Overhaul Spack's URL parsing (#2972)

* Remove fake URLs from Spack

* Ignore long lines for URLs that start with ftp:

* Preliminary changes to version regexes

* New redesign of version regexes

* Allow letters in version-only

* Fix detection of versions that end in Final

* Rearrange a few regexes and add examples

* Add tests for common download repositories

* Add test cases for common tarball naming schemes

* Finalize version regexes

* spack url test -> spack url summary

* Clean up comments

* Rearrange suffix checks

* Use query strings for name detection

* Remove no longer necessary url_for_version functions

* Strip off extraneous information after package name

* Add one more test

* Dot in square brackets does not need to be escaped

* Move renaming outside of parse_name_offset

* Fix versions for a couple more packages

* Fix flake8 and doc tests

* Correctly parse Python, Lua, and Bio++ package names

* Use effective URLs for mfem

* Add checksummed version to mitos

* Remove url_for_version from STAR-CCM+ package

* Revert changes to version numbers with underscores and dashes

* Fix name detection for tbb

* Correctly parse Ruby gems

* Reverted mfem back to shortened URLs.

* Updated instructions for better security

* Remove preferred=True from newest version

* Add tests for new `spack url list` flags

* Add tests for strip_name_suffixes

* Add unit tests for version separators

* Fix bugs related to parseable name but in parseable version

* Remove dead code, update docstring

* Ignore 'binary' at end of version string

* Remove platform from version

* Flip libedit version numbers

* Re-support weird NCO alpha/beta versions

* Rebase and remove one new fake URL

* Add / to beginning of regex to avoid picking up similarly named packages

* Ignore weird tar versions

* Fix bug in url parse --spider when no versions found

* Less strict version matching for spack versions

* Don't rename Python packages

* Be a little more selective, version must begin with a digit

* Re-add fake URLs

* Fix up several other packages

* Ignore more file endings

* Add parsing support for Miniconda

* Update tab completion

* XFAILS are now PASSES for 2 web tests

65 files changed, 154 insertions, 238 deletions

diff --git a/var/spack/repos/builtin/packages/automake/package.py b/var/spack/repos/builtin/packages/automake/package.py
index 8643f5d836..4f022e5cad 100644
--- a/var/spack/repos/builtin/packages/automake/package.py
+++ b/var/spack/repos/builtin/packages/automake/package.py
@@ -29,7 +29,7 @@ class Automake(AutotoolsPackage):
     """Automake -- make file builder part of autotools"""
 
     homepage = 'http://www.gnu.org/software/automake/'
-    url      = 'http://ftp.gnu.org/gnu/automake/automake-1.14.tar.gz'
+    url      = 'http://ftp.gnu.org/gnu/automake/automake-1.15.tar.gz'
 
     version('1.15',   '716946a105ca228ab545fc37a70df3a3')
     version('1.14.1', 'd052a3e884631b9c7892f2efce542d75')
diff --git a/var/spack/repos/builtin/packages/bib2xhtml/package.py b/var/spack/repos/builtin/packages/bib2xhtml/package.py
index b356038180..56038eea18 100644
--- a/var/spack/repos/builtin/packages/bib2xhtml/package.py
+++ b/var/spack/repos/builtin/packages/bib2xhtml/package.py
@@ -33,9 +33,6 @@ class Bib2xhtml(Package):
 
     version('3.0-15-gf506', 'a26ba02fe0053bbbf2277bdf0acf8645')
 
-    def url_for_version(self, v):
-        return ('http://www.spinellis.gr/sw/textproc/bib2xhtml/bib2xhtml-v%s.tar.gz' % v)
-
     def install(self, spec, prefix):
         # Add the bst include files to the install directory
         bst_include = join_path(prefix.share, 'bib2xhtml')
diff --git a/var/spack/repos/builtin/packages/bison/package.py b/var/spack/repos/builtin/packages/bison/package.py
index 133fcc5fc3..e9bfa32b39 100644
--- a/var/spack/repos/builtin/packages/bison/package.py
+++ b/var/spack/repos/builtin/packages/bison/package.py
@@ -31,7 +31,7 @@ class Bison(AutotoolsPackage):
     generalized LR (GLR) parser employing LALR(1) parser tables."""
 
     homepage = "http://www.gnu.org/software/bison/"
-    url      = "http://ftp.gnu.org/gnu/bison/bison-3.0.tar.gz"
+    url      = "http://ftp.gnu.org/gnu/bison/bison-3.0.4.tar.gz"
 
     version('3.0.4', 'a586e11cd4aff49c3ff6d3b6a4c9ccf8')
     version('2.7',   'ded660799e76fb1667d594de1f7a0da9')
diff --git a/var/spack/repos/builtin/packages/blast-plus/package.py b/var/spack/repos/builtin/packages/blast-plus/package.py
index 02db14f478..53f09c03a3 100644
--- a/var/spack/repos/builtin/packages/blast-plus/package.py
+++ b/var/spack/repos/builtin/packages/blast-plus/package.py
@@ -39,14 +39,9 @@ from spack import *
 class BlastPlus(AutotoolsPackage):
     """Basic Local Alignment Search Tool."""
 
-
     homepage = "http://blast.ncbi.nlm.nih.gov/"
     url      = "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-src.tar.gz"
 
-    def url_for_version(self, version):
-        url = "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/{0}/ncbi-blast-{0}+-src.tar.gz"
-        return url.format(version)
-
     version('2.6.0',  'c8ce8055b10c4d774d995f88c7cc6225')
     version('2.2.30', 'f8e9a5eb368173142fe6867208b73715')
 
diff --git a/var/spack/repos/builtin/packages/boost/package.py b/var/spack/repos/builtin/packages/boost/package.py
index 7570987ad8..06df688ea1 100644
--- a/var/spack/repos/builtin/packages/boost/package.py
+++ b/var/spack/repos/builtin/packages/boost/package.py
@@ -141,14 +141,8 @@ class Boost(Package):
     patch('xl_1_62_0_le.patch', when='@1.62.0%xl')
 
     def url_for_version(self, version):
-        """
-        Handle Boost's weird URLs,
-        which write the version two different ways.
-        """
-        parts = [str(p) for p in Version(version)]
-        dots = ".".join(parts)
-        underscores = "_".join(parts)
-        return "http://downloads.sourceforge.net/project/boost/boost/%s/boost_%s.tar.bz2" % (dots, underscores)
+        url = "http://downloads.sourceforge.net/project/boost/boost/{0}/boost_{1}.tar.bz2"
+        return url.format(version.dotted, version.underscored)
 
     def determine_toolset(self, spec):
         if spec.satisfies("platform=darwin"):
diff --git a/var/spack/repos/builtin/packages/bowtie2/package.py b/var/spack/repos/builtin/packages/bowtie2/package.py
index 6dbcea8dd0..dc850d817f 100644
--- a/var/spack/repos/builtin/packages/bowtie2/package.py
+++ b/var/spack/repos/builtin/packages/bowtie2/package.py
@@ -29,7 +29,10 @@ from glob import glob
 class Bowtie2(Package):
     """Bowtie 2 is an ultrafast and memory-efficient tool for aligning
        sequencing reads to long reference sequences"""
+
     homepage = "bowtie-bio.sourceforge.net/bowtie2/index.shtml"
+    url      = "http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.3.1/bowtie2-2.3.1-source.zip"
+
     version('2.3.1', 'b4efa22612e98e0c23de3d2c9f2f2478')
     version('2.2.5', '51fa97a862d248d7ee660efc1147c75f')
 
@@ -38,10 +41,6 @@ class Bowtie2(Package):
     patch('bowtie2-2.2.5.patch', when='@2.2.5', level=0)
     patch('bowtie2-2.3.1.patch', when='@2.3.1', level=0)
 
-    def url_for_version(self, version):
-        url="http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/{0}/bowtie2-{0}-source.zip"
-        return url.format(version)
-
     def install(self, spec, prefix):
         make()
         mkdirp(prefix.bin)
diff --git a/var/spack/repos/builtin/packages/cddlib/package.py b/var/spack/repos/builtin/packages/cddlib/package.py
index 50dc5ad472..002c302599 100644
--- a/var/spack/repos/builtin/packages/cddlib/package.py
+++ b/var/spack/repos/builtin/packages/cddlib/package.py
@@ -31,19 +31,9 @@ class Cddlib(AutotoolsPackage):
     Method of Motzkin et al. for generating all vertices (i.e. extreme points)
     and extreme rays of a general convex polyhedron in R^d given by a system
     of linear inequalities"""
-    homepage = "https://www.inf.ethz.ch/personal/fukudak/cdd_home/"
-    # This is the original download url. It is currently down [2016-08-23],
-    # but should be reinstated or updated once the issue is resolved.
-    # url = "ftp://ftp.ifor.math.ethz.ch/pub/fukuda/cdd/cddlib-094h.tar.gz"
-    url = "http://pkgs.fedoraproject.org/lookaside/pkgs/cddlib/cddlib-094h.tar.gz/1467d270860bbcb26d3ebae424690e7c/cddlib-094h.tar.gz"
 
-    def url_for_version(self, version):
-        # Since the commit id is part of the version, we can't
-        # auto-generate the string, and we need to explicitly list all
-        # known versions here. Currently, there is only one version.
-        if str(version) == '0.94h':
-            return "http://pkgs.fedoraproject.org/lookaside/pkgs/cddlib/cddlib-094h.tar.gz/1467d270860bbcb26d3ebae424690e7c/cddlib-094h.tar.gz"
-        raise InstallError("Unsupported version %s" % str(version))
+    homepage = "https://www.inf.ethz.ch/personal/fukudak/cdd_home/"
+    url      = "ftp://ftp.math.ethz.ch/users/fukudak/cdd/cddlib-094h.tar.gz"
 
     version('0.94h', '1467d270860bbcb26d3ebae424690e7c')
 
