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File R-release.diff of Package R (Revision d613382281cea75d1e66081faa7a36db)

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# cd *inside* the ...../R-3.2.3/  directory, and do
#      zcat ..../R-release.diff.gz | patch -p1 -E
# ---------                          =====
# You need a "g[un]zip capable zcat", and canNOT use Solaris "patch"!
# Rather get ("gzip" and)  "diffutils" from any GNU mirror.
#
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/ChangeLog R-patched/ChangeLog
--- R-release-orig/ChangeLog	2010-03-17 15:43:02.000000000 +0100
+++ R-patched/ChangeLog	2016-01-30 02:41:11.517944000 +0100
@@ -0,0 +1,8 @@
+	* News are in
+	  - the source    doc/NEWS.Rd
+	  - installed R's doc/NEWS and doc/NEWS.pdf
+
+	* Details about single subversion (svn) commits are available, e.g., by
+
+	svn log https://svn.r-project.org/R/trunk
+
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/SVN-REVISION R-patched/SVN-REVISION
--- R-release-orig/SVN-REVISION	2015-12-10 09:01:26.000000000 +0100
+++ R-patched/SVN-REVISION	2016-02-11 02:43:55.286518000 +0100
@@ -1,2 +1,2 @@
-Revision: 69752
-Last Changed Date: 2015-12-10
+Revision: 70149
+Last Changed Date: 2016-02-10
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/VERSION R-patched/VERSION
--- R-release-orig/VERSION	2015-12-10 09:00:04.000000000 +0100
+++ R-patched/VERSION	2015-12-10 17:45:09.849728000 +0100
@@ -1 +1 @@
-3.2.3
+3.2.3 Patched
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/configure R-patched/configure
--- R-release-orig/configure	2015-12-03 00:16:46.000000000 +0100
+++ R-patched/configure	2016-02-06 02:41:09.562652063 +0100
@@ -3778,7 +3778,7 @@
 case "${host_os}" in
    ## Darwin 1.3.1 was OS X 10.0, 1.4.1 was 10.1, 5 is 10.2 etc
    ## with 13 being 10.9.  We no longer support < 10.4 (Tiger)
-   ## http://en.wikipedia.org/wiki/Darwin_OS
+   ## https://en.wikipedia.org/wiki/Darwin_OS
    darwin1.*)
      as_fn_error $? "The earliest supported OS X is 10.4.
      ;;
@@ -20520,6 +20520,8 @@
     ## changes DYLD_LIBRARY_PATH), because they override the system
     ## look-up sequence. Such automatic override has proven to break things
     ## like system frameworks (e.g. ImageIO or OpenGL framework).
+    ## Not so bad in later versions of Darwin,
+    ## where DYLD_FALLBACK_LIBRARY_PATH is used (see below).
     ;;
   *)
     for arg in ${LDFLAGS}; do
@@ -20541,8 +20543,9 @@
 
 ## Record name of environment variable which tells the dynamic linker
 ## where to find shlibs (typically, 'LD_LIBRARY_PATH').
-## Used in etc/ldpaths: override what libtool thinks on OS X
+## Used in etc/ldpaths: As from R 3.0.0 override what libtool thinks on OS X
 ## http://hublog.hubmed.org/archives/001192.html suggests this was in 10.4
+## However, as from 10.11 this variable is not passed down to shells.
 case "${host_os}" in
   darwin*)
     Rshlibpath_var=DYLD_FALLBACK_LIBRARY_PATH
@@ -20811,7 +20814,7 @@
 fi
 
     ## SI says we want '-lcc_dynamic' on Darwin, although currently
-    ## http://developer.apple.com/documentation/MacOSX/ has nothing
+    ## https://developer.apple.com/documentation/MacOSX/ has nothing
     ## official.  Bill Northcott <w.northcott@unsw.edu.au> points out
     ## that it is only needed for GCC 3.x (and earlier) ...
     if test "${GCC}" = yes; then
@@ -23296,7 +23299,7 @@
 # flags.
 r_save_CFLAGS=$CFLAGS
 CFLAGS="$CFLAGS $r_verb"
-(eval echo $as_me:23299: \"$ac_link\") >&5
+(eval echo $as_me:23302: \"$ac_link\") >&5
 r_c_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'`
 echo "$r_c_v_output" >&5
 CFLAGS=$r_save_CFLAGS
@@ -23371,7 +23374,7 @@
 # flags.
 r_save_CFLAGS=$CFLAGS
 CFLAGS="$CFLAGS $r_cv_prog_c_v"
-(eval echo $as_me:23374: \"$ac_link\") >&5
+(eval echo $as_me:23377: \"$ac_link\") >&5
 r_c_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'`
 echo "$r_c_v_output" >&5
 CFLAGS=$r_save_CFLAGS
@@ -27384,7 +27387,7 @@
 ## FreeBSD 7.3 lacks nearbyintl/rintl (nearbyint appeared in 5.2)
 ## Apparently rint was once broken on HP-UX: undefine HAVE_RINT for such platforms
 ## Cygwin and FreeBSD lacked powl (FreeBSD 10 seems to have it).
-## Cygwin has rintl but not nearbyintl
+## Cygwin had rintl but not nearbyintl
 for ac_func in expm1 hypot log1p log1pl log2 log10 nearbyint nearbyintl powl rint rintl
 do
 as_ac_Symbol=`$as_echo "ac_cv_have_decl_$ac_func" | $as_tr_sh`
@@ -27569,7 +27572,7 @@
 fi
 
 
-## Functions from draft C11 extensions, some of which are already in glibc
+## Functions from ISO/IEC TS 18661-4:2015 C11 extensions.
 ## For now, do not define _GNU_SOURCE here.
 ## All but pown have long been in libsunmath
 for ac_func in atanpi atan2pi cospi exp10 pown sinpi tanpi
@@ -27580,7 +27583,7 @@
   cat >>confdefs.h <<_ACEOF
 #define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1
 _ACEOF
- #define __STDC_WANT_IEC_60559_TYPES_EXT__ 1
+ #define __STDC_WANT_IEC_60559_FUNCS_EXT__ 1
 #include <math.h>
 #ifdef HAVE_SUNMATH_H
 #include <sunmath.h>
@@ -33562,6 +33565,7 @@
   $as_echo_n "(cached) " >&6
 else
   if test "${ac_cv_header_netdb_h}" = yes \
+     && test "${ac_cv_header_arpa_inet_h}" = yes \
      && test "${ac_cv_header_netinet_in_h}" = yes \
      && test "${ac_cv_header_sys_socket_h}" = yes \
      && test "${ac_cv_search_connect}" != no \
@@ -35499,9 +35503,11 @@
 
 #include "confdefs.h"
 #include <stdlib.h>
+/* This might get optimized out if not used */
 extern void * __libc_stack_end;
 
 int main () {
+    if(!__libc_stack_end) exit(1);
     exit(0);
 }
 
@@ -36659,11 +36665,11 @@
    -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:36662: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:36668: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>conftest.err)
    ac_status=$?
    cat conftest.err >&5
-   echo "$as_me:36666: \$? = $ac_status" >&5
+   echo "$as_me:36672: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s "$ac_outfile"; then
      # The compiler can only warn and ignore the option if not recognized
      # So say no if there are warnings other than the usual output.
@@ -36758,11 +36764,11 @@
    -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:36761: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:36767: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>out/conftest.err)
    ac_status=$?
    cat out/conftest.err >&5
-   echo "$as_me:36765: \$? = $ac_status" >&5
+   echo "$as_me:36771: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s out/conftest2.$ac_objext
    then
      # The compiler can only warn and ignore the option if not recognized
@@ -36810,11 +36816,11 @@
    -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:36813: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:36819: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>out/conftest.err)
    ac_status=$?
    cat out/conftest.err >&5
-   echo "$as_me:36817: \$? = $ac_status" >&5
+   echo "$as_me:36823: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s out/conftest2.$ac_objext
    then
      # The compiler can only warn and ignore the option if not recognized
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/configure.ac R-patched/configure.ac
--- R-release-orig/configure.ac	2015-09-09 00:15:17.000000000 +0200
+++ R-patched/configure.ac	2016-02-05 07:45:10.470187000 +0100
@@ -2,7 +2,7 @@
 ###
 ### Process this file with autoconf to produce a configure script.
 ###
-### Copyright (C) 1998-2015 R Core Team
+### Copyright (C) 1998-2016 R Core Team
 ###
 ### This file is part of R.
 ###
@@ -18,7 +18,7 @@
 ###
 ### You should have received a copy of the GNU General Public License
 ### along with R; if not, a copy is available at
-### http://www.r-project.org/Licenses/
+### https://www.r-project.org/Licenses/
 
 AC_PREREQ(2.62)
 
@@ -77,7 +77,7 @@
 case "${host_os}" in
    ## Darwin 1.3.1 was OS X 10.0, 1.4.1 was 10.1, 5 is 10.2 etc
    ## with 13 being 10.9.  We no longer support < 10.4 (Tiger)
-   ## http://en.wikipedia.org/wiki/Darwin_OS
+   ## https://en.wikipedia.org/wiki/Darwin_OS
    darwin1.*)
      AC_MSG_ERROR([The earliest supported OS X is 10.4.]
      ;; 
@@ -695,6 +695,8 @@
     ## changes DYLD_LIBRARY_PATH), because they override the system
     ## look-up sequence. Such automatic override has proven to break things
     ## like system frameworks (e.g. ImageIO or OpenGL framework).
+    ## Not so bad in later versions of Darwin, 
+    ## where DYLD_FALLBACK_LIBRARY_PATH is used (see below).
     ;;
   *)
     for arg in ${LDFLAGS}; do
@@ -710,8 +712,9 @@
 
 ## Record name of environment variable which tells the dynamic linker
 ## where to find shlibs (typically, 'LD_LIBRARY_PATH').
-## Used in etc/ldpaths: override what libtool thinks on OS X
+## Used in etc/ldpaths: As from R 3.0.0 override what libtool thinks on OS X
 ## http://hublog.hubmed.org/archives/001192.html suggests this was in 10.4
+## However, as from 10.11 this variable is not passed down to shells.
 case "${host_os}" in
   darwin*)
     Rshlibpath_var=DYLD_FALLBACK_LIBRARY_PATH
@@ -748,7 +751,7 @@
     ## OS X <= 10.2 dlcompat, >= 10.3 included dlcompat in libSystem
     AC_SEARCH_LIBS(dlopen, dl,,[AC_MSG_ERROR([Your OS X is too old.])])
     ## SI says we want '-lcc_dynamic' on Darwin, although currently
-    ## http://developer.apple.com/documentation/MacOSX/ has nothing
+    ## https://developer.apple.com/documentation/MacOSX/ has nothing
     ## official.  Bill Northcott <w.northcott@unsw.edu.au> points out
     ## that it is only needed for GCC 3.x (and earlier) ...
     if test "${GCC}" = yes; then
@@ -1873,7 +1876,7 @@
 ## FreeBSD 7.3 lacks nearbyintl/rintl (nearbyint appeared in 5.2)
 ## Apparently rint was once broken on HP-UX: undefine HAVE_RINT for such platforms
 ## Cygwin and FreeBSD lacked powl (FreeBSD 10 seems to have it).
-## Cygwin has rintl but not nearbyintl
+## Cygwin had rintl but not nearbyintl
 R_CHECK_FUNCS([expm1 hypot log1p log1pl log2 log10 nearbyint nearbyintl powl rint rintl], [#include <math.h>])
 ## va_copy is C99: required as from R 2.13.0
 R_CHECK_FUNCS([va_copy], [#include <stdarg.h>])
@@ -1887,11 +1890,11 @@
 AC_CHECK_HEADERS(sunmath.h)
 AC_CHECK_LIB(sunmath, cospi)
 
-## Functions from draft C11 extensions, some of which are already in glibc
+## Functions from ISO/IEC TS 18661-4:2015 C11 extensions.
 ## For now, do not define _GNU_SOURCE here.
 ## All but pown have long been in libsunmath
 AC_CHECK_FUNCS([atanpi atan2pi cospi exp10 pown sinpi tanpi], 
-[#define __STDC_WANT_IEC_60559_TYPES_EXT__ 1
+[#define __STDC_WANT_IEC_60559_FUNCS_EXT__ 1
 #include <math.h>
 #ifdef HAVE_SUNMATH_H
 #include <sunmath.h>
@@ -2442,9 +2445,11 @@
     [AC_RUN_IFELSE([AC_LANG_SOURCE([[
 #include "confdefs.h"
 #include <stdlib.h>
+/* This might get optimized out if not used */
 extern void * __libc_stack_end;
 
 int main () {
+    if(!__libc_stack_end) exit(1);
     exit(0);
 }
   ]])], [r_cv_libc_stack_end=yes], [r_cv_libc_stack_end=no], 
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/doc/COPYRIGHTS R-patched/doc/COPYRIGHTS
--- R-release-orig/doc/COPYRIGHTS	2015-03-19 00:04:14.000000000 +0100
+++ R-patched/doc/COPYRIGHTS	2016-01-30 02:41:11.579822000 +0100
@@ -326,8 +326,8 @@
     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
+  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
   disclaim any liability to any recipient for claims brought against
   recipient by any third party for infringement of that parties
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/doc/NEWS R-patched/doc/NEWS
--- R-release-orig/doc/NEWS	2015-12-10 09:06:20.000000000 +0100
+++ R-patched/doc/NEWS	2016-02-11 02:51:28.577144000 +0100
@@ -1,177 +1,289 @@
 R News
 
+CHANGES IN R 3.2.3 patched:
+
+  NEW FEATURES:
+
+    • install.packages() and related functions now give a more
+      informative warning when an attempt is made to install a base
+      package.
+
+    • summary(x) now prints with less rounding when x contains infinite
+      values. (Request of PR#16620.)
+
+    • provideDimnames() gets an optional unique argument.
+
+    • shQuote() gains type = "cmd2" for quoting in cmd.exe in Windows.
+      (Response to PR#16636.)
+
+    • The data.frame method of rbind() gains an optional argument
+      stringsAsFactors (instead of only depending on
+      getOption("stringsAsFactors")).
+
+      smooth(x, *) now also works for long vectors.
+
+  DEPRECATED AND DEFUNCT:
+
+    • Use of SUPPORT_OPENMP from header Rconfig.h is deprecated in
+      favour of the standard OpenMP define _OPENMP.
+
+      (This has been the recommendation in the manual for a while now.)
+
+    • The make macro AWK which is long unused by R itself but recorded
+      in file etc/Makeconf is deprecated and will be removed in R
+      3.3.0.
+
+      The C header file S.h is no longer documented: its use should be
+      replaced by R.h.
+
+  BUG FIXES:
+
+    • kmeans(x, centers = <1-row>) now works. (PR#16623)
+
+    • Vectorize() now checks for clashes in argument names.  (PR#16577)
+
+    • file.copy(overwrite = FALSE) would signal a successful copy when
+      none had taken place.  (PR#16576)
+
+    • ngettext() now uses the same default domain as gettext().
+      (PR#14605)
+
+    • array(.., dimnames = *) now warns about non-list dimnames and,
+      from R 3.3.0, will signal the same error for invalid dimnames as
+      matrix() has always done.
+
+    • addmargins() now adds dimnames for the extended margins in all
+      cases, as always documented.
+
+    • heatmap() evaluated its add.expr argument in the wrong
+      environment.  (PR#16583)
+
+    • require() etc now give the correct entry of lib.loc in the
+      warning about an old version of a package masking a newer
+      required one.
+
+    • The internal deparser did not add parentheses when necessary,
+      e.g. before [] or [[]].  (Reported by Lukas Stadler; additional
+      fixes included as well).
+
+    • as.data.frame.vector(*, row.names=*) no longer produces
+      ‘corrupted’ data frames from row names of incorrect length, but
+      rather warns about them.  This will become an error.
+
+    • url connections with method = "libcurl" are destroyed properly.
+      (PR#16681)
+
+    • withCallingHandler() now (again) handles warnings even during S4
+      generic's argument evaluation.  (PR#16111)
+
+    • deparse(..., control = "quoteExpressions") incorrectly quoted
+      empty expressions.  (PR#16686)
+
+    • format()ting datetime objects ("POSIX[cl]?t") could segfault or
+      recycle wrongly.  (PR#16685)
+
+    • plot.ts(<matrix>, las = 1) now does use las.
+
+    • saveRDS(*, compress = "gzip") now works as documented.
+      (PR#16653)
+
+    • (Windows only) The Rgui front end did not always initialize the
+      console properly, and could cause R to crash.  (PR#16998)
+
+    • The as.hclust method for "dendrogram"s failed often when there
+      were ties in the heights.
+
+    • reorder() and midcache.dendrogram() now are non-recursive and
+      hence applicable to somewhat deeply nested dendrograms, thanks to
+      a proposal by Suharto Anggono in PR#16424.
+
+    • cor.test() now calculates very small p values more accurately
+      (affecting the result only in extreme not statistically relevant
+      cases).  (PR#16704)
+
+    • smooth(*, do.ends=TRUE) did not always work correctly in R
+      versions between 3.0.0 and 3.2.3.
+
+    • pretty(D) for date-time objects D now also works well if range(D)
+      is (much) smaller than a second.  In the case of only one unique
+      value in D, the pretty range now is more symmetric around that
+      value than previously.
+
+    • The figures in help pages such as ?points were accidentally
+      damaged, and did not appear in R 3.2.3.  (PR#16708)
+
 CHANGES IN R 3.2.3:
 
   NEW FEATURES:
 
-    * Some recently-added Windows time zone names have been added to
+    • Some recently-added Windows time zone names have been added to
       the conversion table used to convert these to Olson names.
       (Including those relating to changes for Russia in Oct 2014, as
       in PR#16503.)
 
-    * (Windows) Compatibility information has been added to the
+    • (Windows) Compatibility information has been added to the
       manifests for Rgui.exe, Rterm.exe and Rscript.exe.  This should
       allow win.version() and Sys.info() to report the actual Windows
       version up to Windows 10.
 
-    * Windows "wininet" FTP first tries EPSV / PASV mode rather than
+    • Windows "wininet" FTP first tries EPSV / PASV mode rather than
       only using active mode (reported by Dan Tenenbaum).
 
-    * which.min(x) and which.max(x) may be much faster for logical and
+    • which.min(x) and which.max(x) may be much faster for logical and
       integer x and now also work for long vectors.
 
-    * The 'emulation' part of tools::texi2dvi() has been somewhat
+    • The ‘emulation’ part of tools::texi2dvi() has been somewhat
       enhanced, including supporting quiet = TRUE.  It can be selected
       by texi2dvi = "emulation".
 
       (Windows) MiKTeX removed its texi2dvi.exe command in Sept 2015:
       tools::texi2dvi() tries texify.exe if it is not found.
 
-    * (Windows only) Shortcuts for printing and saving have been added
+    • (Windows only) Shortcuts for printing and saving have been added
       to menus in Rgui.exe.  (Request of PR#16572.)
 
-    * loess(..., iterTrace=TRUE) now provides diagnostics for
+    • loess(..., iterTrace=TRUE) now provides diagnostics for
       robustness iterations, and the print() method for
       summary(<loess>) shows slightly more.
 
-    * The included version of PCRE has been updated to 8.38, a bug-fix
+    • The included version of PCRE has been updated to 8.38, a bug-fix
       release.
 
-    * View() now displays nested data frames in a more friendly way.
+    • View() now displays nested data frames in a more friendly way.
       (Request with patch in PR#15915.)
 
   INSTALLATION and INCLUDED SOFTWARE:
 
-    * The included configuration code for libintl has been updated to
+    • The included configuration code for libintl has been updated to
       that from gettext version 0.19.5.1 - this should only affect how
       an external library is detected (and the only known instance is
       under OpenBSD).  (Wish of PR#16464.)
 
-    * configure has a new argument --disable-java to disable the checks
+    • configure has a new argument --disable-java to disable the checks
       for Java.
 
-    * The configure default for MAIN_LDFLAGS has been changed for the
+    • The configure default for MAIN_LDFLAGS has been changed for the
       FreeBSD, NetBSD and Hurd OSes to one more likely to work with
       compilers other than gcc (FreeBSD 10 defaults to clang).
 
-    * configure now supports the OpenMP flags -fopenmp=libomp (clang)
+    • configure now supports the OpenMP flags -fopenmp=libomp (clang)
       and -qopenmp (Intel C).
 
-    * Various macros can be set to override the default behaviour of
+    • Various macros can be set to override the default behaviour of
       configure when detecting OpenMP: see file config.site.
 
-    * Source installation on Windows has been modified to allow for
+    • Source installation on Windows has been modified to allow for
       MiKTeX installations without texi2dvi.exe.  See file
       MkRules.dist.
 
   BUG FIXES:
 
-    * regexpr(pat, x, perl = TRUE) with Python-style named capture did
+    • regexpr(pat, x, perl = TRUE) with Python-style named capture did
       not work correctly when x contained NA strings.  (PR#16484)
 
-    * The description of dataset ToothGrowth has been
+    • The description of dataset ToothGrowth has been
       improved/corrected.  (PR#15953)
 
-    * model.tables(type = "means") and hence TukeyHSD() now support
+    • model.tables(type = "means") and hence TukeyHSD() now support
       "aov" fits without an intercept term.  (PR#16437)
 
-    * close() now reports the status of a pipe() connection opened with
+    • close() now reports the status of a pipe() connection opened with
       an explicit open argument.  (PR#16481)
 
-    * Coercing a list without names to a data frame is faster if the
+    • Coercing a list without names to a data frame is faster if the
       elements are very long. (PR#16467)
 
-    * (Unix-only) Under some rare circumstances piping the output from
+    • (Unix-only) Under some rare circumstances piping the output from
       Rscript or R -f could result in attempting to close the input
       file twice, possibly crashing the process.  (PR#16500)
 
-    * (Windows) Sys.info() was out of step with win.version() and did
+    • (Windows) Sys.info() was out of step with win.version() and did
       not report Windows 8.
 
-    * topenv(baseenv()) returns baseenv() again as in R 3.1.0 and
+    • topenv(baseenv()) returns baseenv() again as in R 3.1.0 and
       earlier.  This also fixes compilerJIT(3) when used in .Rprofile.
 
-    * detach()ing the methods package keeps .isMethodsDispatchOn()
+    • detach()ing the methods package keeps .isMethodsDispatchOn()
       true, as long as the methods namespace is not unloaded.
 
-    * Removed some spurious warnings from configure about the
+    • Removed some spurious warnings from configure about the
       preprocessor not finding header files.  (PR#15989)
 
-    * rchisq(*, df=0, ncp=0) now returns 0 instead of NaN, and
+    • rchisq(*, df=0, ncp=0) now returns 0 instead of NaN, and
       dchisq(*, df=0, ncp=*) also no longer returns NaN in limit cases
       (where the limit is unique).  (PR#16521)
 
-    * pchisq(*, df=0, ncp > 0, log.p=TRUE) no longer underflows (for
+    • pchisq(*, df=0, ncp > 0, log.p=TRUE) no longer underflows (for
       ncp > ~60).
 
-    * nchar(x, "w") returned -1 for characters it did not know about
+    • nchar(x, "w") returned -1 for characters it did not know about
       (e.g. zero-width spaces): it now assumes 1.  It now knows about
       most zero-width characters and a few more double-width
       characters.
 
-    * Help for which.min() is now more precise about behavior with
+    • Help for which.min() is now more precise about behavior with
       logical arguments.  (PR#16532)
 
-    * The print width of character strings marked as "latin1" or
+    • The print width of character strings marked as "latin1" or
       "bytes" was in some cases computed incorrectly.
 
-    * abbreviate() did not give names to the return value if minlength
+    • abbreviate() did not give names to the return value if minlength
       was zero, unlike when it was positive.
 
-    * (Windows only) dir.create() did not always warn when it failed to
+    • (Windows only) dir.create() did not always warn when it failed to
       create a directory.  (PR#16537)
 
-    * When operating in a non-UTF-8 multibyte locale (e.g. an East
+    • When operating in a non-UTF-8 multibyte locale (e.g. an East
       Asian locale on Windows), grep() and related functions did not
       handle UTF-8 strings properly.  (PR#16264)
 
-    * read.dcf() sometimes misread lines longer than 8191 characters.
-      (Reported by Herv'e Pag`es with a patch.)
+    • read.dcf() sometimes misread lines longer than 8191 characters.
+      (Reported by Hervé Pagès with a patch.)
 
-    * within(df, ..) no longer drops columns whose name start with a
+    • within(df, ..) no longer drops columns whose name start with a
       ".".
 
-    * The built-in HTTP server converted entire Content-Type to
+    • The built-in HTTP server converted entire Content-Type to
       lowercase including parameters which can cause issues for
       multi-part form boundaries (PR#16541).
 
-    * Modifying slots of S4 objects could fail when the methods package
+    • Modifying slots of S4 objects could fail when the methods package
       was not attached. (PR#16545)
 
-    * splineDesign(*, outer.ok=TRUE) (splines) is better now
+    • splineDesign(*, outer.ok=TRUE) (splines) is better now
       (PR#16549), and interpSpline() now allows sparse=TRUE for speedup
       with non-small sizes.
 
-    * If the expression in the traceback was too long, traceback() did
-      not report the source line number.  (Patch by Kirill M"uller.)
+    • If the expression in the traceback was too long, traceback() did
+      not report the source line number.  (Patch by Kirill Müller.)
 
-    * The browser did not truncate the display of the function when
+    • The browser did not truncate the display of the function when
       exiting with options("deparse.max.lines") set.  (PR#16581)
 
-    * When bs(*, Boundary.knots=) had boundary knots inside the data
+    • When bs(*, Boundary.knots=) had boundary knots inside the data
       range, extrapolation was somewhat off.  (Patch by Trevor Hastie.)
 
-    * var() and hence sd() warn about factor arguments which are
+    • var() and hence sd() warn about factor arguments which are
       deprecated now. (PR#16564)
 
-    * loess(*, weights = *) stored wrong weights and hence gave
+    • loess(*, weights = *) stored wrong weights and hence gave
       slightly wrong predictions for newdata.  (PR#16587)
 
-    * aperm(a, *) now preserves names(dim(a)).
+    • aperm(a, *) now preserves names(dim(a)).
 
-    * poly(x, ..) now works when either raw=TRUE or coef is specified.
+    • poly(x, ..) now works when either raw=TRUE or coef is specified.
       (PR#16597)
 
-    * data(package=*) is more careful in determining the path.
+    • data(package=*) is more careful in determining the path.
 
-    * prettyNum(*, decimal.mark, big.mark): fixed bug introduced when
+    • prettyNum(*, decimal.mark, big.mark): fixed bug introduced when
       fixing PR#16411.
 
 CHANGES IN R 3.2.2:
 
   SIGNIFICANT USER-VISIBLE CHANGES:
 
-    * It is now easier to use secure downloads from https:// URLs on
+    • It is now easier to use secure downloads from https:// URLs on
       builds which support them: no longer do non-default options need
       to be selected to do so.  In particular, packages can be
       installed from repositories which offer https:// URLs, and those
@@ -182,7 +294,7 @@
       platforms if support for libcurl was compiled in and if that
       supports the https protocol (system installations can be expected
       to do).  So https:// support can be expected except on rather old
-      OSes (an example being OS X 'Snow Leopard', where a non-system
+      OSes (an example being OS X ‘Snow Leopard’, where a non-system
       version of libcurl can be used).
 
       (Windows only) The default method for accessing URLs _via_
@@ -194,17 +306,17 @@
 
   NEW FEATURES:
 
-    * cmdscale() gets new option list. for increased flexibility when a
+    • cmdscale() gets new option list. for increased flexibility when a
       list should be returned.
 
-    * configure now supports texinfo version 6.0, which (unlike the
+    • configure now supports texinfo version 6.0, which (unlike the
       change from 4.x to 5.0) is a minor update.  (Wish of PR#16456.)
 
-    * (Non-Windows only) download.file() with default method = "auto"
+    • (Non-Windows only) download.file() with default method = "auto"
       now chooses "libcurl" if that is available and a https:// or
       ftps:// URL is used.
 
-    * (Windows only) setInternet2(TRUE) is now the default.  The
+    • (Windows only) setInternet2(TRUE) is now the default.  The
       command-line option --internet2 and environment variable
       R_WIN_INTERNET2 are now ignored.
 
@@ -219,261 +331,261 @@
       There are implications for how proxies need to be set (see
       ?download.file).
 
-    * chooseCRANmirror() and chooseBioCmirror() now offer HTTPS mirrors
+    • chooseCRANmirror() and chooseBioCmirror() now offer HTTPS mirrors
       in preference to HTTP mirrors.  This changes the interpretation
       of their ind arguments: see their help pages.
 
-    * capture.output() gets optional arguments type and split to pass
+    • capture.output() gets optional arguments type and split to pass
       to sink(), and hence can be used to capture messages.
 
   C-LEVEL FACILITIES:
 
-    * Header Rconfig.h now defines HAVE_ALLOCA_H if the platform has
+    • Header Rconfig.h now defines HAVE_ALLOCA_H if the platform has
       the alloca.h header (it is needed to define alloca on Solaris and
-      AIX, at least: see 'Writing R Extensions' for how to use it).
+      AIX, at least: see ‘Writing R Extensions’ for how to use it).
 
   INSTALLATION and INCLUDED SOFTWARE:
 
-    * The libtool script generated by configure has been modified to
+    • The libtool script generated by configure has been modified to
       support FreeBSD >= 10 (PR#16410).
 
   BUG FIXES:
 
-    * The HTML help page links to demo code failed due to a change in R
+    • The HTML help page links to demo code failed due to a change in R
       3.2.0.  (PR#16432)
 
-    * If the na.action argument was used in model.frame(), the original
+    • If the na.action argument was used in model.frame(), the original
       data could be modified. (PR#16436)
 
-    * getGraphicsEvent() could cause a crash if a graphics window was
+    • getGraphicsEvent() could cause a crash if a graphics window was
       closed while it was in use. (PR#16438)
 
-    * matrix(x, nr, nc, byrow = TRUE) failed if x was an object of type
+    • matrix(x, nr, nc, byrow = TRUE) failed if x was an object of type
       "expression".
 
-    * strptime() could overflow the allocated storage on the C stack
+    • strptime() could overflow the allocated storage on the C stack
       when the timezone had a non-standard format much longer than the
       standard formats. (Part of PR#16328.)
 
-    * options(OutDec = s) now signals a warning (which will become an
+    • options(OutDec = s) now signals a warning (which will become an
       error in the future) when s is not a string with exactly one
       character, as that has been a documented requirement.
 
-    * prettyNum() gains a new option input.d.mark which together with
+    • prettyNum() gains a new option input.d.mark which together with
       other changes, e.g., the default for decimal.mark, fixes some
       format()ting variants with non-default getOption("OutDec") such
       as in PR#16411.
 
-    * download.packages() failed for type equal to either "both" or
+    • download.packages() failed for type equal to either "both" or
       "binary".  (Reported by Dan Tenenbaum.)
 
-    * The dendrogram method of labels() is much more efficient for
+    • The dendrogram method of labels() is much more efficient for
       large dendrograms, now using rapply().  (Comment #15 of PR#15215)
 
-    * The "port" algorithm of nls() could give spurious errors.
+    • The "port" algorithm of nls() could give spurious errors.
       (Reported by Radford Neal.)
 
-    * Reference classes that inherited from reference classes in
+    • Reference classes that inherited from reference classes in
       another package could invalidate methods of the inherited class.
       Fixing this requires adding the ability for methods to be
-      "external", with the object supplied explicitly as the first
+      “external”, with the object supplied explicitly as the first
       argument, named .self. See "Inter-Package Superclasses" in the
       documentation.
 
-    * readBin() could fail on the SPARC architecture due to alignment
+    • readBin() could fail on the SPARC architecture due to alignment
       issues.  (Reported by Radford Neal.)
 
-    * qt(*, df=Inf, ncp=.) now uses the natural qnorm() limit instead
+    • qt(*, df=Inf, ncp=.) now uses the natural qnorm() limit instead
       of returning NaN. (PR#16475)
 
-    * Auto-printing of S3 and S4 values now searches for print() in the
+    • Auto-printing of S3 and S4 values now searches for print() in the
       base namespace and show() in the methods namespace instead of
       searching the global environment.
 
-    * polym() gains a coefs = NULL argument and returns class "poly"
+    • polym() gains a coefs = NULL argument and returns class "poly"
       just like poly() which gets a new simple=FALSE option.  They now
       lead to correct predict()ions, e.g., on subsets of the original
       data.
 
-    * rhyper(nn, <large>) now works correctly. (PR#16489)
+    • rhyper(nn, <large>) now works correctly. (PR#16489)
 
-    * ttkimage() did not (and could not) work so was removed. Ditto for
+    • ttkimage() did not (and could not) work so was removed. Ditto for
       tkimage.cget() and tkimage.configure(). Added two Ttk widgets and
       missing subcommands for Tk's image command: ttkscale(),
       ttkspinbox(), tkimage.delete(), tkimage.height(),
       tkimage.inuse(), tkimage.type(), tkimage.types(),
       tkimage.width(). (PR#15372, PR#16450)
 
-    * getClass("foo") now also returns a class definition when it is
+    • getClass("foo") now also returns a class definition when it is
       found in the cache more than once.
 
 CHANGES IN R 3.2.1:
 
   NEW FEATURES:
 
-    * utf8ToInt() now checks that its input is valid UTF-8 and returns
+    • utf8ToInt() now checks that its input is valid UTF-8 and returns
       NA if it is not.
 
-    * install.packages() now allows type = "both" with repos = NULL if
+    • install.packages() now allows type = "both" with repos = NULL if
       it can infer the type of file.
 
-    * nchar(x, *) and nzchar(x) gain a new argument keepNA which
+    • nchar(x, *) and nzchar(x) gain a new argument keepNA which
       governs how the result for NAs in x is determined.  For nzchar()
       in general and nchar() in the R 3.2.x series, the default remains
       FALSE which is fully back compatible.  From R 3.3.0, nchar()'s
       default will change to keepNA = NA and you are advised to
       consider this for code portability.
 
-    * news() more flexibly extracts dates from package NEWS.Rd files.
+    • news() more flexibly extracts dates from package NEWS.Rd files.
 
-    * lengths(x) now also works (trivially) for atomic x and hence can
+    • lengths(x) now also works (trivially) for atomic x and hence can
       be used more generally as an efficient replacement of sapply(x,
       length) and similar.
 
-    * The included version of PCRE has been updated to 8.37, a bug-fix
+    • The included version of PCRE has been updated to 8.37, a bug-fix
       release.
 
-    * diag() no longer duplicates a matrix when extracting its
+    • diag() no longer duplicates a matrix when extracting its
       diagonal.
 
-    * as.character.srcref() gains an argument to allow characters
+    • as.character.srcref() gains an argument to allow characters
       corresponding to a range of source references to be extracted.
 
   BUG FIXES:
 
-    * acf() and ccf() now guarantee values strictly in [-1,1] (instead
+    • acf() and ccf() now guarantee values strictly in [-1,1] (instead
       of sometimes very slightly outside). PR#15832.
 
-    * as.integer("111111111111") now gives NA (with a warning) as it
+    • as.integer("111111111111") now gives NA (with a warning) as it
       does for the corresponding numeric or negative number coercions.
       Further, as.integer(M + 0.1) now gives M (instead of NA) when M
       is the maximal representable integer.
 
-    * On some platforms nchar(x, "c") and nchar(x, "w") would return
+    • On some platforms nchar(x, "c") and nchar(x, "w") would return
       values (possibly NA) for inputs which were declared to be UTF-8
       but were not, or for invalid strings without a marked encoding in
       a multi-byte locale, rather than give an error.  Additional
       checks have been added to mitigate this.
 
-    * apply(a, M, function(u) c(X = ., Y = .)) again has dimnames
+    • apply(a, M, function(u) c(X = ., Y = .)) again has dimnames
       containing "X" and "Y" (as in R < 3.2.0).
 
-    * (Windows only) In some cases, the --clean option to R CMD INSTALL
+    • (Windows only) In some cases, the --clean option to R CMD INSTALL
       could fail.  (PR#16178)
 
-    * (Windows only) choose.files() would occasionally include
+    • (Windows only) choose.files() would occasionally include
       characters from the result of an earlier call in the result of a
       later one.  (PR#16270)
 
-    * A change in RSiteSearch() in R 3.2.0 caused it to submit invalid
+    • A change in RSiteSearch() in R 3.2.0 caused it to submit invalid
       URLs.  (PR#16329)
 
-    * Rscript and command line R silently ignored incomplete statements
+    • Rscript and command line R silently ignored incomplete statements
       at the end of a script; now they are reported as parse errors.
       (PR#16350)
 
-    * Parse data for very long strings was not stored.  (PR#16354)
+    • Parse data for very long strings was not stored.  (PR#16354)
 
-    * plotNode(), the workhorse of the plot method for "dendrogram"s is
+    • plotNode(), the workhorse of the plot method for "dendrogram"s is
       no longer recursive, thanks to Suharto Anggono, and hence also
       works for deeply nested dendrograms.  (PR#15215)
 
-    * The parser could overflow internally when given numbers in
+    • The parser could overflow internally when given numbers in
       scientific format with extremely large exponents.  (PR#16358)
 
-    * If the CRAN mirror was not set, install.packages(type = "both")
+    • If the CRAN mirror was not set, install.packages(type = "both")
       and related functions could repeatedly query the user for it.
       (Part of PR#16362)
 
-    * The low-level functions .rowSums() etc. did not check the length
+    • The low-level functions .rowSums() etc. did not check the length
       of their argument, so could segfault. (PR#16367)
 
-    * The quietly argument of library() is now correctly propagated
+    • The quietly argument of library() is now correctly propagated
       from .getRequiredPackages2().
 
-    * Under some circumstances using the internal PCRE when building R
+    • Under some circumstances using the internal PCRE when building R
       from source would cause external libs such as -llzma to be
       omitted from the main link.
 
-    * The .Primitive default methods of the logic operators, i.e., !, &
+    • The .Primitive default methods of the logic operators, i.e., !, &
       and |, now give correct error messages when appropriate, e.g.,
       for `&`(TRUE) or `!`().  (PR#16385)
 
-    * cummax(x) now correctly propagates NAs also when x is of type
+    • cummax(x) now correctly propagates NAs also when x is of type
       integer and begins with an NA.
 
-    * summaryRprof() could fail when the profile contained only two
+    • summaryRprof() could fail when the profile contained only two
       records.  (PR#16395)
 
-    * HTML vignettes opened using vignette() did not support links into
+    • HTML vignettes opened using vignette() did not support links into
       the rest of the HTML help system.  (Links worked properly when
       the vignette was opened using browseVignettes() or from within
       the help system.)
 
-    * arima(*, xreg = .) (for d >= 1) computes estimated variances
+    • arima(*, xreg = .) (for d >= 1) computes estimated variances
       based on a the number of effective observations as in R version
       3.0.1 and earlier.  (PR#16278)
 
-    * slotNames(.) is now correct for "signature" objects (mostly used
+    • slotNames(.) is now correct for "signature" objects (mostly used
       internally in methods).
 
-    * On some systems, the first string comparison after a locale
+    • On some systems, the first string comparison after a locale
       change would result in NA.
 
 CHANGES IN R 3.2.0:
 
   NEW FEATURES:
 
-    * anyNA() gains a recursive argument.
+    • anyNA() gains a recursive argument.
 
-    * When x is missing and names is not false (including the default
+    • When x is missing and names is not false (including the default
       value), Sys.getenv(x, names) returns an object of class "Dlist"
       and hence prints tidily.
 
-    * (Windows.)  shell() no longer consults the environment variable
+    • (Windows.)  shell() no longer consults the environment variable
       SHELL: too many systems have been encountered where it was set
       incorrectly (usually to a path where software was compiled, not
       where it was installed).  R_SHELL, the preferred way to select a
       non-default shell, can be used instead.
 
-    * Some unusual arguments to embedFonts() can now be specified as
+    • Some unusual arguments to embedFonts() can now be specified as
       character vectors, and the defaults have been changed
       accordingly.
 
-    * Functions in the Summary group duplicate less.  (PR#15798)
+    • Functions in the Summary group duplicate less.  (PR#15798)
 
-    * (Unix-alikes.) system(cmd, input = ) now uses
-      'shell-execution-environment' redirection, which will be more
+    • (Unix-alikes.) system(cmd, input = ) now uses
+      ‘shell-execution-environment’ redirection, which will be more
       natural if cmd is not a single command (but requires a
       POSIX-compliant shell). (Wish of PR#15508)
 
-    * read.fwf() and read.DIF() gain a fileEncoding argument, for
+    • read.fwf() and read.DIF() gain a fileEncoding argument, for
       convenience.
 
-    * Graphics devices can add attributes to their description in
+    • Graphics devices can add attributes to their description in
       .Device and .Devices.  Several of those included with R use a
       "filepath" attribute.
 
-    * pmatch() uses hashing in more cases and so is faster at the
+    • pmatch() uses hashing in more cases and so is faster at the
       expense of using more memory. (PR#15697)
 
-    * pairs() gains new arguments to select sets of variables to be
+    • pairs() gains new arguments to select sets of variables to be
       plotted against each other.
 
-    * file.info(, extra_cols = FALSE) allows a minimal set of columns
+    • file.info(, extra_cols = FALSE) allows a minimal set of columns
       to be computed on Unix-alikes: on some systems without
       properly-configured caching this can be significantly faster with
       large file lists.
 
-    * New function dir.exists() in package base to test efficiently
+    • New function dir.exists() in package base to test efficiently
       whether one or more paths exist and are directories.
 
-    * dput() and friends gain new controls hexNumeric and digits17
+    • dput() and friends gain new controls hexNumeric and digits17
       which output double and complex quantities as, respectively,
       binary fractions (exactly, see sprintf("%a")) and as decimals
       with up to 17 significant digits.
 
-    * save(), saveRDS() and serialize() now support ascii = NA which
+    • save(), saveRDS() and serialize() now support ascii = NA which
       writes ASCII files using sprintf("%a") for double/complex
       quantities.  This is read-compatible with ascii = TRUE but avoids
       binary->decimal->binary conversions with potential loss of
@@ -481,7 +593,7 @@
       compliance means that the format cannot be read correctly there
       in R before 3.1.2.
 
-    * The default for formatC(decimal.mark =) has been changed to be
+    • The default for formatC(decimal.mark =) has been changed to be
       getOption("OutDec"); this makes it more consistent with format()
       and suitable for use in print methods, e.g. those for classes
       "density", "ecdf", "stepfun" and "summary.lm".
@@ -493,74 +605,74 @@
 
       (In part, wish of PR#15819.)
 
-    * printNum() and hence format() and formatC() give a warning if
+    • printNum() and hence format() and formatC() give a warning if
       big.mark and decimal.mark are set to the same value (period and
       comma are not uncommonly used for each, and this is a check that
       conventions have not got mixed).
 
-    * merge() can create a result which uses long vectors on 64-bit
+    • merge() can create a result which uses long vectors on 64-bit
       platforms.
 
-    * dget() gains a new argument keep.source which defaults to FALSE
+    • dget() gains a new argument keep.source which defaults to FALSE
       for speed (dput() and dget() are most often used for data objects
       where this can make dget() many times faster).
 
-    * Packages may now use a file of common macro definitions in their
+    • Packages may now use a file of common macro definitions in their
       help files, and may import definitions from other packages.
 
-    * A number of macros have been added in the new share/Rd directory
+    • A number of macros have been added in the new share/Rd directory
       for use in package overview help pages, and promptPackage() now
       makes use of them.
 
