Commit 8b1efab8 authored by Radford Neal's avatar Radford Neal

Files from R-2.14.2.

parent 6e5ebc20
......@@ -33,7 +33,7 @@ ECHO_N = @ECHO_N@
ECHO_T = @ECHO_T@
FFLAGS = @FFLAGS@
FLIBS = @FLIBS@
FLIBS_IN_SO = $(FLIBS)
FLIBS_IN_SO = @FLIBS_IN_SO@
FPICFLAGS = @FPICFLAGS@
F77 = @F77@
GETWD = @GETWD@
......
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Revision: 57956
Last Changed Date: 2011-12-22
Revision: 58522
Last Changed Date: 2012-02-29
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......@@ -782,6 +782,8 @@ R_HEADER_GLIBC2
### * Checks for types.
AC_TYPE_SIGNAL
## xz needs uint64_t
AC_TYPE_UINT64_T
AC_TYPE_PID_T
AC_TYPE_SIZE_T
R_SIZE_MAX
......@@ -833,6 +835,10 @@ AC_OPENMP
### *** Fortran 77 compiler.
R_PROG_F77_FLIBS
if test -z "$FLIBS_IN_SO"; then
FLIBS_IN_SO=${FLIBS}
fi
AC_SUBST(FLIBS_IN_SO)
R_PROG_F77_APPEND_UNDERSCORE
R_PROG_F77_CAN_RUN
R_PROG_F77_CC_COMPAT
......@@ -1668,7 +1674,8 @@ AC_SUBST(FW_VERSION)
if test "x${main_ld_was_given}" = xno -a "${MAIN_LD}" = "${CC}" -a \
"x${dylib_ld_was_given}" = xno -a "${DYLIB_LD}" = "${CC}" -a \
"x${ac_cv_prog_c_openmp}" != "xunsupported"; then
"x${ac_cv_prog_c_openmp}" != "xunsupported" -a \
"x${ac_cv_prog_c_openmp}" != "x"; then
R_OPENMP_CFLAGS="${OPENMP_CFLAGS}"
R_OPENMP_FFLAGS="${OPENMP_FFLAGS}"
R_SH_VAR_ADD(MAIN_LDFLAGS, [${OPENMP_CFLAGS}])
......@@ -1771,7 +1778,7 @@ R_CHECK_FUNCS([access chdir execv ftruncate getcwd geteuid getuid link readlink
[#ifdef HAVE_UNISTD_H
# include <unistd.h>
#endif])
## This was declared obsolescent in POSIX 2008 (use utimes instead)
## utime was declared obsolescent in POSIX 2008 (use utimes instead)
R_CHECK_FUNCS([utime], [#include <utime.h>])
## clock_gettime is POSIX 1993, but not on MacOS X
## Some OSes need -lrt: Linux, Solaris, not FreeBSD.
......@@ -2235,6 +2242,7 @@ AC_SUBST(FCLIBS)
if test "x${shlib_ld_was_given}" = xno -a \
"${SHLIB_LD}" = "${CC}" -a \
"x${ac_cv_prog_c_openmp}" != "xunsupported" -a \
"x${ac_cv_prog_c_openmp}" != "x" -a \
"x${shlib_cxxld_was_given}" = xno -a \
"${SHLIB_CXXLD}" = "${CXX}" -a \
"x${ac_cv_prog_cxx_openmp}" != "xunsupported" -a \
......
......@@ -284,7 +284,7 @@ src/extra/xdr/*
src/extra/zlib/README, *.c, *.h
Taken from zlib-1.2.5 (C) 1995-2010 Jean-loup Gailly and Mark Adler
Taken from zlib-1.2.6 (C) 1995-2012 Jean-loup Gailly and Mark Adler
See src/extra/zlib/README for the licence.
src/main/connections.c, src/main/gzio.h
......@@ -303,6 +303,7 @@ src/extra/pcre/*.[ch]
Copyright (c) 1997-2011 University of Cambridge
All rights reserved.
Copyright(c) 2009-2011 Zoltan Herczeg
See file src/extra/pcre/LICENCE. For binary builds of R that requires
us to include
......@@ -360,27 +361,31 @@ src/extra/tre/LICENSE. For binary builds of R that requires us to
include
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions
are met:
1. Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER AND CONTRIBUTORS
``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.
* Neither the name of the University of Cambridge nor the name of Google
Inc. nor the names of their contributors may be used to endorse or
promote products derived from this software without specific prior
written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
src/library/tools/src/md5.[ch]
......
R FAQ
Frequently Asked Questions on R
Version 2.14.2011-12-16
Version 2.14.2012-02-23
ISBN 3-900051-08-9
Kurt Hornik
......@@ -126,7 +126,7 @@ questions about R.
