checksums: fix packages that needed new download locations

Some packages had incorrect checksums because they needed to be
downloaded from a new place or the package needed tweaking somehow.
These packages to sha256 and the new checksums have been verified by
fetching over https.

41 files changed, 83 insertions, 99 deletions

diff --git a/var/spack/repos/builtin/packages/ape/package.py b/var/spack/repos/builtin/packages/ape/package.py
index 52c0198802..76633a1498 100644
--- a/var/spack/repos/builtin/packages/ape/package.py
+++ b/var/spack/repos/builtin/packages/ape/package.py
@@ -13,7 +13,7 @@ class Ape(Package):
     homepage = "http://www.tddft.org/programs/APE/"
     url      = "http://www.tddft.org/programs/APE/sites/default/files/ape-2.2.1.tar.gz"
 
-    version('2.2.1', 'ab81da85bd749c0c136af088c7f9ad58')
+    version('2.2.1', sha256='1bdb7f987fde81f8a5f335da6b59fa884e6d185d4a0995c90fde7c04376ce9e3')
 
     depends_on('gsl')
     depends_on('libxc@:2.2.2')
diff --git a/var/spack/repos/builtin/packages/archer/package.py b/var/spack/repos/builtin/packages/archer/package.py
index 78ff54e874..7437a3890d 100644
--- a/var/spack/repos/builtin/packages/archer/package.py
+++ b/var/spack/repos/builtin/packages/archer/package.py
@@ -13,7 +13,7 @@ class Archer(CMakePackage):
     homepage = "https://github.com/PRUNERS/ARCHER"
     url      = "https://github.com/PRUNERS/archer/archive/v1.0.0.tar.gz"
 
-    version('1.0.0', '790bfaf00b9f57490eb609ecabfe954a')
+    version('1.0.0', sha256='df814a475606b83c659932caa30a68bed1c62e713386b375c1b78eb8d60e0d15')
 
     depends_on('cmake@3.4.3:', type='build')
     depends_on('llvm')
diff --git a/var/spack/repos/builtin/packages/astra/package.py b/var/spack/repos/builtin/packages/astra/package.py
index 13a912dcbb..c51d069455 100644
--- a/var/spack/repos/builtin/packages/astra/package.py
+++ b/var/spack/repos/builtin/packages/astra/package.py
@@ -11,7 +11,7 @@ class Astra(Package):
 
     homepage = "http://www.desy.de/~mpyflo/"
 
-    version('2016-11-30', '17135b7a4adbacc1843a50a6a2ae2c25', expand=False,
+    version('2016-11-30', sha256='50738bf924724e2dd15f1d924b290ffb0f7c703e5d5ae02ffee2db554338801e', expand=False,
             url='http://www.desy.de/~mpyflo/Astra_for_64_Bit_Linux/Astra')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/converge/package.py b/var/spack/repos/builtin/packages/converge/package.py
index 792bbedeb8..3b990ebd6a 100644
--- a/var/spack/repos/builtin/packages/converge/package.py
+++ b/var/spack/repos/builtin/packages/converge/package.py
@@ -27,13 +27,13 @@ class Converge(Package):
     # In order to view available versions, you need to register for an account:
     # https://download.convergecfd.com/wp-login.php?action=register
 
-    version('2.4.10', '53f5bd4bfb39005bebae46b8d6ee3ce6')
-    version('2.3.23', '2913c3e440f82db069051f8822115e5e')
-    version('2.2.0',  'd949cfe338c83ee736ca0be8f77df6bf',
+    version('2.4.10', sha256='5d3c39894598d2395149cfcc653af13b8b1091177290edd62fcf22c7e830d410')
+    version('2.3.23', sha256='1217d16eaf9d263f917ee468778508bad9dacb7e4397a293cfa6467f39fb4c52')
+    version('2.2.0',  sha256='3885acbaf352c718ea69f0206c858a01be02f0928ffee738e4aceb1dd939a77a',
             url="https://download.convergecfd.com/download/CONVERGE_2.2/Full_Solver_Packages/converge_install_2.2.0_042916.tar.gz")
-    version('2.1.0',  '327a917d46aa3bc8dee9511375ce112c',
+    version('2.1.0',  sha256='6b8896d42cf7b9013cae5456f4dc118306a5bd271d4a15945ceb7dae913e825a',
             url="https://download.convergecfd.com/download/CONVERGE_2.1/Full_Solver_Packages/converge_install_2.1.0_111615.tar.gz")
-    version('2.0.0',  '06f017521c3abc1a922b136e83d606dd',
+    version('2.0.0',  sha256='f32c4824eb33724d85e283481d67ebd0630b1406011c528d775028bb2546f34e',
             url="https://download.convergecfd.com/download/CONVERGE_2.0/Full_Solver_Packages/converge_install_2.0.0_090214.tar.gz")
 
     variant('mpi', default=True, description='Build with MPI support')
diff --git a/var/spack/repos/builtin/packages/cppad/package.py b/var/spack/repos/builtin/packages/cppad/package.py
index 51ae4c0154..de6b4a5c23 100644
--- a/var/spack/repos/builtin/packages/cppad/package.py
+++ b/var/spack/repos/builtin/packages/cppad/package.py
@@ -14,7 +14,7 @@ class Cppad(CMakePackage):
     git      = "https://github.com/coin-or/CppAD.git"
 
     version('develop', branch='master')
-    version('20170114', '565a534dc813fa1289764222cd8c11ea')
+    version('20170114', sha256='fa3980a882be2a668a7522146273a1b4f1d8dabe66ad4aafa8964c8c1fd6f957')
 
     def cmake_args(self):
         # This package does not obey CMAKE_INSTALL_PREFIX
diff --git a/var/spack/repos/builtin/packages/cpprestsdk/package.py b/var/spack/repos/builtin/packages/cpprestsdk/package.py
index 86b24761a1..a4f4a73817 100644
--- a/var/spack/repos/builtin/packages/cpprestsdk/package.py
+++ b/var/spack/repos/builtin/packages/cpprestsdk/package.py
@@ -15,7 +15,7 @@ class Cpprestsdk(CMakePackage):
     homepage = "https://github.com/Microsoft/cpprestsdk"
     url      = "https://github.com/Microsoft/cpprestsdk/archive/v2.9.1.tar.gz"
 