@@ -51,3 +41,7 @@ class Cddlib(AutotoolsPackage):
 
     depends_on("gmp")
     depends_on("libtool", type="build")
+
+    def url_for_version(self, version):
+        url = "ftp://ftp.math.ethz.ch/users/fukudak/cdd/cddlib-{0}.tar.gz"
+        return url.format(version.joined)
diff --git a/var/spack/repos/builtin/packages/cdo/package.py b/var/spack/repos/builtin/packages/cdo/package.py
index 775dc31cf3..90039d4479 100644
--- a/var/spack/repos/builtin/packages/cdo/package.py
+++ b/var/spack/repos/builtin/packages/cdo/package.py
@@ -30,9 +30,13 @@ class Cdo(Package):
     Climate and NWP model Data. """
 
     homepage = "https://code.zmaw.de/projects/cdo"
+    url      = "https://code.zmaw.de/attachments/download/12760/cdo-1.7.2.tar.gz"
+    list_url = "https://code.zmaw.de/projects/cdo/files"
 
-    version('1.7.2', 'f08e4ce8739a4f2b63fc81a24db3ee31', url='https://code.zmaw.de/attachments/download/12760/cdo-1.7.2.tar.gz')
-    version('1.6.9', 'bf0997bf20e812f35e10188a930e24e2', url='https://code.zmaw.de/attachments/download/10198/cdo-1.6.9.tar.gz')
+    version('1.7.2', 'f08e4ce8739a4f2b63fc81a24db3ee31',
+            url='https://code.zmaw.de/attachments/download/12760/cdo-1.7.2.tar.gz')
+    version('1.6.9', 'bf0997bf20e812f35e10188a930e24e2',
+            url='https://code.zmaw.de/attachments/download/10198/cdo-1.6.9.tar.gz')
 
     variant('szip', default=True, description='Enable szip compression for GRIB1')
     variant('hdf5', default=False, description='Enable HDF5 support')
@@ -54,7 +58,7 @@ class Cdo(Package):
     depends_on('proj', when='+proj')
     depends_on('curl', when='+curl')
     depends_on('fftw', when='+fftw')
-    depends_on('magics', when='+magics') 
+    depends_on('magics', when='+magics')
 
     def install(self, spec, prefix):
         config_args = ["--prefix=" + prefix,
diff --git a/var/spack/repos/builtin/packages/cfitsio/package.py b/var/spack/repos/builtin/packages/cfitsio/package.py
index 811b3ca9bc..b382f87f5b 100644
--- a/var/spack/repos/builtin/packages/cfitsio/package.py
+++ b/var/spack/repos/builtin/packages/cfitsio/package.py
@@ -31,6 +31,7 @@ class Cfitsio(AutotoolsPackage):
     """
 
     homepage = 'http://heasarc.gsfc.nasa.gov/fitsio/'
+    url      = 'http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/cfitsio3410.tar.gz'
 
     version('3.410', '8a4a66fcdd816aae41768baa0b025552')
     version('3.370', 'abebd2d02ba5b0503c633581e3bfa116')
diff --git a/var/spack/repos/builtin/packages/cppad/package.py b/var/spack/repos/builtin/packages/cppad/package.py
index 1ec31bbeef..e17a070294 100644
--- a/var/spack/repos/builtin/packages/cppad/package.py
+++ b/var/spack/repos/builtin/packages/cppad/package.py
@@ -29,16 +29,13 @@ class Cppad(CMakePackage):
     """A Package for Differentiation of C++ Algorithms."""
 
     homepage = "https://www.coin-or.org/CppAD/"
+    url      = "http://www.coin-or.org/download/source/CppAD/cppad-20170114.gpl.tgz"
 
     version('20170114', '565a534dc813fa1289764222cd8c11ea')
     version('develop', git='https://github.com/coin-or/CppAD.git')
 
     depends_on('cmake', type='build')
 
-    def url_for_version(self, version):
-        """Handle version-based custom URLs."""
-        return "http://www.coin-or.org/download/source/CppAD/cppad-%s.gpl.tgz" % (version)
-
     def cmake_args(self):
         # This package does not obey CMAKE_INSTALL_PREFIX
         args = [
diff --git a/var/spack/repos/builtin/packages/cryptopp/package.py b/var/spack/repos/builtin/packages/cryptopp/package.py
index c92f262a9a..142bd4f253 100644
--- a/var/spack/repos/builtin/packages/cryptopp/package.py
+++ b/var/spack/repos/builtin/packages/cryptopp/package.py
@@ -36,6 +36,7 @@ class Cryptopp(Package):
     """
 
     homepage = "http://www.cryptopp.com"
+    url      = "http://www.cryptopp.com/cryptopp563.zip"
 
     version('5.6.3', '3c5b70e2ec98b7a24988734446242d07')
     version('5.6.2', '7ed022585698df48e65ce9218f6c6a67')
diff --git a/var/spack/repos/builtin/packages/dakota/package.py b/var/spack/repos/builtin/packages/dakota/package.py
index e8f7d0889b..c40229f83b 100644
--- a/var/spack/repos/builtin/packages/dakota/package.py
+++ b/var/spack/repos/builtin/packages/dakota/package.py
@@ -46,7 +46,6 @@ class Dakota(Package):
 
     homepage = 'https://dakota.sandia.gov/'
     url = 'https://dakota.sandia.gov/sites/default/files/distributions/public/dakota-6.3-public.src.tar.gz'
-    _url_str = 'https://dakota.sandia.gov/sites/default/files/distributions/public/dakota-{version}-public.src.tar.gz'
 
     version('6.3', '05a58d209fae604af234c894c3f73f6d')
 
@@ -64,9 +63,6 @@ class Dakota(Package):
     depends_on('boost')
     depends_on('cmake', type='build')
 
-    def url_for_version(self, version):
-        return Dakota._url_str.format(version=version)
-
     def install(self, spec, prefix):
         options = []
         options.extend(std_cmake_args)
diff --git a/var/spack/repos/builtin/packages/exonerate/package.py b/var/spack/repos/builtin/packages/exonerate/package.py
index 7921e64058..2615d859d6 100644
--- a/var/spack/repos/builtin/packages/exonerate/package.py
+++ b/var/spack/repos/builtin/packages/exonerate/package.py
@@ -29,7 +29,7 @@ class Exonerate(Package):
     """Pairwise sequence alignment of DNA and proteins"""
 
     homepage = "http://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate"
-    url      = "http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/exonerate-2.2.0.tar.gz"
+    url      = "http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/exonerate-2.4.0.tar.gz"
 
     version('2.4.0', '126fbade003b80b663a1d530c56f1904')
 
diff --git a/var/spack/repos/builtin/packages/ferret/package.py b/var/spack/repos/builtin/packages/ferret/package.py
index 15ddfcee16..4dcff54b8f 100644
--- a/var/spack/repos/builtin/packages/ferret/package.py
+++ b/var/spack/repos/builtin/packages/ferret/package.py
@@ -31,11 +31,10 @@ class Ferret(Package):
     """Ferret is an interactive computer visualization and analysis environment
        designed to meet the needs of oceanographers and meteorologists
        analyzing large and complex gridded data sets."""
-    homepage = "http://ferret.noaa.gov/Ferret/"
-    url      = "ftp://ftp.pmel.noaa.gov/ferret/pub/source/fer_source.tar.gz"
+    homepage = "http://ferret.pmel.noaa.gov/Ferret/home"
+    url      = "ftp://ftp.pmel.noaa.gov/ferret/pub/source/fer_source.v696.tar.gz"
 
-    version('6.96', '51722027c864369f41bab5751dfff8cc',
-            url="ftp://ftp.pmel.noaa.gov/ferret/pub/source/fer_source.tar.gz")
+    version('6.96', '51722027c864369f41bab5751dfff8cc')
 
     depends_on("hdf5~mpi~fortran")
     depends_on("netcdf~mpi")
@@ -43,6 +42,10 @@ class Ferret(Package):
     depends_on("readline")
     depends_on("zlib")
 
+    def url_for_version(self, version):
+        return "ftp://ftp.pmel.noaa.gov/ferret/pub/source/fer_source.v{0}.tar.gz".format(
+            version.joined)
+
     def patch(self):
         hdf5_prefix = self.spec['hdf5'].prefix
         netcdff_prefix = self.spec['netcdf-fortran'].prefix
diff --git a/var/spack/repos/builtin/packages/gdk-pixbuf/package.py b/var/spack/repos/builtin/packages/gdk-pixbuf/package.py
index 1159744721..2f3a0b0bd7 100644
--- a/var/spack/repos/builtin/packages/gdk-pixbuf/package.py
+++ b/var/spack/repos/builtin/packages/gdk-pixbuf/package.py
@@ -32,7 +32,9 @@ class GdkPixbuf(AutotoolsPackage):
        GTK+ 2 but it was split off into a separate package in
        preparation for the change to GTK+ 3."""
     homepage = "https://developer.gnome.org/gdk-pixbuf/"
-    url      = "http://ftp.gnome.org/pub/gnome/sources/gdk-pixbuf/2.31/gdk-pixbuf-2.31.1.tar.xz"
+    url      = "http://ftp.gnome.org/pub/gnome/sources/gdk-pixbuf/2.31/gdk-pixbuf-2.31.2.tar.xz"
+    list_url = "http://ftp.acc.umu.se/pub/gnome/sources/gdk-pixbuf/"
+    list_depth = 2
 
     version('2.31.2', '6be6bbc4f356d4b79ab4226860ab8523')
 
diff --git a/var/spack/repos/builtin/packages/go/package.py b/var/spack/repos/builtin/packages/go/package.py
index 6559e90496..c095140c68 100644
--- a/var/spack/repos/builtin/packages/go/package.py
+++ b/var/spack/repos/builtin/packages/go/package.py
@@ -89,13 +89,6 @@ class Go(Package):
             r'# \1\2\3',
         )
 
