Commit d3187efe authored by Dirk Eddelbuettel's avatar Dirk Eddelbuettel

Import Debian changes 3.0.1-1

r-base (3.0.1-1) unstable; urgency=low

  * New upstream version released this morning

  * debian/arm-perl-regexp.patch: Re-apply ARM patch for regexp 

  * debian/rules: Temporarily disabled moving info files. Not all help
    files will be built as a result. We are looking into this.

r-base (3.0.1~20130512-1) unstable; urgency=low

  * Initial rc build (r62731) of R 3.0.1 expected for May 16

  * debian/arm-perl-regexp.patch: Re-apply ARM patch for regexp 
  
  * debian/rules: Temporarily disabled moving info files
parents 1032a355 6a00b1ad
R News R News
CHANGES IN R 3.0.1:
NEW FEATURES:
o chooseCRANmirror() and chooseBioCmirror() gain an ind argument
(like setRepositories()).
o mcparallel has a new argument mc.interactive which can modify the
interactive flag in the child process. The new default is FALSE
which makes child processes non-interactive by default (this
prevents lock-ups due to children waiting for interactive input).
o scan() now warns when end-of-file occurs within a quoted string.
o count.fields() is now consistent with scan() in its handling of
newlines in quoted strings. Instead of triggering an error, this
results in the current line receiving NA as the field count, with
the next line getting the total count of the two lines.
o The default method of image() will plot axes of the class of xlim
and ylim (and hence of x and y if there is a suitable range()
method). Based on a suggestion of Michael Sumner.
o load() now has a verbose argument for debugging support, to print
the names of objects just before loading them.
o When loading a serialized object encounters a reference to a
namespace which cannot be loaded, this is replaced by a reference
to the global environment, with a warning.
o pairs() gains a line.main option for title placement.
o The remaining instances in which serialization to a raw vector
was limited to 2GB have been unlimited on a 64-bit platform, and
in most cases serialization to a vector of more than 1GB will be
substantially faster.
UTILITIES:
o R CMD config now make use of personal Makevars files under ~/.R
and a site file Makevars.site, in the same way as R CMD SHLIB and
R CMD INSTALL. This makes the utility more useful in package
configure scripts.
On Windows finding the personal files may require the environment
variable HOME set.
The old behaviour can be obtained with the new options
--no-user-files and --no-site-files.
PACKAGE INSTALLATION:
o Alternatives to the site and user customization files
Makevars.site and ~/.R/Makevars can be specified _via_ the
environment variables R_MAKEVARS_SITE and R_MAKEVARS_USER
respectively. These can be used to suppress the use of the
default files by setting an empty value (where possible) or a
non-existent path.
BUG FIXES:
o sys.source() did not report error locations when keep.source =
TRUE.
o as.POSIXct.numeric was coercing origin using the tz argument and
not "GMT" as documented (PR#14973).
o The active binding to assign fields in reference classes has been
cleaned up to reduce dependence on the class' package
environment, also fixing bug in initializing read-only fields
(inspired by a report from Hadley Wickham).
o str(d) no longer gives an error when names(d) contain illegal
multibyte strings (PR#15247).
o Profiling of built-in functions with line.profiling= TRUE did not
record the line from which they were called.
o citation(pkg) dropped the header and footer specified in the
CITATION file (PR#15257).
o Quotes were handled differently when reading the first line and
reading the rest, so read.table() misread some files that
contained quote characters (PR#15245).
o cat() with sep a character vector of length greater than one and
more than one argument was using separators inconsistently
(PR#15261).
o On Windows in R 3.0.0, savePlot() failed because of an incorrect
check on the argument count.
o unzip(list = TRUE) returned Names as a factor and not a character
vector (as documented) for the internal method. (Noticed by Sean
O'Riordain.)
o contourLines() now checks more comprehensively for conformance of
its x, y and z arguments (it was used incorrectly in package
R2G2).