-    version('2.9.1', 'c3dd67d8cde8a65c2e994e2ede4439a2')
+    version('2.9.1', sha256='537358760acd782f4d2ed3a85d92247b4fc423aff9c85347dc31dbb0ab9bab16')
 
     depends_on('boost')
 
diff --git a/var/spack/repos/builtin/packages/dislin/package.py b/var/spack/repos/builtin/packages/dislin/package.py
index 53d0e901b2..cfdffeb9ba 100644
--- a/var/spack/repos/builtin/packages/dislin/package.py
+++ b/var/spack/repos/builtin/packages/dislin/package.py
@@ -14,8 +14,7 @@ class Dislin(Package):
     homepage = "http://www.mps.mpg.de/dislin"
     url      = "ftp://ftp.gwdg.de/pub/grafik/dislin/linux/i586_64/dislin-11.0.linux.i586_64.tar.gz"
 
-    version('11.1.linux.i586_64', '34218c257efedaf706f058bdf111ce9d')
-    version('11.0.linux.i586_64', '6fb099b54f41db009cafc702eebb5bc6')
+    version('11.2.linux.i586_64', sha256='13d28188924e0b0b803d72aa4b48be4067e98e890701b0aa6f54a11c7d34dd10')
 
     depends_on('motif')
     depends_on('gl')
diff --git a/var/spack/repos/builtin/packages/fenics/package.py b/var/spack/repos/builtin/packages/fenics/package.py
index 97020e857f..896edb583b 100644
--- a/var/spack/repos/builtin/packages/fenics/package.py
+++ b/var/spack/repos/builtin/packages/fenics/package.py
@@ -102,16 +102,6 @@ class Fenics(CMakePackage):
                 'ufl': 'c75c4781e5104504f158cb42cd87aceffa9052e8e9db6e9764e6a5b6115d7f73',
             }
         },
-        {
-            'version': '1.5.0',
-            'sha256': '9b589a3534299a5e6d22c13c5eb30bb8',
-            'resources': {
-                'ffc': '755be60597d66f13c1e113739e7b9b620ee4271e0f7cc1053553a568bc08e7f4',
-                'fiat': '2b053fa9f70399f8903b987f98a4fa2b06df9559c07c1d5f0b2b5e43c51de670',
-                'instant': '36e042de26d97f5e3d43f2f52544d91ba0f14e1c73c7d07ed7804030b43d935d',
-                'ufl': '2879a5b0937502676fa55765bcb8237ff78e8b70995a118ffe1de042b20e491b',
-            }
-        },
     ]
 
     for release in releases:
diff --git a/var/spack/repos/builtin/packages/fimpute/package.py b/var/spack/repos/builtin/packages/fimpute/package.py
index 6d79f22079..7ee5f361f6 100644
--- a/var/spack/repos/builtin/packages/fimpute/package.py
+++ b/var/spack/repos/builtin/packages/fimpute/package.py
@@ -14,7 +14,7 @@ class Fimpute(Package):
     homepage = "http://www.aps.uoguelph.ca/~msargol/fimpute/"
     url      = "http://www.aps.uoguelph.ca/~msargol/fimpute/FImpute_Linux.zip"
 
-    version('2014-01', 'df934a25c76dabef7d7afcb5b8058d98')
+    version('2014-01', sha256='aecda2dfdd4e3ef6f2331cc1d479e6f297f722fcdca455ca05bb047405534461')
 
     def install(self, spec, prefix):
         mkdirp(prefix.bin)
diff --git a/var/spack/repos/builtin/packages/fseq/package.py b/var/spack/repos/builtin/packages/fseq/package.py
index e3fd92d946..4858114ef0 100644
--- a/var/spack/repos/builtin/packages/fseq/package.py
+++ b/var/spack/repos/builtin/packages/fseq/package.py
@@ -10,9 +10,9 @@ class Fseq(Package):
     """F-Seq: A Feature Density Estimator for High-Throughput Sequence Tags"""
 
     homepage = "http://fureylab.web.unc.edu/software/fseq/"
-    url      = "http://fureylab.med.unc.edu/fseq/fseq_1.84.tgz"
+    url      = "http://html-large-files-dept-fureylab.cloudapps.unc.edu/fureylabfiles/fseq/fseq_1.84.tgz"
 
-    version('1.84', 'f9124ad0f45c60f3a7eb74dde8c945b9')
+    version('1.84', sha256='22d603a51f127cb86cdecde9aeae14d273bb98bcd2b47724763ab3b3241a6e68')
 
     depends_on('java', type=('build', 'run'))
 
diff --git a/var/spack/repos/builtin/packages/gnu-prolog/package.py b/var/spack/repos/builtin/packages/gnu-prolog/package.py
index b0ea5ed293..d332711077 100644
--- a/var/spack/repos/builtin/packages/gnu-prolog/package.py
+++ b/var/spack/repos/builtin/packages/gnu-prolog/package.py
@@ -9,9 +9,9 @@ from spack import *
 class GnuProlog(Package):
     """A free Prolog compiler with constraint solving over finite domains."""
     homepage = "http://www.gprolog.org/"
-    url      = "http://www.gprolog.org/gprolog-1.4.4.tar.gz"
+    url      = "http://www.gprolog.org/gprolog-1.4.5.tar.gz"
 
