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checksums: use sha256 checksums everywhere

Browse Source 
We'd like to use a consistent checksum scheme everywhere so that we can:

    a) incorporate archive checksums into our specs and have a
       consistent hashing algorithm across all specs.

    b) index mirrors with a consistent type of checksum, and not one that
       is dependent on how spack packages are written.

- [x] convert existing md5, sha224, sha512, sha1 checksums to sha256
This commit is contained in:
Todd Gamblin
2019-10-10 22:44:41 -07:00
parent 87fa7c15fc
commit 62927654dd
2344 changed files with 5728 additions and 5754 deletions
Download Patch File Download Diff File Expand all files Collapse all files

10
var/spack/repos/builtin/packages/abinit/package.py
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@@ -30,12 +30,12 @@ class Abinit(AutotoolsPackage):
homepage = 'http://www.abinit.org'
url = 'https://www.abinit.org/sites/default/files/packages/abinit-8.6.3.tar.gz'
version('8.10.3', '969303cf21526cef2a6a08118a3d30ae')
version('8.8.2', '72d7046c7ff31b9f17afe050ecdfb3a5')
version('8.6.3', '6c34d2cec0cf0008dd25b8ec1b6d3ee8')
version('8.2.2', '5f25250e06fdc0815c224ffd29858860')
version('8.10.3', sha256='ed626424b4472b93256622fbb9c7645fa3ffb693d4b444b07d488771ea7eaa75')
version('8.8.2', sha256='15216703bd56a799a249a112b336d07d733627d3756487a4b1cb48ebb625c3e7')
version('8.6.3', sha256='82e8d071088ab8dc1b3a24380e30b68c544685678314df1213180b449c84ca65')
version('8.2.2', sha256='e43544a178d758b0deff3011c51ef7c957d7f2df2ce8543366d68016af9f3ea1')
# Versions before 8.0.8b are not supported.
version('8.0.8b', 'abc9e303bfa7f9f43f95598f87d84d5d')
version('8.0.8b', sha256='37ad5f0f215d2a36e596383cb6e54de3313842a0390ce8d6b48a423d3ee25af2')
variant('mpi', default=True,
description='Builds with MPI support. Requires MPI2+')

4
var/spack/repos/builtin/packages/abyss/package.py
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@@ -15,8 +15,8 @@ class Abyss(AutotoolsPackage):
url = "https://github.com/bcgsc/abyss/releases/download/1.5.2/abyss-1.5.2.tar.gz"
version('2.1.4', sha256='2145a1727556104d6a14db06a9c06f47b96c31cc5ac595ae9c92224349bdbcfc')
version('2.0.2', '1623f55ad7f4586e80f6e74b1f27c798')
version('1.5.2', '10d6d72d1a915e618d41a5cbbcf2364c')
version('2.0.2', sha256='d87b76edeac3a6fb48f24a1d63f243d8278a324c9a5eb29027b640f7089422df')
version('1.5.2', sha256='8a52387f963afb7b63db4c9b81c053ed83956ea0a3981edcad554a895adf84b1')
variant('maxk', values=int, default=0,
description='''set the maximum k-mer length.

8
var/spack/repos/builtin/packages/ack/package.py
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@@ -16,10 +16,10 @@ class Ack(Package):
homepage = "http://beyondgrep.com/"
url = "http://beyondgrep.com/ack-2.14-single-file"
version('2.22', 'eea9d4daef7c262751f15ca9b3b70317', expand=False)
version('2.18', 'e8ebfd7a7ec8476bffd4686bf7b14fd7', expand=False)
version('2.16', '7085b5a5c76fda43ff049410870c8535', expand=False)
version('2.14', 'e74150a1609d28a70b450ef9cc2ed56b', expand=False)
version('2.22', sha256='fd0617585b88517a3d41d3d206c1dc38058c57b90dfd88c278049a41aeb5be38', expand=False)
version('2.18', sha256='6e41057c8f50f661d800099471f769209480efa53b8a886969d7ec6db60a2208', expand=False)
version('2.16', sha256='7f39f08ebb78ed160a41293d7f42ff1bdcdaf57aee859bc4c4888bdf4abee7f2', expand=False)
version('2.14', sha256='1d203cfbc52ce8f49e3992be1cd3e4d7d5dfb7daa3739e8628aa9858ccc5b9df', expand=False)
depends_on('perl')

2
var/spack/repos/builtin/packages/activeharmony/package.py
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@@ -12,7 +12,7 @@ class Activeharmony(Package):
homepage = "http://www.dyninst.org/harmony"
url = "http://www.dyninst.org/sites/default/files/downloads/harmony/ah-4.5.tar.gz"
version('4.5', 'caee5b864716d376e2c25d739251b2a9')
version('4.5', sha256='31d9990c8dd36724d336707d260aa4d976e11eaa899c4c7cc11f80a56cdac684')
def install(self, spec, prefix):
make("CFLAGS=-O3")

4
var/spack/repos/builtin/packages/adept-utils/package.py
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@@ -12,8 +12,8 @@ class AdeptUtils(CMakePackage):
homepage = "https://github.com/llnl/adept-utils"
url = "https://github.com/llnl/adept-utils/archive/v1.0.tar.gz"
version('1.0.1', '731a310717adcb004d9d195130efee7d')
version('1.0', '5c6cd9badce56c945ac8551e34804397')
version('1.0.1', sha256='259f777aeb368ede3583d3617bb779f0fde778319bf2122fdd216bdf223c015e')
version('1.0', sha256='fed29366c9bcf5f3799220ae3b351d2cb338e2aa42133d61584ea650aa8d6ff7')
depends_on('boost')
depends_on('mpi')

14
var/spack/repos/builtin/packages/adios/package.py
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@@ -20,13 +20,13 @@ class Adios(AutotoolsPackage):
maintainers = ['ax3l']
version('develop', branch='master')
version('1.13.1', '958aed11240d7f5a065ab5ee271ecb44')
version('1.13.0', '68af36b821debbdf4748b20320a990ce')
version('1.12.0', '84a1c71b6698009224f6f748c5257fc9')
version('1.11.1', '5639bfc235e50bf17ba9dafb14ea4185')
version('1.11.0', '5eead5b2ccf962f5e6d5f254d29d5238')
version('1.10.0', 'eff450a4c0130479417cfd63186957f3')
version('1.9.0', '310ff02388bbaa2b1c1710ee970b5678')
version('1.13.1', sha256='b1c6949918f5e69f701cabfe5987c0b286793f1057d4690f04747852544e157b')
version('1.13.0', sha256='7b5ee8ff7a5f7215f157c484b20adb277ec0250f87510513edcc25d2c4739f50')
version('1.12.0', sha256='22bc22c157322abec2d1a0817a259efd9057f88c2113e67d918a9a5ebcb3d88d')
version('1.11.1', sha256='9f5c10b9471a721ba57d1cf6e5a55a7ad139a6c12da87b4dc128539e9eef370e')
version('1.11.0', sha256='e89d14ccbe7181777225e0ba6c272c0941539b8ccd440e72ed5a9457441dae83')
version('1.10.0', sha256='6713069259ee7bfd4d03f47640bf841874e9114bab24e7b0c58e310c42a0ec48')
version('1.9.0', sha256='23b2bb70540d51ab0855af0b205ca484fd1bd963c39580c29e3133f9e6fffd46')
variant('shared', default=True,
description='Builds a shared version of the library')

6
var/spack/repos/builtin/packages/adlbx/package.py
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@@ -15,9 +15,9 @@ class Adlbx(AutotoolsPackage):
git = "https://github.com/swift-lang/swift-t.git"
version('master', branch='master')
version('0.9.2', 'a7d9e208eb3b49b8bb857562f6bb61bb')
version('0.9.1', '07151ddef5fb83d8f4b40700013d9daf')
version('0.8.0', '34ade59ce3be5bc296955231d47a27dd')
version('0.9.2', sha256='524902d648001b689a98492402d754a607b8c1d0734699154063c1a4f3410d4a')
version('0.9.1', sha256='8913493fe0c097ff13c721ab057514e5bdb55f6318d4e3512692ab739c3190b3')
version('0.8.0', md5='34ade59ce3be5bc296955231d47a27dd')
depends_on('exmcutils@master', when='@master')
depends_on('exmcutils@:0.5.3', when='@:0.8.0')

8
var/spack/repos/builtin/packages/adol-c/package.py
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@@ -16,10 +16,10 @@ class AdolC(AutotoolsPackage):
git = "https://gitlab.com/adol-c/adol-c.git"
version('develop', branch='master')
version('2.6.3', 'f78f67f70d5874830a1ad1c0f54e54f7')
version('2.6.2', '0f9547584c99c0673e4f81cf64e8d865')
version('2.6.1', '1032b28427d6e399af4610e78c0f087b')
version('2.5.2', '96f81b80e93cca57398066ea4afe28f0')
version('2.6.3', sha256='6ed74580695a0d2c960581e5430ebfcd380eb5da9337daf488bf2e89039e9c21')
version('2.6.2', sha256='f6326e7ba994d02074816132d4461915221069267c31862b31fab7020965c658')
version('2.6.1', sha256='037089e0f64224e5e6255b61af4fe7faac080533fd778b76fe946e52491918b5')
version('2.5.2', sha256='2fa514d9799989d6379738c2bcf75070d9834e4d227eb32a5b278840893b2af9')
variant('advanced_branching', default=False,
description='Enable advanced branching to reduce retaping')

2
var/spack/repos/builtin/packages/aegean/package.py
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@@ -15,7 +15,7 @@ class Aegean(MakefilePackage):
homepage = "http://brendelgroup.github.io/AEGeAn/"
url = "https://github.com/BrendelGroup/AEGeAn/archive/v0.15.2.tar.gz"
version('0.15.2', 'd7d73f5f132ff52340975b636564e949')
version('0.15.2', sha256='734c9dd23ab3415c3966083bfde5fb72c81e6ace84e08ee3fe0d4c338331d975')
depends_on('genometools')

2
var/spack/repos/builtin/packages/albert/package.py
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@@ -13,7 +13,7 @@ class Albert(MakefilePackage):
homepage = "https://people.cs.clemson.edu/~dpj/albertstuff/albert.html"
url = "https://github.com/kentavv/Albert/archive/v4.0a_opt4.tar.gz"
version('4.0a_opt4', '79e3d9623602f2ca5db7d84c81d4eb8c')
version('4.0a_opt4', sha256='80b9ee774789c9cd123072523cfb693c443c3624708a58a5af177a51f36b2c79')
depends_on('readline')

2
var/spack/repos/builtin/packages/alglib/package.py
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@@ -16,7 +16,7 @@ class Alglib(MakefilePackage):
homepage = "http://www.alglib.net"
url = "http://www.alglib.net/translator/re/alglib-3.11.0.cpp.gpl.tgz"
version('3.11.0', 'f87bb05349924d486e8809590dee9f80')
version('3.11.0', sha256='34e391594aac89fb354bdaf58c42849489cd1199197398ba98bb69961f42bdb0')
def url_for_version(self, version):
return 'http://www.alglib.net/translator/re/alglib-{0}.cpp.gpl.tgz'.format(version.dotted)

2
var/spack/repos/builtin/packages/allpaths-lg/package.py
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@@ -13,7 +13,7 @@ class AllpathsLg(AutotoolsPackage):
homepage = "http://www.broadinstitute.org/software/allpaths-lg/blog/"
url = "ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/LATEST_VERSION.tar.gz"
version('52488', 'bde9008e236d87708a48eb83af6d6d5b')
version('52488', sha256='035b49cb21b871a6b111976757d7aee9c2513dd51af04678f33375e620998542')
# compiles with gcc 4.7.0 to 4.9.4)
conflicts('%gcc@:4.6.4,5.1.0:')

2
var/spack/repos/builtin/packages/alsa-lib/package.py
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@@ -14,4 +14,4 @@ class AlsaLib(AutotoolsPackage):
homepage = "https://www.alsa-project.org"
url = "ftp://ftp.alsa-project.org/pub/lib/alsa-lib-1.1.4.1.tar.bz2"
version('1.1.4.1', '29fa3e69122d3cf3e8f0e01a0cb1d183')
version('1.1.4.1', sha256='91bb870c14d1c7c269213285eeed874fa3d28112077db061a3af8010d0885b76')

