1.tar.gz"
+
+    version('2.4.0','661f85c3d23094afbb9ac3c0673840bf',
+           url='https://pypi.python.org/packages/source/j/jsonschema/jsonschema-2.4.0.tar.gz')
+    version('2.5.1', '374e848fdb69a3ce8b7e778b47c30640')
+
+    extends("python")
+    depends_on("py-setuptools@18.1")
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-libxml2/package.py b/var/spack/packages/py-libxml2/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/py-lockfile/package.py b/var/spack/packages/py-lockfile/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/py-mako/package.py b/var/spack/packages/py-mako/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/py-matplotlib/package.py b/var/spack/packages/py-matplotlib/package.py
old mode 100644
new mode 100755
index e7ce3dfd24..b9244daf56
--- a/var/spack/packages/py-matplotlib/package.py
+++ b/var/spack/packages/py-matplotlib/package.py
@@ -12,7 +12,6 @@ class PyMatplotlib(Package):
     extends('python', ignore=r'bin/nosetests.*$')
 
     depends_on('py-pyside')
-    depends_on('py-ipython')
     depends_on('py-pyparsing')
     depends_on('py-six')
     depends_on('py-dateutil')
diff --git a/var/spack/packages/py-mock/package.py b/var/spack/packages/py-mock/package.py
index 3b08428ba0..c43842c187 100644
--- a/var/spack/packages/py-mock/package.py
+++ b/var/spack/packages/py-mock/package.py
@@ -1,17 +1,12 @@
 from spack import *
 
 class PyMock(Package):
-    """mock is a library for testing in Python. It allows you to replace parts
-    of your system under test with mock objects and make assertions about how
-    they have been used."""
+    """A Python Mocking and Patching Library for Testing"""
+    homepage = "http://www.voidspace.org.uk/python/mock/"
+    version("1.0.1", "c3971991738caa55ec7c356bbc154ee2",
+            url="https://pypi.python.org/packages/source/m/mock/mock-1.0.1.tar.gz")
 
-    homepage = "https://github.com/testing-cabal/mock"
-    url      = "https://pypi.python.org/packages/source/m/mock/mock-1.3.0.tar.gz"
-
-    version('1.3.0', '73ee8a4afb3ff4da1b4afa287f39fdeb')
-
-    extends('python')
-    depends_on('py-setuptools@17.1:')
+    extends("python")
 
     def install(self, spec, prefix):
-        python('setup.py', 'install', '--prefix=%s' % prefix)
+        python("setup.py", "install", "--prefix=%s" % prefix)
diff --git a/var/spack/packages/py-mpi4py/package.py b/var/spack/packages/py-mpi4py/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/py-mx/package.py b/var/spack/packages/py-mx/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/py-nose/package.py b/var/spack/packages/py-nose/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/py-numexpr/package.py b/var/spack/packages/py-numexpr/package.py
new file mode 100644
index 0000000000..283ea18772
--- /dev/null
+++ b/var/spack/packages/py-numexpr/package.py
@@ -0,0 +1,12 @@
+from spack import *
+
+class PyNumexpr(Package):
+    """Fast numerical expression evaluator for NumPy"""
+    homepage = "https://github.com/pydata/numexpr"
+    version("2.4", "df7e8d9e9dbb145b56d43c465c2bf854",
+            url="https://pypi.python.org/packages/source/n/numexpr/numexpr-2.4.tar.gz")
+
+    extends("python")
+
+    def install(self, spec, prefix):
+        python("setup.py", "install", "--prefix=%s" % prefix)
diff --git a/var/spack/packages/py-numpy/package.py b/var/spack/packages/py-numpy/package.py
old mode 100644
new mode 100755
index efa109a3e9..6534e063d2
--- a/var/spack/packages/py-numpy/package.py
+++ b/var/spack/packages/py-numpy/package.py
@@ -7,22 +7,9 @@ class PyNumpy(Package):
 
     version('1.9.1', '78842b73560ec378142665e712ae4ad9')
     version('1.9.2', 'a1ed53432dbcd256398898d35bc8e645')
-    
+
     extends('python')
     depends_on('py-nose')
-    depends_on('netlib-blas+fpic')
-    depends_on('netlib-lapack+shared')
-
-    def patch(self):
-        filter_file(
-            "possible_executables = \['(gfortran|g77|ifort|efl)",
-            "possible_executables = ['fc",
-            "numpy/distutils/fcompiler/gnu.py",
-            "numpy/distutils/fcompiler/intel.py")
 