-    version('1.4.4', '37009da471e5217ff637ad1c516448c8')
+    version('1.4.5', sha256='bfdcf00e051e0628b4f9af9d6638d4fde6ad793401e58a5619d1cc6105618c7c')
 
     parallel = False
 
diff --git a/var/spack/repos/builtin/packages/h5hut/package.py b/var/spack/repos/builtin/packages/h5hut/package.py
index ec7b441b8f..48c5fa2020 100644
--- a/var/spack/repos/builtin/packages/h5hut/package.py
+++ b/var/spack/repos/builtin/packages/h5hut/package.py
@@ -12,9 +12,9 @@ class H5hut(AutotoolsPackage):
     High-Performance I/O Library for Particle-based Simulations."""
 
     homepage = "https://amas.psi.ch/H5hut/"
-    url      = "https://amas.psi.ch/H5hut/raw-attachment/wiki/DownloadSources/H5hut-1.99.13.tar.gz"
+    url      = "http://amas.web.psi.ch/Downloads/H5hut/H5hut-2.0.0rc3.tar.gz"
 
-    version('1.99.13', '2a07a449afe50534de006ac6954a421a')
+    version('2.0.0rc3', sha256='1ca9a9478a99e1811ecbca3c02cc49258050d339ffb1a170006eab4ab2a01790')
 
     variant('fortran', default=True, description='Enable Fortran support')
     variant('mpi',     default=True, description='Enable MPI support')
diff --git a/var/spack/repos/builtin/packages/hadoop/package.py b/var/spack/repos/builtin/packages/hadoop/package.py
index 8c51c228a6..04b00e0a85 100644
--- a/var/spack/repos/builtin/packages/hadoop/package.py
+++ b/var/spack/repos/builtin/packages/hadoop/package.py
@@ -13,10 +13,9 @@ class Hadoop(Package):
     """
 
     homepage = "http://hadoop.apache.org/"
-    url      = "http://mirrors.ocf.berkeley.edu/apache/hadoop/common/hadoop-3.1.1/hadoop-3.1.1.tar.gz"
+    url      = "http://apache-mirror.8birdsvideo.com/hadoop/common/hadoop-3.1.2/hadoop-3.1.2-src.tar.gz"
 
-    version('3.1.1', '0b6ab06b59ae75f433de387783f19011')
-    version('2.9.0', 'b443ead81aa2bd5086f99e62e66a8f64')
+    version('3.1.2', sha256='02f277c9fc75d4b13c7697ed6be30dba41667841ab5e37442855267c39bec6b6')
 
     depends_on('java', type='run')
 
diff --git a/var/spack/repos/builtin/packages/harminv/package.py b/var/spack/repos/builtin/packages/harminv/package.py
index 1776f4de2d..3570f87fe1 100644
--- a/var/spack/repos/builtin/packages/harminv/package.py
+++ b/var/spack/repos/builtin/packages/harminv/package.py
@@ -17,7 +17,7 @@ class Harminv(AutotoolsPackage):
     url      = "http://ab-initio.mit.edu/harminv/harminv-1.4.tar.gz"
     list_url = "http://ab-initio.mit.edu/harminv/old"
 
-    version('1.4', 'b95e24a9bc7e07d3d2202d1605e9e86f')
+    version('1.4', sha256='e1b923c508a565f230aac04e3feea23b888b47d8e19b08816a97ee4444233670')
 
     depends_on('blas')
     depends_on('lapack')
diff --git a/var/spack/repos/builtin/packages/hpx5/package.py b/var/spack/repos/builtin/packages/hpx5/package.py
index 762d4d469d..5ea3937c46 100644
--- a/var/spack/repos/builtin/packages/hpx5/package.py
+++ b/var/spack/repos/builtin/packages/hpx5/package.py
@@ -18,16 +18,15 @@ class Hpx5(AutotoolsPackage):
     applications enabling scientists to write code that performs and
     scales better than contemporary runtimes."""
     homepage = "http://hpx.crest.iu.edu"
-    url      = "http://hpx.crest.iu.edu/release/hpx-3.1.0.tar.gz"
-
-    version('4.1.0', '43cb78758506f77416b95276a472f84f')
-    version('4.0.0', 'b40dc03449ae1039cbb48ee149952b22')
-    version('3.1.0', '9e90b8ac46788c009079632828c77628')
-    version('2.0.0', '3d2ff3aab6c46481f9ec65c5b2bfe7a6')
-    version('1.3.0', '2260ecc7f850e71a4d365a43017d8cee')
-    version('1.2.0', '4972005f85566af4afe8b71afbf1480f')
-    version('1.1.0', '646afb460ecb7e0eea713a634933ce4f')
-    version('1.0.0', '8020822adf6090bd59ed7fe465f6c6cb')
+    url      = "https://github.com/adk9/hpx5/archive/v3.1.0.tar.gz"
+
+    version('4.1.0',     sha256='3f01009f5e517c8dfca266dabb49894d688db5adce09608fb1c877263605a9f8')
+    version('4.0.0',     sha256='e35b1161566a65ffbd875c1413ea97a84be0c7b528a3dee99f5e250b2aecbd19')
+    version('3.1.0',     sha256='359d457a26b87abb415605911d791ce0ff6edbb064bc40b0f830960f8f612b84')
+    version('3.0.0',     sha256='10f14ba198a32787cee05962e346bafb922f74a5135fb09a1ba8c32a1e942800')
+    version('2.2.0',     sha256='e34c7513a287d517e67cce5aa3011474c48718e7860c3860ba1290c702be28a8')
+    version('2.1.0',     sha256='675826f669eeb3eab40947715af8c8495e2b3d299223372431dc01c1f7d5d616')
+    version('2.0.0',     sha256='0278728557b6684aeb86228f44d548ac809302f05a0b9c8b433cdd157629e384')
 
