PSARC 2015/541 R 3.2.3
authorRich Burridge <rich.burridge@oracle.com>
Thu, 28 Jan 2016 16:57:12 -0800
changeset 5365 447b67338e7f
parent 5364 17f26e606ed1
child 5366 6eaed9347ba1
PSARC 2015/541 R 3.2.3 22344994 Update R to version 3.2.3
components/r/Makefile
components/r/patches/01-fix-RSiteSearch.patch
components/r/r-cran-base.p5m
components/r/r-cran-boot.p5m
components/r/r-cran-class.p5m
components/r/r-cran-cluster.p5m
components/r/r-cran-codetools.p5m
components/r/r-cran-compiler.p5m
components/r/r-cran-datasets.p5m
components/r/r-cran-foreign.p5m
components/r/r-cran-graphics.p5m
components/r/r-cran-grdevices.p5m
components/r/r-cran-grid.p5m
components/r/r-cran-kernsmooth.p5m
components/r/r-cran-lattice.p5m
components/r/r-cran-mass.p5m
components/r/r-cran-matrix.p5m
components/r/r-cran-methods.p5m
components/r/r-cran-mgcv.p5m
components/r/r-cran-nlme.p5m
components/r/r-cran-nnet.p5m
components/r/r-cran-parallel.p5m
components/r/r-cran-rpart.p5m
components/r/r-cran-spatial.p5m
components/r/r-cran-splines.p5m
components/r/r-cran-stats.p5m
components/r/r-cran-stats4.p5m
components/r/r-cran-survival.p5m
components/r/r-cran-tcltk.p5m
components/r/r-cran-tools.p5m
components/r/r-cran-utils.p5m
components/r/r-recommended.p5m
components/r/r-translations.p5m
components/r/r.license
components/r/r.p5m
components/r/test/results-all.master
--- a/components/r/Makefile	Thu Jan 28 16:55:44 2016 -0800
+++ b/components/r/Makefile	Thu Jan 28 16:57:12 2016 -0800
@@ -26,16 +26,16 @@
 include ../../make-rules/shared-macros.mk
 
 COMPONENT_NAME=		R
-COMPONENT_VERSION=	3.2.0
+COMPONENT_VERSION=	3.2.3
 COMPONENT_PROJECT_URL=	http://www.r-project.org/
 COMPONENT_SRC=		$(COMPONENT_NAME)-$(COMPONENT_VERSION)
 COMPONENT_ARCHIVE=	$(COMPONENT_SRC).tar.gz
 COMPONENT_ARCHIVE_HASH=	\
-    sha256:f5ae953f18ba6f3d55b46556bbbf73441350f9fd22625402b723a2b81ff64f35
+    sha256:b93b7d878138279234160f007cb9b7f81b8a72c012a15566e9ec5395cfd9b6c1
 COMPONENT_ARCHIVE_URL=	http://cran.mtu.edu/src/base/R-3/$(COMPONENT_ARCHIVE)
 COMPONENT_BUGDB=	utility/r
 