o Saved graphics display lists are R version-specific. Attempting
to load workspaces containing them (or some other
version-specific objects) aborted the load in R 3.0.0 and
earlier; now it does a partial load and generates a warning
instead.
o In R 3.0.0, identify() and locator() did not record information
correctly, so replaying a graph (e.g. by copying it to another
device) would fail. (PR#15271)
o Calling file.copy() or dirname() with the invalid input "" (which
was being used in packages, despite not being a file path) could
have caused a segfault.
dirname("") is now "" rather than "." (unless it segfaulted).
o supsmu() could read/write outside its input vectors for very
short inputs (seen in package rms for n = 4).
o as.dendrogram()'s hclust method uses less memory and hence gets
considerably faster for large (n ~ 1000) clusterings, thanks to
Daniel M"ullner. (PR#15174)
o The return value when all workers failed from
parallel::mclapply(mc.presechedule = TRUE) was a list of strings
and not of error objects. (Spotted by Karl Forner and Bernd
Bischl.)
o In R 3.0.0, when help() found multiple pages with the same alias,
the HTML display of all the selections was not produced.
(PR#15282)
o splinefun(method="monoH.FC") now produces a function with first
argument named x and allows deriv=3, as documented. (PR#15273)
o summaryRprof() would only read the first chunksize lines of an
Rprof file produced with line.profiling=TRUE. By default, this is
the first 100 seconds. (PR#15288)
o lsfit() produced an incorrect error message when argument x had
more columns than rows or x had a different number of rows than
y. (Spotted by Renaud Gaujoux.)
o Binary operations on equal length vectors copied the class name
from the second operand when the first had no class name, but did
not set the object bit. (PR#15299)
o The trace() method for reference generator objects failed after
those objects became function definitions.
o write.table() did not check that factors were constructed
correctly, and so caused a segment fault when writing bad ones.
(PR#15300)
o The internal HTTP server no longer chokes on POST requests
without body. It will also pass-through other request types for
custom handlers (with the method stored in Request-Method header)
instead of failing.
CHANGES IN R 3.0.0: CHANGES IN R 3.0.0:
SIGNIFICANT USER-VISIBLE CHANGES: SIGNIFICANT USER-VISIBLE CHANGES:
......
No preview for this file type
Revision: 62481 Revision: 62743
Last Changed Date: 2013-04-03 Last Changed Date: 2013-05-16
Masked Marvel Good Sport
#! /bin/sh #! /bin/sh
# Guess values for system-dependent variables and create Makefiles. # Guess values for system-dependent variables and create Makefiles.
# Generated by GNU Autoconf 2.69 for R 3.0.0. # Generated by GNU Autoconf 2.69 for R 3.0.1.
# #
# Report bugs to <http://bugs.r-project.org>. # Report bugs to <http://bugs.r-project.org>.
# #
...@@ -729,8 +729,8 @@ MAKEFLAGS= ...@@ -729,8 +729,8 @@ MAKEFLAGS=
# Identity of this package. # Identity of this package.
PACKAGE_NAME='R' PACKAGE_NAME='R'
PACKAGE_TARNAME='R' PACKAGE_TARNAME='R'
PACKAGE_VERSION='3.0.0' PACKAGE_VERSION='3.0.1'
PACKAGE_STRING='R 3.0.0' PACKAGE_STRING='R 3.0.1'
PACKAGE_BUGREPORT='http://bugs.r-project.org' PACKAGE_BUGREPORT='http://bugs.r-project.org'
PACKAGE_URL='http://www.r-project.org' PACKAGE_URL='http://www.r-project.org'
...@@ -1768,7 +1768,7 @@ if test "$ac_init_help" = "long"; then ...@@ -1768,7 +1768,7 @@ if test "$ac_init_help" = "long"; then
# Omit some internal or obsolete options to make the list less imposing. # Omit some internal or obsolete options to make the list less imposing.
# This message is too long to be a string in the A/UX 3.1 sh. # This message is too long to be a string in the A/UX 3.1 sh.
cat <<_ACEOF cat <<_ACEOF
\`configure' configures R 3.0.0 to adapt to many kinds of systems. \`configure' configures R 3.0.1 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]... Usage: $0 [OPTION]... [VAR=VALUE]...
