Commit 1786031e authored by Dirk Eddelbuettel's avatar Dirk Eddelbuettel

Import Upstream version 2.1.1

parent 4e20891f
This diff is collapsed.
......@@ -113,13 +113,12 @@ install-strip:
@(for d in $(SUBDIRS); do rsd="$${d} $${rsd}"; done; \
for d in $${rsd}; do (cd $${d} && $(MAKE) $@); done)
@for f in $(INSTFILES); do \
@for f in $(INSTFILES) $(NON_SVN_INSTFILES); do \
rm -f "$(rhome)/$${f}"; \
@rm -rf "$(Rexecbindir)" "$(Rexeclibdir)"
@rm -rf "$(rhome)/demos"
@rm -rf "$(rhome)/gnome"
@rmdir "$(rhome)" 2>/dev/null \
|| echo " dir $(rhome) not removed"
mostlyclean: clean
Dear Emacs, please make this -*-Text-*- mode!
Dear Emacs, please make this -*-Text-*- mode!
* *
......@@ -6,6 +6,198 @@
o now reports the locale in use.
o upgrade.packageStatus() allows user input "c" to cancel the
upgrade, just as update.packages() does.
o glm() now accepts 1D arrays (e.g. tables) as a response,
dropping them to a vector whilst preserving names.
o df() with one infinite df now works (to match pf()).
o Added tclServiceMode() function to the tcltk package to allow
updating to be suspended.
o The Encoding: field of a DESCRIPTION file is now documented,
and used by packageDescription() and library(help=).
o There has been progress on translations: existing translations
have been revised and expanded, and French and Korean have
been added.
The Windows installer supports a wide range of languages for
o lm(qr=FALSE) now works.
o predict.glm() not longer loses names for "response" predictions.
o Typo in menu(graphics=TRUE) meant it failed on Unix if tcltk
was not available.
o When names.dist() was removed, the result of cmdscale() lost
its rownames. The example also lost the labels.
o R CMD check assumed 'tar' was GNU tar and so supported -z.
o read.table() was not handing escaped quotes inside quoted fields
in the first five lines of the file. (PR#7789)
It was also not handling correctly EOF in the first five lines
when reading from stdin(). (PR#7772)
o 'make uninstall' was incomplete.
o make.packages.html() called by help.start() was failing if
there were installed packages with help titles invalid in the
current locale.
o printCoefmat(signif.legend = FALSE) was non-functional. (PR#7802)
o Some methods failed because the expression
deparsed into multiple lines. (PR#7808)
o setRepositories() had a typo. (PR#7810)
o Printing arrays/data frames with multibyte characters in the
column labels was sometimes misaligned or using excessive space.
o The Tcl/Tk console did not support multibyte characters.
o as.POSIXlt() could give infinite recursion if passed a corrupt
"POSIXct" object (generated by an incorrect call to c.POSIXct,
o update.packages() was not passing 'type' correctly to
o Printing the result of an unbalanced model.tables() call
sometimes got confused if terms() had rearranged interaction
terms. (PR#7829)
o .Platform$pkgType was wrong on the CRAN MacOS X build, and
.install.macbinary() was missing.
o as.personList() as used by citation() got confused by names
containing "and". (PR#7797)
o Subscripting an array by a matrix containing zero or negative
values or the wrong number of columns was not handled
consistently. (PR#7824)
o select.list(multiple=TRUE) now detects and tries again for invalid
text input.
o add1.[g]lm could give strange results with interaction terms
when the model and the upper scope had different orders for
the main effects. (PR#7842)
o A bug had sneaked into the anova.mlmlist() code, affecting the
Greenhouse-Geisser epsilon. Code wrongly assumed a matrix to
be symmetric. (Thanks to Bela Bauer.)
o anova.mlmlist() and mauchley.test() are now more tolerant to rank
deficiency in the M and X matrices (also when they are implicitly
generated via model.matrix()).
o anova.mlm had a scoping issue (PR#7898)
o pf() with infinite df is allowed again. It is now more accurate
for extreme ratios of dfs, especially when there is a
non-centrality parameter.
o df() was inaccurate for large df (1e16 or greater).
o dt() was inaccurate for large df (1e9 or greater) with a
non-centrality parameter.
o runmed(*, algorithm="Turlach") seg.faulted in rare cases.
o strwrap() now makes a reasonable job of text that is invalid in the
current locale.
o Reading with encoding "UCS-2LE" will remove any Byte Order
Mark, as most implementations of iconv fail to handle BOMs
(which are present in 'Windows Unicode' files).
o unique() for a list was incorrectly reporting `unimplemented'.
o The parser's contextstack was not protected against overflow,
e.g. more than 50 unmatched '('. (PR#7859)
o source(file, chdir = TRUE) was not checking that 'file' was a
filepath (rather than a URL). For 2.1.0 only, it did not work
even if 'file' was a filepath.
o Hershey fonts were being sized based on pixels not points so came
out too small on devices where pixels were noticeably different
from points (e.g., win.printer() and high-resolution screens).