-TPNO=			22535
+TPNO=			26540
 
 include $(WS_MAKE_RULES)/prep.mk
 include $(WS_MAKE_RULES)/configure.mk
--- a/components/r/patches/01-fix-RSiteSearch.patch	Thu Jan 28 16:55:44 2016 -0800
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,37 +0,0 @@
-Fix Bug 16329 - RSiteSearch fails for all search strings
-https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=16329
-
-Change already intergrated upstream.
-
-diff --git a/src/library/utils/R/RSiteSearch.R b/src/library/utils/R/RSiteSearch.R
-index 4578cb9..9323ddb 100644
---- a/src/library/utils/R/RSiteSearch.R
-+++ b/src/library/utils/R/RSiteSearch.R
[email protected]@ -1,7 +1,7 @@
- #  File src/library/utils/R/RSiteSearch.R
- #  Part of the R package, http://www.R-project.org
- #
--#  Copyright (C) 1995-2012 The R Core Team
-+#  Copyright (C) 1995-2015 The R Core Team
- #
- #  This program is free software; you can redistribute it and/or modify
- #  it under the terms of the GNU General Public License as published by
[email protected]@ -25,7 +25,7 @@ RSiteSearch <- function(string,
- 			matchesPerPage = 20)
- {
-     string <- paste0("http://search.r-project.org/cgi-bin/namazu.cgi?query=",
--		     gsub(" ", "+", string))
-+		     URLencode(gsub(" ", "+", string), reserved = TRUE))
-     mpp <- paste0("max=", matchesPerPage)
-     format <- paste0("result=", match.arg(format))
- 
[email protected]@ -47,8 +47,7 @@ RSiteSearch <- function(string,
-     ## we know this is a http:// URL, so encoding should be safe.
-     ## it seems that firefox on Mac OS needs it for {...}
-     ## OTOH, Namazu does not decode in, say, sort=date:late.
--    qstring <- paste(URLencode(string, reserved = TRUE),
--                     mpp, format, sortby, restr, sep = "&")
-+    qstring <- paste(string, mpp, format, sortby, restr, sep = "&")
-     browseURL(qstring)
-     cat(gettextf("A search query has been submitted to %s",
-                  "http://search.r-project.org"), "\n", sep = "")
--- a/components/r/r-cran-base.p5m	Thu Jan 28 16:55:44 2016 -0800
+++ b/components/r/r-cran-base.p5m	Thu Jan 28 16:57:12 2016 -0800
@@ -18,7 +18,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -32,7 +32,7 @@
     value="org.opensolaris.category.2008:Development/Other Languages"
 set name=info.source-url value=$(COMPONENT_ARCHIVE_URL)
 set name=info.upstream-url value=$(COMPONENT_PROJECT_URL)
-set name=org.opensolaris.arc-caseid value=PSARC/2015/216
+set name=org.opensolaris.arc-caseid value=PSARC/2015/216 value=PSARC/2015/541
 set name=org.opensolaris.consolidation value=$(CONSOLIDATION)
 file path=usr/lib/$(MACH64)/R/library/base/CITATION
 file path=usr/lib/$(MACH64)/R/library/base/DESCRIPTION
--- a/components/r/r-cran-boot.p5m	Thu Jan 28 16:55:44 2016 -0800
+++ b/components/r/r-cran-boot.p5m	Thu Jan 28 16:57:12 2016 -0800
@@ -18,7 +18,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -32,7 +32,7 @@
     value="org.opensolaris.category.2008:Development/Other Languages"
 set name=info.source-url value=$(COMPONENT_ARCHIVE_URL)
 set name=info.upstream-url value=$(COMPONENT_PROJECT_URL)
-set name=org.opensolaris.arc-caseid value=PSARC/2015/216
+set name=org.opensolaris.arc-caseid value=PSARC/2015/216 value=PSARC/2015/541
 set name=org.opensolaris.consolidation value=$(CONSOLIDATION)
 file path=usr/lib/$(MACH64)/R/library/boot/CITATION
 file path=usr/lib/$(MACH64)/R/library/boot/DESCRIPTION
--- a/components/r/r-cran-class.p5m	Thu Jan 28 16:55:44 2016 -0800
+++ b/components/r/r-cran-class.p5m	Thu Jan 28 16:57:12 2016 -0800
@@ -18,7 +18,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -32,7 +32,7 @@
     value="org.opensolaris.category.2008:Development/Other Languages"
 set name=info.source-url value=$(COMPONENT_ARCHIVE_URL)
 set name=info.upstream-url value=$(COMPONENT_PROJECT_URL)
-set name=org.opensolaris.arc-caseid value=PSARC/2015/216
+set name=org.opensolaris.arc-caseid value=PSARC/2015/216 value=PSARC/2015/541
 set name=org.opensolaris.consolidation value=$(CONSOLIDATION)
 file path=usr/lib/$(MACH64)/R/library/class/CITATION
 file path=usr/lib/$(MACH64)/R/library/class/DESCRIPTION
--- a/components/r/r-cran-cluster.p5m	Thu Jan 28 16:55:44 2016 -0800
+++ b/components/r/r-cran-cluster.p5m	Thu Jan 28 16:57:12 2016 -0800
@@ -18,7 +18,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -32,7 +32,7 @@
     value="org.opensolaris.category.2008:Development/Other Languages"
 set name=info.source-url value=$(COMPONENT_ARCHIVE_URL)
 set name=info.upstream-url value=$(COMPONENT_PROJECT_URL)
-set name=org.opensolaris.arc-caseid value=PSARC/2015/216
+set name=org.opensolaris.arc-caseid value=PSARC/2015/216 value=PSARC/2015/541
 set name=org.opensolaris.consolidation value=$(CONSOLIDATION)
 file path=usr/lib/$(MACH64)/R/library/cluster/CITATION
 file path=usr/lib/$(MACH64)/R/library/cluster/DESCRIPTION
@@ -44,6 +44,7 @@
 file path=usr/lib/$(MACH64)/R/library/cluster/Meta/nsInfo.rds
 file path=usr/lib/$(MACH64)/R/library/cluster/Meta/package.rds
 file path=usr/lib/$(MACH64)/R/library/cluster/NAMESPACE
+file path=usr/lib/$(MACH64)/R/library/cluster/NEWS.Rd
 file path=usr/lib/$(MACH64)/R/library/cluster/R/cluster
 file path=usr/lib/$(MACH64)/R/library/cluster/R/cluster.rdb
 file path=usr/lib/$(MACH64)/R/library/cluster/R/cluster.rdx
@@ -113,9 +114,12 @@
 file path=usr/lib/$(MACH64)/R/library/cluster/libs/cluster.so \
     pkg.depend.bypass-generate=libR.so
 file path=usr/lib/$(MACH64)/R/library/cluster/po/de/LC_MESSAGES/R-cluster.mo
+file path=usr/lib/$(MACH64)/R/library/cluster/po/de/LC_MESSAGES/cluster.mo
 file path=usr/lib/$(MACH64)/R/library/cluster/po/[email protected]/LC_MESSAGES/R-cluster.mo
 file path=usr/lib/$(MACH64)/R/library/cluster/po/[email protected]/LC_MESSAGES/cluster.mo
 file path=usr/lib/$(MACH64)/R/library/cluster/po/fr/LC_MESSAGES/R-cluster.mo
+file path=usr/lib/$(MACH64)/R/library/cluster/po/ko/LC_MESSAGES/R-cluster.mo
+file path=usr/lib/$(MACH64)/R/library/cluster/po/ko/LC_MESSAGES/cluster.mo
 file path=usr/lib/$(MACH64)/R/library/cluster/po/pl/LC_MESSAGES/R-cluster.mo
 license COPYING license=GPLv2
 depend type=require fmri=pkg:/runtime/r
--- a/components/r/r-cran-codetools.p5m	Thu Jan 28 16:55:44 2016 -0800
+++ b/components/r/r-cran-codetools.p5m	Thu Jan 28 16:57:12 2016 -0800
@@ -18,7 +18,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -32,7 +32,7 @@
     value="org.opensolaris.category.2008:Development/Other Languages"
 set name=info.source-url value=$(COMPONENT_ARCHIVE_URL)
 set name=info.upstream-url value=$(COMPONENT_PROJECT_URL)
-set name=org.opensolaris.arc-caseid value=PSARC/2015/216
+set name=org.opensolaris.arc-caseid value=PSARC/2015/216 value=PSARC/2015/541
 set name=org.opensolaris.consolidation value=$(CONSOLIDATION)
 file path=usr/lib/$(MACH64)/R/library/codetools/DESCRIPTION
 file path=usr/lib/$(MACH64)/R/library/codetools/INDEX
--- a/components/r/r-cran-compiler.p5m	Thu Jan 28 16:55:44 2016 -0800
+++ b/components/r/r-cran-compiler.p5m	Thu Jan 28 16:57:12 2016 -0800
