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File R-release.diff of Package R (Revision 6af2b02b206065bc02d911f0a9e3238c)

Currently displaying revision 6af2b02b206065bc02d911f0a9e3238c , Show latest

# cd *inside* the .....//  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/SVN-REVISION R-patched/SVN-REVISION
--- R-release-orig/SVN-REVISION	2024-06-14 09:02:21.000000000 +0200
+++ R-patched/SVN-REVISION	2024-08-26 01:32:24.907583689 +0200
@@ -1,2 +1,2 @@
-Revision: 86737
-Last Changed Date: 2024-06-14
+Revision: 87049
+Last Changed Date: 2024-08-21
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/VERSION R-patched/VERSION
--- R-release-orig/VERSION	2024-06-14 09:00:02.000000000 +0200
+++ R-patched/VERSION	2024-07-16 11:38:48.028714071 +0200
@@ -1 +1 @@
-4.4.1
+4.4.1 Patched
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/doc/NEWS R-patched/doc/NEWS
--- R-release-orig/doc/NEWS	2024-06-14 09:05:24.000000000 +0200
+++ R-patched/doc/NEWS	2024-08-26 01:35:04.747707364 +0200
@@ -1,5 +1,21 @@
 R News
 
+CHANGES IN R 4.4.1 patched:
+
+  BUG FIXES:
+
+    * Mathlib function lgammacor(x) no longer warns about underflow to
+      zero for large x.
+
+    * Text widths and heights were incorrectly reported by the Quartz
+      device if the drawing context didn't exist yet (typically when
+      drawing off-screen to a window that is yet to appear, see
+      PR#18591).
+
+    * The Quartz device could segfault in cases where paths with spaces
+      are used in the new glyph drawing API.  Thanks to Tomek
+      Gieorgijewski (PR#18758).
+
 CHANGES IN R 4.4.1:
 
   C-LEVEL FACILITIES:
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	2024-06-04 00:04:01.000000000 +0200
+++ R-patched/doc/NEWS.Rd	2024-08-05 17:45:08.139156246 +0200
@@ -5,6 +5,24 @@
 \title{R News}
 \encoding{UTF-8}
 
+\section{\Rlogo CHANGES IN R 4.4.1 patched}{
+  \subsection{BUG FIXES}{
+    \itemize{
+      \item \I{Mathlib} function \code{lgammacor(x)} no longer warns about
+      underflow to zero for large \code{x}.
+
+      \item Text widths and heights were incorrectly reported by the
+      Quartz device if the drawing context didn't exist yet (typically
+      when drawing off-screen to a window that is yet to appear, see
+      \PR{18591}).
+
+      \item The Quartz device could segfault in cases where paths with
+      spaces are used in the new glyph drawing API.
+      Thanks to \I{Tomek Gieorgijewski} (\PR{18758}).
+    }
+  }
+}
+
 \section{\Rlogo CHANGES IN R 4.4.1}{
   \subsection{C-LEVEL FACILITIES}{
     \itemize{
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/RESOURCES R-patched/doc/RESOURCES
--- R-release-orig/doc/RESOURCES	2024-06-14 09:02:21.000000000 +0200
+++ R-patched/doc/RESOURCES	2024-08-26 01:32:25.123752656 +0200
@@ -9,9 +9,9 @@
 
      <https://CRAN.R-project.org/doc/FAQ/R-FAQ.html>
 
-A text version is in file 'FAQ' in this directory, and an HTML version is
-available as file 'doc/html/faq.html' and via the on-line help (on the index
-page given by 'help.start()').
+A text version is in file ‘FAQ’ in this directory, and an HTML version is
+available as file ‘doc/html/faq.html’ and via the on-line help (on the index
+page given by ‘help.start()’).
 
 2 Mailing lists
 ***************
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	2024-06-14 09:05:24.000000000 +0200
+++ R-patched/doc/html/NEWS.html	2024-08-26 01:35:06.173349216 +0200
@@ -18,6 +18,33 @@
 
 <h2>R News</h2>
 
+<h3><img src="../help/figures/../../html/Rlogo.svg" class="toplogo" alt="[R logo]" /> CHANGES IN R 4.4.1 patched</h3>
+
+
+
+<h4>BUG FIXES</h4>
+
+
+<ul>
+<li> <p>Mathlib function <code>lgammacor(x)</code> no longer warns about
+underflow to zero for large <code>x</code>.
+</p>
+</li>
+<li><p> Text widths and heights were incorrectly reported by the
+Quartz device if the drawing context didn't exist yet (typically
+when drawing off-screen to a window that is yet to appear, see
+<a href="https://bugs.R-project.org/show_bug.cgi?id=18591">PR#18591</a>).
+</p>
+</li>
+<li><p> The Quartz device could segfault in cases where paths with
+spaces are used in the new glyph drawing API.
+Thanks to Tomek Gieorgijewski (<a href="https://bugs.R-project.org/show_bug.cgi?id=18758">PR#18758</a>).
+</p>
+</li></ul>
+
+
+
+
 <h3><img src="../help/figures/../../html/Rlogo.svg" class="toplogo" alt="[R logo]" /> CHANGES IN R 4.4.1</h3>
 