1.1 Legalese
============
This document is copyright (C) 1998-2011 by Kurt Hornik.
This document is copyright (C) 1998-2012 by Kurt Hornik.
This document is free software; you can redistribute it and/or modify it
under the terms of the GNU General Public License as published by the Free
......@@ -159,7 +159,7 @@ site (*note What is CRAN?::).
1.3 Citing this document
========================
In publications, please refer to this FAQ as Hornik (2011), "The R FAQ",
In publications, please refer to this FAQ as Hornik (2012), "The R FAQ",
and give the above, _official_ URL and the ISBN 3-900051-08-9:
@Misc{,
......@@ -258,7 +258,7 @@ i386-freebsd, rs6000-ibm-aix, and sparc-sun-solaris.
2.3 What is the current version of R?
=====================================
The current released version is 2.14.1. Based on this
The current released version is 2.14.2. Based on this
`major.minor.patchlevel' numbering scheme, there are two development
versions of R, a patched version of the current release (`r-patched') and
one working towards the next minor or eventually major (`r-devel') releases
......@@ -645,8 +645,9 @@ binaries for various operating systems (Linux, Mac OS Classic, Mac OS X,
and MS Windows). CRAN also provides access to documentation on R, existing
mailing lists and the R Bug Tracking system.
To "submit" to CRAN, simply upload to
`ftp://CRAN.R-project.org/incoming/' and send an email to
To "submit" to CRAN, check that your submission meets the CRAN
Repository Policy (http://CRAN.R-project.org/web/packages/policies.html),
upload to `ftp://CRAN.R-project.org/incoming/' and send an email to
<CRAN@R-project.org>. Note that CRAN generally does not accept submissions
of precompiled binaries due to security reasons. In particular, binary
packages for Windows and Mac OS X are provided by the respective binary
......
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......@@ -19,32 +19,53 @@
span.sansserif { font-family:sans-serif; font-weight:normal; }
body {margin-left: 5%; margin-right: 5%;}
H1{ background: white;
color: rgb(25%, 25%, 25%);
font-family: monospace;
font-size: xx-large;
text-align: center }
H2{ background: white;
color: rgb(40%, 40%, 40%);
font-family: monospace;
font-size: x-large;
text-align: center }
H3{ background: white;
color: rgb(40%, 40%, 40%);
font-family: monospace;
font-size: large }
H4{ background: white;
color: rgb(40%, 40%, 40%);
font-family: monospace }
H1 {
background: white;
color: rgb(25%, 25%, 25%);
font-family: monospace;
font-size: xx-large;
text-align: center
}
H2 {
background: white;
color: rgb(40%, 40%, 40%);
font-family: monospace;
font-size: x-large;
text-align: center
}
H3 {
background: white;
color: rgb(40%, 40%, 40%);
font-family: monospace;
font-size: large
}
H4 {
background: white;
color: rgb(40%, 40%, 40%);
font-family: monospace
}
span.samp{font-family: monospace}
span.command{font-family: monospace}
span.option{font-family: monospace}
span.file{font-family: monospace}
span.env{font-family: monospace}
ul {
margin-top: 0.25ex;
margin-bottom: 0.25ex;
}
li {
margin-top: 0.25ex;
margin-bottom: 0.25ex;
}
p {
margin-top: 0.6ex;
margin-bottom: 1.2ex;
}
--></style>
</head>
<body>
......
......@@ -3,12 +3,12 @@
@setfilename R-FAQ.info
@settitle R FAQ
@setchapternewpage on
@set FAQ_YEAR 2011
@set FAQ_DATE @value{FAQ_YEAR}-12-16
@set FAQ_YEAR 2012
@set FAQ_DATE @value{FAQ_YEAR}-02-23
@set REL_YEAR 2011
@set REL_MAJOR 2
@set REL_MINOR 14
@set REL_PATCHLEVEL 1
@set REL_PATCHLEVEL 2
@set REL_VERSION @value{REL_MAJOR}.@value{REL_MINOR}.@value{REL_PATCHLEVEL}
@set FAQ_VERSION @value{REL_MAJOR}.@value{REL_MINOR}.@value{FAQ_DATE}
......@@ -873,12 +873,13 @@ Mac OS X, and MS Windows). @CRAN{} also provides access to
documentation on R, existing mailing lists and the R Bug Tracking
system.
To ``submit'' to @CRAN{}, simply upload to
@url{ftp://CRAN.R-project.org/incoming/} and send an email to
@email{CRAN@@R-project.org}. Note that @CRAN{} generally does not
accept submissions of precompiled binaries due to security reasons. In
particular, binary packages for Windows and Mac OS X are provided by the
respective binary package maintainers.