@@ -18,7 +18,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -32,7 +32,7 @@
     value="org.opensolaris.category.2008:Development/Other Languages"
 set name=info.source-url value=$(COMPONENT_ARCHIVE_URL)
 set name=info.upstream-url value=$(COMPONENT_PROJECT_URL)
-set name=org.opensolaris.arc-caseid value=PSARC/2015/216
+set name=org.opensolaris.arc-caseid value=PSARC/2015/216 value=PSARC/2015/541
 set name=org.opensolaris.consolidation value=$(CONSOLIDATION)
 file path=usr/lib/$(MACH64)/R/library/compiler/DESCRIPTION
 file path=usr/lib/$(MACH64)/R/library/compiler/INDEX
--- a/components/r/r-cran-datasets.p5m	Thu Jan 28 16:55:44 2016 -0800
+++ b/components/r/r-cran-datasets.p5m	Thu Jan 28 16:57:12 2016 -0800
@@ -18,7 +18,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -32,7 +32,7 @@
     value="org.opensolaris.category.2008:Development/Other Languages"
 set name=info.source-url value=$(COMPONENT_ARCHIVE_URL)
 set name=info.upstream-url value=$(COMPONENT_PROJECT_URL)
-set name=org.opensolaris.arc-caseid value=PSARC/2015/216
+set name=org.opensolaris.arc-caseid value=PSARC/2015/216 value=PSARC/2015/541
 set name=org.opensolaris.consolidation value=$(CONSOLIDATION)
 file path=usr/lib/$(MACH64)/R/library/datasets/DESCRIPTION
 file path=usr/lib/$(MACH64)/R/library/datasets/INDEX
--- a/components/r/r-cran-foreign.p5m	Thu Jan 28 16:55:44 2016 -0800
+++ b/components/r/r-cran-foreign.p5m	Thu Jan 28 16:57:12 2016 -0800
@@ -18,7 +18,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -33,7 +33,7 @@
     value="org.opensolaris.category.2008:Development/Other Languages"
 set name=info.source-url value=$(COMPONENT_ARCHIVE_URL)
 set name=info.upstream-url value=$(COMPONENT_PROJECT_URL)
-set name=org.opensolaris.arc-caseid value=PSARC/2015/216
+set name=org.opensolaris.arc-caseid value=PSARC/2015/216 value=PSARC/2015/541
 set name=org.opensolaris.consolidation value=$(CONSOLIDATION)
 file path=usr/lib/$(MACH64)/R/library/foreign/COPYRIGHTS
 file path=usr/lib/$(MACH64)/R/library/foreign/DESCRIPTION
--- a/components/r/r-cran-graphics.p5m	Thu Jan 28 16:55:44 2016 -0800
+++ b/components/r/r-cran-graphics.p5m	Thu Jan 28 16:57:12 2016 -0800
@@ -18,7 +18,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -32,7 +32,7 @@
     value="org.opensolaris.category.2008:Development/Other Languages"
 set name=info.source-url value=$(COMPONENT_ARCHIVE_URL)
 set name=info.upstream-url value=$(COMPONENT_PROJECT_URL)
-set name=org.opensolaris.arc-caseid value=PSARC/2015/216
+set name=org.opensolaris.arc-caseid value=PSARC/2015/216 value=PSARC/2015/541
 set name=org.opensolaris.consolidation value=$(CONSOLIDATION)
 file path=usr/lib/$(MACH64)/R/library/graphics/DESCRIPTION
 file path=usr/lib/$(MACH64)/R/library/graphics/INDEX
--- a/components/r/r-cran-grdevices.p5m	Thu Jan 28 16:55:44 2016 -0800
+++ b/components/r/r-cran-grdevices.p5m	Thu Jan 28 16:57:12 2016 -0800
@@ -18,7 +18,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -34,7 +34,7 @@
     value="org.opensolaris.category.2008:Development/Other Languages"
 set name=info.source-url value=$(COMPONENT_ARCHIVE_URL)
 set name=info.upstream-url value=$(COMPONENT_PROJECT_URL)
-set name=org.opensolaris.arc-caseid value=PSARC/2015/216
+set name=org.opensolaris.arc-caseid value=PSARC/2015/216 value=PSARC/2015/541
 set name=org.opensolaris.consolidation value=$(CONSOLIDATION)
 file path=usr/lib/$(MACH64)/R/library/grDevices/DESCRIPTION
 file path=usr/lib/$(MACH64)/R/library/grDevices/INDEX
--- a/components/r/r-cran-grid.p5m	Thu Jan 28 16:55:44 2016 -0800
+++ b/components/r/r-cran-grid.p5m	Thu Jan 28 16:57:12 2016 -0800
@@ -18,7 +18,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -32,7 +32,7 @@
     value="org.opensolaris.category.2008:Development/Other Languages"
 set name=info.source-url value=$(COMPONENT_ARCHIVE_URL)
 set name=info.upstream-url value=$(COMPONENT_PROJECT_URL)
-set name=org.opensolaris.arc-caseid value=PSARC/2015/216
+set name=org.opensolaris.arc-caseid value=PSARC/2015/216 value=PSARC/2015/541
 set name=org.opensolaris.consolidation value=$(CONSOLIDATION)
 file path=usr/lib/$(MACH64)/R/library/grid/DESCRIPTION
 file path=usr/lib/$(MACH64)/R/library/grid/INDEX
--- a/components/r/r-cran-kernsmooth.p5m	Thu Jan 28 16:55:44 2016 -0800
+++ b/components/r/r-cran-kernsmooth.p5m	Thu Jan 28 16:57:12 2016 -0800
@@ -18,7 +18,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -33,7 +33,7 @@
     value="org.opensolaris.category.2008:Development/Other Languages"
 set name=info.source-url value=$(COMPONENT_ARCHIVE_URL)
 set name=info.upstream-url value=$(COMPONENT_PROJECT_URL)
-set name=org.opensolaris.arc-caseid value=PSARC/2015/216
+set name=org.opensolaris.arc-caseid value=PSARC/2015/216 value=PSARC/2015/541
 set name=org.opensolaris.consolidation value=$(CONSOLIDATION)
 file path=usr/lib/$(MACH64)/R/library/KernSmooth/DESCRIPTION
 file path=usr/lib/$(MACH64)/R/library/KernSmooth/INDEX
--- a/components/r/r-cran-lattice.p5m	Thu Jan 28 16:55:44 2016 -0800
+++ b/components/r/r-cran-lattice.p5m	Thu Jan 28 16:57:12 2016 -0800
@@ -18,7 +18,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -32,7 +32,7 @@
     value="org.opensolaris.category.2008:Development/Other Languages"
 set name=info.source-url value=$(COMPONENT_ARCHIVE_URL)
 set name=info.upstream-url value=$(COMPONENT_PROJECT_URL)
-set name=org.opensolaris.arc-caseid value=PSARC/2015/216
+set name=org.opensolaris.arc-caseid value=PSARC/2015/216 value=PSARC/2015/541
 set name=org.opensolaris.consolidation value=$(CONSOLIDATION)
 file path=usr/lib/$(MACH64)/R/library/lattice/CITATION
 file path=usr/lib/$(MACH64)/R/library/lattice/DESCRIPTION
--- a/components/r/r-cran-mass.p5m	Thu Jan 28 16:55:44 2016 -0800
+++ b/components/r/r-cran-mass.p5m	Thu Jan 28 16:57:12 2016 -0800
@@ -18,7 +18,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -34,7 +34,7 @@
     value="org.opensolaris.category.2008:Development/Other Languages"
 set name=info.source-url value=$(COMPONENT_ARCHIVE_URL)
 set name=info.upstream-url value=$(COMPONENT_PROJECT_URL)
-set name=org.opensolaris.arc-caseid value=PSARC/2015/216
+set name=org.opensolaris.arc-caseid value=PSARC/2015/216 value=PSARC/2015/541
 set name=org.opensolaris.consolidation value=$(CONSOLIDATION)
 file path=usr/lib/$(MACH64)/R/library/MASS/CITATION
 file path=usr/lib/$(MACH64)/R/library/MASS/DESCRIPTION
--- a/components/r/r-cran-matrix.p5m	Thu Jan 28 16:55:44 2016 -0800
+++ b/components/r/r-cran-matrix.p5m	Thu Jan 28 16:57:12 2016 -0800
@@ -18,7 +18,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -33,7 +33,7 @@
     value="org.opensolaris.category.2008:Development/Other Languages"
 set name=info.source-url value=$(COMPONENT_ARCHIVE_URL)
 set name=info.upstream-url value=$(COMPONENT_PROJECT_URL)
-set name=org.opensolaris.arc-caseid value=PSARC/2015/216
+set name=org.opensolaris.arc-caseid value=PSARC/2015/216 value=PSARC/2015/541
 set name=org.opensolaris.consolidation value=$(CONSOLIDATION)
