From skostyshak at ufl.edu  Mon Jul  3 08:09:47 2017
From: skostyshak at ufl.edu (Scott Kostyshak)
Date: Mon, 3 Jul 2017 02:09:47 -0400
Subject: [Rd] Patch for R-exts.texi
Message-ID: <20170703060947.22pm6oiyivj7illt@steph>

Attached is a patch for R-exts.texi against r72880.

Here are some of the changes I made:

- Fix a broken link:
    https://developer.apple.com/library/mac/#documentation/DeveloperTools/Conceptual/InstrumentsUserGuide/Introduction/Introduction.html
    ->
    https://developer.apple.com/library/content/documentation/DeveloperTools/Conceptual/InstrumentsUserGuide/index.html

- Changed a few http to https (and checked that the connections are
  indeed secure, as judged by Chromium and Firefox).

- A couple of grammar fixes and "sounds more natural to me" changes.

- "x84_64" -> x86_64

- One change of "which" -> "that"

- The link to Luke's uiowa.edu page involves two changes, removing the
  duplicate URL and changing the protocol to https.

Thanks for your time,

Scott


-- 
Scott Kostyshak
Assistant Professor of Economics
University of Florida
https://people.clas.ufl.edu/skostyshak/

-------------- next part --------------
Index: doc/manual/R-exts.texi
===================================================================
--- doc/manual/R-exts.texi	(revision 72880)
+++ doc/manual/R-exts.texi	(working copy)
@@ -1457,7 +1457,7 @@
 
 @noindent
 then download the sources from
- at uref{http://sourceforge.net/@/projects/@/tcllib/@/files/@/BWidget/} and
+ at uref{https://sourceforge.net/@/projects/@/tcllib/@/files/@/BWidget/} and
 at the command line run something like
 
 @example
@@ -1494,7 +1494,7 @@
 
 @noindent
 and not a version starting
- at samp{http://cran.r-project.org/web/packages/@var{pkgname}}.
+ at samp{https://cran.r-project.org/web/packages/@var{pkgname}}.
 
 @node Configure and cleanup, Checking and building packages, Package structure, Creating R packages
 @section Configure and cleanup
@@ -2117,7 +2117,7 @@
 word, so computations done on OpenMP threads will not make use of
 extended-precision arithmetic which is the default for the main process.
 @c mingw64-public, 2015-02-02.
- at c http://stackoverflow.com/questions/2553725/is-the-fpu-control-word-setting-per-thread-or-per-process
+ at c https://stackoverflow.com/questions/2553725/is-the-fpu-control-word-setting-per-thread-or-per-process
 
 Calling any of the @R{} API from threaded code is `for experts only':
 they will need to read the source code to determine if it is
@@ -7645,7 +7645,7 @@
 which is a GUI version), @command{Shark} (in version of @code{Xcode}
 up to those for Snow Leopard), and @command{Instruments} (part of
 @code{Xcode}, see
- at uref{https://developer.apple.com/library/mac/#documentation/DeveloperTools/Conceptual/InstrumentsUserGuide/Introduction/Introduction.html}).
+ at uref{https://developer.apple.com/library/content/documentation/DeveloperTools/Conceptual/InstrumentsUserGuide/index.html}).
 
 
 @node Debugging, System and foreign language interfaces, Tidying and profiling R code, Top
@@ -8295,8 +8295,8 @@
 to be installed separately, and for checking C++ you may also need
 @pkg{libubsan}.} of @command{gcc} and @command{clang} on common Linux
 and macOS platforms.  See
- at uref{http://clang.llvm.org/@/docs/@/UsersManual.html#controlling-code-generation},
- at uref{http://clang.llvm.org/@/docs/@/AddressSanitizer.html} and
+ at uref{https://clang.llvm.org/@/docs/@/UsersManual.html#controlling-code-generation},
+ at uref{https://clang.llvm.org/@/docs/@/AddressSanitizer.html} and
 @uref{https://code.google.com/@/p/@/address-sanitizer/}.
 
 More thorough checks of C++ code are done if the C++ library has been
@@ -8455,7 +8455,7 @@
 
 Finer control of what is checked can be achieved by other options: for
 @command{clang} see
- at uref{http://clang.llvm.org/@/docs/@/UsersManual.html#controlling-code-generation}. at footnote{or
+ at uref{https://clang.llvm.org/@/docs/@/UsersManual.html#controlling-code-generation}. at footnote{or
 the user manual for your version of @command{clang}, e.g.@: (the paths
 have differed for some versions)
 @uref{http://llvm.org/@/releases/@/4.0.0/@/tools/@/clang/@/docs/@/UsersManual.html}.}
@@ -8560,13 +8560,13 @@
 Recent versions of @command{clang} on @cputype{x86_64} Linux have
 `ThreadSanitizer' (@uref{https://code.google.com/@/p/@/thread-sanitizer/}),
 a `data race detector for C/C++ programs', and `MemorySanitizer'
-(@uref{http://clang.llvm.org/@/docs/@/MemorySanitizer.html},
+(@uref{https://clang.llvm.org/@/docs/@/MemorySanitizer.html},
 @uref{https://code.google.com/@/p/@/memory-sanitizer/@/wiki/@/MemorySanitizer})
 for the detection of uninitialized memory.  Both are based on and
 provide similar functionality to tools in @command{valgrind}.
 