Fix means that default size of Hershey fonts may be slightly
different, for example, smaller by default on PostScript and PDF.
o The branch cuts in the complex versions of the inverse
trigonometric and hyperbolic functions were non-standard.
o truncate() on file() connections was limited to files < 2Gb. It
now works for larger files at least on 64-bit OSes and others
where ftruncate supports such files. (Related to PR#7879)
o proj.aovlist() did not work correctly on objects fitted from a
data frame with row names.
o The coding standards recommendations had
nuke-trailing-whitespace where newer versions of ESS need
ess-nuke-trailing-whitespace. (PR#7888)
o package.skeleton() missed the first newline in the DESCRIPTION file.
o pbirthday() reported p = 1 too often when coincident > 2.
o plot(1:3, exp(1:3), log = "y", ylim = c(30,1)) {reversed
log-scale axis} now works, based on Uwe Ligges' suggestions.
o install.packages() was aborting when a package in a bundle was
chosen from a menu. It failed if more than one package in a
bundle was chosen from the command line.
o qcauchy() suffered from underflow in the extreme tails. (PR#7902)
o Printing of raw matrices/arrays was not implemented. (PR#7912)
o getCallingDLL()'s default first argument did not correspond to
its description and has been changed. The mismatch caused
symbols in .C/.Call/.Fortran calls without a PACKAGE= argument
to be potentially looked up in the wrong namespace.
o Binary save() of raw vectors was not working correctly on
big-endian platforms. (PR#7812)
o as.Date.factor() now accepts a format argument.
o Workaround added for FreeBSD which does not have alloca.h _and_
does not allow alloca() to be declared.
o identify() now respects 'cex'. (PR#660)
Warnings from identify() are now printed immediately even on
consoles with delayed printing.
......@@ -459,7 +651,7 @@ INTERNATIONALIZATION
multi-byte locales on suitably equipped OSes if configured
with option --enable-mbcs (which is the default). [The
changes to font handling in the X11 module are based on the
Japanization patches of Eiji Nakama.]
Japanization patches of Ei-ji Nakama.]
Windows versions of R can be used in `East Asian' locales on
suitable versions of Windows.
......@@ -679,12 +871,12 @@ DEPRECATED & DEFUNCT
o loadURL() is deprecated in favour of load(url()).
o delay() is deprecated. Use delayAssign() instead.
o delay() is deprecated. Use delayedAssign() instead.
o New configure option --enable-utf8 to enable support for
o New configure option --enable-mbcs to enable support for
UTF-8 locales, on by default.
o R_XTRA_[CF]FLAGS are now used during the configuration tests,
This diff is collapsed.
......@@ -145,8 +145,8 @@ fi],
## Allow the user to specify building an R framework (Darwin).
[build R framework (if possible), and specify its
installation prefix @<:@yes, /Library/Frameworks@:>@])],
[MacOS X only: build R framework (if possible), and specify
its installation prefix @<:@yes, /Library/Frameworks@:>@])],
## Can only build frameworks on Darwin.
......@@ -182,7 +182,7 @@ AM_CONDITIONAL(WANT_R_FRAMEWORK, [test "x${want_R_framework}" = xyes])