 file path=usr/lib/$(MACH64)/R/library/Matrix/Copyrights
 file path=usr/lib/$(MACH64)/R/library/Matrix/DESCRIPTION
@@ -107,6 +107,7 @@
 file path=usr/lib/$(MACH64)/R/library/Matrix/html/LU-class.html
 file path=usr/lib/$(MACH64)/R/library/Matrix/html/Matrix-class.html
 file path=usr/lib/$(MACH64)/R/library/Matrix/html/Matrix.html
+file path=usr/lib/$(MACH64)/R/library/Matrix/html/MatrixClass.html
 file path=usr/lib/$(MACH64)/R/library/Matrix/html/MatrixFactorization-class.html
 file path=usr/lib/$(MACH64)/R/library/Matrix/html/R.css
 file path=usr/lib/$(MACH64)/R/library/Matrix/html/RsparseMatrix-class.html
--- a/components/r/r-cran-methods.p5m	Thu Jan 28 16:55:44 2016 -0800
+++ b/components/r/r-cran-methods.p5m	Thu Jan 28 16:57:12 2016 -0800
@@ -17,7 +17,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -32,7 +32,7 @@
     value="org.opensolaris.category.2008:Development/Other Languages"
 set name=info.source-url value=$(COMPONENT_ARCHIVE_URL)
 set name=info.upstream-url value=$(COMPONENT_PROJECT_URL)
-set name=org.opensolaris.arc-caseid value=PSARC/2015/216
+set name=org.opensolaris.arc-caseid value=PSARC/2015/216 value=PSARC/2015/541
 set name=org.opensolaris.consolidation value=$(CONSOLIDATION)
 file path=usr/lib/$(MACH64)/R/library/methods/DESCRIPTION
 file path=usr/lib/$(MACH64)/R/library/methods/INDEX
--- a/components/r/r-cran-mgcv.p5m	Thu Jan 28 16:55:44 2016 -0800
+++ b/components/r/r-cran-mgcv.p5m	Thu Jan 28 16:57:12 2016 -0800
@@ -18,7 +18,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -34,7 +34,7 @@
     value="org.opensolaris.category.2008:Development/Other Languages"
 set name=info.source-url value=$(COMPONENT_ARCHIVE_URL)
 set name=info.upstream-url value=$(COMPONENT_PROJECT_URL)
-set name=org.opensolaris.arc-caseid value=PSARC/2015/216
+set name=org.opensolaris.arc-caseid value=PSARC/2015/216 value=PSARC/2015/541
 set name=org.opensolaris.consolidation value=$(CONSOLIDATION)
 file path=usr/lib/$(MACH64)/R/library/mgcv/CITATION
 file path=usr/lib/$(MACH64)/R/library/mgcv/DESCRIPTION
@@ -148,6 +148,7 @@
 file path=usr/lib/$(MACH64)/R/library/mgcv/html/smooth.construct.cr.smooth.spec.html
 file path=usr/lib/$(MACH64)/R/library/mgcv/html/smooth.construct.ds.smooth.spec.html
 file path=usr/lib/$(MACH64)/R/library/mgcv/html/smooth.construct.fs.smooth.spec.html
+file path=usr/lib/$(MACH64)/R/library/mgcv/html/smooth.construct.gp.smooth.spec.html
 file path=usr/lib/$(MACH64)/R/library/mgcv/html/smooth.construct.html
 file path=usr/lib/$(MACH64)/R/library/mgcv/html/smooth.construct.mrf.smooth.spec.html
 file path=usr/lib/$(MACH64)/R/library/mgcv/html/smooth.construct.ps.smooth.spec.html
@@ -183,8 +184,6 @@
 file path=usr/lib/$(MACH64)/R/library/mgcv/po/ko/LC_MESSAGES/mgcv.mo
 file path=usr/lib/$(MACH64)/R/library/mgcv/po/pl/LC_MESSAGES/R-mgcv.mo
 file path=usr/lib/$(MACH64)/R/library/mgcv/po/pl/LC_MESSAGES/mgcv.mo
-file path=usr/lib/$(MACH64)/R/library/mgcv/po/po/LC_MESSAGES/R-mgcv.mo
-file path=usr/lib/$(MACH64)/R/library/mgcv/po/po/LC_MESSAGES/mgcv.mo
 license COPYING license=GPLv2
 depend type=require fmri=pkg:/runtime/r
 depend type=require fmri=pkg:/system/library/openmp
--- a/components/r/r-cran-nlme.p5m	Thu Jan 28 16:55:44 2016 -0800
+++ b/components/r/r-cran-nlme.p5m	Thu Jan 28 16:57:12 2016 -0800
@@ -18,7 +18,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -33,7 +33,7 @@
     value="org.opensolaris.category.2008:Development/Other Languages"
 set name=info.source-url value=$(COMPONENT_ARCHIVE_URL)
 set name=info.upstream-url value=$(COMPONENT_PROJECT_URL)
-set name=org.opensolaris.arc-caseid value=PSARC/2015/216
+set name=org.opensolaris.arc-caseid value=PSARC/2015/216 value=PSARC/2015/541
 set name=org.opensolaris.consolidation value=$(CONSOLIDATION)
 file path=usr/lib/$(MACH64)/R/library/nlme/CITATION
 file path=usr/lib/$(MACH64)/R/library/nlme/DESCRIPTION
--- a/components/r/r-cran-nnet.p5m	Thu Jan 28 16:55:44 2016 -0800
+++ b/components/r/r-cran-nnet.p5m	Thu Jan 28 16:57:12 2016 -0800
@@ -18,7 +18,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -34,7 +34,7 @@
     value="org.opensolaris.category.2008:Development/Other Languages"
 set name=info.source-url value=$(COMPONENT_ARCHIVE_URL)
 set name=info.upstream-url value=$(COMPONENT_PROJECT_URL)
-set name=org.opensolaris.arc-caseid value=PSARC/2015/216
+set name=org.opensolaris.arc-caseid value=PSARC/2015/216 value=PSARC/2015/541
 set name=org.opensolaris.consolidation value=$(CONSOLIDATION)
 file path=usr/lib/$(MACH64)/R/library/nnet/CITATION
 file path=usr/lib/$(MACH64)/R/library/nnet/DESCRIPTION
--- a/components/r/r-cran-parallel.p5m	Thu Jan 28 16:55:44 2016 -0800
+++ b/components/r/r-cran-parallel.p5m	Thu Jan 28 16:57:12 2016 -0800
@@ -18,7 +18,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -33,7 +33,7 @@
     value="org.opensolaris.category.2008:Development/Other Languages"
 set name=info.source-url value=$(COMPONENT_ARCHIVE_URL)
 set name=info.upstream-url value=$(COMPONENT_PROJECT_URL)
-set name=org.opensolaris.arc-caseid value=PSARC/2015/216
+set name=org.opensolaris.arc-caseid value=PSARC/2015/216 value=PSARC/2015/541
 set name=org.opensolaris.consolidation value=$(CONSOLIDATION)
 file path=usr/lib/$(MACH64)/R/library/parallel/DESCRIPTION
 file path=usr/lib/$(MACH64)/R/library/parallel/INDEX
--- a/components/r/r-cran-rpart.p5m	Thu Jan 28 16:55:44 2016 -0800
+++ b/components/r/r-cran-rpart.p5m	Thu Jan 28 16:57:12 2016 -0800
@@ -18,7 +18,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -32,7 +32,7 @@
     value="org.opensolaris.category.2008:Development/Other Languages"
 set name=info.source-url value=$(COMPONENT_ARCHIVE_URL)
 set name=info.upstream-url value=$(COMPONENT_PROJECT_URL)
-set name=org.opensolaris.arc-caseid value=PSARC/2015/216
+set name=org.opensolaris.arc-caseid value=PSARC/2015/216 value=PSARC/2015/541
 set name=org.opensolaris.consolidation value=$(CONSOLIDATION)
 file path=usr/lib/$(MACH64)/R/library/rpart/DESCRIPTION
 file path=usr/lib/$(MACH64)/R/library/rpart/INDEX
--- a/components/r/r-cran-spatial.p5m	Thu Jan 28 16:55:44 2016 -0800
+++ b/components/r/r-cran-spatial.p5m	Thu Jan 28 16:57:12 2016 -0800
@@ -18,7 +18,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -33,7 +33,7 @@
     value="org.opensolaris.category.2008:Development/Other Languages"
 set name=info.source-url value=$(COMPONENT_ARCHIVE_URL)
 set name=info.upstream-url value=$(COMPONENT_PROJECT_URL)
-set name=org.opensolaris.arc-caseid value=PSARC/2015/216
+set name=org.opensolaris.arc-caseid value=PSARC/2015/216 value=PSARC/2015/541
 set name=org.opensolaris.consolidation value=$(CONSOLIDATION)
 file path=usr/lib/$(MACH64)/R/library/spatial/CITATION
 file path=usr/lib/$(MACH64)/R/library/spatial/DESCRIPTION
--- a/components/r/r-cran-splines.p5m	Thu Jan 28 16:55:44 2016 -0800
+++ b/components/r/r-cran-splines.p5m	Thu Jan 28 16:57:12 2016 -0800
@@ -18,7 +18,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -33,7 +33,7 @@