     def install(self, spec, prefix):
-        with open('site.cfg', 'w') as f:
-            f.write('[DEFAULT]\n')
-            f.write('libraries=lapack,blas\n')
-            f.write('library_dirs=%s/lib:%s/lib\n' % (spec['blas'].prefix, spec['lapack'].prefix))
         python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-pandas/package.py b/var/spack/packages/py-pandas/package.py
old mode 100644
new mode 100755
index 5b9997faa9..07ee12782f
--- a/var/spack/packages/py-pandas/package.py
+++ b/var/spack/packages/py-pandas/package.py
@@ -6,6 +6,8 @@ class PyPandas(Package):
     homepage = "http://pandas.pydata.org/"
     url      = "https://pypi.python.org/packages/source/p/pandas/pandas-0.16.0.tar.gz#md5=bfe311f05dc0c351f8955fbd1e296e73"
 
+    version('0.15.1','f6fd8d49fc801f6f3fa48f9117a6290b',
+           url='https://pypi.python.org/packages/source/p/pandas/pandas-0.15.1.tar.gz')
     version('0.16.0', 'bfe311f05dc0c351f8955fbd1e296e73')
     version('0.16.1', 'fac4f25748f9610a3e00e765474bdea8')
 
diff --git a/var/spack/packages/py-pep8/package.py b/var/spack/packages/py-pep8/package.py
new file mode 100644
index 0000000000..0bcf416922
--- /dev/null
+++ b/var/spack/packages/py-pep8/package.py
@@ -0,0 +1,12 @@
+from spack import *
+
+class PyPep8(Package):
+    """Python style guide checker"""
+    homepage = "http://pep8.readthedocs.org/"
+    version("1.6.1", "76cf60b245f8549cb458ffcd85710738",
+            url="https://pypi.python.org/packages/source/p/pep8/pep8-1.6.1.tar.gz")
+
+    extends("python")
+
+    def install(self, spec, prefix):
+        python("setup.py", "install", "--prefix=%s" % prefix)
diff --git a/var/spack/packages/py-pexpect/package.py b/var/spack/packages/py-pexpect/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/py-pickleshare/package.py b/var/spack/packages/py-pickleshare/package.py
new file mode 100644
index 0000000000..cf9ddb7db8
--- /dev/null
+++ b/var/spack/packages/py-pickleshare/package.py
@@ -0,0 +1,12 @@
+from spack import *
+
+class PyPickleshare(Package):
+    """Tiny 'shelve'-like database with concurrency support"""
+    homepage = "https://github.com/vivainio/pickleshare"
+    version("0.5", "25337740507cb855ad58bfcf60f7710e",
+            url="https://pypi.python.org/packages/source/p/pickleshare/pickleshare-0.5.tar.gz")
+
+    extends("python")
+
+    def install(self, spec, prefix):
+        python("setup.py", "install", "--prefix=%s" % prefix)
diff --git a/var/spack/packages/py-pil/package.py b/var/spack/packages/py-pil/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/py-pip/package.py b/var/spack/packages/py-pip/package.py
new file mode 100644
index 0000000000..89b8570fe4
--- /dev/null
+++ b/var/spack/packages/py-pip/package.py
@@ -0,0 +1,12 @@
+from spack import *
+
+class PyPip(Package):
+    """The PyPA recommended tool for installing Python packages."""
+    homepage = "https://pip.pypa.io/"
+    version("7.1.2", "3823d2343d9f3aaab21cf9c917710196",
+            url="https://pypi.python.org/packages/source/p/pip/pip-7.1.2.tar.gz")
+
+    extends("python")
+
+    def install(self, spec, prefix):
+        python("setup.py", "install", "--prefix=%s" % prefix)
diff --git a/var/spack/packages/py-pmw/package.py b/var/spack/packages/py-pmw/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/py-py/package.py b/var/spack/packages/py-py/package.py
new file mode 100644
index 0000000000..0ef0403124
--- /dev/null
+++ b/var/spack/packages/py-py/package.py
@@ -0,0 +1,12 @@
+from spack import *
+
+class PyPy(Package):
+    """library with cross-python path, ini-parsing, io, code, log facilities"""
+    homepage = "http://pylib.readthedocs.org/"
+    version("1.4.26", "30c3fd92a53f1a5ed6f3591c1fe75c0e",
+            url="https://pypi.python.org/packages/source/p/py/py-1.4.26.tar.gz")
+
+    extends("python")
+
+    def install(self, spec, prefix):
+        python("setup.py", "install", "--prefix=%s" % prefix)
diff --git a/var/spack/packages/py-py4j/package.py b/var/spack/packages/py-py4j/package.py
new file mode 100755
index 0000000000..4c31f57298
--- /dev/null
+++ b/var/spack/packages/py-py4j/package.py
@@ -0,0 +1,15 @@
+from spack import *
+
+
+class PyPy4j(Package):
+    """Enables Python programs to dynamically access arbitrary Java objects"""
+    homepage = "https://www.py4j.org/"
+    url      = "https://pypi.python.org/packages/source/p/py4j/py4j-0.9.tar.gz"
+
+    version('0.9', 'b6fed5faef81a5368e3d50a91a5c9a60')
+
+    extends("python")
+    depends_on("py-setuptools@18.1")
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-pychecker/package.py b/var/spack/packages/py-pychecker/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/py-pycparser/package.py b/var/spack/packages/py-pycparser/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/py-pyelftools/package.py b/var/spack/packages/py-pyelftools/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/py-pygments/package.py b/var/spack/packages/py-pygments/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/py-pylint/package.py b/var/spack/packages/py-pylint/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/py-pypar/package.py b/var/spack/packages/py-pypar/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/py-pyparsing/package.py b/var/spack/packages/py-pyparsing/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/py-pyqt/package.py b/var/spack/packages/py-pyqt/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/py-pyside/package.py b/var/spack/packages/py-pyside/package.py
old mode 100644
new mode 100755
index bb5da44d02..8d093efd2c
--- a/var/spack/packages/py-pyside/package.py
+++ b/var/spack/packages/py-pyside/package.py
@@ -8,12 +8,9 @@ class PyPyside(Package):
 