-    @when('@1.5.0:')
-    def patch(self):
-        pass
-
-    def url_for_version(self, version):
-        return "https://storage.googleapis.com/golang/go{0}.src.tar.gz".format(version)
-
     def install(self, spec, prefix):
         bash = which('bash')
         with working_dir('src'):
diff --git a/var/spack/repos/builtin/packages/gource/package.py b/var/spack/repos/builtin/packages/gource/package.py
index 21994ad42c..7d12697d63 100644
--- a/var/spack/repos/builtin/packages/gource/package.py
+++ b/var/spack/repos/builtin/packages/gource/package.py
@@ -52,10 +52,6 @@ class Gource(AutotoolsPackage):
     parallel = False
     force_autoreconf = True
 
-    def url_for_version(self, version):
-        tmp = 'https://github.com/acaudwell/Gource/releases/download/gource-{0}/gource-{0}.tar.gz'  # NOQA: ignore=E501
-        return tmp.format(version.dotted)
-
     def configure_args(self):
         spec = self.spec
         return [
diff --git a/var/spack/repos/builtin/packages/ibmisc/package.py b/var/spack/repos/builtin/packages/ibmisc/package.py
index f325205507..181ae6d92b 100644
--- a/var/spack/repos/builtin/packages/ibmisc/package.py
+++ b/var/spack/repos/builtin/packages/ibmisc/package.py
@@ -29,9 +29,9 @@ class Ibmisc(CMakePackage):
     """Misc. reusable utilities used by IceBin."""
 
     homepage = "https://github.com/citibeth/ibmisc"
-    url      = "https://github.com/citibeth/ibmisc/tarball/123"
+    url      = "https://github.com/citibeth/ibmisc/archive/v0.1.0.tar.gz"
 
-    version('0.1.0', '12f2a32432a11db48e00217df18e59fa')
+    version('0.1.0', '18c63db3e466c5a6fc2db3f903d06ecb')
 
     variant('everytrace', default=False,
             description='Report errors through Everytrace')
diff --git a/var/spack/repos/builtin/packages/icet/package.py b/var/spack/repos/builtin/packages/icet/package.py
index f8260f1951..ca3251ac40 100644
--- a/var/spack/repos/builtin/packages/icet/package.py
+++ b/var/spack/repos/builtin/packages/icet/package.py
@@ -30,7 +30,7 @@ class Icet(CMakePackage):
        sort-last parallel rendering library."""
 
     homepage = "http://icet.sandia.gov"
-    url = "https://example.com/icet-1.2.3.tar.gz"
+    url      = "https://gitlab.kitware.com/icet/icet/repository/archive.tar.bz2?ref=IceT-2.1.1"
 
     version('develop', branch='master',
             git='https://gitlab.kitware.com/icet/icet.git')
@@ -38,9 +38,5 @@ class Icet(CMakePackage):
 
     depends_on('mpi')
 
-    def url_for_version(self, version):
-        return ("https://gitlab.kitware.com/icet/icet/repository/"
-                "archive.tar.bz2?ref=IceT-{0}".format(version.dotted))
-
     def cmake_args(self):
         return ['-DICET_USE_OPENGL:BOOL=OFF']
diff --git a/var/spack/repos/builtin/packages/image-magick/package.py b/var/spack/repos/builtin/packages/image-magick/package.py
index 9efb0cd368..e32f1967e2 100644
--- a/var/spack/repos/builtin/packages/image-magick/package.py
+++ b/var/spack/repos/builtin/packages/image-magick/package.py
@@ -45,9 +45,6 @@ class ImageMagick(Package):
     depends_on('ghostscript')
     depends_on('ghostscript-fonts')
 
-    def url_for_version(self, version):
-        return "https://github.com/ImageMagick/ImageMagick/archive/{0}.tar.gz".format(version)
-
     def install(self, spec, prefix):
         gs_font_dir = join_path(spec['ghostscript-fonts'].prefix.share, "font")
         configure('--prefix={0}'.format(prefix),
diff --git a/var/spack/repos/builtin/packages/jdk/package.py b/var/spack/repos/builtin/packages/jdk/package.py
index 518a469435..8df01f4b67 100644
--- a/var/spack/repos/builtin/packages/jdk/package.py
+++ b/var/spack/repos/builtin/packages/jdk/package.py
@@ -45,10 +45,10 @@ class Jdk(Package):
         '-H',  # specify required License Agreement cookie
         'Cookie: oraclelicense=accept-securebackup-cookie']
 
-    version('8u66-linux-x64', '88f31f3d642c3287134297b8c10e61bf',
+    version('8u66', '88f31f3d642c3287134297b8c10e61bf',
             url="http://download.oracle.com/otn-pub/java/jdk/8u66-b17/jdk-8u66-linux-x64.tar.gz",
             curl_options=curl_options)
-    version('8u92-linux-x64', '65a1cc17ea362453a6e0eb4f13be76e4',
+    version('8u92', '65a1cc17ea362453a6e0eb4f13be76e4',
             url="http://download.oracle.com/otn-pub/java/jdk/8u92-b14/jdk-8u92-linux-x64.tar.gz",
             curl_options=curl_options)
 
diff --git a/var/spack/repos/builtin/packages/libedit/package.py b/var/spack/repos/builtin/packages/libedit/package.py
index 5dcee61cab..6887d67101 100644
--- a/var/spack/repos/builtin/packages/libedit/package.py
+++ b/var/spack/repos/builtin/packages/libedit/package.py
@@ -30,7 +30,11 @@ class Libedit(AutotoolsPackage):
     homepage = "http://thrysoee.dk/editline/"
     url      = "http://thrysoee.dk/editline/libedit-20150325-3.1.tar.gz"
 
-    version('3.1', '43cdb5df3061d78b5e9d59109871b4f6',
-            url="http://thrysoee.dk/editline/libedit-20150325-3.1.tar.gz")
+    version('3.1-20160903', '0467d27684c453a351fbcefebbcb16a3')
+    version('3.1-20150325', '43cdb5df3061d78b5e9d59109871b4f6')
 
     depends_on('ncurses')
+
+    def url_for_version(self, version):
+        url = "http://thrysoee.dk/editline/libedit-{0}-{1}.tar.gz"
+        return url.format(version[-1], version.up_to(-1))
diff --git a/var/spack/repos/builtin/packages/libgd/package.py b/var/spack/repos/builtin/packages/libgd/package.py
index adce0b7515..c70d8b56fd 100644
--- a/var/spack/repos/builtin/packages/libgd/package.py
+++ b/var/spack/repos/builtin/packages/libgd/package.py
@@ -56,7 +56,3 @@ class Libgd(AutotoolsPackage):
     depends_on('libpng')
     depends_on('libtiff')
     depends_on('fontconfig')
-
-    def url_for_version(self, version):
-        url = "https://github.com/libgd/libgd/releases/download/gd-{0}/libgd-{0}.tar.gz"
-        return url.format(version)
diff --git a/var/spack/repos/builtin/packages/libsodium/package.py b/var/spack/repos/builtin/packages/libsodium/package.py
index a7e3ab10ae..6d21d65345 100644
--- a/var/spack/repos/builtin/packages/libsodium/package.py
+++ b/var/spack/repos/builtin/packages/libsodium/package.py
@@ -30,6 +30,7 @@ class Libsodium(AutotoolsPackage):
     decryption, signatures, password hashing and more."""
     homepage = "https://download.libsodium.org/doc/"
     url      = "https://download.libsodium.org/libsodium/releases/libsodium-1.0.11.tar.gz"
+    list_url = "https://download.libsodium.org/libsodium/releases/old"
 
     version('1.0.11', 'b58928d035064b2a46fb564937b83540')
     version('1.0.10', 'ea89dcbbda0b2b6ff6a1c476231870dd')
diff --git a/var/spack/repos/builtin/packages/libxstream/package.py b/var/spack/repos/builtin/packages/libxstream/package.py
index 3201b58620..0996e6b9e8 100644
--- a/var/spack/repos/builtin/packages/libxstream/package.py
+++ b/var/spack/repos/builtin/packages/libxstream/package.py
@@ -31,9 +31,9 @@ class Libxstream(Package):
     conditions.'''
 
     homepage = 'https://github.com/hfp/libxstream'
-    url      = 'https://github.com/hfp/libxstream.git'
+    url      = 'https://github.com/hfp/libxstream/archive/0.9.0.tar.gz'
 
-    version('0.9.0', git='https://github.com/hfp/libxstream.git')
+    version('0.9.0', 'fd74b7cf5f145ff4925d91be2809571c')
 
     def patch(self):
         kwargs = {'ignore_absent': False, 'backup': True, 'string': True}
diff --git a/var/spack/repos/builtin/packages/meep/package.py b/var/spack/repos/builtin/packages/meep/package.py
index 2c1018e711..00b9c4ea09 100644
--- a/var/spack/repos/builtin/packages/meep/package.py
+++ b/var/spack/repos/builtin/packages/meep/package.py
@@ -30,6 +30,8 @@ class Meep(Package):
     software package developed at MIT to model electromagnetic systems."""
 