     value="org.opensolaris.category.2008:Development/Other Languages"
 set name=info.source-url value=$(COMPONENT_ARCHIVE_URL)
 set name=info.upstream-url value=$(COMPONENT_PROJECT_URL)
-set name=org.opensolaris.arc-caseid value=PSARC/2015/216
+set name=org.opensolaris.arc-caseid value=PSARC/2015/216 value=PSARC/2015/541
 set name=org.opensolaris.consolidation value=$(CONSOLIDATION)
 file path=usr/lib/$(MACH64)/R/library/splines/DESCRIPTION
 file path=usr/lib/$(MACH64)/R/library/splines/INDEX
--- a/components/r/r-cran-stats.p5m	Thu Jan 28 16:55:44 2016 -0800
+++ b/components/r/r-cran-stats.p5m	Thu Jan 28 16:57:12 2016 -0800
@@ -18,7 +18,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -32,7 +32,7 @@
     value="org.opensolaris.category.2008:Development/Other Languages"
 set name=info.source-url value=$(COMPONENT_ARCHIVE_URL)
 set name=info.upstream-url value=$(COMPONENT_PROJECT_URL)
-set name=org.opensolaris.arc-caseid value=PSARC/2015/216
+set name=org.opensolaris.arc-caseid value=PSARC/2015/216 value=PSARC/2015/541
 set name=org.opensolaris.consolidation value=$(CONSOLIDATION)
 file path=usr/lib/$(MACH64)/R/library/stats/COPYRIGHTS.modreg
 file path=usr/lib/$(MACH64)/R/library/stats/DESCRIPTION
--- a/components/r/r-cran-stats4.p5m	Thu Jan 28 16:55:44 2016 -0800
+++ b/components/r/r-cran-stats4.p5m	Thu Jan 28 16:57:12 2016 -0800
@@ -18,7 +18,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -33,7 +33,7 @@
     value="org.opensolaris.category.2008:Development/Other Languages"
 set name=info.source-url value=$(COMPONENT_ARCHIVE_URL)
 set name=info.upstream-url value=$(COMPONENT_PROJECT_URL)
-set name=org.opensolaris.arc-caseid value=PSARC/2015/216
+set name=org.opensolaris.arc-caseid value=PSARC/2015/216 value=PSARC/2015/541
 set name=org.opensolaris.consolidation value=$(CONSOLIDATION)
 file path=usr/lib/$(MACH64)/R/library/stats4/DESCRIPTION
 file path=usr/lib/$(MACH64)/R/library/stats4/INDEX
--- a/components/r/r-cran-survival.p5m	Thu Jan 28 16:55:44 2016 -0800
+++ b/components/r/r-cran-survival.p5m	Thu Jan 28 16:57:12 2016 -0800
@@ -17,7 +17,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -33,7 +33,7 @@
     value="org.opensolaris.category.2008:Development/Other Languages"
 set name=info.source-url value=$(COMPONENT_ARCHIVE_URL)
 set name=info.upstream-url value=$(COMPONENT_PROJECT_URL)
-set name=org.opensolaris.arc-caseid value=PSARC/2015/216
+set name=org.opensolaris.arc-caseid value=PSARC/2015/216 value=PSARC/2015/541
 set name=org.opensolaris.consolidation value=$(CONSOLIDATION)
 file path=usr/lib/$(MACH64)/R/library/survival/CITATION
 file path=usr/lib/$(MACH64)/R/library/survival/COPYRIGHTS
@@ -107,6 +107,7 @@
 file path=usr/lib/$(MACH64)/R/library/survival/html/is.ratetable.html
 file path=usr/lib/$(MACH64)/R/library/survival/html/kidney.html
 file path=usr/lib/$(MACH64)/R/library/survival/html/lines.survfit.html
+file path=usr/lib/$(MACH64)/R/library/survival/html/logLik.coxph.html
 file path=usr/lib/$(MACH64)/R/library/survival/html/logan.html
 file path=usr/lib/$(MACH64)/R/library/survival/html/lung.html
 file path=usr/lib/$(MACH64)/R/library/survival/html/mgus.html
--- a/components/r/r-cran-tcltk.p5m	Thu Jan 28 16:55:44 2016 -0800
+++ b/components/r/r-cran-tcltk.p5m	Thu Jan 28 16:57:12 2016 -0800
@@ -18,7 +18,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -32,7 +32,7 @@
     value="org.opensolaris.category.2008:Development/Other Languages"
 set name=info.source-url value=$(COMPONENT_ARCHIVE_URL)
 set name=info.upstream-url value=$(COMPONENT_PROJECT_URL)
-set name=org.opensolaris.arc-caseid value=PSARC/2015/216
+set name=org.opensolaris.arc-caseid value=PSARC/2015/216 value=PSARC/2015/541
 set name=org.opensolaris.consolidation value=$(CONSOLIDATION)
 file path=usr/lib/$(MACH64)/R/library/tcltk/DESCRIPTION
 file path=usr/lib/$(MACH64)/R/library/tcltk/INDEX
--- a/components/r/r-cran-tools.p5m	Thu Jan 28 16:55:44 2016 -0800
+++ b/components/r/r-cran-tools.p5m	Thu Jan 28 16:57:12 2016 -0800
@@ -18,7 +18,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -33,7 +33,7 @@
     value="org.opensolaris.category.2008:Development/Other Languages"
 set name=info.source-url value=$(COMPONENT_ARCHIVE_URL)
 set name=info.upstream-url value=$(COMPONENT_PROJECT_URL)
-set name=org.opensolaris.arc-caseid value=PSARC/2015/216
+set name=org.opensolaris.arc-caseid value=PSARC/2015/216 value=PSARC/2015/541
 set name=org.opensolaris.consolidation value=$(CONSOLIDATION)
 file path=usr/lib/$(MACH64)/R/library/tools/DESCRIPTION
 file path=usr/lib/$(MACH64)/R/library/tools/INDEX
--- a/components/r/r-cran-utils.p5m	Thu Jan 28 16:55:44 2016 -0800
+++ b/components/r/r-cran-utils.p5m	Thu Jan 28 16:57:12 2016 -0800
@@ -18,7 +18,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -32,7 +32,7 @@
     value="org.opensolaris.category.2008:Development/Other Languages"
 set name=info.source-url value=$(COMPONENT_ARCHIVE_URL)
 set name=info.upstream-url value=$(COMPONENT_PROJECT_URL)
-set name=org.opensolaris.arc-caseid value=PSARC/2015/216
+set name=org.opensolaris.arc-caseid value=PSARC/2015/216 value=PSARC/2015/541
 set name=org.opensolaris.consolidation value=$(CONSOLIDATION)
 file path=usr/lib/$(MACH64)/R/library/utils/DESCRIPTION
 file path=usr/lib/$(MACH64)/R/library/utils/INDEX
--- a/components/r/r-recommended.p5m	Thu Jan 28 16:55:44 2016 -0800
+++ b/components/r/r-recommended.p5m	Thu Jan 28 16:57:12 2016 -0800
@@ -18,7 +18,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -34,7 +34,7 @@
     value="org.opensolaris.category.2008:Development/Other Languages"
 set name=info.source-url value=$(COMPONENT_ARCHIVE_URL)
 set name=info.upstream-url value=$(COMPONENT_PROJECT_URL)
-set name=org.opensolaris.arc-caseid value=PSARC/2015/216
+set name=org.opensolaris.arc-caseid value=PSARC/2015/216 value=PSARC/2015/541
 set name=org.opensolaris.consolidation value=$(CONSOLIDATION)
 depend type=require fmri=pkg:/library/r/r-cran-base
 depend type=require fmri=pkg:/library/r/r-cran-boot
--- a/components/r/r-translations.p5m	Thu Jan 28 16:55:44 2016 -0800
+++ b/components/r/r-translations.p5m	Thu Jan 28 16:57:12 2016 -0800
@@ -18,7 +18,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -33,7 +33,7 @@
     value="org.opensolaris.category.2008:Development/Other Languages"
 set name=info.source-url value=$(COMPONENT_ARCHIVE_URL)
 set name=info.upstream-url value=$(COMPONENT_PROJECT_URL)
-set name=org.opensolaris.arc-caseid value=PSARC/2015/216
+set name=org.opensolaris.arc-caseid value=PSARC/2015/216 value=PSARC/2015/541
 set name=org.opensolaris.consolidation value=$(CONSOLIDATION)
 file path=usr/lib/$(MACH64)/R/library/translations/DESCRIPTION
 file path=usr/lib/$(MACH64)/R/library/translations/da/LC_MESSAGES/R-base.mo
--- a/components/r/r.license	Thu Jan 28 16:55:44 2016 -0800
+++ b/components/r/r.license	Thu Jan 28 16:57:12 2016 -0800
@@ -1,82 +1,82 @@
-		    GNU GENERAL PUBLIC LICENSE
-		       Version 2, June 1991
+GNU GENERAL PUBLIC LICENSE
+		 Version 2, June 1991
 
