Tanim (#9158)

* Added jdk version, added r-ks and r-multicool packages, made some r packages less conservative in their r version requirement

* flake8 fixes

* fix formatting in jdk version cmd

* Added type=('build', 'run') to some R package dependencies,
added some missing dependencies to r-ks. Thanks Adam.

* fix flake8 error

8 files changed, 88 insertions, 5 deletions

diff --git a/var/spack/repos/builtin/packages/jdk/package.py b/var/spack/repos/builtin/packages/jdk/package.py
index ecd2690c7f..b2f6aa92f2 100644
--- a/var/spack/repos/builtin/packages/jdk/package.py
+++ b/var/spack/repos/builtin/packages/jdk/package.py
@@ -57,6 +57,8 @@ class Jdk(Package):
     # symbol in version with '_', otherwise it will be interpreted as a variant
     version('10.0.1_10', 'ae8ed645e6af38432a56a847597ac61d4283b7536688dbab44ab536199d1e5a4', curl_options=curl_options,
             url='http://download.oracle.com/otn-pub/java/jdk/10.0.1+10/fb4372174a714e6b8c52526dc134031e/jdk-10.0.1_linux-x64_bin.tar.gz')
+    version('1.8.0_181-b13', 'ef599e322eee42f6769991dd3e3b1a31', curl_options=curl_options, 
+            url='http://download.oracle.com/otn-pub/java/jdk/8u181-b13/96a7b8442fe848ef90c96a2fad6ed6d1/jdk-8u181-linux-x64.tar.gz')
     version('1.8.0_172-b11', 'eda2945e8c02b84adbf78f46c37b71c1', curl_options=curl_options,
             url='http://download.oracle.com/otn-pub/java/jdk/8u172-b11/a58eab1ec242421181065cdc37240b08/jdk-8u172-linux-x64.tar.gz')
     version('1.8.0_141-b15', '8cf4c4e00744bfafc023d770cb65328c', curl_options=curl_options,
diff --git a/var/spack/repos/builtin/packages/r-chemometrics/package.py b/var/spack/repos/builtin/packages/r-chemometrics/package.py
index 22b16081dd..739bab2c36 100644
--- a/var/spack/repos/builtin/packages/r-chemometrics/package.py
+++ b/var/spack/repos/builtin/packages/r-chemometrics/package.py
@@ -39,7 +39,7 @@ class RChemometrics(RPackage):
     version('1.3.8', '7fad828bd094b5485fbf20bdf7d3d0d1')
     version('1.3.7', 'a9e2f32efb1545421dd96185fd849184')
 
-    depends_on('r@3.4.0:3.4.9')
+    depends_on('r@2.10:', type=('build', 'run'))
     depends_on('r-rpart', type=('build', 'run'))
     depends_on('r-mclust', type=('build', 'run'))
     depends_on('r-lars', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-fnn/package.py b/var/spack/repos/builtin/packages/r-fnn/package.py
index d9b6c0761f..6511e0d081 100644
--- a/var/spack/repos/builtin/packages/r-fnn/package.py
+++ b/var/spack/repos/builtin/packages/r-fnn/package.py
@@ -40,6 +40,6 @@ class RFnn(RPackage):
     version('0.6-3', 'f0f0184e50f9f30a36ed5cff24d6cff2')
     version('0.6-2', '20648ba934ea32b1b00dafb75e1a830c')
 
-    depends_on('r@3.4.0:3.4.9')
+    depends_on('r@3.0.0:', type=('build', 'run'))
     depends_on('r-mvtnorm', type=('build', 'run'))
     depends_on('r-chemometrics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-ks/package.py b/var/spack/repos/builtin/packages/r-ks/package.py
new file mode 100644
index 0000000000..7ca72bdcb7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-ks/package.py
@@ -0,0 +1,45 @@
+##############################################################################
+# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/spack/spack
+# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RKs(RPackage):
+    """Kernel smoothers for univariate and multivariate data."""
+
+    homepage = "https://cran.r-project.org/package=ks"
+    url      = "https://cran.r-project.org/src/contrib/Archive/ks/ks_1.11.2.tar.gz"
+
+    version('1.11.2', sha256='9dfd485096e1e67abc7dfcb7b76a83de110dd15bcfeffe5c899605b3a5592961')
+
+    depends_on('r@2.10:', type=('build', 'run'))
+
+    depends_on('r-fnn@1.1:', type=('build', 'run'))
+    depends_on('r-kernlab', type=('build', 'run'))
+    depends_on('r-mclust', type=('build', 'run'))
+    depends_on('r-multicool', type=('build', 'run'))
+    depends_on('r-mvtnorm@1.0:', type=('build', 'run'))
+    depends_on('r-kernsmooth@2.22:', type=('build', 'run'))
+    depends_on('r-matrix', type=('build', 'run'))
+    depends_on('r-mgcv', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-lars/package.py b/var/spack/repos/builtin/packages/r-lars/package.py
index f03e91abc8..53a733cb7b 100644
--- a/var/spack/repos/builtin/packages/r-lars/package.py
+++ b/var/spack/repos/builtin/packages/r-lars/package.py
@@ -33,7 +33,8 @@ class RLars(RPackage):
     url      = "https://cran.r-project.org/src/contrib/lars_1.2.tar.gz"
     list_url = "https://cran.rstudio.com/src/contrib/Archive/lars"
 
-    depends_on('r@3.4.0:3.4.9')
     version('1.2',   '2571bae325f6cba1ad0202ea61695b8c')
     version('1.1',   'e94f6902aade09b13ec25ba2381384e5')
     version('0.9-8', 'e6f9fffab2d83898f6d3d811f04d177f')
+
+    depends_on('r@2.10:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-multicool/package.py b/var/spack/repos/builtin/packages/r-multicool/package.py
new file mode 100644
index 0000000000..4d112f45c6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-multicool/package.py
@@ -0,0 +1,36 @@
+##############################################################################
+# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/spack/spack
+# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RMulticool(RPackage):
+    """Permutations of multisets in cool-lex order."""
+
+    homepage = "https://cran.r-project.org/package=multicool"
+    url      = "https://cran.r-project.org/src/contrib/Archive/multicool/multicool_0.1-9.tar.gz"
+
+    version('0.1-9', sha256='bdf92571cef1b649952d155395a92b8683099ee13114f73a9d41fc5d7d49d329')
+
+    depends_on('r-rcpp@0.11.2:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-pcapp/package.py b/var/spack/repos/builtin/packages/r-pcapp/package.py
index 1d1b6c6a2e..0ad4a5f94b 100644
--- a/var/spack/repos/builtin/packages/r-pcapp/package.py
+++ b/var/spack/repos/builtin/packages/r-pcapp/package.py
@@ -38,5 +38,4 @@ class RPcapp(RPackage):
         version('1.9-60', '23dd468abb9fedc11e40166446df1017')
         version('1.9-50', 'be44f173404fd6e86ba0a5515711bfa3')
 
-        depends_on('r@3.4.0:3.4.9')
         depends_on('r-mvtnorm', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-som/package.py b/var/spack/repos/builtin/packages/r-som/package.py
index de3f2dfbac..992f4def3b 100644
--- a/var/spack/repos/builtin/packages/r-som/package.py
+++ b/var/spack/repos/builtin/packages/r-som/package.py
@@ -38,4 +38,4 @@ class RSom(RPackage):
     version('0.3-3', 'd4ac444be24f71d08b99974c2f4b96e5')
     version('0.3-2', '4ce28f46df68fbb73905711ba2416fac')
 
-    depends_on('r@3.4.0:3.4.9')
+    depends_on('r@2.10:', type=('build', 'run'))