relicense: remove significant contributions from peetsv

- This is bundled into one commit to make it easy to revert if we do get
  consent from peetsv's company to relicense these contributions.

- Revert "dialign-tx adding patch for gcc@5.4.0 (#6413)"
  - This reverts commit 09eeb991a2ac0d749ffdbfe2f1cc415dd5d5dc85.

- Remove the following LGPL-2.1 packages because we have not gotten
  consent to relicense them:
  - fast-gbs
  - igv
  - metasv
  - perl-xml-libxml
  - py-cnvkit
  - py-crossmap
  - py-pybedtools
  - py-pyfaidx
  - py-pyvcf
  - py-vmd-python
  - r-cghflasso
  - r-dismo
  - r-proc
  - r-spatial
  - r-utf8

17 files changed, 0 insertions, 711 deletions

diff --git a/var/spack/repos/builtin/packages/dialign-tx/dialign-1-0-2-gcc-5-4-0.patch b/var/spack/repos/builtin/packages/dialign-tx/dialign-1-0-2-gcc-5-4-0.patch
deleted file mode 100644
index 5a82f97e7b..0000000000
--- a/var/spack/repos/builtin/packages/dialign-tx/dialign-1-0-2-gcc-5-4-0.patch
+++ /dev/null
@@ -1,80 +0,0 @@
---- a/source/alig.c	2008-12-06 04:10:05.000000000 -0800
-+++ b/source/alig.c	2017-11-21 10:58:31.000000000 -0800
-@@ -520,7 +520,7 @@
-  * datastructure (i.e. frontiers). The given diag must be consistent
-  * to the given alignment !
-  */
--inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg) {
-+char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg) {
- 
-   char alignedSomething = 0;
-   int i,j,k;
-diff -Naur a/source/assemble.c b/source/assemble.c
---- a/source/assemble.c	2008-12-06 04:10:05.000000000 -0800
-+++ b/source/assemble.c	2017-11-21 10:57:55.000000000 -0800
-@@ -10,7 +10,7 @@
- 
- extern void error(char *message);
- extern void merror(char *msg1, char *msg2);
--extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, 
-+extern void calc_weight(struct diag* dg, struct scr_matrix* smatrix, 
- 			struct prob_dist *pdist);
- extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, 
- 		    struct prob_dist *pdist);
-@@ -37,7 +37,7 @@
- extern inline struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos);
- extern struct alignment* copy_alignment( struct alignment *o_algn, struct alignment *algn, char doDgc);
- //extern char adapt_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg);
--extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg);
-+extern char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg);
- //extern inline struct diag_cont* enter_sorted(struct diag_cont* backlog_diags, struct diag_cont *cand);
- //extern inline char fit_fpos_diag(struct alignment *algn, struct diag* dg);
- 
-@@ -574,7 +574,7 @@
-  * returns a value <0 if there is an non-conflicting overlap
-  * returns 0 in all other non-conflicting cases
-  */
--inline char confl_diag(struct alignment *algn, char *layer, struct diag *dg1, struct diag *dg2) {
-+static inline char confl_diag(struct alignment *algn, char *layer, struct diag *dg1, struct diag *dg2) {
-   //  if(dg1->multi_dg || dg2->multi_dg) error(" confl_diag(): cannot accept multi dgs!");
-   int s1_1 = dg1->seq_p1.num;
-   int s1_2 = dg1->seq_p2.num;
-diff -Naur a/source/diag.c b/source/diag.c
---- a/source/diag.c	2008-12-06 04:10:05.000000000 -0800
-+++ b/source/diag.c	2017-11-21 10:55:43.000000000 -0800
-@@ -183,7 +183,7 @@
-  * omitScore = 0:  normal 
-  * omitScore = 1:  no score calculation 
-  */ 
--inline void real_calc_weight(struct diag* dg, struct scr_matrix* smatrix,  
-+static inline void real_calc_weight(struct diag* dg, struct scr_matrix* smatrix,  
- 		 struct prob_dist *pdist, char omitScore, long double **tmp_dist, struct alignment *algn ) { 
-    
-   if(dg->multi_dg) {
-@@ -302,7 +302,7 @@
-   } 
- } 
-  
--inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix,  
-+void calc_weight(struct diag* dg, struct scr_matrix* smatrix,  
- 		 struct prob_dist *pdist) { 
-   real_calc_weight(dg, smatrix, pdist, 0,NULL,NULL); 
- } 
-@@ -312,7 +312,7 @@
- /** 
-  * calculates the overlap weight for the given diag 
-  */ 
--inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,  
-+static inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,  
- 		    struct prob_dist *pdist) { 
-   int sn1 = dg->seq_p1.num; 
-   int sn2 = dg->seq_p2.num; 
-@@ -958,7 +958,7 @@
-  * The pointer returned (and the ones included in the struct)  
-  * has to be deallocted explicitely from memory. 