- Copyright (C) 1989, 1991 Free Software Foundation, Inc.
-                       51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
- Everyone is permitted to copy and distribute verbatim copies
- of this license document, but changing it is not allowed.
+Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+Everyone is permitted to copy and distribute verbatim copies
+of this license document, but changing it is not allowed.
 
-			    Preamble
+			 Preamble
 
-  The licenses for most software are designed to take away your
-freedom to share and change it.  By contrast, the GNU General Public
+The licenses for most software are designed to take away your
+freedom to share and change it. By contrast, the GNU General Public
 License is intended to guarantee your freedom to share and change free
-software--to make sure the software is free for all its users.  This
+software--to make sure the software is free for all its users. This
 General Public License applies to most of the Free Software
 Foundation's software and to any other program whose authors commit to
-using it.  (Some other Free Software Foundation software is covered by
-the GNU Library General Public License instead.)  You can apply it to
+using it. (Some other Free Software Foundation software is covered by
+the GNU Library General Public License instead.) You can apply it to
 your programs, too.
 
-  When we speak of free software, we are referring to freedom, not
-price.  Our General Public Licenses are designed to make sure that you
+When we speak of free software, we are referring to freedom, not
+price. Our General Public Licenses are designed to make sure that you
 have the freedom to distribute copies of free software (and charge for
 this service if you wish), that you receive source code or can get it
 if you want it, that you can change the software or use pieces of it
 in new free programs; and that you know you can do these things.
 
-  To protect your rights, we need to make restrictions that forbid
+To protect your rights, we need to make restrictions that forbid
 anyone to deny you these rights or to ask you to surrender the rights.
 These restrictions translate to certain responsibilities for you if you
 distribute copies of the software, or if you modify it.
 
-  For example, if you distribute copies of such a program, whether
+For example, if you distribute copies of such a program, whether
 gratis or for a fee, you must give the recipients all the rights that
-you have.  You must make sure that they, too, receive or can get the
-source code.  And you must show them these terms so they know their
+you have. You must make sure that they, too, receive or can get the
+source code. And you must show them these terms so they know their
 rights.
 
-  We protect your rights with two steps: (1) copyright the software, and
+We protect your rights with two steps: (1) copyright the software, and
 (2) offer you this license which gives you legal permission to copy,
 distribute and/or modify the software.
 
-  Also, for each author's protection and ours, we want to make certain
+Also, for each author's protection and ours, we want to make certain
 that everyone understands that there is no warranty for this free
-software.  If the software is modified by someone else and passed on, we
+software. If the software is modified by someone else and passed on, we
 want its recipients to know that what they have is not the original, so
 that any problems introduced by others will not reflect on the original
 authors' reputations.
 
-  Finally, any free program is threatened constantly by software
-patents.  We wish to avoid the danger that redistributors of a free
+Finally, any free program is threatened constantly by software
+patents. We wish to avoid the danger that redistributors of a free
 program will individually obtain patent licenses, in effect making the
-program proprietary.  To prevent this, we have made it clear that any
+program proprietary. To prevent this, we have made it clear that any
 patent must be licensed for everyone's free use or not licensed at all.
 
-  The precise terms and conditions for copying, distribution and
+The precise terms and conditions for copying, distribution and
 modification follow.
-
-		    GNU GENERAL PUBLIC LICENSE
-   TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+		 GNU GENERAL PUBLIC LICENSE
+TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
 
-  0. This License applies to any program or other work which contains
+0. This License applies to any program or other work which contains
 a notice placed by the copyright holder saying it may be distributed
-under the terms of this General Public License.  The "Program", below,
+under the terms of this General Public License. The "Program", below,
 refers to any such program or work, and a "work based on the Program"
 means either the Program or any derivative work under copyright law:
 that is to say, a work containing the Program or a portion of it,
 either verbatim or with modifications and/or translated into another
-language.  (Hereinafter, translation is included without limitation in
-the term "modification".)  Each licensee is addressed as "you".
+language. (Hereinafter, translation is included without limitation in
+the term "modification".) Each licensee is addressed as "you".
 
 Activities other than copying, distribution and modification are not
-covered by this License; they are outside its scope.  The act of
+covered by this License; they are outside its scope. The act of
 running the Program is not restricted, and the output from the Program
 is covered only if its contents constitute a work based on the
 Program (independent of having been made by running the Program).
 Whether that is true depends on what the Program does.
 
-  1. You may copy and distribute verbatim copies of the Program's
+1. You may copy and distribute verbatim copies of the Program's
 source code as you receive it, in any medium, provided that you
 conspicuously and appropriately publish on each copy an appropriate
 copyright notice and disclaimer of warranty; keep intact all the
@@ -87,35 +87,35 @@
 You may charge a fee for the physical act of transferring a copy, and
 you may at your option offer warranty protection in exchange for a fee.
 
-  2. You may modify your copy or copies of the Program or any portion
+2. You may modify your copy or copies of the Program or any portion
 of it, thus forming a work based on the Program, and copy and
 distribute such modifications or work under the terms of Section 1
 above, provided that you also meet all of these conditions:
 
-    a) You must cause the modified files to carry prominent notices
-    stating that you changed the files and the date of any change.
+a) You must cause the modified files to carry prominent notices
+stating that you changed the files and the date of any change.
 
-    b) You must cause any work that you distribute or publish, that in
-    whole or in part contains or is derived from the Program or any
-    part thereof, to be licensed as a whole at no charge to all third
-    parties under the terms of this License.
+b) You must cause any work that you distribute or publish, that in
+whole or in part contains or is derived from the Program or any
+part thereof, to be licensed as a whole at no charge to all third
+parties under the terms of this License.
 
-    c) If the modified program normally reads commands interactively
-    when run, you must cause it, when started running for such
-    interactive use in the most ordinary way, to print or display an
-    announcement including an appropriate copyright notice and a
-    notice that there is no warranty (or else, saying that you provide
-    a warranty) and that users may redistribute the program under
-    these conditions, and telling the user how to view a copy of this
-    License.  (Exception: if the Program itself is interactive but
-    does not normally print such an announcement, your work based on
-    the Program is not required to print an announcement.)
-
-These requirements apply to the modified work as a whole.  If
+c) If the modified program normally reads commands interactively
+when run, you must cause it, when started running for such
+interactive use in the most ordinary way, to print or display an
+announcement including an appropriate copyright notice and a
+notice that there is no warranty (or else, saying that you provide
+a warranty) and that users may redistribute the program under
+these conditions, and telling the user how to view a copy of this
+License. (Exception: if the Program itself is interactive but
+does not normally print such an announcement, your work based on
+the Program is not required to print an announcement.)
+
+These requirements apply to the modified work as a whole. If
 identifiable sections of that work are not derived from the Program,
 and can be reasonably considered independent and separate works in
 themselves, then this License, and its terms, do not apply to those
-sections when you distribute them as separate works.  But when you
+sections when you distribute them as separate works. But when you
 distribute the same sections as part of a whole which is a work based
 on the Program, the distribution of the whole must be on the terms of
 this License, whose permissions for other licensees extend to the
@@ -131,32 +131,32 @@
 a storage or distribution medium does not bring the other work under
 the scope of this License.
 