 
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	2024-06-14 09:08:02.000000000 +0200
+++ R-patched/doc/html/R-admin.html	2024-08-26 01:42:11.251696808 +0200
@@ -1,11 +1,11 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!DOCTYPE html>
 <html>
-
+
 <head>
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
-
+
 <head>
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <title>R Resources</title>
@@ -18,21 +18,6 @@
 <link href="dir.html#Top" rel="prev" title="(dir)">
 <style type="text/css">
 <!--
-a.copiable-anchor {visibility: hidden; text-decoration: none; line-height: 0em}
-a.summary-letter {text-decoration: none}
-blockquote.indentedblock {margin-right: 0em}
-div.display {margin-left: 3.2em}
-div.example {margin-left: 3.2em}
-kbd {font-style: oblique}
-pre.display {font-family: inherit}
-pre.format {font-family: inherit}
-pre.menu-comment {font-family: serif}
-pre.menu-preformatted {font-family: serif}
-span.nolinebreak {white-space: nowrap}
-span.roman {font-family: initial; font-weight: normal}
-span.sansserif {font-family: sans-serif; font-weight: normal}
-span:hover a.copiable-anchor {visibility: visible}
-ul.no-bullet {list-style: none}
 @media screen {
     .container {
 	padding-right: 10px;
@@ -171,7 +156,6 @@
 </head>
 
 <body lang="en">
-<h1 class="settitle" align="center">R Resources</h1>
 
 
 
@@ -181,62 +165,62 @@
 </h1>
 <hr>
 
-<span id="Top"></span><h1 class="node-heading">Top</h1>
+<h1 class="node" id="Top">Top</h1>
 
 
 <hr>
-<div class="chapter" id="FAQ">
-<span id="FAQ-1"></span><h3 class="section">1 FAQ</h3>
+<div class="section-level-extent" id="FAQ">
+<h3 class="section chapter-level-set-section" id="FAQ-1">1 FAQ</h3>
 
-<p>A collection of <a href="faq.html">Frequently Asked Questions</a> and their
-answers is maintained by <a href="mailto:Kurt.Hornik@R-project.org">Kurt Hornik</a>
-and can be found at the <acronym>URL</acronym>
+<p>A collection of <a class="uref" href="faq.html">Frequently Asked Questions</a> and their
+answers is maintained by <a class="email" href="mailto:Kurt.Hornik@R-project.org">Kurt Hornik</a>
+and can be found at the <abbr class="acronym">URL</abbr>
 </p>
-<blockquote>
-<p><a href="https://CRAN.R-project.org/doc/FAQ/R-FAQ.html">https://CRAN.R-project.org/doc/FAQ/R-FAQ.html</a>
+<blockquote class="quotation">
+<p><a class="uref" href="https://CRAN.R-project.org/doc/FAQ/R-FAQ.html">https://CRAN.R-project.org/doc/FAQ/R-FAQ.html</a>
 </p></blockquote>
 
 
 <hr>
 </div>
-<div class="chapter" id="Mailing-lists">
-<span id="Mailing-lists-1"></span><h3 class="section">2 Mailing lists</h3>
+<div class="section-level-extent" id="Mailing-lists">
+<h3 class="section chapter-level-set-section" id="Mailing-lists-1">2 Mailing lists</h3>
 
-<p>Thanks to <a href="mailto:Martin.Maechler@R-project.org">Martin Maechler</a> there
+<p>Thanks to <a class="email" href="mailto:Martin.Maechler@R-project.org">Martin Maechler</a> there
 are a number of mailing lists which are used by R users and developers.
 See
 </p>
-<blockquote>
-<p><a href="https://www.R-project.org/mail.html">https://www.R-project.org/mail.html</a>
+<blockquote class="quotation">
+<p><a class="uref" href="https://www.R-project.org/mail.html">https://www.R-project.org/mail.html</a>
 </p></blockquote>
 
 <p>for details.
 </p>
 <hr>
 </div>
-<div class="chapter" id="Archives">
-<span id="Archives-1"></span><h3 class="section">3 Archives</h3>
+<div class="section-level-extent" id="Archives">
+<h3 class="section chapter-level-set-section" id="Archives-1">3 Archives</h3>
 
-<p>The Comprehensive R Archive Network (<acronym>CRAN</acronym>) is a collection of
+<p>The Comprehensive R Archive Network (<abbr class="acronym">CRAN</abbr>) is a collection of
 sites which carry identical material, consisting of the R
 distribution(s), the contributed extensions, documentation for R, and
-binaries, with the master site at <a href="https://CRAN.R-project.org/">https://CRAN.R-project.org/</a> and
+binaries, with the master site at <a class="uref" href="https://CRAN.R-project.org/">https://CRAN.R-project.org/</a> and
 information on daily mirrors available from
 </p>
-<blockquote>
-<p><a href="https://CRAN.R-project.org/mirrors.html">https://CRAN.R-project.org/mirrors.html</a>
+<blockquote class="quotation">
+<p><a class="uref" href="https://CRAN.R-project.org/mirrors.html">https://CRAN.R-project.org/mirrors.html</a>
 </p></blockquote>
 
