New package r-tmixclust (#7658)

* r-tmixclust: new package

* r-cluster: hash changed

* r-cluster: removed 2.0.6 and added the latest 2.0.7-1

2 files changed, 50 insertions, 1 deletions

diff --git a/var/spack/repos/builtin/packages/r-cluster/package.py b/var/spack/repos/builtin/packages/r-cluster/package.py
index 64fec7b0dd..5a7e222a14 100644
--- a/var/spack/repos/builtin/packages/r-cluster/package.py
+++ b/var/spack/repos/builtin/packages/r-cluster/package.py
@@ -34,6 +34,6 @@ class RCluster(RPackage):
     url      = "https://cran.rstudio.com/src/contrib/cluster_2.0.6.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/cluster"
 
-    version('2.0.6', 'e7d0660b05c65f4d886ebf7f046939ab')
+    version('2.0.7-1', 'a37add21b91d3e4f3883d005331e0d45')
     version('2.0.5', '7330f209ebce960bdee1a6d6679cb85a')
     version('2.0.4', 'bb4deceaafb1c42bb1278d5d0dc11e59')
diff --git a/var/spack/repos/builtin/packages/r-tmixclust/package.py b/var/spack/repos/builtin/packages/r-tmixclust/package.py
new file mode 100644
index 0000000000..d36787c8b9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-tmixclust/package.py
@@ -0,0 +1,49 @@
+##############################################################################
+# 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 RTmixclust(RPackage):
+    """Implementation of a clustering method for time series gene expression
+    data based on mixed-effects models with Gaussian variables and
+    non-parametric cubic splines estimation. The method can robustly account
+    for the high levels of noise present in typical gene expression time
+    series datasets."""
+
+    homepage = "https://bioconductor.org/packages/TMixClust/"
+    url      = "https://git.bioconductor.org/packages/TMixClust"
+
+    version('1.0.1', git='https://git.bioconductor.org/packages/TMixClust',
+            commit='0ac800210e3eb9da911767a80fb5582ab33c0cad')
+
+    depends_on('r-gss', type=('build', 'run'))
+    depends_on('r-mvtnorm', type=('build', 'run'))
+    depends_on('r-zoo', type=('build', 'run'))
+    depends_on('r-cluster', type=('build', 'run'))
+    depends_on('r-biocparallel', type=('build', 'run'))
+    depends_on('r-flexclust', type=('build', 'run'))
+    depends_on('r-biobase', type=('build', 'run'))
+    depends_on('r-spem', type=('build', 'run'))
+    depends_on('r@3.4.3:3.4.9', when='@1.0.1')