Update to 3.2.1

Upstream changes:
CHANGES IN R 3.2.1
NEW FEATURES

    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 it can infer the type of file.

    nchar(x, *) and nzchar(x) gain a new argument keepNA which governs how the result for NAs in x is determined. For the R 3.2.x series, the default remains FALSE which is fully back compatible. From R 3.3.0, the 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.

    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 release.

    diag() no longer duplicates a matrix when extracting its diagonal.

    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 of sometimes very slightly outside). PR#15832.

    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 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 containing "X" and "Y" (as in R < 3.2.0).

    (Windows only) In some cases, the --clean option to R CMD INSTALL could fail. (PR#16178)

    (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 URLs. (PR#16329)

    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)

    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 scientific format with extremely large exponents. (PR#16358)

    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 of their argument, so could segfault. (PR#16367)

    The quietly argument of library() is now correctly propagated from .getRequiredPackages2().

    Under some circumstances using the internal PCRE when building R fron 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., !, & 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 integer and begins with an NA.

    summaryRprof() could fail when the profile contained only two records. (PR#16395)

    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 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 internally in methods).

    On some systems, the first string comparison after a locale change would result in NA.

4 files changed, 12 insertions, 29 deletions

diff --git a/math/R/Makefile b/math/R/Makefile
index b806f6aabfc..27cbc23153e 100644
--- a/math/R/Makefile
+++ b/math/R/Makefile
@@ -1,7 +1,6 @@
-# $NetBSD: Makefile,v 1.159 2015/06/29 21:35:04 markd Exp $
+# $NetBSD: Makefile,v 1.160 2015/06/30 02:38:52 wen Exp $
 
-DISTNAME=		R-3.2.0
-PKGREVISION=		3
+DISTNAME=		R-3.2.1
 CATEGORIES=		math
 MASTER_SITES=		${MASTER_SITE_R_CRAN:=base/R-3/}
 
diff --git a/math/R/distinfo b/math/R/distinfo
index c7c8469de25..9fe0b8c8a45 100644
--- a/math/R/distinfo
+++ b/math/R/distinfo
@@ -1,11 +1,10 @@
-$NetBSD: distinfo,v 1.66 2015/06/29 21:35:04 markd Exp $
+$NetBSD: distinfo,v 1.67 2015/06/30 02:38:52 wen Exp $
 
-SHA1 (R-3.2.0.tar.gz) = a6e9a6ca5ef186037a2f8ad2ccc8d7d0147640f1
-RMD160 (R-3.2.0.tar.gz) = a67e255e77baf7db164ee8a869c03137a33a6571
-Size (R-3.2.0.tar.gz) = 29124927 bytes
+SHA1 (R-3.2.1.tar.gz) = 74476c4d356f227bf0f17c8c21e63459861fbc93
+RMD160 (R-3.2.1.tar.gz) = dea095b5c7b32189b6768d5949243bd869564e9f
+Size (R-3.2.1.tar.gz) = 29197870 bytes
 SHA1 (patch-ac) = 1722685e650c651467be8f67c37a5766aefad7af
 SHA1 (patch-ad) = 0a08f293bc1cdc130047868e5d574c2df1f4c6cf
 SHA1 (patch-src_include_GraphicsBase.h) = 5f999e4d124afd38d5c7e18d936942f2c6f27c86
-SHA1 (patch-src_include_Rinterface.h) = 71bcc402eee01eef9d35cb8ba9c186ffed437e85
 SHA1 (patch-src_library_stats_src_Makefile.in) = b468becd011fa4828e50f5d13d700825655c89e8
-SHA1 (patch-src_main_character.c) = 29d302b4530bdc3b49afff6b10f94277e1a94b43
+SHA1 (patch-src_main_character.c) = bd6e9b5b633d86c913c98d9d87c66f982d1ca258
diff --git a/math/R/patches/patch-src_include_Rinterface.h b/math/R/patches/patch-src_include_Rinterface.h
deleted file mode 100644
index 90ade208ced..00000000000
--- a/math/R/patches/patch-src_include_Rinterface.h
+++ /dev/null
@@ -1,15 +0,0 @@
-$NetBSD: patch-src_include_Rinterface.h,v 1.1 2015/06/29 21:35:04 markd Exp $
-
-Fix symbol visibility.
-
---- src/include/Rinterface.h.orig	2015-03-18 23:02:16.000000000 +0000
-+++ src/include/Rinterface.h
-@@ -90,7 +90,7 @@ void R_setStartTime(void);
- void fpu_setup(Rboolean);
- 
- /* in unix/system.c */
--int R_running_as_main_program; 
-+extern int R_running_as_main_program; 
- 
- #ifdef CSTACK_DEFNS
- /* duplicating Defn.h */
diff --git a/math/R/patches/patch-src_main_character.c b/math/R/patches/patch-src_main_character.c
index e485cceb29d..5dbc454650c 100644
--- a/math/R/patches/patch-src_main_character.c
+++ b/math/R/patches/patch-src_main_character.c
@@ -1,8 +1,8 @@
-$NetBSD: patch-src_main_character.c,v 1.1 2015/01/23 15:06:44 joerg Exp $
+$NetBSD: patch-src_main_character.c,v 1.2 2015/06/30 02:38:52 wen Exp $
 
---- src/main/character.c.orig	2015-01-22 19:20:05.000000000 +0000
+--- src/main/character.c.orig	2015-06-29 21:44:13.000000000 +0000
 +++ src/main/character.c
-@@ -1311,7 +1311,7 @@ SEXP attribute_hidden do_strtrim(SEXP ca
+@@ -1360,7 +1360,7 @@ SEXP attribute_hidden do_strtrim(SEXP ca
      return s;
  }
  
@@ -11,12 +11,12 @@ $NetBSD: patch-src_main_character.c,v 1.1 2015/01/23 15:06:44 joerg Exp $
  {
      long int res;
      char *endp;
-@@ -1345,7 +1345,7 @@ SEXP attribute_hidden do_strtoi(SEXP cal
+@@ -1394,7 +1394,7 @@ SEXP attribute_hidden do_strtoi(SEXP cal
  
      PROTECT(ans = allocVector(INTSXP, n = LENGTH(x)));
      for(i = 0; i < n; i++)
 -	INTEGER(ans)[i] = strtoi(STRING_ELT(x, i), base);
 +	INTEGER(ans)[i] = my_strtoi(STRING_ELT(x, i), base);
      UNPROTECT(1);
-     
+ 
      return ans;