 <hr>
 </div>
-<div class="chapter" id="Bug_002dtracking-system">
-<span id="Bug_002dtracking-system-1"></span><h3 class="section">4 Bug-tracking system</h3>
+<div class="section-level-extent" id="Bug_002dtracking-system">
+<h3 class="section chapter-level-set-section" id="Bug_002dtracking-system-1">4 Bug-tracking system</h3>
 
 <p>R has a bug-tracking system (or perhaps a bug-filing system is a more
 precise description) available on the net at
 </p>
-<blockquote>
-<p><a href="https://bugs.R-project.org/">https://bugs.R-project.org/</a>
+<blockquote class="quotation">
+<p><a class="uref" href="https://bugs.R-project.org/">https://bugs.R-project.org/</a>
 </p></blockquote>
 
 </div>
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/doc/manual/R-admin.texi R-patched/doc/manual/R-admin.texi
--- R-release-orig/doc/manual/R-admin.texi	2024-06-02 00:15:00.000000000 +0200
+++ R-patched/doc/manual/R-admin.texi	2024-08-21 17:45:08.424230723 +0200
@@ -5006,15 +5006,14 @@
 define @code{__INTEL_COMPILER}: they also define @code{__clang__} and
 @code{__clang_major__}).
 
-The C++ compiler uses the system's @code{lidstdc++} as its runtime
+The C++ compiler uses the system's @code{libstdc++} as its runtime
 library rather than @I{LLVM}'s @code{libc++}.
 
 Standalone installers (which are free-of-charge) are available from
 @uref{https://www.intel.com/content/www/us/en/developer/articles/tool/oneapi-standalone-components.html}:
 they are also part of the @I{oneAPI} Base and HPC (for Fortran) toolkits.
 
-We tried the compilers in @I{oneAPI} 2024.1.x@footnote{2024.1.2 for
-C/C++, 2024.1.0 for Fortran.} and 2023.x.y using (the paths
+We tried the compilers in @I{oneAPI} 2024.2.1 and 2023.x.y using (the paths
 do differ by compiler version)
 @example
 IP=/path/to/compilers/bin/
@@ -5066,7 +5065,7 @@
 @abbr{LTO}: it is not clear if the Fortran one does.
 
 @c https://community.intel.com/t5/Intel-C-Compiler/Troubles-with-getrusage-when-using-icx/m-p/1509374#M41116
-For some recent versions (including 2023.2.0) all CPU times in e.g.@:
+For some earlier versions (including 2023.2.0) all CPU times in e.g.@:
 @code{proc.time()} are reported as zero.  If you see this, uncomment the
 @samp{INTEL_ICX_FIX} setting in @file{config.site} and re-build.
 
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/doc/manual/R-exts.texi R-patched/doc/manual/R-exts.texi
--- R-release-orig/doc/manual/R-exts.texi	2024-06-05 00:15:01.000000000 +0200
+++ R-patched/doc/manual/R-exts.texi	2024-08-21 17:45:08.458708254 +0200
@@ -2942,6 +2942,11 @@
 @end example
 
 @noindent
+Some maintainers have found it difficult to find @emph{all} the module
+dependencies which leads to hard-to-reproduce installation failures.
+There are tools available to find these, including the Intel compiler's
+flag @option{-gen-dep} and @code{makedepf90}.
+
 Note that it is not portable (although some platforms do accept it) to
 define a module of the same name in multiple source files.
 @c As was done by frailtypack in 2018-12: gfortran accepted this, ODS
@@ -3129,9 +3134,9 @@
 it will not apply to packages using @file{src/Makefile} or building in a
 subdirectory that do not set the C++ standard.  And compilers' default
 C++ standards varies widely and gets changed frequently by vendors --
-for example Apple clang up to at least 15 defaults to C++98, @I{LLVM}
+for example Apple clang up to at least 16 defaults to C++98, @I{LLVM}
 clang 14--15 to C++14, @I{LLVM} clang 16--18 to C++17 and @command{g++}
-11--13 to C++17.
+11--14 to C++17.
 
 For a package with a @file{src/Makefile} (or a Windows analogue),
 a non-default C++ compiler can be selected by including something like
@@ -3193,7 +3198,7 @@
 @subsection C standards
 
 C has had standards C89/C90, C99, C11, C17 (also known as C18), and C23
-is in final draft and expected to be published in early 2024.  C11 was a
+is in final draft and expected to be published in 2024.  C11 was a
 minor change to C99 which introduced some new features and made others
 optional, and C17 is a `bug-fix' update to C11.  On the other hand, C23
 makes extensive changes, including making @code{bool}, @code{true} and
@@ -4969,7 +4974,9 @@
 and ensure that you use the value of environment variable @env{MAKE}
 (and not just @command{make}) in your scripts.  (On some platforms GNU
 make is available under a name such as @command{gmake}, and there
-@code{SystemRequirements} is used to set @env{MAKE}.)
+@code{SystemRequirements} is used to set @env{MAKE}.)  Your
+@code{configure} script (or similar) does need to check that the
+executable pointed to by @env{MAKE} is indeed GNU make.
 