2
var/spack/repos/builtin/packages/amg2013/package.py
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@@ -17,7 +17,7 @@ class Amg2013(MakefilePackage):
homepage = "https://computing.llnl.gov/projects/co-design/amg2013"
url = "https://computing.llnl.gov/projects/co-design/download/amg2013.tgz"
version('master', '9d918d2a69528b83e6e0aba6ba601fef',
version('master', sha256='b03771d84a04e3dbbbe32ba5648cd7b789e5853b938dd501e17d23d43f13c50f',
url='https://computing.llnl.gov/projects/co-design/download/amg2013.tgz')
variant('openmp', default=True, description='Build with OpenMP support')

2
var/spack/repos/builtin/packages/aml/package.py
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@@ -11,7 +11,7 @@ class Aml(AutotoolsPackage):
homepage = "https://xgitlab.cels.anl.gov/argo/aml"
url = "https://www.mcs.anl.gov/research/projects/argo/downloads/aml-0.1.0.tar.gz"
version('0.1.0', 'f704397fe568bcb334ee0cbc4f9e066e')
version('0.1.0', sha256='cc89a8768693f1f11539378b21cdca9f0ce3fc5cb564f9b3e4154a051dcea69b')
depends_on('numactl')

2
var/spack/repos/builtin/packages/ampliconnoise/package.py
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@@ -13,7 +13,7 @@ class Ampliconnoise(MakefilePackage):
homepage = "https://code.google.com/archive/p/ampliconnoise/"
url = "https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/ampliconnoise/AmpliconNoiseV1.29.tar.gz"
version('1.29', 'd6723e6f9cc71d7eb6f1a65ba4643aac')
version('1.29', sha256='0bf946806d77ecaf0994ad8ebf9a5e98ad33c809f6def5c9340a16c367918167')
depends_on('mpi@2:')
depends_on('gsl')

2
var/spack/repos/builtin/packages/andi/package.py
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@@ -13,7 +13,7 @@ class Andi(AutotoolsPackage):
homepage = "https://github.com/EvolBioInf/andi"
url = "https://github.com/EvolBioInf/andi/archive/v0.10.tar.gz"
version('0.10', '3aaba7961798bb4aaa546baa44e469d8')
version('0.10', sha256='1ff371de0b6db4080e402ded2687947dc2d6913e28626edec21dcf5149489ee8')
depends_on('m4', type='build')
depends_on('autoconf', type='build')

4
var/spack/repos/builtin/packages/angsd/package.py
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@@ -16,8 +16,8 @@ class Angsd(MakefilePackage):
homepage = "https://github.com/ANGSD/angsd"
url = "https://github.com/ANGSD/angsd/archive/0.919.tar.gz"
version('0.921', '3702db035396db602c7f74728b1a5a1f')
version('0.919', '79d342f49c24ac00d35934f2617048d4')
version('0.921', sha256='8892d279ce1804f9e17fe2fc65a47e5498e78fc1c1cb84d2ca2527fd5c198772')
version('0.919', sha256='c2ea718ca5a5427109f4c3415e963dcb4da9afa1b856034e25c59c003d21822a')
depends_on('htslib')
conflicts('^htslib@1.6:', when='@0.919')

10
var/spack/repos/builtin/packages/ant/package.py
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@@ -15,11 +15,11 @@ class Ant(Package):
homepage = "http://ant.apache.org/"
url = "https://archive.apache.org/dist/ant/source/apache-ant-1.9.7-src.tar.gz"
version('1.10.0', '2260301bb7734e34d8b96f1a5fd7979c')
version('1.9.9', '22c9d40dabafbec348aaada226581239')
version('1.9.8', '16253d516d5c33c4af9ef8fafcf1004b')
version('1.9.7', 'a2fd9458c76700b7be51ef12f07d4bb1')
version('1.9.6', '29b7507c9053e301d2b85091f2aec6f0')
version('1.10.0', sha256='1f78036c38753880e16fb755516c8070187a78fe4b2e99b59eda5b81b58eccaf')
version('1.9.9', sha256='d6a0c93777ab27db36212d77c5733ac80d17fe24e83f947df23a8e0ad4ac48cc')
version('1.9.8', sha256='5f4daf56e66fc7a71de772920ca27c15eac80cf1fcf41f3b4f2d535724942681')
version('1.9.7', sha256='648b3f3787bb0cb6226978b6d4898eb7e21ae391385357a5f824972dd910a1c8')
version('1.9.6', sha256='550d2aaf828785e30870c227056942c2a552da961db6010cedb2fbcfa8e3268d')
depends_on('java')

2
var/spack/repos/builtin/packages/antlr/package.py
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@@ -16,7 +16,7 @@ class Antlr(AutotoolsPackage):
homepage = "http://www.antlr2.org/"
url = "http://www.antlr2.org/download/antlr-2.7.7.tar.gz"
version('2.7.7', '01cc9a2a454dd33dcd8c856ec89af090')
version('2.7.7', sha256='853aeb021aef7586bda29e74a6b03006bcb565a755c86b66032d8ec31b67dbb9')
# Fixes build with recent versions of GCC
patch('gcc.patch')

2
var/spack/repos/builtin/packages/ants/package.py
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@@ -18,7 +18,7 @@ class Ants(CMakePackage):
homepage = "http://stnava.github.io/ANTs/"
url = "https://github.com/ANTsX/ANTs/archive/v2.2.0.tar.gz"
version('2.2.0', '5661b949268100ac0f7baf6d2702b4dd')
version('2.2.0', sha256='62f8f9ae141cb45025f4bb59277c053acf658d4a3ba868c9e0f609af72e66b4a')
depends_on('zlib', type='link')

2
var/spack/repos/builtin/packages/apex/package.py
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@@ -12,7 +12,7 @@ class Apex(CMakePackage):
homepage = "http://github.com/khuck/xpress-apex"
url = "http://github.com/khuck/xpress-apex/archive/v0.1.tar.gz"
version('0.1', 'e224a0b9033e23a9697ce2a3c307a0a3')
version('0.1', sha256='bb0be37f8f8133fe492998515bcf66a4df452c28a995d317228fbed9b18e6a92')
depends_on("binutils+libiberty")
depends_on("boost@1.54:")

2
var/spack/repos/builtin/packages/applewmproto/package.py
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@@ -16,7 +16,7 @@ class Applewmproto(AutotoolsPackage):
homepage = "http://cgit.freedesktop.org/xorg/proto/applewmproto"
url = "https://www.x.org/archive/individual/proto/applewmproto-1.4.2.tar.gz"
version('1.4.2', 'ecc8a4424a893ce120f5652dba62e9e6')
version('1.4.2', sha256='ff8ac07d263a23357af2d6ff0cca3c1d56b043ddf7797a5a92ec624f4704df2e')
depends_on('pkgconfig', type='build')
depends_on('util-macros', type='build')

2
var/spack/repos/builtin/packages/appres/package.py
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@@ -15,7 +15,7 @@ class Appres(AutotoolsPackage):
homepage = "http://cgit.freedesktop.org/xorg/app/appres"
url = "https://www.x.org/archive/individual/app/appres-1.0.4.tar.gz"
version('1.0.4', 'f82aabe6bbb8960781b63c6945bb361b')
version('1.0.4', sha256='22cb6f639c891ffdbb5371bc50a88278185789eae6907d05e9e0bd1086a80803')
depends_on('libx11')
depends_on('libxt')

4
var/spack/repos/builtin/packages/apr-util/package.py
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@@ -12,8 +12,8 @@ class AprUtil(AutotoolsPackage):
homepage = 'https://apr.apache.org/'
url = 'http://archive.apache.org/dist/apr/apr-util-1.6.0.tar.gz'
version('1.6.0', '3b03dbff60728a4f4c33f5d929e8b35a')
version('1.5.4', '866825c04da827c6e5f53daff5569f42')
version('1.6.0', sha256='483ef4d59e6ac9a36c7d3fd87ad7b9db7ad8ae29c06b9dd8ff22dda1cc416389')
version('1.5.4', sha256='976a12a59bc286d634a21d7be0841cc74289ea9077aa1af46be19d1a6e844c19')
variant('crypto', default=True, description='Enable crypto support')
variant('gdbm', default=False, description='Enable GDBM support')

4
var/spack/repos/builtin/packages/apr/package.py
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@@ -12,5 +12,5 @@ class Apr(AutotoolsPackage):
homepage = 'https://apr.apache.org/'
url = 'http://archive.apache.org/dist/apr/apr-1.6.2.tar.gz'
version('1.6.2', '8672e78514e3fcef2643127c524bf0f9')
version('1.5.2', '98492e965963f852ab29f9e61b2ad700')
version('1.6.2', sha256='4fc24506c968c5faf57614f5d0aebe0e9d0b90afa47a883e1a1ca94f15f4a42e')
version('1.5.2', sha256='1af06e1720a58851d90694a984af18355b65bb0d047be03ec7d659c746d6dbdb')

4
var/spack/repos/builtin/packages/aragorn/package.py
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@@ -13,8 +13,8 @@ class Aragorn(Package):
homepage = "http://mbio-serv2.mbioekol.lu.se/ARAGORN"
url = "http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn1.2.38.tgz"
version('1.2.38', '1df0ed600069e6f520e5cd989de1eaf0')
version('1.2.36', 'ab06032589e45aa002f8616333568e9ab11034b3a675f922421e5f1c3e95e7b5')
version('1.2.38', sha256='4b84e3397755fb22cc931c0e7b9d50eaba2a680df854d7a35db46a13cecb2126')
version('1.2.36', sha256='ab06032589e45aa002f8616333568e9ab11034b3a675f922421e5f1c3e95e7b5')
phases = ['build', 'install']

6
var/spack/repos/builtin/packages/argobots/package.py
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@@ -20,9 +20,9 @@ class Argobots(AutotoolsPackage):
git = "https://github.com/pmodels/argobots.git"
version("develop", branch="master")
version("1.0rc1", "729c018f3353976cb79c07ecaa13319d")
version("1.0b1", "5eeab7b2c639d08bbea22db3026cdf39")
version("1.0a1", "9d29d57d14d718f93b505178f6ba3e08")
version("1.0rc1", sha256="2dc4487556dce602655a6535f501136f0edc3575708029c80b1af6dccd069ce7")
version("1.0b1", sha256="480b85b0e8db288400088a57c2dc5639f556843b06b0492841920c38348a2a3e")
version("1.0a1", sha256="bef93e06026ddeba8809474923176803e64d08e1425672cd7c5b424c797d5d9d")
variant("valgrind", default=False, description="Enable Valgrind")

2
var/spack/repos/builtin/packages/argp-standalone/package.py
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@@ -14,7 +14,7 @@ class ArgpStandalone(AutotoolsPackage):
homepage = "https://www.lysator.liu.se/~nisse/misc"
url = "https://www.lysator.liu.se/~nisse/misc/argp-standalone-1.3.tar.gz"
version('1.3', '720704bac078d067111b32444e24ba69')
version('1.3', sha256='dec79694da1319acd2238ce95df57f3680fea2482096e483323fddf3d818d8be')
# Homebrew (https://github.com/Homebrew/homebrew-core) patches
# argp-standalone to work on Darwin; the patchfile below was taken

2
var/spack/repos/builtin/packages/argtable/package.py
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@@ -14,4 +14,4 @@ class Argtable(AutotoolsPackage):
homepage = "http://argtable.sourceforge.net/"
url = "https://sourceforge.net/projects/argtable/files/argtable/argtable-2.13/argtable2-13.tar.gz/download"
version('2-13', '156773989d0d6406cea36526d3926668')
version('2-13', sha256='8f77e8a7ced5301af6e22f47302fdbc3b1ff41f2b83c43c77ae5ca041771ddbf')

12
var/spack/repos/builtin/packages/armadillo/package.py
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@@ -14,13 +14,13 @@ class Armadillo(CMakePackage):
homepage = "http://arma.sourceforge.net/"
url = "http://sourceforge.net/projects/arma/files/armadillo-7.200.1.tar.xz"
version('8.100.1', 'd9762d6f097e0451d0cfadfbda295e7c')
version('7.950.1', 'c06eb38b12cae49cab0ce05f96147147')
version('8.100.1', sha256='54773f7d828bd3885c598f90122b530ded65d9b195c9034e082baea737cd138d')
version('7.950.1', sha256='a32da32a0ea420b8397a53e4b40ed279c1a5fc791dd492a2ced81ffb14ad0d1b')
# NOTE: v7.900.1 download url seems broken is no v7.950.1?
version('7.900.1', '5ef71763bd429a3d481499878351f3be')
version('7.500.0', '7d316fdf3c3c7ea92b64704180ae315d')
version('7.200.2', 'b21585372d67a8876117fd515d8cf0a2')
version('7.200.1', 'ed86d6df0058979e107502e1fe3e469e')
version('7.900.1', md5='5ef71763bd429a3d481499878351f3be')
version('7.500.0', md5='7d316fdf3c3c7ea92b64704180ae315d')
version('7.200.2', md5='b21585372d67a8876117fd515d8cf0a2')
version('7.200.1', md5='ed86d6df0058979e107502e1fe3e469e')
variant('hdf5', default=False, description='Include HDF5 support')

