25164308 Update R to version 3.3.2
authorRich Burridge <rich.burridge@oracle.com>
Mon, 09 Jan 2017 08:54:39 -0800
changeset 7546 93fdabfd72e4
parent 7545 8720646536ee
child 7547 99009c0665cc
25164308 Update R to version 3.3.2
components/r/Makefile
components/r/patches/02-fix-parfait.patch
components/r/r-cran-base.p5m
components/r/r-cran-methods.p5m
components/r/r-cran-mgcv.p5m
components/r/r-cran-nlme.p5m
components/r/r-cran-stats.p5m
components/r/r-cran-survival.p5m
components/r/r-cran-tools.p5m
components/r/r-cran-utils.p5m
components/r/r.p5m
components/r/test/results-all.master
--- a/components/r/Makefile	Thu Jan 05 06:13:08 2017 -0800
+++ b/components/r/Makefile	Mon Jan 09 08:54:39 2017 -0800
@@ -20,20 +20,20 @@
 #
 
 #
-# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2017, Oracle and/or its affiliates. All rights reserved.
 #
 BUILD_BITS= 64
 include ../../make-rules/shared-macros.mk
 
 COMPONENT_NAME=		R
-COMPONENT_VERSION=	3.2.5
+COMPONENT_VERSION=	3.3.2
 COMPONENT_PROJECT_URL=	http://www.r-project.org/
 COMPONENT_ARCHIVE_HASH=	\
-    sha256:60745672dce5ddc201806fa59f6d4e0ba6554d8ed78d0f9f0d79a629978f80b5
+    sha256:d294ad21e9f574fb4828ebb3a94b8cb34f4f304a41687a994be00dd41a4e514c
 COMPONENT_ARCHIVE_URL=	http://cran.mtu.edu/src/base/R-3/$(COMPONENT_ARCHIVE)
 COMPONENT_BUGDB=	utility/r
 
-TPNO=			28040
+TPNO=			32832
 
 # Requires newer version of system/linker from ON, available in S12 but not
 # 11.3, so do not publish.
--- a/components/r/patches/02-fix-parfait.patch	Thu Jan 05 06:13:08 2017 -0800
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-This problem is still present in the latest version of R and has been
-reported upstream:
-
-  https://bugs.r-project.org/bugzilla/show_bug.cgi?id=16512
-
---- R-3.2.0/src/library/stats/src/Makefile.in.orig	2015-08-17 13:40:12.041006229 -0700
-+++ R-3.2.0/src/library/stats/src/Makefile.in	2015-08-17 13:40:42.269423314 -0700
[email protected]@ -12,6 +12,7 @@
- R_HOME = $(top_builddir)
- ## for $(R_HOME)/etc${R_ARCH}/Makeconf
- R_SHARE_DIR = $(R_HOME)/share
-+R_INCLUDE_DIR = $(R_HOME)/include
- 
- SOURCES_C = init.c kmeans.c \
-   ansari.c bandwidths.c chisqsim.c d2x2xk.c fexact.c kendall.c ks.c \
--- a/components/r/r-cran-base.p5m	Thu Jan 05 06:13:08 2017 -0800
+++ b/components/r/r-cran-base.p5m	Mon Jan 09 08:54:39 2017 -0800
@@ -18,7 +18,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2017, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -171,6 +171,7 @@
 file path=usr/lib/$(MACH64)/R/library/base/html/character.html
 file path=usr/lib/$(MACH64)/R/library/base/html/charmatch.html
 file path=usr/lib/$(MACH64)/R/library/base/html/chartr.html
+file path=usr/lib/$(MACH64)/R/library/base/html/chkDots.html
 file path=usr/lib/$(MACH64)/R/library/base/html/chol.html
 file path=usr/lib/$(MACH64)/R/library/base/html/chol2inv.html
 file path=usr/lib/$(MACH64)/R/library/base/html/class.html
@@ -188,7 +189,6 @@
 file path=usr/lib/$(MACH64)/R/library/base/html/crossprod.html
 file path=usr/lib/$(MACH64)/R/library/base/html/cumsum.html