 If you only need GNU make for parts of the package which are rarely
 needed (for example to create bibliography files under
@@ -6148,14 +6155,18 @@
 @item
 In C++ code
 @example
-using namesapace std; 
+using namespace std; 
 @end example
 @noindent
 is not good practice, and has caused platform-dependent errors if
 included before headers, especially system headers (which may be
 included by other headers). The best practice is to use explicit
 @code{std::} prefixes for all functions declared by the C++ standard to
-be in that namespace.
+be in that namespace.  It is an error to use @code{using namespace
+std} before including any C++ headers, and some recent compilers will
+warn if this is done.
+@c LLVM and Apple clang and Intel icpx do.
+
 
 @item
 @c including @I{LLVM} clang as from 4.0.0
@@ -6312,6 +6323,15 @@
 use C code (which can normally be mixed with C++ code in a package).
 
 @item
+Include only what is essential in @code{extern "C" @{@}} blocks in C++
+code.  In particular it is not portable to include @R{} headers in such
+blocks (although they are themselves C code, they may include C++ system
+headers and the public ones already enclose their declarations in such a
+block).  And maintainers have include @R{} headers from other headers
+included in such a block.
+@c obscure compilation failures seen with clang++/libc++
+
+@item
 @code{reinterpret_cast} in C++ is not safe for pointers: for example the types
 may have different alignment requirements.  Use @code{memcpy} to copy
 the contents to a fresh variable of the destination type.
@@ -12721,7 +12741,7 @@
 
 What happens if the @code{SEXP} is not of the correct type?  Sometimes
 you have no other option except to generate an error.  You can use the
-function @code{error} for this.  It is usually better to coerce the
+function @code{Rf_error} for this.  It is usually better to coerce the
 object to the correct type.  For example, if you find that an
 @code{SEXP} is of the type @code{INTEGER}, but you need a @code{REAL}
 object, you can change the type by using
@@ -14543,7 +14563,9 @@
 should be regarded as undocumented and unstable.
 
 Most of these header files, including all those included by @file{R.h},
-can be used from C++ code.
+can be used from C++ code.  (However, they cannot safely be included in
+a @code{extern "C" @{ @}} block as they may include C++ headers when
+included from C++ code---and whether this succeeds is system-specific).
 
 @quotation Note
 Because @R{} re-maps many of its external names to avoid clashes with
@@ -14789,8 +14811,9 @@
 giving the error message. (Don't do this if the string contains @samp{%}
 or might otherwise be interpreted as a format.)
 
-These are defined in header @file{R_ext/Error.h} included by
-@file{R.h}.
+These are defined in header @file{R_ext/Error.h} included by @file{R.h}.
+@strong{NB}: when @code{R_NO_REMAP} is defined (as is recommeneded for
+C++ code), @code{Rf_error} etc must be used.
 
 @menu
 * Error signaling from Fortran::
@@ -14800,8 +14823,8 @@
 @subsection Error signaling from Fortran
 @cindex Error signaling from Fortran
 
-There are two interface function provided to call @code{error} and
-@code{warning} from Fortran code, in each case with a simple character
+There are two interface function provided to call @code{Rf_error} and
+@code{Rf_warning} from Fortran code, in each case with a simple character
 string argument.  They are defined as
 
 @example
@@ -14920,7 +14943,7 @@
           subroutine putRNGseed() bind(C, name = "PutRNGstate")
           end subroutine putRNGseed
         end interface
-      end module
+      end module rngfuncs
       
       subroutine testit
       use rngfuncs
@@ -14929,7 +14952,7 @@
       X = unifRand()
       print *, X
       call putRNGSeed()
-      end
+      end subroutine testit
 @end example
 
 
@@ -15748,15 +15771,15 @@
 @end deftypefun
 
 @deftypefun double fprec (double @var{x}, double @var{digits})
-Returns the value of @var{x} rounded to @var{digits} decimal digits
-(after the decimal point).
+Returns the value of @var{x} rounded to @var{digits} @emph{significant}
+decimal digits.
 
 This is the function used by @R{}'s @code{signif()}.
 @end deftypefun
 
 @deftypefun double fround (double @var{x}, double @var{digits})
-Returns the value of @var{x} rounded to @var{digits} @emph{significant}
-decimal digits.
+Returns the value of @var{x} rounded to @var{digits} decimal digits
+(after the decimal point).
 