...@@ -1843,7 +1843,7 @@ fi ...@@ -1843,7 +1843,7 @@ fi
if test -n "$ac_init_help"; then if test -n "$ac_init_help"; then
case $ac_init_help in case $ac_init_help in
short | recursive ) echo "Configuration of R 3.0.0:";; short | recursive ) echo "Configuration of R 3.0.1:";;
esac esac
cat <<\_ACEOF cat <<\_ACEOF
...@@ -2062,7 +2062,7 @@ fi ...@@ -2062,7 +2062,7 @@ fi
test -n "$ac_init_help" && exit $ac_status test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then if $ac_init_version; then
cat <<\_ACEOF cat <<\_ACEOF
R configure 3.0.0 R configure 3.0.1
generated by GNU Autoconf 2.69 generated by GNU Autoconf 2.69
Copyright (C) 2012 Free Software Foundation, Inc. Copyright (C) 2012 Free Software Foundation, Inc.
...@@ -3214,7 +3214,7 @@ cat >config.log <<_ACEOF ...@@ -3214,7 +3214,7 @@ cat >config.log <<_ACEOF
This file contains any messages produced by compilers while This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake. running configure, to aid debugging if configure makes a mistake.
It was created by R $as_me 3.0.0, which was It was created by R $as_me 3.0.1, which was
generated by GNU Autoconf 2.69. Invocation command line was generated by GNU Autoconf 2.69. Invocation command line was
$ $0 $@ $ $0 $@
...@@ -42709,7 +42709,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 ...@@ -42709,7 +42709,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
# report actual input values of CONFIG_FILES etc. instead of their # report actual input values of CONFIG_FILES etc. instead of their
# values after options handling. # values after options handling.
ac_log=" ac_log="
This file was extended by R $as_me 3.0.0, which was This file was extended by R $as_me 3.0.1, which was
generated by GNU Autoconf 2.69. Invocation command line was generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES = $CONFIG_FILES CONFIG_FILES = $CONFIG_FILES
...@@ -42776,7 +42776,7 @@ _ACEOF ...@@ -42776,7 +42776,7 @@ _ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`" ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\ ac_cs_version="\\
R config.status 3.0.0 R config.status 3.0.1
configured by $0, generated by GNU Autoconf 2.69, configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\" with options \\"\$ac_cs_config\\"
r-base (3.0.1-1) unstable; urgency=low
* New upstream version released this morning
* debian/arm-perl-regexp.patch: Re-apply ARM patch for regexp
* debian/rules: Temporarily disabled moving info files. Not all help
files will be built as a result. We are looking into this.
-- Dirk Eddelbuettel <edd@debian.org> Thu, 16 May 2013 06:05:31 -0500
r-base (3.0.1~20130512-1) unstable; urgency=low
* Initial rc build (r62731) of R 3.0.1 expected for May 16
* debian/arm-perl-regexp.patch: Re-apply ARM patch for regexp
* debian/rules: Temporarily disabled moving info files
-- Dirk Eddelbuettel <edd@debian.org> Sun, 12 May 2013 14:47:49 -0500
r-base (3.0.0-2) unstable; urgency=low r-base (3.0.0-2) unstable; urgency=low
* debian/r-cran.mk: Revert recent patch to convert '.' in package names * debian/r-cran.mk: Revert recent patch to convert '.' in package names
......