-    * tools::parse_Rd() gains a new permissive argument which converts
+    • tools::parse_Rd() gains a new permissive argument which converts
       unrecognized macros into text.  This is used by
       utils:::format.bibentry to allow LaTeX markup to be ignored.
 
-    * options(OutDec =) can now specify a multi-byte character, e.g.,
+    • options(OutDec =) can now specify a multi-byte character, e.g.,
       options(OutDec = "\u00b7") in a UTF-8 locale.
 
-    * is.recursive(x) is no longer true when x is an external pointer,
+    • is.recursive(x) is no longer true when x is an external pointer,
       a weak reference or byte code; the first enables all.equal(x, x)
       when x <- getClass(.).
 
-    * ls() (aka objects()) and as.list.environment() gain a new
+    • ls() (aka objects()) and as.list.environment() gain a new
       argument sorted.
 
-    * The "source" attribute (which has not been added to functions by
+    • The "source" attribute (which has not been added to functions by
       R since before R version 2.14.0) is no longer treated as special.
 
-    * Function returnValue() has been added to give on.exit() code
+    • Function returnValue() has been added to give on.exit() code
       access to a function's return value for debugging purposes.
 
-    * crossprod(x, y) allows more matrix coercions when x or y are
+    • crossprod(x, y) allows more matrix coercions when x or y are
       vectors, now equalling t(x) %*% y in these cases (also reported
       by Radford Neal).  Similarly, tcrossprod(x,y) and %*% work in
       more cases with vector arguments.
 
-    * Utility function dynGet() useful for detecting cycles, aka
+    • Utility function dynGet() useful for detecting cycles, aka
       infinite recursions.
 
-    * The byte-code compiler and interpreter include new instructions
+    • The byte-code compiler and interpreter include new instructions
       that allow many scalar subsetting and assignment and scalar
       arithmetic operations to be handled more efficiently. This can
       result in significant performance improvements in scalar
       numerical code.
 
-    * apply(m, 2, identity) is now the same as the matrix m when it has
+    • apply(m, 2, identity) is now the same as the matrix m when it has
       _named_ row names.
 
-    * A new function debuggingState() has been added, allowing to
+    • A new function debuggingState() has been added, allowing to
       temporarily turn off debugging.
 
-    * example() gets a new optional argument run.donttest and
+    • example() gets a new optional argument run.donttest and
       tools::Rd2ex() a corresponding commentDonttest, with a default
       such that example(..) in help examples will run \donttest code
       only if used interactively (a change in behaviour).
 
-    * rbind.data.frame() gains an optional argument make.row.names, for
+    • rbind.data.frame() gains an optional argument make.row.names, for
       potential speedup.
 
-    * New function extSoftVersion() to report on the versions of
+    • New function extSoftVersion() to report on the versions of
       third-party software in use in this session.  Currently reports
       versions of zlib, bzlib, the liblzma from xz, PCRE, ICU, TRE and
       the iconv implementation.
@@ -570,74 +682,74 @@
 
       Function tcltk::tclVersion() reports the Tcl/Tk version.
 
-    * Calling callGeneric() without arguments now works with primitive
+    • Calling callGeneric() without arguments now works with primitive
       generics to some extent.
 
-    * vapply(x, FUN, FUN.VALUE) is more efficient notably for large
+    • vapply(x, FUN, FUN.VALUE) is more efficient notably for large
       length(FUN.VALUE); as extension of PR#16061.
 
-    * as.table() now allows tables with one or more dimensions of
+    • as.table() now allows tables with one or more dimensions of
       length 0 (such as as.table(integer())).
 
-    * names(x) <- NULL now clears the names of call and ... objects.
+    • names(x) <- NULL now clears the names of call and ... objects.
 
-    * library() will report a warning when an insufficient dependency
+    • library() will report a warning when an insufficient dependency
       version is masking a sufficient one later on the library search
       path.
 
-    * A new plot() method for class "raster" has been added.
+    • A new plot() method for class "raster" has been added.
 
-    * New check_packages_in_dir_changes() function in package tools for
+    • New check_packages_in_dir_changes() function in package tools for
       conveniently analyzing how changing sources impacts the check
       results of their reverse dependencies.
 
-    * Speed-up from Peter Haverty for ls() and
+    • Speed-up from Peter Haverty for ls() and
       methods:::.requirePackage() speeding up package loading.
       (PR#16133)
 
-    * New get0() function, combining exists() and get() in one call,
+    • New get0() function, combining exists() and get() in one call,
       for efficiency.
 
-    * match.call() gains an envir argument for specifying the
+    • match.call() gains an envir argument for specifying the
       environment from which to retrieve the ... in the call, if any;
       this environment was wrong (or at least undesirable) when the
       definition argument was a function.
 
-    * topenv() has been made .Internal() for speedup, based on Peter
+    • topenv() has been made .Internal() for speedup, based on Peter
       Haverty's proposal in PR#16140.
 
-    * getOption() no longer calls options() in the main case.
+    • getOption() no longer calls options() in the main case.
 
-    * Optional use of libcurl (version 7.28.0 from Oct 2012 or later)
+    • Optional use of libcurl (version 7.28.0 from Oct 2012 or later)
       for Internet access:
 
-        * capabilities("libcurl") reports if this is available.
+        • capabilities("libcurl") reports if this is available.
 
-        * libcurlVersion() reports the version in use, and other
+        • libcurlVersion() reports the version in use, and other
           details of the "libcurl" build including which URL schemes it
           supports.
 
-        * curlGetHeaders() retrieves the headers for http://, https://,
+        • curlGetHeaders() retrieves the headers for http://, https://,
           ftp:// and ftps:// URLs: analysis of these headers can
           provide insights into the `existence' of a URL (it might for
           example be permanently redirected) and is so used in R CMD
           check --as-cran.
 
-        * download.file() has a new optional method "libcurl" which
+        • download.file() has a new optional method "libcurl" which
           will handle more URL schemes, follow redirections, and allows
           simultaneous downloads of multiple URLs.
 
-        * url() has a new method "libcurl" which handles more URL
+        • url() has a new method "libcurl" which handles more URL
           schemes and follows redirections.  The default method is
           controlled by a new option url.method, which applies also to
           the opening of URLs _via_ file() (which happens implicitly in
           functions such as read.table.)
 
-        * When file() or url() is invoked with a https:// or ftps://
+        • When file() or url() is invoked with a https:// or ftps://
           URL which the current method cannot handle, it switches to a
           suitable method if one is available.
 
-    * (Windows.) The DLLs internet.dll and internet2.dll have been
+    • (Windows.) The DLLs internet.dll and internet2.dll have been
       merged.  In this version it is safe to switch (repeatedly)
       between the internal and Windows internet functions within an R
       session.
@@ -649,110 +761,110 @@
       download.file() has new method "wininet", selected as the default
       by --internet2 or setInternet2().
 
-    * parent.env<- can no longer modify the parent of a locked
+    • parent.env<- can no longer modify the parent of a locked
       namespace or namespace imports environment.  Contributed by Karl
       Millar.
 
-    * New function isNamespaceLoaded() for readability and speed.
+    • New function isNamespaceLoaded() for readability and speed.
 
-    * names(env) now returns all the object names of an environment
+    • names(env) now returns all the object names of an environment
       env, equivalently to ls(env, all.names = TRUE, sorted = FALSE)
       and also to the names of the corresponding list,
       names(as.list(env, all.names = TRUE)).  Note that although
       names() returns a character vector, the names have no particular
       ordering.
 
-    * The memory manager now grows the heap more aggressively. This
+    • The memory manager now grows the heap more aggressively. This
       reduces the number of garbage collections, in particular while
       data or code are loaded, at the expense of slightly increasing
       the memory footprint.
 
-    * New function trimws() for removing leading/trailing whitespace.
+    • New function trimws() for removing leading/trailing whitespace.
 
-    * cbind() and rbind() now consider S4 inheritance during S3
+    • cbind() and rbind() now consider S4 inheritance during S3
       dispatch and also obey deparse.level.
 
-    * cbind() and rbind() will delegate recursively to methods::cbind2
+    • cbind() and rbind() will delegate recursively to methods::cbind2
       (methods::rbind2) when at least one argument is an S4 object and
       S3 dispatch fails (due to ambiguity).
 
-    * (Windows.)  download.file(quiet = FALSE) now uses text rather
+    • (Windows.)  download.file(quiet = FALSE) now uses text rather
       than Windows progress bars in non-interactive use.
 
-    * New function hsearch_db() in package utils for building and
+    • New function hsearch_db() in package utils for building and
       retrieving the help search database used by help.search(), along
       with functions for inspecting the concepts and keywords in the
       help search database.
 
-    * New function .getNamespaceInfo(), a no-check version of
+    • New function .getNamespaceInfo(), a no-check version of
       getNamespaceInfo() mostly for internal speedups.
 
-    * The help search system now takes \keyword entries in Rd files
+    • The help search system now takes \keyword entries in Rd files
       which are not standard keywords (as given in KEYWORDS in the R
       documentation directory) as concepts.  For standard keyword
       entries the corresponding descriptions are additionally taken as
       concepts.
 
-    * New lengths() function for getting the lengths of all elements in
+    • New lengths() function for getting the lengths of all elements in
       a list.
 
-    * New function toTitleCase() in package tools, tailored to package
+    • New function toTitleCase() in package tools, tailored to package
       titles.
 
-    * The matrix methods of cbind() and rbind() allow matrices as
+    • The matrix methods of cbind() and rbind() allow matrices as
       inputs which have 2^31 or more elements.  (For cbind(), wish of
       PR#16198.)
 
-    * The default method of image() has an explicit check for a numeric
+    • The default method of image() has an explicit check for a numeric
       or logical matrix (which was always required).
 
-    * URLencode() will not by default encode further URLs which appear
+    • URLencode() will not by default encode further URLs which appear
       to be already encoded.
 
-    * BIC(mod) and BIC(mod, mod2) now give non-NA numbers for arima()
-      fitted models, as nobs(mod) now gives the number of "used"
+    • BIC(mod) and BIC(mod, mod2) now give non-NA numbers for arima()
+      fitted models, as nobs(mod) now gives the number of “used”
       observations for such models.  This fixes PR#16198, quite
       differently than proposed there.
 
-    * The print() methods for "htest", "pairwise.htest" and
+    • The print() methods for "htest", "pairwise.htest" and
       "power.htest" objects now have a digits argument defaulting to (a
       function of) getOption("digits"), and influencing all printed
       numbers coherently.  Unavoidably, this changes the display of
       such test results in some cases.
 
-    * Code completion for namespaces now recognizes all loaded
+    • Code completion for namespaces now recognizes all loaded
       namespaces, rather than only the ones that are also attached.
 
-    * The code completion mechanism can now be replaced by a
+    • The code completion mechanism can now be replaced by a
       user-specified completer function, for (temporary) situations
       where the usual code completion is inappropriate.
 
-    * unzip() will now warn if it is able to detect truncation when
+    • unzip() will now warn if it is able to detect truncation when
       unpacking a file of 4GB or more (related to PR#16243).
 
-    * methods() reports S4 in addition to S3 methods; output is
+    • methods() reports S4 in addition to S3 methods; output is
       simplified when the class argument is used.  .S3methods() and
       methods::.S4methods() report S3 and S4 methods separately.
 
-    * Higher order functions such as the apply functions and Reduce()
+    • Higher order functions such as the apply functions and Reduce()
       now force arguments to the functions they apply in order to
       eliminate undesirable interactions between lazy evaluation and
       variable capture in closures.  This resolves PR#16093.
 
   INSTALLATION and INCLUDED SOFTWARE:
 
-    * The \donttest sections of R's help files can be tested by
+    • The \donttest sections of R's help files can be tested by
       make check TEST_DONTTEST=TRUE .
 
-    * It is possible to request the use of system valgrind headers
+    • It is possible to request the use of system valgrind headers
       _via_ configure option --with-system-valgrind-headers: note the
       possible future incompatibility of such headers discussed in the
       'R Installation and Administration' manual. (Wish of PR#16068.)
 
-    * The included version of liblzma has been updated to xz-utils
+    • The included version of liblzma has been updated to xz-utils
       5.0.7 (minor bug fixes from 5.0.5).
 
-    * configure options --with-system-zlib, --with-system-bzlib and
+    • configure options --with-system-zlib, --with-system-bzlib and
       --with-system-pcre are now the default.  For the time being there
       is fallback to the versions included in the R sources if no
       system versions are found or (unlikely) if they are too old.
@@ -761,16 +873,16 @@
       packages zlib, bzip2/libbz2 and pcre as well as
       xz-devel/liblzma-dev (or similar names) are installed.
 
-    * configure by default looks for the texi2any script from texinfo
+    • configure by default looks for the texi2any script from texinfo
       5.1 or later, rather than the makeinfo program.  (makeinfo is a
       link to the Perl script texi2any in texinfo 5.x.)
 
-    * R CMD INSTALL gains an option --built-timestamp=STAMP allowing
+    • R CMD INSTALL gains an option --built-timestamp=STAMP allowing
       100% reproducible package building, thanks to Dirk Eddelbuettel.
 
   UTILITIES:
 
-    * There is support for testing the \dontrun and \donttest parts of
+    • There is support for testing the \dontrun and \donttest parts of
       examples in packages.
 
       tools::testInstalledPackage() accepts new arguments
@@ -778,90 +890,90 @@
 
       R CMD check gains options --run-dontrun and --run-donttest.
 
-    * The HTML generated by tools::Rd2HTML() and tools::toHTML()
-      methods is now 'XHTML 1.0 Strict'.
+    • The HTML generated by tools::Rd2HTML() and tools::toHTML()
+      methods is now ‘XHTML 1.0 Strict’.
 
-    * The compiler package's utility function setCompilerOptions() now
+    • The compiler package's utility function setCompilerOptions() now
       returns the old values invisibly. The initial optimization level
       can also be set with the environment variable
       R_COMPILER_OPTIMIZE.
 
-    * R CMD build adds a NeedsCompilation field if one is not already
+    • R CMD build adds a NeedsCompilation field if one is not already
       present in the DESCRIPTION file.
 
-    * R CMD check gains option --test-dir to specify an alternative set
+    • R CMD check gains option --test-dir to specify an alternative set
       of tests to run.
 
-    * R CMD check will now by default continue with testing after many
+    • R CMD check will now by default continue with testing after many
       types of errors, and will output a summary count of errors at the
       end if any have occurred.
 
-    * R CMD check now checks that the Title and Description fields are
+    • R CMD check now checks that the Title and Description fields are
       correctly terminated.
 
-    * R CMD check --as-cran now:
+    • R CMD check --as-cran now:
 
-        * checks a README.md file can be processed: this needs pandoc
+        • checks a README.md file can be processed: this needs pandoc
           installed.
 
-        * checks the existence and accessibility of URLs in the
+        • checks the existence and accessibility of URLs in the
           DESCRIPTION, CITATION, NEWS.Rd and README.md files and in the
           help files (provided the build has libcurl support).
 
-        * reports non-ASCII characters in R source files when there is
+        • reports non-ASCII characters in R source files when there is
           no package encoding declared in the DESCRIPTION file.
 
-        * reports (apparent) S3 methods exported but not registered.
+        • reports (apparent) S3 methods exported but not registered.
 
-        * reports overwriting registered S3 methods from
+        • reports overwriting registered S3 methods from
           base/recommended packages.  (Such methods are replaced in the
           affected package for the rest of the session, even if the
           replacing namespace is unloaded.)
 
-        * reports if the Title field does not appear to be in title
-          case (see 'Writing R Extensions': there may be false
+        • reports if the Title field does not appear to be in title
+          case (see ‘Writing R Extensions’: there may be false
           positives, but note that technical words should be
           single-quoted and will then be accepted).
 
       Most of these checks can also be selected by environment
-      variables: see the 'R Internals' manual.
+      variables: see the ‘R Internals’ manual.
 
   C-LEVEL FACILITIES:
 
-    * New C API utility logspace_sum(logx[], n).
+    • New C API utility logspace_sum(logx[], n).
 
-    * Entry points rbinom_mu, rnbinom_mu and rmultinom are remapped (by
+    • Entry points rbinom_mu, rnbinom_mu and rmultinom are remapped (by
       default) to Rf_rbinom_mu etc.  This requires packages using them
       to be re-installed.
 
-    * .C(DUP = FALSE) and .Fortran(DUP = FALSE) are now ignored, so
+    • .C(DUP = FALSE) and .Fortran(DUP = FALSE) are now ignored, so
       arguments are duplicated if DUP = TRUE would do so.  As their
       help has long said, .Call() is much preferred.
 
-    * New entry point R_allocLD, like R_alloc but guaranteed to have
+    • New entry point R_allocLD, like R_alloc but guaranteed to have
       sufficient alignment for long double pointers.
 
-    * isPairList() now returns TRUE for DOTSXP.
+    • isPairList() now returns TRUE for DOTSXP.
 
   WINDOWS BUILD CHANGES:
 
   A number of changes to the Windows build system are in development.
   The following are currently in place.
 
-    * Installation using external binary distributions of zlib, bzip2,
+    • Installation using external binary distributions of zlib, bzip2,
       liblzma, pcre, libpng, jpeglib and libtiff is now required, and
       the build instructions have been revised.
 
-    * A new make target rsync-extsoft has been added to obtain copies
+    • A new make target rsync-extsoft has been added to obtain copies
       of the external libraries from CRAN.
 
-    * Building the manuals now requires texi2any from texinfo 5.1 or
+    • Building the manuals now requires texi2any from texinfo 5.1 or
       later.  CRAN binary builds include the manuals, but by default
       builds from source will not, and they will be accessed from CRAN.
       See the comments in src/gnuwin32/MkRules.dist for how to specify
       the location of texi2any.
 
-    * (Windows) Changes have been made to support an experimental
+    • (Windows) Changes have been made to support an experimental
       Windows toolchain based on GCC 4.9.2.  The default toolchain
       continues to be based on GCC 4.6.3, as the new toolchain is not
       yet stable enough.  A change to a new toolchain is expected
@@ -869,13 +981,13 @@
 
   PACKAGE INSTALLATION:
 
-    * (Windows) The use of macro ZLIB_LIBS in file src/Makevars.win
+    • (Windows) The use of macro ZLIB_LIBS in file src/Makevars.win
       (which has not been documented for a long time) now requires an
-      external libz.a to be available (it is part of the 'goodies' used
+      external libz.a to be available (it is part of the ‘goodies’ used
       to compile Windows binary packages).  It would be simpler to use
       -lz instead.
 
-    * The default for option pkgType on platforms using binary packages
+    • The default for option pkgType on platforms using binary packages
       is now "both", so source packages will be tried if binary
       versions are not available or not up to date.
 
@@ -888,256 +1000,256 @@
 
   DEPRECATED AND DEFUNCT:
 
-    * download.file(method = "lynx") is defunct.
+    • download.file(method = "lynx") is defunct.
 
-    * Building R using the included versions of zlib, bzip2, xz and
+    • Building R using the included versions of zlib, bzip2, xz and
       PCRE is deprecated: these are frozen (bar essential bug-fixes)
       and will be removed for R 3.3.0.
 
-    * The configure option --with-valgrind-instrumentation=3 has been
+    • The configure option --with-valgrind-instrumentation=3 has been
       withdrawn, as it did not work with recent valgrind headers: it is
       now treated as level 2.
 
-    * The MethodsList class in package methods had been deprecated in R
+    • The MethodsList class in package methods had been deprecated in R
       2.11.0 and is defunct now.  Functions using it are defunct if
       they had been deprecated in R 2.11.0, and are deprecated now,
       otherwise.
 
   BUG FIXES:
 
-    * Fixed two obscure bugs in pairlist subassignment, reported by
+    • Fixed two obscure bugs in pairlist subassignment, reported by
       Radford Neal as part of pqR issue 16.
 
-    * Fixes for bugs in handling empty arguments and argument matching
+    • Fixes for bugs in handling empty arguments and argument matching
       by name in log().
 
-    * all.equal() gains methods for environments and refClasses.
+    • all.equal() gains methods for environments and refClasses.
 
-    * [<- and [[<- gain S4 data.frame methods to avoid corruption of S4
+    • [<- and [[<- gain S4 data.frame methods to avoid corruption of S4
       class information by the S3 methods.
 
-    * callNextMethod() should now work within a .local call when ... is
+    • callNextMethod() should now work within a .local call when ... is
       absent from formals(.local).
 
-    * dput(pairlist(x)) generates a call to the pairlist constructor
+    • dput(pairlist(x)) generates a call to the pairlist constructor
       instead of the list constructor.
 
-    * Fix missing() when arguments are propagated through ... .
+    • Fix missing() when arguments are propagated through ... .
       (PR#15707)
 
-    * eigen(m) now defaults to symmetric = TRUE even when the dimnames
+    • eigen(m) now defaults to symmetric = TRUE even when the dimnames
       are asymmetric if the matrix is otherwise symmetric.  (PR#16151)
 
-    * Fix issues with forwarding ... through callGeneric() and
+    • Fix issues with forwarding ... through callGeneric() and
       callNextMethod().  (PR#16141)
 
-    * callGeneric() now works after a callNextMethod().
+    • callGeneric() now works after a callNextMethod().
 
-    * Subclass information is kept consistent when replacing an
-      ordinary S4 class with an "old class" _via_ the S4Class argument
+    • Subclass information is kept consistent when replacing an
+      ordinary S4 class with an “old class” _via_ the S4Class argument
       to setOldClass(). Thus, for example, a data.frame is valid for a
       list argument in the signature, and a factor is valid for vector
       arguments.
 
-    * In qbeta() the inversion of pbeta() is much more sophisticated.
+    • In qbeta() the inversion of pbeta() is much more sophisticated.
       This works better in corner cases some of which failed completely
       previously (PR#15755), or were using too many iterations.
 
-    * Auto-printing no longer duplicates objects when printing is
+    • Auto-printing no longer duplicates objects when printing is
       dispatched to a method.
 
-    * kmeans(x, k) would fail when nrow(x) >= 42949673.  (Comment 6 of
+    • kmeans(x, k) would fail when nrow(x) >= 42949673.  (Comment 6 of
       PR#15364)
 
-    * 'Abbreviated' locale-specific day and month names could have been
+    • ‘Abbreviated’ locale-specific day and month names could have been
       truncated in those rare locales where there are the same as the
       full names.
 
-    * An irrelevant warning message from updating subclass information
+    • An irrelevant warning message from updating subclass information
       was silenced (the namespace would not be writable in this case).
 
 CHANGES IN R 3.1.3:
 
   NEW FEATURES:
 
-    * The internal method of download.file() can now handle files
+    • The internal method of download.file() can now handle files
       larger than 2GB on 32-bit builds which support such files (tested
       on 32-bit R running on 64-bit Windows).
 
-    * kruskal.test() warns on more types of suspicious input.
+    • kruskal.test() warns on more types of suspicious input.
 
-    * The as.dendrogram() method for "hclust" objects gains a check
+    • The as.dendrogram() method for "hclust" objects gains a check
       argument protecting against memory explosion for invalid inputs.
 
-    * capabilities() has a new item long.double which indicates if the
+    • capabilities() has a new item long.double which indicates if the
       build uses a long double type which is longer than double.
 
-    * nlm() no longer modifies the callback argument in place (a new
+    • nlm() no longer modifies the callback argument in place (a new
       vector is allocated for each invocation, which mimics the
       implicit duplication that occurred in R < 3.1.0); note that this
       is a change from the previously documented behavior. (PR#15958)
 
-    * icuSetCollate() now accepts locale = "ASCII" which uses the basic
+    • icuSetCollate() now accepts locale = "ASCII" which uses the basic
       C function strcmp and so collates strings byte-by-byte in
       numerical order.
 
-    * sessionInfo() tries to report the OS version in use (not just
+    • sessionInfo() tries to report the OS version in use (not just
       that compiled under, and including details of Linux
       distributions).
 
-    * model.frame() (used by lm() and many other modelling functions)
+    • model.frame() (used by lm() and many other modelling functions)
       now warns when it drops contrasts from factors.  (Wish of
       PR#16119)
 
-    * install.packages() and friends now accept the value type =
+    • install.packages() and friends now accept the value type =
       "binary" as a synonym for the native binary type on the platform
       (if it has one).
 
-    * Single source or binary files can be supplied for
+    • Single source or binary files can be supplied for
       install.packages(type = "both") and the appropriate type and
       repos = NULL will be inferred.
 
-    * New function pcre_config() to report on some of the configuration
+    • New function pcre_config() to report on some of the configuration
       options of the version of PCRE in use.  In particular, this
       reports if regular expressions using \p{xx} are supported.
 
-    * (Windows.) download.file(cacheOK = FALSE) is now supported when
+    • (Windows.) download.file(cacheOK = FALSE) is now supported when
       internet2.dll is used.
 
-    * browseURL() has been updated to work with Firefox 36.0 which has
+    • browseURL() has been updated to work with Firefox 36.0 which has
       dropped support for the -remote interface.
 
   INSTALLATION and INCLUDED SOFTWARE:
 
-    * The included version of PCRE has been updated to 8.36.
+    • The included version of PCRE has been updated to 8.36.
 
-    * configure accepts MAKEINFO=texi2any as another way to ensure
+    • configure accepts MAKEINFO=texi2any as another way to ensure
       texinfo 5.x is used when both 5.x and 4.x are installed.
 
   UTILITIES:
 
-    * R CMD check now checks the packages used in \donttest sections of
+    • R CMD check now checks the packages used in \donttest sections of
       the examples are specified in the DESCRIPTION file.  (These are
       needed to run the examples interactively.)
 
-    * R CMD check checks for the undeclared use of GNU extensions in
+    • R CMD check checks for the undeclared use of GNU extensions in
       Makefiles, and for Makefiles with a missing final linefeed.
 
       R CMD build will correct line endings in all Makefiles, not just
       those in the src directory.
 
-    * R CMD check notes uses of library() and require() in package
-      code: see the section 'Suggested packages' of 'Writing R
-      Extensions' for good practice.
+    • R CMD check notes uses of library() and require() in package
+      code: see the section ‘Suggested packages’ of ‘Writing R
+      Extensions’ for good practice.
 
   DEPRECATED AND DEFUNCT:
 
-    * The configure option --with-valgrind-instrumentation=3 is
+    • The configure option --with-valgrind-instrumentation=3 is
       deprecated and will be removed in R 3.2.0.
 
   BUG FIXES:
 
-    * (Windows.) Rscript.exe was missing a manifest specifying the
+    • (Windows.) Rscript.exe was missing a manifest specifying the
       modern style for common controls (e.g., the download progress
       bar).
 
-    * If a package had extra documentation files but no vignette, the
+    • If a package had extra documentation files but no vignette, the
       HTML help system produced an empty index page.
 
-    * The parser now gives an error if a null character is included in
+    • The parser now gives an error if a null character is included in
       a string using Unicode escapes. (PR#16046)
 
-    * qr.Q() failed on complex arguments due to pre-3.0(!) typo.
+    • qr.Q() failed on complex arguments due to pre-3.0(!) typo.
       (PR#16054)
 
-    * abs() failed with named arguments when the argument was complex.
+    • abs() failed with named arguments when the argument was complex.
       (PR#16047)
 
-    * "noquote" objects may now be used as columns in data frames.
+    • "noquote" objects may now be used as columns in data frames.
       (PR#15997)
 
-    * Some values with extremely long names were printed incorrectly.
+    • Some values with extremely long names were printed incorrectly.
       (PR#15999)
 
-    * Extremely large exponents on zero expressed in scientific
+    • Extremely large exponents on zero expressed in scientific
       notation (e.g. 0.0e50000) could give NaN.  (PR#15976)
 
-    * download.file() reported downloaded sizes as 0KB if less than
+    • download.file() reported downloaded sizes as 0KB if less than
       1MB, only for R 3.1.2 and only on big-endian platforms.
 
-    * prompt() did not escape percent signs in the automatically
+    • prompt() did not escape percent signs in the automatically
       generated usage section of help files.
 
-    * drop.terms() dropped some of the attributes of the object it was
+    • drop.terms() dropped some of the attributes of the object it was
       working with.  (PR#16029)
 
-    * (Windows.) The command completion in Rgui.exe messed up the
+    • (Windows.) The command completion in Rgui.exe messed up the
       console.  (PR#15791)
 
-    * (Windows.) The choose.files() command returned a blank string
+    • (Windows.) The choose.files() command returned a blank string
       when the user asked for a single file but cancelled the request.
       (PR#16074)
 
-    * Math2 S4 group generics failed to correctly dispatch "structure"-
+    • Math2 S4 group generics failed to correctly dispatch "structure"-
       and "nonStructure"-derived classes.
 
-    * loadNamespace() imposed undocumented restrictions on the
+    • loadNamespace() imposed undocumented restrictions on the
       versionCheck parameter.  (Reported by Geoff Lee.)
 
-    * Rare over-runs detected by AddressSanitizer in substr() and its
+    • Rare over-runs detected by AddressSanitizer in substr() and its
       replacement version have been avoided.
 
       _Inter alia_ that fix gives the documented behaviour for
       substr(x, 1, 2) <- "" (subsequently reported as PR#16214).
 
-    * Loading packages incorrectly defining an S4 generic followed by a
+    • Loading packages incorrectly defining an S4 generic followed by a
       function of the same name caused an erroneous cyclic namespace
       dependency error.
 
-    * Declared vignette encodings are now always passed to the vignette
+    • Declared vignette encodings are now always passed to the vignette
       engine.
 
-    * Port Tomas Kalibera's fix from R-devel that restores the
+    • Port Tomas Kalibera's fix from R-devel that restores the
       loadMethod() fast path, effectively doubling the speed of S4
       dispatch.
 
-    * power.t.test() and power.prop.test() now make use of the
+    • power.t.test() and power.prop.test() now make use of the
       extendInt option of uniroot() and hence work in more extreme
       cases.  (PR#15792)
 
-    * If a package was updated and attached when its namespace was
+    • If a package was updated and attached when its namespace was
       already loaded, it could end up with parts from one version and
       parts from the other.  (PR#16120)
 
-    * tools:::.Rdconv() didn't accept --encoding= due to a typo.
+    • tools:::.Rdconv() didn't accept --encoding= due to a typo.
       (PR#16121)
 
-    * Unix-alike builds without a suitable makeinfo were documented to
+    • Unix-alike builds without a suitable makeinfo were documented to
       link the missing HTML manuals to CRAN, but did not.
 
-    * save(*, ascii=TRUE) and load() now correctly deal with NaN's.
+    • save(*, ascii=TRUE) and load() now correctly deal with NaN's.
       (PR#16137)
 
-    * split.Date() retains fractional representations while avoiding
+    • split.Date() retains fractional representations while avoiding
       incomplete class propagation.
 
-    * R_ext/Lapack.h had not been updated for changes made by LAPACK to
+    • R_ext/Lapack.h had not been updated for changes made by LAPACK to
       the argument lists of its (largely internal) functions dlaed2 and
       dlaed3.  (PR#16157)
 
-    * RShowDoc("NEWS", "txt") had not been updated for the layout
+    • RShowDoc("NEWS", "txt") had not been updated for the layout
       changes of R 3.1.0.
 
-    * The xtfrm() method for class "Surv" has been corrected and its
+    • The xtfrm() method for class "Surv" has been corrected and its
       description expanded.
 
-    * mode(x) <- y would incorrectly evaluate x before changing its
+    • mode(x) <- y would incorrectly evaluate x before changing its
       mode. (PR#16215)
 
-    * besselJ(1, 2^64) and besselY(..) now signal a warning, returning
+    • besselJ(1, 2^64) and besselY(..) now signal a warning, returning
       NaN instead of typically segfaulting. (Issue 3 of PR#15554)
 
-    * HTML conversion of \href markup in .Rd files did not remove the
+    • HTML conversion of \href markup in .Rd files did not remove the
       backslash from \% and so gave an invalid URL.  In a related
       change, the \ escape is now required in such URLs.
 
@@ -1145,19 +1257,19 @@
 
   NEW FEATURES:
 
-    * embedFonts() now defaults to format = "ps2write" for .ps and .eps
+    • embedFonts() now defaults to format = "ps2write" for .ps and .eps
       files.  This is available in Ghostscript 9.x (since 2010) whereas
       the previous default, format = "pswrite", was removed in
       Ghostscript 9.10.
 
-    * For consistency with [dpqr]norm(), [dp]lnorm(sdlog = 0) model a
+    • For consistency with [dpqr]norm(), [dp]lnorm(sdlog = 0) model a
       point mass at exp(mulog) rather than return NaN (for an error).
 
-    * capabilities() now reports if ICU is compiled in for use for
+    • capabilities() now reports if ICU is compiled in for use for
       collation (it is only actually used if a suitable locale is set
       for collation, and never for a C locale).
 
-    * (OS X only.) Package tcltk checks when loaded if it is linked
+    • (OS X only.) Package tcltk checks when loaded if it is linked
       against the CRAN X11-based Tcl/Tk and if so that the Tcl/Tk
       component and the X11 libraries are installed.  This allows more
       informative error messages to be given advising the installation
@@ -1168,430 +1280,430 @@
       from command-line R) check that the X11 libraries are installed
       and if not advises installing XQuartz.
 
-    * icuSetCollate() allows locale = "default", and locale = "none" to
+    • icuSetCollate() allows locale = "default", and locale = "none" to
       use OS services rather than ICU for collation.
 
       Environment variable R_ICU_LOCALE can be used to set the default
       ICU locale, in case the one derived from the OS locale is
       inappropriate (this is currently necessary on Windows).
 
-    * New function icuGetCollate() to report on the ICU collation
+    • New function icuGetCollate() to report on the ICU collation
       locale in use (if any).
 
-    * utils::URLencode() was updated to use unreserved and reserved
+    • utils::URLencode() was updated to use unreserved and reserved
       characters from RFC 3986 (<URL:
       http://tools.ietf.org/html/rfc3986>) instead of RFC 1738.
 
-    * unique(warnings()) and c(warnings()) are now supported.
+    • unique(warnings()) and c(warnings()) are now supported.
 
-    * The Bioconductor 'version' used by setRepositories() now defaults
+    • The Bioconductor ‘version’ used by setRepositories() now defaults
       to 3.0. (It can be set at runtime _via_ environment variable
       R_BIOC_VERSION.)
 
-    * Omegahat is no longer listed as providing Windows binary
+    • Omegahat is no longer listed as providing Windows binary
       packages, e.g. by setRepositories().  It has no binary packages
       available for R 3.1.x and those for earlier versions were 32-bit
       only.
 
   INSTALLATION and INCLUDED SOFTWARE:
 
-    * The configure script reports on the more important
+    • The configure script reports on the more important
       capabilities/options which will not be compiled in.
 
       More types of external BLAS are recognized by name in that
       report.
 
-    * When building R as a shared library, the -L${R_HOME}/lib${R_ARCH}
+    • When building R as a shared library, the -L${R_HOME}/lib${R_ARCH}
       flag is placed earlier in the link commands used during
       installation and when packages are installed: this helps ensure
       that the current build has priority if an R shared library has
       already been installed by e.g. install-libR in a library
-      mentioned in LDFLAGS (and not in 'your system's library
-      directory' as documented). (Wish of PR#15790.)
+      mentioned in LDFLAGS (and not in ‘your system's library
+      directory’ as documented). (Wish of PR#15790.)
 
-    * LaTeX package upquote is no longer required for R's use of
+    • LaTeX package upquote is no longer required for R's use of
       inconsolata.
 
-    * (Windows only) If both 32- and 64-bit versions of R are
+    • (Windows only) If both 32- and 64-bit versions of R are
       installed, the bin/R.exe and bin/Rscript.exe executables now run
       64-bit R.  (To run 32-bit R, overwrite these files with copies of
       bin/i386/Rfe.exe.)
 
   UTILITIES:
 
-    * Running R CMD check with _R_CHECK_DEPENDS_ONLY_ true now makes
+    • Running R CMD check with _R_CHECK_DEPENDS_ONLY_ true now makes
       the VignetteBuilder packages available even if they are listed in
       Suggests, since they are needed to recognise and process
       non-Sweave vignettes.
 
-    * R CMD check now reports empty importFrom declarations in a
+    • R CMD check now reports empty importFrom declarations in a
       NAMESPACE file, as these are common errors (writing
       importFrom(Pkg) where import(Pkg) was intended).
 
-    * R CMD check now by default checks code usage directly on the
+    • R CMD check now by default checks code usage directly on the
       package namespace without loading and attaching the package and
       its suggests and enhances.  For good practice with packages in
-      the Suggests field, see SS1.1.3.1 of 'Writing R Extensions'.  For
+      the Suggests field, see §1.1.3.1 of ‘Writing R Extensions’.  For
       use of lazy-data objects in the package's own code, see ?data.
 
   BUG FIXES:
 
-    * dmultinom() did not handle non-finite probabilities correctly.
+    • dmultinom() did not handle non-finite probabilities correctly.
 
-    * prettyNum(x, zero.print=*) now also works when x contains NAs.
+    • prettyNum(x, zero.print=*) now also works when x contains NAs.
 
-    * A longstanding bug exhibited by nlminb() on Windows was traced to
+    • A longstanding bug exhibited by nlminb() on Windows was traced to
       a compiler bug in gcc 4.6.3; a workaround has been put in place.
       (PR#15244 and PR#15914).
 
-    * Rendering of \command in HTML versions of help pages has been
+    • Rendering of \command in HTML versions of help pages has been
       improved: this is particularly evident on the help page for
       INSTALL.
 
-    * as.hexmode(x) and as.octmode(x) now behave correctly for some
+    • as.hexmode(x) and as.octmode(x) now behave correctly for some
       numeric x, e.g., c(NA, 1) or c(1, pi).
 
-    * drop1() failed if the scope argument had no variables to drop.
+    • drop1() failed if the scope argument had no variables to drop.
       (PR#15935)
 
-    * edit() (and hence fix()) failed if an object had a non-character
+    • edit() (and hence fix()) failed if an object had a non-character
       attribute named "source" (an attribute that had been used in R
       prior to version 2.14.0).
 
-    * callGeneric() could fail if the generic had ... as a formal
+    • callGeneric() could fail if the generic had ... as a formal
       argument. (PR#15937).
 
-    * Forking in package parallel called C entry point exit in the
+    • Forking in package parallel called C entry point exit in the
       child.  This was unsafe (_exit should have been called), and
       could flush stdin of the main R process (seen most often on
       Solaris).
 
       As good practice, stdout is now flushed before forking a child.
 
-    * R objects such as list(`a\b` = 1) now print correctly.
+    • R objects such as list(`a\b` = 1) now print correctly.
 
-    * getAnywhere("C_pbinom") now returns correctly a single object
+    • getAnywhere("C_pbinom") now returns correctly a single object
       (rather than unlisting it).
 
-    * The confint() method for nls() fits failed it these has specified
+    • The confint() method for nls() fits failed it these has specified
       parameter limits despite using an algorithm other than "port".
       (PR#15960)
 
-    * Subclassing an S4 class failed if the class required arguments to
+    • Subclassing an S4 class failed if the class required arguments to
       the generator, through its initialize() method.
 
-    * removeSource() did not properly handle expressions containing
+    • removeSource() did not properly handle expressions containing
       arguments that were supplied as missing, e.g.  x[i,]. (PR#15957)
 
-    * as.environment(list()) now works, and as.list() of such an
+    • as.environment(list()) now works, and as.list() of such an
       environment is now the same as list().
 
-    * Several tcltk functions failed when run in unusual environments.
+    • Several tcltk functions failed when run in unusual environments.
       (PR#15970)
 
-    * options(list()) now works (trivially). (PR#15979)
+    • options(list()) now works (trivially). (PR#15979)
 
-    * merge(<dendrogram>, ..) now works correctly for two `independent'
+    • merge(<dendrogram>, ..) now works correctly for two `independent'
       dendrograms (PR#15648), and still compatibly via adjust = "auto"
       e.g. for two branches of an existing dendrogram.
 
-    * The plot method for "hclust" objects gets an optional argument
+    • The plot method for "hclust" objects gets an optional argument
       check; when that is true (the default) it checks more carefully
       for valid input.
 
-    * (Windows only) If a user chose to install 64 bit R but not 32 bit
+    • (Windows only) If a user chose to install 64 bit R but not 32 bit
       R, the bin/R and bin/Rscript executables failed to run.
       (PR#15981)
 
-    * Various possible buffer overruns have been prevented, and missed
+    • Various possible buffer overruns have been prevented, and missed
       memory protection added. (PR#15990)
 
-    * Rscript no longer passes --args to R when there are no extra
-      ("user") arguments.
+    • Rscript no longer passes --args to R when there are no extra
+      (“user”) arguments.
 
-    * objects like getClass("refClass")@prototype now print() and str()
+    • objects like getClass("refClass")@prototype now print() and str()
       without error.
 
-    * identical() now also looks at the S4 bit.
+    • identical() now also looks at the S4 bit.
 
-    * hist(x, breaks) is more robust in adding a small fuzz to few
+    • hist(x, breaks) is more robust in adding a small fuzz to few
       breaks when some are very large. (PR#15988)
 
-    * sub() and gsub() did not handle regular expressions like "\s{2,}"
-      properly if the text contained NA or non-ascii elements in a
+    • sub() and gsub() did not handle regular expressions like "\s{2,}"
+      properly if the text contained NA or non-ASCII elements in a
       UTF-8 locale.  Part of this was due to a bug in the TRE library.
       (PR#16009)
 
-    * RShowDoc("NEWS") now displays the PDF version.
+    • RShowDoc("NEWS") now displays the PDF version.
 
-    * Matrices and arrays with last dimension zero did not print at all
+    • Matrices and arrays with last dimension zero did not print at all
       or incompletely.  (PR#16012)
 
-    * plot.histogram() and hence hist() now respect the xaxs, yaxs and
+    • plot.histogram() and hence hist() now respect the xaxs, yaxs and
       lab graphics parameters.  (PR#16021)
 
-    * bw.SJ(x) and other bw.*() no longer segfault when x contains
+    • bw.SJ(x) and other bw.*() no longer segfault when x contains
       non-finite values. (PR#16024)
 
-    * R CMD Rd2pdf unintentionally ignored its --os option.
+    • R CMD Rd2pdf unintentionally ignored its --os option.
 
-    * The internal method of download.file() was not reporting file
+    • The internal method of download.file() was not reporting file
       sizes and progress correctly on files larger than 2GB (inherited
       from libxml2).  This is corrected for 64-bit builds (32-bit
       platforms may not support such files, but where possible will be
       supported in future versions of R).
 
-    * Work around a bug in OS X Yosemite where key environment
+    • Work around a bug in OS X Yosemite where key environment
       variables may be duplicated causing issues in subprocesses. The
       duplicates are now removed on R startup (via Rprofile).
       (PR#16042)
 
-    * Adjust X11 auto-launch detection in DISPLAY on OS X to recognize
+    • Adjust X11 auto-launch detection in DISPLAY on OS X to recognize
       latest XQuartz.
 
 CHANGES IN R 3.1.1:
 
   NEW FEATURES:
 
-    * When attach() reports conflicts, it does so compatibly with
+    • When attach() reports conflicts, it does so compatibly with
       library() by using message().
 
-    * R CMD Sweave no longer cleans any files by default, compatibly
+    • R CMD Sweave no longer cleans any files by default, compatibly
       with versions of R prior to 3.1.0.  There are new options
       --clean, --clean=default and --clean=keepOuts.
 
-    * tools::buildVignette() and tools::buildVignettes() with clean =
+    • tools::buildVignette() and tools::buildVignettes() with clean =
       FALSE no longer remove any created files.  buildvignette() gains
       a keep argument for more cleaning customization.
 