 This is the function used by @R{}'s @code{round()}.  (Note that C99/C++11
 provide a @code{round} function but C++98 need not.)
@@ -15811,11 +15834,11 @@
 @end multitable
 @end quotation
 
-There are a set of constants (@code{PI}, @code{DOUBLE_EPS}) (and so on)
-defined (unless @code{STRICT_R_HEADERS} is defined) in the included
-header @file{R_ext/Constants.h}, mainly for compatibility with @Sl{}.
-All but @code{PI} are deprecated and should be replaced by the C99/C++11
-versions used in that file.
+For compatibility with @Sl{} this file defines the constant @code{PI}
+(unless @code{STRICT_R_HEADERS} is defined): this is deprecated and
+should be replaced by @code{M_PI}. @file{Constants.h} includes either C
+header @file{float.h} or C++ header @file{cfloat}, which provide
+constants such as @code{DBL_MAX}.
 
 @findex TRUE
 @findex FALSE
@@ -16235,7 +16258,7 @@
 mechanism so are subject to some overhead.
 
 @code{R_withCallingErrorHandler} establishes a calling handler for
-conditions inheriting form class @code{error}.  It establishes the
+conditions inheriting from class @code{error}.  It establishes the
 handler without calling back into @R{} and will therefore be more
 efficient.
 
Binary files R-release-orig/src/library/Recommended/MASS.tgz and R-patched/src/library/Recommended/MASS.tgz differ
Only in R-release-orig/src/library/Recommended: MASS_7.3-60.2.tar.gz
Binary files R-release-orig/src/library/Recommended/MASS_7.3-61.tar.gz and R-patched/src/library/Recommended/MASS_7.3-61.tar.gz differ
Binary files R-release-orig/src/library/Recommended/foreign.tgz and R-patched/src/library/Recommended/foreign.tgz differ
Only in R-release-orig/src/library/Recommended: foreign_0.8-86.tar.gz
Binary files R-release-orig/src/library/Recommended/foreign_0.8-87.tar.gz and R-patched/src/library/Recommended/foreign_0.8-87.tar.gz differ
Binary files R-release-orig/src/library/Recommended/nlme.tgz and R-patched/src/library/Recommended/nlme.tgz differ
Only in R-release-orig/src/library/Recommended: nlme_3.1-164.tar.gz
Binary files R-release-orig/src/library/Recommended/nlme_3.1-166.tar.gz and R-patched/src/library/Recommended/nlme_3.1-166.tar.gz differ
Binary files R-release-orig/src/library/Recommended/survival.tgz and R-patched/src/library/Recommended/survival.tgz differ
Only in R-release-orig/src/library/Recommended: survival_3.6-4.tar.gz
Binary files R-release-orig/src/library/Recommended/survival_3.7-0.tar.gz and R-patched/src/library/Recommended/survival_3.7-0.tar.gz differ
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/library/base/man/debug.Rd R-patched/src/library/base/man/debug.Rd
--- R-release-orig/src/library/base/man/debug.Rd	2020-06-24 00:15:08.000000000 +0200
+++ R-patched/src/library/base/man/debug.Rd	2024-07-16 11:39:22.000000000 +0200
@@ -108,7 +108,7 @@
 \dontrun{
 debugonce(sample)
 ## only the first call will be debugged
-sampe(10, 1)
+sample(10, 1)
 sample(10, 1)
 }
 }
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/library/base/man/drop.Rd R-patched/src/library/base/man/drop.Rd
--- R-release-orig/src/library/base/man/drop.Rd	2024-03-27 00:02:04.000000000 +0100
+++ R-patched/src/library/base/man/drop.Rd	2024-08-05 17:45:08.000000000 +0200
@@ -1,6 +1,6 @@
 % File src/library/base/man/drop.Rd
 % Part of the R package, https://www.R-project.org
-% Copyright 1995-2021 R Core Team
+% Copyright 1995-2024 R Core Team
 % Distributed under GPL 2 or later
 
 \name{drop}
@@ -21,8 +21,10 @@
   \code{x}, but with any extents of length one removed.  Any
   accompanying \code{dimnames} attribute is adjusted and returned with
   \code{x}: if the result is a vector the \code{names} are taken from
-  the \code{dimnames} (if any).  If the result is a length-one vector,
-  the names are taken from the first dimension with a \I{dimname}.
+  the \code{dimnames} (if any).  However, if the result is a vector
+  of length one, then it does not get \code{names} \emph{unless} exactly
+  one component of the \code{dimnames} is non-\code{NULL}, in which case
+  that component is used.
 