     version('1.2.2', 'c45bc400c8a86d6b35f34c29e379e44d')
 
-    # TODO: make build dependency
-    # depends_on("cmake")
-
     extends('python')
     depends_on('py-setuptools')
-    depends_on('qt@:4')
+    depends_on('qt@5.4.0')
 
     def patch(self):
         """Undo PySide RPATH handling and add Spack RPATH."""
diff --git a/var/spack/packages/py-pytest/package.py b/var/spack/packages/py-pytest/package.py
new file mode 100644
index 0000000000..3611b68862
--- /dev/null
+++ b/var/spack/packages/py-pytest/package.py
@@ -0,0 +1,12 @@
+from spack import *
+
+class PyPytest(Package):
+    """pytest: simple powerful testing with Python"""
+    homepage = "http://pytest.org"
+    version("2.6.4", "14341e122f7e9031a0948eb6b01a2640",
+            url="https://pypi.python.org/packages/source/p/pytest/pytest-2.6.4.tar.gz")
+
+    extends("python")
+
+    def install(self, spec, prefix):
+        python("setup.py", "install", "--prefix=%s" % prefix)
diff --git a/var/spack/packages/py-python-daemon/package.py b/var/spack/packages/py-python-daemon/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/py-python-dateutil/package.py b/var/spack/packages/py-python-dateutil/package.py
new file mode 100644
index 0000000000..8efa114db1
--- /dev/null
+++ b/var/spack/packages/py-python-dateutil/package.py
@@ -0,0 +1,12 @@
+from spack import *
+
+class PyPythonDateutil(Package):
+    """Extensions to the standard Python datetime module"""
+    homepage = "http://labix.org/python-dateutil"
+    version("2.2", "c1f654d0ff7e33999380a8ba9783fd5c",
+            url="https://pypi.python.org/packages/source/p/python-dateutil/python-dateutil-2.2.tar.gz")
+
+    extends("python")
+
+    def install(self, spec, prefix):
+        python("setup.py", "install", "--prefix=%s" % prefix)
diff --git a/var/spack/packages/py-pytz/package.py b/var/spack/packages/py-pytz/package.py
old mode 100644
new mode 100755
index da6311a784..f67bb42854
--- a/var/spack/packages/py-pytz/package.py
+++ b/var/spack/packages/py-pytz/package.py
@@ -5,6 +5,8 @@ class PyPytz(Package):
     homepage = "https://pypi.python.org/pypi/pytz"
     url      = "https://pypi.python.org/packages/source/p/pytz/pytz-2014.10.tar.gz"
 