-    * The Bioconductor 'version' used by setRepositories() can now be
+    • The Bioconductor ‘version’ used by setRepositories() can now be
       set by environment variable R_BIOC_VERSION at runtime, not just
       when R is installed.  (It has been stated that Bioconductor will
-      switch from 'version' 2.14 to 'version' 3.0 during the lifetime
+      switch from ‘version’ 2.14 to ‘version’ 3.0 during the lifetime
       of the R 3.1 series.)
 
-    * Error messages from bugs in embedded Sexpr code in Sweave
+    • Error messages from bugs in embedded Sexpr code in Sweave
       documents now report the source location.
 
-    * type.convert(), read.table() and similar read.*() functions get a
+    • type.convert(), read.table() and similar read.*() functions get a
       new numerals argument, specifying how numeric input is converted
       when its conversion to double precision loses accuracy.  The
       default value, "allow.loss" allows accuracy loss, as in R
       versions before 3.1.0.
 
-    * For some compilers, integer addition could overflow without a
+    • For some compilers, integer addition could overflow without a
       warning.  R's internal code for both integer addition and
       subtraction is more robust now.  (PR#15774)
 
-    * The function determining the default number of knots for
+    • The function determining the default number of knots for
       smooth.spline() is now exported, as .nknots.smspl().
 
-    * dbeta(, a,b), pbeta(), qbeta() and rbeta() are now defined also
+    • dbeta(, a,b), pbeta(), qbeta() and rbeta() are now defined also
       for a = 0, b = 0, or infinite a and b (where they typically
       returned NaN before).
 
-    * Many package authors report that the RStudio graphics device does
+    • Many package authors report that the RStudio graphics device does
       not work correctly with their package's use of dev.new().  The
       new option dev.new(noRStudioGD = TRUE) replaces the RStudio
       override by the default device as selected by R itself, still
       respecting environment variables R_INTERACTIVE_DEVICE and
       R_DEFAULT_DEVICE.
 
-    * readRDS() now returns visibly.
+    • readRDS() now returns visibly.
 
-    * Modifying internal logical scalar constants now results in an
+    • Modifying internal logical scalar constants now results in an
       error instead of a warning.
 
-    * install.packages(repos = NULL) now accepts http:// or ftp:// URLs
+    • install.packages(repos = NULL) now accepts http:// or ftp:// URLs
       of package archives as well as file paths, and will download as
       required.  In most cases repos = NULL can be deduced from the
       extension of the URL.
 
-    * The warning when using partial matching with the $ operator on
+    • The warning when using partial matching with the $ operator on
       data frames is now only given when
       options("warnPartialMatchDollar") is TRUE.
 
-    * Package help requests like package?foo now try the package foo
+    • Package help requests like package?foo now try the package foo
       whether loaded or not.
 
-    * General help requests now default to trying all loaded packages,
+    • General help requests now default to trying all loaded packages,
       not just those on the search path.
 
-    * Added a new function promptImport(), to generate a help page for
+    • Added a new function promptImport(), to generate a help page for
       a function that was imported from another package (and presumably
       re-exported, or help would not be needed).
 
   INSTALLATION and INCLUDED SOFTWARE:
 
-    * configure option --with-internal-tzcode can now be used with
+    • configure option --with-internal-tzcode can now be used with
       variable rsharedir.
 
-    * The included version of PCRE has been updated to 8.35.
+    • The included version of PCRE has been updated to 8.35.
 
-    * There is a new target make uninstall-libR to remove an installed
+    • There is a new target make uninstall-libR to remove an installed
       shared/static libR.
 
       make install-libR now works if a sub-architecture is used,
       although the user will need to specify libdir differently for
       different sub-architectures.
 
-    * There is more extensive advice on which LaTeX packages are
+    • There is more extensive advice on which LaTeX packages are
       required to install R or to make package manuals (as done by R
-      CMD check) in the 'Writing R Extensions' manual.
+      CMD check) in the ‘Writing R Extensions’ manual.
 
-    * Compilers/linkers were handling the visibility control in
+    • Compilers/linkers were handling the visibility control in
       src/extra/xz inconsistently (and apparently in some cases
       incorrectly), so it has been simplified.  (PR#15327)
 
-    * (Windows) There is updated support for the use of ICU for
-      collation: see the 'R Installation and Administration Manual'.
+    • (Windows) There is updated support for the use of ICU for
+      collation: see the ‘R Installation and Administration Manual’.
 
   BUG FIXES:
 
-    * dbinom(x, n), pbinom(), dpois(), etc, are slightly less
+    • dbinom(x, n), pbinom(), dpois(), etc, are slightly less
       restrictive in checking if n is integer-valued.  (Wish of
       PR#15734.)
 
-    * pchisq(x, df, ncp, log.p = TRUE) is more accurate and no longer
+    • pchisq(x, df, ncp, log.p = TRUE) is more accurate and no longer
       underflows for small x and ncp < 80, e.g, for pchisq(1e-5, df =
       100, ncp = 1, log = TRUE).  (Based on PR#15635 and a suggestion
       by Roby Joehanes.)
 
-    * The s ("step into") command in the debugger would cause R to step
+    • The s (“step into”) command in the debugger would cause R to step
       into expressions evaluated there, not just into functions being
       debugged.  (PR#15770)
 
-    * The C code used by strptime() rejected time-zone offsets of more
+    • The C code used by strptime() rejected time-zone offsets of more
       than +1200 (+1245, +1300 and +1400 can occur).  (PR#15768)
 
-    * (Windows only.)  png(type = "cairo", antialias = "gray") was not
+    • (Windows only.)  png(type = "cairo", antialias = "gray") was not
       accepted.  (PR#15760)
 
-    * Use of save(..., envir=) with named objects could fail.
+    • Use of save(..., envir=) with named objects could fail.
       (PR#15758)
 
-    * Sweave() mis-parsed Sexpr expressions that contained backslashes.
+    • Sweave() mis-parsed Sexpr expressions that contained backslashes.
       (PR#15779)
 
-    * The return value from options(foo = NULL) was not the previous
+    • The return value from options(foo = NULL) was not the previous
       value of the option.  (PR#15781)
 
-    * enc2utf8() and enc2native() did not always mark the encoding of
+    • enc2utf8() and enc2native() did not always mark the encoding of
       the return values when it was known.
 
-    * dnbinom(x, size = <large>, mu, log = TRUE) no longer underflows
+    • dnbinom(x, size = <large>, mu, log = TRUE) no longer underflows
       to -Inf for large mu, thanks to a suggestion from Alessandro
       Mammana (MPI MolGen, Berlin).
 
-    * pbeta(x, a, b, log = TRUE) no longer behaves discontinuously (in
+    • pbeta(x, a, b, log = TRUE) no longer behaves discontinuously (in
       a small x-region) because of denormalized numbers.  Also,
-      pbeta(1-1e-12, 1e30, 1.001, log=TRUE) now terminates "in real
-      time".
+      pbeta(1-1e-12, 1e30, 1.001, log=TRUE) now terminates “in real
+      time”.
 
-    * The "CRAN" filter (see available.packages()) no longer removes
+    • The "CRAN" filter (see available.packages()) no longer removes
       duplicates other than of packages on CRAN, and does not fail if
       there is no CRAN repository in getOption("repos").
 
-    * The device listing from dev2bitmap() and bitmap() was truncated
+    • The device listing from dev2bitmap() and bitmap() was truncated
       to 1000 characters: modern versions of GhostScript on most
       platforms have many more devices.
 
-    * (Windows.)  Commands such as Sys.which() and pipe() which needed
-      to find the full path to a command could segfault if the 'long'
-      path name was much longer than the 'short' path name (which
+    • (Windows.)  Commands such as Sys.which() and pipe() which needed
+      to find the full path to a command could segfault if the ‘long’
+      path name was much longer than the ‘short’ path name (which
       Sys.which() returns), as the behaviour of the Windows API call
       had changed.
 
-    * R CMD build will fail with an error if one of the packages
+    • R CMD build will fail with an error if one of the packages
       specified in the VignetteBuilder field is not installed.
       (Without loading those packages it cannot be ascertained which
       files are intended to be vignettes. This means that the
       VignetteBuilder packages have to be installed for package
       checking too.)  (Wish of PR#15775.)
 
-    * Misguided attempts to use chull() with non-finite points now give
+    • Misguided attempts to use chull() with non-finite points now give
       an error (related to PR#15777).
 
-    * For a formula with exactly 32 variables the 32nd variable was
+    • For a formula with exactly 32 variables the 32nd variable was
       aliased to the intercept in some C-level computations of terms,
       so that for example attempting to remove it would remove the
       intercept instead (and leave a corrupt internal structure).
       (PR#15735)
 
-    * anyDuplicated() silently returned wrong values when the first
+    • anyDuplicated() silently returned wrong values when the first
       duplicate was at an index which was too large to be stored in an
       integer vector (although a lot of RAM and patience would have
       been needed to encounter this).
 
-    * tools::Rd2ex(commentDontrun = FALSE) failed if the block had only
+    • tools::Rd2ex(commentDontrun = FALSE) failed if the block had only
       one line.
 
-    * Hexadecimal constants such as 0x110p-5L which were incorrectly
+    • Hexadecimal constants such as 0x110p-5L which were incorrectly
       qualified by L were parsed incorrectly since R 3.0.0, with a
       slightly garbled warning. (PR#15753)
 
-    * system() returned success on some platforms even if the system
+    • system() returned success on some platforms even if the system
       was unable to launch a process. (PR#15796)
 
-    * (Windows Rgui console.)  Unbuffered output was sometimes not
+    • (Windows Rgui console.)  Unbuffered output was sometimes not
       output immediately if the prompt was not on the last line of the
       console.
 
-    * The built-in help server did not declare the encoding for the
+    • The built-in help server did not declare the encoding for the
       DESCRIPTION or other text files to be the package encoding, so
       non-ASCII characters could be displayed incorrectly.
 
-    * R is now trying harder to not cleanup child processes that were
+    • R is now trying harder to not cleanup child processes that were
       not spawned by mcparallel() on platforms that provide information
       about the source process of the SIGCHLD signal. This allows 3rd
       party libraries to manage the exit status of children that they
       spawn without R interfering.
 
-    * mcmapply() was only parallelizing if the number of jobs was
+    • mcmapply() was only parallelizing if the number of jobs was
       bigger than the number of cores. It now parallelizes if the
       number of jobs is more than one.
 
-    * Auto-printing would re-evaluate its argument when trying to
+    • Auto-printing would re-evaluate its argument when trying to
       dispatch to a print method.  This is now avoided when possible.
 
-    * Unserializing (including load() and readRDS()) could silently
+    • Unserializing (including load() and readRDS()) could silently
       return incorrect numeric values from ASCII saves if there was a
       read error.
 
-    * getParseData() could return incorrect values for the parents of
+    • getParseData() could return incorrect values for the parents of
       some elements. (Reported by Andrew Redd.)
 
-    * Attempting to use data frames of 2^31 or more rows with merge()
+    • Attempting to use data frames of 2^31 or more rows with merge()
       or to create a merged data frame of that size now gives a clearer
       error message.
 
-    * parse() did not check its file argument was a connection if it
+    • parse() did not check its file argument was a connection if it
       was not a character string, so e.g. parse(FALSE) attempted to
       read from stdin.
 
       Nor did dump() and dput().
 
-    * The "help.try.all.packages" option was ignored when the shortcut
+    • The "help.try.all.packages" option was ignored when the shortcut
       syntax for help was used, e.g. ?foo.
 
-    * A potential segfault in string allocation has been fixed.  (Found
+    • A potential segfault in string allocation has been fixed.  (Found
       by Radford Neal.)
 
-    * Potential memory protection errors in sort() and D() have been
+    • Potential memory protection errors in sort() and D() have been
       fixed. (Found by Radford Neal.)
 
-    * Fixed a lack of error checking in graphics event functions.
+    • Fixed a lack of error checking in graphics event functions.
       (Found by Radford Neal; a different patch used here than the one
       in pqR.)
 
-    * numericDeriv() sometimes miscalculated the gradient.  (PR#15849,
+    • numericDeriv() sometimes miscalculated the gradient.  (PR#15849,
       reported originally by Radford Neal)
 
 CHANGES IN R 3.1.0:
 
   NEW FEATURES:
 
-    * type.convert() (and hence by default read.table()) returns a
+    • type.convert() (and hence by default read.table()) returns a
       character vector or factor when representing a numeric input as a
       double would lose accuracy.  Similarly for complex inputs.
 
@@ -1599,85 +1711,85 @@
       decimal places that are intended to be read as numeric, specify
       colClasses in read.table() to be "numeric".
 
-    * tools::Rdiff(useDiff = FALSE) is closer to the POSIX definition
+    • tools::Rdiff(useDiff = FALSE) is closer to the POSIX definition
       of diff -b (as distinct from the description in the man pages of
       most systems).
 
-    * New function anyNA(), a version of any(is.na(.)) which is fast
+    • New function anyNA(), a version of any(is.na(.)) which is fast
       for atomic vectors, based on a proposal by Tim Hesterberg. (Wish
       of PR#15239.)
 
-    * arrayInd(*, useNames = TRUE) and, analogously, which(*, arr.ind =
+    • arrayInd(*, useNames = TRUE) and, analogously, which(*, arr.ind =
       TRUE) now make use of names(.dimnames) when available.
 
-    * is.unsorted() now also works for raw vectors.
+    • is.unsorted() now also works for raw vectors.
 
-    * The "table" method for as.data.frame() (also useful as
+    • The "table" method for as.data.frame() (also useful as
       as.data.frame.table()) now passes sep and base arguments to
       provideDimnames().
 
-    * uniroot() gets new optional arguments, notably extendInt,
+    • uniroot() gets new optional arguments, notably extendInt,
       allowing to auto-extend the search interval when needed.  The
       return value has an extra component, init.it.
 
-    * switch(f, ...) now warns when f is a factor, as this typically
+    • switch(f, ...) now warns when f is a factor, as this typically
       happens accidentally where the useR meant to pass a character
       string, but f is treated as integer (as always documented).
 
-    * The parser has been modified to use less memory.
+    • The parser has been modified to use less memory.
 
-    * The way the unary operators (+ - !) handle attributes is now more
+    • The way the unary operators (+ - !) handle attributes is now more
       consistent.  If there is no coercion, all attributes (including
       class) are copied from the input to the result: otherwise only
       names, dims and dimnames are.
 
-    * colorRamp() and colorRampPalette() now allow non-opaque colours
+    • colorRamp() and colorRampPalette() now allow non-opaque colours
       and a ramp in opacity via the new argument alpha = TRUE.
       (Suggested by Alberto Krone-Martins, but optionally as there are
       existing uses which expect only RGB values.)
 
-    * grid.show.layout() and grid.show.viewport() get an optional vp.ex
+    • grid.show.layout() and grid.show.viewport() get an optional vp.ex
       argument.
 
-    * There is a new function find_gs_cmd() in the tools package to
+    • There is a new function find_gs_cmd() in the tools package to
       locate a GhostScript executable.  (This is an enhanced version of
       a previously internal function there.)
 
-    * object.size() gains a format() method.
+    • object.size() gains a format() method.
 
-    * There is a new family, "ArialMT", for the pdf() and postscript()
+    • There is a new family, "ArialMT", for the pdf() and postscript()
       devices.  This will only be rendered correctly on viewers which
       have access to Monotype TrueType fonts (which are sometimes
       requested by journals).
 
-    * The text and PDF news files, including NEWS and NEWS.2, have been
+    • The text and PDF news files, including NEWS and NEWS.2, have been
       moved to the doc directory.
 
-    * combn(x, simplify = TRUE) now gives a factor result for factor
+    • combn(x, simplify = TRUE) now gives a factor result for factor
       input x (previously user error).  (Related to PR#15442.)
 
-    * Added utils::fileSnapshot() and utils::changedFiles() functions
+    • Added utils::fileSnapshot() and utils::changedFiles() functions
       to allow snapshots and comparison of directories of files.
 
-    * make.names(names, unique=TRUE) now tries to preserve existing
+    • make.names(names, unique=TRUE) now tries to preserve existing
       names. (Suggestion of PR#15452.)
 
-    * New functions cospi(x), sinpi(x), and tanpi(x), for more accurate
+    • New functions cospi(x), sinpi(x), and tanpi(x), for more accurate
       computation of cos(pi*x), etc, both in R and the C API.  Using
       these gains accuracy in some cases, e.g., inside lgamma() or
       besselI().  (Suggested by Morten Welinder in PR#15529.)
 
-    * print.table(x, zero.print = ".") now also has an effect when x is
+    • print.table(x, zero.print = ".") now also has an effect when x is
       not integer-valued.
 
-    * There is more support to explore the system's idea of time-zone
+    • There is more support to explore the system's idea of time-zone
       names.  Sys.timezone() tries to give the current system setting
       by name (and succeeds at least on Linux, OS X, Solaris and
       Windows), and OlsonNames() lists the names in the system's Olson
       database. Sys.timezone(location = FALSE) gives the previous
       behaviour.
 
-    * Platforms with a 64-bit time_t type are allowed to handle
+    • Platforms with a 64-bit time_t type are allowed to handle
       conversions between the "POSIXct" and "POSIXlt" classes for
       date-times outside the 32-bit range (before 1902 or after 2037):
       the existing workarounds are used on other platforms.  (Note that
@@ -1690,29 +1802,29 @@
       is 32-bit.  For R for Windows it is 64-bit (for both
       architectures as from this version).
 
-    * The "save.defaults" option can include a value for
+    • The "save.defaults" option can include a value for
       compression_level.  (Wish of PR#15579.)
 
-    * colSums() and friends now have support for arrays and data-frame
+    • colSums() and friends now have support for arrays and data-frame
       columns with 2^31 or more elements.
 
-    * as.factor() is faster when f is an unclassed integer vector (for
+    • as.factor() is faster when f is an unclassed integer vector (for
       example, when called from tapply()).
 
-    * fft() now works with longer inputs, from the 12 million
+    • fft() now works with longer inputs, from the 12 million
       previously supported up to 2 billion.  (PR#15593)
 
-    * Complex svd() now uses LAPACK subroutine ZGESDD, the complex
+    • Complex svd() now uses LAPACK subroutine ZGESDD, the complex
       analogue of the routine used for the real case.
 
-    * Sweave now outputs .tex files in UTF-8 if the input encoding is
+    • Sweave now outputs .tex files in UTF-8 if the input encoding is
       declared to be UTF-8, regardless of the local encoding.  The
       UTF-8 encoding may now be declared using a LaTeX comment
       containing the string %\SweaveUTF8 on a line by itself.
 
-    * file.copy() gains a copy.date argument.
+    • file.copy() gains a copy.date argument.
 
-    * Printing of date-times will make use of the time-zone
+    • Printing of date-times will make use of the time-zone
       abbreviation in use at the time, if known.  For example, for
       Paris pre-1940 this could be LMT, PMT, WET or WEST.  To enable
       this, the "POSIXlt" class has an optional component "zone"
@@ -1721,21 +1833,21 @@
       For platforms which support it, there is also a component
       "gmtoff" recording the offset from GMT where known.
 
-    * (On Windows, by default on OS X and optionally elsewhere.)  The
+    • (On Windows, by default on OS X and optionally elsewhere.)  The
       system C function strftime has been replaced by a more
       comprehensive version with closer conformance to the POSIX 2008
       standard.
 
-    * dnorm(x, log = FALSE) is more accurate (but somewhat slower) for
+    • dnorm(x, log = FALSE) is more accurate (but somewhat slower) for
       |x| > 5; as suggested in PR#15620.
 
-    * Some versions of the tiff() device have further compression
+    • Some versions of the tiff() device have further compression
       options.
 
-    * read.table(), readLines() and scan() have a new argument to
+    • read.table(), readLines() and scan() have a new argument to
       influence the treatment of embedded nuls.
 
-    * Avoid duplicating the right hand side values in complex
+    • Avoid duplicating the right hand side values in complex
       assignments when possible.  This reduces copying of replacement
       values in expressions such as Z$a <- a0 and ans[[i]] <- tmp: some
       package code has relied on there being copies.
@@ -1743,29 +1855,29 @@
       Also, a number of other changes to reduce copying of objects; all
       contributed by or based on suggestions by Michael Lawrence.
 
-    * The fast argument of KalmanLike(), KalmanRun() and
+    • The fast argument of KalmanLike(), KalmanRun() and
       KalmanForecast() has been replaced by update, which instead of
       updating mod in place, optionally returns the updated model in an
       attribute "mod" of the return value.
 
-    * arima() and makeARIMA() get a new optional argument SSinit,
+    • arima() and makeARIMA() get a new optional argument SSinit,
       allowing the choice of a different *s*tate *s*pace initialization
       which has been observed to be more reliable close to
       non-stationarity: see PR#14682.
 
-    * warning() has a new argument noBreaks., to simplify
+    • warning() has a new argument noBreaks., to simplify
       post-processing of output with options(warn = 1).
 
-    * pushBack() gains an argument encoding, to support reading of
+    • pushBack() gains an argument encoding, to support reading of
       UTF-8 characters using scan(), read.table() and related functions
       in a non-UTF-8 locale.
 
-    * all.equal.list() gets a new argument use.names which by default
+    • all.equal.list() gets a new argument use.names which by default
       labels differing components by names (if they match) rather than
       by integer index.  Saved R output in packages may need to be
       updated.
 
-    * The methods for all.equal() and attr.all.equal() now have
+    • The methods for all.equal() and attr.all.equal() now have
       argument check.attributes after ... so it cannot be partially nor
       positionally matched (as it has been, unintentionally).
 
@@ -1780,56 +1892,56 @@
       The message for all.equal.numeric() reports a "scaled difference"
       only for scale != 1.
 
-    * all.equal() now has a "POSIXt" method replacing the "POSIXct"
+    • all.equal() now has a "POSIXt" method replacing the "POSIXct"
       method.
 
-    * The "Date" and "POSIXt" methods of seq() allows by = "quarter"
+    • The "Date" and "POSIXt" methods of seq() allows by = "quarter"
       for completeness (by = "3 months" always worked).
 
-    * file.path() removes any trailing separator on Windows, where they
+    • file.path() removes any trailing separator on Windows, where they
       are invalid (although sometimes accepted).  This is intended to
       enhance the portability of code written by those using POSIX file
       systems (where a trailing / can be used to confine path matching
       to directories).
 
-    * New function agrepl() which like grepl() returns a logical
+    • New function agrepl() which like grepl() returns a logical
       vector.
 
-    * fifo() is now supported on Windows. (PR#15600)
+    • fifo() is now supported on Windows. (PR#15600)
 
-    * sort.list(method = "radix") now allows negative integers (wish of
+    • sort.list(method = "radix") now allows negative integers (wish of
       PR#15644).
 
-    * Some functionality of print.ts() is now available in
+    • Some functionality of print.ts() is now available in
       .preformat.ts() for more modularity.
 
-    * mcparallel() gains an option detach = TRUE which allows execution
+    • mcparallel() gains an option detach = TRUE which allows execution
       of code independently of the current session.  It is based on a
       new estranged = TRUE argument to mcfork() which forks child
       processes such that they become independent of the parent
       process.
 
-    * The pdf() device omits circles and text at extremely small sizes,
+    • The pdf() device omits circles and text at extremely small sizes,
       since some viewers were failing on such files.
 
-    * The rightmost break for the "months", "quarters" and "years"
+    • The rightmost break for the "months", "quarters" and "years"
       cases of hist.POSIXlt() has been increased by a day.  (Inter
       alia, fixes PR#15717.)
 
-    * The handling of DF[i,] <- a where i is of length 0 is improved.
+    • The handling of DF[i,] <- a where i is of length 0 is improved.
       (Inter alia, fixes PR#15718.)
 
-    * hclust() gains a new method "ward.D2" which implements Ward's
+    • hclust() gains a new method "ward.D2" which implements Ward's
       method correctly.  The previous "ward" method is "ward.D" now,
       with the old name still working.  Thanks to research and
       proposals by Pierre Legendre.
 
-    * The sunspot.month dataset has been amended and updated from the
+    • The sunspot.month dataset has been amended and updated from the
       official source, whereas the sunspots and sunspot.year datasets
       will remain immutable. The documentation and source links have
       been updated correspondingly.
 
-    * The summary() method for "lm" fits warns if the fit is
+    • The summary() method for "lm" fits warns if the fit is
       essentially perfect, as most of the summary may be computed
       inaccurately (and with platform-dependent values).
 
@@ -1839,9 +1951,9 @@
 
   INSTALLATION and INCLUDED SOFTWARE:
 
-    * The included version of LAPACK has been updated to 3.5.0.
+    • The included version of LAPACK has been updated to 3.5.0.
 
-    * There is some support for parallel testing of an installation, by
+    • There is some support for parallel testing of an installation, by
       setting TEST_MC_CORES to an integer greater than one to indicate
       the maximum number of cores to be used in parallel. (It is worth
       specifying at least 8 cores if available.)  Most of these require
@@ -1857,14 +1969,14 @@
       The package checks in make check-devel and make check-recommended
       are done in parallel.
 
-    * More of make check will work if recommended packages are not
+    • More of make check will work if recommended packages are not
       installed: but recommended packages remain needed for thorough
       checking of an R build.
 
-    * The version of tzcode included in src/extra/tzone has been
+    • The version of tzcode included in src/extra/tzone has been
       updated.  (Formerly used only on Windows.)
 
-    * The included (64-bit) time-zone conversion code and Olson
+    • The included (64-bit) time-zone conversion code and Olson
       time-zone database can be used instead of the system version: use
       configure option --with-internal-tzcode.  This is the default on
       Windows and OS X.  (Note that this does not currently work if a
@@ -1877,84 +1989,84 @@
       This option also switches to the version of strftime included in
       directory src/extra/tzone.
 
-    * configure now tests for a C++11-compliant compiler by testing
+    • configure now tests for a C++11-compliant compiler by testing
       some basic features.  This by default tries flags for the
       compiler specified by CXX, but an alternative compiler, options
       and standard can be specified by variables CXX1X, CXX1XFLAGS and
       CXX1XSTD (e.g., -std=gnu++11).
 
-    * R can now optionally be compiled to use reference counting
+    • R can now optionally be compiled to use reference counting
       instead of the NAMED mechanism by defining SWITCH_TO_REFCNT in
       Rinternals.h. This may become the default in the future.
 
-    * There is a new option --use-system-tre to use a suitable system
+    • There is a new option --use-system-tre to use a suitable system
       tre library: at present this means a version from their git
       repository, after corrections.  (Wish of PR#15660.)
 
   PACKAGE INSTALLATION:
 
-    * The CRANextra repository is no longer a default repository on
+    • The CRANextra repository is no longer a default repository on
       Windows: all the binary versions of packages from CRAN are now on
       CRAN, although CRANextra contains packages from Omegahat and
       elsewhere used by CRAN packages.
 
-    * Only vignettes sources in directory vignettes are considered to
+    • Only vignettes sources in directory vignettes are considered to
       be vignettes and hence indexed as such.
 
-    * In the DESCRIPTION file,
+    • In the DESCRIPTION file,
       
           License: X11
 
       is no longer recognized as valid.  Use MIT or BSD_2_clause
       instead, both of which need + file LICENSE.
 
-    * For consistency, entries in .Rinstignore are now matched
+    • For consistency, entries in .Rinstignore are now matched
       case-insensitively on all platforms.
 
-    * Help for S4 methods with very long signatures now tries harder to
+    • Help for S4 methods with very long signatures now tries harder to
       split the description in the Usage field to no more than 80
       characters per line (some packages had over 120 characters).
 
-    * R CMD INSTALL --build (not Windows) now defaults to the internal
+    • R CMD INSTALL --build (not Windows) now defaults to the internal
       tar() unless R_INSTALL_TAR is set.
 
-    * There is support for compiling C++11 code in packages on suitable
-      platforms: see 'Writing R Extensions'.
+    • There is support for compiling C++11 code in packages on suitable
+      platforms: see ‘Writing R Extensions’.
 
-    * Fake installs now install the contents of directory inst: some
+    • Fake installs now install the contents of directory inst: some
       packages use this to install e.g. C++ headers for use by other
       packages that are independent of the package itself.  Option
       --no-inst can be used to get the previous behaviour.
 
   DEBUGGING:
 
-    * The behaviour of the code browser has been made more consistent,
+    • The behaviour of the code browser has been made more consistent,
       in part following the suggestions in PR#14985.
 
-    * Calls to browser() are now consistent with calls to the browser
+    • Calls to browser() are now consistent with calls to the browser
       triggered by debug(), in that Enter will default to n rather than
       c.
 
-    * A new browser command s has been added, to "step into" function
+    • A new browser command s has been added, to “step into” function
       calls.
 
-    * A new browser command f has been added, to "finish" the current
+    • A new browser command f has been added, to “finish” the current
       loop or function.
 
-    * Within the browser, the command help will display a short list of
+    • Within the browser, the command help will display a short list of
       available commands.
 
   UTILITIES:
 
-    * Only vignettes sources in directory vignettes are considered to
+    • Only vignettes sources in directory vignettes are considered to
       be vignettes by R CMD check.  That has been the preferred
       location since R 2.14.0 and is now obligatory.
 
-    * For consistency, R CMD build now matches entries in .Rbuildignore
+    • For consistency, R CMD build now matches entries in .Rbuildignore
       and vignettes/.install_extras case-insensitively on all platforms
       (not just on Windows).
 
-    * checkFF() (called by R CMD check by default) can optionally check
+    • checkFF() (called by R CMD check by default) can optionally check
       foreign function calls for consistency with the registered type
       and argument count.  This is the default for R CMD check
       --as-cran or can be enabled by setting environment variable
@@ -1966,205 +2078,205 @@
       Functions suppressForeignCheck() and dontCheck() have been added
       to allow package authors to suppress false positive reports.
 
-    * R CMD check --as-cran warns about a false value of the
+    • R CMD check --as-cran warns about a false value of the
       DESCRIPTION field BuildVignettes for Open Source packages, and
       ignores it.  (An Open Source package needs to have complete
       sources for its vignettes which should be usable on a suitably
       well-equipped system).
 
-    * R CMD check --no-rebuild-vignettes is defunct:
+    • R CMD check --no-rebuild-vignettes is defunct:
       R CMD check --no-build-vignettes has been preferred since R
       3.0.0.
 
-    * R CMD build --no-vignettes is defunct:
+    • R CMD build --no-vignettes is defunct:
       R CMD build --no-build-vignettes has been preferred since R
       3.0.0.
 
-    * R CMD Sweave and R CMD Stangle now process both Sweave and
+    • R CMD Sweave and R CMD Stangle now process both Sweave and
       non-Sweave vignettes.  The tools::buildVignette() function has
       been added to do the same tasks from within R.
 
-    * The flags returned by R CMD config --ldflags and (where
+    • The flags returned by R CMD config --ldflags and (where
       installed) pkg-config --libs libR are now those needed to link a
       front-end against the (shared or static) R library.
 
-    * Sweave.sty has a new option [inconsolata].
+    • Sweave.sty has a new option [inconsolata].
 
-    * R CMD check customizations such as _R_CHECK_DEPENDS_ONLY_ make
+    • R CMD check customizations such as _R_CHECK_DEPENDS_ONLY_ make
       available packages only in LinkingTo only for installation, and
       not for loading/runtime tests.
 
-    * tools::checkFF() reports on .C and .Fortran calls with DUP =
+    • tools::checkFF() reports on .C and .Fortran calls with DUP =
       FALSE if argument check_DUP is true.  This is selected by R CMD
       check by default.
 
-    * R CMD check --use-gct can be tuned to garbage-collect less
+    • R CMD check --use-gct can be tuned to garbage-collect less
       frequently using gctorture2() _via_ the setting of environment
       variable _R_CHECK_GCT_N_.
 
-    * Where supported, tools::texi2dvi() limits the number of passes
+    • Where supported, tools::texi2dvi() limits the number of passes
       tried to 20.
 
   C-LEVEL FACILITIES:
 
-    * (Windows only) A function R_WaitEvent() has been added (with
+    • (Windows only) A function R_WaitEvent() has been added (with
       declaration in headerR.h) to block execution until the next event
       is received by R.
 
-    * Remapping in the Rmath.h header can be suppressed by defining
+    • Remapping in the Rmath.h header can be suppressed by defining
       R_NO_REMAP_RMATH.
 
-    * The remapping of rround() in header Rmath.h has been removed: use
+    • The remapping of rround() in header Rmath.h has been removed: use
       fround() instead.
 
-    * ftrunc() in header Rmath.h is now a wrapper for the C99 function
+    • ftrunc() in header Rmath.h is now a wrapper for the C99 function
       trunc(), which might as well be used in C code: ftrunc() is still
       needed for portable C++ code.
 
-    * The never-documented remapping of prec() to fprec() in header
+    • The never-documented remapping of prec() to fprec() in header
       Rmath.h has been removed.
 
-    * The included LAPACK subset now contains ZGESDD and ZGELSD.
+    • The included LAPACK subset now contains ZGESDD and ZGELSD.
 
-    * The function LENGTH() now checks that it is only applied to
+    • The function LENGTH() now checks that it is only applied to
       vector arguments.  However, in packages length() should be used.
       (In R itself LENGTH() is a macro without the function overhead of
       length().)
 
-    * Calls to SET_VECTOR_ELT() and SET_STRING_ELT() are now checked
+    • Calls to SET_VECTOR_ELT() and SET_STRING_ELT() are now checked
       for indices which are in-range: several packages were writing one
       element beyond the allocated length.
 
-    * allocVector3 has been added which allows custom allocators to be
+    • allocVector3 has been added which allows custom allocators to be
       used for individual vector allocations.
 
   DEPRECATED AND DEFUNCT:
 
-    * chol(pivot = TRUE, LINPACK = TRUE) is defunct.
+    • chol(pivot = TRUE, LINPACK = TRUE) is defunct.
 
       Arguments EISPACK for eigen() and LINPACK for chol(), chol2inv(),
       solve() and svd() are ignored: LAPACK is always used.
 
-    * .find.package() and .path.package() are defunct: only the
+    • .find.package() and .path.package() are defunct: only the
       versions without the initial dot introduced in R 2.13.0 have ever
       been in the API.
 
-    * Partial matching when using the $ operator _on data frames_ now
+    • Partial matching when using the $ operator _on data frames_ now
       throws a warning and may become defunct in the future. If partial
       matching is intended, replace foo$bar by foo[["bar", exact =
       FALSE]].
 
-    * The long-deprecated use of \synopsis in the Usage section of .Rd
+    • The long-deprecated use of \synopsis in the Usage section of .Rd
       files has been removed: such sections are now ignored (with a
       warning).
 
-    * package.skeleton()'s deprecated argument namespace has been
+    • package.skeleton()'s deprecated argument namespace has been
       removed.
 
-    * Many methods are no longer exported by package stats.  They are
+    • Many methods are no longer exported by package stats.  They are
       all registered on their generic, which should be called rather
       than calling a method directly.
 
-    * Functions readNEWS() and checkNEWS() in package tools are
+    • Functions readNEWS() and checkNEWS() in package tools are
       defunct.
 
-    * download.file(method = "lynx") is deprecated.
+    • download.file(method = "lynx") is deprecated.
 
-    * .C(DUP = FALSE) and .Fortran(DUP = FALSE) are now deprecated, and
+    • .C(DUP = FALSE) and .Fortran(DUP = FALSE) are now deprecated, and
       may be disabled in future versions of R.  As their help has long
       said, .Call() is much preferred.
 
       R CMD check notes such usages (by default).
 
-    * The workaround of setting R_OSX_VALGRIND has been removed: it is
+    • The workaround of setting R_OSX_VALGRIND has been removed: it is
       not needed in current valgrind.
 
   BUG FIXES:
 
-    * Calling lm.wfit() with no non-zero weights gave an array-overrun
+    • Calling lm.wfit() with no non-zero weights gave an array-overrun
       in the Fortran code and a not very sensible answer.  It is now
       special-cased with a simpler answer (no qr component).
 
-    * Error messages involving non-syntactic names (e.g., as produced
+    • Error messages involving non-syntactic names (e.g., as produced
       by `\r` when that object does not exist) now encode the control
       characters.  (Reported by Hadley Wickham.)
 
-    * getGraphicsEvent() caused 100% usage of one CPU in Windows.
+    • getGraphicsEvent() caused 100% usage of one CPU in Windows.
       (PR#15500)
 
-    * nls() with no start argument may now work inside another function
+    • nls() with no start argument may now work inside another function
       (scoping issue).
 
-    * pbeta() and similar work better for very large (billions) ncp.
+    • pbeta() and similar work better for very large (billions) ncp.
 
-    * Where time zones have changed abbreviations over the years, the
+    • Where time zones have changed abbreviations over the years, the
       software tries to more consistently use the abbreviation
       appropriate to the time or if that is unknown, the current
       abbreviation.  On some platforms where the C function localtime
       changed the tzname variables the reported abbreviation could have
       been that of the last time converted.
 
-    * all.equal(list(1), identity) now works.
+    • all.equal(list(1), identity) now works.
 
-    * Bug fix for pushing viewports in grid (reported by JJ Allaire and
+    • Bug fix for pushing viewports in grid (reported by JJ Allaire and
       Kevin Ushey).
 
       NOTE for anyone poking around within the graphics engine display
       list (despite the warnings not to) that this changes what is
       recorded by grid on the graphics engine display list.
 
-    * Extra checks have been added for unit resolution and conversion
+    • Extra checks have been added for unit resolution and conversion
       in grid, to catch instances of division-by-zero.  This may
       introduce error messages in existing code and/or produce a
       different result in existing code (but only where a non-finite
       location or dimension may now become zero).
 
-    * Some bugs in TRE have been corrected by updating from the git
+    • Some bugs in TRE have been corrected by updating from the git
       repository.  This allows R to be installed on some platforms for
       which this was a blocker (PR#15087 suggests Linux on ARM and
       HP-UX).
 
-    * ? applied to a call to an S4 generic failed in several cases.
+    • ? applied to a call to an S4 generic failed in several cases.
       (PR#15680)
 
-    * The implicit S4 generics for primitives with ... in their
+    • The implicit S4 generics for primitives with ... in their
       argument list were incorrect. (PR#15690)
 
-    * Bug fixes to methods::callGeneric(). (PR#15691)
+    • Bug fixes to methods::callGeneric(). (PR#15691)
 
-    * The bug fix to aggregrate() in PR#15004 introduced a new bug in
+    • The bug fix to aggregrate() in PR#15004 introduced a new bug in
       the case of no grouping variables. (PR#15699)
 
-    * In rare cases printing deeply nested lists overran a buffer by
+    • In rare cases printing deeply nested lists overran a buffer by
       one byte and on a few platforms segfaulted. (PR#15679)
 
-    * The dendrogram method of as.dendrogram() was hidden accidentally,
+    • The dendrogram method of as.dendrogram() was hidden accidentally,
       (PR#15703), and order.dendrogram(d) gave too much for a leaf d.
       (PR#15702)
 
-    * R would try to kill processes on exit that have pids ever used by
+    • R would try to kill processes on exit that have pids ever used by
       a child process spawned by mcparallel even though the current
       process with that pid was not actually its child.
 
-    * cophenetic() applied to a "dendrogram" object sometimes
+    • cophenetic() applied to a "dendrogram" object sometimes
       incorrectly returned a "Labels" attribute with dimensions.
       (PR#15706)
 
-    * printCoefmat() called from quite a few print() methods now obeys
+    • printCoefmat() called from quite a few print() methods now obeys
       small getOption("width") settings, line wrapping the "signif.
       codes" legend appropriately.  (PR#15708)
 
-    * model.matrix() assumed that the stored dimnames for a matrix was
+    • model.matrix() assumed that the stored dimnames for a matrix was
       NULL or length 2, but length 1 occurred.
 
-    * The clipping region for a device was sometimes used in base
+    • The clipping region for a device was sometimes used in base
       graphics before it was set.
 
 CHANGES IN R 3.0.3:
 
   NEW FEATURES:
 
-    * On Windows there is support for making .texi manuals using
+    • On Windows there is support for making .texi manuals using
       texinfo 5.0 or later: the setting is in file
       src/gnuwin32/MkRules.dist.
 
@@ -2172,56 +2284,56 @@
       been made available at <URL:
       http://www.stats.ox.ac.uk/pub/Rtools/>.
 
-    * write.table() now handles matrices of 2^31 or more elements, for
+    • write.table() now handles matrices of 2^31 or more elements, for
       those with large amounts of patience and disc space.
 
-    * There is a new function, La_version(), to report the version of
+    • There is a new function, La_version(), to report the version of
       LAPACK in use.
 
-    * The HTML version of 'An Introduction to R' now has links to PNG
+    • The HTML version of ‘An Introduction to R’ now has links to PNG
       versions of the figures.
 
-    * There is some support to produce manuals in ebook formats. (See
+    • There is some support to produce manuals in ebook formats. (See
       doc/manual/Makefile.  Suggested by Mauro Cavalcanti.)
 
-    * On a Unix-alike Sys.timezone() returns NA if the environment
+    • On a Unix-alike Sys.timezone() returns NA if the environment
       variable TZ is unset, to distinguish it from an empty string
       which on some OSes means the UTC time zone.
 
-    * The backtick may now be escaped in strings, to allow names
+    • The backtick may now be escaped in strings, to allow names
       containing them to be constructed, e.g. `\``.  (PR#15621)
 
-    * read.table(), readLines() and scan() now warn when an embedded
+    • read.table(), readLines() and scan() now warn when an embedded
       nul is found in the input.  (Related to PR#15625 which was
       puzzled by the behaviour in this unsupported case.)
 
-    * (Windows only.)  file.symlink() works around the undocumented
+    • (Windows only.)  file.symlink() works around the undocumented
       restriction of the Windows system call to backslashes.  (Wish of
       PR#15631.)
 
-    * KalmanForecast(fast = FALSE) is now the default, and the help
+    • KalmanForecast(fast = FALSE) is now the default, and the help
       contains an example of how fast = TRUE can be used in this
       version.  (The usage will change in 3.1.0.)
 
-    * strptime() now checks the locale only when locale-specific
+    • strptime() now checks the locale only when locale-specific
       formats are used and caches the locale in use: this can halve the
       time taken on OSes with slow system functions (e.g., OS X).
 
-    * strptime() and the format() methods for classes "POSIXct",
+    • strptime() and the format() methods for classes "POSIXct",
       "POSIXlt" and "Date" recognize strings with marked encodings:
       this allows, for example, UTF-8 French month names to be read on
       (French) Windows.
 
-    * iconv(to = "utf8") is now accepted on all platforms (some
+    • iconv(to = "utf8") is now accepted on all platforms (some
       implementations did already, but GNU libiconv did not: however
       converted strings were not marked as being in UTF-8).  The
       official name, "UTF-8" is still preferred.
 
-    * available.packages() is better protected against corrupt metadata
+    • available.packages() is better protected against corrupt metadata
       files.  (A recurring problem with Debian package shogun-r:
       PR#14713.)
 
-    * Finalizers are marked to be run at garbage collection, but run
+    • Finalizers are marked to be run at garbage collection, but run
       only at a somewhat safer later time (when interrupts are
       checked).  This circumvents some problems with finalizers running
       arbitrary code during garbage collection (the known instances
@@ -2230,205 +2342,205 @@
 
   INSTALLATION and INCLUDED SOFTWARE:
 
-    * The included version of PCRE has been updated to 8.34.  This
+    • The included version of PCRE has been updated to 8.34.  This
       fixes bugs and makes the behaviour closer to Perl 5.18.  In
-      particular, the concept of 'space' includes VT and hence agrees
+      particular, the concept of ‘space’ includes VT and hence agrees
       with POSIX's.
 
