Commit 218a25a8 authored by Radford Neal's avatar Radford Neal

Files from R-2.12.1.

parent b3ba0ec8
R News
CHANGES IN R VERSION 2.12.1:
NEW FEATURES:
The DVI/PDF reference manual now includes the help pages for all
the standard packages: splines, stats4 and tcltk were previously
omitted (intentionally).
<URL: http://www.rforge.net> has been added to the default set of
repositories known to setRepositories().
xz-utils has been updated to version 5.0.0.
reshape() now makes use of sep when forming names during
reshaping to wide format. (PR#14435)
legend() allows the length of lines to be set by the end user
_via_ the new argument seg.len.
New reference class utility methods copy(), field(),
getRefClass() and getClass() have been added.
When a character value is used for the EXPR argument in switch(),
a warning is given if more than one unnamed alternative value is
given. This will become an error in R 2.13.0.
StructTS(type = "BSM") now allows series with just two seasons.
(Reported by Birgit Erni.)
INSTALLATION:
The PDF reference manual is now built as PDF version 1.5 with
object compression, which on platforms for which this is not the
default (notably MiKTeX) halves its size.
Variable FCLIBS can be set during configuration, for any
additional library flags needed when linking a shared object with
the Fortran 9x compiler. (Needed with Solaris Studio 12.2.)
BUG FIXES:
seq.int() no longer sometimes evaluates arguments twice.
(PR#14388)
The data.frame method of format() failed if a column name was
longer than 256 bytes (the maximum length allowed for an R name).
predict(<lm object>, type ="terms", ...) failed if both terms and
interval were specified. (Reported by Bill Dunlap.)
Also, if se.fit = TRUE the standard errors were reported for all
terms, not just those selected by a non-null terms.
The TRE regular expressions engine could terminate R rather than
give an error when given certain invalid regular expressions.
(PR#14398)
cmdscale(eig = TRUE) was documented to return n-1 eigenvalues but
in fact only returned k. It now returns all n eigenvalues.
cmdscale(add = TRUE) failed to centre the return configuration
and sometimes lost the labels on the points. Its return value
was described wrongly (it is always a list and contains component
ac).
promptClass() in package methods now works for reference classes
and gives a suitably specialized skeleton of documentation.
Also, callSuper() now works via the methods() invocation as well
as for initially specified methods.
download.file() could leave the destination file open if the URL
was not able to be opened. (PR#14414)
Assignment of an environment to functions or as an attribute to
other objects now works for S4 subclasses of "environment".
Use of [[<- for S4 subclasses of "environment" generated an
infinite recursion from the method. The method has been replaced
by internal code.
In a reference class S4 method, callSuper() now works in
initialize() methods when there is no explicit superclass method.
! dropped attributes such as names and dimensions from a
length-zero argument. (PR#14424)
When list2env() created an environment it was missing a PROTECT
call and so was vulnerable to garbage collection.
Sweave() with keep.source=TRUE dropped comments at the start and
end of code chunks. It could also fail when \SweaveInput was
combined with named chunks.
The Fortran code used by nls(algorithm = "port") could
infinite-loop when compiled with high optimization on a modern
version of gcc, and SAFE_FFLAGS is now used to make this less
likely. (PR#14427, seen with 32-bit Windows using gcc 4.5.0 used
from R 2.12.0.)
sapply() with default simplify = TRUE and mapply() with default
SIMPLIFY = TRUE wrongly simplified language-like results, as,
e.g., in mapply(1:2, c(3,7), FUN = function(i,j) call(':',i,j)).
Backreferences to undefined patterns in [g]sub(pcre = TRUE) could
cause a segfault. (PR#14431)
The format() (and hence the print()) method for class "Date"
rounded fractional dates towards zero: it now always rounds them
down.
Reference S4 class creation could generate ambiguous inheritance
patterns under very special circumstances.
[[<- turned S4 subclasses of "environment" into plain
environments.
Long titles for help pages were truncated in package indices and
a few other places.
Additional utilities now work correctly with S4 subclasses of
"environment" (rm, locking tools and active bindings).
spec.ar() now also work for the "ols" method. (Reported by
Hans-Ruedi Kuensch.)