-  */ 
--inline struct simple_diag_col* find_diags_dialign(struct scr_matrix *smatrix,  
-+static inline struct simple_diag_col* find_diags_dialign(struct scr_matrix *smatrix,  
- 				struct prob_dist *pdist, struct seq* seq1,  
- 				struct seq* seq2, struct alignment *algn, 
- 				 long double **tmp_dist, int round) { 
diff --git a/var/spack/repos/builtin/packages/dialign-tx/package.py b/var/spack/repos/builtin/packages/dialign-tx/package.py
index ea7eddaf42..a5ba5ceedc 100644
--- a/var/spack/repos/builtin/packages/dialign-tx/package.py
+++ b/var/spack/repos/builtin/packages/dialign-tx/package.py
@@ -50,5 +50,3 @@ class DialignTx(MakefilePackage):
             install('dialign-tx', prefix.bin)
             # t-coffee recognizes as dialign-t
             install('dialign-tx', join_path(prefix.bin, 'dialign-t'))
-
-    patch('dialign-1-0-2-gcc-5-4-0.patch', when='%gcc@5.4.0')
diff --git a/var/spack/repos/builtin/packages/fast-gbs/package.py b/var/spack/repos/builtin/packages/fast-gbs/package.py
deleted file mode 100644
index feddf105d9..0000000000
--- a/var/spack/repos/builtin/packages/fast-gbs/package.py
+++ /dev/null
@@ -1,54 +0,0 @@
-##############################################################################
-# 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 FastGbs(Package):
-    """A bioinformatic pipeline designed to extract a high-quality SNP catalog
-       starting from FASTQ files obtained from sequencing
-       genotyping-by-sequencing (GBS) libraries."""
-
-    homepage = "https://bitbucket.org/jerlar73/fast-gbs"
-    git      = "https://bitbucket.org/jerlar73/fast-gbs.git"
-
-    version('2017-01-25', commit='3b3cbffa84d269419692067c6a3de08b3b88849c')
-
-    depends_on('parallel', type='run')
-    depends_on('python@2.7:', type='run')
-    depends_on('sabre', type='run')
-    depends_on('py-cutadapt', type='run')
-    depends_on('bwa', type='run')
-    depends_on('samtools', type='run')
-    depends_on('platypus', type='run')
-    depends_on('py-pyvcf', type='run')
-
-    def install(self, spec, prefix):
-        mkdirp(prefix.bin)
-        install('fastgbs.sh', prefix.bin)
-        install('parameters.txt', prefix.bin)
-        install('makeDir.sh', prefix.bin)
-        install('makeBarcodeSabre.py', prefix.bin)
-        install('vcf2txt.py', prefix.bin)
-        install('txt2unix.sh', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/igv/package.py b/var/spack/repos/builtin/packages/igv/package.py
deleted file mode 100644
index b905520629..0000000000
--- a/var/spack/repos/builtin/packages/igv/package.py
+++ /dev/null
@@ -1,54 +0,0 @@
-##############################################################################
-# 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 *
-import glob
-
-
-class Igv(Package):
-    """The Integrative Genomics Viewer (IGV) is a high-performance
-       visualization tool for interactive exploration of large,
-       integrated genomic datasets."""