   PACKAGE INSTALLATION:
 
-    * The new field SysDataCompression in the DESCRIPTION file allows
+    • The new field SysDataCompression in the DESCRIPTION file allows
       user control over the compression used for sysdata.rda objects in
       the lazy-load database.
 
-    * install.packages(dependencies = value) for value = NA (the
+    • install.packages(dependencies = value) for value = NA (the
       default) or value = TRUE omits packages only in LinkingTo for
       binary package installs.
 
   C-LEVEL FACILITIES:
 
-    * The long undocumented remapping of rround() to Rf_fround() in
+    • The long undocumented remapping of rround() to Rf_fround() in
       header Rmath.h is now formally deprecated: use fround() directly.
 
-    * Remapping of prec() and trunc() in the Rmath.h header has been
+    • Remapping of prec() and trunc() in the Rmath.h header has been
       disabled in C++ code (it has caused breakage with libc++
       headers).
 
   BUG FIXES:
 
-    * getParseData() truncated the imaginary part of complex number
+    • getParseData() truncated the imaginary part of complex number
       constants.  (Reported by Yihui Xie.)
 
-    * dbeta(x, a, b) with a or b within a factor of 2 of the largest
+    • dbeta(x, a, b) with a or b within a factor of 2 of the largest
       representable number could infinite-loop.  (Reported by Ioannis
       Kosmidis.)
 
-    * provideDimnames() failed for arrays with a 0 dimension.
+    • provideDimnames() failed for arrays with a 0 dimension.
       (PR#15465)
 
-    * rbind() and cbind() did not handle list objects correctly.
+    • rbind() and cbind() did not handle list objects correctly.
       (PR#15468)
 
-    * replayPlot() now checks if it is replaying a plot from the same
+    • replayPlot() now checks if it is replaying a plot from the same
       session.
 
-    * rasterImage() and grid.raster() now give error on an empty
+    • rasterImage() and grid.raster() now give error on an empty
       (zero-length) raster.  (Reported by Ben North.)
 
-    * plot.lm() would sometimes scramble the labels in plot type 5.
+    • plot.lm() would sometimes scramble the labels in plot type 5.
       (PR#15458 and PR#14837)
 
-    * min() did not handle NA_character_ values properly.  (Reported by
+    • min() did not handle NA_character_ values properly.  (Reported by
       Magnus Thor Torfason.)
 
-    * (Windows only.)  readRegistry() would duplicate default values
+    • (Windows only.)  readRegistry() would duplicate default values
       for keys.  (PR#15455)
 
-    * str(..., strict.width = "cut") did not handle it properly when
+    • str(..., strict.width = "cut") did not handle it properly when
       more than one line needed to be cut.  (Reported by Gerrit
       Eichner.)
 
-    * Removing subclass back-references when S4 classes were removed or
+    • Removing subclass back-references when S4 classes were removed or
       their namespace unloaded had several bugs (e.g., PR#15481).
 
-    * aggregate() could fail when there were too many levels present in
+    • aggregate() could fail when there were too many levels present in
       the by argument.  (PR#15004)
 
-    * namespaceImportFrom() needed to detect primitive functions when
+    • namespaceImportFrom() needed to detect primitive functions when
       checking for duplicated imports (reported by Karl Forner).
 
-    * getGraphicsEvent() did not exit when a user closed the graphics
+    • getGraphicsEvent() did not exit when a user closed the graphics
       window.  (PR#15208)
 
-    * Errors in vignettes were not always captured and displayed
+    • Errors in vignettes were not always captured and displayed
       properly.  (PR#15495)
 
-    * contour() could fail when dealing with extremely small z values.
+    • contour() could fail when dealing with extremely small z values.
       (PR#15454)
 
-    * Several functions did not handle zero-length vectors properly,
+    • Several functions did not handle zero-length vectors properly,
       including browseEnv(), format(), gl(), relist() and
       summary.data.frame().  (E.g., PR#15499)
 
-    * Sweave() did not restore the R output to the console if it was
+    • Sweave() did not restore the R output to the console if it was
       interrupted by a user in the middle of evaluating a code chunk.
       (Reported by Michael Sumner.)
 
-    * Fake installs of packages with vignettes work again.
+    • Fake installs of packages with vignettes work again.
 
-    * Illegal characters in the input caused parse() (and thus
+    • Illegal characters in the input caused parse() (and thus
       source()) to segfault.  (PR#15518)
 
-    * The nonsensical use of nmax = 1 in duplicated() or unique() is
+    • The nonsensical use of nmax = 1 in duplicated() or unique() is
       now silently ignored.
 
-    * qcauchy(p, *) is now fully accurate even when p is very close to
+    • qcauchy(p, *) is now fully accurate even when p is very close to
       1. (PR#15521)
 
-    * The validmu() and valideta() functions in the standard glm()
+    • The validmu() and valideta() functions in the standard glm()
       families now also report non-finite values, rather than failing.
 
-    * Saved vignette results (in a .Rout.save file) were not being
+    • Saved vignette results (in a .Rout.save file) were not being
       compared to the new ones during R CMD check.
 
-    * Double-clicking outside of the list box (e.g., on the scrollbar)
+    • Double-clicking outside of the list box (e.g., on the scrollbar)
       of a Tk listbox widget generated by tk_select.list() no longer
       causes the window to close. (PR#15407)
 
-    * Improved handling of edge cases in parallel::splitindices().
+    • Improved handling of edge cases in parallel::splitindices().
       (PR#15552)
 
-    * HTML display of results from help.search() and ?? sometimes
+    • HTML display of results from help.search() and ?? sometimes
       contained badly constructed links.
 
-    * c() and related functions such as unlist() converted raw vectors
+    • c() and related functions such as unlist() converted raw vectors
       to invalid logical vectors. (PR#15535)
 
-    * (Windows only) When a call to system2() specified one of stdin,
+    • (Windows only) When a call to system2() specified one of stdin,
       stdout or stderr to be a file, but the command was not found
       (e.g., it contained its arguments, or the program was not on the
       PATH), it left the file open and unusable until R terminated.
       (Reported by Mathew McLean.)
 
-    * The bmp() device was not recording res = NA correctly: it is now
+    • The bmp() device was not recording res = NA correctly: it is now
       recorded as 72 ppi.
 
-    * Several potential problems with compiler-specific behaviour have
-      been identified using the 'Undefined Behaviour Sanitizer' in
+    • Several potential problems with compiler-specific behaviour have
+      been identified using the ‘Undefined Behaviour Sanitizer’ in
       conjunction with the clang compiler.
 
-    * hcl() now honours NA inputs (previously they were mapped to
+    • hcl() now honours NA inputs (previously they were mapped to
       black).
 
-    * Some translations in base packages were being looked up in the
+    • Some translations in base packages were being looked up in the
       main catalog rather than that for the package.
 
-    * As a result of the 3.0.2 change about 'the last second before the
-      epoch', most conversions which should have given NA returned that
+    • As a result of the 3.0.2 change about ‘the last second before the
+      epoch’, most conversions which should have given NA returned that
       time.  (The platforms affected include Linux and OS X, but not
       Windows nor Solaris.)
 
-    * rowsum() has more support for matrices and data frames with 2^31
+    • rowsum() has more support for matrices and data frames with 2^31
       or more elements. (PR#15587)
 
-    * predict(<lm object>, interval = "confidence", scale =
+    • predict(<lm object>, interval = "confidence", scale =
       <something>) now works.  (PR#15564)
 
-    * The bug fix in 3.0.2 for PR#15411 was too aggressive, and
+    • The bug fix in 3.0.2 for PR#15411 was too aggressive, and
       sometimes removed spaces that should not have been removed.
       (PR#15583)
 
-    * Running R code in a tcltk callback failed to set the busy flag,
-      which will be needed to tell OS X not to 'App Nap'.
+    • Running R code in a tcltk callback failed to set the busy flag,
+      which will be needed to tell OS X not to ‘App Nap’.
 
-    * The code for date-times before 1902 assumed that the offset from
+    • The code for date-times before 1902 assumed that the offset from
       GMT in 1902 was a whole number of minutes: that was not true of
       Paris (as recorded on some platforms).
 
-    * Using Sys.setlocale to set LC_NUMERIC to "C" (to restore the sane
+    • Using Sys.setlocale to set LC_NUMERIC to "C" (to restore the sane
       behavior) no longer gives a warning.
 
-    * deparse() now deparses complex vectors in a way that re-parses to
+    • deparse() now deparses complex vectors in a way that re-parses to
       the original values.  (PR#15534, patch based on code submitted by
       Alex Bertram.)
 
-    * In some extreme cases (more than 10^15) integer inputs to
+    • In some extreme cases (more than 10^15) integer inputs to
       dpqrxxx() functions might have been rounded up by one (with a
       warning about being non-integer).  (PR#15624)
 
-    * Plotting symbol pch = 14 had the triangle upside down on some
+    • Plotting symbol pch = 14 had the triangle upside down on some
       devices (typically screen devices). The triangle is supposed to
       be point up.  (Reported by Bill Venables.)
 
-    * getSrcref() did not work on method definitions if
+    • getSrcref() did not work on method definitions if
       rematchDefinition() had been used.
 
-    * KalmanForecast(fast = FALSE) reported a (harmless) stack
+    • KalmanForecast(fast = FALSE) reported a (harmless) stack
       imbalance.
 
-    * The count of observations used by KalmanRun() did not take
+    • The count of observations used by KalmanRun() did not take
       missing values into account.
 
-    * In locales where the abbreviated name of one month is a partial
+    • In locales where the abbreviated name of one month is a partial
       match for the full name of a later one, the %B format in
       strptime() could fail.  An example was French on OS X, where juin
       is abbreviated to jui and partially matches juillet.  Similarly
       for weekday names.
 
-    * pbeta(x, a, b, log.p = TRUE) sometimes underflowed to zero for
+    • pbeta(x, a, b, log.p = TRUE) sometimes underflowed to zero for
       very small and very differently sized a, b.  (PR#15641)
 
-    * approx() and approxfun() now handle infinite values with the
+    • approx() and approxfun() now handle infinite values with the
       "constant" method. (PR#15655)
 
-    * stripchart() again respects reversed limits in xlim and ylim.
+    • stripchart() again respects reversed limits in xlim and ylim.
       (PR#15664)
 
 CHANGES IN R 3.0.2:
 
   NEW FEATURES:
 
-    * The NEWS files have been re-organized.
+    • The NEWS files have been re-organized.
 
       This file contains news for R >= 3.0.0: news for the 0.x.y, 1.x.y
       and 2.x.y releases is in files NEWS.0, NEWS.1 and NEWS.2.  The
@@ -2436,137 +2548,137 @@
       version of news from 2.10.0 to 2.15.3 is available as
       doc/html/NEWS.2.html.
 
-    * sum() for integer arguments now uses an integer accumulator of at
+    • sum() for integer arguments now uses an integer accumulator of at
       least 64 bits and so will be more accurate in the very rare case
       that a cumulative sum exceeds 2^53 (necessarily summing more than
       4 million elements).
 
-    * The example() and tools::Rd2ex() functions now have parameters to
+    • The example() and tools::Rd2ex() functions now have parameters to
       allow them to ignore \dontrun markup in examples.  (Suggested by
       Peter Solymos.)
 
-    * str(x) is considerably faster for very large lists, or factors
+    • str(x) is considerably faster for very large lists, or factors
       with 100,000 levels, the latter as in PR#15337.
 
-    * col2rgb() now converts factors to character strings not integer
+    • col2rgb() now converts factors to character strings not integer
       codes (suggested by Bryan Hanson).
 
-    * tail(warnings()) now works, via the new `[` method.
+    • tail(warnings()) now works, via the new `[` method.
 
-    * There is now support for the LaTeX style file zi4.sty which has
+    • There is now support for the LaTeX style file zi4.sty which has
       in some distributions replaced inconsolata.sty.
 
-    * unlist(x) now typically returns all non-list xs unchanged, not
-      just the "vector" ones.  Consequently, format(lst) now also works
+    • unlist(x) now typically returns all non-list xs unchanged, not
+      just the “vector” ones.  Consequently, format(lst) now also works
       when the list lst has non-vector elements.
 
-    * The tools::getVignetteInfo() function has been added to give
+    • The tools::getVignetteInfo() function has been added to give
       information about installed vignettes.
 
-    * New assertCondition(), etc. utilities in tools, useful for
+    • New assertCondition(), etc. utilities in tools, useful for
       testing.
 
-    * Profiling now records non-inlined calls from byte-compiled code
+    • Profiling now records non-inlined calls from byte-compiled code
       to BUILTIN functions.
 
-    * Various functions in stats and elsewhere that use non-standard
+    • Various functions in stats and elsewhere that use non-standard
       evaluation are now more careful to follow the namespace scoping
       rules.  E.g., stats::lm() can now find stats::model.frame() even
       if stats is not on the search path or if some package defines a
       function of that name.
 
-    * If an invalid/corrupt .Random.seed object is encountered in the
+    • If an invalid/corrupt .Random.seed object is encountered in the
       workspace it is ignored with a warning rather than giving an
       error.  (This allows R itself to rely on a working RNG, e.g. to
       choose a random port.)
 
-    * seq() and seq.int() give more explicit error messages if called
+    • seq() and seq.int() give more explicit error messages if called
       with invalid (e.g., NaN) inputs.
 
-    * When parse() finds a syntax error, it now makes partial parse
+    • When parse() finds a syntax error, it now makes partial parse
       information available up to the location of the error.  (Request
       of Reijo Sund.)
 
-    * Methods invoked by NextMethod() had a different dynamic parent to
+    • Methods invoked by NextMethod() had a different dynamic parent to
       the generic. This was causing trouble where S3 methods invoked
       via lazy evaluation could lose track of their generic.
       (PR#15267)
 
-    * Code for the negative binomial distribution now treats the case
+    • Code for the negative binomial distribution now treats the case
       size == 0 as a one-point distribution at zero.
 
-    * abbreviate() handles without warning non-ASCII input strings
+    • abbreviate() handles without warning non-ASCII input strings
       which require no abbreviation.
 
-    * read.dcf() no longer has a limit of 8191 bytes per line. (Wish of
+    • read.dcf() no longer has a limit of 8191 bytes per line. (Wish of
       PR#15250.)
 
-    * formatC(x) no longer copies the class of x to the result, to
+    • formatC(x) no longer copies the class of x to the result, to
       avoid misuse creating invalid objects as in PR#15303.  A warning
       is given if a class is discarded.
 
-    * Dataset npk has been copied from MASS to allow more tests to be
+    • Dataset npk has been copied from MASS to allow more tests to be
       run without recommended packages being installed.
 
-    * The initialization of the regression coefficients for
+    • The initialization of the regression coefficients for
       non-degenerate differenced models in arima() has been changed and
       in some examples avoids a local maximum.  (PR#15396)
 
-    * termplot() now has an argument transform.x to control the display
+    • termplot() now has an argument transform.x to control the display
       of individual terms in the plot.  (PR#15329)
 
-    * format() now supports digits = 0, to display nsmall decimal
+    • format() now supports digits = 0, to display nsmall decimal
       places.
 
-    * There is a new read-only par() parameter called "page", which
+    • There is a new read-only par() parameter called "page", which
       returns a logical value indicating whether the next plot.new()
       call will start a new page.
 
-    * Processing Sweave and Rd documents to PDF now renders backticks
+    • Processing Sweave and Rd documents to PDF now renders backticks
       and single quotes better in several instances, including in \code
       and \samp expressions.
 
-    * utils::modifyList() gets a new argument keep.null allowing NULL
+    • utils::modifyList() gets a new argument keep.null allowing NULL
       components in the replacement to be retained, instead of causing
       corresponding components to be deleted.
 
-    * tools::pkgVignettes() gains argument check; if set to TRUE, it
+    • tools::pkgVignettes() gains argument check; if set to TRUE, it
       will warn when it appears a vignette requests a non-existent
       vignette engine.
 
   UTILITIES:
 
-    * R CMD check --as-cran checks the line widths in usage and
+    • R CMD check --as-cran checks the line widths in usage and
       examples sections of the package Rd files.
 
-    * R CMD check --as-cran now implies --timings.
+    • R CMD check --as-cran now implies --timings.
 
-    * R CMD check looks for command gfile if a suitable file is not
+    • R CMD check looks for command gfile if a suitable file is not
       found.  (Although file is not from GNU, OpenCSW on Solaris
       installs it as gfile.)
 
-    * R CMD build (with the internal tar) checks the permissions of
+    • R CMD build (with the internal tar) checks the permissions of
       configure and cleanup files and adds execute permission to the
       recorded permissions for these files if needed, with a warning.
       This is useful on OSes and file systems which do not support
       execute permissions (notably, on Windows).
 
-    * R CMD build now weaves and tangles all vignettes, so suggested
+    • R CMD build now weaves and tangles all vignettes, so suggested
       packages are not required during package installation if the
       source tarball was prepared with current R CMD build.
 
-    * checkFF() (used by R CMD check) does a better job of detecting
+    • checkFF() (used by R CMD check) does a better job of detecting
       calls from other packages, including not reporting those where a
       function has been copied from another namespace (e.g., as a
       default method).  It now reports calls where .NAME is a symbol
       registered in another package.
 
-    * On Unix-alike systems, R CMD INSTALL now installs packages group
+    • On Unix-alike systems, R CMD INSTALL now installs packages group
       writably whenever the library (lib.loc) is group writable.
       Hence, update.packages() works for other group members (suggested
       originally and from a patch by Dirk Eddelbuettel).
 
-    * R CMD javareconf now supports the use of symbolic links for
+    • R CMD javareconf now supports the use of symbolic links for
       JAVA_HOME on platforms which have realpath.  So it is now
       possible to use
       
@@ -2576,352 +2688,352 @@
       frequently-changing full path such as
       /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.25.x86_64.
 
-    * (Windows only.) Rscript -e requires a non-empty argument for
+    • (Windows only.) Rscript -e requires a non-empty argument for
       consistency with Unix versions of R.  (Also Rterm -e and R -e.)
 
-    * R CMD check does more thorough checking of declared packages and
+    • R CMD check does more thorough checking of declared packages and
       namespaces.  It reports
 
-        * packages declared in more than one of the Depends, Imports,
+        • packages declared in more than one of the Depends, Imports,
           Suggests and Enhances fields of the DESCRIPTION file.
 
-        * namespaces declared in Imports but not imported from, neither
+        • namespaces declared in Imports but not imported from, neither
           in the NAMESPACE file nor using the :: nor ::: operators.
 
-        * packages which are used in library() or requires() calls in
+        • packages which are used in library() or requires() calls in
           the R code but were already put on the search path _via_
           Depends.
 
-        * packages declared in Depends not imported _via_ the NAMESPACE
+        • packages declared in Depends not imported _via_ the NAMESPACE
           file (except the standard packages).  Objects used from
           Depends packages should be imported to avoid conflicts and to
           allow correct operation when the namespace is loaded but not
           attached.
 
-        * objects imported _via_ ::: calls where :: would do.
+        • objects imported _via_ ::: calls where :: would do.
 
-        * objects imported by :: which are not exported.
+        • objects imported by :: which are not exported.
 
-        * objects imported by ::: calls which do not exist.
+        • objects imported by ::: calls which do not exist.
 
-      See 'Writing R Extensions' for good practice.
+      See ‘Writing R Extensions’ for good practice.
 
-    * R CMD check optionally checks for non-standard top-level files
+    • R CMD check optionally checks for non-standard top-level files
       and directories (which are often mistakes): this is enabled for
       --as-cran.
 
-    * LaTeX style file upquote.sty is no longer included (the version
+    • LaTeX style file upquote.sty is no longer included (the version
       was several years old): it is no longer used in R.  A much later
       version is commonly included in LaTeX distributions but does not
       play well with the ae fonts which are the default for Sweave
       vignettes.
 
-    * R CMD build makes more use of the build sub-directory of package
+    • R CMD build makes more use of the build sub-directory of package
       sources, for example to record information about the vignettes.
 
-    * R CMD check analyses ::: calls.
+    • R CMD check analyses ::: calls.
 
   INSTALLATION and INCLUDED SOFTWARE:
 
-    * The macros used for the texinfo manuals have been changed to work
+    • The macros used for the texinfo manuals have been changed to work
       better with the incompatible changes made in texinfo 5.x.
 
-    * The minimum version for a system xz library is now 5.0.3 (was
+    • The minimum version for a system xz library is now 5.0.3 (was
       4.999).  This is in part to avoid 5.0.2, which can compress in
       ways other versions cannot decompress.
 
-    * The included version of PCRE has been updated to 8.33.
+    • The included version of PCRE has been updated to 8.33.
 
-    * The included version of zlib has been updated to 1.2.8, a bug-fix
+    • The included version of zlib has been updated to 1.2.8, a bug-fix
       release.
 
-    * The included version of xz utils's liblzma has been updated to
+    • The included version of xz utils's liblzma has been updated to
       5.0.5.
 
-    * Since javareconf (see above) is used when R is installed, a
+    • Since javareconf (see above) is used when R is installed, a
       stable link for JAVA_HOME can be supplied then.
 
-    * Configuring with --disable-byte-compilation will override the
+    • Configuring with --disable-byte-compilation will override the
       DESCRIPTION files of recommended packages, which typically
       require byte-compilation.
 
-    * More of the installation and checking process will work even when
+    • More of the installation and checking process will work even when
       TMPDIR is set to a path containing spaces, but this is not
       recommended and external software (such as texi2dvi) may fail.
 
   PACKAGE INSTALLATION:
 
-    * Installation is aborted immediately if a LinkingTo package is not
+    • Installation is aborted immediately if a LinkingTo package is not
       installed.
 
-    * R CMD INSTALL has a new option --no-byte-compile which will
+    • R CMD INSTALL has a new option --no-byte-compile which will
       override a ByteCompile field in the package's DESCRIPTION file.
 
-    * License BSD is deprecated: use BSD_3_clause or BSD_2_clause
+    • License BSD is deprecated: use BSD_3_clause or BSD_2_clause
       instead.
 
       License X11 is deprecated: use MIT or BSD_2_clause instead.
 
-    * Version requirements for LinkingTo packages are now recognized:
+    • Version requirements for LinkingTo packages are now recognized:
       they are checked at installation.  (Fields with version
       requirements were previously silently ignored.)
 
-    * The limit of 500 S3method entries in a NAMESPACE file has been
+    • The limit of 500 S3method entries in a NAMESPACE file has been
       removed.
 
-    * The default 'version' of Bioconductor for its packages has been
+    • The default ‘version’ of Bioconductor for its packages has been
       changed to the upcoming 2.13, but this can be set by the
       environment variable R_BIOC_VERSION when R is installed.
 
   C-LEVEL FACILITIES:
 
-    * Rdefines.h has been tweaked so it can be included in C++ code
+    • Rdefines.h has been tweaked so it can be included in C++ code
       after R_ext/Boolean.h (which is included by R.h).
 
       Note that Rdefines.h is not kept up-to-date, and Rinternals.h is
       preferred for new code.
 
-    * eval and applyClosure are now protected against package code
+    • eval and applyClosure are now protected against package code
       supplying an invalid rho.
 
   DEPRECATED AND DEFUNCT:
 
-    * The unused namespace argument to package.skeleton() is now
+    • The unused namespace argument to package.skeleton() is now
       formally deprecated and will be removed in R 3.1.0.
 
-    * plclust() is deprecated: use the plot() method for class "hclust"
+    • plclust() is deprecated: use the plot() method for class "hclust"
       instead.
 
-    * Functions readNEWS() and checkNEWS() in package tools are
+    • Functions readNEWS() and checkNEWS() in package tools are
       deprecated (and they have not worked with current NEWS files for
       a long time).
 
   DOCUMENTATION:
 
-    * 'An Introduction to R' has a new chapter on using R as a
+    • ‘An Introduction to R’ has a new chapter on using R as a
       scripting language including interacting with the OS.
 
   BUG FIXES:
 
-    * help.request() could not determine the current version of R on
+    • help.request() could not determine the current version of R on
       CRAN.  (PR#15241)
 
-    * On Windows, file.info() failed on root directories unless the
+    • On Windows, file.info() failed on root directories unless the
       path was terminated with an explicit ".".  (PR#15302)
 
-    * The regmatches<-() replacement function mishandled results coming
+    • The regmatches<-() replacement function mishandled results coming
       from regexpr().  (PR#15311)
 
-    * The help for setClass() and representation() still suggested the
+    • The help for setClass() and representation() still suggested the
       deprecated argument representation=. (PR#15312)
 
-    * R CMD config failed in an installed build of R 3.0.1 (only) when
+    • R CMD config failed in an installed build of R 3.0.1 (only) when
       a sub-architecture was used.  (Reported by Berwin Turlach.)
 
-    * On Windows, the installer modified the etc/Rconsole and
+    • On Windows, the installer modified the etc/Rconsole and
       etc/Rprofile.site files even when default options were chosen, so
       the MD5 sums did not refer to the installed versions.  (Reported
       by Tal Galili.)
 
-    * plot(hclust(), cex =) respects cex again (and possibly others
+    • plot(hclust(), cex =) respects cex again (and possibly others
       similarly).  (Reported by Peter Langfelder.)
 
-    * If multiple packages were checked by R CMD check, and one was
+    • If multiple packages were checked by R CMD check, and one was
       written for a different OS, it would set --no-install for all
       following packages as well as itself.
 
-    * qr.coef() and related functions did not properly coerce real
+    • qr.coef() and related functions did not properly coerce real
       vectors to complex when necessary.  (PR#15332)
 
-    * ftable(a) now fixes up empty dimnames such that the result is
+    • ftable(a) now fixes up empty dimnames such that the result is
       printable.
 
-    * package.skeleton() was not starting its search for function
+    • package.skeleton() was not starting its search for function
       objects in the correct place if environment was supplied.
       (Reported by Karl Forner.)
 
-    * Parsing code was changing the length field of vectors and
+    • Parsing code was changing the length field of vectors and
       confusing the memory manager.  (PR#15345)
 
-    * The Fortran routine ZHER2K in the reference BLAS had a
+    • The Fortran routine ZHER2K in the reference BLAS had a
       comment-out bug in two places.  This caused trouble with eigen()
       for Hermitian matrices.  (PR#15345 and report from Robin Hankin)
 
-    * vignette() and browseVignettes() did not display non-Sweave
+    • vignette() and browseVignettes() did not display non-Sweave
       vignettes properly.
 
-    * Two warning/error messages have been corrected: the (optional)
+    • Two warning/error messages have been corrected: the (optional)
       warning produced by a partial name match with a pairlist, the
       error message from a zero-length argument to the : operator.
       (Found by Radford Neal; PR#15358, PR#15356)
 
-    * svd() returned NULL rather than omitting components as
+    • svd() returned NULL rather than omitting components as
       documented.  (Found by Radford Neal; PR#15360)
 
-    * mclapply() and mcparallel() with silent = TRUE could break a
+    • mclapply() and mcparallel() with silent = TRUE could break a
       process that uses stdout output unguarded against broken pipes
       (e.g., zip will fail silently). To work around such issues, they
       now replace stdout with a descriptor pointed to /dev/null
       instead. For this purpose, internal closeStdout and closeStderr
       functions have gained the to.null flag.
 
-    * log(), signif() and round() now raise an error if a single named
+    • log(), signif() and round() now raise an error if a single named
       argument is not named x.  (PR#15361)
 
-    * deparse() now deparses raw vectors in a form that is
+    • deparse() now deparses raw vectors in a form that is
       syntactically correct. (PR#15369)
 
-    * The jpeg driver in Sweave created a JPEG file, but gave it a .png
+    • The jpeg driver in Sweave created a JPEG file, but gave it a .png
       extension. (PR#15370)
 
-    * Deparsing of infix operators with named arguments is improved.
+    • Deparsing of infix operators with named arguments is improved.
       (PR#15350)
 
-    * mget(), seq.int() and numericDeriv() did not duplicate arguments
+    • mget(), seq.int() and numericDeriv() did not duplicate arguments
       properly. (PR#15352, PR#15353, PR#15354)
 
-    * kmeans(algorithm = "Hartigan-Wong") now always stops iterating in
+    • kmeans(algorithm = "Hartigan-Wong") now always stops iterating in
       the QTran stage. (PR#15364).
 
-    * read.dcf() re-allocated incorrectly and so could segfault when
+    • read.dcf() re-allocated incorrectly and so could segfault when
       called on a file with lines of more than 100 bytes.
 
-    * On systems where mktime() does not set errno, the last second
+    • On systems where mktime() does not set errno, the last second
       before the epoch could not be converted from POSIXlt to POSIXct.
       (Reported by Bill Dunlap.)
 
-    * add1.glm() miscalculated F-statistics when df > 1. (Bill Dunlap,
+    • add1.glm() miscalculated F-statistics when df > 1. (Bill Dunlap,
       PR#15386).
 
-    * stem() now discards infinite inputs rather than hanging.
+    • stem() now discards infinite inputs rather than hanging.
       (PR#15376)
 
-    * The parser now enforces C99 syntax for floating point hexadecimal
+    • The parser now enforces C99 syntax for floating point hexadecimal
       constants (e.g., 0x1.1p0), rather than returning unintended
       values for malformed constants. (PR#15234)
 
-    * model.matrix() now works with very long LHS names (more than 500
+    • model.matrix() now works with very long LHS names (more than 500
       bytes).  (PR#15377)
 
-    * integrate() reverts to the pre-2.12.0 behaviour: from 2.12.0 to
+    • integrate() reverts to the pre-2.12.0 behaviour: from 2.12.0 to
       3.0.1 it sometimes failed to achieve the requested tolerance and
       reported error estimates that were exceeded.  (PR#15219)
 
-    * strptime() now handles %W fields with value 0. (PR#15915)
+    • strptime() now handles %W fields with value 0. (PR#15915)
 
-    * R is now better protected against people trying to interact with
+    • R is now better protected against people trying to interact with
       the console in startup code.  (PR#15325)
 
-    * Subsetting 1D arrays often lost dimnames (PR#15301).
+    • Subsetting 1D arrays often lost dimnames (PR#15301).
 
-    * Unary + on a logical vector did not coerce to integer, although
+    • Unary + on a logical vector did not coerce to integer, although
       unary - did.
 
-    * na.omit() and na.exclude() added a row to a zero-row data frame.
+    • na.omit() and na.exclude() added a row to a zero-row data frame.
       (PR#15399)
 
-    * All the (where necessary cut-down) vignettes are installed if R
+    • All the (where necessary cut-down) vignettes are installed if R
       was configured with --without-recommended-packages.
 
-    * source() did not display filenames when reporting syntax errors.
+    • source() did not display filenames when reporting syntax errors.
 
-    * Syntax error reports misplaced the caret pointing out the bad
+    • Syntax error reports misplaced the caret pointing out the bad
       token.
 
-    * (Windows only) Starting R with R (instead of Rterm or Rgui) would
+    • (Windows only) Starting R with R (instead of Rterm or Rgui) would
       lose any zero-length strings from the command line arguments.
       (PR#15406)
 
-    * Errors in the encoding specified on the command line via
+    • Errors in the encoding specified on the command line via
       --encoding=foo were not handled properly.  (PR#15405)
 
-    * If x is a symbol, is.vector(x, "name") now returns TRUE, since
-      "name" and "symbol" should be synonyms.  (Reported by Herv'e
-      Pag`es.)
+    • If x is a symbol, is.vector(x, "name") now returns TRUE, since
+      "name" and "symbol" should be synonyms.  (Reported by Hervé
+      Pagès.)
 
-    * R CMD rtags works on platforms (such as OS X) with a
+    • R CMD rtags works on platforms (such as OS X) with a
       XSI-conformant shell command echo. (PR#15231)
 
-    * is.unsorted(NA) returns false as documented (rather than NA).
+    • is.unsorted(NA) returns false as documented (rather than NA).
 
-    * R CMD LINK did not know about sub-architectures.
+    • R CMD LINK did not know about sub-architectures.
 
-    * system() and system2() are better protected against users who
+    • system() and system2() are better protected against users who
       misguidedly have spaces in the temporary directory path.
 
-    * file.show() and edit() are now more likely to work on file paths
+    • file.show() and edit() are now more likely to work on file paths
       containing spaces.  (Where external utilities are used, not the
       norm on Windows nor in R.app which should previously have
       worked.)
 
-    * Packages using the methods package are more likely to work when
+    • Packages using the methods package are more likely to work when
       they import it but it is not attached.  (Several parts of its C
       code were looking for its R functions on the search path rather
       than in its namespace.)
 
-    * lgamma(-x) is no longer NaN for very small x.
+    • lgamma(-x) is no longer NaN for very small x.
 
-    * (Windows) system2() now respects specifying stdout and stderr as
+    • (Windows) system2() now respects specifying stdout and stderr as
       files if called from Rgui. (PR#15393)
 
-    * Closing an x11() device whilst locator() or identify() is in
+    • Closing an x11() device whilst locator() or identify() is in
       progress no longer hangs R.  (PR#15253)
 
-    * list.dirs(full.names = FALSE) was not implemented.  (PR#15170)
+    • list.dirs(full.names = FALSE) was not implemented.  (PR#15170)
 
-    * format() sometimes added unnecessary spaces.  (PR#15411)
+    • format() sometimes added unnecessary spaces.  (PR#15411)
 
-    * all.equal(check.names = FALSE) would ignore the request to ignore
+    • all.equal(check.names = FALSE) would ignore the request to ignore
       the names and would check them as attributes.
 
-    * The symbol set by tools::Rd2txt_options(itemBullet=) was not
+    • The symbol set by tools::Rd2txt_options(itemBullet=) was not
       respected in some locales. (PR#15435)
 
-    * mcMap() was not exported by package parallel. (PR#15439)
+    • mcMap() was not exported by package parallel. (PR#15439)
 
-    * plot() for TukeyHSD objects did not balance dev.hold() and
+    • plot() for TukeyHSD objects did not balance dev.hold() and
       dev.flush() calls on multi-page plots.  (PR#15449)
 
 CHANGES IN R 3.0.1:
 
   NEW FEATURES:
 
-    * chooseCRANmirror() and chooseBioCmirror() gain an ind argument
+    • chooseCRANmirror() and chooseBioCmirror() gain an ind argument
       (like setRepositories()).
 
-    * mcparallel has a new argument mc.interactive which can modify the
+    • mcparallel has a new argument mc.interactive which can modify the
       interactive flag in the child process. The new default is FALSE
       which makes child processes non-interactive by default (this
       prevents lock-ups due to children waiting for interactive input).
 
-    * scan() now warns when end-of-file occurs within a quoted string.
+    • scan() now warns when end-of-file occurs within a quoted string.
 
-    * count.fields() is now consistent with scan() in its handling of
+    • count.fields() is now consistent with scan() in its handling of
       newlines in quoted strings.  Instead of triggering an error, this
       results in the current line receiving NA as the field count, with
       the next line getting the total count of the two lines.
 
-    * The default method of image() will plot axes of the class of xlim
+    • The default method of image() will plot axes of the class of xlim
       and ylim (and hence of x and y if there is a suitable range()
       method).  Based on a suggestion of Michael Sumner.
 
-    * load() now has a verbose argument for debugging support, to print
+    • load() now has a verbose argument for debugging support, to print
       the names of objects just before loading them.
 
-    * When loading a serialized object encounters a reference to a
+    • When loading a serialized object encounters a reference to a
       namespace which cannot be loaded, this is replaced by a reference
       to the global environment, with a warning.
 
-    * pairs() gains a line.main option for title placement.
+    • pairs() gains a line.main option for title placement.
 
-    * The remaining instances in which serialization to a raw vector
+    • The remaining instances in which serialization to a raw vector
       was limited to 2GB have been unlimited on a 64-bit platform, and
       in most cases serialization to a vector of more than 1GB will be
       substantially faster.
 
   UTILITIES:
 
-    * R CMD config now make use of personal Makevars files under ~/.R
+    • R CMD config now make use of personal Makevars files under ~/.R
       and a site file Makevars.site, in the same way as R CMD SHLIB and
       R CMD INSTALL.  This makes the utility more useful in package
       configure scripts.
@@ -2934,7 +3046,7 @@
 
   PACKAGE INSTALLATION:
 
-    * Alternatives to the site and user customization files
+    • Alternatives to the site and user customization files
       Makevars.site and ~/.R/Makevars can be specified _via_ the
       environment variables R_MAKEVARS_SITE and R_MAKEVARS_USER
       respectively.  These can be used to suppress the use of the
@@ -2943,100 +3055,100 @@
 
   BUG FIXES:
 
-    * sys.source() did not report error locations when keep.source =
+    • sys.source() did not report error locations when keep.source =
       TRUE.
 
-    * as.POSIXct.numeric was coercing origin using the tz argument and
+    • as.POSIXct.numeric was coercing origin using the tz argument and
       not "GMT" as documented (PR#14973).
 
-    * The active binding to assign fields in reference classes has been
+    • The active binding to assign fields in reference classes has been
       cleaned up to reduce dependence on the class' package
       environment, also fixing bug in initializing read-only fields
       (inspired by a report from Hadley Wickham).
 
-    * str(d) no longer gives an error when names(d) contain illegal
+    • str(d) no longer gives an error when names(d) contain illegal
       multibyte strings (PR#15247).
 
-    * Profiling of built-in functions with line.profiling= TRUE did not
+    • Profiling of built-in functions with line.profiling= TRUE did not
       record the line from which they were called.
 
-    * citation(pkg) dropped the header and footer specified in the
+    • citation(pkg) dropped the header and footer specified in the
       CITATION file (PR#15257).
 
-    * Quotes were handled differently when reading the first line and
+    • Quotes were handled differently when reading the first line and
       reading the rest, so read.table() misread some files that
       contained quote characters (PR#15245).
 
-    * cat() with sep a character vector of length greater than one and
+    • cat() with sep a character vector of length greater than one and
       more than one argument was using separators inconsistently
       (PR#15261).
 
-    * On Windows in R 3.0.0, savePlot() failed because of an incorrect
+    • On Windows in R 3.0.0, savePlot() failed because of an incorrect
       check on the argument count.
 
-    * unzip(list = TRUE) returned Names as a factor and not a character
+    • unzip(list = TRUE) returned Names as a factor and not a character
       vector (as documented) for the internal method.  (Noticed by Sean
       O'Riordain.)
 
-    * contourLines() now checks more comprehensively for conformance of
+    • contourLines() now checks more comprehensively for conformance of
       its x, y and z arguments (it was used incorrectly in package
       R2G2).
 
-    * Saved graphics display lists are R version-specific.  Attempting
+    • Saved graphics display lists are R version-specific.  Attempting
       to load workspaces containing them (or some other
       version-specific objects) aborted the load in R 3.0.0 and
       earlier; now it does a partial load and generates a warning
       instead.
 
-    * In R 3.0.0, identify() and locator() did not record information
+    • In R 3.0.0, identify() and locator() did not record information
       correctly, so replaying a graph (e.g., by copying it to another
       device) would fail. (PR#15271)
 
-    * Calling file.copy() or dirname() with the invalid input "" (which
+    • Calling file.copy() or dirname() with the invalid input "" (which
       was being used in packages, despite not being a file path) could
       have caused a segfault.
 
       dirname("") is now "" rather than "." (unless it segfaulted).
 
-    * supsmu() could read/write outside its input vectors for very
+    • supsmu() could read/write outside its input vectors for very
       short inputs (seen in package rms for n = 4).
 
-    * as.dendrogram()'s hclust method uses less memory and hence gets
+    • as.dendrogram()'s hclust method uses less memory and hence gets
       considerably faster for large (n ~ 1000) clusterings, thanks to
-      Daniel M"ullner. (PR#15174)
+      Daniel Müllner. (PR#15174)
 
-    * The return value when all workers failed from
+    • The return value when all workers failed from
       parallel::mclapply(mc.preschedule = TRUE) was a list of strings
       and not of error objects.  (Spotted by Karl Forner and Bernd
       Bischl.)
 
-    * In R 3.0.0, when help() found multiple pages with the same alias,
+    • In R 3.0.0, when help() found multiple pages with the same alias,
       the HTML display of all the selections was not produced.
       (PR#15282)
 
-    * splinefun(method="monoH.FC") now produces a function with first
+    • splinefun(method="monoH.FC") now produces a function with first
       argument named x and allows deriv=3, as documented. (PR#15273)
 
-    * summaryRprof() would only read the first chunksize lines of an
+    • summaryRprof() would only read the first chunksize lines of an
       Rprof file produced with line.profiling=TRUE. By default, this is
       the first 100 seconds.  (PR#15288)
 
-    * lsfit() produced an incorrect error message when argument x had
+    • lsfit() produced an incorrect error message when argument x had
       more columns than rows or x had a different number of rows than
       y. (Spotted by Renaud Gaujoux.)
 
-    * Binary operations on equal length vectors copied the class name
+    • Binary operations on equal length vectors copied the class name
       from the second operand when the first had no class name, but did
       not set the object bit. (PR#15299)
 
-    * The trace() method for reference generator objects failed after
+    • The trace() method for reference generator objects failed after
       those objects became function definitions.
 
-    * write.table() did not check that factors were constructed
+    • write.table() did not check that factors were constructed
       correctly, and so caused a segment fault when writing bad ones.
       (PR#15300)
 
-    * The internal HTTP server no longer chokes on POST requests
+    • The internal HTTP server no longer chokes on POST requests
       without body. It will also pass-through other request types for
       custom handlers (with the method stored in Request-Method header)
       instead of failing.
@@ -3045,17 +3157,17 @@
 
   SIGNIFICANT USER-VISIBLE CHANGES:
 
-    * Packages need to be (re-)installed under this version (3.0.0) of
+    • Packages need to be (re-)installed under this version (3.0.0) of
       R.
 
-    * There is a subtle change in behaviour for numeric index values
+    • There is a subtle change in behaviour for numeric index values
       2^31 and larger.  These never used to be legitimate and so were
       treated as NA, sometimes with a warning.  They are now legal for
       long vectors so there is no longer a warning, and x[2^31] <- y
       will now extend the vector on a 64-bit platform and give an error
       on a 32-bit one.
 
-    * It is now possible for 64-bit builds to allocate amounts of
+    • It is now possible for 64-bit builds to allocate amounts of
       memory limited only by the OS.  It may be wise to use OS
       facilities (e.g., ulimit in a bash shell, limit in csh), to set
       limits on overall memory consumption of an R process,
@@ -3067,16 +3179,16 @@
       command-line option --max-mem-size or setting environment
       variable R_MAX_MEM_SIZE.
 
-    * Negative numbers for colours are consistently an error:
+    • Negative numbers for colours are consistently an error:
       previously they were sometimes taken as transparent, sometimes
       mapped into the current palette and sometimes an error.
 
   NEW FEATURES:
 
-    * identical() has a new argument, ignore.environment, used when
+    • identical() has a new argument, ignore.environment, used when
       comparing functions (with default FALSE as before).
 
-    * There is a new option, options(CBoundsCheck=), which controls how
+    • There is a new option, options(CBoundsCheck=), which controls how
       .C() and .Fortran() pass arguments to compiled code.  If true
       (which can be enabled by setting the environment variable
       R_C_BOUNDS_CHECK to yes), raw, integer, double and complex
@@ -3088,218 +3200,218 @@
       This is not intended for routine use, but can be very helpful in
       finding segfaults in package code.
 
-    * In layout(), the limits on the grid size have been raised
+    • In layout(), the limits on the grid size have been raised
       (again).
 
-    * New simple provideDimnames() utility function.
+    • New simple provideDimnames() utility function.
 
-    * Where methods for length() return a double value which is
+    • Where methods for length() return a double value which is
       representable as an integer (as often happens for package
       Matrix), this is converted to an integer.
 