 file path=usr/lib/$(MACH64)/R/library/base/html/curlGetHeaders.html
-file path=usr/lib/$(MACH64)/R/library/base/html/curlVersion.html
 file path=usr/lib/$(MACH64)/R/library/base/html/cut.POSIXt.html
 file path=usr/lib/$(MACH64)/R/library/base/html/cut.html
 file path=usr/lib/$(MACH64)/R/library/base/html/data.class.html
@@ -261,6 +261,7 @@
 file path=usr/lib/$(MACH64)/R/library/base/html/grep.html
 file path=usr/lib/$(MACH64)/R/library/base/html/grepRaw.html
 file path=usr/lib/$(MACH64)/R/library/base/html/groupGeneric.html
+file path=usr/lib/$(MACH64)/R/library/base/html/grouping.html
 file path=usr/lib/$(MACH64)/R/library/base/html/gzcon.html
 file path=usr/lib/$(MACH64)/R/library/base/html/hexmode.html
 file path=usr/lib/$(MACH64)/R/library/base/html/iconv.html
@@ -293,6 +294,7 @@
 file path=usr/lib/$(MACH64)/R/library/base/html/lengths.html
 file path=usr/lib/$(MACH64)/R/library/base/html/levels.html
 file path=usr/lib/$(MACH64)/R/library/base/html/libPaths.html
+file path=usr/lib/$(MACH64)/R/library/base/html/libcurlVersion.html
 file path=usr/lib/$(MACH64)/R/library/base/html/library.dynam.html
 file path=usr/lib/$(MACH64)/R/library/base/html/library.html
 file path=usr/lib/$(MACH64)/R/library/base/html/license.html
@@ -417,9 +419,11 @@
 file path=usr/lib/$(MACH64)/R/library/base/html/sprintf.html
 file path=usr/lib/$(MACH64)/R/library/base/html/srcfile.html
 file path=usr/lib/$(MACH64)/R/library/base/html/standardGeneric.html
+file path=usr/lib/$(MACH64)/R/library/base/html/startsWith.html
 file path=usr/lib/$(MACH64)/R/library/base/html/stop.html
 file path=usr/lib/$(MACH64)/R/library/base/html/stopifnot.html
 file path=usr/lib/$(MACH64)/R/library/base/html/strptime.html
+file path=usr/lib/$(MACH64)/R/library/base/html/strrep.html
 file path=usr/lib/$(MACH64)/R/library/base/html/strsplit.html
 file path=usr/lib/$(MACH64)/R/library/base/html/strtoi.html
 file path=usr/lib/$(MACH64)/R/library/base/html/strtrim.html
@@ -464,6 +468,7 @@
 file path=usr/lib/$(MACH64)/R/library/base/html/unname.html
 file path=usr/lib/$(MACH64)/R/library/base/html/userhooks.html
 file path=usr/lib/$(MACH64)/R/library/base/html/utf8Conversion.html
+file path=usr/lib/$(MACH64)/R/library/base/html/validUTF8.html
 file path=usr/lib/$(MACH64)/R/library/base/html/vector.html
 file path=usr/lib/$(MACH64)/R/library/base/html/warning.html
 file path=usr/lib/$(MACH64)/R/library/base/html/warnings.html
--- a/components/r/r-cran-methods.p5m	Thu Jan 05 06:13:08 2017 -0800
+++ b/components/r/r-cran-methods.p5m	Mon Jan 09 08:54:39 2017 -0800
@@ -17,7 +17,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2017, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -53,10 +53,12 @@
 file path=usr/lib/$(MACH64)/R/library/methods/html/00Index.html
 file path=usr/lib/$(MACH64)/R/library/methods/html/BasicClasses.html
 file path=usr/lib/$(MACH64)/R/library/methods/html/Classes.html
+file path=usr/lib/$(MACH64)/R/library/methods/html/Classes_Details.html
 file path=usr/lib/$(MACH64)/R/library/methods/html/Documentation.html
 file path=usr/lib/$(MACH64)/R/library/methods/html/EmptyMethodsList-class.html