## </NOTE>
[build R as a shared library @<:@no@:>@])],
[build the shared/dynamic library 'libR' @<:@no@:>@])],
## processed after GNOME, which can set this.
......@@ -211,13 +211,13 @@ fi
[Enable support for > 2GB files on Linux @<:@no@:>@])],
[enable support for > 2GB files on Linux @<:@no@:>@])],
[Enable support for UTF-8 and other MBCS locales @<:@yes@:>@])],
[enable support for UTF-8 and other MBCS locales @<:@yes@:>@])],
......@@ -248,7 +248,7 @@ AC_ARG_WITH([readline],
## Aqua.
[use Aqua (if available) @<:@no@:>@])],
[MacOS X only: use Aqua (if available) @<:@no@:>@])],
## Tcl/Tk.
......@@ -466,14 +466,27 @@ R_PROG_MAKEINFO
## Make sure that non-standard directories specified via '-L' are really
## searched in the tests.
## Note: earlier versions used LIBS rather than LDFLAGS.
for arg in ${LDFLAGS}; do
case "${arg}" in
lib=`echo ${arg} | sed "s/^-L//"`
case "${host_os}" in
## Darwin provides a full path in the ID of each library such
## that the linker can add library's path to the binary at link time.
## This allows the dyld to find libraries even without xx_LIBRARY_PATH.
## No paths should be added to R_LD_LIBRARY_PATH (which in turn
## changes DYLD_LIBRARY_PATH), because they override the system
## look-up sequence. Such automatic override has proven to break things
## like system frameworks (e.g. ImageIO or OpenGL framework).
for arg in ${LDFLAGS}; do
case "${arg}" in
lib=`echo ${arg} | sed "s/^-L//"`
## </FIXME>
## Record name of environment variable which tells the dynamic linker
......@@ -1288,7 +1301,7 @@ if test "${use_lapack}" = "yes"; then
if test "${acx_lapack_ok}" != "yes"; then
LAPACK_LIBS="-L\${R_HOME}/lib -lRlapack"
LAPACK_LIBS="-L\$(R_HOME)/lib -lRlapack"
AM_CONDITIONAL(USE_EXTERNAL_LAPACK, [test "${acx_lapack_ok}" = "yes"])
......@@ -1420,6 +1433,8 @@ for arg in ${LDFLAGS} ${FLIBS} ${BLAS_LIBS} ${LAPACK_LIBS} ${X_LIBS} \
lib=`echo ${arg} | sed "s/^-L//"`
## don't add anything for Darwin
case "${host_os}" in darwin*) r_want_lib=false ;; esac
## Do not add non-existent directories.
test -d "${lib}" || continue
## Canonicalize (/usr/lib/gcc-lib/i486-linux/3.3.4/../../..).
......@@ -3,10 +3,12 @@ Australia,Australia,Brisbane,,"PlanetMirror, Brisba
Austria,Austria,Wien,,"Technische Universitaet Wien",
"Brasil (PR)",Brasil,Curitiba,,"Universidade Federal do Parana??","Paulo J. Ribeiro Jr <>"
"Brasil (MG)",Brasil,Vicosa,,"Federal University of Vicosa",
"Brasil (RJ)",Brasil,"Rio de Janeiro",,"Oswaldo Cruz Foundation, Rio de Janeiro",
"Brasil (SP 1)",Brasil,Piracicaba,,"University of Sao Paulo, Piracicaba",
"Brasil (SP 2)",Brasil,"Sao Paulo",,"University of Sao Paulo, Sao Paulo","Fernando Ferreira <>"
"Canada (BC)",Canada,Burnaby,,"Simon Fraser University, Burnaby","Brad McNeney <>"
"Canada (ON)",Canada,Toronto,,"University of Toronto","Jeffrey S. Rosenthal <jeff at>"
China,China,Nanjing,,"Southeast University, Nanjing",
Denmark,Denmark,Aalborg,,", Aalborg",
"France (Toulouse)",France,Toulouse,,"CICT, Toulouse","David Allouche <>"
"France (Lyon)",France,Lyon,,"Dept. of Biometry & Evol. Biology, University of Lyon","Jean Thioulouse <>"
......@@ -18,9 +20,12 @@ Denmark,Denmark,Aalborg,,", Aalborg",mirr
Hungary,Hungary,Budapest,,"Semmelweis University","Laszlo L Tornoci <>"
"Italy (Arezzo)",Italy,Arezzo,,"Ars Machinandi, Arezzo",
"Italy (Ferrara)",Italy,Ferrara,,"Universita di Ferrara","Stefano Volinia <>"
"Italy (Milano)",Italy,Milano,,"Garr Mirror, Milano",
"Japan (Aizu)",Japan,Aizu,,"University of Aizu",
"Japan (Tsukuba)",Japan,Tsukuba,,"University of Tsukuba",
Poland,Poland,Wroclaw,,"University of Wroclaw","Pawel Netzel <>"