-    * Matrix indexing of data frames by two-column numeric indices is
+    • Matrix indexing of data frames by two-column numeric indices is
       now supported for replacement as well as extraction.
 
-    * setNames() now has a default for its object argument, useful for
+    • setNames() now has a default for its object argument, useful for
       a character result.
 
-    * StructTS() has a revised additive constant in the loglik
+    • StructTS() has a revised additive constant in the loglik
       component of the result: the previous definition is returned as
       the loglik0 component.  However, the help page has always warned
       of a lack of comparability of log-likelihoods for non-stationary
       models.  (Suggested by Jouni Helske.)
 
-    * The logic in aggregate.formula() has been revised.  It is now
+    • The logic in aggregate.formula() has been revised.  It is now
       possible to use a formula stored in a variable; previously, it
       had to be given explicitly in the function call.
 
-    * install.packages() has a new argument quiet to reduce the amount
+    • install.packages() has a new argument quiet to reduce the amount
       of output shown.
 
-    * Setting an element of the graphics argument lwd to a negative or
+    • Setting an element of the graphics argument lwd to a negative or
       infinite value is now an error.  Lines corresponding to elements
       with values NA or NaN are silently omitted.
 
       Previously the behaviour was device-dependent.
 
-    * Setting graphical parameters cex, col, lty, lwd and pch in par()
+    • Setting graphical parameters cex, col, lty, lwd and pch in par()
       now requires a length-one argument.  Previously some silently
       took the first element of a longer vector, but not always when
       documented to do so.
 
-    * Sys.which() when used with inputs which would be unsafe in a
+    • Sys.which() when used with inputs which would be unsafe in a
       shell (e.g., absolute paths containing spaces) now uses
       appropriate quoting.
 
-    * as.tclObj() has been extended to handle raw vectors.  Previously,
+    • as.tclObj() has been extended to handle raw vectors.  Previously,
       it only worked in the other direction.  (Contributed by Charlie
       Friedemann, PR#14939.)
 
-    * New functions cite() and citeNatbib() have been added, to allow
+    • New functions cite() and citeNatbib() have been added, to allow
       generation of in-text citations from "bibentry" objects.  A
       cite() function may be added to bibstyle() environments.
 
-    * A sort() method has been added for "bibentry" objects.
+    • A sort() method has been added for "bibentry" objects.
 
-    * The bibstyle() function now defaults to setting the default
+    • The bibstyle() function now defaults to setting the default
       bibliography style. The getBibstyle() function has been added to
       report the name of the current default style.
 
-    * scatter.smooth() now has an argument lpars to pass arguments to
+    • scatter.smooth() now has an argument lpars to pass arguments to
       lines().
 
-    * pairs() has a new log argument, to allow some or all variables to
+    • pairs() has a new log argument, to allow some or all variables to
       be plotted on logarithmic scale.  (In part, wish of PR#14919.)
 
-    * split() gains a sep argument.
+    • split() gains a sep argument.
 
-    * termplot() does a better job when given a model with interactions
+    • termplot() does a better job when given a model with interactions
       (and no longer attempts to plot interaction terms).
 
-    * The parser now incorporates code from Romain Francois' parser
+    • The parser now incorporates code from Romain Francois' parser
       package, to support more detailed computation on the code, such
       as syntax highlighting, comment-based documentation, etc.
       Functions getParseData() and getParseText() access the data.
 
-    * There is a new function rep_len() analogous to rep.int() for when
+    • There is a new function rep_len() analogous to rep.int() for when
       speed is required (and names are not).
 
-    * The undocumented use rep(NULL, length.out = n) for n > 0 (which
+    • The undocumented use rep(NULL, length.out = n) for n > 0 (which
       returns NULL) now gives a warning.
 
-    * demo() gains an encoding argument for those packages with
+    • demo() gains an encoding argument for those packages with
       non-ASCII demos: it defaults to the package encoding where there
       is one.
 
-    * strwrap() converts inputs with a marked encoding to the current
+    • strwrap() converts inputs with a marked encoding to the current
       locale: previously it made some attempt to pass through as bytes
       inputs invalid in the current locale.
 
-    * Specifying both rate and scale to [dpqr]gamma is a warning (if
+    • Specifying both rate and scale to [dpqr]gamma is a warning (if
       they are essentially the same value) or an error.
 
-    * merge() works in more cases where the data frames include
+    • merge() works in more cases where the data frames include
       matrices.  (Wish of PR#14974.)
 
-    * optimize() and uniroot() no longer use a shared parameter object
+    • optimize() and uniroot() no longer use a shared parameter object
       across calls.  (nlm(), nlminb() and optim() with numerical
       derivatives still do, as documented.)
 
-    * The all.equal() method for date-times is now documented: times
+    • The all.equal() method for date-times is now documented: times
       are regarded as equal (by default) if they differ by up to 1
       msec.
 
-    * duplicated() and unique() gain a nmax argument which can be used
+    • duplicated() and unique() gain a nmax argument which can be used
       to make them much more efficient when it is known that there are
       only a small number of unique entries.  This is done
       automatically for factors.
 
-    * Functions rbinom(), rgeom(), rhyper(), rpois(), rnbinom(),
+    • Functions rbinom(), rgeom(), rhyper(), rpois(), rnbinom(),
       rsignrank() and rwilcox() now return integer (not double)
       vectors.  This halves the storage requirements for large
       simulations.
 
-    * sort(), sort.int() and sort.list() now use radix sorting for
+    • sort(), sort.int() and sort.list() now use radix sorting for
       factors of less than 100,000 levels when method is not supplied.
       So does order() if called with a single factor, unless na.last =
       NA.
 
-    * diag() as used to generate a diagonal matrix has been re-written
+    • diag() as used to generate a diagonal matrix has been re-written
       in C for speed and less memory usage.  It now forces the result
-      to be numeric in the case diag(x) since it is said to have 'zero
-      off-diagonal entries'.
+      to be numeric in the case diag(x) since it is said to have ‘zero
+      off-diagonal entries’.
 
-    * backsolve() (and forwardsolve()) are now internal functions, for
+    • backsolve() (and forwardsolve()) are now internal functions, for
       speed and support for large matrices.
 
-    * More matrix algebra functions (e.g., chol() and solve()) accept
+    • More matrix algebra functions (e.g., chol() and solve()) accept
       logical matrices (and coerce to numeric).
 
-    * sample.int() has some support for n >= 2^31: see its help for the
+    • sample.int() has some support for n >= 2^31: see its help for the
       limitations.
 
       A different algorithm is used for (n, size, replace = FALSE, prob
       = NULL) for n > 1e7 and size <= n/2.  This is much faster and
       uses less memory, but does give different results.
 
-    * approxfun() and splinefun() now return a wrapper to an internal
+    • approxfun() and splinefun() now return a wrapper to an internal
       function in the stats namespace rather than a .C() or .Call()
       call.  This is more likely to work if the function is saved and
       used in a different session.
 
-    * The functions .C(), .Call(), .External() and .Fortran() now give
+    • The functions .C(), .Call(), .External() and .Fortran() now give
       an error (rather than a warning) if called with a named first
       argument.
 
-    * Sweave() by default now reports the locations in the source
+    • Sweave() by default now reports the locations in the source
       file(s) of each chunk.
 
-    * clearPushBack() is now a documented interface to a long-existing
+    • clearPushBack() is now a documented interface to a long-existing
       internal call.
 
-    * aspell() gains filters for R code, Debian Control Format and
+    • aspell() gains filters for R code, Debian Control Format and
       message catalog files, and support for R level dictionaries.  In
       addition, package utils now provides functions
       aspell_package_R_files() and aspell_package_C_files() for spell
       checking R and C level message strings in packages.
 
-    * bibentry() gains some support for "incomplete" entries with a
+    • bibentry() gains some support for “incomplete” entries with a
       crossref field.
 
-    * gray() and gray.colors() finally allow alpha to be specified.
+    • gray() and gray.colors() finally allow alpha to be specified.
 
-    * monthplot() gains parameters to control the look of the reference
+    • monthplot() gains parameters to control the look of the reference
       lines.  (Suggestion of Ian McLeod.)
 
-    * Added support for new %~% relation ("is distributed as") in
+    • Added support for new %~% relation (“is distributed as”) in
       plotmath.
 
-    * domain = NA is accepted by gettext() and ngettext(), analogously
+    • domain = NA is accepted by gettext() and ngettext(), analogously
       to stop() etc.
 
-    * termplot() gains a new argument plot = FALSE which returns
+    • termplot() gains a new argument plot = FALSE which returns
       information to allow the plots to be modified for use as part of
       other plots, but does not plot them.  (Contributed by Terry
       Therneau, PR#15076.)
 
-    * quartz.save(), formerly an undocumented part of R.app, is now
+    • quartz.save(), formerly an undocumented part of R.app, is now
       available to copy a device to a quartz() device.  dev.copy2pdf()
       optionally does this for PDF output: quartz.save() defaults to
       PNG.
 
-    * The default method of pairs() now allows text.panel = NULL and
+    • The default method of pairs() now allows text.panel = NULL and
       the use of <foo>.panel = NULL is now documented.
 
-    * setRefClass() and getRefClass() now return class generator
+    • setRefClass() and getRefClass() now return class generator
       functions, similar to setClass(), but still with the reference
       fields and methods as before (suggestion of Romain Francois).
 
-    * New functions bitwNot(), bitwAnd(), bitwOr() and bitwXor(), using
+    • New functions bitwNot(), bitwAnd(), bitwOr() and bitwXor(), using
       the internal interfaces previously used for classes "octmode" and
       "hexmode".
 
       Also bitwShiftL() and bitwShiftR() for shifting bits in elements
       of integer vectors.
 
-    * New option "deparse.cutoff" to control the deparsing of language
+    • New option "deparse.cutoff" to control the deparsing of language
       objects such as calls and formulae when printing.  (Suggested by
       a comment of Sarah Goslee.)
 
-    * colors() gains an argument distinct.
+    • colors() gains an argument distinct.
 
-    * New demo(colors) and demo(hclColors), with utility functions.
+    • New demo(colors) and demo(hclColors), with utility functions.
 
-    * list.files() (aka dir()) gains a new optional argument no.. which
+    • list.files() (aka dir()) gains a new optional argument no.. which
       allows to exclude "." and ".." from listings.
 
-    * Multiple time series are also of class "matrix"; consequently,
+    • Multiple time series are also of class "matrix"; consequently,
       head(), e.g., is more useful.
 
-    * encodeString() preserves UTF-8 marked encodings.  Thus if factor
+    • encodeString() preserves UTF-8 marked encodings.  Thus if factor
       levels are marked as UTF-8 an attempt is made to print them in
       UTF-8 in RGui on Windows.
 
-    * readLines() and scan() (and hence read.table()) in a UTF-8 locale
+    • readLines() and scan() (and hence read.table()) in a UTF-8 locale
       now discard a UTF-8 byte-order-mark (BOM).  Such BOMs are allowed
       but not recommended by the Unicode Standard: however Microsoft
       applications can produce them and so they are sometimes found on
@@ -3308,141 +3420,141 @@
       The encoding name "UTF-8-BOM" for a connection will ensure that a
       UTF-8 BOM is discarded.
 
-    * mapply(FUN, a1, ..) now also works when a1 (or a further such
+    • mapply(FUN, a1, ..) now also works when a1 (or a further such
       argument) needs a length() method (which the documented arguments
-      never do).  (Requested by Herv'e Pag`es; with a patch.)
+      never do).  (Requested by Hervé Pagès; with a patch.)
 
-    * .onDetach() is supported as an alternative to .Last.lib.  Unlike
+    • .onDetach() is supported as an alternative to .Last.lib.  Unlike
       .Last.lib, this does not need to be exported from the package's
       namespace.
 
-    * The srcfile argument to parse() may now be a character string, to
+    • The srcfile argument to parse() may now be a character string, to
       be used in error messages.
 
-    * The format() method for ftable objects gains a method argument,
+    • The format() method for ftable objects gains a method argument,
       propagated to write.ftable() and print(), allowing more compact
       output, notably for LaTeX formatting, thanks to Marius Hofert.
 
-    * The utils::process.events() function has been added to trigger
+    • The utils::process.events() function has been added to trigger
       immediate event handling.
 
-    * Sys.which() now returns NA (not "") for NA inputs (related to
+    • Sys.which() now returns NA (not "") for NA inputs (related to
       PR#15147).
 
-    * The print() method for class "htest" gives fewer trailing spaces
+    • The print() method for class "htest" gives fewer trailing spaces
       (wish of PR#15124).
 
       Also print output from HoltWinters(), nls() and others.
 
-    * loadNamespace() allows a version specification to be given, and
+    • loadNamespace() allows a version specification to be given, and
       this is used to check version specifications given in the Imports
       field when a namespace is loaded.
 
-    * setClass() has a new argument, slots, clearer and less ambiguous
+    • setClass() has a new argument, slots, clearer and less ambiguous
       than representation.  It is recommended for future code, but
       should be back-compatible.  At the same time, the allowed slot
       specification is slightly more general.  See the documentation
       for details.
 
-    * mget() now has a default for envir (the frame from which it is
+    • mget() now has a default for envir (the frame from which it is
       called), for consistency with get() and assign().
 
-    * close() now returns an integer status where available, invisibly.
+    • close() now returns an integer status where available, invisibly.
       (Wish of PR#15088.)
 
-    * The internal method of tar() can now store paths too long for the
+    • The internal method of tar() can now store paths too long for the
       ustar format, using the (widely supported) GNU extension.  It can
       also store long link names, but these are much less widely
       supported.  There is support for larger files, up to the ustar
       limit of 8GB.
 
-    * Local reference classes have been added to package methods.
+    • Local reference classes have been added to package methods.
       These are a technique for avoiding unneeded copying of large
       components of objects while retaining standard R functional
       behavior.  See ?LocalReferenceClasses.
 
-    * untar() has a new argument restore_times which if false (not the
+    • untar() has a new argument restore_times which if false (not the
       default) discards the times in the tarball.  This is useful if
       they are incorrect (some tarballs submitted to CRAN have times in
       a local time zone or many years in the past even though the
       standard required them to be in UTC).
 
-    * replayplot() cannot (and will not attempt to) replay plots
+    • replayplot() cannot (and will not attempt to) replay plots
       recorded under R < 3.0.0.  It may crash the R session if an
       attempt is made to replay plots created in a different build of R
       >= 3.0.0.
 
-    * Palette changes get recorded on the display list, so replaying
+    • Palette changes get recorded on the display list, so replaying
       plots (including when resizing screen devices and using
       dev.copy()) will work better when the palette is changed during a
       plot.
 
-    * chol(pivot = TRUE) now defaults to LAPACK, not LINPACK.
+    • chol(pivot = TRUE) now defaults to LAPACK, not LINPACK.
 
-    * The parse() function has a new parameter keep.source, which
+    • The parse() function has a new parameter keep.source, which
       defaults to options("keep.source").
 
-    * Profiling via Rprof() now optionally records information at the
+    • Profiling via Rprof() now optionally records information at the
       statement level, not just the function level.
 
-    * The Rprof() function now quotes function names in in its output
+    • The Rprof() function now quotes function names in in its output
       file on Windows, to be consistent with the quoting in Unix.
 
-    * Profiling via Rprof() now optionally records information about
+    • Profiling via Rprof() now optionally records information about
       time spent in GC.
 
-    * The HTML help page for a package now displays non-vignette
+    • The HTML help page for a package now displays non-vignette
       documentation files in a more accessible format.
 
-    * To support options(stringsAsFactors = FALSE), model.frame(),
+    • To support options(stringsAsFactors = FALSE), model.frame(),
       model.matrix() and replications() now automatically convert
       character vectors to factors without a warning.
 
-    * The print method for objects of class "table" now detects tables
+    • The print method for objects of class "table" now detects tables
       with 0-extents and prints the results as, e.g., < table of extent
       0 x 1 x 2 >. (Wish of PR#15198.)
 
-    * Deparsing involving calls to anonymous functions has been made
+    • Deparsing involving calls to anonymous functions has been made
       closer to reversible by the addition of extra parentheses.
 
-    * The function utils::packageName() has been added as a lightweight
+    • The function utils::packageName() has been added as a lightweight
       version of methods::getPackageName().
 
-    * find.package(lib.loc = NULL) now treats loaded namespaces
+    • find.package(lib.loc = NULL) now treats loaded namespaces
       preferentially in the same way as attached packages have been for
       a long time.
 
-    * In Windows, the Change Directory dialog now defaults to the
+    • In Windows, the Change Directory dialog now defaults to the
       current working directory, rather than to the last directory
       chosen in that dialog.
 
-    * available.packages() gains a "license/restricts_use" filter which
+    • available.packages() gains a "license/restricts_use" filter which
       retains only packages for which installation can proceed solely
       based on packages which are guaranteed not to restrict use.
 
-    * New check_packages_in_dir() function in package tools for
+    • New check_packages_in_dir() function in package tools for
       conveniently checking source packages along with their reverse
       dependencies.
 
-    * R's completion mechanism has been improved to handle help
+    • R's completion mechanism has been improved to handle help
       requests (starting with a question mark).  In particular, help
       prefixes are now supported, as well as quoted help topics.  To
       support this, completion inside quotes are now handled by R by
       default on all platforms.
 
-    * The memory manager now allows the strategy used to balance
+    • The memory manager now allows the strategy used to balance
       garbage collection and memory growth to be controlled by setting
       the environment variable R_GC_MEM_GROW. See ?Memory for more
       details.
 
-    * ('For experts only', as the introductory manual says.)  The use
+    • (‘For experts only’, as the introductory manual says.)  The use
       of environment variables R_NSIZE and R_VSIZE to control the
       initial (= minimum) garbage collection trigger for number of cons
       cels and size of heap has been restored: they can be overridden
       by the command-line options --min-nsize and --min-vsize; see
       ?Memory.
 
-    * On Windows, the device name for bitmap devices as reported by
+    • On Windows, the device name for bitmap devices as reported by
       .Device and .Devices no longer includes the file name.  This is
       for consistency with other platforms and was requested by the
       lattice maintainer.
@@ -3450,79 +3562,79 @@
       win.metafile() still uses the file name: the exact form is used
       by package tkrplot.
 
-    * set.seed(NULL) re-initializes .Random.seed as done at the
+    • set.seed(NULL) re-initializes .Random.seed as done at the
       beginning of the session if not already set.  (Suggestion of Bill
       Dunlap.)
 
-    * The breaks argument in hist.default() can now be a function that
+    • The breaks argument in hist.default() can now be a function that
       returns the breakpoints to be used (previously it could only
       return the suggested number of breakpoints).
 
-    * File share/licenses/licenses.db has some clarifications,
-      especially as to which variants of 'BSD' and 'MIT' is intended
+    • File share/licenses/licenses.db has some clarifications,
+      especially as to which variants of ‘BSD’ and ‘MIT’ is intended
       and how to apply them to packages.  The problematic licence
-      'Artistic-1.0' has been removed.
+      ‘Artistic-1.0’ has been removed.
 
   LONG VECTORS:
 
   This section applies only to 64-bit platforms.
 
-    * There is support for vectors longer than 2^31 - 1 elements.  This
+    • There is support for vectors longer than 2^31 - 1 elements.  This
       applies to raw, logical, integer, double, complex and character
       vectors, as well as lists.  (Elements of character vectors remain
       limited to 2^31 - 1 bytes.)
 
-    * Most operations which can sensibly be done with long vectors
-      work: others may return the error 'long vectors not supported
-      yet'.  Most of these are because they explicitly work with
+    • Most operations which can sensibly be done with long vectors
+      work: others may return the error ‘long vectors not supported
+      yet’.  Most of these are because they explicitly work with
       integer indices (e.g., anyDuplicated() and match()) or because
       other limits (e.g., of character strings or matrix dimensions)
       would be exceeded or the operations would be extremely slow.
 
-    * length() returns a double for long vectors, and lengths can be
+    • length() returns a double for long vectors, and lengths can be
       set to 2^31 or more by the replacement function with a double
       value.
 
-    * Most aspects of indexing are available.  Generally double-valued
+    • Most aspects of indexing are available.  Generally double-valued
       indices can be used to access elements beyond 2^31 - 1.
 
-    * There is some support for matrices and arrays with each dimension
+    • There is some support for matrices and arrays with each dimension
       less than 2^31 but total number of elements more than that.  Only
       some aspects of matrix algebra work for such matrices, often
       taking a very long time.  In other cases the underlying Fortran
       code has an unstated restriction (as was found for complex
       svd()).
 
-    * dist() can produce dissimilarity objects for more than 65536 rows
+    • dist() can produce dissimilarity objects for more than 65536 rows
       (but for example hclust() cannot process such objects).
 
-    * serialize() to a raw vector is unlimited in size (except by
+    • serialize() to a raw vector is unlimited in size (except by
       resources).
 
-    * The C-level function R_alloc can now allocate 2^35 or more bytes.
+    • The C-level function R_alloc can now allocate 2^35 or more bytes.
 
-    * agrep() and grep() will return double vectors of indices for long
+    • agrep() and grep() will return double vectors of indices for long
       vector inputs.
 
-    * Many calls to .C() have been replaced by .Call() to allow long
+    • Many calls to .C() have been replaced by .Call() to allow long
       vectors to be supported (now or in the future).  Regrettably
       several packages had copied the non-API .C() calls and so failed.
 
-    * .C() and .Fortran() do not accept long vector inputs.  This is a
+    • .C() and .Fortran() do not accept long vector inputs.  This is a
       precaution as it is very unlikely that existing code will have
       been written to handle long vectors (and the R wrappers often
       assume that length(x) is an integer).
 
-    * Most of the methods for sort() work for long vectors.
+    • Most of the methods for sort() work for long vectors.
 
       rank(), sort.list() and order() support long vectors (slowly
       except for radix sorting).
 
-    * sample() can do uniform sampling from a long vector.
+    • sample() can do uniform sampling from a long vector.
 
   PERFORMANCE IMPROVEMENTS:
 
-    * More use has been made of R objects representing registered entry
+    • More use has been made of R objects representing registered entry
       points, which is more efficient as the address is provided by the
       loader once only when the package is loaded.
 
@@ -3535,30 +3647,30 @@
       that .C / .Fortran / .Call calls copied from earlier versions of
       R may no longer work - but they were never part of the API.
 
-    * Many .Call() calls in package base have been migrated to
+    • Many .Call() calls in package base have been migrated to
       .Internal() calls.
 
-    * solve() makes fewer copies, especially when b is a vector rather
+    • solve() makes fewer copies, especially when b is a vector rather
       than a matrix.
 
-    * eigen() makes fewer copies if the input has dimnames.
+    • eigen() makes fewer copies if the input has dimnames.
 
-    * Most of the linear algebra functions make fewer copies when the
+    • Most of the linear algebra functions make fewer copies when the
       input(s) are not double (e.g., integer or logical).
 
-    * A foreign function call (.C() etc) in a package without a PACKAGE
+    • A foreign function call (.C() etc) in a package without a PACKAGE
       argument will only look in the first DLL specified in the
       NAMESPACE file of the package rather than searching all loaded
       DLLs.  A few packages needed PACKAGE arguments added.
 
-    * The @<- operator is now implemented as a primitive, which should
+    • The @<- operator is now implemented as a primitive, which should
       reduce some copying of objects when used.  Note that the operator
       object must now be in package base: do not try to import it
       explicitly from package methods.
 
   PACKAGE INSTALLATION:
 
-    * The transitional support for installing packages without
+    • The transitional support for installing packages without
       namespaces (required since R 2.14.0) has been removed.  R CMD
       build will still add a namespace, but a .First.lib() function
       will need to be converted.
@@ -3570,28 +3682,28 @@
       As an exception, packages without a R directory and no NAMESPACE
       file can still be installed.
 
-    * Packages can specify in their DESCRIPTION file a line like
+    • Packages can specify in their DESCRIPTION file a line like
       
            Biarch: yes
 
       to be installed on Windows with --force-biarch.
 
-    * Package vignettes can now be processed by other engines besides
-      Sweave; see 'Writing R Extensions' and the tools::vignetteEngine
+    • Package vignettes can now be processed by other engines besides
+      Sweave; see ‘Writing R Extensions’ and the tools::vignetteEngine
       help topic for details.
 
-    * The *.R tangled source code for vignettes is now included in
+    • The *.R tangled source code for vignettes is now included in
       tarballs when R CMD build is used to produce them.  In R 3.0.0,
       *.R files not in the sources will be produced at install time,
       but eventually this will be dropped.
 
-    * The package type "mac.binary" now looks in a path in the
+    • The package type "mac.binary" now looks in a path in the
       repository without any Mac subtype (which used to be universal or
       leopard): it looks in bin/macosx/contrib/3.0 rather than
       bin/macosx/leopard/contrib/2.15).  This is the type used for the
       CRAN binary distribution for OS X as from R 3.0.0.
 
-    * File etc/Makeconf makes more use of the macros $(CC), $(CXX),
+    • File etc/Makeconf makes more use of the macros $(CC), $(CXX),
       $(F77) and $(FC), so the compiler in use can be changed by
       setting just these (and if necessary the corresponding flags and
       FLIBS) in file ~/.R/Makevars.
@@ -3601,40 +3713,40 @@
 
   UTILITIES:
 
-    * R CMD check now gives a warning rather than a note if it finds
+    • R CMD check now gives a warning rather than a note if it finds
       calls to abort, assert or exit in compiled code, and has been
       able to find the .o file in which the calls occur.
 
       Such calls can terminate the R process which loads the package.
 
-    * The location of the build and check environment files can now be
+    • The location of the build and check environment files can now be
       specified by the environment variables R_BUILD_ENVIRON and
       R_CHECK_ENVIRON, respectively.
 
-    * R CMD Sweave gains a --compact option to control possibly
+    • R CMD Sweave gains a --compact option to control possibly
       reducing the size of the PDF file it creates when --pdf is given.
 
-    * R CMD build now omits Eclipse's .metadata directories, and R CMD
+    • R CMD build now omits Eclipse's .metadata directories, and R CMD
       check warns if it finds them.
 
-    * R CMD check now does some checks on functions defined within
+    • R CMD check now does some checks on functions defined within
       reference classes, including of .Call() etc calls.
 
-    * R CMD check --as-cran notes assignments to the global
+    • R CMD check --as-cran notes assignments to the global
       environment, calls to data() which load into the global
       environment, and calls to attach().
 
-    * R CMD build by default uses the internal method of tar() to
+    • R CMD build by default uses the internal method of tar() to
       prepare the tarball.  This is more likely to produce a tarball
       compatible with R CMD INSTALL and R CMD check: an external tar
       program, including options, can be specified _via_ the
       environment variable R_BUILD_TAR.
 
-    * tools::massageExamples() is better protected against packages
+    • tools::massageExamples() is better protected against packages
       which re-define base functions such as cat() and get() and so can
       cause R CMD check to fail when checking examples.
 
-    * R CMD javareconf has been enhanced to be more similar to the code
+    • R CMD javareconf has been enhanced to be more similar to the code
       used by configure.
 
       There is now a test that a JNI program can be compiled (like
@@ -3643,7 +3755,7 @@
       It makes use of custom settings from configuration recorded in
       etc/javaconf.
 
-    * The --no-vignettes argument of R CMD build has been renamed to
+    • The --no-vignettes argument of R CMD build has been renamed to
       the more accurate --no-build-vignettes: its action has always
       been to (re)build vignettes and never omitted them.
 
@@ -3652,40 +3764,40 @@
 
   DEPRECATED AND DEFUNCT:
 
-    * The ENCODING argument to .C() is defunct.  Use iconv() instead.
+    • The ENCODING argument to .C() is defunct.  Use iconv() instead.
 
-    * The .Internal(eval.with.vis) non-API function has been removed.
+    • The .Internal(eval.with.vis) non-API function has been removed.
 
-    * Support for the converters for use with .C() has been removed,
+    • Support for the converters for use with .C() has been removed,
       including the oft misused non-API header R_ext/RConverters.h.
 
-    * The previously deprecated uses of array() with a 0-length dim
+    • The previously deprecated uses of array() with a 0-length dim
       argument and tapply() with a 0-length INDEX list are now errors.
 
-    * Translation packages are defunct.
+    • Translation packages are defunct.
 
-    * Calling rep() or rep.int() on a pairlist or other non-vector
+    • Calling rep() or rep.int() on a pairlist or other non-vector
       object is now an error.
 
-    * Several non-API entry points have been transferred to packages
+    • Several non-API entry points have been transferred to packages
       (e.g., R_zeroin2) or replaced by different non-API entry points
       (e.g., R_tabulate).
 
-    * The 'internal' graphics device invoked by
+    • The ‘internal’ graphics device invoked by
       .Call("R_GD_nullDevice", package = "grDevices") has been removed:
       use pdf(file = NULL) instead.
 
-    * The .Fortran() entry point "dqrls" which has not been used by R
+    • The .Fortran() entry point "dqrls" which has not been used by R
       since version 2.15.1 is no longer available.
 
-    * Functions traceOn() and traceOff() in package methods are now
+    • Functions traceOn() and traceOff() in package methods are now
       defunct.
 
-    * Function CRAN.packages() is finally defunct.
+    • Function CRAN.packages() is finally defunct.
 
-    * Use of col2rgb(0) is defunct: use par("bg") or NA instead.
+    • Use of col2rgb(0) is defunct: use par("bg") or NA instead.
 
-    * The long-defunct functions Rd_parse(), anovalist.lm(),
+    • The long-defunct functions Rd_parse(), anovalist.lm(),
       categpry(), clearNames(), gammaCody(), glm.fit.null(),
       lm.fit.null(), lm.wfit.null(), manglePackageNames(),
       mauchley.test(), package.contents(), print.coefmat(),
@@ -3694,57 +3806,57 @@
       zip.file.extract() have been removed entirely (but are still
       documented in the help system).
 
-    * The unused dataPath argument to attachNamespace() has been
+    • The unused dataPath argument to attachNamespace() has been
       removed.
 
-    * grid.prompt() has been removed: use devAskNewPage() instead.
+    • grid.prompt() has been removed: use devAskNewPage() instead.
 
-    * The long-deprecated intensities component is no longer returned
+    • The long-deprecated intensities component is no longer returned
       by hist().
 
-    * mean() for data frames and sd() for data frames and matrices are
+    • mean() for data frames and sd() for data frames and matrices are
       defunct.
 
-    * chol(pivot = FALSE, LINPACK = TRUE), ch2inv(LINPACK = TRUE),
+    • chol(pivot = FALSE, LINPACK = TRUE), ch2inv(LINPACK = TRUE),
       eigen(EISPACK = TRUE), solve(LINPACK = TRUE) and svd(LINPACK =
       TRUE) are defunct: LAPACK will be used, with a warning.
 
-    * The keep.source argument to library() and require() is defunct.
+    • The keep.source argument to library() and require() is defunct.
       This option needs to be set at install time.
 
-    * Documentation for real(), as.real() and is.real() has been moved
-      to 'defunct' and the functions removed.
+    • Documentation for real(), as.real() and is.real() has been moved
+      to ‘defunct’ and the functions removed.
 
-    * The maxRasters argument of pdf() (unused since R 2.14.0) has been
+    • The maxRasters argument of pdf() (unused since R 2.14.0) has been
       removed.
 
-    * The unused fontsmooth argument has been removed from the quartz()
+    • The unused fontsmooth argument has been removed from the quartz()
       device.
 
-    * All the (non-API) EISPACK entry points in R have been removed.
+    • All the (non-API) EISPACK entry points in R have been removed.
 
-    * chol(pivot = TRUE, LINPACK = TRUE) is deprecated.
+    • chol(pivot = TRUE, LINPACK = TRUE) is deprecated.
 
-    * The long-deprecated use of \synopsis in the Usage section of .Rd
+    • The long-deprecated use of \synopsis in the Usage section of .Rd
       files will be removed in R 3.1.0.
 
-    * .find.package() and .path.package() are deprecated: only the
+    • .find.package() and .path.package() are deprecated: only the
       public versions without the dot have ever been in the API.
 
-    * In a package's DESCRIPTION file,
+    • In a package's DESCRIPTION file,
       
           License: X11
 
-      is deprecated, since it includes 'Copyright (C) 1996 X
-      Consortium' which cannot be appropriate for a current R package.
-      Use 'MIT' or 'BSD_2_clause' instead.
+      is deprecated, since it includes ‘Copyright (C) 1996 X
+      Consortium’ which cannot be appropriate for a current R package.
+      Use ‘MIT’ or ‘BSD_2_clause’ instead.
 
   CODE MIGRATION:
 
-    * The C code underlying base graphics has been migrated to the
+    • The C code underlying base graphics has been migrated to the
       graphics package (and hence no longer uses .Internal() calls).
 
-    * Most of the .Internal() calls used in the stats package have been
+    • Most of the .Internal() calls used in the stats package have been
       migrated to C code in that package.
 
       This means that a number of .Internal() calls which have been
@@ -3752,14 +3864,14 @@
       .Internal(cov), .Internal(optimhess) and
       .Internal(update.formula).
 
-    * Some .External() calls to the base package (really to the R
+    • Some .External() calls to the base package (really to the R
       executable or shared library) have been moved to more appropriate
       packages.  Packages should not have been using such calls, but
       some did (mainly those used by integrate()).
 
   PACKAGE parallel:
 
-    * There is a new function mcaffinity() which allows getting or
+    • There is a new function mcaffinity() which allows getting or
       setting the CPU affinity mask for the current R process on
       systems that supports this (currently only Linux has been tested
       successfully).  It has no effect on systems which do not support
@@ -3771,11 +3883,11 @@
       control in the OS by its own bookkeeping via mcaffinity() related
       to processes and threads it spawns.
 
-    * mcparallel() has a new argument mc.affinity which attempts to set
+    • mcparallel() has a new argument mc.affinity which attempts to set
       the affinity of the child process according to the specification
       contained therein.
 
-    * The port used by socket clusters is chosen randomly: this should
+    • The port used by socket clusters is chosen randomly: this should
       help to avoid clashes observed when two users of a multi-user
       machine try to create a cluster at the same time.  To reproduce
       the previous behaviour set environment variable R_PARALLEL_PORT
@@ -3783,71 +3895,71 @@
 
   C-LEVEL FACILITIES:
 
-    * There has been some minor re-organization of the non-API header
+    • There has been some minor re-organization of the non-API header
       files.  In particular, Rinternals.h no longer includes the
       non-API header R_exts/PrtUtil.h, and that no longer includes
       R_exts/Print.h.
 
-    * Passing NULL to .C() is now an error.
+    • Passing NULL to .C() is now an error.
 
-    * .C() and .Fortran() now warn if "single" arguments are used with
+    • .C() and .Fortran() now warn if "single" arguments are used with
       DUP = FALSE, as changes to such arguments are not returned to the
       caller.
 
-    * C entry points R_qsort and R_qsort_I now have start and end as
+    • C entry points R_qsort and R_qsort_I now have start and end as
       size_t to allow them to work with longer vectors on 64-bit
       platforms.  Code using them should be recompiled.
 
-    * A few recently added C entry points were missing the remapping to
+    • A few recently added C entry points were missing the remapping to
       Rf_, notably [dpq]nbinom_mu.
 
-    * Some of the interface pointers formerly available only to R.app
+    • Some of the interface pointers formerly available only to R.app
       are now available to front-ends on all Unix-alikes: one has been
       added for the interface to View().
 
-    * PACKAGE = "" is now an error in .C() etc calls: it was always
+    • PACKAGE = "" is now an error in .C() etc calls: it was always
       contrary to the documentation.
 
-    * Entry point rcont2 has been migrated to package stats and so is
+    • Entry point rcont2 has been migrated to package stats and so is
       no longer available.
 
-    * R_SVN_REVISION in Rversion.h is now an integer (rather than a
+    • R_SVN_REVISION in Rversion.h is now an integer (rather than a
       string) and hence usable as e.g.  #if R_SVN_REVISION < 70000.
 
-    * The entry points rgb2hsv and hsv2rgb have been migrated to
+    • The entry points rgb2hsv and hsv2rgb have been migrated to
       package grDevices and so are no longer available.
 
-    * R_GE_version has been increased to 10 and name2col removed (use
+    • R_GE_version has been increased to 10 and name2col removed (use
       R_GE_str2col instead).  R internal colour codes are now defined
       using the typedef rcolor.
 
-    * The REPROTECT macro now checks that the protect index is valid.
+    • The REPROTECT macro now checks that the protect index is valid.
 
-    * Several non-API entry points no longer used by R have been
+    • Several non-API entry points no longer used by R have been
       removed, including the Fortran entry points chol, chol2inv, cg,
       ch and rg, and the C entry points Brent_fmin, fft_factor and
       fft_work.
 
-    * If a .External call is registered with a number of arguments
+    • If a .External call is registered with a number of arguments
       (other than -1), the number of arguments passed is checked for
       each call (as for other foreign function calls).
 
-    * It is now possible to write custom connection implementations
+    • It is now possible to write custom connection implementations
       outside core R using R_ext/Connections.h.  Please note that the
       implementation of connections is still considered internal and
       may change in the future (see the above file for details).
 
   INTERNATIONALIZATION:
 
-    * The management of translations has been converted to R code: see
+    • The management of translations has been converted to R code: see
       ?tools::update_pkg_po.
 
-    * The translations for the R interpreter and RGui.exe are now part
+    • The translations for the R interpreter and RGui.exe are now part
       of the base package (rather than having sources in directory po
       and being installed to share/locale).  Thus the base package
       supports three translation domains, R-base, R and RGui.
 
-    * The compiled translations which ship with R are all installed to
+    • The compiled translations which ship with R are all installed to
       the new package translations for easier updating.  The first
       package of that name found on .libPaths() at the start of the R
       session will be used.  (It is possible messages will be used
@@ -3856,128 +3968,128 @@
       R_TRANSLATIONS to point to the location of the intended
       translations package to use this right from the start.)
 
-    * The translations form a separate group in the Windows installer,
+    • The translations form a separate group in the Windows installer,
       so can be omitted if desired.
 
-    * The markup for many messages has been changed to make them easier
-      to translate, incorporating suggestions from Lukasz Daniel.
+    • The markup for many messages has been changed to make them easier
+      to translate, incorporating suggestions from Łukasz Daniel.
 
   INSTALLATION:
 
-    * There is again support for building without using the C 'long
-      double' type.  This is required by C99, but system
+    • There is again support for building without using the C ‘long
+      double’ type.  This is required by C99, but system
       implementations can be slow or flawed.  Use configure option
       --disable-long-double.
 
-    * make pdf and make install-pdf now make and install the full
+    • make pdf and make install-pdf now make and install the full
       reference index (including all base and recommended packages).
 
-    * The 'reference manual' on the Windows GUI menu and included in
+    • The 'reference manual' on the Windows GUI menu and included in
       the installer is now the full reference index, including all base
       and recommended packages.
 
-    * R help pages and manuals have no ISBNs because ISBN rules no
+    • R help pages and manuals have no ISBNs because ISBN rules no
       longer allow constantly changing content to be assigned an ISBN.
 
-    * The Windows installer no longer installs a Start Menu link to the
+    • The Windows installer no longer installs a Start Menu link to the
       static help pages; as most pages are generated dynamically, this
       led to a lot of broken links.
 
-    * Any custom settings for Java configuration are recorded in file
+    • Any custom settings for Java configuration are recorded in file
       etc/javaconf for subsequent use by R CMD javareconf.
 
-    * There is now support for makeinfo version 5.0 (which requires a
+    • There is now support for makeinfo version 5.0 (which requires a
       slightly different .texi syntax).
 
-    * The minimum versions for --use-system-zlib and --use-system-pcre
+    • The minimum versions for --use-system-zlib and --use-system-pcre
       are now tested as 1.2.5 and 8.10 respectively.
 
-    * On Windows, the stack size is reduced to 16MB on 32-bit systems:
+    • On Windows, the stack size is reduced to 16MB on 32-bit systems:
       misguided users were launching many threads without controlling
       the stack size.
 
-    * configure no longer looks for file ~/.Rconfig: ~/.R/config has
+    • configure no longer looks for file ~/.Rconfig: ~/.R/config has
       long been preferred.
 
   BUG FIXES:
 
-    * When R CMD build is run in an encoding other than the one
+    • When R CMD build is run in an encoding other than the one
       specified in the package's DESCRIPTION file it tries harder to
       expand the authors@R field in the specified encoding.  (PR#14958)
 
-    * If R CMD INSTALL is required to expand the authors@R field of the
+    • If R CMD INSTALL is required to expand the authors@R field of the
       DESCRIPTION file, it tries harder to do so in the encoding
       specified for the package (rather than using ASCII escapes).
 
-    * Fix in package grid for pushing a viewport into a layout cell,
+    • Fix in package grid for pushing a viewport into a layout cell,
       where the layout is within a viewport that has zero physical
       width OR where the layout has zero total relative width (likewise
       for height).  The layout column widths (or row heights) in this
       case were being calculated with non-finite values.  (Reported by
       Winston Chang.)
 
-    * solve(A, b) for a vector b gave the answer names from colnames(A)
+    • solve(A, b) for a vector b gave the answer names from colnames(A)
       for LINPACK = TRUE but not in the default case.
 
-    * La.svd() accepts logical matrices (as documented, and as svd()
+    • La.svd() accepts logical matrices (as documented, and as svd()
       did).
 
-    * legend() now accepts negative pch values, in the same way
+    • legend() now accepts negative pch values, in the same way
       points() long has.
 
-    * Parse errors when installing files now correctly display the name
+    • Parse errors when installing files now correctly display the name
       of the file containing the bad code.
 
-    * In Windows, tcltk windows were not always properly constructed.
+    • In Windows, tcltk windows were not always properly constructed.
       (PR#15150)
 
-    * The internal functions implementing parse(), tools::parseLatex()
+    • The internal functions implementing parse(), tools::parseLatex()
       and tools::parse_Rd() were not reentrant, leading to errors in
       rare circumstances such as a garbage collection triggering a
       recursive call.
 
-    * Field assignments in reference class objects via $<- were not
+    • Field assignments in reference class objects via $<- were not
       being checked because the magic incantation to turn methods on
       for that primitive operator had been inadvertently omitted.
 
-    * setHook(hookname, value, action="replace") set the hook to be the
+    • setHook(hookname, value, action="replace") set the hook to be the
       value, rather than a list containing the value as documented.
       (PR#15167)
 
-    * If a package used a NEWS.Rd file, the main HTML package index
+    • If a package used a NEWS.Rd file, the main HTML package index
       page did not link to it.  (Reported by Dirk Eddelbuettel.)
 
-    * The primitive implementation of @<- was not checking the class of
+    • The primitive implementation of @<- was not checking the class of
       the replacement.  It now does a check, quicker but less general
       than slot<-. See the help.
 
-    * split(x, f) now recycles classed objects x in the same way as
+    • split(x, f) now recycles classed objects x in the same way as
       vectors.  (Reported by Martin Morgan.)
 
-    * pbeta(.28, 1/2, 2200, lower.tail=FALSE, log.p=TRUE) is no longer
+    • pbeta(.28, 1/2, 2200, lower.tail=FALSE, log.p=TRUE) is no longer
       -Inf; ditto for corresponding pt() and pf() calls, such as pt(45,
       df=5000, lower.tail=FALSE, log.p=TRUE). (PR#15162)
 
-    * The Windows graphics device would crash R if a user attempted to
+    • The Windows graphics device would crash R if a user attempted to
       load the graphics history from a variable that was not a saved
       history. (PR#15230)
 
-    * The workspace size for the predict() method for loess() could
+    • The workspace size for the predict() method for loess() could
       exceed the maximum integer size.  (Reported by Hiroyuki
       Kawakatsu.)
 