The initialization of objects from S4 subclasses of "environment"
now allocates a new environment object.
R CMD check has more protection against (probably erroneous)
example or test output which is invalid in the current locale.
qr.X() with column names and pivoting now also pivots the column
names. (PR#14438)
unit.pmax() and unit.pmin() in package grid gave incorrect
results when all inputs were of length 1. (PR#14443)
The parser for NAMESPACE files ignored misspelled directives,
rather than signalling an error. For 2.12.x a warning will be
issued, but this will be correctly reported as an error in later
releases. (Reported by Charles Berry.)
Fix for subsetting of "raster" objects when only one of i or j is
specified.
grid.raster() in package grid did not accept "nativeRaster"
objects (like rasterImage() does).
Rendering raster images in PDF output was resetting the clipping
region.
Rendering of raster images on Cairo X11 device was wrong,
particularly when a small image was being scaled up using
interpolation.
With Cairo < 1.6, will be better than before, though still a
little clunky. With Cairo >= 1.6, should be sweet as.
Several bugs fixed in read.DIF(): single column inputs caused
errors, cells marked as "character" could be converted to other
types, and (in Windows) copying from the clipboard failed.
CHANGES IN R VERSION 2.12.0:
NEW FEATURES:
Reading a packages's CITATION file now defaults to ASCII rather
Reading a package's CITATION file now defaults to ASCII rather
than Latin-1: a package with a non-ASCII CITATION file should
declare an encoding in its DESCRIPTION file and use that encoding
for the CITATION file.
......@@ -72,7 +235,8 @@ CHANGES IN R VERSION 2.12.0:
• There are several small changes to output which ‘zap’ small
numbers, e.g. in printing quantiles of residuals in summaries
from "lm" and "glm" fits, and in test statisics in print.anova().
from "lm" and "glm" fits, and in test statistics in
print.anova().
• Special names such as "dim", "names", etc, are now allowed as
slot names of S4 classes, with "class" the only remaining
......@@ -285,7 +449,7 @@ CHANGES IN R VERSION 2.12.0:
(portably) ignore standard output.
system(intern = TRUE) and pipe() connections are guaranteed to be
avaliable on all builds of R.
available on all builds of R.
Sys.which() has been altered to return "" if the command is not
found (even on Solaris).
......@@ -1311,7 +1475,7 @@ CHANGES IN R VERSION 2.11.0:
Various ar() fitting methods have more protection for singular
fits.
callNextMethod now works again with the drop= argument in `[`
callNextMethod now works again with the drop= argument in [
parse() and parse_Rd() miscounted columns when multibyte UTF-8
characters were present.
......@@ -1515,7 +1679,7 @@ CHANGES IN R VERSION 2.10.1 patched:
user.child instead) on systems with HAVE_GETRUSAGE. (PR#14210)
• Changing both line texture and line cap (end) resulted in the
latter to be ommitted form the PDF code. In addition, line cap
latter to be omitted form the PDF code. In addition, line cap
(end) and join are now set explicitly in PDF output to ensure
correct defaults.
......@@ -1761,7 +1925,7 @@ CHANGES IN R VERSION 2.10.0:
• [g]sub(perl=TRUE) now also supports "\E" in order to *end* "\U"
and "\L" case changes, thanks to a patch from Bill Dunlap.
• factor(), `levels<-`(), etc, now ensure that the resulting factor
• factor(), levels()<-, etc, now ensure that the resulting factor
levels are unique (as was always the implied intention). Factors
with duplicated levels are still constructible by low-level
means, but are now declared illegal.
......@@ -1785,7 +1949,7 @@ CHANGES IN R VERSION 2.10.0:
• available.packages() by default only returns information on the
latest versions of packages whose version requirements are
satisified by the currently running R.
satisfied by the currently running R.