 file path=usr/lib/$(MACH64)/R/library/methods/html/EnvironmentClass.html
 file path=usr/lib/$(MACH64)/R/library/methods/html/GenericFunctions.html
+file path=usr/lib/$(MACH64)/R/library/methods/html/Introduction.html
 file path=usr/lib/$(MACH64)/R/library/methods/html/LanguageClasses.html
 file path=usr/lib/$(MACH64)/R/library/methods/html/LinearMethodsList-class.html
 file path=usr/lib/$(MACH64)/R/library/methods/html/MethodDefinition-class.html
@@ -65,6 +67,9 @@
 file path=usr/lib/$(MACH64)/R/library/methods/html/Methods.html
 file path=usr/lib/$(MACH64)/R/library/methods/html/MethodsList-class.html
 file path=usr/lib/$(MACH64)/R/library/methods/html/MethodsList.html
+file path=usr/lib/$(MACH64)/R/library/methods/html/Methods_Details.html
+file path=usr/lib/$(MACH64)/R/library/methods/html/Methods_for_Nongenerics.html
+file path=usr/lib/$(MACH64)/R/library/methods/html/Methods_for_S3.html
 file path=usr/lib/$(MACH64)/R/library/methods/html/NextMethod.html
 file path=usr/lib/$(MACH64)/R/library/methods/html/ObjectsWithPackage-class.html
 file path=usr/lib/$(MACH64)/R/library/methods/html/R.css
@@ -109,11 +114,15 @@
 file path=usr/lib/$(MACH64)/R/library/methods/html/promptClass.html
 file path=usr/lib/$(MACH64)/R/library/methods/html/promptMethods.html
 file path=usr/lib/$(MACH64)/R/library/methods/html/refClass.html
+file path=usr/lib/$(MACH64)/R/library/methods/html/removeMethod.html
 file path=usr/lib/$(MACH64)/R/library/methods/html/representation.html
 file path=usr/lib/$(MACH64)/R/library/methods/html/selectSuperClasses.html
+file path=usr/lib/$(MACH64)/R/library/methods/html/setAs.html
 file path=usr/lib/$(MACH64)/R/library/methods/html/setClass.html
 file path=usr/lib/$(MACH64)/R/library/methods/html/setClassUnion.html
 file path=usr/lib/$(MACH64)/R/library/methods/html/setGeneric.html
+file path=usr/lib/$(MACH64)/R/library/methods/html/setGroupGeneric.html
+file path=usr/lib/$(MACH64)/R/library/methods/html/setIs.html
 file path=usr/lib/$(MACH64)/R/library/methods/html/setLoadActions.html
 file path=usr/lib/$(MACH64)/R/library/methods/html/setMethod.html
 file path=usr/lib/$(MACH64)/R/library/methods/html/setOldClass.html
--- a/components/r/r-cran-mgcv.p5m	Thu Jan 05 06:13:08 2017 -0800
+++ b/components/r/r-cran-mgcv.p5m	Mon Jan 09 08:54:39 2017 -0800
@@ -18,7 +18,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2017, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -74,6 +74,7 @@
 file path=usr/lib/$(MACH64)/R/library/mgcv/html/columb.html
 file path=usr/lib/$(MACH64)/R/library/mgcv/html/concurvity.html
 file path=usr/lib/$(MACH64)/R/library/mgcv/html/coxph.html
+file path=usr/lib/$(MACH64)/R/library/mgcv/html/coxpht.html
 file path=usr/lib/$(MACH64)/R/library/mgcv/html/exclude.too.far.html
 file path=usr/lib/$(MACH64)/R/library/mgcv/html/extract.lme.cov.html
 file path=usr/lib/$(MACH64)/R/library/mgcv/html/family.mgcv.html
@@ -101,6 +102,8 @@
 file path=usr/lib/$(MACH64)/R/library/mgcv/html/gamm.html
 file path=usr/lib/$(MACH64)/R/library/mgcv/html/gaulss.html