-    * ftable(x, row.vars, col.vars) now also works when the *.vars
+    • ftable(x, row.vars, col.vars) now also works when the *.vars
       arguments are (integer or character vectors) of length zero.
 
-    * Calling cat() on a malformed UTF-8 string could cause the Windows
+    • Calling cat() on a malformed UTF-8 string could cause the Windows
       GUI to lock up. (PR#15227)
 
-    * removeClass(cc) gave "node stack overflow" for some class
+    • removeClass(cc) gave "node stack overflow" for some class
       definitions containing "array" or "matrix".
 
 CHANGES in previous versions:
 
-  * Older news can be found in text format in files NEWS.0, NEWS.1 and
+  • Older news can be found in text format in files NEWS.0, NEWS.1 and
     NEWS.2 in the doc directory.  News in HTML format for R versions
     from 2.10.0 to 2.15.3 is in doc/html/NEWS.2.html.
 
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/doc/NEWS.Rd R-patched/doc/NEWS.Rd
--- R-release-orig/doc/NEWS.Rd	2015-12-07 00:15:08.000000000 +0100
+++ R-patched/doc/NEWS.Rd	2016-02-10 17:45:10.736519000 +0100
@@ -5,6 +5,127 @@
 \title{R News}
 \encoding{UTF-8}
 
+\section{\Rlogo CHANGES IN R 3.2.3 patched}{
+  \subsection{NEW FEATURES}{
+    \itemize{
+      \item \code{install.packages()} and related functions now give a
+      more informative warning when an attempt is made to install a base
+      package.
+
+      \item \code{summary(x)} now prints with less rounding when
+      \code{x} contains infinite values. (Request of \PR{16620}.)
+
+      \item \code{provideDimnames()} gets an optional \code{unique} argument.
+
+      \item \code{shQuote()} gains \code{type = "cmd2"} for quoting
+      in \command{cmd.exe} in Windows.  (Response to \PR{16636}.)
+
+      \item The \code{data.frame} method of \code{rbind()} gains an
+      optional argument \code{stringsAsFactors} (instead of only
+      depending on \code{getOption("stringsAsFactors")}).
+
+      \code{smooth(x, *)} now also works for long vectors.
+    }
+  }
+
+  \subsection{DEPRECATED AND DEFUNCT}{
+    \itemize{
+      \item Use of \samp{SUPPORT_OPENMP} from header \file{Rconfig.h} is
+      deprecated in favour of the standard OpenMP define \samp{_OPENMP}.
+
+      (This has been the recommendation in the manual for a while now.)
+
+      \item The \command{make} macro \code{AWK} which is long unused by
+      \R itself but recorded in file \file{etc/Makeconf} is deprecated
+      and will be removed in \R 3.3.0.
+
+      The C header file \file{S.h} is no longer documented: its use
+      should be replaced by \file{R.h}.
+    }
+  }
+
+  \subsection{BUG FIXES}{
+    \itemize{
+      \item \code{kmeans(x, centers = <1-row>)} now works. (\PR{16623})
+
+      \item \code{Vectorize()} now checks for clashes in argument names.
+      (\PR{16577})
+
+      \item \code{file.copy(overwrite = FALSE)} would signal a successful
+      copy when none had taken place.  (\PR{16576})
+
+      \item \code{ngettext()} now uses the same default domain as
+      \code{gettext()}.  (\PR{14605})
+
+      \item \code{array(.., dimnames = *)} now warns about
+      non-\code{list} dimnames and, from \R 3.3.0, will signal the same
+      error for invalid dimnames as \code{matrix()} has always done.
+
+      \item \code{addmargins()} now adds dimnames for the extended
+      margins in all cases, as always documented.
+
+      \item \code{heatmap()} evaluated its \code{add.expr} argument
+      in the wrong environment.  (\PR{16583})
+
+      \item \code{require()} etc now give the correct entry of
+      \code{lib.loc} in the warning about an old version of a package
+      masking a newer required one.
+
+      \item The internal deparser did not add parentheses when
+      necessary,  e.g. before \code{[]} or \code{[[]]}.  (Reported by
+      Lukas Stadler; additional fixes included as well).
+
+      \item \code{as.data.frame.vector(*, row.names=*)} no longer
+      produces \sQuote{corrupted} data frames from row names of incorrect
+      length, but rather warns about them.  This will become an error.
+
+      \item \code{url} connections with \code{method = "libcurl"} are
+      destroyed properly. (\PR{16681})
+
+      \item \code{withCallingHandler()} now (again) handles warnings
+      even during S4 generic's argument evaluation.  (\PR{16111})
+
+      \item \code{deparse(..., control = "quoteExpressions")}
+      incorrectly quoted empty expressions.  (\PR{16686})
+
+      \item \code{format()}ting datetime objects (\code{"POSIX[cl]?t"})
+      could segfault or recycle wrongly.  (\PR{16685})
+
+      \item \code{plot.ts(<matrix>, las = 1)} now does use \code{las}.
+
+      \item \code{saveRDS(*, compress = "gzip")} now works as
+      documented.  (\PR{16653})
+
+      \item (Windows only) The \command{Rgui} front end did not
+      always initialize the console properly, and could cause
+      \R to crash.  (\PR{16998})
+
+      \item The \code{as.hclust} method for \code{"dendrogram"}s failed often
+      when there were ties in the heights.
+
+      \item \code{reorder()} and \code{midcache.dendrogram()} now are
+      non-recursive and hence applicable to somewhat deeply nested
+      dendrograms, thanks to a proposal by Suharto Anggono in \PR{16424}.
+
+      \item \code{cor.test()} now calculates very small p values
+      more accurately (affecting the result only in extreme not
+      statistically relevant cases).  (\PR{16704})
+
+      \item \code{smooth(*, do.ends=TRUE)} did not always work correctly
+      in \R versions between 3.0.0 and 3.2.3.
+
+      \item \code{pretty(D)} for date-time objects \code{D} now also
+      works well if \code{range(D)} is (much) smaller than a second.  In
+      the case of only one unique value in \code{D}, the pretty range
+      now is more symmetric around that value than previously.
+      
+      \item The figures in help pages such as \code{?points} were 
+      accidentally damaged, and did not appear in \R 3.2.3.  
+      (\PR{16708})
+    }
+  }
+}
+
 \section{\Rlogo CHANGES IN R 3.2.3}{
   \subsection{NEW FEATURES}{
     \itemize{
@@ -41,10 +162,10 @@
       \item \code{loess(..., iterTrace=TRUE)} now provides diagnostics
       for robustness iterations, and the \code{print()} method for
       \code{summary(<loess>)} shows slightly more.
-      
+
       \item The included version of PCRE has been updated to 8.38, a
       bug-fix release.
-      
+
       \item \code{View()} now displays nested data frames in a more
       friendly way.  (Request with patch in \PR{15915}.)
     }
@@ -1495,7 +1616,7 @@
 
       \item \code{sub()} and \code{gsub()} did not handle regular
       expressions like \code{"\\s{2,}"} properly if the text
-      contained \code{NA} or non-ascii elements in a UTF-8
+      contained \code{NA} or non-ASCII elements in a UTF-8
       locale.  Part of this was due to a bug in the TRE library.
       (\PR{16009})
 
Binary files R-release-orig/doc/NEWS.pdf and R-patched/doc/NEWS.pdf differ
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/doc/html/NEWS.html R-patched/doc/html/NEWS.html
--- R-release-orig/doc/html/NEWS.html	2015-12-10 09:06:20.000000000 +0100
+++ R-patched/doc/html/NEWS.html	2016-02-11 02:51:31.881251000 +0100
@@ -7,6 +7,171 @@
 
 <h2>R News</h2>
 
+<h3><img src="../help/figures/../../html/logo.jpg" alt="../../html/logo.jpg" /> CHANGES IN R 3.2.3 patched</h3>
+
+
+
+<h4>NEW FEATURES</h4>
+
+
+<ul>
+<li> <p><code>install.packages()</code> and related functions now give a
+more informative warning when an attempt is made to install a base
+package.
+</p>
+</li>
+<li> <p><code>summary(x)</code> now prints with less rounding when
+<code>x</code> contains infinite values. (Request of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16620">PR#16620</a>.)
+</p>
+</li>
+<li> <p><code>provideDimnames()</code> gets an optional <code>unique</code> argument.
+</p>
+</li>
+<li> <p><code>shQuote()</code> gains <code>type = "cmd2"</code> for quoting
+in <code>cmd.exe</code> in Windows.  (Response to <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16636">PR#16636</a>.)
+</p>
+</li>
+<li><p> The <code>data.frame</code> method of <code>rbind()</code> gains an
+optional argument <code>stringsAsFactors</code> (instead of only
+depending on <code>getOption("stringsAsFactors")</code>).
+</p>
+<p><code>smooth(x, *)</code> now also works for long vectors.
+</p>
+</li></ul>
+
+
+
+
+<h4>DEPRECATED AND DEFUNCT</h4>
+
+
+<ul>
+<li><p> Use of <span class="samp">SUPPORT_OPENMP</span> from header &lsquo;<span class="file">Rconfig.h</span>&rsquo; is
+deprecated in favour of the standard OpenMP define <span class="samp">_OPENMP</span>.
+</p>
+<p>(This has been the recommendation in the manual for a while now.)
+</p>
+</li>
+<li><p> The <code>make</code> macro <code>AWK</code> which is long unused by
+<span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> itself but recorded in file &lsquo;<span class="file">etc/Makeconf</span>&rsquo; is deprecated
+and will be removed in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.3.0.
+</p>
+<p>The C header file &lsquo;<span class="file">S.h</span>&rsquo; is no longer documented: its use
+should be replaced by &lsquo;<span class="file">R.h</span>&rsquo;.
+</p>
+</li></ul>
+
+
+
+
+<h4>BUG FIXES</h4>
+
+
+<ul>
+<li> <p><code>kmeans(x, centers = &lt;1-row&gt;)</code> now works. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16623">PR#16623</a>)
+</p>
+</li>
+<li> <p><code>Vectorize()</code> now checks for clashes in argument names.
+(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16577">PR#16577</a>)
+</p>
+</li>
+<li> <p><code>file.copy(overwrite = FALSE)</code> would signal a successful
+copy when none had taken place.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16576">PR#16576</a>)
+</p>
+</li>
+<li> <p><code>ngettext()</code> now uses the same default domain as
+<code>gettext()</code>.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14605">PR#14605</a>)
+</p>
+</li>
+<li> <p><code>array(.., dimnames = *)</code> now warns about
+non-<code>list</code> dimnames and, from <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.3.0, will signal the same
+error for invalid dimnames as <code>matrix()</code> has always done.
+</p>
+</li>
+<li> <p><code>addmargins()</code> now adds dimnames for the extended
+margins in all cases, as always documented.
+</p>
+</li>
+<li> <p><code>heatmap()</code> evaluated its <code>add.expr</code> argument
+in the wrong environment.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16583">PR#16583</a>)
+</p>
+</li>
+<li> <p><code>require()</code> etc now give the correct entry of
+<code>lib.loc</code> in the warning about an old version of a package
+masking a newer required one.
+</p>
+</li>
+<li><p> The internal deparser did not add parentheses when
+necessary,  e.g. before <code>[]</code> or <code>[[]]</code>.  (Reported by
+Lukas Stadler; additional fixes included as well).
+</p>
+</li>
+<li> <p><code>as.data.frame.vector(*, row.names=*)</code> no longer
+produces &lsquo;corrupted&rsquo; data frames from row names of incorrect
+length, but rather warns about them.  This will become an error.
+</p>
+</li>
+<li> <p><code>url</code> connections with <code>method = "libcurl"</code> are
+destroyed properly. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16681">PR#16681</a>)
+</p>
+</li>
+<li> <p><code>withCallingHandler()</code> now (again) handles warnings
+even during S4 generic's argument evaluation.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16111">PR#16111</a>)
+</p>
+</li>
+<li> <p><code>deparse(..., control = "quoteExpressions")</code>
+incorrectly quoted empty expressions.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16686">PR#16686</a>)
+</p>
+</li>
+<li> <p><code>format()</code>ting datetime objects (<code>"POSIX[cl]?t"</code>)
+could segfault or recycle wrongly.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16685">PR#16685</a>)
+</p>
+</li>
+<li> <p><code>plot.ts(&lt;matrix&gt;, las = 1)</code> now does use <code>las</code>.
+</p>
+</li>
+<li> <p><code>saveRDS(*, compress = "gzip")</code> now works as
+documented.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16653">PR#16653</a>)
+</p>
+</li>
+<li><p> (Windows only) The <code>Rgui</code> front end did not
+always initialize the console properly, and could cause
+<span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> to crash.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16998">PR#16998</a>)
+</p>
+</li>
+<li><p> The <code>as.hclust</code> method for <code>"dendrogram"</code>s failed often
+when there were ties in the heights.
+</p>
+</li>
+<li> <p><code>reorder()</code> and <code>midcache.dendrogram()</code> now are
+non-recursive and hence applicable to somewhat deeply nested
+dendrograms, thanks to a proposal by Suharto Anggono in <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16424">PR#16424</a>.
+</p>
+</li>
+<li> <p><code>cor.test()</code> now calculates very small p values
+more accurately (affecting the result only in extreme not
+statistically relevant cases).  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16704">PR#16704</a>)
+</p>
+</li>
+<li> <p><code>smooth(*, do.ends=TRUE)</code> did not always work correctly
+in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> versions between 3.0.0 and 3.2.3.
+</p>
+</li>
+<li> <p><code>pretty(D)</code> for date-time objects <code>D</code> now also
+works well if <code>range(D)</code> is (much) smaller than a second.  In
+the case of only one unique value in <code>D</code>, the pretty range
+now is more symmetric around that value than previously.
+</p>
+</li>
+<li><p> The figures in help pages such as <code>?points</code> were 
+accidentally damaged, and did not appear in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.2.3.  
+(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16708">PR#16708</a>)
+</p>
+</li></ul>
+
+
+
+
 <h3><img src="../help/figures/../../html/logo.jpg" alt="../../html/logo.jpg" /> CHANGES IN R 3.2.3</h3>
 
 
@@ -1946,7 +2111,7 @@
 </li>
 <li> <p><code>sub()</code> and <code>gsub()</code> did not handle regular
 expressions like <code>"\s{2,}"</code> properly if the text
-contained <code>NA</code> or non-ascii elements in a UTF-8
+contained <code>NA</code> or non-ASCII elements in a UTF-8
 locale.  Part of this was due to a bug in the TRE library.
 (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16009">PR#16009</a>)
 </p>
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/doc/html/R-admin.html R-patched/doc/html/R-admin.html
--- R-release-orig/doc/html/R-admin.html	2015-12-10 09:12:12.000000000 +0100
+++ R-patched/doc/html/R-admin.html	2016-02-11 03:03:41.551388001 +0100
@@ -1,6 +1,6 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
 <html>
- allowing "random access" into the dendrogram
 .add.dendrInd <- function(x)
@@ -184,23 +186,46 @@
 
     type <- match.arg(type) ## currently only "hclust"
     stopifnot( inherits(x, "dendrogram") )
+    verbose <- getOption("verbose", 0) >= 2 # non-public
     setmid <- function(d, type) {
-	if(is.leaf(d))# no "midpoint"
-	    return(d)
-	k <- length(d)
-	if(k < 1)
-	    stop("dendrogram node with non-positive #{branches}")
-	r <- d # incl. attributes!
-	midS <- 0
-	for(j in 1L:k) {
-	    r[[j]] <- unclass(setmid(d[[j]], type))
-	    midS <- midS + .midDend(r[[j]])
-	}
-	if(!quiet && type == "hclust" && k != 2)
-	    warning("midcache() of non-binary dendrograms only partly implemented")
-	## compatible to as.dendrogram.hclust() {MM: doubtful if k > 2}
-	attr(r, "midpoint") <- (.memberDend(d[[1L]]) + midS) / 2
-	r
+	depth <- 0L
+	kk <- integer()
+	jj <- integer()
+	dd <- list()
+	repeat {
+	    if(!is.leaf(d)) {# no "midpoint" for leaf
+		k <- length(d)
+		if(k < 1)
+		    stop("dendrogram node with non-positive #{branches}")
+		depth <- depth + 1L
+		if(verbose) cat(sprintf(" depth(+)=%4d, k=%d\n", depth, k))
+		kk[depth] <- k
+		if(storage.mode(jj) != storage.mode(kk)) # (long vectors)
+		    storage.mode(jj) <- storage.mode(kk)
+		dd[[depth]] <- d
+		d <- d[[jj[depth] <- 1L]]
+		next
+	    }
+	    while(depth) {
+		k <- kk[depth]
+		j <- jj[depth]
+		r <- dd[[depth]] # incl. attributes!
+		r[[j]] <- unclass(d)
+		if(j < k) break
+		depth <- depth - 1L
+		if(verbose) cat(sprintf(" depth(-)=%4d, k=%d\n", depth, k))
+		midS <- sum(vapply(r, .midDend, 0))
+		if(!quiet && type == "hclust" && k != 2)
+		    warning("midcache() of non-binary dendrograms only partly implemented")
+		## compatible to as.dendrogram.hclust() {MM: doubtful if k > 2}
+		attr(r, "midpoint") <- (.memberDend(r[[1L]]) + midS) / 2
+		d <- r
+	    }
+	    if(!depth) break
+	    dd[[depth]] <- r
+	    d <- r[[jj[depth] <- j + 1L]]
+	}
+	d
     }
     setmid(x, type=type)
 }
@@ -533,21 +558,21 @@
     ## get the left borders limit[k] of all children k=1..K, and
     ## the handle point `x' for the edge connecting to the parent.
     inner <- !is.leaf(subtree) && x1 != x2
-    if(inner) {
-	K <- length(subtree)
-	mTop <- .memberDend(subtree)
-	limit <- integer(K)
-	xx1 <- x1
-	for(k in 1L:K) {
-	    m <- .memberDend(subtree[[k]])
-	    ##if(is.null(m)) m <- 1
-	    xx1 <- xx1 + (if(center) (x2-x1) * m/mTop else m)
-	    limit[k] <- xx1
-	}
-	limit <- c(x1, limit)
-    } else { ## leaf
-	limit <- c(x1, x2)
-    }
+    limit <- c(x1,
+	       if(inner) {
+		   K <- length(subtree)
+		   mTop <- .memberDend(subtree)
+		   limit <- integer(K)
+		   xx1 <- x1
+		   for(k in 1L:K) {
+		       m <- .memberDend(subtree[[k]])
+		       ##if(is.null(m)) m <- 1
+		       xx1 <- xx1 + (if(center) (x2-x1) * m/mTop else m)
+		       limit[k] <- xx1
+		   }
+		   limit
+	       } else ## leaf
+		   x2)
     mid <- attr(subtree, "midpoint")
     center <- center || (inner && !is.numeric(mid))
     x <- if(center) mean(c(x1,x2)) else x1 + (if(inner) mid else 0)
@@ -626,22 +651,40 @@
 	stop("'reorder.dendrogram' requires a dendrogram")
     agglo.FUN <- match.fun(agglo.FUN)
     oV <- function(x, wts) {
-	if(is.leaf(x)) {
-	    attr(x, "value") <- wts[x[1L]]
-	    return(x)
-	}
-        k <- length(x)
-        if(k == 0L) stop("invalid (length 0) node in dendrogram")
-        vals <- numeric(k)
-        for(j in 1L:k) {
-            ## insert/compute 'wts' recursively down the branches:
-            b <- oV(x[[j]], wts)
-            x[[j]] <- b
-            vals[j] <- attr(b, "value")
-        }
-        iOrd <- sort.list(vals)
-	attr(x, "value") <- agglo.FUN(vals[iOrd])
-        x[] <- x[iOrd]
+	depth <- 0L
+	kk <- jj <- integer()
+	xx <- list()
+	repeat {
+	    if(is.leaf(x))
+		attr(x, "value") <- wts[x[1L]]
+	    else {
+		k <- length(x)
+		if(k == 0L) stop("invalid (length 0) node in dendrogram")
+		depth <- depth + 1L
+		kk[depth] <- k
+		if(storage.mode(jj) != storage.mode(kk))
+		    storage.mode(jj) <- storage.mode(kk)
+		## insert/compute 'wts' recursively down the branches:
+		xx[[depth]] <- x
+		x <- x[[jj[depth] <- 1L]]
+		next
+	    }
+	    while(depth) {
+		b <- x
+		x <- xx[[depth]]
+		j <- jj[depth]
+		x[[j]] <- b
+		if(j < kk[depth]) break
+		depth <- depth - 1L
+		vals <- vapply(x, attr, numeric(1L), which="value")
+		iOrd <- sort.list(vals)
+		attr(x, "value") <- agglo.FUN(vals[iOrd])
+		x[] <- x[iOrd]
+	    }
+	    if(!depth) break
+	    xx[[depth]] <- x
+	    x <- x[[jj[depth] <- j + 1L]]
+	}
         x
     }
     midcache.dendrogram( oV(x, wts) )
@@ -885,7 +928,7 @@
     if(!is.null(ylab)) mtext(ylab, side = 4, line = margins[2L] - 1.25)
 
     if (!missing(add.expr))
-	eval(substitute(add.expr))
+	eval.parent(substitute(add.expr))
 
     ## the two dendrograms :
     par(mar = c(margins[1L], 0, 0, 0))
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/library/stats/R/family.R R-patched/src/library/stats/R/family.R
--- R-release-orig/src/library/stats/R/family.R	2015-08-26 00:16:01.000000000 +0200
+++ R-patched/src/library/stats/R/family.R	2016-01-30 02:41:09.000000000 +0100
@@ -532,9 +532,8 @@
     })
     validmu <- function(mu) TRUE
     simfun <- function(object, nsim) {
-        if(is.null(tryCatch(loadNamespace("SuppDists"),
-                            error = function(e) NULL)))
-            stop("need CRAN package 'SuppDists' for the 'inverse.gaussian' family")
+        if(!requireNamespace("SuppDists", quietly = TRUE))
+            stop("need CRAN package 'SuppDists' for simulation from the 'inverse.gaussian' family")
         wts <- object$prior.weights
         if (any(wts != 1)) message("using weights as inverse variances")
         ftd <- fitted(object)
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/library/stats/R/kmeans.R R-patched/src/library/stats/R/kmeans.R
--- R-release-orig/src/library/stats/R/kmeans.R	2015-08-26 00:16:02.000000000 +0200
+++ R-patched/src/library/stats/R/kmeans.R	2015-12-11 17:45:11.000000000 +0100
@@ -93,7 +93,6 @@
                     "MacQueen" = 3L)
     storage.mode(x) <- "double"
     if(length(centers) == 1L) {
-	if (centers == 1) nmeth <- 3L
 	k <- centers
         ## we need to avoid duplicates here
         if(nstart == 1L)
@@ -116,6 +115,7 @@
     }
     k <- as.integer(k)
     if(is.na(k)) stop("'invalid value of 'k'")
+    if (k == 1L) nmeth <- 3L # Hartigan-Wong, (Fortran) needs k > 1
     iter.max <- as.integer(iter.max)
     if(is.na(iter.max) || iter.max < 1L) stop("'iter.max' must be positive")
     if(ncol(x) != ncol(centers))
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/library/stats/R/smooth.R R-patched/src/library/stats/R/smooth.R
--- R-release-orig/src/library/stats/R/smooth.R	2015-08-26 00:16:02.000000000 +0200
+++ R-patched/src/library/stats/R/smooth.R	2016-02-10 17:45:09.000000000 +0100
@@ -1,7 +1,7 @@
 #  File src/library/stats/R/smooth.R
 #  Part of the R package, https://www.R-project.org
 #
-#  Copyright (C) 1995-2013 The R Core Team
+#  Copyright (C) 1995-2016 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
@@ -21,16 +21,15 @@
 
 smooth <- function(x, kind = c("3RS3R", "3RSS", "3RSR", "3R", "3", "S"),
                    twiceit = FALSE,
-                   endrule = "Tukey", do.ends = FALSE)
+                   endrule = c("Tukey", "copy"), do.ends = FALSE)
 {
     if(!is.numeric(x)) stop("attempt to smooth non-numeric values")
     if(anyNA(x)) stop("attempt to smooth NA values")
+    endrule <- match.arg(endrule)
     rules <- c("copy","Tukey")#- exact order matters!
     if(is.na(iend <- pmatch(endrule, rules))) stop("invalid 'endrule' argument")
-    n <- as.integer(length(x))
-    if(is.na(n)) stop("invalid length(x)")
     kind <- match.arg(kind)
-    if(substr(kind ,1L, 3L) == "3RS" && !do.ends) iend <- -iend
+    if(substr(kind, 1L, 3L) == "3RS" && !do.ends) iend <- -iend
     else if(kind == "S") iend <- as.logical(do.ends)
     type <- match(kind, c("3RS3R", "3RSS", "3RSR", "3R", "3", "S"))
     smo <- .Call(C_Rsm, as.double(x), type, iend)
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/library/stats/R/ts.R R-patched/src/library/stats/R/ts.R
--- R-release-orig/src/library/stats/R/ts.R	2015-08-26 00:16:02.000000000 +0200
+++ R-patched/src/library/stats/R/ts.R	2016-02-01 17:45:11.000000000 +0100
@@ -495,10 +495,10 @@
 		do.xax <- i %% nr == 0 || i == nser
 		if(axes) {
 		    axis(y.side, xpd = NA, cex.axis = cex.axis,
-                         col.axis = col.axis, font.axis = font.axis)
+			 col.axis = col.axis, font.axis = font.axis, ...)
 		    if(do.xax)
 			axis(1, xpd = NA, cex.axis = cex.axis,
-                             col.axis = col.axis, font.axis = font.axis)
+			     col.axis = col.axis, font.axis = font.axis, ...)
 		}
 		if(ann) {
 		    mtext(nm[i], y.side, line=3, cex=cex.lab, col=col.lab,
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/library/stats/man/complete.cases.Rd R-patched/src/library/stats/man/complete.cases.Rd
--- R-release-orig/src/library/stats/man/complete.cases.Rd	2015-08-26 00:16:29.000000000 +0200
+++ R-patched/src/library/stats/man/complete.cases.Rd	2016-01-02 17:45:09.000000000 +0100
@@ -1,6 +1,6 @@
 % File src/library/stats/man/complete.cases.Rd
 % Part of the R package, https://www.R-project.org
-% Copyright 1995-2007 R Core Team
+% Copyright 1995-2015 R Core Team
 % Distributed under GPL 2 or later
 
 \name{complete.cases}
@@ -20,6 +20,14 @@
   A logical vector specifying which observations/rows have no missing
   values across the entire sequence.
 }
+\note{
+  A current limitation of this function is that it uses low level
+  functions to determine lengths and missingness, ignoring the 
+  class.  This will lead to spurious errors when some columns
+  have classes with \code{\link{length}} or \code{\link{is.na}}
+  methods, for example \code{"\link{POSIXlt}"}, as described
+  in \PR{16648}.
+}
 \seealso{
   \code{\link{is.na}},
   \code{\link{na.omit}},
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/library/stats/man/family.Rd R-patched/src/library/stats/man/family.Rd
--- R-release-orig/src/library/stats/man/family.Rd	2015-08-26 00:16:27.000000000 +0200
+++ R-patched/src/library/stats/man/family.Rd	2015-12-30 17:45:09.000000000 +0100
@@ -1,6 +1,6 @@
 % File src/library/stats/man/family.Rd
 % Part of the R package, https://www.R-project.org
-% Copyright 1995-2014 R Core Team
+% Copyright 1995-2015 R Core Team
 % Distributed under GPL 2 or later
 
 \name{family}
@@ -137,9 +137,9 @@
   \item{initialize}{expression.  This needs to set up whatever data
     objects are needed for the family as well as \code{n} (needed for
     AIC in the binomial family) and \code{mustart} (see \code{\link{glm}}.}
-  \item{valid.mu}{logical function.  Returns \code{TRUE} if a mean
+  \item{validmu}{logical function.  Returns \code{TRUE} if a mean
     vector \code{mu} is within the domain of \code{variance}.}
-  \item{valid.eta}{logical function.   Returns \code{TRUE} if a linear
+  \item{valideta}{logical function.   Returns \code{TRUE} if a linear
     predictor \code{eta} is within the domain of \code{linkinv}.}
   \item{simulate}{(optional) function \code{simulate(object, nsim)} to be
     called by the \code{"lm"} method of \code{\link{simulate}}.  It will
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/library/stats/man/smooth.Rd R-patched/src/library/stats/man/smooth.Rd
--- R-release-orig/src/library/stats/man/smooth.Rd	2015-08-26 00:16:29.000000000 +0200
+++ R-patched/src/library/stats/man/smooth.Rd	2016-02-10 17:45:10.000000000 +0100
@@ -1,6 +1,6 @@
 % File src/library/stats/man/smooth.Rd
 % Part of the R package, https://www.R-project.org
-% Copyright 1995-2007 R Core Team
+% Copyright 1995-2016 R Core Team
 % Distributed under GPL 2 or later
 
 \name{smooth}
@@ -11,7 +11,7 @@
 }
 \usage{
 smooth(x, kind = c("3RS3R", "3RSS", "3RSR", "3R", "3", "S"),
-       twiceit = FALSE, endrule = "Tukey", do.ends = FALSE)
+       twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends = FALSE)
 }
 \arguments{
   \item{x}{a vector or time series}
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/library/stats/src/smooth.c R-patched/src/library/stats/src/smooth.c
--- R-release-orig/src/library/stats/src/smooth.c	2015-08-26 00:16:08.000000000 +0200
+++ R-patched/src/library/stats/src/smooth.c	2016-02-10 17:45:10.000000000 +0100
@@ -263,14 +263,14 @@
 	    double *z = (double *) R_alloc(n, sizeof(double));
 	    double *w = (double *) R_alloc(n, sizeof(double));
 	    iter = sm_3RS3R(REAL(x), REAL(y), z, w, n, abs(iend), 
-			      iend ? TRUE : FALSE);
+			    /* split_ends: */ (iend < 0) ? TRUE : FALSE);
 	    break;
 	}
 	case 2:
 	{
 	    double *z = (double *) R_alloc(n, sizeof(double));
 	    iter = sm_3RSS(REAL(x), REAL(y), z, n, abs(iend), 
-			      iend ? TRUE : FALSE);
+			   /* split_ends: */ (iend < 0) ? TRUE : FALSE);
 	    break;
 	}
 	case 3:
@@ -278,7 +278,7 @@
 	    double *z = (double *) R_alloc(n, sizeof(double));
 	    double *w = (double *) R_alloc(n, sizeof(double));
 	    iter = sm_3RSR(REAL(x), REAL(y), z, w, n, abs(iend), 
-			   iend ? TRUE : FALSE);
+			   /* split_ends: */ (iend < 0) ? TRUE : FALSE);
 	    break;
 	}
 	case 4:
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/library/stats/tests/glm.Rout.save R-patched/src/library/stats/tests/glm.Rout.save
--- R-release-orig/src/library/stats/tests/glm.Rout.save	2015-12-04 00:15:09.000000000 +0100
+++ R-patched/src/library/stats/tests/glm.Rout.save	2016-01-22 17:45:10.000000000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -29,4 +29,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.101   0.014   0.107 
+  0.147   0.022   0.158 
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/library/stats/tests/ks-test.Rout.save R-patched/src/library/stats/tests/ks-test.Rout.save
--- R-release-orig/src/library/stats/tests/ks-test.Rout.save	2015-12-04 00:15:09.000000000 +0100
+++ R-patched/src/library/stats/tests/ks-test.Rout.save	2016-01-22 17:45:10.000000000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -114,4 +114,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.127   0.017   0.135 
+  0.113   0.011   0.114 
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/library/stats/tests/nls.Rout.save R-patched/src/library/stats/tests/nls.Rout.save
--- R-release-orig/src/library/stats/tests/nls.Rout.save	2015-12-04 00:15:09.000000000 +0100
+++ R-patched/src/library/stats/tests/nls.Rout.save	2016-01-22 17:45:10.000000000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -703,4 +703,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  1.095   0.021   1.106 
+  1.101   0.021   1.112 
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/library/stats/tests/simulate.Rout.save R-patched/src/library/stats/tests/simulate.Rout.save
--- R-release-orig/src/library/stats/tests/simulate.Rout.save	2015-12-04 00:15:09.000000000 +0100
+++ R-patched/src/library/stats/tests/simulate.Rout.save	2016-01-22 17:45:10.000000000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -406,4 +406,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.164   0.021   0.176 
+  0.172   0.016   0.178 
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/library/tools/R/QC.R R-patched/src/library/tools/R/QC.R
--- R-release-orig/src/library/tools/R/QC.R	2015-11-14 00:15:11.000000000 +0100
+++ R-patched/src/library/tools/R/QC.R	2015-12-11 17:45:13.000000000 +0100
@@ -8127,7 +8127,7 @@
     ## ASCII letters, digits and hyphen.
     ## We could also check that the local and domain parts are no longer
     ## than 64 and 255 characters, respectively.
-    ## See http://en.wikipedia.org/wiki/Email_address.
+    ## See https://en.wikipedia.org/wiki/Email_address.
     ASCII_letters_and_digits <-
         "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789"
     l <- sprintf("[%s%s]", ASCII_letters_and_digits, "!#$%*/?|^{}`~&'+=_-")
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/library/tools/R/check.R R-patched/src/library/tools/R/check.R
--- R-release-orig/src/library/tools/R/check.R	2015-08-26 00:16:54.000000000 +0200
+++ R-patched/src/library/tools/R/check.R	2016-01-30 02:41:09.000000000 +0100
@@ -1,7 +1,7 @@
 #  File src/library/tools/R/check.R
 #  Part of the R package, https://www.R-project.org
 #
-#  Copyright (C) 1995-2015 The R Core Team
+#  Copyright (C) 1995-2016 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
@@ -215,9 +215,10 @@
                      env = "R_DEFAULT_PACKAGES='utils,grDevices,graphics,stats'")
             {
                 out <- R_runR(cmd, R_opts2, env)
+                ## htmltools produced non-UTF-8 output in Dec 2015
                 if (R_check_suppress_RandR_message)
                     grep('^Xlib: *extension "RANDR" missing on display', out,
-                         invert = TRUE, value = TRUE)
+                         invert = TRUE, value = TRUE, useBytes = TRUE)
                 else out
             }
 
@@ -642,7 +643,7 @@
         ## entries because these really are a part of R: hence, skip the
         ## check.
         check_license <- if (!is_base_pkg) {
-            Check_license <- Sys.getenv("_R_CHECK_LICENSE_", NA)
+            Check_license <- Sys.getenv("_R_CHECK_LICENSE_", NA_character_)
             if(is.na(Check_license)) {
                 ## The check code conditionalizes *output* on _R_CHECK_LICENSE_.
                 Sys.setenv('_R_CHECK_LICENSE_' = "TRUE")
@@ -1693,6 +1694,9 @@
             ## Current example is TeachingDemos
             out <- grep("^Loading required package:", out,
                         invert = TRUE, value = TRUE)
+            ## and methods can give Notes, e.g. from metaheur
+            out <- grep("^Note: the specification for", out,
+                        invert = TRUE, value = TRUE)
             err <- grep("^Error", out)
             if (length(err)) {
                 errorLog(Log)
@@ -2727,7 +2731,8 @@
                     lines <- lines[max(1, ll-12):ll]
                     if (R_check_suppress_RandR_message)
                         lines <- grep('^Xlib: *extension "RANDR" missing on display',
-                                      lines, invert = TRUE, value = TRUE)
+                                      lines, invert = TRUE, value = TRUE,
+                                      useBytes = TRUE)
                     printLog(Log, sprintf("Running the tests in %s failed.\n", sQuote(file)))
                     printLog(Log, "Last 13 lines of output:\n")
                     printLog0(Log, .format_lines_with_indent(lines), "\n")
@@ -3340,8 +3345,7 @@
                 ## Case B. All output from installation redirected,
                 ## or already available in the log file.
                 checkingLog(Log,
-                            "whether package ",
-                            sQuote(desc["Package"]),
+			    "whether package ", sQuote(desc["Package"]),
                             " can be installed")
                 outfile <- file.path(pkgoutdir, "00install.out")
                 if (grepl("^check", install)) {
@@ -3640,7 +3644,7 @@
             printLog(Log, sprintf("  installed size is %4.1fMb\n", total/1024))
             rest <- res2[-nrow(res2), ]
             rest[, 2L] <- sub("./", "", rest[, 2L])
-            # keep only top-level directories
+            ## keep only top-level directories
             rest <- rest[!grepl("/", rest[, 2L]), ]
             rest <- rest[rest[, 1L] > 1024, ] # > 1Mb
             if(nrow(rest)) {
@@ -4087,7 +4091,7 @@
     options(showErrorCalls=FALSE, warn = 1)
 
     ## Read in check environment file.
-    Renv <- Sys.getenv("R_CHECK_ENVIRON", unset = NA)
+    Renv <- Sys.getenv("R_CHECK_ENVIRON", unset = NA_character_)
     if(!is.na(Renv)) {
         ## Do not read any check environment file if R_CHECK_ENVIRON is
         ## set to empty of something non-existent.
@@ -4380,9 +4384,9 @@
         Sys.setenv("_R_SHLIB_BUILD_OBJECTS_SYMBOL_TABLES_" = "TRUE")
         Sys.setenv("_R_CHECK_DOT_FIRSTLIB_" = "TRUE")
         Sys.setenv("_R_CHECK_PACKAGES_USED_CRAN_INCOMING_NOTES_" = "TRUE")
-        prev <- Sys.getenv("_R_CHECK_LIMIT_CORES_", NA)
+        prev <- Sys.getenv("_R_CHECK_LIMIT_CORES_", NA_character_)
         if(is.na(prev)) Sys.setenv("_R_CHECK_LIMIT_CORES_" = "TRUE")
-        prev <- Sys.getenv("_R_CHECK_SCREEN_DEVICE_", NA)
+        prev <- Sys.getenv("_R_CHECK_SCREEN_DEVICE_", NA_character_)
         if(is.na(prev)) Sys.setenv("_R_CHECK_SCREEN_DEVICE_" = "stop")
         Sys.setenv("_R_CHECK_CODE_USAGE_VIA_NAMESPACES_" = "TRUE")
         Sys.setenv("_R_CHECK_S3_METHODS_NOT_REGISTERED_" = "TRUE")
@@ -4401,7 +4405,8 @@
     } else {
         ## do it this way so that INSTALL produces symbols.rds
         ## when called from check but not in general.
-        if(is.na(Sys.getenv("_R_SHLIB_BUILD_OBJECTS_SYMBOL_TABLES_", NA)))
+        if(is.na(Sys.getenv("_R_SHLIB_BUILD_OBJECTS_SYMBOL_TABLES_",
+                            NA_character_)))
             Sys.setenv("_R_SHLIB_BUILD_OBJECTS_SYMBOL_TABLES_" = "TRUE")
     }
 
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/library/tools/R/license.R R-patched/src/library/tools/R/license.R
--- R-release-orig/src/library/tools/R/license.R	2015-08-26 00:16:53.000000000 +0200
+++ R-patched/src/library/tools/R/license.R	2015-12-11 17:45:12.000000000 +0100
@@ -19,7 +19,7 @@
 ## <NOTE>
 ## We want *standardized* license specs so that we can compute on them.
 ## In particular, we want to know whether licenses are recognizable as
-## FOSS (http://en.wikipedia.org/wiki/Free_and_open-source_software)
+## FOSS (https://en.wikipedia.org/wiki/Free_and_open-source_software)
 ## licenses.
 ##
 ## A license spec is standardized ("canonical") if it is an alternative
@@ -47,12 +47,12 @@
 ## by the FSF (and not rejected by the OSI).
 ##
 ## See
-##   http://www.gnu.org/licenses/license-list.html
-##   http://opensource.org/licenses/alphabetical
+##   https://www.gnu.org/licenses/license-list.html
+##   https://opensource.org/licenses/alphabetical
 ## fot the FSF and OSI license lists, and also
-##   http://www.fsf.org/licensing/licenses
-##   http://en.wikipedia.org/wiki/List_of_FSF_approved_software_licences
-##   http://en.wikipedia.org/wiki/List_of_OSI_approved_software_licences
+##   https://www.fsf.org/licensing/licenses
+##   https://en.wikipedia.org/wiki/List_of_FSF_approved_software_licences
+##   https://en.wikipedia.org/wiki/List_of_OSI_approved_software_licences
 ## for more information.
 ## </NOTE>
 
@@ -82,7 +82,7 @@
                                  .Platform$path.sep, fixed = TRUE))
     paths <- c(paths,
                file.path(R.home("share"), "licenses", "license.db"))
-    ldb <- Reduce(function(u, v) merge(u, v, all = TRUE), 
+    ldb <- Reduce(function(u, v) merge(u, v, all = TRUE),
                   lapply(unique(normalizePath(paths)), read.dcf))
     ## Merging matrices gives a data frame.
     ldb <- as.matrix(ldb)
@@ -269,11 +269,11 @@
 ## Nasty issues.
 ## * There really is no GPL version 2.0.
 ##   Unfortunately, the FSF uses 2.0 in URLs or links
-##   (http://www.gnu.org/licenses/old-licenses/gpl-2.0.html)
+##   (https://www.gnu.org/licenses/old-licenses/gpl-2.0.html)
 ##   The text clearly says "Version 2, June 1991".
 ## * There really is no LGPL version 2.0.
 ##   Unfortunately, the FSF uses 2.0 in URLs or links
-##   (http://www.gnu.org/licenses/old-licenses/).
+##   (https://www.gnu.org/licenses/old-licenses/).
 ##   The text clearly says "Version 2, June 1991".
 ## * CeCILL is a bit of a mess: the current version is referred to as
 ##   "version 2" (http://www.cecill.info/licences.en.html) but
@@ -284,7 +284,7 @@
 list("Artistic-2.0" =
      c("The Artistic License, Version 2.0",
        "Artistic 2.0",
-       "Artistic-2.0, see http://www.opensource.org/licenses/artistic-license-2.0.php"
+       "Artistic-2.0, see https://opensource.org/licenses/artistic-license-2.0.php"
        ),
 
      "BSL" =
@@ -301,7 +301,7 @@
      c("GNU Public License",
        "Gnu GPL",
        "GNU GPL",
-       "GPL (http://www.gnu.org/copyleft/gpl.html)"
+       "GPL (https://www.gnu.org/copyleft/gpl.html)"
        ),
 
      "GPL-2" =
@@ -368,10 +368,10 @@
        "GPL version 2 (or newer)",
        "GPL version 2 or later.",
        "GPL version 2 or newer",
-       "GPL version 2 or newer (http://www.gnu.org/copyleft/gpl.html)",
+       "GPL version 2 or newer (https://www.gnu.org/copyleft/gpl.html)",
        "GPL version 2 or newer (see README).",
        "GPL version 2 or newer.",
-       "GPL version 2 or newer. http://www.gnu.org/copyleft/gpl.html",
+       "GPL version 2 or newer. https://www.gnu.org/copyleft/gpl.html",
        "GPL version 2, or, at your option, any newer version.",
        "GPL Version 2 (or later)",
        "GPL version 2 (or later)",
@@ -399,7 +399,7 @@
        ),
 
      "LGPL" =
-     c("LGPL (see <http://www.opensource.org/licenses/lgpl-license.php>).",
+     c("LGPL (see <https://opensource.org/licenses/lgpl-license.php>).",
        "GNU LGPL (same as wxWidgets)."
        ),
 
@@ -541,7 +541,7 @@
             !is.null(x) && all(!is.na(x) & (x == v))
         ## (More generally we could test for positive length of x: but
         ## a length test is needed because all(NULL) |=> TRUE.)
-        
+
         expansions <- lapply(components,
                              expand_license_spec_component_from_db)
 
@@ -626,7 +626,7 @@
                   standardization = standardization,
                   is_verified = is_verified,
                   components = components,
-                  expansions = expansions,    
+                  expansions = expansions,
                   extensions = extensions,
                   pointers = pointers,
                   is_FOSS = is_FOSS,
@@ -767,7 +767,7 @@
         }
         TRUE
     }
-    
+
     if(x == "Unlimited" ||
        grepl(x, ldb_vars$re_license_file))
         return(NULL)
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/library/tools/R/sysdata.R R-patched/src/library/tools/R/sysdata.R
--- R-release-orig/src/library/tools/R/sysdata.R	2015-03-19 00:03:12.000000000 +0100
+++ R-patched/src/library/tools/R/sysdata.R	2015-12-11 17:45:13.000000000 +0100
@@ -1,11 +1,11 @@
 make_sysdata_rda <-
-function()    
+function()
 {
     IANA_URI_scheme_db <- get_IANA_URI_scheme_db()
 
     IANA_HTTP_status_code_db <- get_IANA_HTTP_status_code_db()
 
-    ## See <http://en.wikipedia.org/wiki/List_of_HTTP_status_codes>.
+    ## See <https://en.wikipedia.org/wiki/List_of_HTTP_status_codes>.
     table_of_HTTP_status_codes <- IANA_HTTP_status_code_db$Description
     names(table_of_HTTP_status_codes) <- IANA_HTTP_status_code_db$Value
 
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/library/tools/R/urltools.R R-patched/src/library/tools/R/urltools.R
--- R-release-orig/src/library/tools/R/urltools.R	2015-09-05 00:15:09.000000000 +0200
+++ R-patched/src/library/tools/R/urltools.R	2015-12-11 17:45:13.000000000 +0100
@@ -274,7 +274,7 @@
     db[db$Description != "Unassigned", ]
 }
 
-## See <http://en.wikipedia.org/wiki/List_of_FTP_server_return_codes>
+## See <https://en.wikipedia.org/wiki/List_of_FTP_server_return_codes>
 ## and <http://tools.ietf.org/html/rfc959>,
 ## Section 4.2.2 "Numeric Order List of Reply Codes",
 ## and <https://tools.ietf.org/html/rfc2228>,
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/library/tools/src/text.c R-patched/src/library/tools/src/text.c
--- R-release-orig/src/library/tools/src/text.c	2015-08-26 00:16:55.000000000 +0200
+++ R-patched/src/library/tools/src/text.c	2016-01-05 02:41:10.000000000 +0100
@@ -120,7 +120,8 @@
 		if(used == 0) break;
 		s += used;
 	    } else
-		s++; pos++;
+		s++; 
+	    pos++;
 	}
 	if(end > -1) {
 	    INTEGER(ans)[i] = start + 1; /* index from one */
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/library/utils/R/packages2.R R-patched/src/library/utils/R/packages2.R
--- R-release-orig/src/library/utils/R/packages2.R	2015-08-26 00:16:34.000000000 +0200
+++ R-patched/src/library/utils/R/packages2.R	2015-12-13 17:45:10.000000000 +0100
@@ -19,6 +19,12 @@
 if (.Platform$OS.type == "windows")
     .install.macbinary <- function(...) NULL	# globalVariables isn't available, so use this to suppress the warning
 
+isBasePkg <- function(pkg) {
+  priority <- tryCatch(packageDescription(pkg, fields = "Priority"),
+                       error = function(e) e, warning = function(e) e)
+  identical(priority, "base")
+}
+
 getDependencies <-
     function(pkgs, dependencies = NA, available = NULL, lib = .libPaths()[1L],
              binary = FALSE)
@@ -53,6 +59,13 @@
 				 "packages %s are not available (%s)"),
 			paste(sQuote(p0[miss]), collapse = ", "), msg),
                 domain = NA, call. = FALSE)
+        base <- vapply(p0[miss], isBasePkg, FALSE)
+        if (sum(base))
+          warning(sprintf(ngettext(sum(base),
+                                   "package %s is a base package, and should not be updated",
+                                   "packages %s are base packages, and should not be updated"),
+                          paste(sQuote(p0[miss][base]), collapse = ", ")),
+                  domain = NA, call. = FALSE)
         if (sum(miss) == 1L &&
             !is.na(w <- match(tolower(p0[miss]),
                               tolower(row.names(available))))) {
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/library/utils/R/rtags.R R-patched/src/library/utils/R/rtags.R
--- R-release-orig/src/library/utils/R/rtags.R	2015-08-26 00:16:35.000000000 +0200
+++ R-patched/src/library/utils/R/rtags.R	2015-12-11 17:45:12.000000000 +0100
@@ -23,7 +23,7 @@
 ### parser.  Support for vi-style tags could be useful, but it needs
 ### the tags file needs to be sorted, making file-by-file processing
 ### difficult. It may be easier to write a script to convert an etags
-### format file (see http://http://en.wikipedia.org/wiki/Ctags).
+### format file (see http://https://en.wikipedia.org/wiki/Ctags).
 
