Merge remote branch 'origin/develop' into develop

lib/spack/spack/compilers/pgi.py

@@ -77,4 +77,4 @@ def default_version(cls, comp):
         on PowerPC.
         """
         return get_compiler_version(
-            comp, '-V', r'pg[^ ]* ([0-9.-]+) [^ ]+ target on ')
+            comp, '-V', r'pg[^ ]* ([0-9.]+)-[0-9]+ [^ ]+ target on ')

var/spack/repos/builtin/packages/bcl2fastq2/package.py

@@ -39,7 +39,11 @@ class Bcl2fastq2(Package):
     homepage = "https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-18.html"
     url      = "https://support.illumina.com/content/dam/illumina-support/documents/downloads/software/bcl2fastq/bcl2fastq2-v2-18-0-12-tar.zip"
 
-    version('2-18-0-12', 'fbe06492117f65609c41be0c27e3215c')
+    version('2.18.0.12', 'fbe06492117f65609c41be0c27e3215c')
+    # 2.17.1.14 is no longer distributed.  If you have a copy of the
+    # source tarball, you can drop it into a local mirror w/ the name
+    # mirror/bcl2fastq2/bcl2fastq2-2.17.1.14.zip and go from there.
+    version('2.17.1.14', '7426226c6db095862e636b95c38608d3')
 
     depends_on('boost@1.54.0')
     depends_on('cmake@2.8.9:')

var/spack/repos/builtin/packages/caffe/package.py

@@ -73,7 +73,8 @@ class Caffe(CMakePackage):
 
     def cmake_args(self):
         spec = self.spec
-        args = ['-DBLAS={0}'.format(spec['blas'].name),
+        args = ['-DBLAS={0}'.format('open' if spec['blas'].name == 'openblas'
+                else spec['blas'].name),
                 '-DCPU_ONLY=%s' % ('~gpu' in spec),
                 '-DUSE_CUDNN=%s' % ('+gpu' in spec),
                 '-DBUILD_python=%s' % ('+python' in spec),

var/spack/repos/builtin/packages/cairo/package.py

@@ -51,4 +51,8 @@ class Cairo(AutotoolsPackage):
     def configure_args(self):
         args = ["--disable-trace",  # can cause problems with libiberty
                 "--enable-tee"]
+        if '+X' in self.spec:
+            args.extend(["--enable-xlib", "--enable-xcb"])
+        else:
+            args.extend(["--disable-xlib", "--disable-xcb"])
         return args

var/spack/repos/builtin/packages/libpciaccess/package.py

@@ -29,8 +29,9 @@ class Libpciaccess(AutotoolsPackage):
     """Generic PCI access library."""
 
     homepage = "http://cgit.freedesktop.org/xorg/lib/libpciaccess/"
-    url      = "http://xorg.freedesktop.org/archive/individual/lib/libpciaccess-0.13.4.tar.gz"
+    url      = "http://xorg.freedesktop.org/archive/individual/lib/libpciaccess-0.13.5.tar.gz"
 
+    version('0.13.5', '81468664fde96d1df2c3216fdf3c4a20')
     version('0.13.4', 'cc1fad87da60682af1d5fa43a5da45a4')
 
     depends_on('libtool', type='build')

var/spack/repos/builtin/packages/mesa-glu/package.py

@@ -34,4 +34,6 @@ class MesaGlu(AutotoolsPackage):
 
     version('9.0.0', 'bbc57d4fe3bd3fb095bdbef6fcb977c4')
 
