From 0ce15003763b3c05c0d77b1875d10f7c295b2936 Mon Sep 17 00:00:00 2001 From: Brian Van Essen Date: Fri, 1 Mar 2019 14:46:13 -0600 Subject: Package Updates for ECP CANDLE Supervisor (#10760) * Add EQ-R package * Add Fansi, Pillar, UTF8 (R) packages * Add new versions for py-mdanalysis, r-cli, r-dplyr, r-pkgconfig, r-rlang, r-tibble, stc, and turbine packages * Add hdf5 support for turbine * Specify configure directory for stc package --- var/spack/repos/builtin/packages/eqr/package.py | 54 ++++++++++++++++++++++ .../builtin/packages/py-mdanalysis/package.py | 12 ++++- var/spack/repos/builtin/packages/r-cli/package.py | 1 + .../repos/builtin/packages/r-dplyr/package.py | 1 + .../repos/builtin/packages/r-fansi/package.py | 21 +++++++++ .../repos/builtin/packages/r-pillar/package.py | 31 +++++++++++++ .../repos/builtin/packages/r-pkgconfig/package.py | 2 + .../repos/builtin/packages/r-rlang/package.py | 3 ++ .../repos/builtin/packages/r-tibble/package.py | 8 ++++ var/spack/repos/builtin/packages/r-utf8/package.py | 21 +++++++++ var/spack/repos/builtin/packages/stc/package.py | 6 +++ .../repos/builtin/packages/turbine/package.py | 18 +++++++- 12 files changed, 175 insertions(+), 3 deletions(-) create mode 100644 var/spack/repos/builtin/packages/eqr/package.py create mode 100644 var/spack/repos/builtin/packages/r-fansi/package.py create mode 100644 var/spack/repos/builtin/packages/r-pillar/package.py create mode 100644 var/spack/repos/builtin/packages/r-utf8/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/eqr/package.py b/var/spack/repos/builtin/packages/eqr/package.py new file mode 100644 index 0000000000..e31f88bb39 --- /dev/null +++ b/var/spack/repos/builtin/packages/eqr/package.py @@ -0,0 +1,54 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * +import os + + +class Eqr(AutotoolsPackage): + """ + EMEWS Queues for R (EQ/R) + Installs EQ/R. + """ + + git = "https://github.com/emews/EQ-R" + + version('develop', branch='master') + + configure_directory = 'src' + + homepage = "http://emews.org" + url = "https://github.com/emews/EQ-R/archive/1.0.tar.gz" + version('1.0', sha256='68047cb0edf088eaaefc5e36cefda9818292e5c832593e10a1dd9c73c27661b6') + + depends_on('autoconf', type='build') + depends_on('automake', type='build') + depends_on('libtool', type='build') + depends_on('m4', type='build') + depends_on('mpi') + depends_on('r-rinside') + depends_on('r-rcpp') + depends_on('r') + depends_on('tcl') + depends_on('swig') + + def setup_environment(self, spack_env, run_env): + spec = self.spec + spack_env.set('CC', spec['mpi'].mpicc) + spack_env.set('CXX', spec['mpi'].mpicxx) + spack_env.set('CXXLD', spec['mpi'].mpicxx) + + def configure_args(self): + args = ['--with-tcl=' + self.spec['tcl'].prefix] + r_location = '{0}/rlib/R'.format(self.spec['r'].prefix) + if not os.path.exists(r_location): + rscript = which('Rscript') + if rscript is not None: + r_location = rscript('-e', 'cat(R.home())') + else: + msg = 'couldn\'t locate Rscript on your PATH' + raise RuntimeError(msg) + args.append('--with-r={0}'.format(r_location)) + return args diff --git a/var/spack/repos/builtin/packages/py-mdanalysis/package.py b/var/spack/repos/builtin/packages/py-mdanalysis/package.py index 7d733cea27..f98a0fb063 100644 --- a/var/spack/repos/builtin/packages/py-mdanalysis/package.py +++ b/var/spack/repos/builtin/packages/py-mdanalysis/package.py @@ -14,8 +14,16 @@ class PyMdanalysis(PythonPackage): topology formats.)""" homepage = "http://www.mdanalysis.org" - url = "https://pypi.io/packages/source/M/MDAnalysis/MDAnalysis-0.15.0.tar.gz" - + url = "https://pypi.io/packages/source/M/MDAnalysis/MDAnalysis-0.19.2.tar.gz" + + version('0.19.2', sha256='c5395bbafa5efca2e1aee4715d26129844140c47cb8301da0293106cb969de7d') + version('0.19.1', sha256='ff1d694f8598c0833ec340de6a6adb3b5e62b92d0fa94ee6401718ba972db3cc') + version('0.19.0', sha256='248e3b37fc6150e31c609cc18a3927c32aee37b76d29cbfedf635e7e1aa982cf') + version('0.18.0', sha256='a08acea1755112411e7db55e3f282e164b47a59e15794b38744cce6c596f252a') + version('0.17.0', sha256='9bd61760334698cc7b8a57ad26456451e926e9c9e66722594ad8816561348cde') + version('0.16.2', sha256='407d9a9ff1ab8a5e47973714d06fabff220f8d08a28792dee93e88e70e995b0a') + version('0.16.1', sha256='3dc8f5d639ab3a0d152cbd7259ae9372ec8a9bac0f8cb7d3b80ce5adc1e3ee57') + version('0.16.0', sha256='c4824fa1fddd336daa39371436187ebb023366885fb250c2827ed7fce2546bd4') version('0.15.0', '19e5a8e6c2bfe85f6209d1d7a36e4f20') variant('analysis', default=True, diff --git a/var/spack/repos/builtin/packages/r-cli/package.py b/var/spack/repos/builtin/packages/r-cli/package.py index 8c3066f089..883a34e8eb 100644 --- a/var/spack/repos/builtin/packages/r-cli/package.py +++ b/var/spack/repos/builtin/packages/r-cli/package.py @@ -15,6 +15,7 @@ class RCli(RPackage): url = "https://cran.r-project.org/src/contrib/cli_1.0.0.tar.gz" list_url = "https://cran.r-project.org/src/contrib/Archive/cli" + version('1.0.1', 'ef80fbcde15760fd55abbf9413b306e3971b2a7034ab8c415fb52dc0088c5ee4') version('1.0.0', 'e6c4169541d394d6d435c4b430b1dd77') depends_on('r-assertthat', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-dplyr/package.py b/var/spack/repos/builtin/packages/r-dplyr/package.py index ac034b5513..b2aed2c626 100644 --- a/var/spack/repos/builtin/packages/r-dplyr/package.py +++ b/var/spack/repos/builtin/packages/r-dplyr/package.py @@ -34,3 +34,4 @@ class RDplyr(RPackage): depends_on('r-rlang@0.3.0:', type=('build', 'run')) depends_on('r-tibble@1.4.2:', type=('build', 'run')) depends_on('r-tidyselect@0.2.3:', type=('build', 'run')) + depends_on('r-bh@1.58.0-1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-fansi/package.py b/var/spack/repos/builtin/packages/r-fansi/package.py new file mode 100644 index 0000000000..41695ebc72 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-fansi/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RFansi(RPackage): + """Counterparts to R string manipulation functions that account + for the effects of ANSI text formatting control sequences.""" + + homepage = "https://cran.r-project.org/package=fansi" + url = "https://cran.r-project.org/src/contrib/fansi_0.4.0.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/fansi" + + version('0.4.0', sha256='e104e9d01c7ff8a847f6b332ef544c0ef912859f9c6a514fe2e6f3b34fcfc209') + version('0.3.0', sha256='dd6401d5c91ff4c45d752cceddd5379d1ae39a8a1196f236b0bc0ec6d691b88c') + version('0.2.3', sha256='db6dfef8bfe6682d58b654b6a6a1d59cb07225ca41755176b465ab8611fd96c9') + version('0.2.2', sha256='71dfdda467985a4d630ecf93d4bc60446a8a78d69dbd7ac24cc45822329d4bce') + version('0.2.1', sha256='abe709d69ddd6610aaa24e049c7a97c16a2c2dbe0873d4e3b8af57e486ef05c5') diff --git a/var/spack/repos/builtin/packages/r-pillar/package.py b/var/spack/repos/builtin/packages/r-pillar/package.py new file mode 100644 index 0000000000..d23c6eb662 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-pillar/package.py @@ -0,0 +1,31 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RPillar(RPackage): + """Provides a 'pillar' generic designed for formatting columns of data + using the full range of colours provided by modern terminals.""" + + homepage = "https://cran.r-project.org/package=pillar" + url = "https://cran.r-project.org/src/contrib/pillar_1.3.1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/pillar" + + version('1.3.1', sha256='b338b55f956dd7134f379d39bb94dfb25e13cf27999d6a6e6dc9f292755acbf6') + version('1.3.0', sha256='aed845ae4888be9a7340eed57536e3fe6cb46e89d905897fb9b0635797cfcae0') + version('1.2.3', sha256='c81d1b5c6b55d789a6717dc3c7be1200eb0efbcfc5013db00d553d9cafd6f0e7') + version('1.2.2', sha256='676d6e64754ce42c2789ca3521eeb576c873afc3b09adfdf2c97f03cbcddb8ce') + version('1.2.1', sha256='6de997a43416f436039f2b8b47c46ea08d2508f8ad341e0e1fd878704a3dcde7') + version('1.2.0', sha256='fd042b525b27e5f700e5299f50d25710501a4f35556b6a04b430776568962416') + version('1.1.0', sha256='58a29e8d0d3a47150caf8cb1aba5dc5eca233ac8d4626f4b23beb8b5ae9003be') + version('1.0.1', sha256='7b37189ab9ab0bbf2e6f49e9d5e678acb31500739d3c3ea2b5326b457716277d') + version('1.0.0', sha256='7478d0765212c5f0333b8866231a6fe350393b7fa49840e6fed3516ac64540dc') + + depends_on('r-cli', type=('build', 