8
var/spack/repos/builtin/packages/arpack-ng/package.py
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@@ -42,10 +42,10 @@ class ArpackNg(Package):
version('3.7.0', sha256='972e3fc3cd0b9d6b5a737c9bf6fd07515c0d6549319d4ffb06970e64fa3cc2d6')
version('3.6.3', sha256='64f3551e5a2f8497399d82af3076b6a33bf1bc95fc46bbcabe66442db366f453')
version('3.6.2', sha256='673c8202de996fd3127350725eb1818e534db4e79de56d5dcee8c00768db599a')
version('3.6.0', 'f2607c1d5f80e922d55751fbed86a8ec')
version('3.5.0', '9762c9ae6d739a9e040f8201b1578874')
version('3.4.0', 'ae9ca13f2143a7ea280cb0e2fd4bfae4')
version('3.3.0', 'ed3648a23f0a868a43ef44c97a21bad5')
version('3.6.0', sha256='3c88e74cc10bba81dc2c72c4f5fff38a800beebaa0b4c64d321c28c9203b37ea')
version('3.5.0', sha256='50f7a3e3aec2e08e732a487919262238f8504c3ef927246ec3495617dde81239')
version('3.4.0', sha256='69e9fa08bacb2475e636da05a6c222b17c67f1ebeab3793762062248dd9d842f')
version('3.3.0', sha256='ad59811e7d79d50b8ba19fd908f92a3683d883597b2c7759fdcc38f6311fe5b3')
variant('shared', default=True,
description='Enables the build of shared libraries')

8
var/spack/repos/builtin/packages/arrow/package.py
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@@ -15,10 +15,10 @@ class Arrow(CMakePackage):
homepage = "http://arrow.apache.org"
url = "https://github.com/apache/arrow/archive/apache-arrow-0.9.0.tar.gz"
version('0.12.1', 'aae68622edc3dcadaa16b2d25ae3f00290d5233100321993427b03bcf5b1dd3b')
version('0.11.0', '0ac629a7775d86108e403eb66d9f1a3d3bdd6b3a497a86228aa4e8143364b7cc')
version('0.9.0', 'ebbd36c362b9e1d398ca612f6d2531ec')
version('0.8.0', '56436f6f61ccc68686b7e0ea30bf4d09')
version('0.12.1', sha256='aae68622edc3dcadaa16b2d25ae3f00290d5233100321993427b03bcf5b1dd3b')
version('0.11.0', sha256='0ac629a7775d86108e403eb66d9f1a3d3bdd6b3a497a86228aa4e8143364b7cc')
version('0.9.0', sha256='65f89a3910b6df02ac71e4d4283db9b02c5b3f1e627346c7b6a5982ae994af91')
version('0.8.0', sha256='c61a60c298c30546fc0b418a35be66ef330fb81b06c49928acca7f1a34671d54')
depends_on('boost@1.60:')
depends_on('cmake@3.2.0:', type='build')

2
var/spack/repos/builtin/packages/asciidoc/package.py
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@@ -13,7 +13,7 @@ class Asciidoc(AutotoolsPackage):
homepage = "http://asciidoc.org"
url = "http://downloads.sourceforge.net/project/asciidoc/asciidoc/8.6.9/asciidoc-8.6.9.tar.gz"
version('8.6.9', 'c59018f105be8d022714b826b0be130a')
version('8.6.9', sha256='78db9d0567c8ab6570a6eff7ffdf84eadd91f2dfc0a92a2d0105d323cab4e1f0')
depends_on('libxml2')
depends_on('libxslt')

2
var/spack/repos/builtin/packages/asciidoctor/package.py
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@@ -12,7 +12,7 @@ class Asciidoctor(Package):
homepage = "https://asciidoctor.org/"
url = "https://rubygems.org/downloads/asciidoctor-1.5.8.gem"
version('1.5.8', '5f55200cab8d1cfcf561e66d3f477159', expand=False)
version('1.5.8', sha256='9deaa93eacadda48671e18395b992eafba35d08f25ddbe28d25bb275831a8d62', expand=False)
extends('ruby')

2
var/spack/repos/builtin/packages/aspcud/package.py
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@@ -18,7 +18,7 @@ class Aspcud(CMakePackage):
homepage = "https://potassco.org/aspcud"
url = "https://github.com/potassco/aspcud/archive/v1.9.4.tar.gz"
version('1.9.4', '35e5c663a25912e4bdc94f168e827ed2')
version('1.9.4', sha256='3645f08b079e1cc80e24cd2d7ae5172a52476d84e3ec5e6a6c0034492a6ea885')
depends_on('boost', type=('build'))
depends_on('cmake', type=('build'))

2
var/spack/repos/builtin/packages/aspell/package.py
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@@ -16,7 +16,7 @@ class Aspell(AutotoolsPackage):
extendable = True # support activating dictionaries
version('0.60.6.1', 'e66a9c9af6a60dc46134fdacf6ce97d7')
version('0.60.6.1', sha256='f52583a83a63633701c5f71db3dc40aab87b7f76b29723aeb27941eff42df6e1')
patch('darwin.patch', when='platform=darwin')
patch('issue-519.patch', when='@:0.60.6.1')

2
var/spack/repos/builtin/packages/aspell6-de/package.py
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@@ -12,4 +12,4 @@ class Aspell6De(AspellDictPackage):
homepage = "http://aspell.net/"
url = "https://ftpmirror.gnu.org/aspell/dict/de/aspell6-de-20030222-1.tar.bz2"
version('6-de-20030222-1', '5950c5c8a36fc93d4d7616591bace6a6')
version('6-de-20030222-1', sha256='ba6c94e11bc2e0e6e43ce0f7822c5bba5ca5ac77129ef90c190b33632416e906')

2
var/spack/repos/builtin/packages/aspell6-en/package.py
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@@ -12,4 +12,4 @@ class Aspell6En(AspellDictPackage):
homepage = "http://aspell.net/"
url = "https://ftpmirror.gnu.org/aspell/dict/en/aspell6-en-2017.01.22-0.tar.bz2"
version('2017.01.22-0', 'a6e002076574de9dc4915967032a1dab')
version('2017.01.22-0', sha256='93c73fae3eab5ea3ca6db3cea8770715a820f1b7d6ea2b932dd66a17f8fd55e1')

2
var/spack/repos/builtin/packages/aspell6-es/package.py
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@@ -12,4 +12,4 @@ class Aspell6Es(AspellDictPackage):
homepage = "http://aspell.net/"
url = "https://ftpmirror.gnu.org/aspell/dict/es/aspell6-es-1.11-2.tar.bz2"
version('1.11-2', '8406336a89c64e47e96f4153d0af70c4')
version('1.11-2', sha256='ad367fa1e7069c72eb7ae37e4d39c30a44d32a6aa73cedccbd0d06a69018afcc')

2
var/spack/repos/builtin/packages/aspera-cli/package.py
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@@ -13,7 +13,7 @@ class AsperaCli(Package):
homepage = "https://asperasoft.com"
url = "https://download.asperasoft.com/download/sw/cli/3.7.7/aspera-cli-3.7.7.608.927cce8-linux-64-release.sh"
version('3.7.7', 'e92140d809e7e65112a5d1cd49c442cf',
version('3.7.7', sha256='83efd03b699bdb1cac6c62befb3812342d6122217f4944f732ae7a135d578966',
url='https://download.asperasoft.com/download/sw/cli/3.7.7/aspera-cli-3.7.7.608.927cce8-linux-64-release.sh',
expand=False)

2
var/spack/repos/builtin/packages/assimp/package.py
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@@ -13,7 +13,7 @@ class Assimp(CMakePackage):
homepage = "https://www.assimp.org"
url = "https://github.com/assimp/assimp/archive/v4.0.1.tar.gz"
version('4.0.1', '23a6301c728a413aafbfa1cca19ba91f')
version('4.0.1', sha256='60080d8ab4daaab309f65b3cffd99f19eb1af8d05623fff469b9b652818e286e')
variant('shared', default=True,
description='Enables the build of shared libraries')

2
var/spack/repos/builtin/packages/astral/package.py
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@@ -16,7 +16,7 @@ class Astral(Package):
version('5.6.1', sha256='b49a67c9fe19c0c92a89dc2f1a3928840e698a53054a595c61546ca98448a076',
url='https://github.com/smirarab/ASTRAL/archive/untagged-697f19dbce69929ece09.tar.gz')
version('4.10.7', '38c81020570254e3f5c75d6c3c27fc6d')
version('4.10.7', sha256='314b49e0129ec06a7c78a1b60d590259ede6a5e75253407031e108d8048fcc79')
depends_on('java', type=('build', 'run'))
depends_on('zip', type='build')

10
var/spack/repos/builtin/packages/astyle/package.py
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@@ -17,11 +17,11 @@ class Astyle(MakefilePackage):
# Gentoo alternative
# url = "http://distfiles.gentoo.org/distfiles/astyle_3.0.1_linux.tar.gz"
version('3.1', '7712622f62661b1d8cb1062d7fedc390')
version('3.0.1', 'c301f09679efa2e1eb6e6b5fd33788b4')
version('2.06', 'ff588e7fcede824591cf5b9085df109d')
version('2.05.1', '4142d178047d7040da3e0e2f1b030a1a')
version('2.04', '30b1193a758b0909d06e7ee8dd9627f6')
version('3.1', sha256='cbcc4cf996294534bb56f025d6f199ebfde81aa4c271ccbd5ee1c1a3192745d7')
version('3.0.1', sha256='6c3ab029e0e4a75e2e603d449014374aa8269218fdd03a4aaa46ab743b1912fd')
version('2.06', sha256='3b7212210dc139e8f648e004b758c0be1b3ceb1694b22a879202d2b833db7c7e')
version('2.05.1', sha256='fbdfc6f1966a972d19a215927266c76d4183eee235ed1e2bd7ec551c2a270eac')
version('2.04', sha256='70b37f4853c418d1e2632612967eebf1bdb93dfbe558c51d7d013c9b4e116b60')
parallel = False

4
var/spack/repos/builtin/packages/at-spi2-atk/package.py
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@@ -15,8 +15,8 @@ class AtSpi2Atk(MesonPackage):
list_url = "http://ftp.gnome.org/pub/gnome/sources/at-spi2-atk"
list_depth = 1
version('2.26.2', '355c7916a69513490cb83ad34016b169')
version('2.26.1', 'eeec6cead3350dca48a235271c105b3e')
version('2.26.2', sha256='61891f0abae1689f6617a963105a3f1dcdab5970c4a36ded9c79a7a544b16a6e')
version('2.26.1', sha256='b4f0c27b61dbffba7a5b5ba2ff88c8cee10ff8dac774fa5b79ce906853623b75')
depends_on('pkgconfig', type='build')
depends_on('at-spi2-core@2.28.0:')

2
var/spack/repos/builtin/packages/at-spi2-core/package.py
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@@ -16,7 +16,7 @@ class AtSpi2Core(MesonPackage):
list_url = "http://ftp.gnome.org/pub/gnome/sources/at-spi2-core"
list_depth = 1
version('2.28.0', '9c42f79636ed1c0e908b7483d789b32e')
version('2.28.0', sha256='42a2487ab11ce43c288e73b2668ef8b1ab40a0e2b4f94e80fca04ad27b6f1c87')
depends_on('glib@2.56.1:')
depends_on('dbus@1.12.8:')

6
var/spack/repos/builtin/packages/atk/package.py
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@@ -18,9 +18,9 @@ class Atk(Package):
list_depth = 1
version('2.30.0', sha256='dd4d90d4217f2a0c1fee708a555596c2c19d26fef0952e1ead1938ab632c027b')
version('2.28.1', 'dfb5e7474220afa3f4ca7e45af9f3a11')
version('2.20.0', '5187b0972f4d3905f285540b31395e20')
version('2.14.0', 'ecb7ca8469a5650581b1227d78051b8b')
version('2.28.1', sha256='cd3a1ea6ecc268a2497f0cd018e970860de24a6d42086919d6bf6c8e8d53f4fc')
version('2.20.0', sha256='493a50f6c4a025f588d380a551ec277e070b28a82e63ef8e3c06b3ee7c1238f0')
version('2.14.0', sha256='2875cc0b32bfb173c066c22a337f79793e0c99d2cc5e81c4dac0d5a523b8fbad')
depends_on('meson@0.40.1:', type='build', when='@2.28:')
depends_on('meson@0.46.0:', type='build', when='@2.29:')