...@@ -457,9 +457,9 @@ install-arch-stamp: ...@@ -457,9 +457,9 @@ install-arch-stamp:
touch install-indep-stamp touch install-indep-stamp
# edd 06 Dec 2006 lintian wants them compressed with -9, and R # edd 06 Dec 2006 lintian wants them compressed with -9, and R
# seems to pre-zip them lower # seems to pre-zip them lower
gunzip -9v $(debtmp)/usr/share/info/*.gz # edd 12 May 2013 FIXME gunzip -9v $(debtmp)/usr/share/info/*.gz
# move files for r-doc-info # move files for r-doc-info
dh_movefiles --sourcedir=debian/$(corepackage) -p$(infopackage) # edd 12 May 2013 FIXME dh_movefiles --sourcedir=debian/$(corepackage) -p$(infopackage)
# deal with stupid automake / install-info issue (cf #235713) # deal with stupid automake / install-info issue (cf #235713)
rm -vf $(debinf)/usr/share/info/dir \ rm -vf $(debinf)/usr/share/info/dir \
$(debinf)/usr/share/info/dir.old $(debinf)/usr/share/info/dir.old
......
...@@ -50,7 +50,7 @@ Ireland,Ireland,Dublin,http://ftp.heanet.ie/mirrors/cran.r-project.org/,"HEAnet, ...@@ -50,7 +50,7 @@ Ireland,Ireland,Dublin,http://ftp.heanet.ie/mirrors/cran.r-project.org/,"HEAnet,
"Korea (Seoul 2)",Korea,Seoul,http://biostat.cau.ac.kr/CRAN/,"Chung-Ang University, Seoul","Sunghow # gmail.com",1,kr "Korea (Seoul 2)",Korea,Seoul,http://biostat.cau.ac.kr/CRAN/,"Chung-Ang University, Seoul","Sunghow # gmail.com",1,kr
Latvia,Latvia,Riga,http://mirrors.webhostinggeeks.com/cran/,Webhostinggeeks,"whg.igp # gmail.com",1,lv Latvia,Latvia,Riga,http://mirrors.webhostinggeeks.com/cran/,Webhostinggeeks,"whg.igp # gmail.com",1,lv
"Mexico (Mexico City)",Mexico,"Mexico City",http://cran.itam.mx/,"Instituto Tecnologico Autonomo de Mexico","Ernesto Barrios <ebarrios # Itam.mx>",1,mx "Mexico (Mexico City)",Mexico,"Mexico City",http://cran.itam.mx/,"Instituto Tecnologico Autonomo de Mexico","Ernesto Barrios <ebarrios # Itam.mx>",1,mx
"Mexico (Texcoco)",Mexico,Texcoco,http://www.est.colpos.mx/R-mirror/,"Colegio de Postgraduados, Texcoco","perpdgo # colpos.mx",1,mx "Mexico (Texcoco)",Mexico,Texcoco,http://www.est.colpos.mx/R-mirror/,"Colegio de Postgraduados, Texcoco","perpdgo # gmail.com",1,mx
"Netherlands (Amsterdam)",Netherlands,Amsterdam,http://cran.xl-mirror.nl/,"XL-Data, Amsterdam","werner # xl-mirror.nl",1,nl "Netherlands (Amsterdam)",Netherlands,Amsterdam,http://cran.xl-mirror.nl/,"XL-Data, Amsterdam","werner # xl-mirror.nl",1,nl
"Netherlands (Utrecht)",Netherlands,Utrecht,http://cran-mirror.cs.uu.nl/,"Utrecht University","webmaster # cs.uu.nl",1,nl "Netherlands (Utrecht)",Netherlands,Utrecht,http://cran-mirror.cs.uu.nl/,"Utrecht University","webmaster # cs.uu.nl",1,nl
"New Zealand","New Zealand",Auckland,http://cran.stat.auckland.ac.nz/,"University of Auckland","w.schmidt # auckland.ac.nz",1,nz "New Zealand","New Zealand",Auckland,http://cran.stat.auckland.ac.nz/,"University of Auckland","w.schmidt # auckland.ac.nz",1,nz
...@@ -60,7 +60,7 @@ Poland,Poland,Wroclaw,http://r.meteo.uni.wroc.pl/,"University of Wroclaw","Pawe ...@@ -60,7 +60,7 @@ Poland,Poland,Wroclaw,http://r.meteo.uni.wroc.pl/,"University of Wroclaw","Pawe
Russia,Russia,Moscow,http://cran.gis-lab.info/,GIS-Lab.info,"sim # gis-lab.info",1,ru Russia,Russia,Moscow,http://cran.gis-lab.info/,GIS-Lab.info,"sim # gis-lab.info",1,ru