   Array subsetting (\code{\link{[}}) performs this reduction unless used
   with \code{drop = FALSE}, but sometimes it is useful to invoke
@@ -34,6 +36,13 @@
 }
 \examples{
 dim(drop(array(1:12, dim = c(1,3,1,1,2,1,2)))) # = 3 2 2
-drop(1:3 \%*\% 2:4)  # scalar product
+drop(1:3 \%*\% 2:4)  # scalar product - w/o drop(.), would return 1x1 matrix
+
+# Behavior when result is length-1 vector:
+(x <- x1 <- x2 <- array(0, c(1L, 1L), list("a", "b")))
+colnames(x1) <- rownames(x2) <- NULL
+names(drop(x )) # NULL
+names(drop(x1)) #  "a"
+names(drop(x2)) #  "b"
 }
 \keyword{array}
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/library/base/man/is.recursive.Rd R-patched/src/library/base/man/is.recursive.Rd
--- R-release-orig/src/library/base/man/is.recursive.Rd	2024-03-27 00:02:04.000000000 +0100
+++ R-patched/src/library/base/man/is.recursive.Rd	2024-07-16 11:39:22.000000000 +0200
@@ -1,6 +1,6 @@
 % File src/library/base/man/is.recursive.Rd
 % Part of the R package, https://www.R-project.org
-% Copyright 1995-2023 R Core Team
+% Copyright 1995-2024 R Core Team
 % Distributed under GPL 2 or later
 
 \name{is.recursive}
@@ -14,6 +14,7 @@
 \description{
   \code{is.atomic} returns \code{TRUE} if \code{x} is of an atomic type
   and \code{FALSE} otherwise.
+  \code{is.atomic(NULL)} returns \code{FALSE} since \R version 4.4.0.
 
   \code{is.recursive} returns \code{TRUE} if \code{x} has a recursive
   (list-like) structure and \code{FALSE} otherwise.
@@ -60,6 +61,10 @@
 is.a.r(expression(x+1)) # FALSE TRUE
 is.a.r(quote(exp))      # FALSE FALSE
 is.a.r(NULL)            # FALSE FALSE
+
+# Reproduce pre-4.4 behavior of is.atomic()
+is.atomicN <- function(x) is.atomic(x) || is.null(x)
+is.atomicN(NULL) # TRUE
 }
 \keyword{programming}
 \keyword{classes}
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/library/base/man/print.default.Rd R-patched/src/library/base/man/print.default.Rd
--- R-release-orig/src/library/base/man/print.default.Rd	2024-06-01 00:15:01.000000000 +0200
+++ R-patched/src/library/base/man/print.default.Rd	2024-07-16 11:39:23.000000000 +0200
@@ -51,7 +51,8 @@
 \details{
   The default for printing \code{NA}s is to print \code{NA} (without
   quotes) unless this is a character \code{NA} \emph{and} \code{quote =
-    FALSE}, when \samp{<NA>} is printed.
+    FALSE}, when \samp{<NA>} is printed.  When \code{na.print} is not \code{NULL},
+  it handles how character \code{NA} is displayed, with no interaction with \code{quote}.
 
   The same number of decimal places is used throughout a vector.  This
   means that \code{digits} specifies the minimum number of significant
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/library/grDevices/src/devQuartz.c R-patched/src/library/grDevices/src/devQuartz.c
--- R-release-orig/src/library/grDevices/src/devQuartz.c	2023-11-01 00:15:01.000000000 +0100
+++ R-patched/src/library/grDevices/src/devQuartz.c	2024-07-24 07:45:08.000000000 +0200
@@ -1939,10 +1939,16 @@
 static double RQuartz_StrWidth(const char *text, CTXDESC)
 {
     DEVSPEC;
-    if (!ctx) NOCTXR(strlen(text) * 10.0); /* for sanity reasons */
-    RQuartz_SetFont(ctx, gc, xd);
 
-    CGFontRef font = CGContextGetFont(ctx);
+    CGFontRef font = 0;
+    if (!ctx) { /* if there is no context then don't set the font */
+        xd->async = 1; /* flag us as not having a context */
+        font = RQuartz_Font(gc, NULL);
+        if (!font) return (strlen(text) * 10.0); /* for sanity reasons */
+    } else {
+        RQuartz_SetFont(ctx, gc, xd);
+        font = CGContextGetFont(ctx);
+    }
     float aScale   = (float)((gc->cex * gc->ps * xd->tscale) /
 			     CGFontGetUnitsPerEm(font));
     UniChar *buffer;
@@ -2547,15 +2553,24 @@
 		   pDevDesc dd)
 {
     DRAWSPEC;
-    if (!ctx) { /* dummy data if we have no context, for sanity reasons */
-        *ascent = 10.0;
-        *descent= 2.0;
-        *width  = 9.0;
-        NOCTX;
+    CGFontRef font = 0;
+
+    if (!ctx) {
+        xd->async = 1; /* flag us as not having a context */
+        font = RQuartz_Font(gc, NULL);
+        if (!font) {
+            /* dummy data if we have no font at all, for sanity reasons */
+            *ascent = 10.0;
+            *descent= 2.0;
+            *width  = 9.0;
+            return;
+        }
+    } else {
+        RQuartz_SetFont(ctx, gc, xd);
+        font = CGContextGetFont(ctx);
     }
-    RQuartz_SetFont(ctx, gc, xd);
+
     {
-	CGFontRef font = CGContextGetFont(ctx);
         float aScale   = (float)((gc->cex * gc->ps * xd->tscale) /
 				 CGFontGetUnitsPerEm(font));
 	UniChar  *buffer, single;
@@ -3002,14 +3017,12 @@
 
     Rboolean grouping = QuartzBegin(&ctx, &layer, xd);
 