-  3. You may copy and distribute the Program (or a work based on it,
+3. You may copy and distribute the Program (or a work based on it,
 under Section 2) in object code or executable form under the terms of
 Sections 1 and 2 above provided that you also do one of the following:
 
-    a) Accompany it with the complete corresponding machine-readable
-    source code, which must be distributed under the terms of Sections
-    1 and 2 above on a medium customarily used for software interchange; or,
+a) Accompany it with the complete corresponding machine-readable
+source code, which must be distributed under the terms of Sections
+1 and 2 above on a medium customarily used for software interchange; or,
 
-    b) Accompany it with a written offer, valid for at least three
-    years, to give any third party, for a charge no more than your
-    cost of physically performing source distribution, a complete
-    machine-readable copy of the corresponding source code, to be
-    distributed under the terms of Sections 1 and 2 above on a medium
-    customarily used for software interchange; or,
+b) Accompany it with a written offer, valid for at least three
+years, to give any third party, for a charge no more than your
+cost of physically performing source distribution, a complete
+machine-readable copy of the corresponding source code, to be
+distributed under the terms of Sections 1 and 2 above on a medium
+customarily used for software interchange; or,
 
-    c) Accompany it with the information you received as to the offer
-    to distribute corresponding source code.  (This alternative is
-    allowed only for noncommercial distribution and only if you
-    received the program in object code or executable form with such
-    an offer, in accord with Subsection b above.)
+c) Accompany it with the information you received as to the offer
+to distribute corresponding source code. (This alternative is
+allowed only for noncommercial distribution and only if you
+received the program in object code or executable form with such
+an offer, in accord with Subsection b above.)
 
 The source code for a work means the preferred form of the work for
-making modifications to it.  For an executable work, complete source
+making modifications to it. For an executable work, complete source
 code means all the source code for all modules it contains, plus any
 associated interface definition files, plus the scripts used to
-control compilation and installation of the executable.  However, as a
+control compilation and installation of the executable. However, as a
 special exception, the source code distributed need not include
 anything that is normally distributed (in either source or binary
 form) with the major components (compiler, kernel, and so on) of the
@@ -168,40 +168,40 @@
 access to copy the source code from the same place counts as
 distribution of the source code, even though third parties are not
 compelled to copy the source along with the object code.
-
-  4. You may not copy, modify, sublicense, or distribute the Program
-except as expressly provided under this License.  Any attempt
+
+4. You may not copy, modify, sublicense, or distribute the Program
+except as expressly provided under this License. Any attempt
 otherwise to copy, modify, sublicense or distribute the Program is
 void, and will automatically terminate your rights under this License.
 However, parties who have received copies, or rights, from you under
 this License will not have their licenses terminated so long as such
 parties remain in full compliance.
 
-  5. You are not required to accept this License, since you have not
-signed it.  However, nothing else grants you permission to modify or
-distribute the Program or its derivative works.  These actions are
-prohibited by law if you do not accept this License.  Therefore, by
+5. You are not required to accept this License, since you have not
+signed it. However, nothing else grants you permission to modify or
+distribute the Program or its derivative works. These actions are
+prohibited by law if you do not accept this License. Therefore, by
 modifying or distributing the Program (or any work based on the
 Program), you indicate your acceptance of this License to do so, and
 all its terms and conditions for copying, distributing or modifying
 the Program or works based on it.
 
-  6. Each time you redistribute the Program (or any work based on the
+6. Each time you redistribute the Program (or any work based on the
 Program), the recipient automatically receives a license from the
 original licensor to copy, distribute or modify the Program subject to
-these terms and conditions.  You may not impose any further
+these terms and conditions. You may not impose any further
 restrictions on the recipients' exercise of the rights granted herein.
 You are not responsible for enforcing compliance by third parties to
 this License.
 
-  7. If, as a consequence of a court judgment or allegation of patent
+7. If, as a consequence of a court judgment or allegation of patent
 infringement or for any other reason (not limited to patent issues),
 conditions are imposed on you (whether by court order, agreement or
 otherwise) that contradict the conditions of this License, they do not
-excuse you from the conditions of this License.  If you cannot
+excuse you from the conditions of this License. If you cannot
 distribute so as to satisfy simultaneously your obligations under this
 License and any other pertinent obligations, then as a consequence you
-may not distribute the Program at all.  For example, if a patent
+may not distribute the Program at all. For example, if a patent
 license would not permit royalty-free redistribution of the Program by
 all those who receive copies directly or indirectly through you, then
 the only way you could satisfy both it and this License would be to
@@ -216,7 +216,7 @@
 patents or other property right claims or to contest validity of any
 such claims; this section has the sole purpose of protecting the
 integrity of the free software distribution system, which is
-implemented by public license practices.  Many people have made
+implemented by public license practices. Many people have made
 generous contributions to the wide range of software distributed
 through that system in reliance on consistent application of that
 system; it is up to the author/donor to decide if he or she is willing
@@ -225,49 +225,49 @@
 
 This section is intended to make thoroughly clear what is believed to
 be a consequence of the rest of this License.
-
-  8. If the distribution and/or use of the Program is restricted in
+
+8. If the distribution and/or use of the Program is restricted in
 certain countries either by patents or by copyrighted interfaces, the
 original copyright holder who places the Program under this License
 may add an explicit geographical distribution limitation excluding
 those countries, so that distribution is permitted only in or among
-countries not thus excluded.  In such case, this License incorporates
+countries not thus excluded. In such case, this License incorporates
 the limitation as if written in the body of this License.
 
-  9. The Free Software Foundation may publish revised and/or new versions
-of the General Public License from time to time.  Such new versions will
+9. The Free Software Foundation may publish revised and/or new versions
+of the General Public License from time to time. Such new versions will
 be similar in spirit to the present version, but may differ in detail to
 address new problems or concerns.
 
-Each version is given a distinguishing version number.  If the Program
+Each version is given a distinguishing version number. If the Program
 specifies a version number of this License which applies to it and "any
 later version", you have the option of following the terms and conditions
 either of that version or of any later version published by the Free
-Software Foundation.  If the Program does not specify a version number of
+Software Foundation. If the Program does not specify a version number of
 this License, you may choose any version ever published by the Free Software
 Foundation.
 
-  10. If you wish to incorporate parts of the Program into other free
+10. If you wish to incorporate parts of the Program into other free
 programs whose distribution conditions are different, write to the author
-to ask for permission.  For software which is copyrighted by the Free
+to ask for permission. For software which is copyrighted by the Free
 Software Foundation, write to the Free Software Foundation; we sometimes
-make exceptions for this.  Our decision will be guided by the two goals
+make exceptions for this. Our decision will be guided by the two goals
 of preserving the free status of all derivatives of our free software and
 of promoting the sharing and reuse of software generally.
 
-			    NO WARRANTY
+			 NO WARRANTY
 
-  11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
-FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.  EXCEPT WHEN
+11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
+FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
 OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
 PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
 OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
-MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.  THE ENTIRE RISK AS
-TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU.  SHOULD THE
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS
+TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE
 PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
 REPAIR OR CORRECTION.
 
-  12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
 WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
 REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
 INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
@@ -277,35 +277,35 @@
 PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
 POSSIBILITY OF SUCH DAMAGES.
 
-		     END OF TERMS AND CONDITIONS
-
-	    How to Apply These Terms to Your New Programs
+		 END OF TERMS AND CONDITIONS
 
-  If you develop a new program, and you want it to be of the greatest
+	 How to Apply These Terms to Your New Programs
+
+If you develop a new program, and you want it to be of the greatest
 possible use to the public, the best way to achieve this is to make it
 free software which everyone can redistribute and change under these terms.
 
-  To do so, attach the following notices to the program.  It is safest
+To do so, attach the following notices to the program. It is safest
 to attach them to the start of each source file to most effectively
 convey the exclusion of warranty; and each file should have at least
 the "copyright" line and a pointer to where the full notice is found.
 