 
 
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/library/utils/R/str.R R-patched/src/library/utils/R/str.R
--- R-release-orig/src/library/utils/R/str.R	2015-08-26 00:16:34.000000000 +0200
+++ R-patched/src/library/utils/R/str.R	2016-02-02 17:45:06.000000000 +0100
@@ -1,7 +1,7 @@
 #  File src/library/utils/R/str.R
 #  Part of the R package, https://www.R-project.org
 #
-#  Copyright (C) 1995-2015 The R Core Team
+#  Copyright (C) 1995-2016 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
@@ -54,13 +54,13 @@
     ## use 'give.length' when specified, else default = give.head
     if(length(larg <- list(...))) {
 	nl <- names(larg)
-	iGiveHead <- which(nl == "give.head")
+	which.head <- which(nl == "give.head")
 	if (any(Bgl <- nl == "give.length"))
 	    give.length <- larg[[which(Bgl)]]
-	else if(length(iGiveHead))
-	    give.length <- larg[[iGiveHead]]
-	if(length(iGiveHead)) # eliminate it from arg.list
-	    larg <- larg[ - iGiveHead ]
+	else if(length(which.head))
+	    give.length <- larg[[which.head]]
+	if(length(which.head)) # eliminate it from arg.list
+	    larg <- larg[ - which.head ]
 	if(is.numeric(larg[["nest.lev"]]) &&
 	   is.numeric(larg[["vec.len"]])) # typical call from data.frame
 	    ## reduce length for typical call:
@@ -203,7 +203,7 @@
     has.class <- S4 || !is.null(cl) # S3 or S4
     mod <- ""; char.like <- FALSE
     if(give.attr) a <- attributes(object)#-- save for later...
-    deParse <- function(.) deparse(., width.cutoff = min(500,max(20, width-10)))
+    deParse <- function(.) deparse(., width.cutoff = min(500, max(20, width-10)))
     n.of. <- function(n, singl, plural) paste(n, ngettext(n, singl, plural))
     n.of <- function(n, noun) n.of.(n, noun, paste0(noun,"s"))
     if (is.null(object))
@@ -548,7 +548,7 @@
 					#O: encodeString(object, quote= '"', na.encode= FALSE)
 	    formObj <- function(x) paste(as.character(x), collapse=" ")
 	}
-	else {
+	else { # not char.like
 	    if(!exists("format.fun", inherits=TRUE)) #-- define one --
 		format.fun <-
 		    if(mod == "num" || mod == "cplx") format else as.character
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/library/utils/R/tar.R R-patched/src/library/utils/R/tar.R
--- R-release-orig/src/library/utils/R/tar.R	2015-08-26 00:16:37.000000000 +0200
+++ R-patched/src/library/utils/R/tar.R	2015-12-11 17:45:12.000000000 +0100
@@ -140,7 +140,7 @@
 
     ## A tar file is a set of 512 byte records,
     ## a header record followed by file contents (zero-padded).
-    ## See http://en.wikipedia.org/wiki/Tar_%28file_format%29
+    ## See https://en.wikipedia.org/wiki/Tar_%28file_format%29
     if(is.character(tarfile) && length(tarfile) == 1L) {
         con <- gzfile(path.expand(tarfile), "rb") # reads compressed formats
         on.exit(close(con))
Binary files R-release-orig/src/library/utils/inst/doc/Sweave.pdf and R-patched/src/library/utils/inst/doc/Sweave.pdf differ
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/main/Makefile.in R-patched/src/main/Makefile.in
--- R-release-orig/src/main/Makefile.in	2015-08-26 00:18:39.000000000 +0200
+++ R-patched/src/main/Makefile.in	2015-12-11 17:45:15.016384000 +0100
@@ -154,9 +154,9 @@
 
 libR.a: $(OBJECTS) $(STATIC_LIBS)
 	-@mkdir libs
-	@(cd libs; for l in $(STATIC_LIBS); do $(AR) x ../$$l; done)
+	@(cd libs; for l in $(STATIC_LIBS); do $(AR) -x ../$$l; done)
 	@rm -rf $@
-	$(AR) cr $@ $(OBJECTS) libs/*o
+	$(AR) -cr $@ $(OBJECTS) libs/*o
 	$(RANLIB) $@
 	@rm -rf libs
 
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/main/Rstrptime.h R-patched/src/main/Rstrptime.h
--- R-release-orig/src/main/Rstrptime.h	2015-12-04 00:15:10.000000000 +0100
+++ R-patched/src/main/Rstrptime.h	2015-12-11 17:45:15.096485000 +0100
@@ -513,7 +513,7 @@
 		    if (val % 100 >= 60) return NULL;
 		    val = (val / 100) * 100 + ((val % 100) * 50) / 30;
 		}
-		/* http://en.wikipedia.org/wiki/List_of_UTC_time_offsets */
+		/* https://en.wikipedia.org/wiki/List_of_UTC_time_offsets */
 		if (val > 1400) return NULL;
 		off = ((val * 3600) / 100);
 		if (neg) off = -off;
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/main/arithmetic.h R-patched/src/main/arithmetic.h
--- R-release-orig/src/main/arithmetic.h	2015-08-26 00:18:39.000000000 +0200
+++ R-patched/src/main/arithmetic.h	2016-01-20 17:45:10.169203000 +0100
@@ -39,7 +39,7 @@
 
 /* some systems get this wrong, possibly depend on what libs are loaded */
 static R_INLINE double R_log(double x) {
-    return x > 0 ? log(x) : x < 0 ? R_NaN : R_NegInf;
+    return x > 0 ? log(x) : x == 0 ? R_NegInf : R_NaN;
 }
 
 /* Note that the behaviour of log(0) required is not necessarily that
@@ -50,10 +50,10 @@
 static R_INLINE double logbase(double x, double base)
 {
 #ifdef HAVE_LOG10
-    if(base == 10) return x > 0 ? log10(x) : x < 0 ? R_NaN : R_NegInf;
+    if(base == 10) return x > 0 ? log10(x) : x == 0 ? R_NegInf : R_NaN;
 #endif
 #ifdef HAVE_LOG2
-    if(base == 2) return x > 0 ? log2(x) : x < 0 ? R_NaN : R_NegInf;
+    if(base == 2) return x > 0 ? log2(x) : x == 0 ? R_NegInf : R_NaN;
 #endif
     return R_log(x) / R_log(base);
 }
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/main/array.c R-patched/src/main/array.c
--- R-release-orig/src/main/array.c	2015-11-18 00:15:05.000000000 +0100
+++ R-patched/src/main/array.c	2015-12-21 17:13:30.668705000 +0100
@@ -189,7 +189,7 @@
 	    ;
 	}
     }
-    if(!isNull(dimnames)&& length(dimnames) > 0)
+    if(!isNull(dimnames) && length(dimnames) > 0)
 	ans = dimnamesgets(ans, dimnames);
     UNPROTECT(1);
     return ans;
@@ -1645,12 +1645,13 @@
     }
 
     ans = dimgets(ans, dims);
-    if (TYPEOF(dimnames) == VECSXP && LENGTH(dimnames)) {
-	PROTECT(ans);
-	ans = dimnamesgets(ans, dimnames);
-	UNPROTECT(1);
+    if(!isNull(dimnames) && length(dimnames) > 0) {
+	// R 3.2.3 patched only: do not signal an error yet for wrong dimnames
+	if (TYPEOF(dimnames) != VECSXP)
+	    warning(_("non-list dimnames are disregarded; will be an error in R 3.3.0"));
+	else
+	    ans = dimnamesgets(ans, dimnames);
     }
-
     UNPROTECT(2);
     return ans;
 }
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/main/datetime.c R-patched/src/main/datetime.c
--- R-release-orig/src/main/datetime.c	2015-08-26 00:18:46.000000000 +0200
+++ R-patched/src/main/datetime.c	2016-01-30 02:41:11.015232000 +0100
@@ -913,7 +913,12 @@
     if(n > 0) N = (m > n) ? m:n; else N = 0;
     PROTECT(ans = allocVector(STRSXP, N));
     char tm_zone[20];
-    Rboolean have_zone = LENGTH(x) >= 10 && LENGTH(VECTOR_ELT(x, 9)) == n;
+#ifdef HAVE_TM_GMTOFF
+    Rboolean have_zone = LENGTH(x) >= 11 && XLENGTH(VECTOR_ELT(x, 9)) == n &&
+	XLENGTH(VECTOR_ELT(x, 10)) == n;
+#else
+    Rboolean have_zone = LENGTH(x) >= 10 && XLENGTH(VECTOR_ELT(x, 9)) == n;
+#endif
     for(R_xlen_t i = 0; i < N; i++) {
 	double secs = REAL(VECTOR_ELT(x, 0))[i%nlen[0]], fsecs = floor(secs);
 	// avoid (int) NAN
@@ -927,7 +932,7 @@
 	tm.tm_yday  = INTEGER(VECTOR_ELT(x, 7))[i%nlen[7]];
 	tm.tm_isdst = INTEGER(VECTOR_ELT(x, 8))[i%nlen[8]];
 	if(have_zone) {
-	    strncpy(tm_zone, CHAR(STRING_ELT(VECTOR_ELT(x, 9), i)), 20);
+	    strncpy(tm_zone, CHAR(STRING_ELT(VECTOR_ELT(x, 9), i%n)), 20);
             tm_zone[20 - 1] = '\0';
 #ifdef HAVE_TM_ZONE
 	    tm.tm_zone = tm_zone;
@@ -1003,8 +1008,8 @@
 		// Now assume tzone abbreviated name is < 40 bytes,
 		// but they are currently 3 or 4 bytes.
 		if(UseTZ) {
-		    if(LENGTH(x) >= 10) {
-			const char *p = CHAR(STRING_ELT(VECTOR_ELT(x, 9), i));
+		    if(have_zone) {
+			const char *p = CHAR(STRING_ELT(VECTOR_ELT(x, 9), i%n));
 			if(strlen(p)) {strcat(buff, " "); strcat(buff, p);}
 		    } else if(!isNull(tz)) {
 			int ii = 0;
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/main/deparse.c R-patched/src/main/deparse.c
--- R-release-orig/src/main/deparse.c	2015-08-26 00:18:41.000000000 +0200
+++ R-patched/src/main/deparse.c	2016-01-29 17:45:10.087059000 +0100
@@ -1,7 +1,7 @@
 /*
  *  R : A Computer Language for Statistical Data Analysis
  *  Copyright (C) 1995, 1996  Robert Gentleman and Ross Ihaka
- *  Copyright (C) 1997--2015  The R Core Team
+ *  Copyright (C) 1997--2016  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
@@ -129,6 +129,7 @@
     int maxlines;
     Rboolean active;
     int isS4;
+    Rboolean fnarg; /* fn argument, so parenthesize = as assignment */
 } LocalParseData;
 
 static SEXP deparse1WithCutoff(SEXP call, Rboolean abbrev, int cutoff,
@@ -641,6 +642,7 @@
 		    d->opts = localOpts;
 		}
 		print2buff(" = ", d);
+		d->fnarg = TRUE;
 		deparse2buff(CAR(a), d);
 	    }
 	    a = CDR(a);
@@ -709,7 +711,7 @@
 	    sym = SYMVALUE(op);
 	    if (TYPEOF(sym) == BUILTINSXP
 	        || TYPEOF(sym) == SPECIALSXP) {
-	        if (PPINFO(sym).precedence >= PREC_DOLLAR
+		if (PPINFO(sym).precedence >= PREC_SUBSET
 	            || PPINFO(sym).kind == PP_FUNCALL
 	            || PPINFO(sym).kind == PP_PAREN
 	            || PPINFO(sym).kind == PP_CURLY) return FALSE; /* x$f(z) or x[n](z) or f(z) or (f) or {f} */
@@ -731,9 +733,12 @@
 static void deparse2buff(SEXP s, LocalParseData *d)
 {
     PPinfo fop;
-    Rboolean lookahead = FALSE, lbreak = FALSE, parens;
+    Rboolean lookahead = FALSE, lbreak = FALSE, parens, fnarg = d->fnarg, 
+             outerparens, doquote;
     SEXP op, t;
     int localOpts = d->opts, i, n;
+    
+    d->fnarg = FALSE;
 
     if (!d->active) return;
 
@@ -744,7 +749,8 @@
 	print2buff("NULL", d);
 	break;
     case SYMSXP:
-	if (localOpts & QUOTEEXPRESSIONS) {
+	doquote = (localOpts & QUOTEEXPRESSIONS) && strlen(CHAR(PRINTNAME(s)));
+	if (doquote) {
 	    attr1(s, d);
 	    print2buff("quote(", d);
 	}
@@ -754,7 +760,7 @@
 	    print2buff(quotify(PRINTNAME(s), '`'), d);
 	else
 	    print2buff(CHAR(PRINTNAME(s)), d);
-	if (localOpts & QUOTEEXPRESSIONS) {
+	if (doquote) {
 	    print2buff(")", d);
 	    attr2(s, d);
 	}
@@ -971,7 +977,11 @@
 		    print2buff(")", d);
 		    break;
 		case PP_SUBSET:
+		    if ((parens = needsparens(fop, CAR(s), 1)))
+			print2buff("(", d);		
 		    deparse2buff(CAR(s), d);
+		    if (parens)
+			print2buff(")", d);		    
 		    if (PRIMVAL(SYMVALUE(op)) == 1)
 			print2buff("[", d);
 		    else
@@ -1023,6 +1033,8 @@
 		    break;
 		case PP_ASSIGN:
 		case PP_ASSIGN2:
+		    if ((outerparens = (fnarg && !strcmp(CHAR(PRINTNAME(op)), "="))))
+		    	print2buff("(", d);
 		    if ((parens = needsparens(fop, CAR(s), 1)))
 			print2buff("(", d);
 		    deparse2buff(CAR(s), d);
@@ -1036,6 +1048,8 @@
 		    deparse2buff(CADR(s), d);
 		    if (parens)
 			print2buff(")", d);
+		    if (outerparens)
+			print2buff(")", d);
 		    break;
 		case PP_DOLLAR:
 		    if ((parens = needsparens(fop, CAR(s), 1)))
@@ -1584,17 +1598,22 @@
 	    if(formals) {
 		if (CAR(arglist) != R_MissingArg) {
 		    print2buff(" = ", d);
+		    d->fnarg = TRUE;
 		    deparse2buff(CAR(arglist), d);
 		}
 	    }
 	    else {
 		print2buff(" = ", d);
 		if (CAR(arglist) != R_MissingArg) {
+		    d->fnarg = TRUE;
 		    deparse2buff(CAR(arglist), d);
 		}
 	    }
 	}
-	else deparse2buff(CAR(arglist), d);
+	else {
+	  d->fnarg = TRUE;
+	  deparse2buff(CAR(arglist), d);
+	}
 	arglist = CDR(arglist);
 	if (arglist != R_NilValue) {
 	    print2buff(", ", d);
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/main/errors.c R-patched/src/main/errors.c
--- R-release-orig/src/main/errors.c	2015-08-26 00:18:40.000000000 +0200
+++ R-patched/src/main/errors.c	2015-12-15 02:41:10.544709000 +0100
@@ -1033,7 +1033,7 @@
 SEXP attribute_hidden do_ngettext(SEXP call, SEXP op, SEXP args, SEXP rho)
 {
 #ifdef ENABLE_NLS
-    const char *domain = "";
+    const char *domain = "", *cfn;;
     char *buf;
     SEXP ans, sdom = CADDDR(args);
 #endif
@@ -1055,8 +1055,11 @@
 	     cptr != NULL && cptr->callflag != CTXT_TOPLEVEL;
 	     cptr = cptr->nextcontext)
 	    if (cptr->callflag & CTXT_FUNCTION) {
+		/* stop() etc have internal call to .makeMessage */
+		cfn = CHAR(STRING_ELT(deparse1s(CAR(cptr->call)), 0));
+		if(streql(cfn, "stop") || streql(cfn, "warning")
+		   || streql(cfn, "message")) continue;
 		rho = cptr->cloenv;
-		break;
 	    }
 	while(rho != R_EmptyEnv) {
 	    if (rho == R_GlobalEnv) break;
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/main/eval.c R-patched/src/main/eval.c
--- R-release-orig/src/main/eval.c	2015-10-28 00:15:05.000000000 +0100
+++ R-patched/src/main/eval.c	2016-01-13 02:41:19.907816000 +0100
@@ -877,7 +877,7 @@
 {
     SEXP formals, actuals, savedrho;
     volatile SEXP body, newrho;
-    SEXP f, a, tmp;
+    SEXP f, a, tmp, savesrc;
     RCNTXT cntxt;
 
     /* formals = list of formal parameters */
@@ -964,6 +964,7 @@
 	the generic as the sysparent of the method because the method
 	is a straight substitution of the generic.  */
 
+    PROTECT(savesrc = R_Srcref);
     if( R_GlobalContext->callflag == CTXT_GENERIC )
 	begincontext(&cntxt, CTXT_RETURN, call,
 		     newrho, R_GlobalContext->sysparent, arglist, op);
@@ -1045,13 +1046,14 @@
 	PROTECT(tmp = eval(body, newrho));
     }
     cntxt.returnValue = tmp; /* make it available to on.exit */
+    R_Srcref = savesrc;
     endcontext(&cntxt);
 
     if (RDEBUG(op) && R_current_debug_state()) {
 	Rprintf("exiting from: ");
 	PrintCall(call, rho);
     }
-    UNPROTECT(3);
+    UNPROTECT(4);
     return (tmp);
 }
 
@@ -5782,7 +5784,7 @@
 	  /* duplicate arguments and protect */
 	  PROTECT(args = duplicate(CDR(call)));
 	  /* insert evaluated promise for LHS as first argument */
-	  /* promise won't be captured so don't track refrences */
+	  /* promise won't be captured so don't track references */
 	  prom = R_mkEVPROMISE_NR(R_TmpvalSymbol, lhs);
 	  SETCAR(args, prom);
 	  /* insert evaluated promise for RHS as last argument */
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/main/inspect.c R-patched/src/main/inspect.c
--- R-release-orig/src/main/inspect.c	2015-08-26 00:18:44.000000000 +0200
+++ R-patched/src/main/inspect.c	2016-01-30 02:41:10.956699000 +0100
@@ -1,4 +1,4 @@
-/*
+  /*
  *  R : A Computer Language for Statistical Data Analysis
  *  Copyright (C) 2009-2014 The R Core Team.
  *
@@ -105,7 +105,7 @@
 	if (BINDING_IS_LOCKED(v)) { if (a) Rprintf(","); Rprintf("LCK"); a = 1; }
     }
     if (TYPEOF(v) == ENVSXP) {
-        if (FRAME_IS_LOCKED(v)) { if (a) Rprintf(","); Rprintf("LCK"); a = 1; }
+	if (FRAME_IS_LOCKED(v)) { if (a) Rprintf(","); Rprintf("LCK"); a = 1; }
 	if (IS_GLOBAL_FRAME(v)) { if (a) Rprintf(","); Rprintf("GL"); a = 1; }
     }
     if (LEVELS(v)) { if (a) Rprintf(","); Rprintf("gp=0x%x", LEVELS(v)); a = 1; }
@@ -119,7 +119,7 @@
     if (TYPEOF(v) == ENVSXP) /* NOTE: this is not a trivial OP since it involves looking up things
 				in the environment, so for a low-level debugging we may want to
 				avoid it .. */
-        PrintEnvironment(v);
+	PrintEnvironment(v);
     if (TYPEOF(v) == CHARSXP) {
 	if (IS_BYTES(v)) Rprintf("[bytes] ");
 	if (IS_LATIN1(v)) Rprintf("[latin1] ");
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/main/main.c R-patched/src/main/main.c
--- R-release-orig/src/main/main.c	2015-10-28 00:15:05.000000000 +0100
+++ R-patched/src/main/main.c	2016-01-30 02:41:10.986493000 +0100
@@ -718,7 +718,7 @@
 	char *p, Rlocale[1000]; /* Windows' locales can be very long */
 	p = getenv("LC_ALL");
 	strncpy(Rlocale, p ? p : "", 1000);
-        Rlocale[1000 - 1] = '\0';
+	Rlocale[1000 - 1] = '\0';
 	if(!(p = getenv("LC_CTYPE"))) p = Rlocale;
 	/* We'd like to use warning, but need to defer.
 	   Also cannot translate. */
@@ -981,7 +981,14 @@
     }
 
     /* trying to do this earlier seems to run into bootstrapping issues. */
-    R_init_jit_enabled();
+    doneit = 0;
+    SETJMP(R_Toplevel.cjmpbuf);
+    R_GlobalContext = R_ToplevelContext = R_SessionContext = &R_Toplevel;
+    if (!doneit) {
+	doneit = 1;
+	R_init_jit_enabled();
+    } else
+	R_Suicide(_("unable to initialize the JIT\n"));
     R_Is_Running = 2;
 }
 
@@ -1100,7 +1107,7 @@
 static void PrintCall(SEXP call, SEXP rho)
 {
     int old_bl = R_BrowseLines,
-        blines = asInteger(GetOption1(install("deparse.max.lines")));
+	blines = asInteger(GetOption1(install("deparse.max.lines")));
     if(blines != NA_INTEGER && blines > 0)
 	R_BrowseLines = blines;
     PrintValueRec(call, rho);
@@ -1138,8 +1145,8 @@
 
     /* return if 'expr' is not TRUE */
     if( !asLogical(CADDR(argList)) ) {
-        UNPROTECT(1);
-        return R_NilValue;
+	UNPROTECT(1);
+	return R_NilValue;
     }
 
     /* Save the evaluator state information */
@@ -1152,17 +1159,17 @@
     saveGlobalContext = R_GlobalContext;
 
     if (!RDEBUG(rho)) {
-        int skipCalls = asInteger(CADDDR(argList));
+	int skipCalls = asInteger(CADDDR(argList));
 	cptr = R_GlobalContext;
 	while ( ( !(cptr->callflag & CTXT_FUNCTION) || skipCalls--)
 		&& cptr->callflag )
 	    cptr = cptr->nextcontext;
 	Rprintf("Called from: ");
-        if( cptr != R_ToplevelContext ) {
+	if( cptr != R_ToplevelContext ) {
 	    PrintCall(cptr->call, rho);
 	    SET_RDEBUG(cptr->cloenv, 1);
-        } else
-            Rprintf("top level \n");
+	} else
+	    Rprintf("top level \n");
 
 	R_BrowseLines = 0;
     }
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/main/platform.c R-patched/src/main/platform.c
--- R-release-orig/src/main/platform.c	2015-09-19 00:15:06.000000000 +0200
+++ R-patched/src/main/platform.c	2016-01-05 02:41:11.372368000 +0100
@@ -2411,6 +2411,9 @@
 		nfail++;
 		goto copy_error;
 	    }
+	} else if (!over) {
+	  nfail++;
+	  goto copy_error;
 	}
 	if(fp1) fclose(fp1); fp1 = NULL;
 	if(fp2) fclose(fp2); fp2 = NULL;
@@ -2444,7 +2447,7 @@
 	    error(_("invalid '%s' argument"), "to");
 	over = asLogical(CAR(args)); args = CDR(args);
 	if (over == NA_LOGICAL)
-	    error(_("invalid '%s' argument"), "over");
+	    error(_("invalid '%s' argument"), "overwrite");
 	recursive = asLogical(CAR(args)); args = CDR(args);
 	if (recursive == NA_LOGICAL)
 	    error(_("invalid '%s' argument"), "recursive");
@@ -2633,10 +2636,11 @@
 		nfail++;
 		goto copy_error;
 	    }
-	    if(fp2) fclose(fp2); fp2 = NULL;
+	    if(fp2) {fclose(fp2); fp2 = NULL;}
 	    if(perms) chmod(dest, sb.st_mode & mask);
 	    if(dates) copyFileTime(this, dest);
-	}
+	} else if (!over)
+	    nfail++;
 copy_error:
 	if(fp2) fclose(fp2);
 	if(fp1) fclose(fp1);
@@ -2664,7 +2668,7 @@
 	    error(_("invalid '%s' argument"), "to");
 	over = asLogical(CAR(args)); args = CDR(args);
 	if (over == NA_LOGICAL)
-	    error(_("invalid '%s' argument"), "over");
+	    error(_("invalid '%s' argument"), "overwrite");
 	recursive = asLogical(CAR(args)); args = CDR(args);
 	if (recursive == NA_LOGICAL)
 	    error(_("invalid '%s' argument"), "recursive");
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/main/plot.c R-patched/src/main/plot.c
--- R-release-orig/src/main/plot.c	2015-08-26 00:18:42.000000000 +0200
+++ R-patched/src/main/plot.c	2016-01-05 02:41:11.255842000 +0100
@@ -133,8 +133,10 @@
 	    n = 0;
 	    if (0.5 * dn >= umin) n++;
 	    for (;;) {
-		if (dn > umax) break;		n++;
-		if (5 * dn > umax) break;	n++;
+		if (dn > umax) break;
+		n++;
+		if (5 * dn > umax) break;
+		n++;
 		dn *= 10;
 	    }
 	    if (!n)
@@ -159,9 +161,12 @@
 	    if (0.2 * dn >= umin) n++;
 	    if (0.5 * dn >= umin) n++;
 	    for (;;) {
-		if (dn > umax) break;		n++;
-		if (2 * dn > umax) break;	n++;
-		if (5 * dn > umax) break;	n++;
+		if (dn > umax) break;
+		n++;
+		if (2 * dn > umax) break;
+		n++;
+		if (5 * dn > umax) break;
+		n++;
 		dn *= 10;
 	    }
 	    if (!n)
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/main/print.c R-patched/src/main/print.c
--- R-release-orig/src/main/print.c	2015-08-26 00:18:46.000000000 +0200
+++ R-patched/src/main/print.c	2016-01-28 17:45:11.270468000 +0100
@@ -1,7 +1,7 @@
 /*
  *  R : A Computer Language for Statistical Data Analysis
  *  Copyright (C) 1995-1998	Robert Gentleman and Ross Ihaka.
- *  Copyright (C) 2000-2015	The R Core Team.
+ *  Copyright (C) 2000-2016	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
@@ -66,8 +66,7 @@
 #include "Print.h"
 #include "Fileio.h"
 #include "Rconnections.h"
-#include <S.h>
-
+#include <R_ext/RS.h>
 
 /* Global print parameter struct: */
 R_print_par_t R_print;
@@ -193,9 +192,9 @@
     if (!isInteger(t) || !useSource)
 	t = deparse1w(s, 0, useSource | DEFAULTDEPARSE);
     else {
-        PROTECT(t = lang2(install("as.character"), t));
-        t = eval(t, R_BaseEnv);
-        UNPROTECT(1);
+	PROTECT(t = lang2(install("as.character"), t));
+	t = eval(t, R_BaseEnv);
+	UNPROTECT(1);
     }
     PROTECT(t);
     for (i = 0; i < LENGTH(t); i++)
@@ -742,8 +741,8 @@
 	Rprintf("<CHARSXP: ");
 	Rprintf("%s", EncodeString(s, 0, '"', Rprt_adj_left));
 	Rprintf(">\n");
-        return; /* skip attribute printing for CHARSXP; they are used */
-                /* in managing the CHARSXP cache. */
+	return; /* skip attribute printing for CHARSXP; they are used */
+		/* in managing the CHARSXP cache. */
     case EXPRSXP:
 	PrintExpression(s);
 	break;
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/main/printutils.c R-patched/src/main/printutils.c
--- R-release-orig/src/main/printutils.c	2015-09-13 00:15:05.000000000 +0200
+++ R-patched/src/main/printutils.c	2016-01-05 02:41:11.311826000 +0100
@@ -639,13 +639,15 @@
 		if(res == 0) {k = 0; wc = L'\0';}
 		if(0x20 <= k && k < 0x7f && iswprint(wc)) {
 		    switch(wc) {
-		    case L'\\': *q++ = '\\'; *q++ = '\\'; p++;
-			break;
+		    case L'\\': *q++ = '\\'; *q++ = '\\'; p++; break;
 		    case L'\'':
 		    case L'"':
 		    case L'`':
-			if(quote == *p)  *q++ = '\\'; *q++ = *p++;
-			break;
+			{
+			    if(quote == *p)  *q++ = '\\'; 
+			    *q++ = *p++;
+			    break;
+			}
 		    default:
 			for(j = 0; j < res; j++) *q++ = *p++;
 			break;
@@ -715,7 +717,11 @@
 		    case '\'':
 		    case '"':
 		    case '`':
-			if(quote == *p)  *q++ = '\\'; *q++ = *p; break;
+		    {
+			if(quote == *p)  *q++ = '\\';
+			*q++ = *p; 
+			break;
+		    }
 		    default: *q++ = *p; break;
 		    }
 		} else switch(*p) {
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/main/rlocale_data.h R-patched/src/main/rlocale_data.h
--- R-release-orig/src/main/rlocale_data.h	2015-09-11 00:15:11.000000000 +0200
+++ R-patched/src/main/rlocale_data.h	2016-01-05 02:41:11.341799000 +0100
@@ -1299,6 +1299,7 @@
     {0x100000,0x10fffd,{1,1,1,1,2,1,1}}, // EA ambiguous
 };
 
+#if defined(__APPLE__) || defined(Win32) || defined(_AIX)
 /* ------------------- iswalpha -------------------- */
 static const struct interval table_walpha[] = {
     { 0x41, 0x5a },
@@ -3521,7 +3522,7 @@
 };
 static const int table_wxdigit_count =
   (sizeof(table_wxdigit)/sizeof(struct interval));
-
+#endif
 
 /* -------------------helper for wcwidth -------------------- */
 
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/main/saveload.c R-patched/src/main/saveload.c
--- R-release-orig/src/main/saveload.c	2015-09-05 00:15:11.000000000 +0200
+++ R-patched/src/main/saveload.c	2016-01-05 02:41:11.402852000 +0100
@@ -222,7 +222,7 @@
 	x = R_NegInf;
     else
 	res  = sscanf(d->smbuf, "%lg", &x);
-	if(res != 1) error(_("read error"));
+    if(res != 1) error(_("read error"));
     return x;
 }
 
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/main/sort.c R-patched/src/main/sort.c
--- R-release-orig/src/main/sort.c	2015-09-05 00:15:11.000000000 +0200
+++ R-patched/src/main/sort.c	2016-01-05 02:41:11.283731000 +0100
@@ -864,7 +864,7 @@
 
     if (n < 2) return;
     for (t = 0; incs[t] > n; t++);
-    for (h = incs[t]; t < NI; h = incs[++t])
+    for (h = incs[t]; t < NI; h = incs[++t]) {
 	R_CheckUserInterrupt();
 	for (i = h; i < n; i++) {
 	    itmp = indx[i];
@@ -877,6 +877,7 @@
 	    }
 	    indx[j] = itmp;
 	}
+    }
 }
 #endif
 
@@ -1348,11 +1349,14 @@
 		switch(ties_kind) {
 		case AVERAGE:
 		    for (k = i; k <= j; k++)
-			rk[in[k]] = (i + j + 2) / 2.; break;
+			rk[in[k]] = (i + j + 2) / 2.; 
+		    break;
 		case MAX:
-		    for (k = i; k <= j; k++) rk[in[k]] = j+1; break;
+		    for (k = i; k <= j; k++) rk[in[k]] = j+1;
+		    break;
 		case MIN:
-		    for (k = i; k <= j; k++) rk[in[k]] = i+1; break;
+		    for (k = i; k <= j; k++) rk[in[k]] = i+1;
+		    break;
 		}
 	    }
 	} else
@@ -1368,11 +1372,14 @@
 		switch(ties_kind) {
 		case AVERAGE:
 		    for (k = i; k <= j; k++)
-			rk[in[k]] = (i + j + 2) / 2.; break;
+			rk[in[k]] = (i + j + 2) / 2.;
+		    break;
 		case MAX:
-		    for (k = i; k <= j; k++) ik[in[k]] = j+1; break;
+		    for (k = i; k <= j; k++) ik[in[k]] = j+1;
+		    break;
 		case MIN:
-		    for (k = i; k <= j; k++) ik[in[k]] = i+1; break;
+		    for (k = i; k <= j; k++) ik[in[k]] = i+1; 
+		    break;
 		}
 	    }
 	}
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/main/subassign.c R-patched/src/main/subassign.c
--- R-release-orig/src/main/subassign.c	2015-08-26 00:18:41.000000000 +0200
+++ R-patched/src/main/subassign.c	2016-01-13 02:41:19.828275000 +0100
@@ -1914,6 +1914,11 @@
     input = allocVector(STRSXP, 1);
 
     nlist = CADR(args);
+    if (TYPEOF(nlist) == PROMSXP) {
+	PROTECT(input);
+	nlist = eval(nlist, env);
+	UNPROTECT(1);
+    }
     iS = isSymbol(nlist);
     if (iS)
 	SET_STRING_ELT(input, 0, PRINTNAME(nlist));
@@ -1927,6 +1932,9 @@
     /* replace the second argument with a string */
     SETCADR(args, input);
 
+    /* if nlist is a string, it may be destroyed below, but it is ok
+       because we later only use its first element which is protected
+       implicitly through args/input */
     if(R_DispatchOrEvalSP(call, op, "$<-", args, env, &ans))
       return(ans);
 
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/main/subset.c R-patched/src/main/subset.c
--- R-release-orig/src/main/subset.c	2015-08-26 00:18:44.000000000 +0200
+++ R-patched/src/main/subset.c	2016-01-13 02:41:19.863525000 +0100
@@ -1141,6 +1141,8 @@
     input = PROTECT(allocVector(STRSXP, 1));
 
     nlist = CADR(args);
+    if (TYPEOF(nlist) == PROMSXP)
+	nlist = eval(nlist, env);
     if(isSymbol(nlist) )
 	SET_STRING_ELT(input, 0, PRINTNAME(nlist));
     else if(isString(nlist) )
@@ -1164,13 +1166,13 @@
     /* evaluation retains any missing argument indicators. */
 
     if(R_DispatchOrEvalSP(call, op, "$", args, env, &ans)) {
-	UNPROTECT(2);
+	UNPROTECT(2); /* input, args */
 	if (NAMED(ans))
 	    SET_NAMED(ans, 2);
 	return(ans);
     }
 
-    UNPROTECT(2);
+    UNPROTECT(2); /* input, args */
     return R_subset3_dflt(CAR(ans), STRING_ELT(input, 0), call);
 }
 
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/main/sysutils.c R-patched/src/main/sysutils.c
--- R-release-orig/src/main/sysutils.c	2015-08-26 00:18:44.000000000 +0200
+++ R-patched/src/main/sysutils.c	2016-01-30 02:41:10.929668000 +0100
@@ -255,7 +255,7 @@
     if (n2 < 1)
 	error(_("no 'tempdir'"));
     if (n3 < 1)
-        error(_("no 'fileext'"));
+	error(_("no 'fileext'"));
     slen = (n1 > n2) ? n1 : n2;
     slen = (n3 > slen) ? n3 : slen;
     PROTECT(ans = allocVector(STRSXP, slen));
@@ -275,8 +275,9 @@
 FILE *R_popen(const char *command, const char *type)
 {
     FILE *fp;
-#ifdef __APPLE__
+#ifdef OLD__APPLE__
     /* Luke recommends this to fix PR#1140 */
+    /* As of 2016-01-06 on El Capitan this may no longer be needed -- LT */
     sigset_t ss;
     sigemptyset(&ss);
     sigaddset(&ss, SIGPROF);
@@ -297,16 +298,21 @@
 {
     int res;
 #ifdef __APPLE__
+# ifdef OLD__APPLE__
     /* Luke recommends this to fix PR#1140 */
+    /* As of 2016-01-06 on El Capitan this may no longer be needed -- LT */
     sigset_t ss;
     sigemptyset(&ss);
     sigaddset(&ss, SIGPROF);
     sigprocmask(SIG_BLOCK, &ss,  NULL);
+# endif
 #ifdef HAVE_AQUA
     if(ptr_CocoaSystem) res = ptr_CocoaSystem(command); else
 #endif
     res = system(command);
+# ifdef OLD__APPLE__
     sigprocmask(SIG_UNBLOCK, &ss, NULL);
+# endif
 #else // not APPLE
     res = system(command);
 #endif
@@ -788,15 +794,15 @@
 
     if (IS_ASCII(x)) return NT_NONE;
     if (IS_UTF8(x)) {
-        if (utf8locale || x == NA_STRING) return NT_NONE;
-        return NT_FROM_UTF8;
+	if (utf8locale || x == NA_STRING) return NT_NONE;
+	return NT_FROM_UTF8;
     }
     if (IS_LATIN1(x)) {
-        if (x == NA_STRING || latin1locale) return NT_NONE;
-        return NT_FROM_LATIN1;
+	if (x == NA_STRING || latin1locale) return NT_NONE;
+	return NT_FROM_LATIN1;
     }
     if (IS_BYTES(x))
-        error(_("translating strings with \"bytes\" encoding is not allowed"));
+	error(_("translating strings with \"bytes\" encoding is not allowed"));
     return NT_NONE;
 }
 
@@ -806,10 +812,10 @@
 /* Translates string in "ans" to native encoding returning it as string
    buffer "cbuff" */
 static void translateToNative(const char *ans, R_StringBuffer *cbuff,
-                              nttype_t ttype) {
+			      nttype_t ttype) {
 
     if (ttype == NT_NONE)
-        error(_("internal error: no translation needed"));
+	error(_("internal error: no translation needed"));
 
     void * obj;
     const char *inbuf;
@@ -825,7 +831,7 @@
 		error(_("unsupported conversion from '%s' in codepage %d"),
 		      "latin1", localeCP);
 #else
-	        error(_("unsupported conversion from '%s' to '%s'"),
+		error(_("unsupported conversion from '%s' to '%s'"),
 		      "latin1", "");
 #endif
 	    latin1_obj = obj;
@@ -840,7 +846,7 @@
 		error(_("unsupported conversion from '%s' in codepage %d"),
 		      "latin1", localeCP);
 #else
-	        error(_("unsupported conversion from '%s' to '%s'"),
+		error(_("unsupported conversion from '%s' to '%s'"),
 		      "latin1", "");
 #endif
 	    utf8_obj = obj;
@@ -1378,7 +1384,7 @@
 	    char tocode[128];
 	    /* locale set fuzzy case */
 	    strncpy(tocode, locale2charset(NULL), sizeof(tocode));
-            tocode[sizeof(tocode) - 1] = '\0';
+	    tocode[sizeof(tocode) - 1] = '\0';
 	    if((void *)(-1) == (cd = Riconv_open(tocode, UNICODE)))
 		return (size_t)(-1);
 #else
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/main/times.c R-patched/src/main/times.c
--- R-release-orig/src/main/times.c	2015-08-26 00:18:42.000000000 +0200
+++ R-patched/src/main/times.c	2015-12-11 17:45:15.063074000 +0100
@@ -1,6 +1,6 @@
 /*
  *  R : A Computer Language for Statistical Data Analysis
- *  Copyright (C) 2000-2014  The R Core Team.
+ *  Copyright (C) 2000-2015  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
@@ -126,7 +126,7 @@
     /* No known current OSes */
     /* Disallowed by POSIX (1988-):
        http://www.mail-archive.com/leapsecs@rom.usno.navy.mil/msg00109.html
-       http://en.wikipedia.org/wiki/Unix_time
+       https://en.wikipedia.org/wiki/Unix_time
     */
     if (!ISNAN(ans)) {
 	ans -= n_leapseconds;
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/main/util.c R-patched/src/main/util.c
--- R-release-orig/src/main/util.c	2015-08-26 00:18:40.000000000 +0200
+++ R-patched/src/main/util.c	2016-01-05 02:41:11.199717000 +0100
@@ -653,8 +653,12 @@
     isort_with_index(INTEGER(yi), iy, ny);
 
     /* 1. determine result sizes */
-    for (i = 0; i < nx; i++) if (INTEGER(xi)[i] > 0) break; nx_lone = i;
-    for (i = 0; i < ny; i++) if (INTEGER(yi)[i] > 0) break; ny_lone = i;
+    for (i = 0; i < nx; i++) 
+	if (INTEGER(xi)[i] > 0) break; 
+    nx_lone = i;
+    for (i = 0; i < ny; i++) 
+	if (INTEGER(yi)[i] > 0) break;
+    ny_lone = i;
     double dnans = 0;
     for (i = nx_lone, j = ny_lone; i < nx; i = nnx, j = nny) {
 	int tmp = INTEGER(xi)[i];
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/modules/internet/libcurl.c R-patched/src/modules/internet/libcurl.c
--- R-release-orig/src/modules/internet/libcurl.c	2015-09-05 00:15:12.000000000 +0200
+++ R-patched/src/modules/internet/libcurl.c	2016-01-28 07:45:08.075491000 +0100
@@ -633,11 +633,24 @@
     curl_multi_remove_handle(ctxt->mh, ctxt->hnd);
     curl_easy_cleanup(ctxt->hnd);
     curl_multi_cleanup(ctxt->mh);
-    free(ctxt->buf);
-
     con->isopen = FALSE;
 }
 
+static void Curl_destroy(Rconnection con)
+{
+    RCurlconn ctxt;
+
+    if (NULL == con)
+        return;
+    ctxt = (RCurlconn)(con->private);
+
+    if (NULL == ctxt)
+        return;
+
+    free(ctxt->buf);
+    free(ctxt);
+}
+
 static int Curl_fgetc_internal(Rconnection con)
 {
     unsigned char c;
@@ -669,6 +682,7 @@
     new->canwrite = FALSE;
     new->open = &Curl_open;
     new->close = &Curl_close;
+    new->destroy = &Curl_destroy;
     new->fgetc_internal = &Curl_fgetc_internal;
     new->fgetc = &dummy_fgetc;
     new->read = &Curl_read;
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/modules/internet/nanohttp.c R-patched/src/modules/internet/nanohttp.c
--- R-release-orig/src/modules/internet/nanohttp.c	2015-08-26 00:18:56.000000000 +0200
+++ R-patched/src/modules/internet/nanohttp.c	2016-01-05 02:41:12.227429000 +0100
@@ -367,7 +367,10 @@
 	    break;
 	}
 	if(indx >= 40959)
-	    RxmlMessage(2, _("RxmlNanoHTTPScanURL: overlong (invalid?) URL"));	buf[indx++] = *cur++;
+	    RxmlMessage(2, _("RxmlNanoHTTPScanURL: overlong (invalid?) URL"));
+	else {
+	    buf[indx++] = *cur++;
+	}
     }
     if (*cur == 0) return;
 
@@ -395,7 +398,10 @@
 	    break;
 	}
 	if(indx >= 40959)
-	    RxmlMessage(2, _("RxmlNanoHTTPScanURL: overlong (invalid?) URL"));	buf[indx++] = *cur++;
+	    RxmlMessage(2, _("RxmlNanoHTTPScanURL: overlong (invalid?) URL"));
+	else { 
+	    buf[indx++] = *cur++;
+	}
     }
     if (*cur == 0)
         ctxt->path = xmlMemStrdup("/");
@@ -452,7 +458,9 @@
 	}
 	if(indx >= 4095)
 	    RxmlMessage(2, _("RxmlNanoHTTPScanProxy: overlong (invalid?) URL"));
-	buf[indx++] = *cur++;
+	else {
+	    buf[indx++] = *cur++;
+	}
     }
     if (*cur == 0) return;
 
@@ -487,7 +495,10 @@
 	    break;
 	}
 	if(indx >= 4095)
-	    RxmlMessage(2, _("RxmlNanoHTTPScanProxy: overlong (invalid?) URL"));	buf[indx++] = *cur++;
+	    RxmlMessage(2, _("RxmlNanoHTTPScanProxy: overlong (invalid?) URL"));
+	else {
+	    buf[indx++] = *cur++;
+	}
     }
 }
 
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/modules/lapack/README R-patched/src/modules/lapack/README
--- R-release-orig/src/modules/lapack/README	2014-03-13 00:03:24.000000000 +0100
+++ R-patched/src/modules/lapack/README	2016-01-23 17:45:09.499663000 +0100
@@ -7,19 +7,6 @@
 compiler and compatible with the Rcomplex type.
 Neither will be compiled if an external LAPACK is used.
 