-    char url[501];
-    snprintf(url, 500, "file://%s", R_GE_glyphFontFile(font));
-    CFStringRef cfFontFileName = 
-        CFStringCreateWithCString(NULL, url, kCFStringEncodingUTF8);
-    CFURLRef cfFontURL = CFURLCreateWithString(NULL, cfFontFileName, NULL);
+    const char* path = R_GE_glyphFontFile(font);
+    CFURLRef cfFontURL = CFURLCreateFromFileSystemRepresentation(NULL, (const UInt8*)path, strlen(path), false);
+    if (!cfFontURL)
+        error(_("Invalid font path: \"%s\""), path);
     CFArrayRef cfFontDescriptors = 
         CTFontManagerCreateFontDescriptorsFromURL(cfFontURL);
-    CFRelease(cfFontFileName);
     CFRelease(cfFontURL);
     int n_fonts = CFArrayGetCount(cfFontDescriptors);
     if (n_fonts > 0) {
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/library/grDevices/src/devices.c R-patched/src/library/grDevices/src/devices.c
--- R-release-orig/src/library/grDevices/src/devices.c	2023-03-24 00:02:03.000000000 +0100
+++ R-patched/src/library/grDevices/src/devices.c	2024-07-24 07:45:08.000000000 +0200
@@ -226,7 +226,7 @@
     UNPROTECT(1);
 
     /* Further capabilities can be filled in by device */
-    if (dd->deviceVersion >= R_GE_group) {
+    if (dd->deviceVersion >= R_GE_group && dd->capabilities) {
         devcap = dd->capabilities(capabilities);
     } else {
         devcap = capabilities;
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/library/graphics/man/mtext.Rd R-patched/src/library/graphics/man/mtext.Rd
--- R-release-orig/src/library/graphics/man/mtext.Rd	2024-03-27 00:02:05.000000000 +0100
+++ R-patched/src/library/graphics/man/mtext.Rd	2024-08-05 17:45:08.000000000 +0200
@@ -1,6 +1,6 @@
 % File src/library/graphics/man/mtext.Rd
 % Part of the R package, https://www.R-project.org
-% Copyright 1995-2011 R Core Team
+% Copyright 1995-2024 R Core Team
 % Distributed under GPL 2 or later
 
 \name{mtext}
@@ -35,8 +35,8 @@
     parallel to the axis the default is to centre the string.}
   \item{padj}{adjustment for each string perpendicular to the reading
     direction (which is controlled by \code{adj}).  For strings parallel
-    to the axes, \code{padj = 0} means left or bottom alignment,
-    and \code{padj = 1} means right or top alignment (relative to the line).
+    to the axes, \code{padj = 0} means bottom alignment,
+    and \code{padj = 1} means top alignment (relative to the axis line).
     
     If \code{padj} is not a finite value (the default), the value of
     \code{par("las")} determines the adjustment.  For strings plotted
@@ -103,5 +103,10 @@
 ##--- log axis :
 plot(1:10, exp(1:10), log = "y", main = "log =\"y\"", xlab = "xlab")
 for(s in 1:4) mtext(paste("mtext(...,side=", s ,")"), side = s)
+
+##--- illustrating padj behavior :
+plot(0, axes=FALSE, ann=FALSE, frame.plot=TRUE)
+for(si in 1:4) mtext(c("padj=0", "-----------", "padj=1"),
+                     side = si, padj = c(0, 0.5, 1))
 }
 \keyword{aplot}
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diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/library/tools/R/utils.R R-patched/src/library/tools/R/utils.R
--- R-release-orig/src/library/tools/R/utils.R	2024-06-01 00:15:01.000000000 +0200
+++ R-patched/src/library/tools/R/utils.R	2024-07-16 11:40:42.000000000 +0200
@@ -1909,6 +1909,8 @@
                          "dim.rename.nc", "open.nc", "print.nc"),
              Rmpfr = c("mpfr.is.0", "mpfr.is.integer"),
              SMPracticals = "exp.gibbs",
+             SparseM = c("as.matrix.csc","as.matrix.csr", "as.matrix.ssc", "as.matrix.ssr", "as.matrix.coo",
+                         "is.matrix.csc","is.matrix.csr", "is.matrix.ssc", "is.matrix.ssr", "is.matrix.coo"),
              TANOVA = "sigma.hat",
              TeachingDemos = "sigma.test",
              XML = "text.SAX",
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/library/utils/R/sessionInfo.R R-patched/src/library/utils/R/sessionInfo.R
--- R-release-orig/src/library/utils/R/sessionInfo.R	2024-03-27 00:02:08.000000000 +0100
+++ R-patched/src/library/utils/R/sessionInfo.R	2024-07-16 11:41:21.000000000 +0200
@@ -78,7 +78,8 @@
                                       "11" = "Big Sur",
                                       "12" = "Monterey",
                                       "13" = "Ventura",
-                                      "14" = "Sonoma"),
+                                      "14" = "Sonoma",
+                                      "15" = "Sequoia"),
                                ver)
                    else
                        sprintf("macOS %s", ver)
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/library/utils/src/windows/util.c R-patched/src/library/utils/src/windows/util.c
--- R-release-orig/src/library/utils/src/windows/util.c	2023-03-24 00:02:05.000000000 +0100
+++ R-patched/src/library/utils/src/windows/util.c	2024-07-16 11:41:35.000000000 +0200
@@ -1,7 +1,7 @@
 /*
  *  R : A Computer Language for Statistical Data Analysis
  *  file util.c
- *  Copyright (C) 2005--2023  The R Core Team
+ *  Copyright (C) 2005--2024  The R Core Team
  *  Copyright (C) 1998--2003  Guido Masarotto and Brian Ripley
  *  Copyright (C) 2004	      The R Foundation
  *
@@ -292,15 +292,17 @@
 