Korea,Korea,Seoul,,"Seoul National University","SungGON Yi <>"
"Poland (Lublin)",Poland,Lublin,,"Skubiszewski Medical University, Lublin","Lukasz Komsta <>"
"Poland (Wroclaw)",Poland,Wroclaw,,"University of Wroclaw","Pawel Netzel <>"
Portugal,Portugal,Porto,,"Universidade do Porto",
"Slovenia (Besnica)",Slovenia,Besnica,,", Besnica","Tomy Kurtis <>"
"Slovenia (Ljubljana)",Slovenia,Ljubljana,,", Ljubljana",
......@@ -30,13 +35,15 @@ Spain,Spain,Madrid,,"Spanish National Research Netw
"Switzerland (Bern 1)",Switzerland,Bern,,"Universitaet Bern","Thomas Schweizer <>"
"Switzerland (Bern 2)",Switzerland,Bern,,"Prokmu Hosting, Bern",
Turkey,Turkey,Istanbul,,"Istanbul Bilgi University","Vehbi Sinan TUNALIOGLU <>"
Taiwan,Taiwan,Taipei,,"National Taiwan University, Taipei","Rong-En Fan <>"
"Taiwan (Taichung)",Taiwan,Taichung,,"Providence University, Taichung",
"Taiwan (Taipeh)",Taiwan,Taipei,,"National Taiwan University, Taipei","Rong-En Fan <>"
"UK (Bristol)",UK,Bristol,,"University of Bristol","Guy Nason <>"
"UK (London)",UK,London,,"Sourcekeg, London",
"USA (CA 1)",USA,Berkeley,,"University of California, Berkeley, CA",
"USA (CA 2)",USA,"Los Angeles",,"University of California, Los Angeles, CA",
"USA (MA)",USA,Boston,,"Dana Farber Cancer Institute, Boston, MA","Jeff Gentry <>"
"USA (IA)",USA,Ames,,"Iowa State University, Ames, IA","Dave Edsall <>"
"USA (MI)",USA,Houghton,,"Michigan Technological University, Houghton, MI","Robert Froese <>"
"USA (MO)",USA,"St. Louis",,"Washington University, St. Louis, MO",
"USA (NC)",USA,"Chapel Hill",,"University of North Carolina, Chapel Hill, NC","""Nancy C. Wilson"" <>"
"USA (PA 1)",USA,Pittsburgh,,"Pair Networks, Pittsburgh, PA",
"USA (PA 2)",USA,Pittsburgh,,"Statlib, Carnegie Mellon University, Pittsburgh, PA",
......@@ -83,7 +83,7 @@ uninstall:
@for d in $(SUBDIRS); do \
(cd $${d} && $(MAKE) $@); \
@for f in $(CLEANFILES) $(INSTFILES) $(OBJECTS); do \
rm -f "$(rhome)/$(subdir)/$${f}"; \
@rmdir "$(rhome)/$(subdir)" 2>/dev/null \
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......@@ -2080,9 +2080,8 @@ spreadsheet file.
@code{Perl} users have contributed a module
@code{OLE::SpreadSheet::ParseExcel} and a program @code{} to
convert Excel spreadsheets to CSV files. Bundle @pkg{gregmisc}
provides a basic wrapper in its @code{read.xls} function in package
convert Excel spreadsheets to CSV files. Package @pkg{gdata} provides a
basic wrapper in its @code{read.xls} function.
......@@ -234,6 +234,9 @@ start with a space or tab. The @samp{Package}, @samp{Version},
@samp{Maintainer} fields are mandatory, the remaining fields
(@samp{Date}, @samp{Depends}, @samp{URL}, @dots{}) are optional.
The @file{DESCRIPTION} file should be written entirely in ASCII for
maximal portability.
The @samp{Package} and @samp{Version} fields give the name and the
version of the package, respectively. The name should consist of
letters, numbers, and the dot character and start with a letter. The
......@@ -367,6 +370,13 @@ The optional @samp{ZipData} field controls whether the automatic
Windows build will zip up the data directory or no: set this to
@samp{no} if your package will not work with a zipped data directory.
If the @file{DESCRIPTION} file is not entirely in ASCII it should
contain an @samp{Encoding} field specifying an encoding. This is
currently used as the encoding of the @file{DESCRIPTION} file itself,
and may in the future be taken as the encoding for other documentation
in the package. Only encoding names @code{latin1}, @code{latin2} and
@code{UTF-8} are known to be portable.