     # Don't second-guess what compiler we are using on Cray
     patch("configure.patch", when='@4.0.0')
diff --git a/var/spack/repos/builtin/packages/hstr/package.py b/var/spack/repos/builtin/packages/hstr/package.py
index b3669e0921..1a933f22fb 100644
--- a/var/spack/repos/builtin/packages/hstr/package.py
+++ b/var/spack/repos/builtin/packages/hstr/package.py
@@ -14,7 +14,7 @@ class Hstr(AutotoolsPackage):
     homepage = "https://github.com/dvorka/hstr"
     url      = "https://github.com/dvorka/hstr/archive/1.22.tar.gz"
 
-    version('1.22', '620dab922fadf2858938fbe36d9f99fd')
+    version('1.22', sha256='384fee04e4c80a1964dcf443131c1da4a20dd474fb48132a51d3de0a946ba996')
 
     depends_on('autoconf', type='build')
     depends_on('automake', type='build')
diff --git a/var/spack/repos/builtin/packages/libbeato/package.py b/var/spack/repos/builtin/packages/libbeato/package.py
index 8c6db5eb77..58fde449ea 100644
--- a/var/spack/repos/builtin/packages/libbeato/package.py
+++ b/var/spack/repos/builtin/packages/libbeato/package.py
@@ -12,6 +12,6 @@ class Libbeato(AutotoolsPackage):
     from UCSC's Genome Browser Group."""
 
     homepage = "https://github.com/CRG-Barcelona/libbeato"
-    url      = "https://github.com/CRG-Barcelona/libbeato/archive/master.tar.gz"
+    git      = "https://github.com/CRG-Barcelona/libbeato.git"
 
-    version('master', 'ee6f0f0f3f09c4f601fcfed3b13e7395')
+    version('master', brancch='master')
diff --git a/var/spack/repos/builtin/packages/lsof/package.py b/var/spack/repos/builtin/packages/lsof/package.py
index a65c0503f6..8bc2c8897a 100644
--- a/var/spack/repos/builtin/packages/lsof/package.py
+++ b/var/spack/repos/builtin/packages/lsof/package.py
@@ -12,7 +12,7 @@ class Lsof(Package):
     homepage = "https://people.freebsd.org/~abe/"
     url      = "https://www.mirrorservice.org/sites/lsof.itap.purdue.edu/pub/tools/unix/lsof/lsof_4.89.tar.gz"
 
-    version('4.89', '8afbaff3ee308edc130bdc5df0801c8f')
+    version('4.89', sha256='ff4ac555966b587f06338475c8fcc0f41402b4c8e970e730f6f83b62be8b5c0d')
 
     def install(self, spec, prefix):
         tar = which('tar')
diff --git a/var/spack/repos/builtin/packages/nektar/package.py b/var/spack/repos/builtin/packages/nektar/package.py
index 86e929ead5..d2cc96d92b 100644
--- a/var/spack/repos/builtin/packages/nektar/package.py
+++ b/var/spack/repos/builtin/packages/nektar/package.py
@@ -12,7 +12,7 @@ class Nektar(CMakePackage):
     homepage = "https://www.nektar.info/"
     url      = "https://gitlab.nektar.info/nektar/nektar/-/archive/v4.4.1/nektar-v4.4.1.tar.bz2"
 
-    version('4.4.1', '1be7d061c3cafd9a0f1eb8d281d99b89')
+    version('4.4.1', sha256='71cfd93d848a751ae9ae5e5ba336cee4b4827d4abcd56f6b8dc5c460ed6b738c')
 
     variant('mpi', default=True, description='Builds with mpi support')
     variant('fftw', default=True, description='Builds with fftw support')
diff --git a/var/spack/repos/builtin/packages/ocaml/package.py b/var/spack/repos/builtin/packages/ocaml/package.py
index 73a64f861c..e3d3cb9c83 100644
--- a/var/spack/repos/builtin/packages/ocaml/package.py
+++ b/var/spack/repos/builtin/packages/ocaml/package.py
@@ -11,10 +11,10 @@ class Ocaml(Package):
        functional, imperative and object-oriented styles"""
 
     homepage = "http://ocaml.org/"
-    url      = "http://caml.inria.fr/pub/distrib/ocaml-4.03/ocaml-4.03.0.tar.gz"
+    url      = "https://caml.inria.fr/pub/distrib/ocaml-4.06/ocaml-4.06.0.tar.gz"
 
-    version('4.06.0', '66e5439eb63dbb8b8224cba5d1b20947')
-    version('4.03.0', '43812739ea1b4641cf480f57f977c149')
+    version('4.06.0', sha256='c17578e243c4b889fe53a104d8927eb8749c7be2e6b622db8b3c7b386723bf50')
+    version('4.03.0', sha256='7fdf280cc6c0a2de4fc9891d0bf4633ea417046ece619f011fd44540fcfc8da2')
 
     depends_on('ncurses')
 
diff --git a/var/spack/repos/builtin/packages/octopus/package.py b/var/spack/repos/builtin/packages/octopus/package.py
index d6dc0a2402..4e7aa3322e 100644
--- a/var/spack/repos/builtin/packages/octopus/package.py
+++ b/var/spack/repos/builtin/packages/octopus/package.py
@@ -10,12 +10,12 @@ class Octopus(Package):
     """A real-space finite-difference (time-dependent) density-functional
     theory code."""
 