Singapore,Singapore,Singapore,http://cran.stat.nus.edu.sg/,"National University of Singapore","Zhang Rong <ccezr # nus.edu.sg>",1,sg Singapore,Singapore,Singapore,http://cran.stat.nus.edu.sg/,"National University of Singapore","Zhang Rong <ccezr # nus.edu.sg>",1,sg
Slovakia,Slovakia,Bratislava,http://cran.fyxm.net/,"FYXM.net, Bratislava","docko # docko.sk",1,sk Slovakia,Slovakia,Bratislava,http://cran.fyxm.net/,"FYXM.net, Bratislava","docko # docko.sk",1,sk
"South Africa (Cape Town)","South Africa","Cape Town"," http://r.adu.org.za/","University of Cape Town","michael.brooks # uct.ac.za",1,za "South Africa (Cape Town)","South Africa","Cape Town",http://r.adu.org.za/,"University of Cape Town","michael.brooks # uct.ac.za",1,za
"South Africa (Johannesburg)","South Africa",Johannesburg,http://cran.mirror.ac.za/,"TENET, Johannesburg","Patrick Holahan <patrickh # tenet.ac.za>",1,za "South Africa (Johannesburg)","South Africa",Johannesburg,http://cran.mirror.ac.za/,"TENET, Johannesburg","Patrick Holahan <patrickh # tenet.ac.za>",1,za
"Spain (Madrid)",Spain,Madrid,http://cran.es.r-project.org/,"Spanish National Research Network, Madrid","Jose Manuel Macias <jmanuel.macias # rediris.es>",1,es "Spain (Madrid)",Spain,Madrid,http://cran.es.r-project.org/,"Spanish National Research Network, Madrid","Jose Manuel Macias <jmanuel.macias # rediris.es>",1,es
Sweden,Sweden,Uppsala,http://ftp.sunet.se/pub/lang/CRAN/,"Swedish University Computer Network, Uppsala","Goran Brostrom <gb # stat.umu.se>",1,se Sweden,Sweden,Uppsala,http://ftp.sunet.se/pub/lang/CRAN/,"Swedish University Computer Network, Uppsala","Goran Brostrom <gb # stat.umu.se>",1,se
...@@ -72,10 +72,9 @@ Turkey,Turkey,Denizli,http://cran.pau.edu.tr,"Pamukkale University, Denizli","Ug ...@@ -72,10 +72,9 @@ Turkey,Turkey,Denizli,http://cran.pau.edu.tr,"Pamukkale University, Denizli","Ug
"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 (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 "UK (London)",UK,London,http://cran.ma.imperial.ac.uk/,"Imperial College London","s.rochford # imperial.ac.uk",1,uk
"UK (St Andrews)",UK,"St Andrews",http://star-www.st-andrews.ac.uk/cran/,"St Andrews University","Lee Kelvin <lsk9 # St-andrews.ac.uk>",1,uk "UK (St Andrews)",UK,"St Andrews",http://star-www.st-andrews.ac.uk/cran/,"St Andrews University","Lee Kelvin <lsk9 # St-andrews.ac.uk>",1,uk
"USA (AZ)",USA,Scottsdale,http://cran.opensourceresources.org/,opensourceresources.org,"mike.winslow1 # gmail.com",0,us
"USA (CA 1)",USA,Berkeley,http://cran.cnr.Berkeley.edu,"University of California, Berkeley, CA","casterln # nature.berkeley.edu",1,us "USA (CA 1)",USA,Berkeley,http://cran.cnr.Berkeley.edu,"University of California, Berkeley, CA","casterln # nature.berkeley.edu",1,us
"USA (CA 2)",USA,"Los Angeles",http://cran.stat.ucla.edu/,"University of California, Los Angeles, CA","Jose Hales-Garcia <jose # stat.ucla.edu>",1,us "USA (CA 2)",USA,"Los Angeles",http://cran.stat.ucla.edu/,"University of California, Los Angeles, CA","Jose Hales-Garcia <jose # stat.ucla.edu>",1,us