'run')) + depends_on('r-crayon', type=('build', 'run')) + depends_on('r-fansi', type=('build', 'run')) + depends_on('r-rlang', type=('build', 'run')) + depends_on('r-utf8', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pkgconfig/package.py b/var/spack/repos/builtin/packages/r-pkgconfig/package.py index a741025d30..1f589b5b61 100644 --- a/var/spack/repos/builtin/packages/r-pkgconfig/package.py +++ b/var/spack/repos/builtin/packages/r-pkgconfig/package.py @@ -14,4 +14,6 @@ class RPkgconfig(RPackage): homepage = "https://cran.rstudio.com/web/packages/pkgconfig/index.html" url = "https://cran.rstudio.com/src/contrib/pkgconfig_2.0.1.tar.gz" list_url = "https://cran.r-project.org/src/contrib/Archive/pkgconfig" + + version('2.0.2', sha256='25997754d1adbe7a251e3bf9879bb52dced27dd8b84767d558f0f644ca8d69ca') version('2.0.1', 'a20fd9588e37995995fa62dc4828002e') diff --git a/var/spack/repos/builtin/packages/r-rlang/package.py b/var/spack/repos/builtin/packages/r-rlang/package.py index ff52f9893f..2fada49290 100644 --- a/var/spack/repos/builtin/packages/r-rlang/package.py +++ b/var/spack/repos/builtin/packages/r-rlang/package.py @@ -14,6 +14,9 @@ class RRlang(RPackage): url = "https://cran.r-project.org/src/contrib/rlang_0.2.2.tar.gz" list_url = "https://cran.r-project.org/src/contrib/Archive/rlang" + version('0.3.1', sha256='30427b2be2288e88acd30c4ea348ee06043a649fd73623a63148b1ad96317151') + version('0.3.0.1', sha256='29451db0a3cabd75761d32df47a5d43ccadbde07ecb693ffdd73f122a0b9f348') + version('0.3.0', sha256='9ab10ea3e19b2d60a289602ebbefa83509f430db1c8161e523896c374241b893') version('0.2.2', 'df2abf3a1936c503ed1edd4350ffb5f0') version('0.1.4', 'daed5104d557c0cbfb4a654ec8ffb579') version('0.1.2', '170f8cf7b61898040643515a1746a53a') diff --git a/var/spack/repos/builtin/packages/r-tibble/package.py b/var/spack/repos/builtin/packages/r-tibble/package.py index 5afcc00edd..29b2f614cd 100644 --- a/var/spack/repos/builtin/packages/r-tibble/package.py +++ b/var/spack/repos/builtin/packages/r-tibble/package.py @@ -13,6 +13,10 @@ class RTibble(RPackage): homepage = "https://github.com/tidyverse/tibble" url = "https://cran.rstudio.com/src/contrib/tibble_1.3.4.tar.gz" list_url = "https://cran.r-project.org/src/contrib/Archive/tibble" + version('2.0.1', sha256='7ab2cc295eecf00a5310993c99853cd6622ad468e7a60d004b8a73957a713d13') + version('2.0.0', sha256='05ad2d62e949909548c4bb8ac596810321f11b330afa9717d0889dc35edd99ba') + version('1.4.2', sha256='11670353ff7059a55066dd075d1534d6a27bc5c3583fb9bc291bf750a75c5b17') + version('1.4.1', sha256='32267fae1ca86abdd37c4683f9d2b1a47b8b65e1977ea3900aa197066c57aa29') version('1.3.4', '298e81546f999fb0968625698511b8d3') version('1.2', 'bdbc3d67aa16860741add6d6ec20ea13') version('1.1', '2fe9f806109d0b7fadafb1ffafea4cb8') @@ -23,3 +27,7 @@ class RTibble(RPackage): depends_on('r-lazyeval@0.1.10:', type=('build', 'run'), when='@:1.3.0') depends_on('r-rcpp', type=('build', 'run')) depends_on('r-rlang', type=('build', 'run'), when='@1.3.1:') + depends_on('r-cli', type=('build', 'run'), when='@1.4.2:') + depends_on('r-crayon', type=('build', 'run'), when='@1.4.2:') + depends_on('r-pillar', type=('build', 'run'), when='@1.4.2:') + depends_on('r-pkgconfig', type=('build', 'run'), when='@1.4.2:') diff --git a/var/spack/repos/builtin/packages/r-utf8/package.py b/var/spack/repos/builtin/packages/r-utf8/package.py new file mode 100644 index 0000000000..2e40f83bfa --- /dev/null +++ b/var/spack/repos/builtin/packages/r-utf8/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RUtf8(RPackage): + """Process and print 'UTF-8' encoded international text + (Unicode). Input, validate, normalize, encode, format, and display.""" + + homepage = "https://cran.r-project.org/package=utf8" + url = "https://cran.r-project.org/src/contrib/utf8_1.1.4.