-    homepage = "http://www.tddft.org/programs/octopus/"
-    url      = "http://www.tddft.org/programs/octopus/down.php?file=6.0/octopus-6.0.tar.gz"
+    homepage = "https://octopus-code.org/"
+    url      = "http://octopus-code.org/down.php?file=6.0/octopus-6.0.tar.gz"
 
-    version('7.3', '87e51fa4a3a999706ea4ea5e9136996f')
-    version('6.0', '5d1168c2a8d7fd9cb9492eaebaa7182e')
-    version('5.0.1', '2b6392ab67b843f9d4ca7413fc07e822')
+    version('7.3',   sha256='ad843d49d4beeed63e8b9a2ca6bfb2f4c5a421f13a4f66dc7b02f6d6a5c4d742')
+    version('6.0',   sha256='4a802ee86c1e06846aa7fa317bd2216c6170871632c9e03d020d7970a08a8198')
+    version('5.0.1', sha256='3423049729e03f25512b1b315d9d62691cd0a6bd2722c7373a61d51bfbee14e0')
 
     variant('scalapack', default=False,
             description='Compile with Scalapack')
diff --git a/var/spack/repos/builtin/packages/openmc/package.py b/var/spack/repos/builtin/packages/openmc/package.py
index 247e6fe86d..5627ac0dc6 100644
--- a/var/spack/repos/builtin/packages/openmc/package.py
+++ b/var/spack/repos/builtin/packages/openmc/package.py
@@ -18,7 +18,7 @@ class Openmc(CMakePackage):
     url = "https://github.com/openmc-dev/openmc/tarball/v0.10.0"
     git = "https://github.com/openmc-dev/openmc.git"
 
-    version('0.10.0', 'abb57bd1b226eb96909dafeec31369b0')
+    version('0.10.0', sha256='47650cb45e2c326ae439208d6f137d75ad3e5c657055912d989592c6e216178f')
     version('develop')
 
     depends_on("hdf5+hl")
diff --git a/var/spack/repos/builtin/packages/parmgridgen/package.py b/var/spack/repos/builtin/packages/parmgridgen/package.py
index 457770edb2..74305fc907 100644
--- a/var/spack/repos/builtin/packages/parmgridgen/package.py
+++ b/var/spack/repos/builtin/packages/parmgridgen/package.py
@@ -16,9 +16,9 @@ class Parmgridgen(Package):
     """
 
     homepage = "http://www-users.cs.umn.edu/~moulitsa/software.html"
-    url = "http://www-users.cs.umn.edu/~moulitsa/download/ParMGridGen-1.0.tar.gz"
+    url = "http://www.stasyan.com/devel/distfiles/ParMGridGen-1.0.tar.gz"
 
-    version('1.0', '2872fa95b7fb91d6bd525490eed62038')
+    version('1.0', sha256='62cdb6e48cfc59124e5d5d360c2841e0fc2feecafe65bda110b74e942740b395')
 
     variant('mpi', default=True,
             description='Activate the compilation of parallel libraries')
diff --git a/var/spack/repos/builtin/packages/pgi/package.py b/var/spack/repos/builtin/packages/pgi/package.py
index b3c7bcbb23..c61611e22f 100644
--- a/var/spack/repos/builtin/packages/pgi/package.py
+++ b/var/spack/repos/builtin/packages/pgi/package.py
@@ -20,17 +20,12 @@ class Pgi(Package):
 
     homepage = "http://www.pgroup.com/"
 
-    version('19.4', sha256='23eee0d4da751dd6f247d624b68b03538ebd172e63a053c41bb67013f07cf68e')
-    version('19.1', sha256='3e05a6db2bf80b5d15f6ff83188f20cb89dc23e233417921e5c0822e7e57d34f')
+    version('19.4',  sha256='23eee0d4da751dd6f247d624b68b03538ebd172e63a053c41bb67013f07cf68e')
+    version('19.1',  sha256='3e05a6db2bf80b5d15f6ff83188f20cb89dc23e233417921e5c0822e7e57d34f')
     version('18.10', sha256='4b3ff83d2a13de6001bed599246eff8e63ef711b8952d4a9ee12efd666b3e326')
-    version('18.4',  'b55461f9f0986acbd51902c51c2074b9')
-    version('17.10', '85ad6506e7ada610ab11ddb35d697efa')
-    version('17.4',  'a311d2756ddda657860bad8e5725597b')
-    version('17.3',  '6eefc42f85e756cbaba76467ed640902')
-    version('16.10', '9bb6bfb7b1052f9e6a45829ba7a24e47')
-    version('16.5',  'a40e8852071b5d600cb42f31631b3de1')
-    version('16.3',  '618cb7ddbc57d4e4ed1f21a0ab25f427')
-    version('15.7',  '84a689217b17cdaf78c39270c70bea5d')
+    version('18.4',  sha256='81e0dcf6000b026093ece180d42d77854c23269fb8409cedcf51c674ca580a0f')
+    version('17.10', sha256='9da8f869fb9b70c0c4423c903d40a9e22d54b997af359a43573c0841165cd1b6')
+    version('17.4',  sha256='115c212d526695fc116fe44f1e722793e60b6f7d1b341cd7e77a95da8e7f6c34')
 