• tools::write_PACKAGES() has a new argument latestOnly, which
defaults to TRUE when only the latest versions in the repository
......@@ -2044,7 +2208,7 @@ CHANGES IN R VERSION 2.10.0:
• A different regular expression engine is used for basic and
extended regexps and is also for approximate matching. This is
based on the TRE library of Ville Laurikari, a modifed copy of
based on the TRE library of Ville Laurikari, a modified copy of
which is included in the R sources.
This is often faster, especially in a MBCS locale.
......
No preview for this file type
Revision: 53317
Last Changed Date: 2010-10-15
Revision: 53855
Last Changed Date: 2010-12-16
......@@ -191,6 +191,8 @@
## SHLIB_FCLD=${FC}
## Unlike SHLIB_CXXLDFLAGS, SHLIB_FCLDFLAGS is never additional
## SHLIB_FCLDFLAGS=${SHLIB_LDFLAGS}
## Additional libraries needed to link a shared object, e.g. on x86 Solaris
## FCLIBS=
## Tcl/Tk settings.
## Use TCLTK_LIBS for all '-L' and '-l' options needed for linking
......
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......@@ -1714,11 +1714,9 @@ AC_CHECK_DECLS([putenv], , , [#include <stdlib.h>])
## this is a GNU extension so usually hidden
AC_CHECK_FUNCS(vasprintf)
AC_CHECK_DECLS([vasprintf], , , [#include <stdio.h>])
## mempcpy is a GNU extension used by regex.c. That defines
## _GNU_SOURCE, so should be declared on glibc systems.
## gettext will also check for this.
## mempcpy is a GNU extension used by the included gettext
AC_CHECK_FUNCS(mempcpy)
## realpath is a BSD extension.
## realpath is a POSIX 2001 (and BSD)
## Some early GNU libc systems had it in unistd.h.
AC_CHECK_FUNCS(realpath)
AC_CHECK_DECLS([realpath], , , [#include <stdlib.h>
......@@ -2136,6 +2134,9 @@ AC_LANG_POP()
: ${SHLIB_FCLDFLAGS="${SHLIB_LDFLAGS}"}
AC_SUBST(SHLIB_FCLD)
AC_SUBST(SHLIB_FCLDFLAGS)
## x86 Solaris' f95 needs additional libs when building a DSO
FCLIBS=${FCLIBS}
AC_SUBST(FCLIBS)
## Look for FCPICFLAGS
......
......@@ -10,7 +10,7 @@ Belgium,Belgium,Antwerp,http://www.freestatistics.org/cran/,"K.U.Leuven Associat
"Canada (NS)",Canada,Halifax,http://mirror.its.dal.ca/cran/,"Dalhousie University, Halifax","mirror # lists.dal.ca",1,ca
"Canada (ON)",Canada,Toronto,http://probability.ca/cran/,"University of Toronto","Jeffrey S. Rosenthal <jeff at math.toronto.edu>",1,ca
"Canada (QC 1)",Canada,Montreal,http://cran.skazkaforyou.com/,"iWeb, Montreal","mirrors # skazkaforyou.com",1,ca
"Canada (QC 2)",Canada,Montreal,http://cran.parentinginformed.com/,"iWeb, Montreal","jmiller # parentinginformed.com",1,ca
"Canada (QC 2)",Canada,Montreal,http://cran.parentingamerica.com/,"iWeb, Montreal","jmiller # Parentingamerica.com",1,ca
Chile,Chile,Santiago,http://dirichlet.mat.puc.cl/,"Pontificia Universidad Catolica de Chile, Santiago","Fernando Quintana <quintana # mat.puc.cl>",1,cl
"China (Beijing 1)",China,Bejing,http://ftp.ctex.org/mirrors/CRAN/,CTEX.ORG,"Aloft Wu <aloft # ctex.org>",1,cn
"China (Beijing 2)",China,Bejing,http://cran.csdb.cn/,"Computer Network Information Center, CAS, Beijing","Hull # cnic.cn",1,cn
......@@ -55,7 +55,8 @@ Switzerland,Switzerland,Zuerich,http://stat.ethz.ch/CRAN/,"ETH Zuerich","Martin.