"USA (IA)",USA,Ames,http://streaming.stat.iastate.edu/CRAN/,"Iowa State University, Ames, IA","Ted Peterson <cpterson # iastate.edu>",1,us "USA (IA)",USA,Ames,http://streaming.stat.iastate.edu/CRAN/,"Iowa State University, Ames, IA","Ted Peterson <statit # iastate.edu>",1,us
"USA (IN)",USA,Bloomington,http://ftp.ussg.iu.edu/CRAN/,"Indiana University","rtadmin # indiana.edu",1,us "USA (IN)",USA,Bloomington,http://ftp.ussg.iu.edu/CRAN/,"Indiana University","rtadmin # indiana.edu",1,us
"USA (KS)",USA,Lawrence,http://rweb.quant.ku.edu/cran/,"University of Kansas, Lawrence, KS","Paul Johnson <pauljohn # ku.edu>",1,us "USA (KS)",USA,Lawrence,http://rweb.quant.ku.edu/cran/,"University of Kansas, Lawrence, KS","Paul Johnson <pauljohn # ku.edu>",1,us
"USA (MD)",USA,Bethesda,http://watson.nci.nih.gov/cran_mirror/,"National Cancer Institute, Bethesda, MD","Sean Davis <sdavis2 # mail.nih.gov>",1,us "USA (MD)",USA,Bethesda,http://watson.nci.nih.gov/cran_mirror/,"National Cancer Institute, Bethesda, MD","Sean Davis <sdavis2 # mail.nih.gov>",1,us
......
R FAQ R FAQ
Frequently Asked Questions on R Frequently Asked Questions on R
Version 3.0.2013-03-31 Version 3.0.2013-05-12
Kurt Hornik Kurt Hornik
...@@ -256,7 +256,7 @@ i386-freebsd, rs6000-ibm-aix, and sparc-sun-solaris. ...@@ -256,7 +256,7 @@ i386-freebsd, rs6000-ibm-aix, and sparc-sun-solaris.
2.3 What is the current version of R? 2.3 What is the current version of R?
===================================== =====================================
The current released version is 3.0.0. Based on this The current released version is 3.0.1. Based on this
`major.minor.patchlevel' numbering scheme, there are two development `major.minor.patchlevel' numbering scheme, there are two development
versions of R, a patched version of the current release (`r-patched') and 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 one working towards the next minor or eventually major (`r-devel') releases
......
...@@ -7,6 +7,183 @@ ...@@ -7,6 +7,183 @@
\title{ R News} \title{ R News}
\encoding{UTF-8} \encoding{UTF-8}
\section{\Rlogo CHANGES IN R 3.0.1}{
\subsection{NEW FEATURES}{
\itemize{
\item \code{chooseCRANmirror()} and \code{chooseBioCmirror()} gain
an \code{ind} argument (like \code{setRepositories()}).
\item \code{mcparallel} has a new argument \code{mc.interactive}
which can modify the interactive flag in the child process. The
new default is \code{FALSE} which makes child processes
non-interactive by default (this prevents lock-ups due to children
waiting for interactive input).
\item \code{scan()} now warns when end-of-file occurs within
a quoted string.
\item \code{count.fields()} is now consistent with \code{scan()}
in its handling of newlines in quoted strings. Instead of
triggering an error, this results in the current line receiving
\code{NA} as the field count, with the next line getting the total
count of the two lines.
\item The default method of \code{image()} will plot axes of the
class of \code{xlim} and \code{ylim} (and hence of \code{x} and
\code{y} if there is a suitable \code{range()} method). Based on
a suggestion of Michael Sumner.
\item \code{load()} now has a \code{verbose} argument for
debugging support, to print the names of objects just before
loading them.