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var/spack/repos/builtin/packages/atlas/package.py
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@@ -20,18 +20,18 @@ class Atlas(Package):
# Developer (unstable)
version('3.11.41', sha256='477d567a8d683e891d786e9e8bb6ad6659daa9ba18e8dd0e2f70b7a54095f8de')
version('3.11.39', '5f3252fa980f5f060f93edd4669321e2')
version('3.11.34', '0b6c5389c095c4c8785fd0f724ec6825')
version('3.11.39', sha256='584bd44572746142bf19348139530c18f4538ce41d94330ff86ede38c36eddc9')
version('3.11.34', sha256='b6d42af3afd4fe54ef3a04a070fc7e75f6d8ac9f7d4886b636fe27ebfcbdf91f')
# Stable
version('3.10.3', 'd6ce4f16c2ad301837cfb3dade2f7cef', preferred=True)
version('3.10.2', 'a4e21f343dec8f22e7415e339f09f6da')
version('3.10.3', sha256='2688eb733a6c5f78a18ef32144039adcd62fabce66f2eb51dd59dde806a6d2b7', preferred=True)
version('3.10.2', sha256='3aab139b118bf3fcdb4956fbd71676158d713ab0d3bccb2ae1dc3769db22102f')
# not all packages (e.g. Trilinos@12.6.3) stopped using deprecated in 3.6.0
# Lapack routines. Stick with 3.5.0 until this is fixed.
resource(name='lapack',
url='http://www.netlib.org/lapack/lapack-3.5.0.tgz',
md5='b1d3e3e425b2e44a06760ff173104bdf',
sha256='9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352',
destination='spack-resource-lapack',
when='@3:')

2
var/spack/repos/builtin/packages/atom-dft/package.py
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@@ -13,7 +13,7 @@ class AtomDft(MakefilePackage):
homepage = "https://departments.icmab.es/leem/siesta/Pseudopotentials/"
url = "https://departments.icmab.es/leem/siesta/Pseudopotentials/Code/atom-4.2.6.tgz"
version('4.2.6', 'c0c80cf349f951601942ed6c7cb0256b')
version('4.2.6', sha256='489f0d883af35525647a8b8f691e7845c92fe6b5a25b13e1ed368edfd0391ed2')
depends_on('libgridxc')
depends_on('xmlf90')

4
var/spack/repos/builtin/packages/atompaw/package.py
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@@ -18,8 +18,8 @@ class Atompaw(Package):
homepage = "http://users.wfu.edu/natalie/papers/pwpaw/man.html"
url = "http://users.wfu.edu/natalie/papers/pwpaw/atompaw-4.0.0.13.tar.gz"
version('4.0.0.13', 'af4a042380356f6780183c4b325aad1d')
version('3.1.0.3', 'c996a277e11707887177f47bbb229aa6')
version('4.0.0.13', sha256='cbd73f11f3e9cc3ff2e5f3ec87498aeaf439555903d0b95a72f3b0a021902020')
version('3.1.0.3', sha256='15fe9a0369bdcc366370a0ecaa67e803ae54534b479ad63c4c7494a04fa3ea78')
depends_on("lapack")
depends_on("blas")

2
var/spack/repos/builtin/packages/atop/package.py
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@@ -11,7 +11,7 @@ class Atop(Package):
homepage = "http://www.atoptool.nl/index.php"
url = "http://www.atoptool.nl/download/atop-2.2-3.tar.gz"
version('2.2-3', '034dc1544f2ec4e4d2c739d320dc326d')
version('2.2-3', sha256='c785b8a2355be28b3de6b58a8ea4c4fcab8fadeaa57a99afeb03c66fac8e055d')
depends_on('zlib')
depends_on('ncurses')

4
var/spack/repos/builtin/packages/augustus/package.py
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@@ -18,9 +18,9 @@ class Augustus(MakefilePackage):
version('3.3.2', sha256='d09f972cfd88deb34b19b69878eb8af3bbbe4f1cde1434b69cedc2aa6247a0f2')
version('3.3.1', sha256='011379606f381ee21b9716f83e8a1a57b2aaa01aefeebd2748104efa08c47cab',
url='https://github.com/Gaius-Augustus/Augustus/archive/v3.3.1-tag1.tar.gz')
version('3.3', '93691d9aafc7d3d0e1adf31ec308507f',
version('3.3', sha256='b5eb811a4c33a2cc3bbd16355e19d530eeac6d1ac923e59f48d7a79f396234ee',
url='http://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-3.3.tar.gz')
version('3.2.3', 'b8c47ea8d0c45aa7bb9a82626c8ff830',
version('3.2.3', sha256='a1af128aefd228dea0c46d6f5234910fdf068a2b9133175ca8da3af639cb4514',
url='http://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-3.2.3.tar.gz')
depends_on('perl', type=('build', 'run'))

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var/spack/repos/builtin/packages/autoconf/package.py
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@@ -12,10 +12,10 @@ class Autoconf(AutotoolsPackage):
homepage = 'https://www.gnu.org/software/autoconf/'
url = 'https://ftpmirror.gnu.org/autoconf/autoconf-2.69.tar.gz'
version('2.69', '82d05e03b93e45f5a39b828dc9c6c29b')
version('2.62', '6c1f3b3734999035d77da5024aab4fbd')
version('2.59', 'd4d45eaa1769d45e59dcb131a4af17a0')
version('2.13', '9de56d4a161a723228220b0f425dc711')
version('2.69', sha256='954bd69b391edc12d6a4a51a2dd1476543da5c6bbf05a95b59dc0dd6fd4c2969')
version('2.62', sha256='83aa747e6443def0ebd1882509c53f5a2133f502ddefa21b3de141c433914bdd')
version('2.59', sha256='9cd05c73c5fcb1f5ccae53dd6cac36bb8cb9c7b3e97ffae5a7c05c72594c88d8')
version('2.13', sha256='f0611136bee505811e9ca11ca7ac188ef5323a8e2ef19cffd3edb3cf08fd791e')
# Note: m4 is not a pure build-time dependency of autoconf. m4 is
# needed when autoconf runs, not only when autoconf is built.

2
var/spack/repos/builtin/packages/autodock-vina/package.py
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@@ -13,7 +13,7 @@ class AutodockVina(MakefilePackage):
homepage = "http://vina.scripps.edu/"
url = "http://vina.scripps.edu/download/autodock_vina_1_1_2.tgz"
version('1_1_2', 'b467b71ee77dd155b65b1c5364e4220f')
version('1_1_2', sha256='b86412d316960b1e4e319401719daf57ff009229d91654d623c3cf09339f6776')
depends_on('boost@1.65.0')

2
var/spack/repos/builtin/packages/autogen/package.py
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@@ -17,7 +17,7 @@ class Autogen(AutotoolsPackage):
list_url = "https://ftp.gnu.org/gnu/autogen"
list_depth = 1
version('5.18.12', '551d15ccbf5b5fc5658da375d5003389')
version('5.18.12', sha256='805c20182f3cb0ebf1571d3b01972851c56fb34348dfdc38799fd0ec3b2badbe')
variant('xml', default=True, description='Enable XML support')

2
var/spack/repos/builtin/packages/automaded/package.py
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@@ -21,7 +21,7 @@ class Automaded(CMakePackage):
homepage = "https://github.com/llnl/AutomaDeD"
url = "https://github.com/llnl/AutomaDeD/archive/v1.0.tar.gz"
version('1.0', '16a3d4def2c4c77d0bc4b21de8b3ab03')
version('1.0', sha256='600740cdd594cc6968c7bcb285d0829eb0ddbd5597c32c06c6ae5d9929a2625d')
depends_on('mpi')
depends_on('boost')

12
var/spack/repos/builtin/packages/automake/package.py
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@@ -12,12 +12,12 @@ class Automake(AutotoolsPackage):
homepage = 'http://www.gnu.org/software/automake/'
url = 'https://ftpmirror.gnu.org/automake/automake-1.15.tar.gz'
version('1.16.1', '608a97523f97db32f1f5d5615c98ca69326ced2054c9f82e65bade7fc4c9dea8')
version('1.15.1', '988e32527abe052307d21c8ca000aa238b914df363a617e38f4fb89f5abf6260')
version('1.15', '7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924')
version('1.14.1', '814c2333f350ce00034a1fe718e0e4239998ceea7b0aff67e9fd273ed6dfc23b')
version('1.13.4', '4c93abc0bff54b296f41f92dd3aa1e73e554265a6f719df465574983ef6f878c')
version('1.11.6', '53dbf1945401c43f4ce19c1971baecdbf8bc32e0f37fa3f49fe7b6992d0d2030')
version('1.16.1', sha256='608a97523f97db32f1f5d5615c98ca69326ced2054c9f82e65bade7fc4c9dea8')
version('1.15.1', sha256='988e32527abe052307d21c8ca000aa238b914df363a617e38f4fb89f5abf6260')
version('1.15', sha256='7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924')
version('1.14.1', sha256='814c2333f350ce00034a1fe718e0e4239998ceea7b0aff67e9fd273ed6dfc23b')
version('1.13.4', sha256='4c93abc0bff54b296f41f92dd3aa1e73e554265a6f719df465574983ef6f878c')
version('1.11.6', sha256='53dbf1945401c43f4ce19c1971baecdbf8bc32e0f37fa3f49fe7b6992d0d2030')
depends_on('autoconf', type='build')
depends_on('perl', type=('build', 'run'))

2
var/spack/repos/builtin/packages/axel/package.py
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@@ -12,7 +12,7 @@ class Axel(AutotoolsPackage):
homepage = "https://github.com/axel-download-accelerator/axel"
url = "https://github.com/axel-download-accelerator/axel/archive/v2.16.1.tar.gz"
version('2.16.1', '3aaa7052458c66c1547bf1133609d0f2')
version('2.16.1', sha256='64529add74df3db828f704b42d4ec3fcdacb8142c84f051f9213637c337e706c')
depends_on('m4', type='build')
depends_on('autoconf', type='build')

12
var/spack/repos/builtin/packages/bamtools/package.py
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@@ -13,12 +13,12 @@ class Bamtools(CMakePackage):
homepage = "https://github.com/pezmaster31/bamtools"
url = "https://github.com/pezmaster31/bamtools/archive/v2.4.0.tar.gz"
version('2.5.1', '98e90632058f85bd5eed6088b3ff912e')
version('2.5.0', 'dd4185bdba6e3adf2c24b7f93a57233d')
version('2.4.1', '41cadf513f2744256851accac2bc7baa')
version('2.4.0', '6139d00c1b1fe88fe15d094d8a74d8b9')
version('2.3.0', 'd327df4ba037d6eb8beef65d7da75ebc')
version('2.2.3', '6eccd3e45e4ba12a68daa3298998e76d')
version('2.5.1', sha256='4abd76cbe1ca89d51abc26bf43a92359e5677f34a8258b901a01f38c897873fc')
version('2.5.0', sha256='85e02e04998a67cbda7ab68cdab36cee133db024e814b34e06bb617b627caf9c')
version('2.4.1', sha256='933a0c1a83c88c1dac8078c0c0e82f6794c75cb927265399404bc2cc2611204b')
version('2.4.0', sha256='f1fe82b8871719e0fb9ed7be73885f5d0815dd5c7277ee33bd8f67ace961e13e')
version('2.3.0', sha256='288046e6d5d41afdc5fce8608c5641cf2b8e670644587c1315b90bbe92f039af')
version('2.2.3', sha256='92ddef44801a1f8f01ce1a397f83e0f8b5e1ae8ad92c620f2dafaaf8d54cf178')
depends_on('zlib', type='link')

2
var/spack/repos/builtin/packages/bamutil/package.py
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@@ -15,7 +15,7 @@ class Bamutil(MakefilePackage):
homepage = "http://genome.sph.umich.edu/wiki/BamUtil"
url = "http://genome.sph.umich.edu/w/images/7/70/BamUtilLibStatGen.1.0.13.tgz"
version('1.0.13', '08b7d0bb1d60be104a11f0e54ddf4a79')
version('1.0.13', sha256='16c1d01c37d1f98b98c144f3dd0fda6068c1902f06bd0989f36ce425eb0c592b')
depends_on('zlib', type=('build', 'link'))