"Taiwan (Taichung)",Taiwan,Taichung,http://cran.cs.pu.edu.tw/,"Providence University, Taichung","hcchang # cs.pu.edu.tw",1,tw
"Taiwan (Taipei 1)",Taiwan,Taipei,http://cran.csie.ntu.edu.tw/,"National Taiwan University, Taipei","Rong-En Fan <rafan # infor.org>",1,tw
"Taiwan (Taipei 2)",Taiwan,Taipei,http://cran.stat.tku.edu.tw/,"Tamkang University, Taipei","steve # stat.tku.edu.tw",1,tw
"Thailand (Bangkog)",Thailand,Bangkok,http://mirror.kapook.com/cran/,"Kapook.com, Bangkok","thawachchai # bunditcenter.com",1,th
"Thailand (Bangkog 1)",Thailand,Bangkok,http://mirror.kapook.com/cran/,"Kapook.com, Bangkok","thawachchai # bunditcenter.com",1,th
"Thailand (Bangkog 2)",Thailand,Bangkok,http://www.mirror.in.th/osarchive/CRAN/,"Software Industry Promotion Agency,  Bangkok","iempairote # Buu.ac.th",1,th
"Thailand (Hatyai)",Thailand,Hatyai,http://mirrors.psu.ac.th/pub/cran/,"Prince of Songkla University, Hatyai","wipat.s # psu.ac.th",1,th
"UK (Bristol)",UK,Bristol,http://www.stats.bris.ac.uk/R/,"University of Bristol","Guy Nason <G.P.Nason # bristol.ac.uk>",1,uk
"UK (London)",UK,London,http://cran.ma.imperial.ac.uk/,"Imperial College London","s.rochford # imperial.ac.uk",1,uk
......
R FAQ
Frequently Asked Questions on R
Version 2.12.2010-10-11
Version 2.12.2010-12-13
ISBN 3-900051-08-9
Kurt Hornik
......@@ -255,7 +255,7 @@ i386-freebsd, rs6000-ibm-aix, and sparc-sun-solaris.
2.3 What is the current version of R?
=====================================
The current released version is 2.12.0. Based on this
The current released version is 2.12.1. 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
......
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......@@ -56,7 +56,7 @@ R_RD4PDF = @R_RD4PDF@
texinputs_BASE = $(R_PKGS_BASE:=-pkg.tex)
texinputs_RECOMMENDED = $(R_PKGS_RECOMMENDED:=-pkg.tex)
R_PKGS_refman = base datasets grDevices graphics grid methods stats tools utils
R_PKGS_refman = base datasets grDevices graphics grid methods splines stats stats4 tcltk tools utils
refman_TEXINPUTS = $(R_PKGS_refman:=-pkg.tex)
refman_DEPENDENCIES = version.tex $(top_srcdir)/share/texmf/tex/latex/Rd.sty
fullrefman_TEXINPUTS = $(texinputs_BASE) @USE_RECOMMENDED_PACKAGES_TRUE@ $(texinputs_RECOMMENDED)
......@@ -216,11 +216,8 @@ fullrefman.dvi: $(refman_DEPENDENCIES) stamp-fullrefman-dvi
do $(ECHO) $${f}; done) | LC_COLLATE=C $(SORT)`; \
for f in $${texinputs}; do $(ECHO) "\\input{$${f}}"; done; \
$(ECHO) "\\part{}"; \
texinputs=`(for f in $(fullrefman_TEXINPUTS); \
texinputs=`(for f in $(texinputs_RECOMMENDED); \
do $(ECHO) $${f}; done) | LC_COLLATE=C $(SORT)`; \
for f in $(refman_TEXINPUTS); do \
texinputs=`$(ECHO) "$${texinputs}" | sed "/$${f}/d"`; \
done; \
for f in $${texinputs}; do $(ECHO) "\\input{$${f}}"; done; \
cat $(srcdir)/refman.bot) > fullrefman.tex
@TEXINPUTS="$(top_srcdir)/share/texmf/tex/latex:$$TEXINPUTS" \
......@@ -324,11 +321,8 @@ fullrefman.pdf: $(refman_DEPENDENCIES) stamp-fullrefman-pdf
do $(ECHO) $${f}; done) | LC_COLLATE=C $(SORT)`; \
for f in $${texinputs}; do $(ECHO) "\\input{$${f}}"; done; \
$(ECHO) "\\part{}"; \
texinputs=`(for f in $(fullrefman_TEXINPUTS); \
texinputs=`(for f in $(texinputs_RECOMMENDED); \
do $(ECHO) $${f}; done) | LC_COLLATE=C $(SORT)`; \
for f in $(refman_TEXINPUTS); do \
texinputs=`$(ECHO) "$${texinputs}" | sed "/$${f}/d"`; \
done; \
for f in $${texinputs}; do $(ECHO) "\\input{$${f}}"; done; \
cat $(srcdir)/refman.bot) > fullrefman.tex
@TEXINPUTS="$(top_srcdir)/share/texmf/tex/latex:$$TEXINPUTS" \
......