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/utf8" + + version('1.1.3', sha256='43b394c3274ba0f66719d28dc4a7babeb87187e766de8d8ca716e0548091440f') + version('1.1.2', sha256='148517aadb75d82aba61f63afe2a30d254abebbdc7e32dd0830e12ff443915b9') + version('1.1.1', sha256='0e30c824e43cdc0a3339f4688e3271737d02ea10768a46137e0e41936051cb3d') + version('1.1.0', sha256='6a8ae2c452859800c3ef12993a55892588fc35df8fa1360f3d182ed97244dc4f') + version('1.0.0', sha256='7562a80262cbc2017eee76c0d3c9575f240fab291f868a11724fa04a116efb80') diff --git a/var/spack/repos/builtin/packages/stc/package.py b/var/spack/repos/builtin/packages/stc/package.py index 705bc42671..1263f794a3 100644 --- a/var/spack/repos/builtin/packages/stc/package.py +++ b/var/spack/repos/builtin/packages/stc/package.py @@ -12,13 +12,19 @@ class Stc(AutotoolsPackage): homepage = 'http://swift-lang.org/Swift-T' url = 'http://swift-lang.github.io/swift-t-downloads/spack/stc-0.0.0.tar.gz' + git = "https://github.com/swift-lang/swift-t.git" + configure_directory = 'stc/code' + version('develop', branch='master') version('0.8.2', '883b0657f1aac9b81158ef0a8989be4c') depends_on('java', type=('build', 'run')) depends_on('ant', type='build') depends_on('turbine', type=('build', 'run')) depends_on('zsh', type=('build', 'run')) + depends_on('autoconf', type='build') + depends_on('automake', type='build') + depends_on('libtool', type='build') def configure_args(self): args = ['--with-turbine=' + self.spec['turbine'].prefix] diff --git a/var/spack/repos/builtin/packages/turbine/package.py b/var/spack/repos/builtin/packages/turbine/package.py index 42e23229e1..8ce10e7d54 100644 --- a/var/spack/repos/builtin/packages/turbine/package.py +++ b/var/spack/repos/builtin/packages/turbine/package.py @@ -12,7 +12,10 @@ class Turbine(AutotoolsPackage): homepage = 'http://swift-lang.org/Swift-T' url = 'http://swift-lang.github.io/swift-t-downloads/spack/turbine-0.0.0.tar.gz' + git = "https://github.com/swift-lang/swift-t.git" + configure_directory = 'turbine/code' + version('develop', branch='master') version('1.2.3', 'f2e393c292c4248b4e77a19f8272ae88') version('1.2.1', 'c8976b22849aafe02a8fb4259dfed434') version('1.1.0', '9a347cf16df02707cb529f96c265a082') @@ -21,6 +24,8 @@ class Turbine(AutotoolsPackage): description='Enable calling python') variant('r', default=False, description='Enable calling R') + variant('hdf5', default=False, + description='Enable HDF5 support') depends_on('adlbx@:0.8.0', when='@:1.1.0') depends_on('adlbx', when='@1.2.1:') depends_on('adlbx') @@ -29,6 +34,12 @@ class Turbine(AutotoolsPackage): depends_on('swig', type='build') depends_on('python', when='+python') depends_on('r', when='+r') + depends_on('r-rinside', when='+r') + depends_on('hdf5', when='+hdf5') + depends_on('mpi') + depends_on('autoconf', type='build') + depends_on('automake', type='build') + depends_on('libtool', type='build') def setup_environment(self, spack_env, run_env): spec = self.spec @@ -41,7 +52,12 @@ class Turbine(AutotoolsPackage): args = ['--with-c-utils=' + self.spec['exmcutils'].prefix, '--with-adlb=' + self.spec['adlbx'].prefix, '--with-tcl=' + self.spec['tcl'].prefix, - '--with-mpi=' + self.spec['mpi'].prefix] + '--with-mpi=' + self.spec['mpi'].prefix, + '--disable-static-pkg'] + if '+hdf5' in self.spec: + args.append('--with-hdf5=ON') + else: + args.append('--with-hdf5=OFF') if '+python' in self.spec: args.append('--with-python-exe={0}'.format( self.spec['python'].command.path)) -- cgit v1.2.3-70-g09d2