+    version('2014.9','d42bda2f4c1e873e02fbd1e4acfd1b8c',
+           url='https://pypi.python.org/packages/source/p/pytz/pytz-2014.9.tar.gz')
     version('2014.10', 'eb1cb941a20c5b751352c52486aa1dd7')
     version('2015.4', '417a47b1c432d90333e42084a605d3d8')
 
diff --git a/var/spack/packages/py-pyzmq/package.py b/var/spack/packages/py-pyzmq/package.py
new file mode 100755
index 0000000000..f5551182b3
--- /dev/null
+++ b/var/spack/packages/py-pyzmq/package.py
@@ -0,0 +1,16 @@
+from spack import *
+
+class PyPyzmq(Package):
+    """official Python binding for the ZeroMQ Messaging Library"""
+    homepage = "https://github.com/zeromq/pyzmq"
+    url      = "https://pypi.python.org/packages/source/p/pyzmq/pyzmq-14.7.0.tar.gz"
+
+    version('14.4.1','a6a7fb6950b1bf5333c6795f3edf196c',
+           url='https://pypi.python.org/packages/source/p/pyzmq/pyzmq-14.4.1.tar.gz')
+    version('14.7.0', '87e3abb33af5794db5ae85c667bbf324')
+
+    extends('python')
+    depends_on('py-setuptools@18.1')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-rpy2/package.py b/var/spack/packages/py-rpy2/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/py-scientificpython/package.py b/var/spack/packages/py-scientificpython/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/py-scikit-learn/package.py b/var/spack/packages/py-scikit-learn/package.py
old mode 100644
new mode 100755
index 5b078ce901..744b37e7e0
--- a/var/spack/packages/py-scikit-learn/package.py
+++ b/var/spack/packages/py-scikit-learn/package.py
@@ -9,6 +9,9 @@ class PyScikitLearn(Package):
     version('0.16.1', '363ddda501e3b6b61726aa40b8dbdb7e')
 
     extends('python')
+    depends_on('python@2.7.10')
+    depends_on('py-numpy@1.9.2')
+    depends_on('py-scipy@0.15.1')
 
     def install(self, spec, prefix):
         python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-scipy/package.py b/var/spack/packages/py-scipy/package.py
old mode 100644
new mode 100755
index 3a1124cc15..bcbdb2100f
--- a/var/spack/packages/py-scipy/package.py
+++ b/var/spack/packages/py-scipy/package.py
@@ -5,14 +5,14 @@ class PyScipy(Package):
     homepage = "https://pypi.python.org/pypi/scipy"
     url      = "https://pypi.python.org/packages/source/s/scipy/scipy-0.15.0.tar.gz"
 
+    version('0.14.0','d7c7f4ccf8b07b08d6fe49d5cd51f85d',
+           url='https://pypi.python.org/packages/source/s/scipy/scipy-0.14.0.tar.gz')
     version('0.15.0', '639112f077f0aeb6d80718dc5019dc7a')
     version('0.15.1', 'be56cd8e60591d6332aac792a5880110')
 
     extends('python')
     depends_on('py-nose')
     depends_on('py-numpy')
-    depends_on('blas')
-    depends_on('lapack')
 
     def install(self, spec, prefix):
         python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-seaborn/package.py b/var/spack/packages/py-seaborn/package.py
new file mode 100644
index 0000000000..1e228b0622
--- /dev/null
+++ b/var/spack/packages/py-seaborn/package.py
@@ -0,0 +1,12 @@
+from spack import *
+
+class PySeaborn(Package):
+    """Seaborn: statistical data visualization"""
+    homepage = "http://stanford.edu/~mwaskom/software/seaborn/"
+    version("0.5.1", "2ce6ea7d3c67858c0b1f5793fa2043b8",
+            url="https://pypi.python.org/packages/source/s/seaborn/seaborn-0.5.1.tar.gz")
+
+    extends("python")
+
+    def install(self, spec, prefix):
+        python("setup.py", "install", "--prefix=%s" % prefix)
diff --git a/var/spack/packages/py-setuptools/package.py b/var/spack/packages/py-setuptools/package.py
old mode 100644
new mode 100755
index 760ad4d6db..053fe1ba80
--- a/var/spack/packages/py-setuptools/package.py
+++ b/var/spack/packages/py-setuptools/package.py
@@ -3,11 +3,12 @@
 class PySetuptools(Package):
     """Easily download, build, install, upgrade, and uninstall Python packages."""
     homepage = "https://pypi.python.org/pypi/setuptools"
-    url      = "https://pypi.python.org/packages/source/s/setuptools/setuptools-11.3.tar.gz"
 