-
-    homepage = "http://software.broadinstitute.org/software/igv/"
-
-    version('2.4.5', '4c45e1b281d8e3d8630aa485c5df6949',
-        url='http://data.broadinstitute.org/igv/projects/downloads/2.4/IGVSource_2.4.5.zip')
-    version('2.3.50', '7fdb903a59d556fad25e668b38e860f8',
-        url='http://data.broadinstitute.org/igv/projects/downloads/2.3/IGVSource_2.3.50.zip')
-
-    depends_on('jdk@8:', type=('build', 'run'), when='@2.4:')
-    depends_on('jdk@7u0:7u999', type=('build', 'run'), when='@2.3:2.3.999')
-    depends_on('ant', type='build')
-
-    def install(self, spec, prefix):
-        ant = self.spec['ant'].command
-        ant('all')
-        mkdirp(prefix.bin)
-        install('igv.sh', prefix.bin)
-        install('igv.jar', prefix.bin)
-        mkdirp(prefix.lib)
-        files = [x for x in glob.glob("lib/*jar")]
-        for f in files:
-            install(f, prefix.lib)
diff --git a/var/spack/repos/builtin/packages/metasv/package.py b/var/spack/repos/builtin/packages/metasv/package.py
deleted file mode 100644
index 540b2da2b9..0000000000
--- a/var/spack/repos/builtin/packages/metasv/package.py
+++ /dev/null
@@ -1,41 +0,0 @@
-##############################################################################
-# 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 Metasv(PythonPackage):
-    """An accurate and integrative structural-variant caller
-       for next generation sequencing"""
-
-    homepage = "http://bioinform.github.io/metasv/"
-    url      = "https://github.com/bioinform/metasv/archive/0.5.4.tar.gz"
-
-    version('0.5.4', 'de2e21ac4f86bc4d1830bdfff95d8391')
-
-    depends_on('py-pybedtools@0.6.9', type=('build', 'run'))
-    depends_on('py-pysam@0.7.7', type=('build', 'run'))
-    depends_on('py-pyvcf@0.6.7', type=('build', 'run'))
-    depends_on('py-setuptools', type=('build', 'run'))
-    depends_on('py-cython', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-xml-libxml/package.py b/var/spack/repos/builtin/packages/perl-xml-libxml/package.py
deleted file mode 100644
index 7bb689544c..0000000000
--- a/var/spack/repos/builtin/packages/perl-xml-libxml/package.py
+++ /dev/null
@@ -1,35 +0,0 @@
-##############################################################################
-# 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 PerlXmlLibxml(PerlPackage):
-    """This module is an interface to libxml2, providing XML and HTML parsers
-       with DOM, SAX and XMLReader interfaces"""
-
-    homepage = "http://search.cpan.org/~shlomif/XML-LibXML-2.0132/LibXML.pod"
-    url      = "http://search.cpan.org/CPAN/authors/id/S/SH/SHLOMIF/XML-LibXML-2.0132.tar.gz"
-
-    version('2.0132', '43546fd9a3974f19323f9fb04861ece9')
diff --git a/var/spack/repos/builtin/packages/py-cnvkit/package.py b/var/spack/repos/builtin/packages/py-cnvkit/package.py
deleted file mode 100644
index 045c940206..0000000000
--- a/var/spack/repos/builtin/packages/py-cnvkit/package.py
+++ /dev/null
@@ -1,48 +0,0 @@
-##############################################################################
-# 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 PyCnvkit(PythonPackage):
-    """A command-line toolkit and Python library for detecting copy number
-       variants and alterations genome-wide from high-throughput sequencing."""
-
-    homepage = "http://cnvkit.readthedocs.io/en/stable/"
-    url      = "https://github.com/etal/cnvkit/archive/v0.9.2.tar.gz"
-
-    version('0.9.2', '16612c4dcc9570f6ef9fecc42caf1745')
-
-    depends_on('py-setuptools',        type='build')
-    depends_on('py-biopython@1.62:',   type=('build', 'run'))
-    depends_on('py-future@0.15.2:',    type=('build', 'run'))
-    depends_on('py-matplotlib@1.3.1:', type=('build', 'run'))
-    depends_on('py-numpy@1.9:',        type=('build', 'run'))
-    depends_on('py-pandas@0.18.1:',    type=('build', 'run'))
-    depends_on('py-pyfaidx@0.4.7:',    type=('build', 'run'))
-    depends_on('py-pysam@0.10.0:0.13', type=('build', 'run'))
-    depends_on('py-reportlab@3.0:',    type=('build', 'run'))
-    depends_on('py-scipy@0.15.0:',     type=('build', 'run'))
-    depends_on('bcftools@1.6',         type=('build', 'run'))
-    depends_on('samtools@1.6',         type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-crossmap/package.py b/var/spack/repos/builtin/packages/py-crossmap/package.py
deleted file mode 100644
index ad94df9bc4..0000000000
--- a/var/spack/repos/builtin/packages/py-crossmap/package.py
+++ /dev/null
@@ -1,41 +0,0 @@
-##############################################################################
-# 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 PyCrossmap(PythonPackage):
-    """CrossMap is a program for convenient conversion of genome
-       coordinates (or annotation files) between different assemblies"""
-
-    homepage = "http://crossmap.sourceforge.net"
-    url      = "https://downloads.sourceforge.net/project/crossmap/CrossMap-0.2.7.tar.gz"
-
-    version('0.2.7', '91dadec9644ee3038f20ee7a6eb8dfb7')
-
-    depends_on('python@2.7:2.7.999', type=('build', 'run'))
-    depends_on('py-cython@0.17:', type='build')
-    depends_on('py-pysam', type=('build', 'run'))
-    depends_on('py-setuptools', type='build')
-    depends_on('py-bx-python', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-pybedtools/package.py b/var/spack/repos/builtin/packages/py-pybedtools/package.py
deleted file mode 100644
index 55d6d34f1f..0000000000
--- a/var/spack/repos/builtin/packages/py-pybedtools/package.py
+++ /dev/null
@@ -1,44 +0,0 @@
-##############################################################################
-# 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 PyPybedtools(PythonPackage):
-    """pybedtools wraps and extends BEDTools and offers
-    feature-level manipulations from within Python."""