6
var/spack/repos/builtin/packages/barrnap/package.py
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@@ -12,9 +12,9 @@ class Barrnap(Package):
homepage = "https://github.com/tseemann/barrnap"
url = "https://github.com/tseemann/barrnap/archive/0.8.tar.gz"
version('0.8', 'd02ccb800d60fa824bae946dd4fa2358')
version('0.7', 'ef2173e250f06cca7569c03404c9d4ab6a908ef7643e28901fbe9a732d20c09b')
version('0.6', '272642a41634623bda34dccdce487ab791925fa769e3e575d53014956a1f9dce')
version('0.8', sha256='82004930767e92b61539c0de27ff837b8b7af01236e565f1473c63668cf0370f')
version('0.7', sha256='ef2173e250f06cca7569c03404c9d4ab6a908ef7643e28901fbe9a732d20c09b')
version('0.6', sha256='272642a41634623bda34dccdce487ab791925fa769e3e575d53014956a1f9dce')
depends_on('hmmer@3.1b:', type='run')

4
var/spack/repos/builtin/packages/bash-completion/package.py
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@@ -14,8 +14,8 @@ class BashCompletion(AutotoolsPackage):
git = "https://github.com/scop/bash-completion.git"
version('develop', branch='master')
version('2.7', 'f72c9e2e877d188c3159956a3496a450e7279b76')
version('2.3', '67e50f5f3c804350b43f2b664c33dde811d24292')
version('2.7', sha256='dba2b88c363178622b61258f35d82df64dc8d279359f599e3b93eac0375a416c')
version('2.3', sha256='d92fcef5f6e3bbc68a84f0a7b063a1cd07b4000cc6e275cd1ff83863ab3b322a')
# Build dependencies
depends_on('automake', type='build')

8
var/spack/repos/builtin/packages/bash/package.py
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@@ -12,10 +12,10 @@ class Bash(AutotoolsPackage):
homepage = "https://www.gnu.org/software/bash/"
url = "https://ftpmirror.gnu.org/bash/bash-4.4.tar.gz"
version('5.0', sha256='b4a80f2ac66170b2913efbfb9f2594f1f76c7b1afd11f799e22035d63077fb4d')
version('4.4.12', '7c112970cbdcadfc331e10eeb5f6aa41')
version('4.4', '148888a7c95ac23705559b6f477dfe25')
version('4.3', '81348932d5da294953e15d4814c74dd1')
version('5.0', sha256='b4a80f2ac66170b2913efbfb9f2594f1f76c7b1afd11f799e22035d63077fb4d')
version('4.4.12', sha256='57d8432be54541531a496fd4904fdc08c12542f43605a9202594fa5d5f9f2331')
version('4.4', sha256='d86b3392c1202e8ff5a423b302e6284db7f8f435ea9f39b5b1b20fd3ac36dfcb')
version('4.3', sha256='afc687a28e0e24dc21b988fa159ff9dbcf6b7caa92ade8645cc6d5605cd024d4')
depends_on('ncurses')
depends_on('readline@5.0:')

2
var/spack/repos/builtin/packages/bats/package.py
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@@ -12,7 +12,7 @@ class Bats(Package):
homepage = "https://github.com/sstephenson/bats"
url = "https://github.com/sstephenson/bats/archive/v0.4.0.tar.gz"
version('0.4.0', 'aeeddc0b36b8321930bf96fce6ec41ee')
version('0.4.0', sha256='480d8d64f1681eee78d1002527f3f06e1ac01e173b761bc73d0cf33f4dc1d8d7')
def install(self, spec, prefix):
bash = which("bash")

36
var/spack/repos/builtin/packages/bazel/package.py
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@@ -17,24 +17,24 @@ class Bazel(Package):
homepage = "https://www.bazel.io"
url = "https://github.com/bazelbuild/bazel/releases/download/0.11.1/bazel-0.11.1-dist.zip"
version('0.17.2', '9805c0593e781295126af6b8be8cc7a9')
version('0.16.1', 'c333d903c5275286e79316eb19dd742d')
version('0.15.0', 'fb6b928b62f068697bd66ad6d13aad53')
version('0.14.1', '841900316b3ec9b996babe1c5b0b92e1')
version('0.13.0', '64a5124025c1618b550faec64a9b6fa3')
version('0.12.0', 'b5d67564ceecfe2005a885fe2ffe0da3')
version('0.11.1', '80daac6b100b7f8e2b17d133150eba44')
version('0.11.0', 'e6caf93a805b45c33367028e575b91dd')
version('0.10.1', 'a7e5b9576993b752e31bd2d3259a14c5')
version('0.10.0', 'c2f15b34255099d25e94fce7283e5cd2')
version('0.9.0', '7fda74c163108f7c180bbc513bc8123b')
version('0.4.5', '2b737be42678900470ae9e48c975ac5b2296d9ae23c007bf118350dbe7c0552b')
version('0.4.4', '5e7c52b89071efc41277e2f0057d258f')
version('0.3.1', '5c959467484a7fc7dd2e5e4a1e8e866b')
version('0.3.0', '33a2cb457d28e1bee9282134769b9283')
version('0.2.3', '393a491d690e43caaba88005efe6da91')
version('0.2.2b', '75081804f073cbd194da1a07b16cba5f')
version('0.2.2', '644bc4ea7f429d835e74f255dc1054e6')
version('0.17.2', sha256='b6e87acfa0a405bb8b3417c58477b66d5bc27dc0d31ba6fa12bc255b9278d33b')
version('0.16.1', sha256='09c66b94356c82c52f212af52a81ac28eb06de1313755a2f23eeef84d167b36c')
version('0.15.0', sha256='c3b716e6625e6b8c323350c95cd3ae0f56aeb00458dddd10544d5bead8a7b602')
version('0.14.1', sha256='d49cdcd82618ae7a7a190e6f0a80d9bf85c1a66b732f994f37732dc14ffb0025')
version('0.13.0', sha256='82e9035084660b9c683187618a29aa896f8b05b5f16ae4be42a80b5e5b6a7690')
version('0.12.0', sha256='3b3e7dc76d145046fdc78db7cac9a82bc8939d3b291e53a7ce85315feb827754')
version('0.11.1', sha256='e8d762bcc01566fa50952c8028e95cfbe7545a39b8ceb3a0d0d6df33b25b333f')
version('0.11.0', sha256='abfeccc94728cb46be8dbb3507a23ccffbacef9fbda96a977ef4ea8d6ab0d384')
version('0.10.1', sha256='708248f6d92f2f4d6342006c520f22dffa2f8adb0a9dc06a058e3effe7fee667')
version('0.10.0', sha256='47e0798caaac4df499bce5fe554a914abd884a855a27085a4473de1d737d9548')
version('0.9.0', sha256='efb28fed4ffcfaee653e0657f6500fc4cbac61e32104f4208da385676e76312a')
version('0.4.5', sha256='2b737be42678900470ae9e48c975ac5b2296d9ae23c007bf118350dbe7c0552b')
version('0.4.4', sha256='d52a21dda271ae645711ce99c70cf44c5d3a809138e656bbff00998827548ebb')
version('0.3.1', md5='5c959467484a7fc7dd2e5e4a1e8e866b')
version('0.3.0', md5='33a2cb457d28e1bee9282134769b9283')
version('0.2.3', md5='393a491d690e43caaba88005efe6da91')
version('0.2.2b', md5='75081804f073cbd194da1a07b16cba5f')
version('0.2.2', md5='644bc4ea7f429d835e74f255dc1054e6')
depends_on('java@8:', type=('build', 'link', 'run'))
depends_on('zip')

2
var/spack/repos/builtin/packages/bbmap/package.py
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@@ -13,7 +13,7 @@ class Bbmap(Package):
url = "https://downloads.sourceforge.net/project/bbmap/BBMap_38.63.tar.gz"
version('38.63', sha256='089064104526c8d696164aefa067f935b888bc71ef95527c72a98c17ee90a01f')
version('37.36', '1e1086e1fae490a7d03c5a065b1c262f')
version('37.36', sha256='befe76d7d6f3d0f0cd79b8a01004a2283bdc0b5ab21b0743e9dbde7c7d79e8a9')
depends_on('java')

2
var/spack/repos/builtin/packages/bc/package.py
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@@ -14,7 +14,7 @@ class Bc(AutotoolsPackage):
homepage = "https://www.gnu.org/software/bc"
url = "https://ftpmirror.gnu.org/bc/bc-1.07.tar.gz"
version('1.07', 'e91638a947beadabf4d7770bdbb3d512')
version('1.07', sha256='55cf1fc33a728d7c3d386cc7b0cb556eb5bacf8e0cb5a3fcca7f109fc61205ad')
depends_on('ed', type='build')
depends_on('texinfo', type='build')

12
var/spack/repos/builtin/packages/bcftools/package.py
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@@ -16,12 +16,12 @@ class Bcftools(AutotoolsPackage):
url = "https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2"
version('1.9', sha256='6f36d0e6f16ec4acf88649fb1565d443acf0ba40f25a9afd87f14d14d13070c8')
version('1.8', 'ba6c2fb7eb6dcb208f00ab8b22df475c')
version('1.7', 'c972db68d17af9da3a18963f4e5aeca8')
version('1.6', 'c4dba1e8cb55db0f94b4c47724b4f9fa')
version('1.4', '50ccf0a073bd70e99cdb3c8be830416e')
version('1.3.1', '575001e9fca37cab0c7a7287ad4b1cdb')
version('1.2', '8044bed8fce62f7072fc6835420f0906')
version('1.8', sha256='4acbfd691f137742e0be63d09f516434f0faf617a5c60f466140e0677915fced')
version('1.7', sha256='dd4f63d91b0dffb0f0ce88ac75c2387251930c8063f7799611265083f8d302d1')
version('1.6', sha256='293010736b076cf684d2873928924fcc3d2c231a091084c2ac23a8045c7df982')
version('1.4', sha256='8fb1b0a47ed4e1f9d7c70129d7993aa650da1688fd931b10646d1c4707ae234d')
version('1.3.1', sha256='12c37a4054cbf1980223e2b3a80a7fdb3fd850324a4ba6832e38fdba91f1b924')
version('1.2', sha256='53c628339020dd45334a007c9cefdaf1cba3f1032492ec813b116379fa684fd6')
depends_on('libzip', when='@1.8:')

8
var/spack/repos/builtin/packages/bcl2fastq2/package.py
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@@ -19,13 +19,13 @@ class Bcl2fastq2(Package):
homepage = "https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html"
version('2.20.0.422', '4dc99f1af208498b7279b66556329488')
version('2.19.1.403', 'baba7a02767fd868e87cb36781d2be26')
version('2.18.0.12', 'fbe06492117f65609c41be0c27e3215c')
version('2.20.0.422', sha256='8dd3044767d044aa4ce46de0de562b111c44e5b8b7348e04e665eb1b4f101fe3')
version('2.19.1.403', sha256='cf13580f2c1ebcc3642b4d98a02ad01e41a44e644db7d31730f9767b25521806')
version('2.18.0.12', md5='fbe06492117f65609c41be0c27e3215c')
# 2.17.1.14 is no longer distributed. If you have a copy of the
# source tarball, you can drop it into a local mirror w/ the name
# mirror/bcl2fastq2/bcl2fastq2-2.17.1.14.zip and go from there.
version('2.17.1.14', '7426226c6db095862e636b95c38608d3')
version('2.17.1.14', md5='7426226c6db095862e636b95c38608d3')
conflicts('platform=darwin',
msg='malloc.h/etc requirements break build on macs')

2
var/spack/repos/builtin/packages/bdftopcf/package.py
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@@ -17,7 +17,7 @@ class Bdftopcf(AutotoolsPackage):
homepage = "http://cgit.freedesktop.org/xorg/app/bdftopcf"
url = "https://www.x.org/archive/individual/app/bdftopcf-1.0.5.tar.gz"
version('1.0.5', '456416d33e0d41a96b5a3725d99e1be3')
version('1.0.5', sha256='78a5ec945de1d33e6812167b1383554fda36e38576849e74a9039dc7364ff2c3')
depends_on('libxfont')

4
var/spack/repos/builtin/packages/bdw-gc/package.py
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@@ -14,8 +14,8 @@ class BdwGc(AutotoolsPackage):
url = "https://www.hboehm.info/gc/gc_source/gc-8.0.0.tar.gz"
version('8.0.0', sha256='8f23f9a20883d00af2bff122249807e645bdf386de0de8cbd6cce3e0c6968f04')
version('7.6.0', 'bf46ccbdaccfa3186c2ab87191c8855a')
version('7.4.4', '96d18b0448a841c88d56e4ab3d180297')
version('7.6.0', sha256='a14a28b1129be90e55cd6f71127ffc5594e1091d5d54131528c24cd0c03b7d90')
version('7.4.4', sha256='e5ca9b628b765076b6ab26f882af3a1a29cde786341e08b9f366604f74e4db84')
variant('libatomic-ops', default=True,
description='Use external libatomic-ops')