 file path=usr/lib/$(MACH64)/R/library/mgcv/html/get.var.html
+file path=usr/lib/$(MACH64)/R/library/mgcv/html/gevlss.html
+file path=usr/lib/$(MACH64)/R/library/mgcv/html/identifiability.html
 file path=usr/lib/$(MACH64)/R/library/mgcv/html/in.out.html
 file path=usr/lib/$(MACH64)/R/library/mgcv/html/inSide.html
 file path=usr/lib/$(MACH64)/R/library/mgcv/html/influence.gam.html
@@ -128,6 +131,7 @@
 file path=usr/lib/$(MACH64)/R/library/mgcv/html/notExp2.html
 file path=usr/lib/$(MACH64)/R/library/mgcv/html/null.space.dimension.html
 file path=usr/lib/$(MACH64)/R/library/mgcv/html/ocat.html
+file path=usr/lib/$(MACH64)/R/library/mgcv/html/one.se.rule.html
 file path=usr/lib/$(MACH64)/R/library/mgcv/html/pcls.html
 file path=usr/lib/$(MACH64)/R/library/mgcv/html/pdIdnot.html
 file path=usr/lib/$(MACH64)/R/library/mgcv/html/pdTens.html
@@ -165,6 +169,7 @@
 file path=usr/lib/$(MACH64)/R/library/mgcv/html/smooth.construct.tensor.smooth.spec.html
 file path=usr/lib/$(MACH64)/R/library/mgcv/html/smooth.construct.tp.smooth.spec.html
 file path=usr/lib/$(MACH64)/R/library/mgcv/html/smooth.terms.html
+file path=usr/lib/$(MACH64)/R/library/mgcv/html/smooth2random.html
 file path=usr/lib/$(MACH64)/R/library/mgcv/html/smoothCon.html
 file path=usr/lib/$(MACH64)/R/library/mgcv/html/sp.vcov.html
 file path=usr/lib/$(MACH64)/R/library/mgcv/html/spasm.construct.html
--- a/components/r/r-cran-nlme.p5m	Thu Jan 05 06:13:08 2017 -0800
+++ b/components/r/r-cran-nlme.p5m	Mon Jan 09 08:54:39 2017 -0800
@@ -18,7 +18,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2017, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -38,6 +38,7 @@
 file path=usr/lib/$(MACH64)/R/library/nlme/CITATION
 file path=usr/lib/$(MACH64)/R/library/nlme/DESCRIPTION
 file path=usr/lib/$(MACH64)/R/library/nlme/INDEX
+file path=usr/lib/$(MACH64)/R/library/nlme/LICENCE
 file path=usr/lib/$(MACH64)/R/library/nlme/Meta/Rd.rds
 file path=usr/lib/$(MACH64)/R/library/nlme/Meta/data.rds
 file path=usr/lib/$(MACH64)/R/library/nlme/Meta/hsearch.rds
@@ -364,6 +365,7 @@
 file path=usr/lib/$(MACH64)/R/library/nlme/scripts/ch05.R
 file path=usr/lib/$(MACH64)/R/library/nlme/scripts/ch06.R
 file path=usr/lib/$(MACH64)/R/library/nlme/scripts/ch08.R
+file path=usr/lib/$(MACH64)/R/library/nlme/scripts/runme.R
 file path=usr/lib/$(MACH64)/R/library/nlme/scripts/sims.rda
 license COPYING license=GPLv2
 depend type=require fmri=pkg:/runtime/r
--- a/components/r/r-cran-stats.p5m	Thu Jan 05 06:13:08 2017 -0800
+++ b/components/r/r-cran-stats.p5m	Mon Jan 09 08:54:39 2017 -0800
@@ -18,7 +18,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2017, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -313,6 +313,7 @@
 file path=usr/lib/$(MACH64)/R/library/stats/html/selfStart.html
 file path=usr/lib/$(MACH64)/R/library/stats/html/setNames.html
 file path=usr/lib/$(MACH64)/R/library/stats/html/shapiro.test.html
+file path=usr/lib/$(MACH64)/R/library/stats/html/sigma.html
 file path=usr/lib/$(MACH64)/R/library/stats/html/simulate.html
 file path=usr/lib/$(MACH64)/R/library/stats/html/smooth.html