-
-    homepage = "http://daler.github.io/pybedtools"
-    url      = "https://pypi.io/packages/source/p/pybedtools/pybedtools-0.7.10.tar.gz"
-
-    version('0.7.10', 'f003c67e22c48b77f070538368ece70c')
-    version('0.6.9',  'b7df049036422d8c6951412a90e83dca')
-
-    depends_on('py-setuptools', type='build')
-    depends_on('bedtools2',     type=('build', 'run'))
-    depends_on('py-numpy',      type=('build', 'run'))
-    depends_on('py-pandas',     type=('build', 'run'))
-    depends_on('py-pysam@0.8.1:', type=('build', 'run'), when='@0.7.0:')
-    depends_on('py-pysam@0.7.7',  type=('build', 'run'), when='@0.6.9')
-    depends_on('py-six',        type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-pyfaidx/package.py b/var/spack/repos/builtin/packages/py-pyfaidx/package.py
deleted file mode 100644
index deee8cb745..0000000000
--- a/var/spack/repos/builtin/packages/py-pyfaidx/package.py
+++ /dev/null
@@ -1,37 +0,0 @@
-##############################################################################
-# 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 PyPyfaidx(PythonPackage):
-    """pyfaidx: efficient pythonic random access to fasta subsequences"""
-
-    homepage = "https://pypi.python.org/pypi/pyfaidx"
-    url      = "https://pypi.io/packages/source/p/pyfaidx/pyfaidx-0.5.3.1.tar.gz"
-
-    version('0.5.3.1', '128074c48fdef23d41e47af73b45f040')
-
-    depends_on('py-setuptools@0.7:', type='build')
-    depends_on('py-six', type='build')
diff --git a/var/spack/repos/builtin/packages/py-pyvcf/package.py b/var/spack/repos/builtin/packages/py-pyvcf/package.py
deleted file mode 100644
index 3a7cb21263..0000000000
--- a/var/spack/repos/builtin/packages/py-pyvcf/package.py
+++ /dev/null
@@ -1,39 +0,0 @@
-##############################################################################
-# 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 PyPyvcf(PythonPackage):
-    """PyVCF - A Variant Call Format Parser for Python"""
-
-    homepage = "https://github.com/jamescasbon/PyVCF"
-    url      = "https://pypi.io/packages/source/P/PyVCF/PyVCF-0.6.8.tar.gz"
-
-    version('0.6.8', '3cc70aa59e62dab7b4a85bd5a9f2e714')
-    version('0.6.7', '51b57ce99e0c2f7be2a18d08d8f87734')
-
-    depends_on('py-setuptools', type='build')
-    depends_on('py-cython', type='build')
-    depends_on('py-pysam', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-vmd-python/package.py b/var/spack/repos/builtin/packages/py-vmd-python/package.py
deleted file mode 100644
index 57c15c5ffb..0000000000
--- a/var/spack/repos/builtin/packages/py-vmd-python/package.py
+++ /dev/null
@@ -1,41 +0,0 @@
-##############################################################################
-# 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 PyVmdPython(PythonPackage):
-    """Installable VMD as a python module"""
-
-    homepage = "https://github.com/Eigenstate"
-    url      = "https://github.com/Eigenstate/vmd-python/archive/v2.0.10.tar.gz"
-
-    version('2.0.10', '8c746d961497a676053b66e3dd692794')
-
-    depends_on('python@2.7:2.8', type=('build', 'run'))
-    depends_on('py-numpy', type=('build', 'run'))
-    depends_on('py-setuptools', type='run')
-    depends_on('tcl')
-    depends_on('netcdf')
-    depends_on('expat')
diff --git a/var/spack/repos/builtin/packages/r-cghflasso/package.py b/var/spack/repos/builtin/packages/r-cghflasso/package.py
deleted file mode 100644
index 7ef6fe07d7..0000000000
--- a/var/spack/repos/builtin/packages/r-cghflasso/package.py
+++ /dev/null
@@ -1,36 +0,0 @@
-##############################################################################
-# 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 RCghflasso(RPackage):
-    """Spatial smoothing and hot spot detection using the fused
-       lasso regression"""
-
-    homepage = "https://cran.r-project.org/package=cghFLasso"
-    url      = "https://cran.r-project.org/src/contrib/cghFLasso_0.2-1.tar.gz"