\item When loading a serialized object encounters a reference to a
namespace which cannot be loaded, this is replaced by a reference
to the global environment, with a warning.
\item \code{pairs()} gains a \code{line.main} option for title placement.
\item The remaining instances in which serialization to a raw
vector was limited to 2GB have been unlimited on a 64-bit
platform, and in most cases serialization to a vector of more than
1GB will be substantially faster.
}
}
\subsection{UTILITIES}{
\itemize{
\item \command{R CMD config} now make use of personal
\file{Makevars} files under \file{~/.R} and a site file
\file{Makevars.site}, in the same way as \command{R CMD SHLIB} and
\command{R CMD INSTALL}. This makes the utility more useful in
package \command{configure} scripts.
On Windows finding the personal files may require the environment
variable \env{HOME} set.
The old behaviour can be obtained with the new options
\option{--no-user-files} and \option{--no-site-files}.
}
}
\subsection{PACKAGE INSTALLATION}{
\itemize{
\item Alternatives to the site and user customization files
\file{Makevars.site} and \file{~/.R/Makevars} can be specified
\emph{via} the environment variables \env{R_MAKEVARS_SITE} and
\env{R_MAKEVARS_USER} respectively. These can be used to suppress
the use of the default files by setting an empty value (where
possible) or a non-existent path.
}
}
\subsection{BUG FIXES}{
\itemize{
\item \code{sys.source()} did not report error locations when
\code{keep.source = TRUE}.
\item \code{as.POSIXct.numeric} was coercing \code{origin} using
the \code{tz} argument and not \code{"GMT"} as documented
(\PR{14973}).
\item The active binding to assign fields in reference classes
has been cleaned up to reduce dependence on the class' package
environment, also fixing bug in initializing read-only fields
(inspired by a report from Hadley Wickham).
\item \code{str(d)} no longer gives an error when \code{names(d)}
contain illegal multibyte strings (\PR{15247}).
\item Profiling of built-in functions with \code{line.profiling=
TRUE} did not record the line from which they were called.
\item \code{citation(pkg)} dropped the header and footer specified
in the \file{CITATION} file (\PR{15257}).
\item Quotes were handled differently when reading the first line
and reading the rest, so \code{read.table()} misread some files
that contained quote characters (\PR{15245}).
\item \code{cat()} with \code{sep} a character vector of length
greater than one and more than one argument was using separators
inconsistently (\PR{15261}).
\item On Windows in \R 3.0.0, \code{savePlot()} failed because of
an incorrect check on the argument count.
\item \code{unzip(list = TRUE)} returned \code{Names} as a factor
and not a character vector (as documented) for the internal method.
(Noticed by Sean O'Riordain.)
\item \code{contourLines()} now checks more comprehensively for
conformance of its \code{x}, \code{y} and \code{z} arguments (it
was used incorrectly in package \CRANpkg{R2G2}).
\item Saved graphics display lists are \R version-specific.
Attempting to load workspaces containing them (or some other
version-specific objects) aborted the load in \R 3.0.0 and
earlier; now it does a partial load and generates a warning
instead.
\item In \R 3.0.0, \code{identify()} and \code{locator()} did
not record information correctly, so replaying a graph (e.g. by
copying it to another device) would fail. (\PR{15271})
\item Calling \code{file.copy()} or \code{dirname()} with the
invalid input \code{""} (which was being used in packages, despite
not being a file path) could have caused a segfault.
\code{dirname("")} is now \code{""} rather than \code{"."} (unless
it segfaulted).
\item \code{supsmu()} could read/write outside its input vectors
for very short inputs (seen in package \CRANpkg{rms} for \code{n = 4}).
\item \code{as.dendrogram()}'s \code{hclust} method uses less
memory and hence gets considerably faster for large (n ~ 1000)
clusterings, thanks to Daniel Müllner. (\PR{15174})
\item The return value when all workers failed from
\code{parallel::mclapply(mc.presechedule = TRUE)} was a list of
strings and not of error objects. (Spotted by Karl Forner and
Bernd Bischl.)