 file path=usr/lib/$(MACH64)/R/library/stats/html/smooth.spline.html
--- a/components/r/r-cran-survival.p5m	Thu Jan 05 06:13:08 2017 -0800
+++ b/components/r/r-cran-survival.p5m	Mon Jan 09 08:54:39 2017 -0800
@@ -17,7 +17,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2017, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -48,7 +48,6 @@
 file path=usr/lib/$(MACH64)/R/library/survival/Meta/vignette.rds
 file path=usr/lib/$(MACH64)/R/library/survival/NAMESPACE
 file path=usr/lib/$(MACH64)/R/library/survival/NEWS.Rd
-file path=usr/lib/$(MACH64)/R/library/survival/NEWS.Rd.orig
 file path=usr/lib/$(MACH64)/R/library/survival/R/survival
 file path=usr/lib/$(MACH64)/R/library/survival/R/survival.rdb
 file path=usr/lib/$(MACH64)/R/library/survival/R/survival.rdx
@@ -72,6 +71,8 @@
 file path=usr/lib/$(MACH64)/R/library/survival/doc/timedep.R
 file path=usr/lib/$(MACH64)/R/library/survival/doc/timedep.Rnw
 file path=usr/lib/$(MACH64)/R/library/survival/doc/timedep.pdf
+file path=usr/lib/$(MACH64)/R/library/survival/doc/validate.R
+file path=usr/lib/$(MACH64)/R/library/survival/doc/validate.Rnw
 file path=usr/lib/$(MACH64)/R/library/survival/doc/validate.pdf
 file path=usr/lib/$(MACH64)/R/library/survival/help/AnIndex
 file path=usr/lib/$(MACH64)/R/library/survival/help/aliases.rds
@@ -101,8 +102,10 @@
 file path=usr/lib/$(MACH64)/R/library/survival/html/coxph.object.html
 file path=usr/lib/$(MACH64)/R/library/survival/html/coxph.wtest.html
 file path=usr/lib/$(MACH64)/R/library/survival/html/dsurvreg.html
+file path=usr/lib/$(MACH64)/R/library/survival/html/finegray.html
 file path=usr/lib/$(MACH64)/R/library/survival/html/flchain.html
 file path=usr/lib/$(MACH64)/R/library/survival/html/frailty.html
+file path=usr/lib/$(MACH64)/R/library/survival/html/genfan.html
 file path=usr/lib/$(MACH64)/R/library/survival/html/heart.html
 file path=usr/lib/$(MACH64)/R/library/survival/html/is.ratetable.html
 file path=usr/lib/$(MACH64)/R/library/survival/html/kidney.html
@@ -138,6 +141,7 @@
 file path=usr/lib/$(MACH64)/R/library/survival/html/rats2.html
 file path=usr/lib/$(MACH64)/R/library/survival/html/residuals.coxph.html
 file path=usr/lib/$(MACH64)/R/library/survival/html/residuals.survreg.html
+file path=usr/lib/$(MACH64)/R/library/survival/html/retinopathy.html
 file path=usr/lib/$(MACH64)/R/library/survival/html/ridge.html
 file path=usr/lib/$(MACH64)/R/library/survival/html/stanford2.html
 file path=usr/lib/$(MACH64)/R/library/survival/html/strata.html
@@ -150,10 +154,12 @@
 file path=usr/lib/$(MACH64)/R/library/survival/html/survdiff.html
 file path=usr/lib/$(MACH64)/R/library/survival/html/survexp.fit.html
 file path=usr/lib/$(MACH64)/R/library/survival/html/survexp.html
+file path=usr/lib/$(MACH64)/R/library/survival/html/survexp.object.html
 file path=usr/lib/$(MACH64)/R/library/survival/html/survexp.us.html
 file path=usr/lib/$(MACH64)/R/library/survival/html/survfit.coxph.html
 file path=usr/lib/$(MACH64)/R/library/survival/html/survfit.formula.html
 file path=usr/lib/$(MACH64)/R/library/survival/html/survfit.html