......@@ -58,7 +58,7 @@ R_RD4PDF = times,hyper
texinputs_BASE = $(R_PKGS_BASE:=-pkg.tex)
texinputs_RECOMMENDED = $(R_PKGS_RECOMMENDED:=-pkg.tex)
R_PKGS_refman = base datasets grDevices graphics grid methods stats tools utils
R_PKGS_refman = base datasets grDevices graphics grid methods splines stats stats4 tcltk tools utils
refman_TEXINPUTS = $(R_PKGS_refman:=-pkg.tex)
refman_DEPENDENCIES = version.tex $(top_srcdir)/share/texmf/tex/latex/Rd.sty
fullrefman_TEXINPUTS = $(texinputs_BASE) $(texinputs_RECOMMENDED)
......@@ -156,11 +156,8 @@ fullrefman.dvi: $(fullrefman_TEXINPUTS) $(refman_DEPENDENCIES) \
do $(ECHO) $${f}; done) | LC_COLLATE=C $(SORT)`; \
for f in $${texinputs}; do $(ECHO) "\\input{$${f}}"; done; \
$(ECHO) "\\part{}"; \
texinputs=`(for f in $(fullrefman_TEXINPUTS); \
texinputs=`(for f in $(texinputs_RECOMMENDED); \
do $(ECHO) $${f}; done) | LC_COLLATE=C $(SORT)`; \
for f in $(refman_TEXINPUTS); do \
texinputs=`$(ECHO) "$${texinputs}" | sed "/$${f}/d"`; \
done; \
for f in $${texinputs}; do $(ECHO) "\\input{$${f}}"; done; \
cat $(srcdir)/refman.bot) > fullrefman.tex
@$(RM) -f *.aux fullrefman.toc fullrefman.ind
......@@ -215,11 +212,8 @@ fullrefman.pdf: $(fullrefman_TEXINPUTS) $(refman_DEPENDENCIES) \
do $(ECHO) $${f}; done) | LC_COLLATE=C $(SORT)`; \
for f in $${texinputs}; do $(ECHO) "\\input{$${f}}"; done; \
$(ECHO) "\\part{}"; \
texinputs=`(for f in $(fullrefman_TEXINPUTS); \
texinputs=`(for f in $(texinputs_RECOMMENDED); \
do $(ECHO) $${f}; done) | LC_COLLATE=C $(SORT)`; \
for f in $(refman_TEXINPUTS); do \
texinputs=`$(ECHO) "$${texinputs}" | sed "/$${f}/d"`; \
done; \
for f in $${texinputs}; do $(ECHO) "\\input{$${f}}"; done; \
cat $(srcdir)/refman.bot) > fullrefman.tex
@$(RM) -f *.aux fullrefman.toc fullrefman.ind
......
......@@ -4,11 +4,11 @@
@settitle R FAQ
@setchapternewpage on
@set FAQ_YEAR 2010
@set FAQ_DATE @value{FAQ_YEAR}-10-11
@set FAQ_DATE @value{FAQ_YEAR}-12-13
@set REL_YEAR 2010
@set REL_MAJOR 2
@set REL_MINOR 12
@set REL_PATCHLEVEL 0
@set REL_PATCHLEVEL 1
@set REL_VERSION @value{REL_MAJOR}.@value{REL_MINOR}.@value{REL_PATCHLEVEL}
@set FAQ_VERSION @value{REL_MAJOR}.@value{REL_MINOR}.@value{FAQ_DATE}
......
