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.

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')

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')

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):

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('2.4.10', sha256='5d3c39894598d2395149cfcc653af13b8b1091177290edd62fcf22c7e830d410')
-    version('2.3.23', '2913c3e440f82db069051f8822115e5e')
+    version('2.3.23', sha256='1217d16eaf9d263f917ee468778508bad9dacb7e4397a293cfa6467f39fb4c52')
-    version('2.2.0',  'd949cfe338c83ee736ca0be8f77df6bf',
+    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')

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

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')
 

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('11.2.linux.i586_64', sha256='13d28188924e0b0b803d72aa4b48be4067e98e890701b0aa6f54a11c7d34dd10')
-    version('11.0.linux.i586_64', '6fb099b54f41db009cafc702eebb5bc6')
 
     depends_on('motif')
     depends_on('gl')

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:

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)

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'))
 

var/spack/repos/builtin/packages/gnu-prolog/package.py

@@ -9,9 +9,9 @@
 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
 

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')

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('3.1.2', sha256='02f277c9fc75d4b13c7697ed6be30dba41667841ab5e37442855267c39bec6b6')
-    version('2.9.0', 'b443ead81aa2bd5086f99e62e66a8f64')
 
     depends_on('java', type='run')
 

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')

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"
+    url      = "https://github.com/adk9/hpx5/archive/v3.1.0.tar.gz"
 
-    version('4.1.0', '43cb78758506f77416b95276a472f84f')
+    version('4.1.0',     sha256='3f01009f5e517c8dfca266dabb49894d688db5adce09608fb1c877263605a9f8')
-    version('4.0.0', 'b40dc03449ae1039cbb48ee149952b22')
+    version('4.0.0',     sha256='e35b1161566a65ffbd875c1413ea97a84be0c7b528a3dee99f5e250b2aecbd19')
-    version('3.1.0', '9e90b8ac46788c009079632828c77628')
+    version('3.1.0',     sha256='359d457a26b87abb415605911d791ce0ff6edbb064bc40b0f830960f8f612b84')
-    version('2.0.0', '3d2ff3aab6c46481f9ec65c5b2bfe7a6')
+    version('3.0.0',     sha256='10f14ba198a32787cee05962e346bafb922f74a5135fb09a1ba8c32a1e942800')
-    version('1.3.0', '2260ecc7f850e71a4d365a43017d8cee')
+    version('2.2.0',     sha256='e34c7513a287d517e67cce5aa3011474c48718e7860c3860ba1290c702be28a8')
-    version('1.2.0', '4972005f85566af4afe8b71afbf1480f')
+    version('2.1.0',     sha256='675826f669eeb3eab40947715af8c8495e2b3d299223372431dc01c1f7d5d616')
-    version('1.1.0', '646afb460ecb7e0eea713a634933ce4f')
+    version('2.0.0',     sha256='0278728557b6684aeb86228f44d548ac809302f05a0b9c8b433cdd157629e384')
-    version('1.0.0', '8020822adf6090bd59ed7fe465f6c6cb')
 
     # Don't second-guess what compiler we are using on Cray
     patch("configure.patch", when='@4.0.0')

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')

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')

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')

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')

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('4.06.0', sha256='c17578e243c4b889fe53a104d8927eb8749c7be2e6b622db8b3c7b386723bf50')
-    version('4.03.0', '43812739ea1b4641cf480f57f977c149')
+    version('4.03.0', sha256='7fdf280cc6c0a2de4fc9891d0bf4633ea417046ece619f011fd44540fcfc8da2')
 
     depends_on('ncurses')
 

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/"
+    homepage = "https://octopus-code.org/"
-    url      = "http://www.tddft.org/programs/octopus/down.php?file=6.0/octopus-6.0.tar.gz"
+    url      = "http://octopus-code.org/down.php?file=6.0/octopus-6.0.tar.gz"
 
-    version('7.3', '87e51fa4a3a999706ea4ea5e9136996f')
+    version('7.3',   sha256='ad843d49d4beeed63e8b9a2ca6bfb2f4c5a421f13a4f66dc7b02f6d6a5c4d742')
-    version('6.0', '5d1168c2a8d7fd9cb9492eaebaa7182e')
+    version('6.0',   sha256='4a802ee86c1e06846aa7fa317bd2216c6170871632c9e03d020d7970a08a8198')
-    version('5.0.1', '2b6392ab67b843f9d4ca7413fc07e822')
+    version('5.0.1', sha256='3423049729e03f25512b1b315d9d62691cd0a6bd2722c7373a61d51bfbee14e0')
 
     variant('scalapack', default=False,
             description='Compile with Scalapack')

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")

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')

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('19.4',  sha256='23eee0d4da751dd6f247d624b68b03538ebd172e63a053c41bb67013f07cf68e')
-    version('19.1', sha256='3e05a6db2bf80b5d15f6ff83188f20cb89dc23e233417921e5c0822e7e57d34f')
+    version('19.1',  sha256='3e05a6db2bf80b5d15f6ff83188f20cb89dc23e233417921e5c0822e7e57d34f')
     version('18.10', sha256='4b3ff83d2a13de6001bed599246eff8e63ef711b8952d4a9ee12efd666b3e326')
-    version('18.4',  'b55461f9f0986acbd51902c51c2074b9')
+    version('18.4',  sha256='81e0dcf6000b026093ece180d42d77854c23269fb8409cedcf51c674ca580a0f')
-    version('17.10', '85ad6506e7ada610ab11ddb35d697efa')
+    version('17.10', sha256='9da8f869fb9b70c0c4423c903d40a9e22d54b997af359a43573c0841165cd1b6')
-    version('17.4',  'a311d2756ddda657860bad8e5725597b')
+    version('17.4',  sha256='115c212d526695fc116fe44f1e722793e60b6f7d1b341cd7e77a95da8e7f6c34')
-    version('17.3',  '6eefc42f85e756cbaba76467ed640902')
-    version('16.10', '9bb6bfb7b1052f9e6a45829ba7a24e47')
-    version('16.5',  'a40e8852071b5d600cb42f31631b3de1')
-    version('16.3',  '618cb7ddbc57d4e4ed1f21a0ab25f427')
-    version('15.7',  '84a689217b17cdaf78c39270c70bea5d')
 
     variant('network', default=True,
             description="Perform a network install")

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")
 

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',

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')

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)

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'))

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"
+    homepage = "https://pypi.python.org/pypi/pyperf"
-    url = "https://github.com/vstinner/perf/archive/1.5.1.tar.gz"
+    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'))

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('0.6.1', sha256='cc48dd7579da2f4b0e4cff0c8220811f5ba7019493bb408819c1532acf53d13a')
-    version('0.6.0', 'b93661e07668fa0b461236dca164eedf')
+    version('0.6.0', sha256='4636e276445e96563f628e071cacd5df31dc587d83899e7d03fa8b31760f2cd2')
 
     depends_on('py-setuptools', type=('build', 'run'))
     depends_on('py-six', type=('build', 'run'))

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'))

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']
 

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')

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'))

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'))

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')

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'))
 

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/"
+    # Moved from original homepage
-    url      = "https://people.seas.harvard.edu/~apw/stress/stress-1.0.4.tar.gz"
+    # 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')

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')

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')