@quotation Note
There should be no @samp{Built} or @samp{Packaged} fields, as these are
added by the package management tools.
......@@ -7859,7 +7869,10 @@ customization to set the @code{c-default-style} to @code{"bsd"} and
;; ess-close-brace-offset 0 0 0 0 0
(add-hook 'local-write-file-hooks
(lambda ()
(setq ess-nuke-trailing-whitespace-p 'ask)
;; or even
;; (setq ess-nuke-trailing-whitespace-p t)
@end group
;;; Perl
This diff is collapsed.
......@@ -1705,6 +1705,12 @@ operation.
[1] 1 4
@end example
Negative indices are not allowed in indexing matrices. @code{NA} and
zero values are allowed: rows in an index matrix containing a zero are
ignored, whereas rows containing an @code{NA} produce an @code{NA} in
the result.
Both in the case of using a single
@cindex index
index and in matrix indexing, a @code{names} attribute is used if
......@@ -62,7 +62,7 @@ uninstall:
&& test "`cd \"$(rhome)\"; $(GETWD)`" \
!= "`cd $(top_builddir); $(GETWD)`"; then \
(cd "$(rhome)/$(subdir)" && \
rmdir "$(rhome)/$(subdir)" 2> /dev/null \
|| echo " subdir $(subdir) not removed"; \
......@@ -896,10 +896,7 @@ with_gnu_ld=$acl_cv_prog_gnu_ld
dnl From libtool-1.4. Sets the variable LD.
[ --with-gnu-ld assume the C compiler uses GNU ld [default=no]],
test "$withval" = no || with_gnu_ld=yes, with_gnu_ld=no)
# The user is always right.
......@@ -220,7 +220,7 @@ test "x$enable_libtool_lock" != xno && enable_libtool_lock=yes
[try to use only PIC/non-PIC objects @<:@default=use both@:>@])],
[libtool: try to use only PIC/non-PIC objects @<:@default=use both@:>@])],
test -z "$pic_mode" && pic_mode=default
......@@ -1630,7 +1630,7 @@ test "$dynamic_linker" = no && can_build_shared=no
[include additional configurations @<:@automatic@:>@])],
[libtool: include additional configurations @<:@automatic@:>@])],
if test -f "$ltmain" && test -n "$tagnames"; then
......@@ -1748,7 +1748,7 @@ AC_DEFUN([AC_ENABLE_SHARED],
[define([AC_ENABLE_SHARED_DEFAULT], ifelse($1, no, no, yes))dnl
[build shared libraries @<:@default=]AC_ENABLE_SHARED_DEFAULT[@:>@])],
[libtool: build shared libraries @<:@default=]AC_ENABLE_SHARED_DEFAULT[@:>@])],
case $enableval in
yes) enable_shared=yes ;;
......@@ -1787,7 +1787,7 @@ AC_DEFUN([AC_ENABLE_STATIC],
[define([AC_ENABLE_STATIC_DEFAULT], ifelse($1, no, no, yes))dnl
[build static libraries @<:@default=]AC_ENABLE_STATIC_DEFAULT[@:>@])],
[libtool: build static libraries @<:@default=]AC_ENABLE_STATIC_DEFAULT[@:>@])],
case $enableval in
yes) enable_static=yes ;;
......@@ -1826,7 +1826,7 @@ AC_DEFUN([AC_ENABLE_FAST_INSTALL],
[define([AC_ENABLE_FAST_INSTALL_DEFAULT], ifelse($1, no, no, yes))dnl
[optimize for fast installation @<:@default=]AC_ENABLE_FAST_INSTALL_DEFAULT[@:>@])],
[libtool: optimize for fast installation @<:@default=]AC_ENABLE_FAST_INSTALL_DEFAULT[@:>@])],
case $enableval in
yes) enable_fast_install=yes ;;
......@@ -1966,7 +1966,7 @@ fi
[assume the C compiler uses GNU ld @<:@default=no@:>@])],
[libtool: assume the C compiler uses GNU ld @<:@default=no@:>@])],
[test "$withval" = no || with_gnu_ld=yes],
......@@ -17,8 +17,10 @@
## add both RGui-ll.po and files to RGUI_CATALOGS
RGui-de.po \
RGui-fr.po \
RGui-it.po \
RGui-ja.po \
RGui-ko.po \
VPATH = @srcdir@
......@@ -313,7 +315,7 @@ update-po: Makefile
$(MAKE) $(DOMAIN).pot-update