     homepage = "http://ab-initio.mit.edu/wiki/index.php/Meep"
+    url      = "http://ab-initio.mit.edu/meep/meep-1.3.tar.gz"
+    list_url = "http://ab-initio.mit.edu/meep/old"
 
     version('1.3',   '18a5b9e18008627a0411087e0bb60db5')
     version('1.2.1', '9be2e743c3a832ae922de9d955d016c5')
diff --git a/var/spack/repos/builtin/packages/metis/package.py b/var/spack/repos/builtin/packages/metis/package.py
index f15d544b7b..c927c22a1b 100644
--- a/var/spack/repos/builtin/packages/metis/package.py
+++ b/var/spack/repos/builtin/packages/metis/package.py
@@ -37,7 +37,8 @@ class Metis(Package):
        partitioning schemes."""
 
     homepage = "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview"
-    base_url = "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis"
+    url      = "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz"
+    list_url = "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD"
 
     version('5.1.0', '5465e67079419a69e0116de24fce58fe')
     version('5.0.2', 'acb521a4e8c2e6dd559a7f9abd0468c5')
@@ -55,12 +56,11 @@ class Metis(Package):
     patch('install_gklib_defs_rename.patch', when='@5:')
 
     def url_for_version(self, version):
-        verdir = 'OLD/' if version < Version('4.0.3') else ''
-        return '%s/%smetis-%s.tar.gz' % (Metis.base_url, verdir, version)
-
-    @when('@:4')
-    def patch(self):
-        pass
+        url = "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis"
+        if version < Version('4.0.3'):
+            url += "/OLD"
+        url += "/metis-{0}.tar.gz".format(version)
+        return url
 
     @when('@5:')
     def patch(self):
@@ -84,7 +84,7 @@ class Metis(Package):
             filter_file('#define MAX_JBUFS 128', '#define MAX_JBUFS 24',
                         join_path(source_path, 'GKlib', 'error.c'))
 
-    @when('@:4')
+    @when('@:4')  # noqa: F811
     def install(self, spec, prefix):
         # Process library spec and options
         if any('+{0}'.format(v) in spec for v in ['gdb', 'int64', 'real64']):
@@ -175,7 +175,7 @@ class Metis(Package):
             Executable(test_bin('mesh2dual'))(test_graph('metis.mesh'))
             """
 
-    @when('@5:')
+    @when('@5:')  # noqa: F811
     def install(self, spec, prefix):
         source_directory = self.stage.source_path
         build_directory = join_path(source_directory, 'build')
@@ -187,7 +187,7 @@ class Metis(Package):
         if '+shared' in spec:
             options.append('-DSHARED:BOOL=ON')
         else:
-            # Remove all RPATH options 
+            # Remove all RPATH options
             # (RPATHxxx options somehow trigger cmake to link dynamically)
             rpath_options = []
             for o in options:
diff --git a/var/spack/repos/builtin/packages/mfem/package.py b/var/spack/repos/builtin/packages/mfem/package.py
index a25583e164..b3fe5197a0 100644
--- a/var/spack/repos/builtin/packages/mfem/package.py
+++ b/var/spack/repos/builtin/packages/mfem/package.py
@@ -31,15 +31,32 @@ class Mfem(Package):
     homepage = 'http://www.mfem.org'
     url      = 'https://github.com/mfem/mfem'
 
+    # mfem is downloaded from a URL shortener at request of upstream
+    # author Tzanio Kolev <tzanio@llnl.gov>.  See here:
+    #     https://github.com/mfem/mfem/issues/53
+    #
+    # The following procedure should be used to verify security when a
+    # new verison is added:
+    #
+    # 1. Verify that no checksums on old versions have changed.
+    #
+    # 2. Verify that the shortened URL for the new version is listed at:
+    #    http://mfem.org/download/
+    #
+    # 3. Use http://getlinkinfo.com or similar to verify that the
+    #    underling download link for the latest version comes has the
+    #    prefix: http://mfem.github.io/releases
+    #
+    # If this quick verification procedure fails, additional discussion
+    # will be required to verify the new version.
+
     version('3.2',
             '2938c3deed4ec4f7fd5b5f5cfe656845282e86e2dcd477d292390058b7b94340',
-            url='http://goo.gl/Y9T75B', preferred=True, extension='.tar.gz')
+            url='http://goo.gl/Y9T75B', extension='.tar.gz')
 
     version('3.1',
             '841ea5cf58de6fae4de0f553b0e01ebaab9cd9c67fa821e8a715666ecf18fc57',
             url='http://goo.gl/xrScXn', extension='.tar.gz')
-#    version('3.1', git='https://github.com/mfem/mfem.git',
-#            commit='dbae60fe32e071989b52efaaf59d7d0eb2a3b574')
 
     variant('metis', default=False, description='Activate support for metis')
     variant('hypre', default=False, description='Activate support for hypre')
diff --git a/var/spack/repos/builtin/packages/mitos/package.py b/var/spack/repos/builtin/packages/mitos/package.py
index d577a1b285..4ccddb3592 100644
--- a/var/spack/repos/builtin/packages/mitos/package.py
+++ b/var/spack/repos/builtin/packages/mitos/package.py
@@ -30,13 +30,12 @@ class Mitos(Package):
     performance data to view with MemAxes"""
 
     homepage = "https://github.com/llnl/Mitos"
-    url = "https://github.com/llnl/Mitos"
+    url      = "https://github.com/LLNL/Mitos/archive/v0.9.1.tar.gz"
 
     version('0.9.2',
             git='https://github.com/llnl/Mitos.git',
             commit='8cb143a2e8c00353ff531a781a9ca0992b0aaa3d')
-
-    version('0.9.1', git='https://github.com/llnl/Mitos.git', tag='v0.9.1')
+    version('0.9.1', 'c6cb57f3cae54f5157affd97ef7ef79e')
 
     depends_on('dyninst@8.2.1:')
     depends_on('hwloc')
diff --git a/var/spack/repos/builtin/packages/moab/package.py b/var/spack/repos/builtin/packages/moab/package.py
index b783d7b81b..14925cfd3e 100644
--- a/var/spack/repos/builtin/packages/moab/package.py
+++ b/var/spack/repos/builtin/packages/moab/package.py
@@ -35,7 +35,7 @@ class Moab(Package):
     mesh in chunks rather than through individual entities, while also
     versatile enough to support individual entity access."""
     homepage = "https://bitbucket.org/fathomteam/moab"
-    url      = "http://ftp.mcs.anl.gov/pub/fathom/moab-4.6.3.tar.gz"
+    url      = "http://ftp.mcs.anl.gov/pub/fathom/moab-4.9.1.tar.gz"
 
     version('4.9.1', '19cc2189fa266181ad9109b18d0b2ab8')
     version('4.9.0', '40695d0a159040683cfa05586ad4a7c2')
diff --git a/var/spack/repos/builtin/packages/mxml/package.py b/var/spack/repos/builtin/packages/mxml/package.py
index cd53c67dff..435fd748b3 100644
--- a/var/spack/repos/builtin/packages/mxml/package.py
+++ b/var/spack/repos/builtin/packages/mxml/package.py
@@ -41,9 +41,6 @@ class Mxml(AutotoolsPackage):
     version('2.6', '68977789ae64985dddbd1a1a1652642e')
     version('2.5', 'f706377fba630b39fa02fd63642b17e5')
 
-    def url_for_version(self, version):
-        return "https://github.com/michaelrsweet/mxml/releases/download/release-{0}/mxml-{0}.tar.gz".format(version)
-
     # module swap PrgEnv-intel PrgEnv-$COMP
     # (Can use whatever compiler you want to use)
     # Case statement to change CC and CXX flags
diff --git a/var/spack/repos/builtin/packages/nettle/package.py b/var/spack/repos/builtin/packages/nettle/package.py
index 2b6693a18c..e9df8489c9 100644
--- a/var/spack/repos/builtin/packages/nettle/package.py
+++ b/var/spack/repos/builtin/packages/nettle/package.py
@@ -30,7 +30,7 @@ class Nettle(AutotoolsPackage):
     that is designed to fit easily in many contexts."""
 
     homepage = "https://www.lysator.liu.se/~nisse/nettle/"
-    url      = "http://ftp.gnu.org/gnu/nettle/nettle-2.7.1.tar.gz"
+    url      = "http://ftp.gnu.org/gnu/nettle/nettle-3.2.tar.gz"
 
     version('3.2',   'afb15b4764ebf1b4e6d06c62bd4d29e4')
     version('2.7.1', '003d5147911317931dd453520eb234a5')
diff --git a/var/spack/repos/builtin/packages/nextflow/package.py b/var/spack/repos/builtin/packages/nextflow/package.py
index 563ecd9b40..05f21f70b7 100644
--- a/var/spack/repos/builtin/packages/nextflow/package.py
+++ b/var/spack/repos/builtin/packages/nextflow/package.py
@@ -29,6 +29,7 @@ class Nextflow(Package):
     """Data-driven computational pipelines"""
 
     homepage = "http://www.nextflow.io"
+    url      = "https://github.com/nextflow-io/nextflow/releases/download/v0.24.1/nextflow"
 
     version('0.24.1', '80ec8c4fe8e766e0bdd1371a50410d1d',
             expand=False)
@@ -39,10 +40,6 @@ class Nextflow(Package):
 
     depends_on('jdk')
 