-    version('11.3.1', '01f69212e019a2420c1693fb43593930')
-    version('16.0', '0ace0b96233516fc5f7c857d086aa3ad')
-    version('18.1', 'f72e87f34fbf07f299f6cb46256a0b06')
+    version('18.1', 'f72e87f34fbf07f299f6cb46256a0b06',
+            url='https://pypi.python.org/packages/source/s/setuptools/setuptools-18.1.tar.gz')
+    version('11.3.1', '01f69212e019a2420c1693fb43593930',
+            url="https://pypi.python.org/packages/source/s/setuptools/setuptools-11.3.tar.gz")
+    version('16.0', '0ace0b96233516fc5f7c857d086aa3ad',)
 
     extends('python')
 
diff --git a/var/spack/packages/py-shiboken/package.py b/var/spack/packages/py-shiboken/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/py-sip/package.py b/var/spack/packages/py-sip/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/py-six/package.py b/var/spack/packages/py-six/package.py
old mode 100644
new mode 100755
index 05c5bd00a9..e9946a1e56
--- a/var/spack/packages/py-six/package.py
+++ b/var/spack/packages/py-six/package.py
@@ -5,6 +5,8 @@ class PySix(Package):
     homepage = "https://pypi.python.org/pypi/six"
     url      = "https://pypi.python.org/packages/source/s/six/six-1.9.0.tar.gz"
 
+    version('1.8.0','1626eb24cc889110c38f7e786ec69885',
+           url='https://pypi.python.org/packages/source/s/six/six-1.8.0.tar.gz')
     version('1.9.0', '476881ef4012262dfc8adc645ee786c4')
 