     n = length(text);
     if(n > 0) {
-	int len = 1;
+	int len = 0;
 	if(raw) len = n;
-	else if (format == CF_UNICODETEXT)
+	else if (format == CF_UNICODETEXT) {
+	    len = 2; /* terminator */
 	    for(i = 0; i < n; i++)
 		len += 2 * (wcslen(wtransChar(STRING_ELT(text, i))) + 2);
-	else if (format == CF_TEXT || format == CF_OEMTEXT || format == CF_DIF)
+	} else if (format == CF_TEXT || format == CF_OEMTEXT || format == CF_DIF) {
+	    len = 1; /* terminator */
 	    for(i = 0; i < n; i++)
 		len += strlen(translateChar(STRING_ELT(text, i))) + 2;
-	else
+	} else
 	    error("'raw = FALSE' and format is a not a known text format");
 
 	if ( (hglb = GlobalAlloc(GHND, len)) &&
diff -ru -P -x .mirror -x ls_lR -x Old R-release-orig/src/nmath/lgammacor.c R-patched/src/nmath/lgammacor.c
--- R-release-orig/src/nmath/lgammacor.c	2024-03-27 00:02:08.000000000 +0100
+++ R-patched/src/nmath/lgammacor.c	2024-08-05 17:45:08.527645623 +0200
@@ -25,11 +25,12 @@
  *  DESCRIPTION
  *
  *    Compute the log gamma correction factor for x >= 10 so that
+ *                                               ---------
  *
  *    log(gamma(x)) = .5*log(2*pi) + (x-.5)*log(x) -x + lgammacor(x)
  *
- *    [ lgammacor(x) is called	Del(x)	in other contexts (e.g. dcdflib)]
- *
+ *    [ lgammacor(x) is called	Del(x)	in other contexts (e.g. dcdflib)], or  stirlerr(x)
+ *				~~~~~~					       ~~~~~~~~~~~
  *  NOTES
  *
  *    This routine is a translation into C of a Fortran subroutine
@@ -68,18 +69,20 @@
  *   xmax = DBL_MAX / 48 =  2^1020 / 3 */
 #define nalgm 5
 #define xbig  94906265.62425156
-#define xmax  3.745194030963158e306
 
     if (x < 10) // possibly consider stirlerr()
 	ML_WARN_return_NAN
+#ifndef IEEE_754
+#   define xmax  3.745194030963158e306
     else if (x >= xmax) {
 	ML_WARNING(ME_UNDERFLOW, "lgammacor");
 	/* allow to underflow below */
     }
+#endif
     else if (x < xbig) {
 	double tmp = 10 / x;
 	return chebyshev_eval(tmp * tmp * 2 - 1, algmcs, nalgm) / x;
     }
-    // else, xbig <= x < xmax :
+    // x >= xbig
     return 1 / (x * 12);
 }
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	2024-03-27 00:02:08.000000000 +0100
+++ R-patched/tests/Examples/graphics-Ex.Rout.save	2024-08-05 17:45:08.662712136 +0200
@@ -1,7 +1,7 @@
 
-R Under development (unstable) (2023-09-08 r85109) -- "Unsuffered Consequences"
-Copyright (C) 2023 The R Foundation for Statistical Computing
-Platform: aarch64-apple-darwin22.6.0
+R version 4.4.1 Patched (2024-07-31 r86978) -- "Race for Your Life"
+Copyright (C) 2024 The R Foundation for Statistical Computing
+Platform: x86_64-pc-linux-gnu
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.
@@ -1720,6 +1720,11 @@
 > plot(1:10, exp(1:10), log = "y", main = "log =\"y\"", xlab = "xlab")
 > for(s in 1:4) mtext(paste("mtext(...,side=", s ,")"), side = s)
 > 
+> ##--- illustrating padj behavior :
+> plot(0, axes=FALSE, ann=FALSE, frame.plot=TRUE)
+> for(si in 1:4) mtext(c("padj=0", "-----------", "padj=1"),
++                      side = si, padj = c(0, 0.5, 1))
+> 
 > 
 > 
 > cleanEx()

Places

File R-release.diff of Package R (Revision 6af2b02b206065bc02d911f0a9e3238c)

Places