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......@@ -90,12 +90,12 @@ principal authors of the packages mentioned are
@quotation
@multitable {foreign xxxx} {A longggggggggggggggggggggggggggggggggg description}
@item @pkg{CORBA} @tab Duncan Temple Lang
@item @pkg{DBI} David A. James
@item @pkg{dataframes2xls} Guido van Steen
@item @pkg{DBI} @tab David A. James
@item @pkg{dataframes2xls} @tab Guido van Steen
@item @pkg{foreign} @tab Thomas Lumley, Saikat DebRoy, Douglas Bates, Duncan Murdoch and Roger Bivand
@item @pkg{gdata} @tab Gregory R. Warnes
@item @pkg{hdf5} @tab Marcus Daniels
@item @pkg{ncdf} @tab David Pierce
@item @pkg{ncdf}, @pkg{ncdf4} @tab David Pierce
@item @pkg{rJava} @tab Simon Urbanek
@item @pkg{RMySQL} @tab David James and Saikat DebRoy
@item @pkg{RNetCDF} @tab Pavel Michna
......@@ -262,7 +262,7 @@ is specified. Excel is one such system.
@findex write.csv2
A common field separator to use in the file is a comma, as that is
unlikely to appear in any of the fields, in English-speaking countries.
unlikely to appear in any of the fields in English-speaking countries.
Such files are known as CSV (comma separated values) files, and wrapper
function @code{write.csv} provides appropriate defaults. In some locales
the comma is used as the decimal point (set this in @code{write.table}
......@@ -303,6 +303,29 @@ a
@noindent
The second is the form of escape commonly used by spreadsheets.
@item @strong{Encodings}
@cindex Encodings
Text files do not contain metadata on their encodings, so for non-ASCII
data the file needs to be targetted to the application intended to read
it. All of these functions can write to a @emph{connection} which
allows an encoding to be specified for the file, and as from @R{} 2.13.0
@code{write.table} has a @code{fileEncoding} argument to make this
easier.
The hard part is to know what file encoding to use. For use on Windows,
it is best to use what Windows calls `Unicode'@footnote{Even then,
Windows applications may expect a Byte Order Mark which the
implementation of @code{iconv} used by @R{} may or may not add depending
on the platform.}, that is @code{"UTF-16LE"}. Using UTF-8 is a good way
to make portable files that will not easily be confused with any other
encoding, but even Mac OS X applications (where UTF-8 is the system
encoding) may not recognize them, and Windows applications are most
unlikely to. Apparently Excel:mac 2004/8 expects @code{.csv} files in
@code{"macroman"} encoding (the encoding used in much earlier versions
of Mac OS).
@end enumerate
@findex write.matrix
......@@ -791,10 +814,10 @@ Another way to do this is to use the function
...
@end example
The @code{reshape} has a more complicated syntax than @code{stack} but
can be used for data where the `long' form has more than the one column
in this example. With @code{direction="wide"}, @code{reshape} can also
perform the opposite transformation.
The @code{reshape} function has a more complicated syntax than
@code{stack} but can be used for data where the `long' form has more
than the one column in this example. With @code{direction="wide"},
@code{reshape} can also perform the opposite transformation.
@node Flat contingency tables, , Re-shaping data, Spreadsheet-like data
@section Flat contingency tables
......@@ -932,8 +955,8 @@ export the data in an ordinary @acronym{SPSS} format.
@cindex Stata
@findex read.dta
@findex write.dta
Stata @file{.dta} files are a binary file format. Files from versions 5,
6, 7/SE and 8 of Stata can be read and written by functions
Stata @file{.dta} files are a binary file format. Files from versions 5
up to at least 11 of Stata can be read and written by functions
@code{read.dta} and @code{write.dta}. Stata variables with value labels
are optionally converted to (and from) @R{} factor.
......@@ -1200,13 +1223,13 @@ PostgreSQL.