     extends('python')
diff --git a/var/spack/packages/py-statsmodels/package.py b/var/spack/packages/py-statsmodels/package.py
new file mode 100644
index 0000000000..393c772738
--- /dev/null
+++ b/var/spack/packages/py-statsmodels/package.py
@@ -0,0 +1,12 @@
+from spack import *
+
+class PyStatsmodels(Package):
+    """Statistical computations and models for use with SciPy"""
+    homepage = "http://statsmodels.sourceforge.net/"
+    version("0.6.1", "f7580ebf7d2a2c9b87abfad190dcb9a3",
+            url="https://pypi.python.org/packages/source/s/statsmodels/statsmodels-0.6.1.tar.gz")
+
+    extends("python")
+
+    def install(self, spec, prefix):
+        python("setup.py", "install", "--prefix=%s" % prefix)
diff --git a/var/spack/packages/py-sympy/package.py b/var/spack/packages/py-sympy/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/py-tables/package.py b/var/spack/packages/py-tables/package.py
new file mode 100644
index 0000000000..637ccf34cd
--- /dev/null
+++ b/var/spack/packages/py-tables/package.py
@@ -0,0 +1,12 @@
+from spack import *
+
+class PyTables(Package):
+    """Hierarchical datasets for Python"""
+    homepage = "http://www.pytables.org/"
+    version("3.1.1", "38d917f0c6dfb0bc28ce9ea0c3492524",
+            url="https://pypi.python.org/packages/source/t/tables/tables-3.1.1.tar.gz")
+
+    extends("python")
+
+    def install(self, spec, prefix):
+        python("setup.py", "install", "--prefix=%s" % prefix)
diff --git a/var/spack/packages/py-tornado/package.py b/var/spack/packages/py-tornado/package.py
new file mode 100755
index 0000000000..4fc2d42c7b
--- /dev/null
+++ b/var/spack/packages/py-tornado/package.py
@@ -0,0 +1,17 @@
+from spack import *
+
+class PyTornado(Package):
+    """Python web framework and asynchronous networking library"""
+    homepage = "http://www.tornadoweb.org/"
+    url = "https://pypi.python.org/packages/source/t/tornado/tornado-4.2.1.tar.gz"
+
+    version('4.0.2','985c0e704b765c33a6193d49d1935588',
+           url='https://pypi.python.org/packages/source/t/tornado/tornado-4.0.2.tar.gz')
+    version('4.2.1', 'd523204389cfb70121bb69709f551b20')
+
+    extends('python')
+    depends_on('py-certifi')
+    depends_on('py-setuptools@18.1')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-traitlets/package.py b/var/spack/packages/py-traitlets/package.py
new file mode 100755
index 0000000000..7b7f5c64cc
--- /dev/null
+++ b/var/spack/packages/py-traitlets/package.py
@@ -0,0 +1,14 @@
+from spack import *
+
+class PyTraitlets(Package):
+    """A lightweight Traits like module"""
+    homepage = "http://traitlets.readthedocs.org/"
+    url      = "https://github.com/ipython/traitlets/archive/4.0.0.tar.gz"
+
+    version('4.0.0', 'b5b95ea5941fd9619b4704dfd8201568')
+
+    extends('python')
+    depends_on("py-setuptools@18.1")
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-triangle-plot/package.py b/var/spack/packages/py-triangle-plot/package.py
new file mode 100644
index 0000000000..29c5f92857
--- /dev/null
+++ b/var/spack/packages/py-triangle-plot/package.py
@@ -0,0 +1,12 @@
+from spack import *
+
+class PyTrianglePlot(Package):
+    """Make some beautiful corner plots of samples."""
+    homepage = "https://github.com/dfm/triangle.py"
+    version("0.0.6", "970a35a9bde6002d673e3188fe39f0ed",
+            url="https://pypi.python.org/packages/source/t/triangle_plot/triangle_plot-0.0.6.tar.gz")
+
+    extends("python")
+
+    def install(self, spec, prefix):
+        python("setup.py", "install", "--prefix=%s" % prefix)
diff --git a/var/spack/packages/py-virtualenv/package.py b/var/spack/packages/py-virtualenv/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/py-yapf/package.py b/var/spack/packages/py-yapf/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/python/package.py b/var/spack/packages/python/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/qhull/package.py b/var/spack/packages/qhull/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/qt/package.py b/var/spack/packages/qt/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/qthreads/package.py b/var/spack/packages/qthreads/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/ravel/package.py b/var/spack/packages/ravel/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/readline/package.py b/var/spack/packages/readline/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/rose/add_spack_compiler_recognition.patch b/var/spack/packages/rose/add_spack_compiler_recognition.patch
old mode 100644
new mode 100755
diff --git a/var/spack/packages/rose/package.py b/var/spack/packages/rose/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/ruby/package.py b/var/spack/packages/ruby/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/samtools/package.py b/var/spack/packages/samtools/package.py
deleted file mode 100644
index 72900398d8..0000000000
--- a/var/spack/packages/samtools/package.py
+++ /dev/null
@@ -1,18 +0,0 @@
-from spack import *
-
-class Samtools(Package):
-    """SAM Tools provide various utilities for manipulating alignments in the SAM format, 
-       including sorting, merging, indexing and generating
-       alignments in a per-position format"""
-
-    homepage = "www.htslib.org"
-    version('1.2','988ec4c3058a6ceda36503eebecd4122',url = "https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2")
-
-    depends_on("zlib")
-    depends_on("mpc")
-    parallel=False
-    patch("samtools1.2.patch",level=0)
-
-    def install(self, spec, prefix):
-        make("prefix=%s" % prefix, "install")
-
diff --git a/var/spack/packages/samtools/samtools1.2.patch b/var/spack/packages/samtools/samtools1.2.patch
deleted file mode 100644
index ead3ab4e2c..0000000000
--- a/var/spack/packages/samtools/samtools1.2.patch
+++ /dev/null
@@ -1,20 +0,0 @@
---- Makefile	2015-02-03 08:27:34.000000000 -0800
-+++ Makefile.new	2015-07-21 10:38:27.881406892 -0700
-@@ -26,7 +26,7 @@
- CFLAGS   = -g -Wall -O2
- LDFLAGS  =
- LDLIBS   =
--DFLAGS=     -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1
-+DFLAGS=     -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0
- LOBJS=      bam_aux.o bam.o bam_import.o sam.o \
-             sam_header.o bam_plbuf.o
- AOBJS=      bam_index.o bam_plcmd.o sam_view.o \
-@@ -37,7 +37,7 @@
-             faidx.o stats.o stats_isize.o bam_flags.o bam_split.o \
-             bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o
- INCLUDES=   -I. -I$(HTSDIR)
--LIBCURSES=  -lcurses # -lXCurses
-+#LIBCURSES=  -lcurses # -lXCurses
- 
- prefix      = /usr/local
- exec_prefix = $(prefix)
diff --git a/var/spack/packages/scalasca/package.py b/var/spack/packages/scalasca/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/scorep/package.py b/var/spack/packages/scorep/package.py
old mode 100644
new mode 100755
index f013bd1cbb..32a772e3db
--- a/var/spack/packages/scorep/package.py
+++ b/var/spack/packages/scorep/package.py
@@ -1,10 +1,11 @@
 # FIXME: Add copyright statement
 
 from spack import *
+from contextlib import closing
 
 class Scorep(Package):
-    """The Score-P measurement infrastructure is a highly scalable and
-       easy-to-use tool suite for profiling, event tracing, and online
+    """The Score-P measurement infrastructure is a highly scalable and 
+       easy-to-use tool suite for profiling, event tracing, and online 
        analysis of HPC applications."""
 