-For 'base' R addition of a new .Call()able Lapack routine,
-all these files must be updated {path relative to R's topdir}:
-
-  src/gnuwin32/Rdll.hide
-  src/include/R_ext/Lapack.h
-  src/include/Rmodules/Rlapack.h
-  src/main/basedecl.h
-  src/main/lapack.c
-  src/main/registration.c
-  src/modules/lapack/Lapack.c
-  src/modules/lapack/Lapack.h
-  src/modules/lapack/cmplx.f or dlapack.f
-
 We have tried to avoid including any single-precision routines.
 
 dlapack.f is the concatenation of
@@ -106,6 +93,11 @@
 dgtrfs.f	dlar1v.f	dorgtr.f	dstegr.f
 dgtsv.f		dlar2v.f	dorm2l.f	dstein.f
 
+dgeqpf dgegv dggsvd dggsvp dgegs dgelsx dlahrd dlatzm dtzrqf
+are 'deprecated' in LAPACK 3.6.0 and may not be included in
+external libraries.
+
+
 cmplx.f is the concatenation of
 
 dzsum1.f ilazlc.f ilazlr.f izmax1.f zbdsqr.f
@@ -128,4 +120,38 @@
 zungr2.f zungrq.f zungtr.f zunm2r.f zunmbr.f
 zunmhr.f zunml2.f zunmlq.f zunmqr.f
 
-R.patch suppresses warnings with Fortran array-bounds checking.
+zlahr2 zlaqr0 zlaqr1 zlaqr2 zlaqr3 zlaqr4 zlaqr5 zlartg zpotf2 zpotrf
+zrot ztrexc
+were added in 2.5.0.
+
+izmax1 zdrscl zgecon zlacn2 zlantr ztrcon
+were added in 2.7.0.
+
+dzsum1 ilazlc ilazlr zunmhr
+were added in 2.15.2.
+
+zgelsd zgesdd zlacp2 zlacrm zlals0 zlalsa zlalsd zlarcm
+were added in R 3.1.0.
+
+zlahrd is 'deprecated' in LAPACK 3.6.0 and may not be included in
+external libraries.
+
+-------------------------------------------------
+
+R.patch suppresses compilation warnings, and helps with Fortran
+array-bounds checking.
+
+-------------------------------------------------
+
+For 'base' R addition of a new .Call()able Lapack routine,
+all these files must be updated {path relative to R's topdir}:
+
+  src/gnuwin32/Rdll.hide
+  src/include/R_ext/Lapack.h
+  src/include/Rmodules/Rlapack.h
+  src/main/basedecl.h
+  src/main/lapack.c
+  src/main/registration.c
+  src/modules/lapack/Lapack.c
+  src/modules/lapack/Lapack.h
+  src/modules/lapack/cmplx.f or dlapack.f
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/nmath/Makefile.in R-patched/src/nmath/Makefile.in
--- R-release-orig/src/nmath/Makefile.in	2015-03-19 00:03:59.000000000 +0100
+++ R-patched/src/nmath/Makefile.in	2015-12-11 17:45:15.386041000 +0100
@@ -72,8 +72,8 @@
 	@$(MAKE) libnmath.a
 
 libnmath.a: $(OBJECTS)
-	rm -rf $@
-	$(AR) cr $@ $(OBJECTS)
+	@rm -rf $@
+	$(AR) -cr $@ $(OBJECTS)
 	$(RANLIB) $@
 
 mostlyclean: clean
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/nmath/dbeta.c R-patched/src/nmath/dbeta.c
--- R-release-orig/src/nmath/dbeta.c	2015-08-26 00:18:53.000000000 +0200
+++ R-patched/src/nmath/dbeta.c	2016-01-05 02:41:11.987732000 +0100
@@ -53,16 +53,16 @@
     // limit cases for (a,b), leading to point masses
     if(a == 0 || b == 0 || !R_FINITE(a) || !R_FINITE(b)) {
 	if(a == 0 && b == 0) { // point mass 1/2 at each of {0,1} :
-	    if (x == 0 || x == 1) return(ML_POSINF); /* else */ return(R_D__0);
+	    if (x == 0 || x == 1) return(ML_POSINF); else return(R_D__0);
 	}
 	if (a == 0 || a/b == 0) { // point mass 1 at 0
-	    if (x == 0) return(ML_POSINF); /* else */ return(R_D__0);
+	    if (x == 0) return(ML_POSINF); else return(R_D__0);
 	}
 	if (b == 0 || b/a == 0) { // point mass 1 at 1
-	    if (x == 1) return(ML_POSINF); /* else */ return(R_D__0);
+	    if (x == 1) return(ML_POSINF); else return(R_D__0);
 	}
 	// else, remaining case:  a = b = Inf : point mass 1 at 1/2
-	if (x == 0.5) return(ML_POSINF); /* else */ return(R_D__0);
+	if (x == 0.5) return(ML_POSINF); else return(R_D__0);
     }
 
     if (x == 0) {
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/nmath/df.c R-patched/src/nmath/df.c
--- R-release-orig/src/nmath/df.c	2015-08-26 00:18:52.000000000 +0200
+++ R-patched/src/nmath/df.c	2016-01-05 02:41:11.931289000 +0100
@@ -47,8 +47,7 @@
     if (x < 0.)  return(R_D__0);
     if (x == 0.) return(m > 2 ? R_D__0 : (m == 2 ? R_D__1 : ML_POSINF));
     if (!R_FINITE(m) && !R_FINITE(n)) { /* both +Inf */
-	if(x == 1.) return ML_POSINF;
-	/* else */  return R_D__0;
+	if(x == 1.) return ML_POSINF; else return R_D__0;
     }
     if (!R_FINITE(n)) /* must be +Inf by now */
 	return(dgamma(x, m/2, 2./m, give_log));
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/nmath/dnf.c R-patched/src/nmath/dnf.c
--- R-release-orig/src/nmath/dnf.c	2015-08-26 00:18:53.000000000 +0200
+++ R-patched/src/nmath/dnf.c	2016-01-05 02:41:11.960281000 +0100
@@ -55,8 +55,7 @@
      */
     if (!R_FINITE(df1) && !R_FINITE(df2)) { /* both +Inf */
 	/* PR: not sure about this (taken from  ncp==0)  -- FIXME ? */
-	if(x == 1.) return ML_POSINF;
-	/* else */  return R_D__0;
+	if(x == 1.) return ML_POSINF; else return R_D__0;
     }
     if (!R_FINITE(df2)) /* i.e.  = +Inf */
 	return df1* dnchisq(x*df1, df1, ncp, give_log);
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/nmath/lbeta.c R-patched/src/nmath/lbeta.c
--- R-release-orig/src/nmath/lbeta.c	2015-08-26 00:18:53.000000000 +0200
+++ R-patched/src/nmath/lbeta.c	2016-01-05 02:41:12.014169000 +0100
@@ -69,9 +69,10 @@
 	return lgammafn(p) + corr + p - p * log(p + q)
 		+ (q - 0.5) * log1p(-p / (p + q));
     }
-    else
+    else {
 	/* p and q are small: p <= q < 10. */
 	/* R change for very small args */
 	if (p < 1e-306) return lgamma(p) + (lgamma(q) - lgamma(p+q));
-	return log(gammafn(p) * (gammafn(q) / gammafn(p + q)));
+	else return log(gammafn(p) * (gammafn(q) / gammafn(p + q)));
+    }
 }
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/nmath/pbeta.c R-patched/src/nmath/pbeta.c
--- R-release-orig/src/nmath/pbeta.c	2015-08-26 00:18:53.000000000 +0200
+++ R-patched/src/nmath/pbeta.c	2016-01-05 02:41:12.041989000 +0100
@@ -50,10 +50,7 @@
 	if (b == 0 || b/a == 0) // point mass 1 at 1 ==> P(X <= x) = 0, all x < 1
 	    return R_DT_0;
 	// else, remaining case:  a = b = Inf : point mass 1 at 1/2
-	if (x < 0.5)
-	    return R_DT_0;
-	// else,  x >= 0.5 :
-	    return R_DT_1;
+	if (x < 0.5) return R_DT_0; else return R_DT_1;
     }
     // Now:  0 < a < Inf;  0 < b < Inf
 
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/nmath/standalone/Makefile.in R-patched/src/nmath/standalone/Makefile.in
--- R-release-orig/src/nmath/standalone/Makefile.in	2015-08-26 00:18:53.000000000 +0200
+++ R-patched/src/nmath/standalone/Makefile.in	2015-12-11 17:45:15.000000000 +0100
@@ -121,7 +121,8 @@
 	@touch $@
 
 libRmath.a: $(libRmath_a_OBJECTS)
-	$(AR) cr $@ $(libRmath_a_OBJECTS)
+	@rm -rf $@
+	$(AR) -cr $@ $(libRmath_a_OBJECTS)
 	$(RANLIB) $@
 
 ## under peculiar circumstances, $(LIBM) here helps.
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/unix/Makefile.in R-patched/src/unix/Makefile.in
--- R-release-orig/src/unix/Makefile.in	2015-09-03 00:15:06.000000000 +0200
+++ R-patched/src/unix/Makefile.in	2015-12-11 17:45:10.067400000 +0100
@@ -53,8 +53,8 @@
 	(cd ../include; $(MAKE) $(@F))
 
 libunix.a: $(OBJECTS)
-	rm -rf $@
-	$(AR) cr $@ $(OBJECTS)
+	@rm -rf $@
+	$(AR) -cr $@ $(OBJECTS)
 	$(RANLIB) $@
 
 mostlyclean: clean
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/Examples/datasets-Ex.Rout.save R-patched/tests/Examples/datasets-Ex.Rout.save
--- R-release-orig/tests/Examples/datasets-Ex.Rout.save	2015-12-04 00:15:21.000000000 +0100
+++ R-patched/tests/Examples/datasets-Ex.Rout.save	2016-01-22 17:45:15.202908000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -3458,7 +3458,7 @@
 > ###
 > options(digits = 7L)
 > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed:  1.276 0.03 1.308 0 0 
+Time elapsed:  1.284 0.031 1.316 0 0 
 > grDevices::dev.off()
 null device 
           1 
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/Examples/grDevices-Ex.Rout.save R-patched/tests/Examples/grDevices-Ex.Rout.save
--- R-release-orig/tests/Examples/grDevices-Ex.Rout.save	2015-12-04 00:15:21.000000000 +0100
+++ R-patched/tests/Examples/grDevices-Ex.Rout.save	2016-01-22 17:45:15.237816000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -266,7 +266,7 @@
 [3,] "#999999"
 [4,] "#CCCCCC"
 [5,] "#FFFFFF"
-> #   locigal vectors are black and white ...
+> #   logical vectors are black and white ...
 > as.raster(1:10 %% 2 == 0)
       [,1]     
  [1,] "#000000"
@@ -3764,7 +3764,7 @@
 > ###
 > options(digits = 7L)
 > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed:  7.687 0.141 7.83 0 0 
+Time elapsed:  7.772 0.131 7.905 0 0 
 > grDevices::dev.off()
 null device 
           1 
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/Examples/graphics-Ex.Rout.save R-patched/tests/Examples/graphics-Ex.Rout.save
--- R-release-orig/tests/Examples/graphics-Ex.Rout.save	2015-12-10 00:15:20.000000000 +0100
+++ R-patched/tests/Examples/graphics-Ex.Rout.save	2016-01-22 17:45:15.056865000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-08 r69745) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -2066,7 +2066,7 @@
 > points.default # to see how it calls "plot.xy(xy.coords(x, y), ...)"
 function (x, y = NULL, type = "p", ...) 
 plot.xy(xy.coords(x, y), type = type, ...)
-<bytecode: 0x2c65bf8>
+<bytecode: 0x20eab38>
 <environment: namespace:graphics>
 > 
 > 
@@ -2936,7 +2936,7 @@
     u <- par("usr")
     xy * c(u[2L] - u[1L], u[4L] - u[3L])/par("pin")
 }
-<bytecode: 0x27e10b8>
+<bytecode: 0x2460308>
 <environment: namespace:graphics>
 > 
 > ## plot labels offset 0.12 inches to the right
@@ -3016,7 +3016,7 @@
 > ###
 > options(digits = 7L)
 > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed:  1.793 0.033 1.827 0 0 
+Time elapsed:  1.808 0.026 1.834 0 0 
 > grDevices::dev.off()
 null device 
           1 
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/Examples/grid-Ex.Rout.save R-patched/tests/Examples/grid-Ex.Rout.save
--- R-release-orig/tests/Examples/grid-Ex.Rout.save	2015-12-04 00:15:21.000000000 +0100
+++ R-patched/tests/Examples/grid-Ex.Rout.save	2016-01-22 17:45:15.169138000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -2058,7 +2058,7 @@
 > ###
 > options(digits = 7L)
 > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed:  1.003 0.021 1.023 0 0 
+Time elapsed:  1.022 0.015 1.036 0 0 
 > grDevices::dev.off()
 null device 
           1 
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/Examples/splines-Ex.Rout.save R-patched/tests/Examples/splines-Ex.Rout.save
--- R-release-orig/tests/Examples/splines-Ex.Rout.save	2015-12-04 00:15:21.000000000 +0100
+++ R-patched/tests/Examples/splines-Ex.Rout.save	2016-01-22 17:45:15.279490000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -582,7 +582,7 @@
 > ###
 > options(digits = 7L)
 > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed:  0.106 0.003 0.11 0 0 
+Time elapsed:  0.104 0.004 0.108 0 0 
 > grDevices::dev.off()
 null device 
           1 
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/Examples/stats-Ex.Rout.save R-patched/tests/Examples/stats-Ex.Rout.save
--- R-release-orig/tests/Examples/stats-Ex.Rout.save	2015-12-04 00:15:21.000000000 +0100
+++ R-patched/tests/Examples/stats-Ex.Rout.save	2016-01-22 17:45:15.313559945 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -3792,7 +3792,7 @@
 > 
 > asOneSidedFormula("age")
 ~age
-<environment: 0x3fae4e8>
+<environment: 0x2a13488>
 > asOneSidedFormula(~ age)
 ~age
 > 
@@ -4755,7 +4755,7 @@
     r[cbind(1L:p, 1L:p)] <- 1
     r
 }
-<bytecode: 0x3e0e4d8>
+<bytecode: 0x3e1a010>
 <environment: namespace:stats>
 > stopifnot(all.equal(Cl, cov2cor(cov(longley))),
 +           all.equal(cor(longley, method = "kendall"),
@@ -7279,7 +7279,7 @@
 > environment(as.formula("y ~ x"))
 <environment: R_GlobalEnv>
 > environment(as.formula("y ~ x", env = new.env()))
-<environment: 0x15d4a70>
+<environment: 0x2924058>
 > 
 > 
 > ## Create a formula for a model with a large number of variables:
@@ -11762,14 +11762,14 @@
 $linkfun
 function (mu) 
 mu^lambda
-<bytecode: 0x3bcc468>
-<environment: 0x3bc2fb8>
+<bytecode: 0x34af1b8>
+<environment: 0x34a6960>
 
 $linkinv
 function (eta) 
 pmax(eta^(1/lambda), .Machine$double.eps)
-<bytecode: 0x3bcc580>
-<environment: 0x3bc2fb8>
+<bytecode: 0x34af2d0>
+<environment: 0x34a6960>
 
 > 
 > 
@@ -15642,8 +15642,8 @@
 > unclass(sfun0)
 function (v) 
 .approxfun(x, y, v, method, yleft, yright, f)
-<bytecode: 0x2a7afb8>
-<environment: 0x399ac60>
+<bytecode: 0x3b927f8>
+<environment: 0x7279078>
 attr(,"call")
 stepfun(1:3, y0, f = 0)
 > ls(envir = environment(sfun0))
@@ -17920,7 +17920,7 @@
 > ###
 > options(digits = 7L)
 > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed:  4.349 0.095 4.446 0 0 
+Time elapsed:  4.338 0.106 4.447 0 0 
 > grDevices::dev.off()
 null device 
           1 
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/Examples/stats4-Ex.Rout.save R-patched/tests/Examples/stats4-Ex.Rout.save
--- R-release-orig/tests/Examples/stats4-Ex.Rout.save	2015-12-04 00:15:21.000000000 +0100
+++ R-patched/tests/Examples/stats4-Ex.Rout.save	2016-01-22 17:45:15.140436000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -184,7 +184,7 @@
 > ###
 > options(digits = 7L)
 > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed:  0.291 0.006 0.297 0 0 
+Time elapsed:  0.297 0.005 0.303 0 0 
 > grDevices::dev.off()
 null device 
           1 
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/Examples/tools-Ex.Rout.save R-patched/tests/Examples/tools-Ex.Rout.save
--- R-release-orig/tests/Examples/tools-Ex.Rout.save	2015-12-04 00:15:21.000000000 +0100
+++ R-patched/tests/Examples/tools-Ex.Rout.save	2016-01-22 17:45:15.099516000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -188,7 +188,7 @@
 > bibstyle("unsorted", sortKeys = function(refs) seq_along(refs),
 +     fmtPrefix = function(paper) paste0("[", paper$.index, "]"),
 +        .init = TRUE)
-<environment: 0x2f81600>
+<environment: 0x309e8b0>
 > print(refs, .bibstyle = "unsorted")
 [1] R Core Team (2013). _R: A Language and Environment for Statistical
 Computing_. R Foundation for Statistical Computing, Vienna, Austria.
@@ -981,7 +981,7 @@
 > ###
 > options(digits = 7L)
 > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed:  0.197 0.002 0.199 0 0 
+Time elapsed:  0.234 0.006 0.242 0 0 
 > grDevices::dev.off()
 null device 
           1 
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/R-intro.Rout.save R-patched/tests/R-intro.Rout.save
--- R-release-orig/tests/R-intro.Rout.save	2015-12-04 00:15:18.000000000 +0100
+++ R-patched/tests/R-intro.Rout.save	2016-01-22 17:45:14.448763000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/any-all.Rout.save R-patched/tests/any-all.Rout.save
--- R-release-orig/tests/any-all.Rout.save	2015-12-04 00:15:20.000000000 +0100
+++ R-patched/tests/any-all.Rout.save	2016-01-22 17:45:14.894113000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/arith-true.Rout.save R-patched/tests/arith-true.Rout.save
--- R-release-orig/tests/arith-true.Rout.save	2015-12-04 00:15:20.000000000 +0100
+++ R-patched/tests/arith-true.Rout.save	2016-01-22 17:45:14.984913000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -323,5 +323,5 @@
 > 
 > ## Last Line:
 > cat('Time elapsed: ', proc.time() - .proctime00,'\n')
-Time elapsed:  0.217 0.006 0.222 0 0 
+Time elapsed:  0.222 0.001 0.223 0 0 
 > 
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/arith.Rout.save R-patched/tests/arith.Rout.save
--- R-release-orig/tests/arith.Rout.save	2015-12-04 00:15:19.000000000 +0100
+++ R-patched/tests/arith.Rout.save	2016-01-22 17:45:14.634088000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/array-subset.Rout.save R-patched/tests/array-subset.Rout.save
--- R-release-orig/tests/array-subset.Rout.save	2015-12-04 00:15:19.000000000 +0100
+++ R-patched/tests/array-subset.Rout.save	2016-01-22 17:45:14.695931000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/complex.Rout.save R-patched/tests/complex.Rout.save
--- R-release-orig/tests/complex.Rout.save	2015-12-04 00:15:19.000000000 +0100
+++ R-patched/tests/complex.Rout.save	2016-01-22 17:45:14.751973000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/d-p-q-r-tests.Rout.save R-patched/tests/d-p-q-r-tests.Rout.save
--- R-release-orig/tests/d-p-q-r-tests.Rout.save	2015-12-04 00:15:20.000000000 +0100
+++ R-patched/tests/d-p-q-r-tests.Rout.save	2016-01-22 17:45:14.868204000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -1322,5 +1322,5 @@
 > 
 > 
 > cat("Time elapsed: ", proc.time() - .ptime,"\n")
-Time elapsed:  0.961 0.012 0.974 0 0 
+Time elapsed:  0.959 0.014 0.973 0 0 
 > 
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/datasets.Rout.save R-patched/tests/datasets.Rout.save
--- R-release-orig/tests/datasets.Rout.save	2015-12-04 00:15:20.000000000 +0100
+++ R-patched/tests/datasets.Rout.save	2016-01-22 17:45:14.779638000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/datetime.Rout.save R-patched/tests/datetime.Rout.save
--- R-release-orig/tests/datetime.Rout.save	2015-12-04 00:15:19.000000000 +0100
+++ R-patched/tests/datetime.Rout.save	2016-01-22 17:45:14.723983000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/datetime2.Rout.save R-patched/tests/datetime2.Rout.save
--- R-release-orig/tests/datetime2.Rout.save	2015-12-04 00:15:22.000000000 +0100
+++ R-patched/tests/datetime2.Rout.save	2016-01-22 17:45:16.424898000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/demos.Rout.save R-patched/tests/demos.Rout.save
--- R-release-orig/tests/demos.Rout.save	2015-12-04 00:15:19.000000000 +0100
+++ R-patched/tests/demos.Rout.save	2016-01-22 17:45:14.607118000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -1510,5 +1510,5 @@
 > par(op)
 > 
 > cat("Time elapsed: ", proc.time() - .ptime, "\n")
-Time elapsed:  0.986 0.022 1.01 0 0 
+Time elapsed:  1.043 0.017 1.06 0 0 
 > 
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/eval-etc.Rout.save R-patched/tests/eval-etc.Rout.save
--- R-release-orig/tests/eval-etc.Rout.save	2015-12-04 00:15:22.000000000 +0100
+++ R-patched/tests/eval-etc.Rout.save	2016-01-22 17:45:16.191484000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/iec60559.Rout.save R-patched/tests/iec60559.Rout.save
--- R-release-orig/tests/iec60559.Rout.save	2015-12-04 00:15:19.000000000 +0100
+++ R-patched/tests/iec60559.Rout.save	2016-01-22 17:45:14.664931000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/internet.Rout.save R-patched/tests/internet.Rout.save
--- R-release-orig/tests/internet.Rout.save	2015-12-10 00:15:20.000000000 +0100
+++ R-patched/tests/internet.Rout.save	2016-01-22 17:45:15.023502000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-08 r69745) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -29,7 +29,7 @@
 > 
 > # test do_download.
 > nrow(available.packages(contrib.url("http://cran.r-project.org")))
-[1] 7588
+[1] 7809
 > 
 > # test url connections on http
 > zz <- url("http://cran.r-project.org/")
@@ -44,7 +44,7 @@
  [8] "<link rel=\"stylesheet\" type=\"text/css\" href=\"R.css\">"                                               
  [9] "</head>"                                                                                                  
 [10] ""                                                                                                         
-[11] "<FRAMESET cols=\"1*, 4*\" border=0>"                                                                      
+[11] "<FRAMESET cols=\"1*, 4*\" style=\"border: none;\">"                                                       
 [12] "<FRAMESET rows=\"120, 1*\">"                                                                              
 [13] "<FRAME src=\"logo.html\" name=\"logo\" frameborder=0>"                                                    
 [14] "<FRAME src=\"navbar.html\" name=\"contents\" frameborder=0>"                                              
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/isas-tests.Rout.save R-patched/tests/isas-tests.Rout.save
--- R-release-orig/tests/isas-tests.Rout.save	2015-12-04 00:15:19.000000000 +0100
+++ R-patched/tests/isas-tests.Rout.save	2016-01-22 17:45:14.547093000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -2568,6 +2568,6 @@
 > f <- try(as.ts( x ), silent = TRUE)
 >   if(!inherits(f, 'try-error')) report(identical(f, as.ts( f )))
 > cat('Time elapsed: ', proc.time() - .proctime00,'\n')
-Time elapsed:  0.12 0.013 0.132 0 0 
+Time elapsed:  0.118 0.015 0.134 0 0 
 > 
 > 
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/lapack.Rout.save R-patched/tests/lapack.Rout.save
--- R-release-orig/tests/lapack.Rout.save	2015-12-04 00:15:18.000000000 +0100
+++ R-patched/tests/lapack.Rout.save	2016-01-22 17:45:14.485861000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/lm-tests.Rout.save R-patched/tests/lm-tests.Rout.save
--- R-release-orig/tests/lm-tests.Rout.save	2015-12-04 00:15:22.000000000 +0100
+++ R-patched/tests/lm-tests.Rout.save	2016-01-22 17:45:16.307952000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/method-dispatch.Rout.save R-patched/tests/method-dispatch.Rout.save
--- R-release-orig/tests/method-dispatch.Rout.save	2015-12-04 00:15:22.000000000 +0100
+++ R-patched/tests/method-dispatch.Rout.save	2016-01-22 17:45:16.366349000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/ok-errors.Rout.save R-patched/tests/ok-errors.Rout.save
--- R-release-orig/tests/ok-errors.Rout.save	2015-12-04 00:15:20.000000000 +0100
+++ R-patched/tests/ok-errors.Rout.save	2016-01-22 17:45:14.952112000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/p-r-random-tests.Rout.save R-patched/tests/p-r-random-tests.Rout.save
--- R-release-orig/tests/p-r-random-tests.Rout.save	2015-12-04 00:15:20.000000000 +0100
+++ R-patched/tests/p-r-random-tests.Rout.save	2016-01-22 17:45:14.838856000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -278,6 +278,6 @@
 > 
 > 
 > cat('Time elapsed: ', proc.time() - .proctime00,'\n')
-Time elapsed:  1.215 0.003 1.22 0 0 
+Time elapsed:  1.233 0.003 1.236 0 0 
 > 
 > 
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/print-tests.Rout.save R-patched/tests/print-tests.Rout.save
--- R-release-orig/tests/print-tests.Rout.save	2015-12-04 00:15:19.000000000 +0100
+++ R-patched/tests/print-tests.Rout.save	2016-01-22 17:45:14.514105000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/reg-IO.Rout.save R-patched/tests/reg-IO.Rout.save
--- R-release-orig/tests/reg-IO.Rout.save	2015-12-04 00:15:22.000000000 +0100
+++ R-patched/tests/reg-IO.Rout.save	2016-01-22 17:45:16.449348000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/reg-IO2.Rout.save R-patched/tests/reg-IO2.Rout.save
--- R-release-orig/tests/reg-IO2.Rout.save	2015-12-04 00:15:19.000000000 +0100
+++ R-patched/tests/reg-IO2.Rout.save	2016-01-22 17:45:14.575015000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/reg-S4.Rout.save R-patched/tests/reg-S4.Rout.save
--- R-release-orig/tests/reg-S4.Rout.save	2015-12-04 00:15:22.000000000 +0100
+++ R-patched/tests/reg-S4.Rout.save	2016-01-22 17:45:16.276225000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/reg-examples3.Rout.save R-patched/tests/reg-examples3.Rout.save
--- R-release-orig/tests/reg-examples3.Rout.save	2015-12-04 00:15:22.000000000 +0100
+++ R-patched/tests/reg-examples3.Rout.save	2016-01-22 17:45:16.339094000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/reg-plot.Rout.save R-patched/tests/reg-plot.Rout.save
--- R-release-orig/tests/reg-plot.Rout.save	2015-12-04 00:15:22.000000000 +0100
+++ R-patched/tests/reg-plot.Rout.save	2016-01-22 17:45:16.133876000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/reg-tests-1c.R R-patched/tests/reg-tests-1c.R
--- R-release-orig/tests/reg-tests-1c.R	2015-04-22 00:15:10.000000000 +0200
+++ R-patched/tests/reg-tests-1c.R	2016-01-13 02:41:20.170252000 +0100
@@ -722,5 +722,15 @@
 	  is.na(as.integer(as.character(-100*MI))))
 ## The two cases with positive numbers  failed in R <= 3.2.0
 
+`$.foo` <- function(x, fun) paste("foo: ", NextMethod())
+x <- list(a = 1, b = 2)
+class(x) <- "foo"
+x$b  # failed prior to R 3.3.0
+
+`$<-.foo` <- function(x, value, fun) {
+    attr(x, "modified") <- "yes"
+    NextMethod()
+}
+x$y <- 10  # failed prior to R 3.3.0
 
 proc.time()
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/reg-tests-2.Rout.save R-patched/tests/reg-tests-2.Rout.save
--- R-release-orig/tests/reg-tests-2.Rout.save	2015-12-04 00:15:20.000000000 +0100
+++ R-patched/tests/reg-tests-2.Rout.save	2016-01-22 17:45:14.809303000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -6405,15 +6405,15 @@
 > print.function
 function (x, ...)  
  - attr(*, "srcref")=Class 'srcref'  atomic [1:8] 1 19 1 63 19 63 1 1
-  .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x41b05e8> 
+  .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x2963018> 
 > f
 function ()  
  - attr(*, "srcref")=Class 'srcref'  atomic [1:8] 1 17 1 28 17 28 1 1
-  .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x41bf660> 
+  .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x297cfa8> 
  - attr(*, "note")= chr "just a note"
  - attr(*, "yada")=function ()  
   ..- attr(*, "srcref")=Class 'srcref'  atomic [1:8] 2 24 2 48 24 48 2 2
-  .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x41bf660> 
+  .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x297cfa8> 
 > rm(print.function)
 > ## auto-printing and printing differed up to R 2.9.x
 > 
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/reg-tests-3.Rout.save R-patched/tests/reg-tests-3.Rout.save
--- R-release-orig/tests/reg-tests-3.Rout.save	2015-12-04 00:15:22.000000000 +0100
+++ R-patched/tests/reg-tests-3.Rout.save	2016-01-22 17:45:16.396830000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tests/simple-true.Rout.save R-patched/tests/simple-true.Rout.save
--- R-release-orig/tests/simple-true.Rout.save	2015-12-04 00:15:20.000000000 +0100
+++ R-patched/tests/simple-true.Rout.save	2016-01-22 17:45:14.925715000 +0100
@@ -1,6 +1,6 @@
 
-R version 3.2.3 RC (2015-12-02 r69719) -- "Wooden Christmas-Tree"
-Copyright (C) 2015 The R Foundation for Statistical Computing
+R version 3.2.3 Patched (2016-01-22 r69982) -- "Wooden Christmas-Tree"
+Copyright (C) 2016 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tools/GETCONFIG R-patched/tools/GETCONFIG
--- R-release-orig/tools/GETCONFIG	2015-07-22 00:15:06.000000000 +0200
+++ R-patched/tools/GETCONFIG	2016-01-03 17:45:11.185703000 +0100
@@ -24,6 +24,7 @@
 echo "${line}"
 line=`grep "HAVE_AQUA" config.h`
 echo "${line}"
+echo "/* Deprecated: use _OPENMP instead */"
 line=`grep "SUPPORT_OPENMP" config.h`
 echo "${line}"
 line=`grep "SIZEOF_SIZE_T" config.h`
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tools/config.guess R-patched/tools/config.guess
--- R-release-orig/tools/config.guess	2015-07-26 00:15:03.000000000 +0200
+++ R-patched/tools/config.guess	2016-01-08 02:41:06.923108000 +0100
@@ -1,8 +1,8 @@
 #! /bin/sh
 # Attempt to guess a canonical system name.
-#   Copyright 1992-2015 Free Software Foundation, Inc.
+#   Copyright 1992-2016 Free Software Foundation, Inc.
 
-timestamp='2015-07-03'
+timestamp='2016-01-01'
 
 # This file is free software; you can redistribute it and/or modify it
 # under the terms of the GNU General Public License as published by
@@ -27,7 +27,7 @@
 # Originally written by Per Bothner; maintained since 2000 by Ben Elliston.
 #
 # You can get the latest version of this script from:
-# http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD
+# http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess
 #
 # Please send patches to <config-patches@gnu.org>.
 
@@ -50,7 +50,7 @@
 GNU config.guess ($timestamp)
 
 Originally written by Per Bothner.
-Copyright 1992-2015 Free Software Foundation, Inc.
+Copyright 1992-2016 Free Software Foundation, Inc.
 
 This is free software; see the source for copying conditions.  There is NO
 warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
@@ -249,6 +249,9 @@
     *:MirBSD:*:*)
 	echo ${UNAME_MACHINE}-unknown-mirbsd${UNAME_RELEASE}
 	exit ;;
+    *:Sortix:*:*)
+	echo ${UNAME_MACHINE}-unknown-sortix
+	exit ;;
     alpha:OSF1:*:*)
 	case $UNAME_RELEASE in
 	*4.0)
@@ -962,6 +965,9 @@
     ia64:Linux:*:*)
 	echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
 	exit ;;
+    k1om:Linux:*:*)
+	echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
+	exit ;;
     m32r*:Linux:*:*)
 	echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
 	exit ;;
@@ -1117,7 +1123,7 @@
 	# uname -m prints for DJGPP always 'pc', but it prints nothing about
 	# the processor, so we play safe by assuming i586.
 	# Note: whatever this is, it MUST be the same as what config.sub
-	# prints for the "djgpp" host, or else GDB configury will decide that
+	# prints for the "djgpp" host, or else GDB configure will decide that
 	# this is a cross-build.
 	echo i586-pc-msdosdjgpp
 	exit ;;
@@ -1387,6 +1393,9 @@
     x86_64:VMkernel:*:*)
 	echo ${UNAME_MACHINE}-unknown-esx
 	exit ;;
+    amd64:Isilon\ OneFS:*:*)
+	echo x86_64-unknown-onefs
+	exit ;;
 esac
 
 cat >&2 <<EOF
@@ -1396,9 +1405,9 @@
 the operating system you are using. It is advised that you
 download the most up to date version of the config scripts from
 
-  http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD
+  http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess
 and
-  http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD
+  http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub
 
 If the version you run ($0) is already up to date, please
 send the following data and any information you think might be
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/tools/config.sub R-patched/tools/config.sub
--- R-release-orig/tools/config.sub	2015-07-26 00:15:04.000000000 +0200
+++ R-patched/tools/config.sub	2016-01-08 02:41:06.952729000 +0100
@@ -1,8 +1,8 @@
 #! /bin/sh
 # Configuration validation subroutine script.
-#   Copyright 1992-2015 Free Software Foundation, Inc.
+#   Copyright 1992-2016 Free Software Foundation, Inc.
 
-timestamp='2015-07-24'
+timestamp='2016-01-01'
 
 # This file is free software; you can redistribute it and/or modify it
 # under the terms of the GNU General Public License as published by
@@ -33,7 +33,7 @@
 # Otherwise, we print the canonical config type on stdout and succeed.
 
 # You can get the latest version of this script from:
-# http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD
+# http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub
 
 # This file is supposed to be the same for all GNU packages
 # and recognize all the CPU types, system types and aliases
@@ -53,8 +53,7 @@
 me=`echo "$0" | sed -e 's,.*/,,'`
 
 usage="\
-Usage: $0 [OPTION] CPU-MFR-OPSYS
-       $0 [OPTION] ALIAS
+Usage: $0 [OPTION] CPU-MFR-OPSYS or ALIAS
 
 Canonicalize a configuration name.
 
@@ -68,7 +67,7 @@
 version="\
 GNU config.sub ($timestamp)
 
-Copyright 1992-2015 Free Software Foundation, Inc.
+Copyright 1992-2016 Free Software Foundation, Inc.
 
 This is free software; see the source for copying conditions.  There is NO
 warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
@@ -306,7 +305,7 @@
 	| riscv32 | riscv64 \
 	| rl78 | rx \
 	| score \
-	| sh | sh[1234] | sh[24]a | sh[24]aeb | sh[23]e | sh[34]eb | sheb | shbe | shle | sh[1234]le | sh3ele \
+	| sh | sh[1234] | sh[24]a | sh[24]aeb | sh[23]e | sh[234]eb | sheb | shbe | shle | sh[1234]le | sh3ele \
 	| sh64 | sh64le \
 	| sparc | sparc64 | sparc64b | sparc64v | sparc86x | sparclet | sparclite \
 	| sparcv8 | sparcv9 | sparcv9b | sparcv9v \
@@ -430,6 +429,7 @@
 	| pdp10-* | pdp11-* | pj-* | pjl-* | pn-* | power-* \
 	| powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* \
 	| pyramid-* \
+	| riscv32-* | riscv64-* \
 	| rl78-* | romp-* | rs6000-* | rx-* \
 	| sh-* | sh[1234]-* | sh[24]a-* | sh[24]aeb-* | sh[23]e-* | sh[34]eb-* | sheb-* | shbe-* \
 	| shle-* | sh[1234]le-* | sh3ele-* | sh64-* | sh64le-* \
@@ -520,7 +520,7 @@
 		basic_machine=i386-pc
 		os=-aros
 		;;
-        asmjs)
+	asmjs)
 		basic_machine=asmjs-unknown
 		;;
 	aux)
@@ -1378,7 +1378,7 @@
 	      | -hpux* | -unos* | -osf* | -luna* | -dgux* | -auroraux* | -solaris* \
 	      | -sym* | -kopensolaris* | -plan9* \
 	      | -amigaos* | -amigados* | -msdos* | -newsos* | -unicos* | -aof* \
-	      | -aos* | -aros* | -cloudabi* \
+	      | -aos* | -aros* | -cloudabi* | -sortix* \
 	      | -nindy* | -vxsim* | -vxworks* | -ebmon* | -hms* | -mvs* \
 	      | -clix* | -riscos* | -uniplus* | -iris* | -rtu* | -xenix* \
 	      | -hiux* | -386bsd* | -knetbsd* | -mirbsd* | -netbsd* \
@@ -1398,7 +1398,8 @@
 	      | -os2* | -vos* | -palmos* | -uclinux* | -nucleus* \
 	      | -morphos* | -superux* | -rtmk* | -rtmk-nova* | -windiss* \
 	      | -powermax* | -dnix* | -nx6 | -nx7 | -sei* | -dragonfly* \
-	      | -skyos* | -haiku* | -rdos* | -toppers* | -drops* | -es* | -tirtos*)
+	      | -skyos* | -haiku* | -rdos* | -toppers* | -drops* | -es* \
+	      | -onefs* | -tirtos*)
 	# Remember, each alternative MUST END IN *, to match a version number.
 		;;
 	-qnx*)

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File R-release.diff of Package R (Revision d613382281cea75d1e66081faa7a36db)

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