4
var/spack/repos/builtin/packages/bear/package.py
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@@ -12,8 +12,8 @@ class Bear(CMakePackage):
homepage = "https://github.com/rizsotto/Bear"
url = "https://github.com/rizsotto/Bear/archive/2.0.4.tar.gz"
version('2.2.0', '87250cc3a9a697e7d1e8972253a35259')
version('2.0.4', 'fd8afb5e8e18f8737ba06f90bd77d011')
version('2.2.0', sha256='6bd61a6d64a24a61eab17e7f2950e688820c72635e1cf7ea8ea7bf9482f3b612')
version('2.0.4', sha256='33ea117b09068aa2cd59c0f0f7535ad82c5ee473133779f1cc20f6f99793a63e')
depends_on('python')
depends_on('cmake@2.8:', type='build')

4
var/spack/repos/builtin/packages/beast1/package.py
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@@ -13,8 +13,8 @@ class Beast1(Package):
homepage = "http://beast.community/"
version('1.10.4', sha256='be652c4d55953f7c6c7a9d3eb3de203c77dc380e81ad81cfe0492408990c36a8')
version('1.10.0', 'bcf2f2c074319360ec8a2ebad57d2e57')
version('1.8.4', 'cb8752340c1f77a22d39ca4fe09687b0')
version('1.10.0', md5='bcf2f2c074319360ec8a2ebad57d2e57')
version('1.8.4', sha256='c14e93976008463108aefa34ecc23287ab70703caccf4962e36e295207120d78')
variant('beagle', default=True, description='Build with libbeagle support')

2
var/spack/repos/builtin/packages/beast2/package.py
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@@ -18,7 +18,7 @@ class Beast2(Package):
url = "https://github.com/CompEvol/beast2/releases/download/v2.4.6/BEAST.v2.4.6.Linux.tgz"
version('2.5.2', sha256='2feb2281b4f7cf8f7de1a62de50f52a8678ed0767fc72f2322e77dde9b8cd45f')
version('2.4.6', 'b446f4ab121df9b991f7bb7ec94c8217')
version('2.4.6', sha256='84029c5680cc22f95bef644824130090f5f12d3d7f48d45cb4efc8e1d6b75e93')
depends_on('java')

6
var/spack/repos/builtin/packages/bedops/package.py
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@@ -15,9 +15,9 @@ class Bedops(MakefilePackage):
homepage = "https://bedops.readthedocs.io"
url = "https://github.com/bedops/bedops/archive/v2.4.30.tar.gz"
version('2.4.35', 'b425b3e05fd4cd1024ef4dd8bf04b4e5')
version('2.4.34', 'fc467d96134a0efe8b134e638af87a1a')
version('2.4.30', '4e5d9f7b7e5432b28aef8d17a22cffab')
version('2.4.35', sha256='da0265cf55ef5094834318f1ea4763d7a3ce52a6900e74f532dd7d3088c191fa')
version('2.4.34', sha256='533a62a403130c048d3378e6a975b73ea88d156d4869556a6b6f58d90c52ed95')
version('2.4.30', sha256='218e0e367aa79747b2f90341d640776eea17befc0fdc35b0cec3c6184098d462')
@property
def build_targets(self):

10
var/spack/repos/builtin/packages/bedtools2/package.py
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@@ -15,11 +15,11 @@ class Bedtools2(Package):
homepage = "https://github.com/arq5x/bedtools2"
url = "https://github.com/arq5x/bedtools2/archive/v2.26.0.tar.gz"
version('2.27.1', '8e0afcab95a824e42a6e99c5436a8438')
version('2.27.0', '052f22eb214ef2e7e7981b3c01167302')
version('2.26.0', '52227e7efa6627f0f95d7d734973233d')
version('2.25.0', '534fb4a7bf0d0c3f05be52a0160d8e3d')
version('2.23.0', '4fa3671b3a3891eefd969ad3509222e3')
version('2.27.1', sha256='edcac089d84e63a51f85c3c189469daa7d42180272130b046856faad3cf79112')
version('2.27.0', sha256='e91390b567e577d337c15ca301e264b0355441f5ab90fa4f971622e3043e0ca0')
version('2.26.0', sha256='15db784f60a11b104ccbc9f440282e5780e0522b8d55d359a8318a6b61897977')
version('2.25.0', sha256='159122afb9978015f7ec85d7b17739b01415a5738086b20a48147eeefcf08cfb')
version('2.23.0', sha256='9dacaa561d11ce9835d1d51e5aeb092bcbe117b7119663ec9a671abac6a36056')
depends_on('zlib')

2
var/spack/repos/builtin/packages/beforelight/package.py
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@@ -15,7 +15,7 @@ class Beforelight(AutotoolsPackage):
homepage = "http://cgit.freedesktop.org/xorg/app/beforelight"
url = "https://www.x.org/archive/individual/app/beforelight-1.0.5.tar.gz"
version('1.0.5', 'f0433eb6df647f36bbb5b38fb2beb22a')
version('1.0.5', sha256='93bb3c457d6d5e8def3180fdee07bc84d1b7f0e5378a95812e2193cd51455cdc')
depends_on('libx11')
depends_on('libxscrnsaver')

10
var/spack/repos/builtin/packages/benchmark/package.py
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@@ -19,11 +19,11 @@ class Benchmark(CMakePackage):
version('develop', branch='master')
version('1.5.0', sha256='3c6a165b6ecc948967a1ead710d4a181d7b0fbcaa183ef7ea84604994966221a')
version('1.4.1', sha256='f8e525db3c42efc9c7f3bc5176a8fa893a9a9920bbd08cef30fb56a51854d60d')
version('1.4.0', 'ccfaf2cd93ae20191b94f730b945423e')
version('1.3.0', '19ce86516ab82d6ad3b17173cf307aac')
version('1.2.0', '48d0b090cd7a84af2c4a28c8dc963c74')
version('1.1.0', '66b2a23076cf70739525be0092fc3ae3')
version('1.0.0', '1474ff826f8cd68067258db75a0835b8')
version('1.4.0', sha256='616f252f37d61b15037e3c2ef956905baf9c9eecfeab400cb3ad25bae714e214')
version('1.3.0', sha256='f19559475a592cbd5ac48b61f6b9cedf87f0b6775d1443de54cfe8f53940b28d')
version('1.2.0', sha256='3dcc90c158838e2ac4a7ad06af9e28eb5877cf28252a81e55eb3c836757d3070')
version('1.1.0', sha256='e7334dd254434c6668e33a54c8f839194c7c61840d52f4b6258eee28e9f3b20e')
version('1.0.0', sha256='d2206c263fc1a7803d4b10e164e0c225f6bcf0d5e5f20b87929f137dee247b54')
variant('build_type', default='RelWithDebInfo',
description='The build type to build',

8
var/spack/repos/builtin/packages/berkeley-db/package.py
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@@ -12,10 +12,10 @@ class BerkeleyDb(AutotoolsPackage):
homepage = "http://www.oracle.com/technetwork/database/database-technologies/berkeleydb/overview/index.html"
url = "http://download.oracle.com/berkeley-db/db-5.3.28.tar.gz"
version('5.3.28', 'b99454564d5b4479750567031d66fe24')
version('6.0.35', 'c65a4d3e930a116abaaf69edfc697f25')
version('6.1.29', '7f4d47302dfec698fe088e5285c9098e')
version('6.2.32', '33491b4756cb44b91c3318b727e71023')
version('5.3.28', sha256='e0a992d740709892e81f9d93f06daf305cf73fb81b545afe72478043172c3628')
version('6.0.35', sha256='24421affa8ae436fe427ae4f5f2d1634da83d3d55a5ad6354a98eeedb825de55')
version('6.1.29', sha256='b3c18180e4160d97dd197ba1d37c19f6ea2ec91d31bbfaf8972d99ba097af17d')
version('6.2.32', sha256='a9c5e2b004a5777aa03510cfe5cd766a4a3b777713406b02809c17c8e0e7a8fb')
configure_directory = 'dist'
build_directory = 'spack-build'

2
var/spack/repos/builtin/packages/bertini/package.py
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@@ -14,7 +14,7 @@ class Bertini(AutotoolsPackage):
homepage = "https://bertini.nd.edu/"
url = "https://bertini.nd.edu/BertiniSource_v1.5.tar.gz"
version('1.5', 'e3f6cc6e7f9a0cf1d73185e8671af707')
version('1.5', sha256='a9a68a96e180fe6a93ba1bc1d61f522784c9a053b049b2cbd98008b5b6deec3c')
variant('mpi', default=True, description='Compile in parallel')

2
var/spack/repos/builtin/packages/bigreqsproto/package.py
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@@ -15,7 +15,7 @@ class Bigreqsproto(AutotoolsPackage):
homepage = "http://cgit.freedesktop.org/xorg/proto/bigreqsproto"
url = "https://www.x.org/archive/individual/proto/bigreqsproto-1.1.2.tar.gz"
version('1.1.2', '9b83369ac7a5eb2bf54c8f34db043a0e')
version('1.1.2', sha256='de68a1a9dd1a1219ad73531bff9f662bc62fcd777387549c43cd282399f4a6ea')
depends_on('pkgconfig', type='build')
depends_on('util-macros', type='build')

18
var/spack/repos/builtin/packages/binutils/package.py
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@@ -14,16 +14,16 @@ class Binutils(AutotoolsPackage):
url = "https://ftpmirror.gnu.org/binutils/binutils-2.28.tar.bz2"
version('2.32', sha256='de38b15c902eb2725eac6af21183a5f34ea4634cb0bcef19612b50e5ed31072d')
version('2.31.1', 'ffcc382695bf947da6135e7436b8ed52d991cf270db897190f19d6f9838564d0')
version('2.29.1', '9af59a2ca3488823e453bb356fe0f113')
version('2.28', '9e8340c96626b469a603c15c9d843727')
version('2.27', '2869c9bf3e60ee97c74ac2a6bf4e9d68')
version('2.26', '64146a0faa3b411ba774f47d41de239f')
version('2.31.1', sha256='ffcc382695bf947da6135e7436b8ed52d991cf270db897190f19d6f9838564d0')
version('2.29.1', sha256='1509dff41369fb70aed23682351b663b56db894034773e6dbf7d5d6071fc55cc')
version('2.28', sha256='6297433ee120b11b4b0a1c8f3512d7d73501753142ab9e2daa13c5a3edd32a72')
version('2.27', sha256='369737ce51587f92466041a97ab7d2358c6d9e1b6490b3940eb09fb0a9a6ac88')
version('2.26', sha256='c2ace41809542f5237afc7e3b8f32bb92bc7bc53c6232a84463c423b0714ecd9')
version('2.25.1', sha256='b5b14added7d78a8d1ca70b5cb75fef57ce2197264f4f5835326b0df22ac9f22')
version('2.25', 'd9f3303f802a5b6b0bb73a335ab89d66')
version('2.24', 'e0f71a7b2ddab0f8612336ac81d9636b')
version('2.23.2', '4f8fa651e35ef262edc01d60fb45702e')
version('2.20.1', '2b9dc8f2b7dbd5ec5992c6e29de0b764')
version('2.25', sha256='22defc65cfa3ef2a3395faaea75d6331c6e62ea5dfacfed3e2ec17b08c882923')
version('2.24', sha256='e5e8c5be9664e7f7f96e0d09919110ab5ad597794f5b1809871177a0f0f14137')
version('2.23.2', sha256='fe914e56fed7a9ec2eb45274b1f2e14b0d8b4f41906a5194eac6883cfe5c1097')
version('2.20.1', sha256='71d37c96451333c5c0b84b170169fdcb138bbb27397dc06281905d9717c8ed64')
variant('plugins', default=False,
description="enable plugins, needed for gold linker")

2
var/spack/repos/builtin/packages/bioawk/package.py
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@@ -15,7 +15,7 @@ class Bioawk(MakefilePackage):
homepage = "https://github.com/lh3/bioawk"
url = "https://github.com/lh3/bioawk/archive/v1.0.zip"
version('1.0', 'e423942689f944369de270900978be28')
version('1.0', sha256='316a6561dda41e8327b85106db3704e94e23d7a89870392d19ef8559f7859e2d')
depends_on('zlib')
depends_on('bison', type=('build'))