+file path=usr/lib/$(MACH64)/R/library/survival/html/survfit.matrix.html
 file path=usr/lib/$(MACH64)/R/library/survival/html/survfit.object.html
 file path=usr/lib/$(MACH64)/R/library/survival/html/survfitcoxph.fit.html
 file path=usr/lib/$(MACH64)/R/library/survival/html/survival-internal.html
--- a/components/r/r-cran-tools.p5m	Thu Jan 05 06:13:08 2017 -0800
+++ b/components/r/r-cran-tools.p5m	Mon Jan 09 08:54:39 2017 -0800
@@ -18,7 +18,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2017, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -58,6 +58,7 @@
 file path=usr/lib/$(MACH64)/R/library/tools/html/HTMLlinks.html
 file path=usr/lib/$(MACH64)/R/library/tools/html/QC.html
 file path=usr/lib/$(MACH64)/R/library/tools/html/R.css
+file path=usr/lib/$(MACH64)/R/library/tools/html/Rcmd.html
 file path=usr/lib/$(MACH64)/R/library/tools/html/Rd2HTML.html
 file path=usr/lib/$(MACH64)/R/library/tools/html/Rd2txt_options.html
 file path=usr/lib/$(MACH64)/R/library/tools/html/RdTextFilter.html
@@ -92,6 +93,7 @@
 file path=usr/lib/$(MACH64)/R/library/tools/html/loadRdMacros.html
 file path=usr/lib/$(MACH64)/R/library/tools/html/makeLazyLoading.html
 file path=usr/lib/$(MACH64)/R/library/tools/html/make_translations_pkg.html
+file path=usr/lib/$(MACH64)/R/library/tools/html/makevars.html
 file path=usr/lib/$(MACH64)/R/library/tools/html/md5sum.html
 file path=usr/lib/$(MACH64)/R/library/tools/html/package.dependencies.html
 file path=usr/lib/$(MACH64)/R/library/tools/html/package_dependencies.html
--- a/components/r/r-cran-utils.p5m	Thu Jan 05 06:13:08 2017 -0800
+++ b/components/r/r-cran-utils.p5m	Mon Jan 09 08:54:39 2017 -0800
@@ -18,7 +18,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2017, Oracle and/or its affiliates. All rights reserved.
 #
 
 set name=pkg.fmri \
@@ -42,6 +42,8 @@
 file path=usr/lib/$(MACH64)/R/library/utils/Meta/nsInfo.rds
 file path=usr/lib/$(MACH64)/R/library/utils/Meta/package.rds
 file path=usr/lib/$(MACH64)/R/library/utils/NAMESPACE
+file path=usr/lib/$(MACH64)/R/library/utils/R/sysdata.rdb
+file path=usr/lib/$(MACH64)/R/library/utils/R/sysdata.rdx
 file path=usr/lib/$(MACH64)/R/library/utils/R/utils
 file path=usr/lib/$(MACH64)/R/library/utils/R/utils.rdb
 file path=usr/lib/$(MACH64)/R/library/utils/R/utils.rdx
@@ -130,6 +132,7 @@
 file path=usr/lib/$(MACH64)/R/library/utils/html/hsearch-utils.html
 file path=usr/lib/$(MACH64)/R/library/utils/html/install.packages.html
 file path=usr/lib/$(MACH64)/R/library/utils/html/installed.packages.html
+file path=usr/lib/$(MACH64)/R/library/utils/html/isS3method.html
 file path=usr/lib/$(MACH64)/R/library/utils/html/localeToCharset.html
 file path=usr/lib/$(MACH64)/R/library/utils/html/ls_str.html
 file path=usr/lib/$(MACH64)/R/library/utils/html/maintainer.html
--- a/components/r/r.p5m	Thu Jan 05 06:13:08 2017 -0800
+++ b/components/r/r.p5m	Mon Jan 09 08:54:39 2017 -0800
@@ -18,7 +18,7 @@
 #
 # CDDL HEADER END
 #
-# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2015, 2017, Oracle and/or its affiliates. All rights reserved.