-    <one line to give the program's name and a brief idea of what it does.>
-    Copyright (C) <year>  <name of author>
+
+Copyright (C) 
 
-    This program is free software; you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation; either version 2 of the License, or
-    (at your option) any later version.
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
 
-    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
-    GNU General Public License for more details.
+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
+GNU General Public License for more details.
 
-    You should have received a copy of the GNU General Public License
-    along with this program; if not, write to the Free Software
-    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
+You should have received a copy of the GNU General Public License
+along with this program; if not, write to the Free Software
+Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 
 Also add information on how to contact you by electronic and paper mail.
@@ -313,30 +313,30 @@
 If the program is interactive, make it output a short notice like this
 when it starts in an interactive mode:
 
-    Gnomovision version 69, Copyright (C) year name of author
-    Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
-    This is free software, and you are welcome to redistribute it
-    under certain conditions; type `show c' for details.
+Gnomovision version 69, Copyright (C) year name of author
+Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+This is free software, and you are welcome to redistribute it
+under certain conditions; type `show c' for details.
 
 The hypothetical commands `show w' and `show c' should show the appropriate
-parts of the General Public License.  Of course, the commands you use may
+parts of the General Public License. Of course, the commands you use may
 be called something other than `show w' and `show c'; they could even be
 mouse-clicks or menu items--whatever suits your program.
 
 You should also get your employer (if you work as a programmer) or your
 school, if any, to sign a "copyright disclaimer" for the program, if
-necessary.  Here is a sample; alter the names:
+necessary. Here is a sample; alter the names:
 
-  Yoyodyne, Inc., hereby disclaims all copyright interest in the program
-  `Gnomovision' (which makes passes at compilers) written by James Hacker.
+Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+`Gnomovision' (which makes passes at compilers) written by James Hacker.
 
-  <signature of Ty Coon>, 1 April 1989
-  Ty Coon, President of Vice
+, 1 April 1989
+Ty Coon, President of Vice
 
 This General Public License does not permit incorporating your program into
-proprietary programs.  If your program is a subroutine library, you may
+proprietary programs. If your program is a subroutine library, you may
 consider it more useful to permit linking proprietary applications with the
-library.  If this is what you want to do, use the GNU Library General
+library. If this is what you want to do, use the GNU Library General
 Public License instead of this License.
 
 ---------------------------------------------------------------------------
@@ -347,24 +347,24 @@
 matching package (library and tools) with support for approximate
 matching.
 
-Copyright (c) 2001-2009 Ville Laurikari <[email protected]>
+Copyright (c) 2001-2009 Ville Laurikari 
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions
 are met:
 
-  1. Redistributions of source code must retain the above copyright
-     notice, this list of conditions and the following disclaimer.
+1. Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
 
-  2. Redistributions in binary form must reproduce the above copyright
-     notice, this list of conditions and the following disclaimer in the
-     documentation and/or other materials provided with the distribution.
+2. Redistributions in binary form must reproduce the above copyright
+notice, this list of conditions and the following disclaimer in the
+documentation and/or other materials provided with the distribution.
 
 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER AND CONTRIBUTORS
 ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
 LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
-A PARTICULAR PURPOSE ARE DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
 HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
 SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
 LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
@@ -378,12 +378,12 @@
 R-3.2.0/src/modules/lapack/LICENSE:
 
 Copyright (c) 1992-2011 The University of Tennessee and The University
-                        of Tennessee Research Foundation.  All rights
-                        reserved.
+of Tennessee Research Foundation. All rights
+reserved.
 Copyright (c) 2000-2011 The University of California Berkeley. All
-                        rights reserved.
-Copyright (c) 2006-2012 The University of Colorado Denver.  All rights
-                        reserved.
+rights reserved.
+Copyright (c) 2006-2012 The University of Colorado Denver. All rights
+reserved.
 
 $COPYRIGHT$
 
@@ -396,20 +396,20 @@
 met:
 
 - Redistributions of source code must retain the above copyright
-  notice, this list of conditions and the following disclaimer.
+notice, this list of conditions and the following disclaimer.
 
 - Redistributions in binary form must reproduce the above copyright
-  notice, this list of conditions and the following disclaimer listed
-  in this license in the documentation and/or other materials
-  provided with the distribution.
+notice, this list of conditions and the following disclaimer listed
+in this license in the documentation and/or other materials
+provided with the distribution.
 
 - Neither the name of the copyright holders nor the names of its
-  contributors may be used to endorse or promote products derived from
-  this software without specific prior written permission.
+contributors may be used to endorse or promote products derived from
+this software without specific prior written permission.
 
 The copyright holders provide no reassurances that the source code
 provided does not infringe any patent, copyright, or any other
-intellectual property rights of third parties.  The copyright holders
+intellectual property rights of third parties. The copyright holders
 disclaim any liability to any recipient for claims brought against
 recipient by any third party for infringement of that parties
 intellectual property rights.
--- a/components/r/r.p5m	Thu Jan 28 16:55:44 2016 -0800
+++ b/components/r/r.p5m	Thu Jan 28 16:57:12 2016 -0800
@@ -18,7 +18,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
 #
 
 <transform file path=usr.*/man/.+ -> default mangler.man.stability volatile>
@@ -34,7 +34,7 @@
     value="org.opensolaris.category.2008:Development/Other Languages"
 set name=info.source-url value=$(COMPONENT_ARCHIVE_URL)
 set name=info.upstream-url value=$(COMPONENT_PROJECT_URL)
-set name=org.opensolaris.arc-caseid value=PSARC/2015/216
+set name=org.opensolaris.arc-caseid value=PSARC/2015/216 value=PSARC/2015/541
 set name=org.opensolaris.consolidation value=$(CONSOLIDATION)
 file usr/bin/$(MACH64)/R path=usr/bin/R
 file usr/bin/$(MACH64)/Rscript path=usr/bin/Rscript
@@ -66,6 +66,7 @@
 file path=usr/lib/$(MACH64)/R/bin/pager
 file path=usr/lib/$(MACH64)/R/bin/rtags
 file path=usr/lib/$(MACH64)/R/doc/AUTHORS
+file path=usr/lib/$(MACH64)/R/doc/BioC_mirrors.csv
 file path=usr/lib/$(MACH64)/R/doc/COPYING
 file path=usr/lib/$(MACH64)/R/doc/COPYRIGHTS
 file path=usr/lib/$(MACH64)/R/doc/CRAN_mirrors.csv
--- a/components/r/test/results-all.master	Thu Jan 28 16:55:44 2016 -0800
+++ b/components/r/test/results-all.master	Thu Jan 28 16:57:12 2016 -0800
@@ -3,7 +3,7 @@
   comparing 'tools-Ex.Rout' to 'tools-Ex.Rout.save' ...
 Testing examples for package 'utils'
 Testing examples for package 'grDevices'
-  comparing 'grDevices-Ex.Rout' to 'grDevices-Ex.Rout.save' ... OK
+  comparing 'grDevices-Ex.Rout' to 'grDevices-Ex.Rout.save' ...
 Testing examples for package 'graphics'
   comparing 'graphics-Ex.Rout' to 'graphics-Ex.Rout.save' ... OK
 Testing examples for package 'stats'
@@ -55,7 +55,7 @@
   comparing 'iec60559.Rout' to '$(SOURCE_DIR)/tests/iec60559.Rout.save' ... OK
 running regression tests ...
 running code in 'reg-tests-1a.R' ... OK
-running code in 'reg-tests-1b.R' ...$(SOURCE_DIR)/tests/Makefile.common:93: recipe for target 'reg-tests-1b.Rout' failed
+running code in 'reg-tests-1b.R' ... OK
 running code in 'reg-tests-1c.R' ... OK
 running code in 'reg-tests-2.R' ... OK
   comparing 'reg-tests-2.Rout' to '$(SOURCE_DIR)/tests/reg-tests-2.Rout.save' ... OK