     variant('network', default=True,
             description="Perform a network install")
diff --git a/var/spack/repos/builtin/packages/porta/package.py b/var/spack/repos/builtin/packages/porta/package.py
index fac5198ce8..d3bc8a466b 100644
--- a/var/spack/repos/builtin/packages/porta/package.py
+++ b/var/spack/repos/builtin/packages/porta/package.py
@@ -11,9 +11,9 @@ class Porta(Package):
     """PORTA is a collection of routines for analyzing polytopes and
     polyhedra"""
     homepage = "http://porta.zib.de"
-    url      = "http://porta.zib.de/porta-1.4.1.tgz"
+    url      = "http://porta.zib.de/porta-1.4.1.zip"
 
-    version('1.4.1', '585179bf19d214ed364663a5d17bd5fc')
+    version('1.4.1', sha256='21e3784f46f4f2154100a0c39cbd9211a26e513ffe0c9f70ab75a3bb2810b059')
 
     depends_on("libtool", type="build")
 
diff --git a/var/spack/repos/builtin/packages/psi4/package.py b/var/spack/repos/builtin/packages/psi4/package.py
index f9c422baab..be9d5046eb 100644
--- a/var/spack/repos/builtin/packages/psi4/package.py
+++ b/var/spack/repos/builtin/packages/psi4/package.py
@@ -13,9 +13,9 @@ class Psi4(CMakePackage):
     a variety of molecular properties."""
 
     homepage = "http://www.psicode.org/"
-    url = "https://github.com/psi4/psi4/archive/0.5.tar.gz"
+    url = "https://github.com/psi4/psi4/archive/v1.3.2.tar.gz"
 
-    version('0.5', '53041b8a9be3958384171d0d22f9fdd0')
+    version('1.3.2', sha256='ed76c67803b6420f35f57a6dd31c47108b9145b8c9fced5c94cdc179f6b5fbf3')
 
     variant('build_type', default='Release',
             description='The build type to build',
diff --git a/var/spack/repos/builtin/packages/pslib/package.py b/var/spack/repos/builtin/packages/pslib/package.py
index 1be61a940b..7cb6601b2c 100644
--- a/var/spack/repos/builtin/packages/pslib/package.py
+++ b/var/spack/repos/builtin/packages/pslib/package.py
@@ -10,9 +10,9 @@ class Pslib(AutotoolsPackage):
     """C-library to create PostScript files on the fly."""
 
     homepage = "http://pslib.sourceforge.net/"
-    url      = "https://kent.dl.sourceforge.net/project/pslib/pslib/0.4.5/pslib-0.4.5.tar.gz"
+    url      = "https://sourceforge.net/projects/pslib/files/pslib/0.4.5/pslib-0.4.5.tar.gz"
 
-    version('0.4.5', '03f39393628a6d758799b9f845047e27')
+    version('0.4.5', sha256='7a33928982b281660206bb3749a4a563e3ac987eea64f41696f212df345212be')
 
     depends_on('jpeg')
     depends_on('libpng')
diff --git a/var/spack/repos/builtin/packages/pstreams/package.py b/var/spack/repos/builtin/packages/pstreams/package.py
index 48ae581996..fc4bbff2d7 100644
--- a/var/spack/repos/builtin/packages/pstreams/package.py
+++ b/var/spack/repos/builtin/packages/pstreams/package.py
@@ -11,9 +11,9 @@ class Pstreams(Package):
     """C++ wrapper for the POSIX.2 functions popen(3) and pclose(3)"""
 
     homepage = "http://pstreams.sourceforge.net/"
-    url      = "https://superb-sea2.dl.sourceforge.net/project/pstreams/pstreams/Release%201.0/pstreams-1.0.1.tar.gz"
+    url      = "https://sourceforge.net/projects/pstreams/files/pstreams/Release%201.0/pstreams-1.0.1.tar.gz"
 
-    version('1.0.1', '23199e3d12a644a2a0c66ec889d4c064')
+    version('1.0.1', sha256='a5f1f2e014392cd0e2cdb508a429e11afe64140db05b7f0a83d7534faa1a9226')
 
     def install(self, spec, prefix):
         mkdirp(prefix.include)
diff --git a/var/spack/repos/builtin/packages/py-opppy/package.py b/var/spack/repos/builtin/packages/py-opppy/package.py
index a005332ab0..b6edea8226 100644
--- a/var/spack/repos/builtin/packages/py-opppy/package.py
+++ b/var/spack/repos/builtin/packages/py-opppy/package.py
@@ -16,7 +16,7 @@ class PyOpppy(PythonPackage):
     git = "https://github.com/lanl/opppy.git"
 
     version('master', branch='master')
-    version('0.1.1', '852a1329ce68d678623beed3fd01ea98')
+    version('0_1_1', sha256='505c023853e75552abc65de9777a125ecb6a99a1cb4e605a4f702af837e3168b')
 
     depends_on('py-setuptools', type=('build', 'run'))
     depends_on('py-numpy@1.6:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-perf/package.py b/var/spack/repos/builtin/packages/py-perf/package.py
index 211479fb94..2d2c025691 100644
--- a/var/spack/repos/builtin/packages/py-perf/package.py
+++ b/var/spack/repos/builtin/packages/py-perf/package.py
@@ -11,10 +11,10 @@ class PyPerf(PythonPackage):
     analyze benchmarks.
     """
 