 #
 
 <transform file path=usr.*/man/.+ -> default mangler.man.stability volatile>
@@ -84,6 +84,8 @@
 file path=usr/lib/$(MACH64)/R/doc/html/NEWS.2.html
 file path=usr/lib/$(MACH64)/R/doc/html/NEWS.html
 file path=usr/lib/$(MACH64)/R/doc/html/R.css
+file path=usr/lib/$(MACH64)/R/doc/html/Rlogo.pdf
+file path=usr/lib/$(MACH64)/R/doc/html/Rlogo.svg
 file path=usr/lib/$(MACH64)/R/doc/html/Search.html
 file path=usr/lib/$(MACH64)/R/doc/html/SearchOn.html
 file path=usr/lib/$(MACH64)/R/doc/html/about.html
@@ -91,7 +93,6 @@
 file path=usr/lib/$(MACH64)/R/doc/html/index.html
 file path=usr/lib/$(MACH64)/R/doc/html/left.jpg
 file path=usr/lib/$(MACH64)/R/doc/html/logo.jpg
-file path=usr/lib/$(MACH64)/R/doc/html/logosm.jpg
 file path=usr/lib/$(MACH64)/R/doc/html/packages-head-utf8.html
 file path=usr/lib/$(MACH64)/R/doc/html/packages.html
 file path=usr/lib/$(MACH64)/R/doc/html/resources.html
--- a/components/r/test/results-all.master	Thu Jan 05 06:13:08 2017 -0800
+++ b/components/r/test/results-all.master	Mon Jan 09 08:54:39 2017 -0800
@@ -1,7 +1,9 @@
 Testing examples for package 'base'
+  comparing 'base-Ex.Rout' to 'base-Ex.Rout.prev' ...
 Testing examples for package 'tools'
   comparing 'tools-Ex.Rout' to 'tools-Ex.Rout.save' ...
 Testing examples for package 'utils'
+  comparing 'utils-Ex.Rout' to 'utils-Ex.Rout.prev' ... OK
 Testing examples for package 'grDevices'
   comparing 'grDevices-Ex.Rout' to 'grDevices-Ex.Rout.save' ... OK
 Testing examples for package 'graphics'
@@ -11,6 +13,7 @@
 Testing examples for package 'datasets'
   comparing 'datasets-Ex.Rout' to 'datasets-Ex.Rout.save' ... OK
 Testing examples for package 'methods'
+  comparing 'methods-Ex.Rout' to 'methods-Ex.Rout.prev' ... OK
 Testing examples for package 'grid'
   comparing 'grid-Ex.Rout' to 'grid-Ex.Rout.save' ... OK
 Testing examples for package 'splines'
@@ -18,8 +21,11 @@
 Testing examples for package 'stats4'
   comparing 'stats4-Ex.Rout' to 'stats4-Ex.Rout.save' ... OK
 Testing examples for package 'tcltk'
+  comparing 'tcltk-Ex.Rout' to 'tcltk-Ex.Rout.prev' ... OK
 Testing examples for package 'compiler'
+  comparing 'compiler-Ex.Rout' to 'compiler-Ex.Rout.prev' ... OK
 Testing examples for package 'parallel'
+  comparing 'parallel-Ex.Rout' to 'parallel-Ex.Rout.prev' ...