-    def url_for_version(self, version):
-        base_url = 'https://github.com/nextflow-io/nextflow/releases/download/v{0}/nextflow'
-        return base_url.format(version)
-
     def install(self, spec, prefix):
         mkdirp(prefix.bin)
         install("nextflow", join_path(prefix.bin, "nextflow"))
diff --git a/var/spack/repos/builtin/packages/oce/package.py b/var/spack/repos/builtin/packages/oce/package.py
index c3488c137a..950621da40 100644
--- a/var/spack/repos/builtin/packages/oce/package.py
+++ b/var/spack/repos/builtin/packages/oce/package.py
@@ -32,6 +32,7 @@ class Oce(Package):
     Open CASCADE library.
     """
     homepage = "https://github.com/tpaviot/oce"
+    url      = "https://github.com/tpaviot/oce/archive/OCE-0.18.tar.gz"
 
     version('0.18',   '226e45e77c16a4a6e127c71fefcd171410703960ae75c7ecc7eb68895446a993')
     version('0.17.2', 'bf2226be4cd192606af677cf178088e5')
@@ -46,10 +47,6 @@ class Oce(Package):
     depends_on('cmake@2.8:', type='build')
     depends_on('tbb', when='+tbb')
 
-    def url_for_version(self, version):
-        return 'https://github.com/tpaviot/oce/archive/OCE-%s.tar.gz' % (
-            version.dotted)
-
     # There is a bug in OCE which appears with Clang (version?) or GCC 6.0
     # and has to do with compiler optimization, see
     # https://github.com/tpaviot/oce/issues/576
diff --git a/var/spack/repos/builtin/packages/octopus/package.py b/var/spack/repos/builtin/packages/octopus/package.py
index 88350f50bc..8999b081e3 100644
--- a/var/spack/repos/builtin/packages/octopus/package.py
+++ b/var/spack/repos/builtin/packages/octopus/package.py
@@ -30,17 +30,11 @@ class Octopus(Package):
     theory code."""
 
     homepage = "http://www.tddft.org/programs/octopus/"
-    base_url = "http://www.tddft.org/programs/octopus/down.php?file="
+    url      = "http://www.tddft.org/programs/octopus/down.php?file=6.0/octopus-6.0.tar.gz"
 
     version('6.0', '5d1168c2a8d7fd9cb9492eaebaa7182e')
     version('5.0.1', '2b6392ab67b843f9d4ca7413fc07e822')
 
-    # Sample url is:
-    # "http://www.tddft.org/programs/octopus/down.php?file=5.0.1/octopus-5.0.1.tar.gz"
-    def url_for_version(self, version):
-        return '{0}/{1}/octopus-{1}.tar.gz'.format(Octopus.base_url,
-                                                   version.dotted)
-
     variant('scalapack', default=False,
             description='Compile with Scalapack')
     variant('metis', default=True,
diff --git a/var/spack/repos/builtin/packages/openjpeg/package.py b/var/spack/repos/builtin/packages/openjpeg/package.py
index 9790c52e7d..b22de4452a 100644
--- a/var/spack/repos/builtin/packages/openjpeg/package.py
+++ b/var/spack/repos/builtin/packages/openjpeg/package.py
@@ -43,7 +43,3 @@ class Openjpeg(CMakePackage):
     version('2.0',   'cdf266530fee8af87454f15feb619609')
     version('1.5.2', '545f98923430369a6b046ef3632ef95c')
     version('1.5.1', 'd774e4b5a0db5f0f171c4fc0aabfa14e')
-
-    def url_for_version(self, version):
-        fmt = 'https://github.com/uclouvain/openjpeg/archive/version.{0}.tar.gz'
-        return fmt.format(version.dotted)
diff --git a/var/spack/repos/builtin/packages/panda/package.py b/var/spack/repos/builtin/packages/panda/package.py
index e30c2c869d..fb14bd5643 100644
--- a/var/spack/repos/builtin/packages/panda/package.py
+++ b/var/spack/repos/builtin/packages/panda/package.py
@@ -29,9 +29,9 @@ from spack import *
 class Panda(Package):
     """PANDA: Parallel AdjaceNcy Decomposition Algorithm"""
     homepage = "http://comopt.ifi.uni-heidelberg.de/software/PANDA/index.html"
-    url      = "http://comopt.ifi.uni-heidelberg.de/software/PANDA/downloads/current_panda.tar"
+    url      = "http://comopt.ifi.uni-heidelberg.de/software/PANDA/downloads/panda-2016-03-07.tar"
 
-    version('current', 'b06dc312ee56e13eefea9c915b70fcef')
+    version('2016-03-07', 'b06dc312ee56e13eefea9c915b70fcef')
 
     # Note: Panda can also be built without MPI support
 
diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py
index 0e6cd5390a..b07c796dd7 100644
--- a/var/spack/repos/builtin/packages/parmetis/package.py
+++ b/var/spack/repos/builtin/packages/parmetis/package.py
@@ -33,7 +33,8 @@ class Parmetis(Package):
        computing fill-reducing orderings of sparse matrices."""
 
     homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview'
-    base_url = 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis'
+    url      = 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/parmetis-4.0.3.tar.gz'
+    list_url = 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD'
 
     version('4.0.3', 'f69c479586bf6bb7aff6a9bc0c739628')
     version('4.0.2', '0912a953da5bb9b5e5e10542298ffdce')
@@ -54,8 +55,11 @@ class Parmetis(Package):
     patch('pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch')
 
     def url_for_version(self, version):
-        verdir = 'OLD/' if version < Version('3.2.0') else ''
-        return '%s/%sparmetis-%s.tar.gz' % (Parmetis.base_url, verdir, version)
+        url = 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis'
+        if version < Version('3.2.0'):
+            url += '/OLD'
+        url += '/parmetis-{0}.tar.gz'.format(version)
+        return url
 
     def install(self, spec, prefix):
         source_directory = self.stage.source_path
@@ -72,7 +76,7 @@ class Parmetis(Package):
         if '+shared' in spec:
             options.append('-DSHARED:BOOL=ON')
         else:
-            # Remove all RPATH options 
+            # Remove all RPATH options
             # (RPATHxxx options somehow trigger cmake to link dynamically)
             rpath_options = []
             for o in options:
diff --git a/var/spack/repos/builtin/packages/prank/package.py b/var/spack/repos/builtin/packages/prank/package.py
index d627e8a0b6..09b73e795f 100644
--- a/var/spack/repos/builtin/packages/prank/package.py
+++ b/var/spack/repos/builtin/packages/prank/package.py
@@ -29,7 +29,7 @@ class Prank(Package):
     """A powerful multiple sequence alignment browser."""
 
     homepage = "http://wasabiapp.org/software/prank/"
-    url      = "http://wasabiapp.org/download/prank/prank.source.140603.tgz"
+    url      = "http://wasabiapp.org/download/prank/prank.source.150803.tgz"
 
     version('150803', '71ac2659e91c385c96473712c0a23e8a')
 
diff --git a/var/spack/repos/builtin/packages/py-autopep8/package.py b/var/spack/repos/builtin/packages/py-autopep8/package.py
index c892e2979c..6c92def415 100644
--- a/var/spack/repos/builtin/packages/py-autopep8/package.py
+++ b/var/spack/repos/builtin/packages/py-autopep8/package.py
@@ -30,10 +30,10 @@ class PyAutopep8(PythonPackage):
     PEP 8 style guide."""
 
     homepage = "https://github.com/hhatto/autopep8"
-    url      = "https://github.com/hhatto/autopep8/archive/v1.2.4.tar.gz"
+    url      = "https://pypi.io/packages/source/a/autopep8/autopep8-1.2.4.tar.gz"
 
-    version('1.2.4', '0458db85159a9e1b45f3e71ce6c158da')
-    version('1.2.2', 'def3d023fc9dfd1b7113602e965ad8e1')
+    version('1.2.4', 'fcea19c0c5e505b425e2a78afb771f5c')
+    version('1.2.2', '3d97f9c89d14a0975bffd32a2c61c36c')
 
     extends('python', ignore='bin/pep8')
     depends_on('python@2.6:2.7,3.2:')
@@ -41,10 +41,3 @@ class PyAutopep8(PythonPackage):
     depends_on('py-pycodestyle@1.5.7:1.7.0', type=('build', 'run'))
 
     depends_on('py-setuptools', type='build')
-
-    def url_for_version(self, version):
-        url = "https://github.com/hhatto/autopep8/archive/{0}{1}.tar.gz"
-        if version >= Version('1.2.3'):
-            return url.format('v', version)
-        else:
-            return url.format('ver', version)
diff --git a/var/spack/repos/builtin/packages/py-cdo/package.py b/var/spack/repos/builtin/packages/py-cdo/package.py
index 3f1306a183..2bf4a2623c 100644
--- a/var/spack/repos/builtin/packages/py-cdo/package.py
+++ b/var/spack/repos/builtin/packages/py-cdo/package.py
@@ -30,10 +30,9 @@ class PyCdo(PythonPackage):
     Operators from Python."""
 
     homepage = "https://pypi.python.org/pypi/cdo"
-    url      = "https://pypi.python.org/packages/sources/c/cdo/cdo-1.3.2.tar.gz"
+    url      = "https://pypi.io/packages/source/c/cdo/cdo-1.3.2.tar.gz"
 