@menu
* DBI / RMySQL::
* DBI::
* RODBC::
@end menu
@node DBI / RMySQL, RODBC, R interface packages, R interface packages
@subsection Packages DBI and RMySQL
@node DBI, RODBC, R interface packages, R interface packages
@subsection Packages using DBI
@cindex MySQL database system
Package @pkg{RMySQL} on @acronym{CRAN} provides an interface to the
......@@ -1230,7 +1253,7 @@ object, and then a call to @code{dbConnect} opens a database connection
which can subsequently be closed by a call to the generic function
@code{dbDisconnect}. Use @code{dbDriver("Oracle")},
@code{dbdDriver("PostgreSQL")} or @code{dbDriver("SQLite")} with those
DBMSs and packages @pkg{ROracle}, @pkg{PostgreSQL} or @pkg{RSQLite}
DBMSs and packages @pkg{ROracle}, @pkg{RPostgreSQL} or @pkg{RSQLite}
respectively.
@findex dbSendQuery
......@@ -1294,7 +1317,7 @@ Arkansas 8.8 190 50 19.5
> dbDisconnect(con)
@end smallexample
@node RODBC, , DBI / RMySQL, R interface packages
@node RODBC, , DBI, R interface packages
@subsection Package RODBC
@cindex ODBC
@cindex Open Database Connectivity
......@@ -1591,10 +1614,10 @@ handle binary files.
@findex netCDF
@cindex network Common Data Form
Packages @pkg{hdf5}, @pkg{RNetCDF} and @pkg{ncdf} on @acronym{CRAN}
provide interfaces to @acronym{NASA}'s HDF5 (Hierarchical Data Format,
see @uref{http://hdf.ncsa.uiuc.edu/HDF5/}) and to UCAR's netCDF data
files (network Common Data Form, see
Packages @pkg{hdf5}, @pkg{RNetCDF}, @pkg{ncdf} and @pkg{ncdf4} on
@acronym{CRAN} provide interfaces to @acronym{NASA}'s HDF5 (Hierarchical
Data Format, see @uref{http://hdf.ncsa.uiuc.edu/HDF5/}) and to UCAR's
netCDF data files (network Common Data Form, see
@uref{http://www.unidata.ucar.edu/packages/netcdf/}).
Both of these are systems to store scientific data in array-oriented
......@@ -1603,6 +1626,13 @@ allows @emph{groups} of arrays, and the @R{} interface maps lists
to HDF5 groups, and can write numeric and character vectors and
matrices.
NetCDF's version 4 format (confusingly, implemented in netCDF 4.1.1 and
later, but not in 4.0.1) includes the use of various HDF5 formats. This
is handled by package @pkg{ncdf4} whereas @pkg{RNetCDF} and @pkg{ncdf}
handle version 3 files.
The availability of software to support these formats is somewhat
limited by platform, especially on Windows.
@node dBase files (DBF), , Binary data formats, Binary files
@section dBase files (DBF)
......
......@@ -1215,7 +1215,7 @@ On Windows there is normally a choice between linking to an import
library or directly to a DLL. Where possible, the latter is much more
reliable: import libraries are tied to a specific toolchain, and in
particular on 64-bit Windows two different conventions are common, and
@R{} 2.11.x and 2.12.x use different ones. So for example instead of
@R{} 2.11.x and 2.12.x use different ones. So for example instead of
@example
PKG_LIBS = -L$(XML_DIR)/lib -lxml2
......@@ -1697,13 +1697,13 @@ installed in an available library tree (see the Note: below).
Similarly, if the @file{.Rd} documentation files contain any
@code{\Sexpr} macros (@pxref{Dynamic pages}), the package will be
temporarily installed to execute them. Post-execution binary copies
of those pages containing build-time macros will be saved in
@file{build/partial.rdb}. If there are any install-time or
render-time macros, a @file{.pdf} version of the package manual will be built
and installed in the @file{build/} subdirectory. (This allows CRAN or
other repositories to display the manual even if they are unable to
install the package.)
temporarily installed to execute them. Post-execution binary copies of
those pages containing build-time macros will be saved in