 running strict specific tests
 running code in 'eval-etc.R' ... OK
   comparing 'eval-etc.Rout' to '$(SOURCE_DIR)/tests/eval-etc.Rout.save' ... OK
@@ -35,8 +41,6 @@
   comparing 'ok-errors.Rout' to '$(SOURCE_DIR)/tests/ok-errors.Rout.save' ... OK
 running code in 'method-dispatch.R' ... OK
   comparing 'method-dispatch.Rout' to '$(SOURCE_DIR)/tests/method-dispatch.Rout.save' ... OK
-running code in 'array-subset.R' ... OK
-  comparing 'array-subset.Rout' to '$(SOURCE_DIR)/tests/array-subset.Rout.save' ... OK
 running code in 'any-all.R' ... OK
   comparing 'any-all.Rout' to '$(SOURCE_DIR)/tests/any-all.Rout.save' ... OK
 running code in 'd-p-q-r-tests.R' ... OK
@@ -54,15 +58,17 @@
 running code in 'iec60559.R' ... OK
   comparing 'iec60559.Rout' to '$(SOURCE_DIR)/tests/iec60559.Rout.save' ... OK
 running regression tests ...
+running code in 'array-subset.R' ... OK
 running code in 'reg-tests-1a.R' ... OK
 running code in 'reg-tests-1b.R' ... OK
-running code in 'reg-tests-1c.R' ... OK
+running code in 'reg-tests-1c.R' ...make[4]: [$(SOURCE_DIR)/tests/Makefile.common:96: reg-tests-1c.Rout] Error 1 (ignored)
 running code in 'reg-tests-2.R' ... OK
   comparing 'reg-tests-2.Rout' to '$(SOURCE_DIR)/tests/reg-tests-2.Rout.save' ... OK
 running code in 'reg-examples1.R' ... OK
 running code in 'reg-examples2.R' ... OK
 running code in 'reg-packages.R' ... OK
 running code in 'p-qbeta-strict-tst.R' ... OK
+running code in 'r-strict-tst.R' ... OK
 running code in 'reg-IO.R' ... OK
   comparing 'reg-IO.Rout' to '$(SOURCE_DIR)/tests/reg-IO.Rout.save' ... OK
 running code in 'reg-IO2.R' ... OK
@@ -71,6 +77,7 @@
   comparing 'reg-plot.pdf' to '$(SOURCE_DIR)/tests/reg-plot.pdf.save' ... OK
 running code in 'reg-S4.R' ... OK
   comparing 'reg-S4.Rout' to '$(SOURCE_DIR)/tests/reg-S4.Rout.save' ... OK
+running code in 'reg-S4-examples.R' ... OK
 running code in 'reg-BLAS.R' ... OK
 running code in 'reg-tests-3.R' ... OK
   comparing 'reg-tests-3.Rout' to '$(SOURCE_DIR)/tests/reg-tests-3.Rout.save' ... OK
@@ -80,5 +87,5 @@
   comparing 'reg-plot-latin1.pdf' to '$(SOURCE_DIR)/tests/reg-plot-latin1.pdf.save' ...261c261
 running tests of Internet functions
   expect some differences
-running code in 'internet.R' ...$(SOURCE_DIR)/tests/Makefile.common:93: recipe for target 'internet.Rout' failed
-  comparing 'internet.Rout' to '$(SOURCE_DIR)/tests/internet.Rout.save' ...17c17
+running code in 'internet.R' ...make[4]: [$(SOURCE_DIR)/tests/Makefile.common:96: internet.Rout] Error 1 (ignored)
+  comparing 'internet.Rout' to '$(SOURCE_DIR)/tests/internet.Rout.save' ...11c11