4
var/spack/repos/builtin/packages/bismark/package.py
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@@ -13,8 +13,8 @@ class Bismark(Package):
homepage = "https://www.bioinformatics.babraham.ac.uk/projects/bismark"
url = "https://github.com/FelixKrueger/Bismark/archive/0.19.0.tar.gz"
version('0.19.0', 'f403654aded77bf0d1dac1203867ded1')
version('0.18.2', '42334b7e3ed53ba246f30f1f846b4af8')
version('0.19.0', sha256='91707737f96a0574956a282b635abad7560e7d90bee188a67a7807b2470deae2')
version('0.18.2', sha256='83391c5b5af33047178e7774ac25f5a69ce9315c13ae02f016baf7c50b73e702')
depends_on('bowtie2', type='run')
depends_on('perl', type='run')

6
var/spack/repos/builtin/packages/bison/package.py
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@@ -16,9 +16,9 @@ class Bison(AutotoolsPackage):
homepage = "http://www.gnu.org/software/bison/"
url = "https://ftpmirror.gnu.org/bison/bison-3.0.4.tar.gz"
version('3.0.5', '41ad57813157b61bfa47e33067a9d6f0')
version('3.0.4', 'a586e11cd4aff49c3ff6d3b6a4c9ccf8')
version('2.7', 'ded660799e76fb1667d594de1f7a0da9')
version('3.0.5', sha256='cd399d2bee33afa712bac4b1f4434e20379e9b4099bce47189e09a7675a2d566')
version('3.0.4', sha256='b67fd2daae7a64b5ba862c66c07c1addb9e6b1b05c5f2049392cfd8a2172952e')
version('2.7', sha256='19bbe7374fd602f7a6654c131c21a15aebdc06cc89493e8ff250cb7f9ed0a831')
depends_on('diffutils', type='build')
depends_on('m4', type=('build', 'run'))

2
var/spack/repos/builtin/packages/bitmap/package.py
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@@ -12,7 +12,7 @@ class Bitmap(AutotoolsPackage):
homepage = "http://cgit.freedesktop.org/xorg/app/bitmap"
url = "https://www.x.org/archive/individual/app/bitmap-1.0.8.tar.gz"
version('1.0.8', '0ca600041bb0836ae7c9f5db5ce09091')
version('1.0.8', sha256='1a2fbd10a2ca5cd93f7b77bbb0555b86d8b35e0fc18d036b1607c761755006fc')
depends_on('libx11')
depends_on('libxmu')

2
var/spack/repos/builtin/packages/blasr-libcpp/package.py
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@@ -15,7 +15,7 @@ class BlasrLibcpp(Package):
homepage = "https://github.com/PacificBiosciences/blasr_libcpp"
url = "https://github.com/PacificBiosciences/blasr_libcpp/archive/5.3.1.tar.gz"
version('5.3.1', 'ca770042cbca508d5ff12dff0d645045')
version('5.3.1', sha256='45a673255bfe7e29ed1f5bdb6410aa45cb6b907400d038c3da9daf1058b09156')
depends_on('pbbam')
depends_on('hdf5+cxx@1.8.12:1.8.99')

2
var/spack/repos/builtin/packages/blasr/package.py
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@@ -13,7 +13,7 @@ class Blasr(Package):
homepage = "https://github.com/PacificBiosciences/blasr/wiki"
url = "https://github.com/PacificBiosciences/blasr/archive/5.3.1.tar.gz"
version('5.3.1', '53c93f499aa4bc10781c87bafc33df2a')
version('5.3.1', sha256='ff7da5a03096294572e6c64340354da5c5ee1c86c277e7b899f2c170c1ac4049')
depends_on('ncurses')
depends_on('hdf5+cxx@1.8.12:1.8.99')

4
var/spack/repos/builtin/packages/blast-plus/package.py
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@@ -26,8 +26,8 @@ class BlastPlus(AutotoolsPackage):
version('2.9.0', sha256='a390cc2d7a09422759fc178db84de9def822cbe485916bbb2ec0d215dacdc257')
version('2.8.1', sha256='e03dd1a30e37cb8a859d3788a452c5d70ee1f9102d1ee0f93b2fbd145925118f')
version('2.7.1', sha256='10a78d3007413a6d4c983d2acbf03ef84b622b82bd9a59c6bd9fbdde9d0298ca')
version('2.6.0', 'c8ce8055b10c4d774d995f88c7cc6225')
version('2.2.30', 'f8e9a5eb368173142fe6867208b73715')
version('2.6.0', sha256='0510e1d607d0fb4389eca50d434d5a0be787423b6850b3a4f315abc2ef19c996')
version('2.2.30', sha256='26f72d51c81b9497f33b7274109565c36692572faef4d72377f79b7e59910e40')
# homebrew sez: Fixed upstream in future version > 2.6
# But this bug sez that it will be fixed in 2.6

2
var/spack/repos/builtin/packages/blat/package.py
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@@ -13,7 +13,7 @@ class Blat(Package):
homepage = "https://genome.ucsc.edu/FAQ/FAQblat.html"
url = "https://users.soe.ucsc.edu/~kent/src/blatSrc35.zip"
version('35', '16e546b8843b85e0b0f2fa603cd78724')
version('35', sha256='06d9bcf114ec4a4b21fef0540a0532556b6602322a5a2b33f159dc939ae53620')
depends_on('libpng')

32
var/spack/repos/builtin/packages/blaze/package.py
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@@ -26,19 +26,19 @@ class Blaze(CMakePackage):
version('3.5', sha256='f50d4a57796b8012d3e6d416667d9abe6f4d95994eb9deb86cd4491381dec624')
version('3.4', sha256='fd474ab479e81d31edf27d4a529706b418f874caa7b046c67489128c20dda66f')
version('3.3', sha256='138cbb7b95775c10bf56a5ab3596a32205751299b19699984b6ed55b1bf989d0')
version('3.2', '47bd4a4f1b6292f5a6f71ed9d5287480')
version('3.1', '2938e015f0d274e8d62ee5c4c0c1e9f3')
version('3.0', '0c4cefb0be7b5a27ed8a377941be1ab1')
version('2.6', 'f7b515eeffd5cce92eb02dc6f8905f4d')
version('2.5', '53a862763c275046ff0a8f07dfd3985b')
version('2.4', '7cf2e963a73d3c95ced0f7eaa0ae3677')
version('2.3', '2f8ca52d23447ac75a03bb43b12ef774')
version('2.2', '686a514108d7f3c6c7325ed57c171a59')
version('2.1', 'e5e419a2b35f0a36cd9d7527a250c56a')
version('2.0', 'aeb6a865e9e3810ee55456f961458a8e')
version('1.5', '5b77b605ee5ad35631bb3039737142c9')
version('1.4', '3f06d710161954ccae0975d87f1069ca')
version('1.3', 'ebd7f91fc5fca4108bfd16a86f9abd82')
version('1.2', 'b1511324456c3f70fce198a2b63e71ef')
version('1.1', '5e52ebe68217f2e50d66dfdb9803d51e')
version('1.0', 'a46508a2965ace9d89ded30a386d9548')
version('3.2', sha256='fb7e83d3a8c1ba04d3a51234708092b75a1abf3b7c4d0db5e6cf3cbed771b869')
version('3.1', sha256='a122d6758d9ada7ab516417f7b5ad186a4a9b390bba682f009df6585f5550716')
version('3.0', sha256='d66abaf4633d60b6e6472f6ecd7db7b4fb5f74a4afcfdf00c92e1ea61f2e0870')
version('2.6', sha256='a6b927db14b43fad483670dfa2acd7ecc94fd53085cdf18f262d2dc613857fb6')
version('2.5', sha256='5faeca8a26e04f70a5b3f94e88ef1fbe96a89e3722cd89e5f9d4bc8267b33d41')
version('2.4', sha256='34af70c8bb4da5fd0017b7c47e5efbfef9aadbabc5aae416582901a4059d1fa3')
version('2.3', sha256='785089db7f15684c24018b931f9f564954a79389166ac1f3e256a56c667d49f2')
version('2.2', sha256='448e70a440d71afa6325bae254ca7367b10e61431084adbf2ac679dbd5da78d2')
version('2.1', sha256='b982c03236c6a7ae396850eba0ef8fb1642ddf6448531063bf7239d9ff3290fd')
version('2.0', sha256='7bdf555e97455a2f42f40396b32caa9cf3e52bdd1877e0289115825113f4dcb2')
version('1.5', sha256='5c69b605b712616dcd29fa25abecb20b977ef318207ef96176ab67b2ad891e1e')
version('1.4', sha256='2e48d2e5a3a06abb23716829501bb0b825c58ad156faab6df0cfeef1bcdfbc82')
version('1.3', sha256='361bfbf2d2bf8557d123da3af8abc70e4c3b13d9c94a8227aeb751e06acdb8cf')
version('1.2', sha256='16f56d4f61dca229fa7e17a0d1e348a1f3246c65cded2df5db33babebf8f9b9d')
version('1.1', sha256='6add20eb9c176ea9f8091c49b101f46d1a1a6bd9c31553a6eff5e53603f0527f')
version('1.0', sha256='ee13cfd467c1a4b0fe7cc58b61b846eae862167a90dd2e60559626a30418b5a3')

2
var/spack/repos/builtin/packages/bliss/package.py
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@@ -14,7 +14,7 @@ class Bliss(Package):
homepage = "http://www.tcs.hut.fi/Software/bliss/"
url = "http://www.tcs.hut.fi/Software/bliss/bliss-0.73.zip"
version('0.73', '72f2e310786923b5c398ba0fc40b42ce')
version('0.73', sha256='f57bf32804140cad58b1240b804e0dbd68f7e6bf67eba8e0c0fa3a62fd7f0f84')
# Note: Bliss can also be built without gmp, but we don't support this yet

4
var/spack/repos/builtin/packages/blitz/package.py
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@@ -11,8 +11,8 @@ class Blitz(AutotoolsPackage):
homepage = "http://github.com/blitzpp/blitz"
url = "https://github.com/blitzpp/blitz/archive/1.0.1.tar.gz"
version('1.0.1', 'fe43e2cf6c9258bc8b369264dd008971')
version('1.0.0', '971c43e22318bbfe8da016e6ef596234')
version('1.0.1', sha256='b62fc3f07b64b264307b01fec5e4f2793e09a68dcb5378984aedbc2e4b3adcef')
version('1.0.0', sha256='79c06ea9a0585ba0e290c8140300e3ad19491c45c1d90feb52819abc3b58a0c1')
build_targets = ['lib']

4
var/spack/repos/builtin/packages/bmake/package.py
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@@ -12,8 +12,8 @@ class Bmake(Package):
homepage = "http://www.crufty.net/help/sjg/bmake.htm"
url = "http://www.crufty.net/ftp/pub/sjg/bmake-20180512.tar.gz"
version('20180512', '48ba5933833a7f224d76ce482eedfec0')
version('20171207', '5d7f2f85f16c4a6ba34ceea68957447f')
version('20180512', sha256='ac3cd262065fcc20c1dec7c95f06306c8138b3e17025b949343a06a8980a5508')
version('20171207', sha256='1703667e53a0498c0903b20612ebcbb41b886a94b238624cfeadd91a4111d39a')
phases = ['configure', 'build', 'install']

8
var/spack/repos/builtin/packages/bml/package.py
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@@ -17,10 +17,10 @@ class Bml(CMakePackage):
version('develop', branch='master')
version('1.3.1', sha256='17145eda96aa5e550dcbff1ee7ce62b45723af8210b1ab70c5975ec792fa3d13')
version('1.3.0', '2bf8546b27a89666dab3e8f4873cd117')
version('1.2.3', '8133137fb56a27fade44d1588449c2ac')
version('1.2.2', 'c86959cb0188e9d0a9a2cbad03b2782d')
version('1.1.0', '271adecee08aee678be9eeceee06b6fb')
version('1.3.0', sha256='d9465079fe77210eb2af2dcf8ed96802edf5bb76bfbfdbcc97e206c8cd460b07')
version('1.2.3', sha256='9a2ee6c47d2445bfdb34495497ea338a047e9e4767802af47614d9ff94b0c523')
version('1.2.2', sha256='89ab78f9fe8395fe019cc0495a1d7b69875b5708069faeb831ddb9a6a9280a8a')
version('1.1.0', sha256='29162f1f7355ad28b44d3358206ccd3c7ac7794ee13788483abcbd2f8063e7fc')
variant('shared', default=True, description='Build shared libs')
variant('mpi', default=True, description='Build with MPI Support')

