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

12 files changed, 175 insertions, 3 deletions

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))