-    homepage = "https://pypi.python.org/pypi/perf"
-    url = "https://github.com/vstinner/perf/archive/1.5.1.tar.gz"
+    homepage = "https://pypi.python.org/pypi/pyperf"
+    url = "https://github.com/vstinner/pyperf/archive/1.5.1.tar.gz"
 
-    version('1.5.1', 'e3dc532fdbaf44f2d921556164bd74e5')
+    version('1.5.1', sha256='9c271862bc2911be8eb01031a4a86cbc3f5bb615971514383802d3dcf46f18ed')
 
     depends_on('py-setuptools', type='build')
     depends_on('py-six', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-performance/package.py b/var/spack/repos/builtin/packages/py-performance/package.py
index 3d07e1562b..9abc3c4d48 100644
--- a/var/spack/repos/builtin/packages/py-performance/package.py
+++ b/var/spack/repos/builtin/packages/py-performance/package.py
@@ -17,8 +17,8 @@ class PyPerformance(PythonPackage):
     homepage = 'http://pyperformance.readthedocs.io/'
     url = 'https://github.com/python/performance/archive/0.6.1.tar.gz'
 
-    version('0.6.1', '95477b584a284582b66c922a5335b427')
-    version('0.6.0', 'b93661e07668fa0b461236dca164eedf')
+    version('0.6.1', sha256='cc48dd7579da2f4b0e4cff0c8220811f5ba7019493bb408819c1532acf53d13a')
+    version('0.6.0', sha256='4636e276445e96563f628e071cacd5df31dc587d83899e7d03fa8b31760f2cd2')
 
     depends_on('py-setuptools', type=('build', 'run'))
     depends_on('py-six', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-tomopy/package.py b/var/spack/repos/builtin/packages/py-tomopy/package.py
index 93a82bf0e9..b838561efd 100644
--- a/var/spack/repos/builtin/packages/py-tomopy/package.py
+++ b/var/spack/repos/builtin/packages/py-tomopy/package.py
@@ -19,7 +19,7 @@ class PyTomopy(PythonPackage):
         'tomopy.prep', 'tomopy.misc', 'tomopy.io', 'doc.demo'
     ]
 
-    version('1.0.0', '986ac2c85a4af9ada0403b4c746d2cd4')
+    version('1.0.0', sha256='ee45f7a062e5a66d6f18a904d2e204e48d85a1ce1464156f9e2f6353057dfe4c')
 
     depends_on('py-setuptools', type='build')
     depends_on('py-numpy', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-udunits/package.py b/var/spack/repos/builtin/packages/py-udunits/package.py
index f0f37ff051..b7fb343439 100644
--- a/var/spack/repos/builtin/packages/py-udunits/package.py
+++ b/var/spack/repos/builtin/packages/py-udunits/package.py
@@ -12,7 +12,7 @@ class PyUdunits(PythonPackage):
     homepage = "https://github.com/SciTools/cf_units"
     url      = "https://github.com/SciTools/cf_units/archive/v1.1.3.tar.gz"
 
-    version('1.1.3', '61ea2239c87b4c1d5d30147800a9e750')
+    version('1.1.3', sha256='cc27f4f06c99d242c36beb8dc5c517e1b1124a8c65ca3f76f372b9674aa320ba')
 
     maintainers = ['citibeth']
 
diff --git a/var/spack/repos/builtin/packages/r-abadata/package.py b/var/spack/repos/builtin/packages/r-abadata/package.py
index 8c79dce6c5..2f4f6f1ebc 100644
--- a/var/spack/repos/builtin/packages/r-abadata/package.py
+++ b/var/spack/repos/builtin/packages/r-abadata/package.py
@@ -17,6 +17,6 @@ class RAbadata(RPackage):
     All datasets are restricted to protein coding genes."""
 
     homepage = "https://bioconductor.org/packages/ABAData/"
-    url      = "https://bioconductor.org/packages/release/data/experiment/src/contrib/ABAData_1.6.0.tar.gz"
+    url      = "https://bioconductor.org/packages/release/data/experiment/src/contrib/ABAData_1.14.0.tar.gz"
 
-    version('1.6.0', '9adfb9fbb39ad05cf72852a229476fb7')
+    version('1.14.0', sha256='d203d968044c292cdfab57a4d6bf52dfb60470bd78b4c9bd88892577ac42b2b7')
diff --git a/var/spack/repos/builtin/packages/r-acde/package.py b/var/spack/repos/builtin/packages/r-acde/package.py
index 107c7937bc..4b49104897 100644
--- a/var/spack/repos/builtin/packages/r-acde/package.py
+++ b/var/spack/repos/builtin/packages/r-acde/package.py
@@ -20,8 +20,8 @@ class RAcde(RPackage):
     (2015, pending publication)."""
 
     homepage = "https://www.bioconductor.org/packages/acde/"
-    url      = "https://www.bioconductor.org/packages/release/bioc/src/contrib/acde_1.6.0.tar.gz"
+    url      = "https://bioconductor.org/packages/release/bioc/src/contrib/acde_1.14.0.tar.gz"
 
-    version('1.6.0', 'e92ce91f75bab3bb1d79995bec1b42cc')
+    version('1.14.0', sha256='e8d9ad688610d4b72cab729141dc46fce580c97128d929885336bb138345b788')
 
     depends_on('r-boot', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-affydata/package.py b/var/spack/repos/builtin/packages/r-affydata/package.py
index a310286ef7..c5bcc2c329 100644
--- a/var/spack/repos/builtin/packages/r-affydata/package.py
+++ b/var/spack/repos/builtin/packages/r-affydata/package.py
@@ -12,9 +12,9 @@ class RAffydata(RPackage):
     package affy."""
 