6
var/spack/repos/builtin/packages/bolt/package.py
View File

@@ -22,9 +22,9 @@ class Bolt(CMakePackage):
git = "https://github.com/pmodels/bolt.git"
version("master", branch="master")
version("1.0rc2", "f5ca4f9fb05d6e4edbbd32635828c833")
version("1.0rc1", "77733ba2ad9440c29b36d1c1411a9793")
version("1.0b1", "df76beb3a7f13ae2dcaf9ab099eea87b")
version("1.0rc2", sha256="662ab0bb9583e8d733e8af62a97b41828e8bfe4bd65902f1195b986901775a45")
version("1.0rc1", sha256="c08cde0695b9d1252ab152425be96eb29c70d764e3083e276c013804883a15a4")
version("1.0b1", sha256="fedba46ad2f8835dd1cec1a9a52bcc9d8923071dc40045d0360517d09cd1a57d")
depends_on('argobots')
depends_on('autoconf', type='build')

4
var/spack/repos/builtin/packages/bookleaf-cpp/package.py
View File

@@ -16,8 +16,8 @@ class BookleafCpp(CMakePackage):
version('develop', branch='develop')
version('2.0.2', sha256='787ade5045415d71d9bad55fe9f93598f3a0548d13e2ff80e752cc99f62fe6d3')
version('2.0.1', '34a5a9e7b2b5ffc98562656a4406ba5b')
version('2.0', '69819ebcbae5eaa63d1a4de2c77cac85')
version('2.0.1', sha256='1286f916f59d1f3bf325041854e8c203894e293c5e26d5b19b9362ee02082983')
version('2.0', sha256='3c14344c31385bec9e089f9babf815566c4fcf98a47822f663afa2cefb0e90e1')
variant('typhon', default=True, description='Use Typhon')
variant('parmetis', default=False, description='Use ParMETIS')

80
var/spack/repos/builtin/packages/boost/package.py
View File

@@ -24,50 +24,50 @@ class Boost(Package):
list_depth = 1
version('develop', branch='develop', submodules=True)
version('1.70.0', '5b2e5ccc454503cfbba6c1221f5d495f0de279ea')
version('1.69.0', 'ea6eee4b5999f9c02105386850f63a53f0250eaa')
version('1.68.0', '18863a7cae4d58ae85eb63d400f774f60a383411')
version('1.67.0', '694ae3f4f899d1a80eb7a3b31b33be73c423c1ae')
version('1.66.0', 'b6b284acde2ad7ed49b44e856955d7b1ea4e9459')
version('1.65.1', '41d7542ce40e171f3f7982aff008ff0d')
version('1.65.0', '5512d3809801b0a1b9dd58447b70915d')
version('1.70.0', sha256='430ae8354789de4fd19ee52f3b1f739e1fba576f0aded0897c3c2bc00fb38778')
version('1.69.0', sha256='8f32d4617390d1c2d16f26a27ab60d97807b35440d45891fa340fc2648b04406')
version('1.68.0', sha256='7f6130bc3cf65f56a618888ce9d5ea704fa10b462be126ad053e80e553d6d8b7')
version('1.67.0', sha256='2684c972994ee57fc5632e03bf044746f6eb45d4920c343937a465fd67a5adba')
version('1.66.0', sha256='5721818253e6a0989583192f96782c4a98eb6204965316df9f5ad75819225ca9')
version('1.65.1', sha256='9807a5d16566c57fd74fb522764e0b134a8bbe6b6e8967b83afefd30dcd3be81')
version('1.65.0', sha256='ea26712742e2fb079c2a566a31f3266973b76e38222b9f88b387e3c8b2f9902c')
# NOTE: 1.64.0 seems fine for *most* applications, but if you need
# +python and +mpi, there seem to be errors with out-of-date
# API calls from mpi/python.
# See: https://github.com/spack/spack/issues/3963
version('1.64.0', '93eecce2abed9d2442c9676914709349')
version('1.63.0', '1c837ecd990bb022d07e7aab32b09847')
version('1.62.0', '5fb94629535c19e48703bdb2b2e9490f')
version('1.61.0', '6095876341956f65f9d35939ccea1a9f')
version('1.60.0', '65a840e1a0b13a558ff19eeb2c4f0cbe')
version('1.59.0', '6aa9a5c6a4ca1016edd0ed1178e3cb87')
version('1.58.0', 'b8839650e61e9c1c0a89f371dd475546')
version('1.57.0', '1be49befbdd9a5ce9def2983ba3e7b76')
version('1.56.0', 'a744cf167b05d72335f27c88115f211d')
version('1.55.0', 'd6eef4b4cacb2183f2bf265a5a03a354')
version('1.54.0', '15cb8c0803064faef0c4ddf5bc5ca279')
version('1.53.0', 'a00d22605d5dbcfb4c9936a9b35bc4c2')
version('1.52.0', '3a855e0f919107e0ca4de4d84ad3f750')
version('1.51.0', '4b6bd483b692fd138aef84ed2c8eb679')
version('1.50.0', '52dd00be775e689f55a987baebccc462')
version('1.49.0', '0d202cb811f934282dea64856a175698')
version('1.48.0', 'd1e9a7a7f532bb031a3c175d86688d95')
version('1.47.0', 'a2dc343f7bc7f83f8941e47ed4a18200')
version('1.46.1', '7375679575f4c8db605d426fc721d506')
version('1.46.0', '37b12f1702319b73876b0097982087e0')
version('1.45.0', 'd405c606354789d0426bc07bea617e58')
version('1.44.0', 'f02578f5218f217a9f20e9c30e119c6a')
version('1.43.0', 'dd49767bfb726b0c774f7db0cef91ed1')
version('1.42.0', '7bf3b4eb841b62ffb0ade2b82218ebe6')
version('1.41.0', '8bb65e133907db727a2a825c5400d0a6')
version('1.40.0', 'ec3875caeac8c52c7c129802a8483bd7')
version('1.39.0', 'a17281fd88c48e0d866e1a12deecbcc0')
version('1.38.0', '5eca2116d39d61382b8f8235915cb267')
version('1.37.0', '8d9f990bfb7e83769fa5f1d6f065bc92')
version('1.36.0', '328bfec66c312150e4c2a78dcecb504b')
version('1.35.0', 'dce952a7214e72d6597516bcac84048b')
version('1.34.1', '2d938467e8a448a2c9763e0a9f8ca7e5')
version('1.34.0', 'ed5b9291ffad776f8757a916e1726ad0')
version('1.64.0', sha256='7bcc5caace97baa948931d712ea5f37038dbb1c5d89b43ad4def4ed7cb683332')
version('1.63.0', sha256='beae2529f759f6b3bf3f4969a19c2e9d6f0c503edcb2de4a61d1428519fcb3b0')
version('1.62.0', sha256='36c96b0f6155c98404091d8ceb48319a28279ca0333fba1ad8611eb90afb2ca0')
version('1.61.0', sha256='a547bd06c2fd9a71ba1d169d9cf0339da7ebf4753849a8f7d6fdb8feee99b640')
version('1.60.0', sha256='686affff989ac2488f79a97b9479efb9f2abae035b5ed4d8226de6857933fd3b')
version('1.59.0', sha256='727a932322d94287b62abb1bd2d41723eec4356a7728909e38adb65ca25241ca')
version('1.58.0', sha256='fdfc204fc33ec79c99b9a74944c3e54bd78be4f7f15e260c0e2700a36dc7d3e5')
version('1.57.0', sha256='910c8c022a33ccec7f088bd65d4f14b466588dda94ba2124e78b8c57db264967')
version('1.56.0', sha256='134732acaf3a6e7eba85988118d943f0fa6b7f0850f65131fff89823ad30ff1d')
version('1.55.0', sha256='fff00023dd79486d444c8e29922f4072e1d451fc5a4d2b6075852ead7f2b7b52')
version('1.54.0', sha256='047e927de336af106a24bceba30069980c191529fd76b8dff8eb9a328b48ae1d')
version('1.53.0', sha256='f88a041b01882b0c9c5c05b39603ec8383fb881f772f6f9e6e6fd0e0cddb9196')
version('1.52.0', sha256='222b6afd7723f396f5682c20130314a10196d3999feab5ba920d2a6bf53bac92')
version('1.51.0', sha256='fb2d2335a29ee7fe040a197292bfce982af84a645c81688a915c84c925b69696')
version('1.50.0', sha256='c9ace2b8c81fa6703d1d17c7e478de3bc51101c5adbdeb3f6cb72cf3045a8529')
version('1.49.0', sha256='dd748a7f5507a7e7af74f452e1c52a64e651ed1f7263fce438a06641d2180d3c')
version('1.48.0', sha256='1bf254b2d69393ccd57a3cdd30a2f80318a005de8883a0792ed2f5e2598e5ada')
version('1.47.0', sha256='815a5d9faac4dbd523fbcf3fe1065e443c0bbf43427c44aa423422c6ec4c2e31')
version('1.46.1', sha256='e1dfbf42b16e5015c46b98e9899c423ca4d04469cbeee05e43ea19236416d883')
version('1.46.0', sha256='2f90f60792fdc25e674b8a857a0bcbb8d01199651719c90d5c4f8c61c08eba59')
version('1.45.0', sha256='55ed3ec51d5687e8224c988e22bef215dacce04e037d9f689569a80c4377a6d5')
version('1.44.0', sha256='45c328029d97d1f1dc7ff8c9527cd0c5cc356636084a800bca2ee4bfab1978db')
version('1.43.0', sha256='344f100b1aa410e812cabf0e4130728a80be042bf346135516b9187853806120')
version('1.42.0', sha256='4b1eb95bd250ce15ac66435d6167f225b072b0d3a7eb72477a31847a9ca9e609')
version('1.41.0', sha256='1ef94e6749eaf13318284b4f629be063544c7015b45e38113b975ac1945cc726')
version('1.40.0', sha256='36cf4a239b587067a4923fdf6e290525a14c3af29829524fa73f3dec6841530c')
version('1.39.0', sha256='44785eae8c6cce61a29a8a51f9b737e57b34d66baa7c0bcd4af188832b8018fd')
version('1.38.0', sha256='3ee3a45af4d2fabf343b9e05cfbe033c35d63719b45a6554d5849e4a34216066')
version('1.37.0', sha256='d52ef49f70b1b9addc4e0d1a3a2a1966227f0d173c3301bac3e6d399eeac5472')
version('1.36.0', sha256='9a4a0cfbbd227c20a13519a2c41f2e707dc0d89e518a3c7bfcd381f7b7fbcdef')
version('1.35.0', sha256='f8bf7368a22ccf2e2cf77048ab2129744be4c03f8488c76ad31c0aa229b280da')
version('1.34.1', sha256='0f866c75b025a4f1340117a106595cc0675f48ba1e5a9b5c221ec7f19e96ec4c')
version('1.34.0', sha256='455cb8fa41b759272768257c2e7bdc5c47ec113245dfa533f275e787a855efd2')
default_install_libs = set(['atomic',
'chrono',

2
var/spack/repos/builtin/packages/boostmplcartesianproduct/package.py
View File

@@ -15,7 +15,7 @@ class Boostmplcartesianproduct(Package):
homepage = "http://www.organicvectory.com/index.php?option=com_content&view=article&id=75:boostmplcartesianproduct&catid=42:boost&Itemid=78"
url = "https://github.com/quinoacomputing/BoostMPLCartesianProduct/tarball/20161205"
version('20161205', 'b0c8534ee807484ffd161723cbc8fc04')
version('20161205', sha256='1fa8e367e4dc545b34016bf57d802858ce38baf40aff20f7c93b329895a18572')
def install(self, spec, prefix):
install_tree('boost/mpl', join_path(prefix.include, 'boost', 'mpl'))

2
var/spack/repos/builtin/packages/bowtie/package.py
View File

@@ -28,7 +28,7 @@ class Bowtie(MakefilePackage):
version('1.2.0', sha256='dc4e7951b8eca56ce7714c47fd4e84f72badd5312ee9546c912af1963570f894')
# Keeping the old 1.2 version around for reproducibility, it's not
# clearly identical to 1.2.0.
version('1.2', md5='6d97f0ea1a65af11d17cc270cfac4af9', url='https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.0/bowtie-1.2-source.zip')
version('1.2', sha256='b1052de4253007890f6436e6361d40148bc2a5a9dd01827bb9f34097747e65f8', url='https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.0/bowtie-1.2-source.zip')
# 1.2.2 and 1.2.2_p1 fail to build with %gcc@8.3.0
# with and without issue-87 patch

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