-    depends_on('mesa')
+    variant('mesa', default=True,
+       description='Usually depends on mesa, disable for accelerated OpenGL')
+    depends_on('mesa', when='+mesa')

var/spack/repos/builtin/packages/mummer/Makefile.patch

@@ -0,0 +1,24 @@
+--- a/Makefile	2017-05-15 17:33:05.132803923 -0700
++++ b/Makefile	2017-05-16 16:01:29.264842369 -0700
+@@ -35,6 +35,13 @@
+ TIGR_SRC_DIR  := $(TOP_DIR)/src/tigr
+ KURTZ_SRC_DIR := $(TOP_DIR)/src/kurtz
+ 
++ifndef INSTALL_TOP_DIR
++INSTALL_TOP_DIR     := $(TOP_DIR)
++endif
++INSTALL_BIN_DIR := $(INSTALL_TOP_DIR)/bin
++INSTALL_AUX_BIN_DIR := $(INSTALL_TOP_DIR)/aux_bin
++INSTALL_SCRIPT_DIR    := $(INSTALL_TOP_DIR)/scripts
++
+ CC   := $(filter /%,$(shell /bin/sh -c 'type gcc'))
+ CXX  := $(filter /%,$(shell /bin/sh -c 'type g++'))
+ SED  := $(filter /%,$(shell /bin/sh -c 'type sed'))
+@@ -52,6 +59,7 @@
+ 
+ #-- EXPORT THESE VARIABLES TO OTHER MAKEFILES
+ export BIN_DIR AUX_BIN_DIR CXX CC CFLAGS CXXFLAGS LDFLAGS
++export INSTALL_BIN_DIR INSTALL_AUX_BIN_DIR INSTALL_SCRIPT_DIR
+ 
+ 
+ 

var/spack/repos/builtin/packages/mummer/package.py

@@ -34,22 +34,34 @@ class Mummer(Package):
     version('3.23', 'f2422b3d2638dba4baedb71b1acdffa2')
 
     depends_on('gnuplot')
+    depends_on('perl', type=('build', 'run'))
+
+    patch('Makefile.patch')
+    patch('scripts-Makefile.patch')
 
     def install(self, spec, prefix):
         if self.run_tests:
             make('check')
-        make('install')
+        make('INSTALL_TOP_DIR={0}'.format(prefix))
-        mkdirp(prefix.bin)
+        bd = prefix.bin
+        abd = join_path(prefix, 'aux_bin')
+        sd = join_path(prefix, 'scripts')
+        mkdirp(bd)
+        mkdirp(abd)
+        mkdirp(sd)
 
-        bins = ["show-tiling", "show-snps", "show-coords", "show-aligns", 
+        bins = ["show-tiling", "show-snps", "show-coords", "show-aligns",
-                "show-diff", "delta-filter", "combineMUMs", "mummer", 
+                "show-diff", "delta-filter", "combineMUMs", "mummer",
-                "repeat-match", "annotate", "mgaps", "gaps", "dnadiff", 
+                "repeat-match", "annotate", "mgaps", "gaps", "dnadiff",
-                "nucmer2xfig", "run-mummer3", "mummerplot", "promer", 
+                "nucmer2xfig", "run-mummer3", "mummerplot", "promer",
                 "run-mummer1", "nucmer", "mapview", "exact-tandems"]
         aux_bins = ["aux_bin/postnuc", "aux_bin/postpro",
                     "aux_bin/prenuc", "aux_bin/prepro"]
-                  
+        scripts = ["scripts/Foundation.pm"]
-        for b in bins:
+
-            install(b, join_path(prefix.bin, b))
+        for f in bins:
-        for b in aux_bins:
+            install(f, join_path(bd, f))
-            install(b, join_path(prefix.bin, b[8:]))
+        for f in aux_bins:
+            install(f, join_path(abd, f[8:]))
+        for f in scripts:
+            install(f, join_path(sd, f[8:]))