     # FIXME: add a proper url for your package's homepage here.
@@ -19,7 +20,7 @@ class Scorep(Package):
     depends_on("mpi")
     depends_on("papi")
     # depends_on("otf2@1.2:1.2.1") # only Score-P 1.2.x
-    depends_on("otf2")
+    depends_on("otf2") 
     depends_on("opari2")
     depends_on("cube@4.2:4.2.3")
 
@@ -52,12 +53,12 @@ def install(self, spec, prefix):
         # Use a custom compiler configuration, otherwise the score-p
         # build system messes with spack's compiler settings.
         # Create these three files in the build directory
-        with open("platform-backend-user-provided", "w") as backend_file:
+        with closing(open("platform-backend-user-provided", "w")) as backend_file:
             backend_file.write(self.backend_user_provided)
-        with open("platform-frontend-user-provided", "w") as frontend_file:
+        with closing(open("platform-frontend-user-provided", "w")) as frontend_file:
             frontend_file.write(self.frontend_user_provided)
-        with open("platform-mpi-user-provided", "w") as mpi_file:
-            mpi_file.write(self.mpi_user_provided)
+        with closing(open("platform-mpi-user-provided", "w")) as mpi_file:
+            mpi_file.write(self.mpi_user_provided)            
 
         configure_args = ["--prefix=%s" % prefix,
                           "--with-custom-compilers",
diff --git a/var/spack/packages/scotch/package.py b/var/spack/packages/scotch/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/scr/package.py b/var/spack/packages/scr/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/silo/package.py b/var/spack/packages/silo/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/snappy/package.py b/var/spack/packages/snappy/package.py
deleted file mode 100644
index c8f9ceef7d..0000000000
--- a/var/spack/packages/snappy/package.py
+++ /dev/null
@@ -1,15 +0,0 @@
-import os
-from spack import *
-
-class Snappy(Package):
-    """A fast compressor/decompressor: https://code.google.com/p/snappy"""
-
-    homepage = "https://code.google.com/p/snappy"
-    url      = "https://github.com/google/snappy/releases/download/1.1.3/snappy-1.1.3.tar.gz"
-
-    version('1.1.3', '7358c82f133dc77798e4c2062a749b73')
-
-    def install(self, spec, prefix):
-        configure("--prefix=" + prefix)
-        make()
-        make("install")
diff --git a/var/spack/packages/spindle/package.py b/var/spack/packages/spindle/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/sqlite/package.py b/var/spack/packages/sqlite/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/stat/configure_mpicxx.patch b/var/spack/packages/stat/configure_mpicxx.patch
old mode 100644
new mode 100755
diff --git a/var/spack/packages/stat/package.py b/var/spack/packages/stat/package.py
old mode 100644
new mode 100755
index 5d81e62731..c40d65ae78
--- a/var/spack/packages/stat/package.py
+++ b/var/spack/packages/stat/package.py
@@ -9,20 +9,17 @@ class Stat(Package):
     version('2.1.0', 'ece26beaf057aa9134d62adcdda1ba91')
     version('2.0.0', 'c7494210b0ba26b577171b92838e1a9b')
 
-    variant('dysect', default=False, description="enable DySectAPI")
-
     depends_on('libelf')
     depends_on('libdwarf')
     depends_on('dyninst')
     depends_on('graphlib')
-    depends_on('graphviz')
     depends_on('launchmon')
     depends_on('mrnet')
 
     patch('configure_mpicxx.patch', when='@2.1.0')
 
     def install(self, spec, prefix):
-        configure_args = [
+        configure(
             "--enable-gui",
             "--prefix=%s" % prefix,
             "--disable-examples", # Examples require MPI: avoid this dependency.
@@ -30,11 +27,7 @@ def install(self, spec, prefix):
             "--with-mrnet=%s"       % spec['mrnet'].prefix,
             "--with-graphlib=%s"    % spec['graphlib'].prefix,
             "--with-stackwalker=%s" % spec['dyninst'].prefix,
-            "--with-libdwarf=%s"    % spec['libdwarf'].prefix
-            ]
-        if '+dysect' in spec:
-            configure_args.append('--enable-dysectapi')
-        configure(*configure_args)
+            "--with-libdwarf=%s"    % spec['libdwarf'].prefix)
 