To ``submit'' to @CRAN{}, check that your submission meets the
@url{http://CRAN.R-project.org/web/packages/policies.html, CRAN
Repository Policy}, upload to @url{ftp://CRAN.R-project.org/incoming/}
and send an email to @email{CRAN@@R-project.org}. Note that @CRAN{}
generally does not accept submissions of precompiled binaries due to
security reasons. In particular, binary packages for Windows and Mac OS
X are provided by the respective binary package maintainers.
@quotation Note
It is very important that you indicate the copyright (license)
......
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......@@ -32,13 +32,17 @@ $\t\$%
@strong{\p\}
@end macro
@macro CRANpkg {p}
@url{http://CRAN.R-project.org/package=\p\, @strong{\p\}}
@end macro
@macro cputype {c}
@samp{\c\}
@end macro
@c -- edit these here alone -- in order keep consistency
@macro Rcopyright{year}
Copyright @copyright{} \year\--2011 R Development Core Team
Copyright @copyright{} \year\--2012 R Development Core Team
@end macro
@macro permission{}
......
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......@@ -3034,7 +3034,7 @@ In addition there are functions @code{ptukey} and @code{qtukey} for the
distribution of the studentized range of samples from a normal
distribution, and @code{dmultinom} and @code{rmultinom} for the
multinomial distribution. Further distributions are available in
contributed packages, notably @pkg{SuppDists}.
contributed packages, notably @CRANpkg{SuppDists}.
Here are some examples
......@@ -3452,7 +3452,7 @@ of @var{expr_1}.
As an example, suppose @code{ind} is a vector of class indicators and we
wish to produce separate plots of @code{y} versus @code{x} within
classes. One possibility here is to use @code{coplot()},@footnote{to be
discussed later, or use @code{xyplot} from package @pkg{lattice}.}
discussed later, or use @code{xyplot} from package @CRANpkg{lattice}.}
which will produce an array of plots corresponding to each level of the
factor. Another way to do this, now putting all plots on the one
display, is as follows:
......@@ -5257,7 +5257,7 @@ problems.
@itemize @bullet
@item
@cindex Mixed models
@strong{Mixed models.} The recommended @pkg{nlme} package provides
@strong{Mixed models.} The recommended @CRANpkg{nlme} package provides
functions @code{lme()} and @code{nlme()}
@findex lme
@findex nlme
......@@ -5285,12 +5285,12 @@ with code for projection pursuit regression.
fitting regression models in a way resistant to the influence of extreme
outliers in the data. Function @code{lqs}
@findex lqs
in the recommended package @pkg{MASS} provides state-of-art algorithms
in the recommended package @CRANpkg{MASS} provides state-of-art algorithms
for highly-resistant fits. Less resistant but statistically more
efficient methods are available in packages, for example function
@code{rlm}
@findex rlm
in package @pkg{MASS}.
in package @CRANpkg{MASS}.
@item
@cindex Additive models
......@@ -5300,13 +5300,13 @@ usually one for each determining variable. Functions @code{avas} and
@code{ace}
@findex avas
@findex ace
in package @pkg{acepack} and functions @code{bruto} and @code{mars}
in package @CRANpkg{acepack} and functions @code{bruto} and @code{mars}
@findex bruto
@findex mars
in package @pkg{mda} provide some examples of these techniques in
in package @CRANpkg{mda} provide some examples of these techniques in
user-contributed packages to @R{}. An extension is @strong{Generalized
Additive Models}, implemented in user-contributed packages @pkg{gam} and
@pkg{mgcv}.
Additive Models}, implemented in user-contributed packages @CRANpkg{gam} and
@CRANpkg{mgcv}.
@item
@cindex Tree-based models
......@@ -5326,7 +5326,7 @@ are well adapted to displaying the results of a tree-based model fit in
a graphical way.
Tree models are available in @R{} @emph{via} the user-contributed
packages @pkg{rpart} and @pkg{tree}.
packages @CRANpkg{rpart} and @CRANpkg{tree}.
@end itemize
......@@ -5371,7 +5371,7 @@ can be manipulated to customize your plots.
This manual only describes what are known as `base' graphics. A
separate graphics sub-system in package @pkg{grid} coexists with base --
it is more powerful but harder to use. There is a recommended package
@pkg{lattice} which builds on @pkg{grid} and provides ways to produce
@CRANpkg{lattice} which builds on @pkg{grid} and provides ways to produce
multi-panel plots akin to those in the @emph{Trellis} system in @Sl{}.