var/spack/repos/builtin/packages/mummer/scripts-Makefile.patch

@@ -0,0 +1,74 @@
+--- a/scripts/Makefile	2011-12-16 18:49:26.000000000 -0800
++++ b/scripts/Makefile	2017-05-16 16:05:48.697853000 -0700
+@@ -37,56 +37,56 @@
+ #-- not so PHONY rules --#
+ exact-tandems: exact-tandems.csh
+ 	$(SED)  -e 's?__CSH_PATH?$(CSH)?g' \
+-		-e 's?__BIN_DIR?$(BIN_DIR)?g' \
+-		-e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
++		-e 's?__BIN_DIR?$(INSTALL_BIN_DIR)?g' \
++		-e 's?__SCRIPT_DIR?$(INSTALL_SCRIPT_DIR)?g' \
+ 		exact-tandems.csh > $(BIN_DIR)/exact-tandems
+ 	chmod 755 $(BIN_DIR)/exact-tandems
+ 
+ mapview: mapview.pl
+ 	$(SED)  -e 's?__PERL_PATH?$(PERL)?g' \
+-		-e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
++		-e 's?__SCRIPT_DIR?$(INSTALL_SCRIPT_DIR)?g' \
+                 mapview.pl > $(BIN_DIR)/mapview
+ 	chmod 755 $(BIN_DIR)/mapview
+ 
+ mummerplot: mummerplot.pl Foundation.pm
+ 	$(SED)  -e 's?__PERL_PATH?$(PERL)?g' \
+-                -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
+-                -e 's?__BIN_DIR?$(BIN_DIR)?g' \
++                -e 's?__SCRIPT_DIR?$(INSTALL_SCRIPT_DIR)?g' \
++                -e 's?__BIN_DIR?$(INSTALL_BIN_DIR)?g' \
+                 mummerplot.pl > $(BIN_DIR)/mummerplot
+ 	chmod 755 $(BIN_DIR)/mummerplot
+ 
+ dnadiff: dnadiff.pl Foundation.pm
+ 	$(SED) -e 's?__PERL_PATH?$(PERL)?g' \
+-               -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
+-               -e 's?__BIN_DIR?$(BIN_DIR)?g' \
++               -e 's?__SCRIPT_DIR?$(INSTALL_SCRIPT_DIR)?g' \
++               -e 's?__BIN_DIR?$(INSTALL_BIN_DIR)?g' \
+                  dnadiff.pl > $(BIN_DIR)/dnadiff
+ 	chmod 755 $(BIN_DIR)/dnadiff
+ 
+ nucmer: nucmer.pl Foundation.pm
+ 	$(SED)  -e 's?__PERL_PATH?$(PERL)?g' \
+-                -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
+-                -e 's?__AUX_BIN_DIR?$(AUX_BIN_DIR)?g' \
+-                -e 's?__BIN_DIR?$(BIN_DIR)?g' \
++                -e 's?__SCRIPT_DIR?$(INSTALL_SCRIPT_DIR)?g' \
++                -e 's?__AUX_BIN_DIR?$(INSTALL_AUX_BIN_DIR)?g' \
++                -e 's?__BIN_DIR?$(INSTALL_BIN_DIR)?g' \
+                  nucmer.pl > $(BIN_DIR)/nucmer
+ 	chmod 755 $(BIN_DIR)/nucmer
+ 
+ promer: promer.pl Foundation.pm
+ 	$(SED)  -e 's?__PERL_PATH?$(PERL)?g' \
+-                -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
+-                -e 's?__AUX_BIN_DIR?$(AUX_BIN_DIR)?g' \
+-                -e 's?__BIN_DIR?$(BIN_DIR)?g' \
++                -e 's?__SCRIPT_DIR?$(INSTALL_SCRIPT_DIR)?g' \
++                -e 's?__AUX_BIN_DIR?$(INSTALL_AUX_BIN_DIR)?g' \
++                -e 's?__BIN_DIR?$(INSTALL_BIN_DIR)?g' \
+                 promer.pl > $(BIN_DIR)/promer
+ 	chmod 755 $(BIN_DIR)/promer
+ 
+ run-mummer1: run-mummer1.csh
+ 	$(SED)  -e 's?__CSH_PATH?$(CSH)?g' \
+-		-e 's?__BIN_DIR?$(BIN_DIR)?g' \
++		-e 's?__BIN_DIR?$(INSTALL_BIN_DIR)?g' \
+ 		run-mummer1.csh > $(BIN_DIR)/run-mummer1
+ 	chmod 755 $(BIN_DIR)/run-mummer1
+ 
+ run-mummer3: run-mummer3.csh
+ 	$(SED)  -e 's?__CSH_PATH?$(CSH)?g' \
+-		-e 's?__BIN_DIR?$(BIN_DIR)?g' \
++		-e 's?__BIN_DIR?$(INSTALL_BIN_DIR)?g' \
+ 		run-mummer3.csh > $(BIN_DIR)/run-mummer3
+ 	chmod 755 $(BIN_DIR)/run-mummer3
+ 