         make(parallel=False)
         make("install")
diff --git a/var/spack/packages/sundials/package.py b/var/spack/packages/sundials/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/swig/package.py b/var/spack/packages/swig/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/task/package.py b/var/spack/packages/task/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/taskd/package.py b/var/spack/packages/taskd/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/tau/package.py b/var/spack/packages/tau/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/tcl/package.py b/var/spack/packages/tcl/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/the_silver_searcher/package.py b/var/spack/packages/the_silver_searcher/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/thrift/package.py b/var/spack/packages/thrift/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/tk/package.py b/var/spack/packages/tk/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/tmux/package.py b/var/spack/packages/tmux/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/tmuxinator/package.py b/var/spack/packages/tmuxinator/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/uncrustify/package.py b/var/spack/packages/uncrustify/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/util-linux/package.py b/var/spack/packages/util-linux/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/vim/package.py b/var/spack/packages/vim/package.py
old mode 100644
new mode 100755
index 4099b3257f..d0cf80b898
--- a/var/spack/packages/vim/package.py
+++ b/var/spack/packages/vim/package.py
@@ -35,26 +35,15 @@ class Vim(Package):
     variant('ruby', default=False, description="build with Ruby")
     depends_on('ruby', when='+ruby')
 
-    variant('cscope', default=False, description="build with cscope support")
-    depends_on('cscope', when='+cscope')
-
-    variant('gui', default=False, description="build with gui (gvim)")
-    # virtual dependency?
-
     def install(self, spec, prefix):
       feature_set = None
       for fs in self.feature_sets:
         if "+" + fs in spec:
           if feature_set is not None:
-            tty.error("Only one feature set allowed, both %s and %s specified"
-                      % (feature_set, fs))
+            tty.error("Only one feature set allowed, both {} and {} specified".format(
+              feature_set,
+              fs))
           feature_set = fs
-      if '+gui' in spec:
-        if feature_set is not None:
-          if feature_set is not 'huge':
-            tty.error("+gui variant requires 'huge' feature set, %s was specified"
-                      % feature_set)
-        feature_set = 'huge'
       if feature_set is None:
         feature_set = 'normal'
 
@@ -71,12 +60,6 @@ def install(self, spec, prefix):
       else:
         configure_args.append("--enable-rubyinterp=dynamic")
 
-      if '+gui' in spec:
-        configure_args.append("--enable-gui=auto")
-
-      if '+cscope' in spec:
-        configure_args.append("--enable-cscope")
-
       configure("--prefix=%s" % prefix, *configure_args)
 
       make()
diff --git a/var/spack/packages/vtk/package.py b/var/spack/packages/vtk/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/wget/package.py b/var/spack/packages/wget/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/wx/package.py b/var/spack/packages/wx/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/wxpropgrid/package.py b/var/spack/packages/wxpropgrid/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/xcb-proto/package.py b/var/spack/packages/xcb-proto/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/xz/package.py b/var/spack/packages/xz/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/yasm/package.py b/var/spack/packages/yasm/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/zeromq/package.py b/var/spack/packages/zeromq/package.py
deleted file mode 100644
index b5a1e3d4cd..0000000000
--- a/var/spack/packages/zeromq/package.py
+++ /dev/null
@@ -1,20 +0,0 @@
-from spack import *
-
-class Zeromq(Package):
-    """ The ZMQ networking/concurrency library and core API """
-    homepage = "http://zguide.zeromq.org/"
-    url      = "http://download.zeromq.org/zeromq-4.1.2.tar.gz"
-
-    version('4.1.2', '159c0c56a895472f02668e692d122685')
-    version('4.1.1', '0a4b44aa085644f25c177f79dc13f253')
-    version('4.0.7', '9b46f7e7b0704b83638ef0d461fd59ab')
-    version('4.0.6', 'd47dd09ed7ae6e7fd6f9a816d7f5fdf6')
-    version('4.0.5', '73c39f5eb01b9d7eaf74a5d899f1d03d')
-
-    depends_on("libsodium")
-
-    def install(self, spec, prefix):
-        configure("--with-libsodium","--prefix=%s" % prefix)
-
-        make()
-        make("install")
diff --git a/var/spack/packages/zlib/package.py b/var/spack/packages/zlib/package.py
old mode 100644
new mode 100755
diff --git a/var/spack/packages/zsh/package.py b/var/spack/packages/zsh/package.py
old mode 100644
new mode 100755