-    version('1.3.2', '4b3686ec1b9b891f166c1c466c6db745',
-            url="https://pypi.python.org/packages/d6/13/908e7c1451e1f5fb68405f341cdcb3196a16952ebfe1f172cb788f864aa9/cdo-1.3.2.tar.gz")
+    version('1.3.2', '4b3686ec1b9b891f166c1c466c6db745')
 
     depends_on('cdo')
 
diff --git a/var/spack/repos/builtin/packages/py-markdown/package.py b/var/spack/repos/builtin/packages/py-markdown/package.py
index 23c8167021..af10f1c5d3 100644
--- a/var/spack/repos/builtin/packages/py-markdown/package.py
+++ b/var/spack/repos/builtin/packages/py-markdown/package.py
@@ -50,7 +50,3 @@ class PyMarkdown(PythonPackage):
 
     depends_on('py-setuptools', type='build')
     depends_on('python@2.7:2.8,3.2:3.4')
-
-    def url_for_version(self, version):
-        base_url = "https://github.com/waylan/Python-Markdown/archive"
-        return "{0}/{1}-final.tar.gz".format(base_url, version)
diff --git a/var/spack/repos/builtin/packages/py-proj/package.py b/var/spack/repos/builtin/packages/py-proj/package.py
index 949aab88c3..cf230eb49f 100644
--- a/var/spack/repos/builtin/packages/py-proj/package.py
+++ b/var/spack/repos/builtin/packages/py-proj/package.py
@@ -32,9 +32,8 @@ class PyProj(PythonPackage):
 
     # This is not a tagged release of pyproj.
     # The changes in this "version" fix some bugs, especially with Python3 use.
-    version('1.9.5.1.1', 'd035e4bc704d136db79b43ab371b27d2',
-        url='https://www.github.com/jswhit/pyproj/tarball/0be612cc9f972e38b50a90c946a9b353e2ab140f')
-
+    version('1.9.5.1.1', git='https://www.github.com/jswhit/pyproj.git',
+            commit='0be612cc9f972e38b50a90c946a9b353e2ab140f')
     version('1.9.5.1', 'a4b80d7170fc82aee363d7f980279835')
 
     depends_on('py-cython', type='build')
diff --git a/var/spack/repos/builtin/packages/py-pypar/package.py b/var/spack/repos/builtin/packages/py-pypar/package.py
index 6ba999c063..c95698d83d 100644
--- a/var/spack/repos/builtin/packages/py-pypar/package.py
+++ b/var/spack/repos/builtin/packages/py-pypar/package.py
@@ -38,6 +38,3 @@ class PyPypar(PythonPackage):
     depends_on('py-numpy', type=('build', 'run'))
 
     build_directory = 'source'
-
-    def url_for_version(self, version):
-        return "https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/pypar/pypar-%s.tgz" % version
diff --git a/var/spack/repos/builtin/packages/py-rtree/package.py b/var/spack/repos/builtin/packages/py-rtree/package.py
index 55f98ad19e..a3604b467d 100644
--- a/var/spack/repos/builtin/packages/py-rtree/package.py
+++ b/var/spack/repos/builtin/packages/py-rtree/package.py
@@ -28,22 +28,9 @@ from spack import *
 class PyRtree(PythonPackage):
     """Python interface to the RTREE.4 Library."""
     homepage = "http://toblerity.org/rtree/"
-    url      = "https://github.com/Toblerity/rtree/tarball/0.8.2"
+    url      = "https://pypi.io/packages/source/R/Rtree/Rtree-0.8.3.tar.gz"
 
-    # Not an official release yet.  But changes in here are required
-    # to work with Spack.  As it does with all packages, Spack
-    # installs libspatialindex in a non-system location.  Without the
-    # changes in this fork, py-rtree requires an environment variables
-    # to be set *at runtime*, in order to find libspatialindex.  That
-    # is not feasible within the Spack worldview.
-    version('0.8.2.2', 'b1fe96a73153db49ea6ce45a063d82cb',
-        url='https://github.com/citibeth/rtree/tarball/95a678cc7350857a1bb631bc41254efcd1fc0a0d')
-
-    version('0.8.2.1', '394696ca849dd9f3a5ef24fb02a41ef4',
-        url='https://github.com/citibeth/rtree/tarball/3a87d86f66a3955676b2507d3bf424ade938a22b')
-
-    # Does not work with Spack
-    # version('0.8.2', '593c7ac6babc397b8ba58f1636c1e0a0')
+    version('0.8.3', 'a27cb05a85eed0a3605c45ebccc432f8')
 
     depends_on('py-setuptools', type='build')
     depends_on('libspatialindex')
diff --git a/var/spack/repos/builtin/packages/r-lava/package.py b/var/spack/repos/builtin/packages/r-lava/package.py
index c38f9003ea..263e859c48 100644
--- a/var/spack/repos/builtin/packages/r-lava/package.py
+++ b/var/spack/repos/builtin/packages/r-lava/package.py
@@ -29,7 +29,7 @@ class RLava(RPackage):
     """Estimation and simulation of latent variable models."""
 
     homepage = "https://cran.r-project.org/package=lava"
-    url      = "https://cran.r-project.org/src/contrib/lava_1.4.6.tar.gz"
+    url      = "https://cran.r-project.org/src/contrib/lava_1.4.7.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/lava"
 
     version('1.4.7', '28039248a7039ba9281d172e4dbf9543')
diff --git a/var/spack/repos/builtin/packages/root/package.py b/var/spack/repos/builtin/packages/root/package.py
index a96d7f6bbc..a5939ace8f 100644
--- a/var/spack/repos/builtin/packages/root/package.py
+++ b/var/spack/repos/builtin/packages/root/package.py
@@ -30,7 +30,7 @@ import sys
 class Root(Package):
     """ROOT is a data analysis framework."""
     homepage = "https://root.cern.ch"
-    url      = "https://root.cern.ch/download/root_v6.07.02.source.tar.gz"
+    url      = "https://root.cern.ch/download/root_v6.06.06.source.tar.gz"
 
     version('6.06.06', '4308449892210c8d36e36924261fea26')
     version('6.06.04', '55a2f98dd4cea79c9c4e32407c2d6d17')
@@ -83,7 +83,3 @@ class Root(Package):
         spack_env.set('ROOTSYS', self.prefix)
         spack_env.set('ROOT_VERSION', 'v6')
         spack_env.prepend_path('PYTHONPATH', self.prefix.lib)
-
-    def url_for_version(self, version):
-        """Handle ROOT's unusual version string."""
-        return "https://root.cern.ch/download/root_v%s.source.tar.gz" % version
diff --git a/var/spack/repos/builtin/packages/rose/package.py b/var/spack/repos/builtin/packages/rose/package.py
index 02b09f0126..5f0d12427c 100644
--- a/var/spack/repos/builtin/packages/rose/package.py
+++ b/var/spack/repos/builtin/packages/rose/package.py
@@ -35,10 +35,11 @@ class Rose(Package):
        (Developed at Lawrence Livermore National Lab)"""
 
     homepage = "http://rosecompiler.org/"
-    url      = "https://github.com/rose-compiler/edg4x-rose"
+    url      = "https://github.com/rose-compiler/rose/archive/v0.9.7.tar.gz"
 
+    version('0.9.7', 'e14ce5250078df4b09f4f40559d46c75')
     version('master', branch='master',
-            git='https://github.com/rose-compiler/edg4x-rose.git')
+            git='https://github.com/rose-compiler/rose.git')
 
     patch('add_spack_compiler_recognition.patch')
 
@@ -46,7 +47,7 @@ class Rose(Package):
     depends_on("automake@1.14", type='build')
     depends_on("libtool@2.4", type='build')
     depends_on("boost@1.54.0")
-    depends_on("jdk@8u25-linux-x64")
+    depends_on("jdk@8u25")
 
     def install(self, spec, prefix):
         # Bootstrap with autotools
diff --git a/var/spack/repos/builtin/packages/rust-bindgen/package.py b/var/spack/repos/builtin/packages/rust-bindgen/package.py
index c411bc15d1..00ccbb71cf 100644
--- a/var/spack/repos/builtin/packages/rust-bindgen/package.py
+++ b/var/spack/repos/builtin/packages/rust-bindgen/package.py
@@ -29,9 +29,9 @@ import os
 class RustBindgen(Package):
     """The rust programming language toolchain"""
     homepage = "http://www.rust-lang.org"
-    url = "https://github.com/crabtw/rust-bindgen"
+    url = "https://github.com/servo/rust-bindgen/archive/v0.20.5.tar.gz"
 
-    version('0.16', tag='0.16', git='https://github.com/crabtw/rust-bindgen')
+    version('0.20.5', '3e4d70a5bec540324fdd95bc9e82bebc')
 
     extends("rust")
     depends_on("llvm")
diff --git a/var/spack/repos/builtin/packages/scorep/package.py b/var/spack/repos/builtin/packages/scorep/package.py
index 6b3345d83b..1a5a591c3f 100644
--- a/var/spack/repos/builtin/packages/scorep/package.py
+++ b/var/spack/repos/builtin/packages/scorep/package.py
@@ -32,14 +32,11 @@ class Scorep(Package):
     """
 
     homepage = "http://www.vi-hps.org/projects/score-p"
-    url      = "http://www.vi-hps.org/upload/packages/scorep/scorep-1.2.3.tar.gz"
+    url      = "http://www.vi-hps.org/upload/packages/scorep/scorep-2.0.2.tar.gz"
 
-    version('2.0.2', '8f00e79e1b5b96e511c5ebecd10b2888',
-            url='http://www.vi-hps.org/upload/packages/scorep/scorep-2.0.2.tar.gz')
-    version('1.4.2', '3b9a042b13bdd5836452354e6567f71e',
-            url='http://www.vi-hps.org/upload/packages/scorep/scorep-1.4.2.tar.gz')
-    version('1.3', '9db6f957b7f51fa01377a9537867a55c',
-            url='http://www.vi-hps.org/upload/packages/scorep/scorep-1.3.tar.gz')
+    version('2.0.2', '8f00e79e1b5b96e511c5ebecd10b2888')
+    version('1.4.2', '3b9a042b13bdd5836452354e6567f71e')
+    version('1.3',   '9db6f957b7f51fa01377a9537867a55c')
 