var/spack/repos/builtin/packages/opencoarrays/package.py

@@ -36,6 +36,7 @@ class Opencoarrays(CMakePackage):
     homepage = "http://www.opencoarrays.org/"
     url      = "https://github.com/sourceryinstitute/OpenCoarrays/releases/download/1.8.4/OpenCoarrays-1.8.4.tar.gz"
 
+    version('1.8.10', '9ba1670647db4d986634abf743abfd6a')
     version('1.8.4', '7c9eaffc3a0b5748d0d840e52ec9d4ad')
     version('1.8.0', 'ca78d1507b2a118c75128c6c2e093e27')
     version('1.7.4', '85ba87def461e3ff5a164de2e6482930')

var/spack/repos/builtin/packages/r-rgl/package.py

@@ -0,0 +1,54 @@
+##############################################################################
+# Copyright (c) 2013-2016, 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/llnl/spack
+# Please also see the LICENSE file 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 RRgl(RPackage):
+    """Provides medium to high level functions for 3D interactive graphics,
+    including functions modelled on base graphics (plot3d(), etc.) as well as
+    functions for constructing representations of geometric objects (cube3d(),
+    etc.). Output may be on screen using OpenGL, or to various standard
+    3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats,
+    including PNG, Postscript, SVG, PGF."""
+
+    homepage = "https://r-forge.r-project.org/projects/rgl"
+    url      = "https://cloud.r-project.org/src/contrib/rgl_0.98.1.tar.gz"
+
+    list_url = 'https://cloud.r-project.org/src/contrib/Archive/rgl'
+
+    version('0.98.1', 'bd69e1d33f1590feb4b6dc080b133e5b')
+
+    depends_on('r@3.2:3.9')
+    depends_on('zlib', type=('link'))
+    depends_on('libpng', type=('link'))
+    depends_on('freetype', type=('link'))
+    depends_on('mesa', type=('link'))
+    depends_on('mesa-glu', type=('link'))
+    depends_on('r-htmlwidgets', type=('build', 'run'))
+    depends_on('r-htmltools', type=('build', 'run'))
+    depends_on('r-knitr', type=('build', 'run'))
+    depends_on('r-jsonlite', type=('build', 'run'))
+    depends_on('r-shiny', type=('build', 'run'))
+    depends_on('r-magrittr', type=('build', 'run'))

var/spack/repos/builtin/packages/virtualgl/package.py

@@ -0,0 +1,45 @@
+##############################################################################
+# Copyright (c) 2013-2016, 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/llnl/spack
+# Please also see the LICENSE file 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 Virtualgl(CMakePackage):
+    """VirtualGL redirects 3D commands from a Unix/Linux OpenGL application
+       onto a server-side GPU and converts the rendered 3D images into a video
+       stream with which remote clients can interact to view and control the
+       3D application in real time."""
+
+    homepage = "http://www.virtualgl.org/Main/HomePage"
+    url      = "http://downloads.sourceforge.net/project/virtualgl/2.5.2/VirtualGL-2.5.2.tar.gz"
+
+    version('2.5.2', '1a9f404f4a35afa9f56381cb33ed210c')
+
+    depends_on("libjpeg-turbo")
+    # virtualgl require OpenGL but also wants to link libglu
+    # on systems without development packages, provide with spack and depends
+    # on mesa-glu, but we do not want Mesa OpenGL sw emulation, so added
+    # variant on mesa-glu to disable dependencies on sw emulated OpenGL
+    depends_on("mesa-glu~mesa")