 @command{clang} has a `Static Analyser' which can be run on the source
-files during compilation: see @uref{http://clang-analyzer.llvm.org/}.
+files during compilation: see @uref{https://clang-analyzer.llvm.org/}.
 
 @node Using `Dr. Memory', Fortran array bounds checking, Other analyses with `clang', Checking memory access
 @subsection Using `Dr. Memory'
@@ -9429,7 +9429,7 @@
 @uref{https://www.r-project.org/@/doc/@/Rnews/Rnews_2001-3.pdf}).
 
 Once routines are registered, they can be referred to as @R{} objects if
-they this is arranged in the @code{useDynLib} call in the package's
+this is arranged in the @code{useDynLib} call in the package's
 @file{NAMESPACE} file (see @ref{useDynLib}).  So for example the
 @pkg{stats} package has
 @example
@@ -9516,7 +9516,7 @@
 the OS (and even if it is 32- or 64-bit), on the version of @R{} and
 what else is loaded into @R{} at the time.
 
-To fix ideas, first consider @code{x84_64} OS 10.7 and @R{} 2.15.2.  A
+To fix ideas, first consider @code{x86_64} OS 10.7 and @R{} 2.15.2.  A
 simple @code{.Call} function might be
 @example
 foo <- function(x) .Call("foo", x)
@@ -9696,7 +9696,7 @@
 suffices. (For most platforms one can omit all the arguments.)
 
 @item
-(Optional but highly recommended.)  Restrict @code{.Call} etc to using the
+(Optional but highly recommended.)  Restrict @code{.Call} etc to use the
 symbols you chose to register by editing @file{src/init.c} to contain
 
 @example
@@ -9749,7 +9749,7 @@
 unintentionally exports the newly created @R{} objects.
 
 @item
-Restrict @code{.Call} to using the @R{} symbols by editing
+Restrict @code{.Call} to use the @R{} symbols by editing
 @file{src/init.c} to contain
 
 @example
@@ -9781,7 +9781,7 @@
 @noindent
 If there were any entry points not intended to be used by the package we
 should try to avoid exporting them, for example by making them
- at code{static}.  Now the two relevant entry points are only accessed
+ at code{static}.  Now that the two relevant entry points are only accessed
 @emph{via} the registration table, we can hide them.  There are two ways
 to do so on some Unix-alikes.  We can hide individual entry points
 @emph{via}
@@ -9899,8 +9899,8 @@
 A package that wishes to make use of header files in other packages
 needs to declare them as a comma-separated list in the field
 @samp{LinkingTo} in the @file{DESCRIPTION} file.  This then arranges
-that the @file{include} directories in the installed linked-to packages
-are added to the include paths for C and C++ code.
+for the @file{include} directories in the installed linked-to packages
+to be added to the include paths for C and C++ code.
 
 It must specify at footnote{whether or not @samp{LinkingTo} is used.}
 @samp{Imports} or @samp{Depends} of those packages, for they have to be
@@ -9911,7 +9911,7 @@
 
 @acronym{CRAN} examples of the use of this mechanism include @CRANpkg{coxme}
 linking to @CRANpkg{bdsmatrix} and @CRANpkg{xts} linking to
- at CRANpkg{zoo}
+ at CRANpkg{zoo}.
 
 @node Creating shared objects, Interfacing C++ code, Registering native routines, System and foreign language interfaces
 @section Creating shared objects
@@ -9955,7 +9955,7 @@
 by setting the macro @samp{OBJECTS} in file @file{Makevars}, together
 with suitable rules to make the objects.
 
-Flags which are already set (for example in file
+Flags that are already set (for example in file
 @file{etc at var{R_ARCH}/Makeconf}) can be overridden by the environment
 variable @env{MAKEFLAGS} (at least for systems using a POSIX-compliant
 @code{make}), as in (Bourne shell syntax)
@@ -12121,8 +12121,7 @@
 @end example
 
 A toy example of the use of weak references can be found at
- at uref{http://homepage.stat.uiowa.edu/~luke/R/references/weakfinex.html,
- at code{homepage.@/stat.@/uiowa.@/edu/@/~luke/@/R/references/@/weakfinex.html}},
+ at uref{https://homepage.stat.uiowa.edu/~luke/R/references/weakfinex.html},
 but that is used to add finalizers to external pointers which can now be
 done more directly.  At the time of writing no @acronym{CRAN} or
 Bioconductor package uses weak references.


[Rd] Patch for R-exts.texi
Scott Kostyshak