\item In \R 3.0.0, when \code{help()} found multiple pages with
the same alias, the HTML display of all the selections was not
produced. (\PR{15282})
\item \code{splinefun(method="monoH.FC")} now produces a
function with first argument named \code{x} and allows
\code{deriv=3}, as documented. (\PR{15273})
\item \code{summaryRprof()} would only read the first
\code{chunksize} lines of an \code{Rprof} file produced with
\code{line.profiling=TRUE}. By default, this is the first 100
seconds. (\PR{15288})
\item \code{lsfit()} produced an incorrect error message when
argument \code{x} had more columns than rows or \code{x} had a
different number of rows than \code{y}. (Spotted by Renaud Gaujoux.)
\item Binary operations on equal length vectors copied the
class name from the second operand when the first had no
class name, but did not set the object bit. (\PR{15299})
\item The \code{trace()} method for reference generator objects
failed after those objects became function definitions.
\item \code{write.table()} did not check that factors were
constructed correctly, and so caused a segment fault when
writing bad ones. (\PR{15300})
\item The internal HTTP server no longer chokes on POST requests
without body. It will also pass-through other request types for
custom handlers (with the method stored in Request-Method header)
instead of failing.
}
}
}
\section{\Rlogo CHANGES IN R 3.0.0}{ \section{\Rlogo CHANGES IN R 3.0.0}{
\subsection{SIGNIFICANT USER-VISIBLE CHANGES}{ \subsection{SIGNIFICANT USER-VISIBLE CHANGES}{
\itemize{ \itemize{
...@@ -761,7 +938,7 @@ ...@@ -761,7 +938,7 @@
\item \code{.find.package()} and \code{.path.package()} are \item \code{.find.package()} and \code{.path.package()} are
deprecated: only the public versions without the dot have ever deprecated: only the public versions without the dot have ever
been in the API. been in the API.
\item In a package's \file{DESCRIPTION} file, \preformatted{ License: X11} \item In a package's \file{DESCRIPTION} file, \preformatted{ License: X11}
is deprecated, since it includes is deprecated, since it includes
\sQuote{Copyright (C) 1996 X Consortium} which cannot be \sQuote{Copyright (C) 1996 X Consortium} which cannot be
......
...@@ -8,6 +8,237 @@ ...@@ -8,6 +8,237 @@
<h2> R News</h2> <h2> R News</h2>
<h3><img src="../help/figures/../../html/logo.jpg" alt="../../html/logo.jpg" /> CHANGES IN R 3.0.1</h3>
<h4>NEW FEATURES</h4>
<ul>
<li> <p><code>chooseCRANmirror()</code> and <code>chooseBioCmirror()</code> gain
an <code>ind</code> argument (like <code>setRepositories()</code>).
</p>
</li>
<li> <p><code>mcparallel</code> has a new argument <code>mc.interactive</code>
which can modify the interactive flag in the child process. The
new default is <code>FALSE</code> which makes child processes
non-interactive by default (this prevents lock-ups due to children
waiting for interactive input).
</p>
</li>
<li> <p><code>scan()</code> now warns when end-of-file occurs within
a quoted string.
</p>
</li>
<li> <p><code>count.fields()</code> is now consistent with <code>scan()</code>
in its handling of newlines in quoted strings. Instead of
triggering an error, this results in the current line receiving
<code>NA</code> as the field count, with the next line getting the total
count of the two lines.
</p>
</li>
<li><p> The default method of <code>image()</code> will plot axes of the
class of <code>xlim</code> and <code>ylim</code> (and hence of <code>x</code> and
<code>y</code> if there is a suitable <code>range()</code> method). Based on
a suggestion of Michael Sumner.
</p>
</li>
<li> <p><code>load()</code> now has a <code>verbose</code> argument for
debugging support, to print the names of objects just before
loading them.
</p>
</li>
<li><p> When loading a serialized object encounters a reference to a
namespace which cannot be loaded, this is replaced by a reference