     ##########
     # Dependencies for SCORE-P are quite tight. See the homepage for more
diff --git a/var/spack/repos/builtin/packages/scotch/package.py b/var/spack/repos/builtin/packages/scotch/package.py
index b878349485..8efb629487 100644
--- a/var/spack/repos/builtin/packages/scotch/package.py
+++ b/var/spack/repos/builtin/packages/scotch/package.py
@@ -31,8 +31,7 @@ class Scotch(Package):
        partitioning, graph clustering, and sparse matrix ordering."""
 
     homepage = "http://www.labri.fr/perso/pelegrin/scotch/"
-    url = "http://gforge.inria.fr/frs/download.php/latestfile/298/scotch_6.0.3.tar.gz"  # noqa: E501
-    base_url = "http://gforge.inria.fr/frs/download.php/latestfile/298"
+    url      = "http://gforge.inria.fr/frs/download.php/latestfile/298/scotch_6.0.4.tar.gz"
     list_url = "http://gforge.inria.fr/frs/?group_id=248"
 
     version('6.0.4', 'd58b825eb95e1db77efe8c6ff42d329f')
@@ -71,12 +70,10 @@ class Scotch(Package):
     # from the Scotch hosting site.  These alternative archives include a
     # superset of the behavior in their default counterparts, so we choose to
     # always grab these versions for older Scotch versions for simplicity.
-    def url_for_version(self, version):
-        return super(Scotch, self).url_for_version(version)
-
     @when('@:6.0.0')
     def url_for_version(self, version):
-        return '%s/scotch_%s_esmumps.tar.gz' % (Scotch.base_url, version)
+        url = "http://gforge.inria.fr/frs/download.php/latestfile/298/scotch_{0}_esmumps.tar.gz"
+        return url.format(version)
 
     def patch(self):
         self.configure()
diff --git a/var/spack/repos/builtin/packages/silo/package.py b/var/spack/repos/builtin/packages/silo/package.py
index 6a9326517b..eca5d1a605 100644
--- a/var/spack/repos/builtin/packages/silo/package.py
+++ b/var/spack/repos/builtin/packages/silo/package.py
@@ -30,7 +30,7 @@ class Silo(Package):
        data to binary, disk files."""
 
     homepage = "http://wci.llnl.gov/simulation/computer-codes/silo"
-    base_url = "https://wci.llnl.gov/content/assets/docs/simulation/computer-codes/silo"
+    url      = "https://wci.llnl.gov/content/assets/docs/simulation/computer-codes/silo/silo-4.10.2/silo-4.10.2.tar.gz"
 
     version('4.10.2', '9ceac777a2f2469ac8cef40f4fab49c8')
     version('4.9', 'a83eda4f06761a86726e918fc55e782a')
@@ -67,6 +67,3 @@ class Silo(Package):
 
         make()
         make('install')
-
-    def url_for_version(self, version):
-        return '%s/silo-%s/silo-%s.tar.gz' % (Silo.base_url, version, version)
diff --git a/var/spack/repos/builtin/packages/star-ccm-plus/package.py b/var/spack/repos/builtin/packages/star-ccm-plus/package.py
index ba1516b62a..4197aec339 100644
--- a/var/spack/repos/builtin/packages/star-ccm-plus/package.py
+++ b/var/spack/repos/builtin/packages/star-ccm-plus/package.py
@@ -31,6 +31,7 @@ class StarCcmPlus(Package):
     """STAR-CCM+ (Computational Continuum Mechanics) CFD solver."""
 
     homepage = "http://mdx.plm.automation.siemens.com/star-ccm-plus"
+    url      = "file://{0}/STAR-CCM+11.06.010_02_linux-x86_64.tar.gz".format(os.getcwd())
 
     version('11.06.010_02', 'd349c6ac8293d8e6e7a53533d695588f')
 
@@ -40,10 +41,6 @@ class StarCcmPlus(Package):
     license_required = True
     license_vars = ['CDLMD_LICENSE_FILE', 'LM_LICENSE_FILE']
 
-    def url_for_version(self, version):
-        return "file://{0}/STAR-CCM+{1}_linux-x86_64.tar.gz".format(
-            os.getcwd(), version)
-
     def install(self, spec, prefix):
         # There is a known issue with the LaunchAnywhere application.
         # Specifically, it cannot handle long prompts or prompts
diff --git a/var/spack/repos/builtin/packages/sublime-text/package.py b/var/spack/repos/builtin/packages/sublime-text/package.py
index 81d8690db8..1cfb117a05 100644
--- a/var/spack/repos/builtin/packages/sublime-text/package.py
+++ b/var/spack/repos/builtin/packages/sublime-text/package.py
@@ -33,8 +33,8 @@ class SublimeText(Package):
     homepage = "http://www.sublimetext.com/"
     url      = "https://download.sublimetext.com/sublime_text_3_build_3126_x64.tar.bz2"
 
-    version('3126',  'acc34252b0ea7dff1f581c5db1564dcb')
-    version('2.0.2', '699cd26d7fe0bada29eb1b2cd7b50e4b')
+    version('3_build_3126', 'acc34252b0ea7dff1f581c5db1564dcb')
+    version('2.0.2',        '699cd26d7fe0bada29eb1b2cd7b50e4b')
 
     # Sublime text comes as a pre-compiled binary.
     # Since we can't link to Spack packages, we'll just have to
diff --git a/var/spack/repos/builtin/packages/tcl/package.py b/var/spack/repos/builtin/packages/tcl/package.py
index 79d4bc7544..8ddfc903b3 100644
--- a/var/spack/repos/builtin/packages/tcl/package.py
+++ b/var/spack/repos/builtin/packages/tcl/package.py
@@ -34,6 +34,7 @@ class Tcl(AutotoolsPackage):
        that is truly cross platform, easily deployed and highly
        extensible."""
     homepage = "http://www.tcl.tk"
+    url      = "http://prdownloads.sourceforge.net/tcl/tcl8.6.5-src.tar.gz"
 
     version('8.6.6', '5193aea8107839a79df8ac709552ecb7')
     version('8.6.5', '0e6426a4ca9401825fbc6ecf3d89a326')
@@ -45,10 +46,6 @@ class Tcl(AutotoolsPackage):
 
     configure_directory = 'unix'
 
-    def url_for_version(self, version):
-        base_url = 'http://prdownloads.sourceforge.net/tcl'
-        return '{0}/tcl{1}-src.tar.gz'.format(base_url, version)
-
     def setup_environment(self, spack_env, run_env):
         # When using Tkinter from within spack provided python+tk, python
         # will not be able to find Tcl/Tk unless TCL_LIBRARY is set.
diff --git a/var/spack/repos/builtin/packages/tetgen/package.py b/var/spack/repos/builtin/packages/tetgen/package.py
index 6e5ed79c36..2ccc9504e2 100644
--- a/var/spack/repos/builtin/packages/tetgen/package.py
+++ b/var/spack/repos/builtin/packages/tetgen/package.py
@@ -34,7 +34,7 @@ class Tetgen(Package):
        boundary conforming Delaunay meshes, and Voronoi paritions.
     """
 
-    homepage = "http://www.tetgen.org"
+    homepage = "http://wias-berlin.de/software/tetgen/"
 
     version('1.5.0', '3b9fd9cdec121e52527b0308f7aad5c1', url='http://www.tetgen.org/1.5/src/tetgen1.5.0.tar.gz')
     version('1.4.3', 'd6a4bcdde2ac804f7ec66c29dcb63c18', url='http://www.tetgen.org/files/tetgen1.4.3.tar.gz')
diff --git a/var/spack/repos/builtin/packages/tinyxml/package.py b/var/spack/repos/builtin/packages/tinyxml/package.py
index 1789d9022e..9cb4b715df 100644
--- a/var/spack/repos/builtin/packages/tinyxml/package.py
+++ b/var/spack/repos/builtin/packages/tinyxml/package.py
@@ -34,6 +34,10 @@ class Tinyxml(CMakePackage):
 
     version('2.6.2', 'cba3f50dd657cb1434674a03b21394df9913d764')
 
+    def url_for_version(self, version):
+        url = "https://sourceforge.net/projects/tinyxml/files/tinyxml/{0}/tinyxml_{1}.tar.gz"
+        return url.format(version.dotted, version.underscored)
+
     def patch(self):
         copyfile(join_path(os.path.dirname(__file__),
                            "CMakeLists.txt"), "CMakeLists.txt")
diff --git a/var/spack/repos/builtin/packages/tk/package.py b/var/spack/repos/builtin/packages/tk/package.py
index 4d9651315a..fdcb29a785 100644
--- a/var/spack/repos/builtin/packages/tk/package.py
+++ b/var/spack/repos/builtin/packages/tk/package.py
@@ -33,6 +33,7 @@ class Tk(AutotoolsPackage):
        applications that run unchanged across Windows, Mac OS X, Linux
        and more."""
     homepage = "http://www.tcl.tk"
+    url      = "http://prdownloads.sourceforge.net/tcl/tk8.6.5-src.tar.gz"
 
     version('8.6.6', 'dd7dbb3a6523c42d05f6ab6e86096e99')
     version('8.6.5', '11dbbd425c3e0201f20d6a51482ce6c4')
@@ -43,10 +44,6 @@ class Tk(AutotoolsPackage):
 
     configure_directory = 'unix'
 