@menu
......@@ -6217,7 +6217,7 @@ however, so you must create them explicitly using @code{oma} or
More complicated arrangements of multiple figures can be produced by the
@code{split.screen()} and @code{layout()} functions, as well as by the
@pkg{grid} and @pkg{lattice} packages.
@pkg{grid} and @CRANpkg{lattice} packages.
@node Device drivers, Dynamic graphics, Graphics parameters, Graphics
@section Device drivers
......@@ -6405,10 +6405,10 @@ available from
@end quotation
@noindent
and these can be accessed from @R{} via the package @pkg{rggobi}, described at
and these can be accessed from @R{} via the package @CRANpkg{rggobi}, described at
@uref{http://www.ggobi.org/rggobi}.
Also, package @pkg{rgl} provides ways to interact with 3D plots, for example
Also, package @CRANpkg{rgl} provides ways to interact with 3D plots, for example
of surfaces.
@node Packages, A sample session, Graphics, Top
......@@ -6431,7 +6431,7 @@ To see which packages are installed at your site, issue the command
@end example
@noindent
with no arguments. To load a particular package (e.g., the @pkg{boot}
with no arguments. To load a particular package (e.g., the @CRANpkg{boot}
package containing functions from Davison & Hinkley (1997)), use a
command like
......
......@@ -318,9 +318,6 @@ an active binding. (For the definition of an `active binding' see the
header comments in file @file{src/main/envir.c}.) Bit 15 is used for an
environment to indicate if it participates in the global cache.
Almost all other uses seem to be only of bits 0 and 1, although one
reserves the first four bits.
@findex ARGSUSED
@findex SET_ARGUSED
The macros @code{ARGUSED} and @code{SET_ARGUSED} are used when matching
......@@ -352,8 +349,8 @@ recursive loops).
Bit 0 is used for @code{HASHASH}, on the @code{PRINTNAME} of the
@code{TAG} of the frame of an environment.
Bits 0 and 1 are used for weak references (to indicate 'ready to
finalize', 'finalize on exit').
Bits 0 and 1 are used for weak references (to indicate `ready to
finalize', `finalize on exit').
Bit 0 is used by the condition handling system (on a @code{VECSXP}) to
indicate a calling handler.
......@@ -469,8 +466,8 @@ for the @code{nul} terminator).
@code{length}, @code{truelength} followed by a block of C @code{double}s
@item CPLXSXP
@code{length}, @code{truelength} followed by a block of C99
@code{double complex}s, or equivalent structures.
@code{length}, @code{truelength} followed by a block of C99 @code{double
complex}s.
@item STRSXP
@code{length}, @code{truelength} followed by a block of pointers
......@@ -491,7 +488,7 @@ are internally identical (and identical to @code{STRSXP}) but differ in
the interpretations placed on the elements.
@item BCODESXP
For the future byte-code compiler.
For the `byte-code' objects generated by the compiler.
@item EXTPTRSXP
Has three pointers, to the pointer, the protection value (an @R{} object
......@@ -639,7 +636,7 @@ table.
@node Hash table, , Namespaces, Environments and variable lookup
@subsection Hash table
Environments in @R{} usually have a hash table, although that is not the
Environments in @R{} usually have a hash table, and nowadays that is the
default in @code{new.env()}. It is stored as a @code{VECSXP} where
@code{length} is used for the allocated size of the table and
@code{truelength} is the number of primary slots in use---the pointer to
......@@ -773,8 +770,8 @@ attr(,"comm")
@cindex context
@emph{Contexts} are the internal mechanism used to keep track of where a
computation has got to (and from where), so that control-flow constructs
can work and reasonable information can be produced on error conditions,
(such as @emph{via} traceback) and otherwise (the @code{sys.@var{xxx}}
can work and reasonable information can be produced on error conditions
(such as @emph{via} traceback), and otherwise (the @code{sys.@var{xxx}}
functions).
Execution contexts are a stack of C @code{structs}:
......@@ -803,7 +800,7 @@ typedef struct RCNTXT @{
@end example
@noindent
plus additional fields for the future byte-code compiler. The `types'
plus additional fields for the byte-code compiler. The `types'
are from
@example
......@@ -1149,11 +1146,10 @@ and @code{readRDS} can read @command{gzip}, @command{bzip2} and
@R{} has used the same serialization format since @R{} 1.4.0 in December
2001. Earlier formats are still supported via @code{load} and
@code{save} but such formats are not described here. (Files of some of
these formats can still be found in @file{data} directories of
packages.) The current serialization format is called `version 2', and
has been expanded in back-compatible ways since @R{} 1.4.0, for example
to support additional @code{SEXPTYPE}s.