     homepage = "https://www.bioconductor.org/packages/affydata/"
-    url      = "https://www.bioconductor.org/packages/release/data/experiment/src/contrib/affydata_1.24.0.tar.gz"
+    url      = "https://www.bioconductor.org/packages/release/data/experiment/src/contrib/affydata_1.32.0.tar.gz"
 
-    version('1.24.0', '0b6938685c450a56d65dd5628ebed42d')
+    version('1.32.0', sha256='059e05a2b8908720801d684d5617d5d5e45db7a5999c5659a22daf87658538d1')
 
     depends_on('r@3.4.0:3.4.9', when=('@1.24.0'))
     depends_on('r-affy', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/raft/package.py b/var/spack/repos/builtin/packages/raft/package.py
index f8426c663a..fda2e02a50 100644
--- a/var/spack/repos/builtin/packages/raft/package.py
+++ b/var/spack/repos/builtin/packages/raft/package.py
@@ -16,7 +16,7 @@ class Raft(CMakePackage):
     git      = "https://bitbucket.org/gill_martinez/raft_aps.git"
 
     version('develop', branch='master')
-    version('1.2.3', '4d1b106d9b3493e63dde96f7dd44b834')
+    version('1.2.3', sha256='c41630e74491c8db272dcf4707e9b11cdcb226c0b7e978ca6eba8006f47bdae6')
 
     depends_on('mpi')
     depends_on('cmake', type='build')
diff --git a/var/spack/repos/builtin/packages/snpeff/package.py b/var/spack/repos/builtin/packages/snpeff/package.py
index c9e8e1dcd5..d0c60c586e 100644
--- a/var/spack/repos/builtin/packages/snpeff/package.py
+++ b/var/spack/repos/builtin/packages/snpeff/package.py
@@ -13,9 +13,9 @@ class Snpeff(Package):
     amino acid changes)."""
 
     homepage = "http://snpeff.sourceforge.net/"
-    url      = "https://kent.dl.sourceforge.net/project/snpeff/snpEff_latest_core.zip"
+    url      = "https://downloads.sourceforge.net/project/snpeff/snpEff_latest_core.zip"
 
-    version('2017-11-24', '1fa84a703580a423e27f1e14a945901c')
+    version('2017-11-24', sha256='d55a7389a78312947c1e7dadf5e6897b42d3c6e942e7c1b8ec68bb35d2ae2244')
 
     depends_on('jdk', type=('build', 'run'))
 
diff --git a/var/spack/repos/builtin/packages/stress/package.py b/var/spack/repos/builtin/packages/stress/package.py
index 6531962011..93cb340220 100644
--- a/var/spack/repos/builtin/packages/stress/package.py
+++ b/var/spack/repos/builtin/packages/stress/package.py
@@ -12,7 +12,9 @@ class Stress(AutotoolsPackage):
     the system. It is written in C, and is free software licensed under the
     GPLv2."""
 
-    homepage = "https://people.seas.harvard.edu/~apw/stress/"
-    url      = "https://people.seas.harvard.edu/~apw/stress/stress-1.0.4.tar.gz"
+    # Moved from original homepage
+    # homepage = "https://people.seas.harvard.edu/~apw/stress/"
+    homepage = "https://github.com/javiroman/system-stress"
+    url      = "https://github.com/javiroman/system-stress/archive/v1.0.4.tar.gz"
 
-    version('1.0.4', '890a4236dd1656792f3ef9a190cf99ef')
+    version('1.0.4', sha256='b03dbb9664d7f8dcb3eadc918c2e8eb822f5a3ba47d9bd51246540bac281bd75')
diff --git a/var/spack/repos/builtin/packages/xdmf3/package.py b/var/spack/repos/builtin/packages/xdmf3/package.py
index c14560816f..772135846c 100644
--- a/var/spack/repos/builtin/packages/xdmf3/package.py
+++ b/var/spack/repos/builtin/packages/xdmf3/package.py
@@ -18,7 +18,7 @@ class Xdmf3(CMakePackage):
 
     # There is no official release of XDMF and development has largely ceased,
     # but the current version, 3.x, is maintained on the master branch.
-    version('2019-01-14', '8d9c98081d89ac77a132d56bc8bef53581db4078')
+    version('2019-01-14', commit='8d9c98081d89ac77a132d56bc8bef53581db4078')
 
     variant('shared', default=True, description='Enable shared libraries')
     variant('mpi', default=True, description='Enable MPI')
diff --git a/var/spack/repos/builtin/packages/yorick/package.py b/var/spack/repos/builtin/packages/yorick/package.py
index 59cc2751cf..caffcfa11d 100644
--- a/var/spack/repos/builtin/packages/yorick/package.py
+++ b/var/spack/repos/builtin/packages/yorick/package.py
@@ -22,7 +22,7 @@ class Yorick(Package):
     git      = "https://github.com/dhmunro/yorick.git"
 
     version('master', branch='master')
-    version('2.2.04', '1b5b0da6ad81b2d9dba64d991ec17939')
+    version('2.2.04', sha256='4a4f3a18aed533cc5fadbb3d4bafb48f04834a22cbff6ad5c19d9dba74facbda')
     version('f90-plugin', branch='f90-plugin')
 
     variant('X', default=False, description='Enable X11 support')