-    list_url = "https://cran.r-project.org/src/contrib/Archive/cghFLasso"
-
-    version('0.2-1', '9a714a6dda3de9e905d23dadfa5d37f1')
diff --git a/var/spack/repos/builtin/packages/r-dismo/package.py b/var/spack/repos/builtin/packages/r-dismo/package.py
deleted file mode 100644
index 01c5a70413..0000000000
--- a/var/spack/repos/builtin/packages/r-dismo/package.py
+++ /dev/null
@@ -1,40 +0,0 @@
-##############################################################################
-# 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 RDismo(RPackage):
-    """Functions for species distribution modeling, that is, predicting
-       entire geographic distributions form occurrences at a number of
-       sites and the environment at these sites"""
-
-    homepage = "http://rspatial.org/sdm"
-    url      = "https://cran.r-project.org/src/contrib/dismo_1.1-4.tar.gz"
-
-    version('1.1-4', '0ed11729bcf4c2ffa01a3e2ac88dabfc')
-
-    depends_on('r@3.2:', type=('build', 'run'))
-    depends_on('r-raster@2.5-2:', type=('build', 'run'))
-    depends_on('r-sp@1.2-0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-proc/package.py b/var/spack/repos/builtin/packages/r-proc/package.py
deleted file mode 100644
index d06e823000..0000000000
--- a/var/spack/repos/builtin/packages/r-proc/package.py
+++ /dev/null
@@ -1,44 +0,0 @@
-##############################################################################
-# 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 RProc(RPackage):
-    """Tools for visualizing, smoothing and comparing receiver operating
-       characteristic (ROC curves). (Partial) area under the curve (AUC)
-       can be compared with statistical tests based on U-statistics or
-       bootstrap. Confidence intervals can be computed for (p)AUC or
-       ROC curves."""
-
-    homepage = "https://web.expasy.org/pROC/"
-    url      = "https://cran.r-project.org/src/contrib/pROC_1.12.1.tar.gz"
-    list_url = "https://cran.r-project.org/src/contrib/Archive/pROC"
-
-    version('1.12.1', 'ef5fb446fd75c1a3a5e7abf9b7aa4f75')
-
-    depends_on('r@2.14:', type=('build', 'run'))
-    depends_on('r-plyr', type=('build', 'run'))
-    depends_on('r-rcpp@0.11.1:', type=('build', 'run'))
-    depends_on('r-ggplot2', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-spatial/package.py b/var/spack/repos/builtin/packages/r-spatial/package.py
deleted file mode 100644
index 6435d70f0e..0000000000
--- a/var/spack/repos/builtin/packages/r-spatial/package.py
+++ /dev/null
@@ -1,37 +0,0 @@
-##############################################################################
-# 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 RSpatial(RPackage):
-    """Functions for kriging and point pattern analysis."""
-
-    homepage = "http://www.stats.ox.ac.uk/pub/MASS4/"
-    url      = "https://cran.r-project.org/src/contrib/spatial_7.3-10.tar.gz"
-    list_url = "https://cran.r-project.org/src/contrib/Archive/spatial"
-
-    version('7.3-10', 'e544e3e3fd92e6868f29b8da2925b214')
-
-    depends_on('r@3.0.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-utf8/package.py b/var/spack/repos/builtin/packages/r-utf8/package.py
deleted file mode 100644
index bd5e5fd7c6..0000000000
--- a/var/spack/repos/builtin/packages/r-utf8/package.py
+++ /dev/null
@@ -1,38 +0,0 @@
-##############################################################################
-# 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 RUtf8(RPackage):
-    """Process and print 'UTF-8' encoded international text (Unicode).
-       Input, validate, normalize, encode, format, and display."""
-
-    homepage = "https://github.com/patperry/r-utf8"
-    url      = "https://cran.r-project.org/src/contrib/utf8_1.1.3.tar.gz"
-    list_url = "https://cran.r-project.org/src/contrib/Archive/utf8"
-
-    version('1.1.3', '3a4d84328eb3314e8ebb84d3553f7015')
-
-    depends_on('r@2.1.0:', type=('build', 'run'))