-    def url_for_version(self, version):
-        base_url = "http://prdownloads.sourceforge.net/tcl"
-        return "{0}/tk{1}-src.tar.gz".format(base_url, version)
-
     def setup_environment(self, spack_env, run_env):
         # When using Tkinter from within spack provided python+tk, python
         # will not be able to find Tcl/Tk unless TK_LIBRARY is set.
diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 3de72ea6c8..0e0d86fa3c 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -44,7 +44,7 @@ class Trilinos(CMakePackage):
     A unique design feature of Trilinos is its focus on packages.
     """
     homepage = "https://trilinos.org/"
-    base_url = "https://github.com/trilinos/Trilinos/archive"
+    url      = "https://github.com/trilinos/Trilinos/archive/trilinos-release-12-10-1.tar.gz"
 
     version('develop',
             git='https://github.com/trilinos/Trilinos.git', tag='develop')
@@ -63,10 +63,6 @@ class Trilinos(CMakePackage):
     version('11.14.2', 'e7c3cdbbfe3279a8a68838b873ad6d51')
     version('11.14.1', 'b7760b142eef66c79ed13de7c9560f81')
 
-    def url_for_version(self, version):
-        return '%s/trilinos-release-%s.tar.gz' % \
-            (Trilinos.base_url, version.dashed)
-
     variant('xsdkflags',        default=False,
             description='Compile using the default xSDK configuration')
     variant('metis',        default=True,
@@ -125,6 +121,10 @@ class Trilinos(CMakePackage):
 
     patch('umfpack_from_suitesparse.patch', when='@:12.8.1')
 
+    def url_for_version(self, version):
+        url = "https://github.com/trilinos/Trilinos/archive/trilinos-release-{0}.tar.gz"
+        return url.format(version.dashed)
+
     # check that the combination of variants makes sense
     def variants_check(self):
         if '+superlu-dist' in self.spec and self.spec.satisfies('@:11.4.3'):
diff --git a/var/spack/repos/builtin/packages/unison/package.py b/var/spack/repos/builtin/packages/unison/package.py
index 181e1e6410..aa890ea869 100644
--- a/var/spack/repos/builtin/packages/unison/package.py
+++ b/var/spack/repos/builtin/packages/unison/package.py
@@ -34,7 +34,7 @@ class Unison(Package):
        other."""
 
     homepage = "https://www.cis.upenn.edu/~bcpierce/unison/"
-    url      = "https://www.seas.upenn.edu/~bcpierce/unison//download/releases/stable/unison-2.48.3.tar.gz"
+    url      = "https://www.seas.upenn.edu/~bcpierce/unison//download/releases/stable/unison-2.48.4.tar.gz"
 
     version('2.48.4', '5334b78c7e68169df7de95f4c6c4b60f')
 
diff --git a/var/spack/repos/builtin/packages/voropp/package.py b/var/spack/repos/builtin/packages/voropp/package.py
index 0e39769927..0fc84ef252 100644
--- a/var/spack/repos/builtin/packages/voropp/package.py
+++ b/var/spack/repos/builtin/packages/voropp/package.py
@@ -31,19 +31,10 @@ class Voropp(MakefilePackage):
     scientific fields."""
 
     homepage = "http://math.lbl.gov/voro++/about.html"
-
-    # This url is wrong but it passes the test the ++ make the url parser fail,
-    # the correct url is constructed by url_for_version that has to be used in
-    # any case due to the difference between the package name and the url
-    url      = "http://math.lbl.gov/voropp/download/dir/voropp-0.4.6.tar.gz"
+    url      = "http://math.lbl.gov/voro++/download/dir/voro++-0.4.6.tar.gz"
 
     version('0.4.6', '2338b824c3b7b25590e18e8df5d68af9')
 
-    def url_for_version(self, version):
-        url = "http://math.lbl.gov/voro++/download/dir/voro++-{0}.tar.gz".format(  # noqa: E501
-            str(version))
-        return url
-
     def edit(self, spec, prefix):
         filter_file(r'CC=g\+\+',
                     'CC={0}'.format(self.compiler.cxx),
diff --git a/var/spack/repos/builtin/packages/vtk/package.py b/var/spack/repos/builtin/packages/vtk/package.py
index c577949c3a..dafeae6dbb 100644
--- a/var/spack/repos/builtin/packages/vtk/package.py
+++ b/var/spack/repos/builtin/packages/vtk/package.py
@@ -33,6 +33,7 @@ class Vtk(CMakePackage):
 
     homepage = "http://www.vtk.org"
     url      = "http://www.vtk.org/files/release/7.1/VTK-7.1.0.tar.gz"
+    list_url = "http://www.vtk.org/download/"
 
     version('7.1.0', 'a7e814c1db503d896af72458c2d0228f')
     version('7.0.0', '5fe35312db5fb2341139b8e4955c367d')
diff --git a/var/spack/repos/builtin/packages/xsdktrilinos/package.py b/var/spack/repos/builtin/packages/xsdktrilinos/package.py
index ea49054435..7e88b2f9eb 100644
--- a/var/spack/repos/builtin/packages/xsdktrilinos/package.py
+++ b/var/spack/repos/builtin/packages/xsdktrilinos/package.py
@@ -32,16 +32,12 @@ class Xsdktrilinos(CMakePackage):
     Trilinos.
     """
     homepage = "https://trilinos.org/"
-    base_url = "https://github.com/trilinos/xSDKTrilinos/archive"
+    url      = "https://github.com/trilinos/xSDKTrilinos/archive/trilinos-release-12-8-1.tar.gz"
 
     version('develop', git='https://github.com/trilinos/xSDKTrilinos.git', tag='master')
     version('12.8.1', '9cc338ded17d1e10ea6c0dc18b22dcd4')
     version('12.6.4', '44c4c54ccbac73bb8939f68797b9454a')
 
-    def url_for_version(self, version):
-        return '%s/trilinos-release-%s.tar.gz' % \
-            (Xsdktrilinos.base_url, version.dashed)
-
     variant('hypre',        default=True,
             description='Compile with Hypre preconditioner')
     variant('petsc',        default=True,
@@ -59,6 +55,10 @@ class Xsdktrilinos(CMakePackage):
     depends_on('trilinos@12.8.1', when='@12.8.1')
     depends_on('trilinos@develop', when='@develop')
 
+    def url_for_version(self, version):
+        url = "https://github.com/trilinos/xSDKTrilinos/archive/trilinos-release-{0}.tar.gz"
+        return url.format(version.dashed)
+
     def cmake_args(self):
         spec = self.spec
 
diff --git a/var/spack/repos/builtin/packages/yorick/package.py b/var/spack/repos/builtin/packages/yorick/package.py
index 52a4d8787d..9cbd417e4e 100644
--- a/var/spack/repos/builtin/packages/yorick/package.py
+++ b/var/spack/repos/builtin/packages/yorick/package.py
@@ -31,7 +31,7 @@ import glob
 class Yorick(Package):
     """Yorick is an interpreted programming language for scientific simulations
        or calculations, postprocessing or steering large simulation codes,
-       interactive scientific graphics, and reading, writing, or translating 
+       interactive scientific graphics, and reading, writing, or translating
        files of numbers. Yorick includes an interactive graphics package, and a
        binary file package capable of translating to and from the raw numeric
        formats of all modern computers. Yorick is written in ANSI C and runs on
@@ -39,9 +39,9 @@ class Yorick(Package):
     """
 
     homepage = "http://dhmunro.github.io/yorick-doc/"
-    url =  "https://github.com/dhmunro/yorick/archive/y_2_2_04.tar.gz"
+    url      = "https://github.com/dhmunro/yorick/archive/y_2_2_04.tar.gz"
 
-    version('2.2.04', md5='1b5b0da6ad81b2d9dba64d991ec17939')
+    version('2.2.04', '1b5b0da6ad81b2d9dba64d991ec17939')
     version('master', branch='master',
             git='https://github.com/dhmunro/yorick.git')
     version('f90-plugin', branch='f90-plugin',
@@ -51,6 +51,10 @@ class Yorick(Package):
 
     depends_on('libx11', when='+X')
 
+    def url_for_version(self, version):
+        url = "https://github.com/dhmunro/yorick/archive/y_{0}.tar.gz"
+        return url.format(version.underscored)
+
     def install(self, spec, prefix):
         os.environ['FORTRAN_LINKAGE'] = '-Df_linkage'
 
diff --git a/var/spack/repos/builtin/packages/zoltan/package.py b/var/spack/repos/builtin/packages/zoltan/package.py
index 21c90a05e4..b6720b7b1e 100644
--- a/var/spack/repos/builtin/packages/zoltan/package.py
+++ b/var/spack/repos/builtin/packages/zoltan/package.py
@@ -41,7 +41,7 @@ class Zoltan(Package):
     """
 
     homepage = "http://www.cs.sandia.gov/zoltan"
-    base_url = "http://www.cs.sandia.gov/~kddevin/Zoltan_Distributions"
+    url      = "http://www.cs.sandia.gov/~kddevin/Zoltan_Distributions/zoltan_distrib_v3.83.tar.gz"
 
     version('3.83', '1ff1bc93f91e12f2c533ddb01f2c095f')
     version('3.8', '9d8fba8a990896881b85351d4327c4a9')
@@ -56,9 +56,6 @@ class Zoltan(Package):
 
     depends_on('mpi', when='+mpi')
 
-    def url_for_version(self, version):
-        return '%s/zoltan_distrib_v%s.tar.gz' % (Zoltan.base_url, version)
-
     def install(self, spec, prefix):
         # FIXME: The older Zoltan versions fail to compile the F90 MPI wrappers
         # because of some complicated generic type problem.