Commit 6e5ebc20 authored by Radford Neal's avatar Radford Neal

Files from R-2.14.1.

parent c3c05085
R News
CHANGES IN R VERSION 2.14.0 patched:
NEW FEATURES:
o parallel::detectCores() is now able to find the number of
physical cores (rather than CPUs) on Sparc Solaris.
It can also do so on most versions of Windows; however the
default remains detectCores(logical = TRUE) on that platform.
o Reference classes now keep a record of which fields are locked.
$lock() with no arguments returns the names of the locked fields.
o HoltWinters() reports a warning rather than an error for some
optimization failures (where the answer might be a reasonable
one).
o tools::dependsOnPkg() now accepts the shorthand dependencies =
"all".
o parallel::clusterExport() now allows specification of an
environment from which to export.
o The quartz() device now does tilde expansion on its file
argument.
o tempfile() on a Unix-alike now takes the process ID into account.
This is needed with multicore (and as part of parallel) because
the parent and all the children share a session temporary
directory, and they can share the C random number stream used to
produce the uniaue part. Further, two children can call
tempfile() simultaneously.
o Option print in Sweave's RweaveLatex() driver now emulates
auto-printing rather than printing (which can differ for an S4
object by calling show() rather than print()).
o filled.contour() now accepts infinite values: previously it might
have generated invalid graphics files (e.g. containing NaN
values).
INSTALLATION:
o On 64-bit Linux systems, configure now only sets LIBnn to lib64
if /usr/lib64 exists. This may obviate setting LIBnn explicitly
on Debian-derived systems.
It is still necessary to set LIBnn = lib (or lib32) for 32-bit
builds of R on a 64-bit OS on those Linux distributions capable
for supporting that concept.
o configure looks for inconsolata.sty, and if not found adjusts the
default R_RD4PDF to not use it (with a warning, since it is
needed for high-quality rendering of manuals).
PACKAGE INSTALLATION:
o R CMD INSTALL will now do a test load for all sub-architectures
for which code was compiled (rather than just the primary
sub-architecture).
UTILITIES:
o When checking examples under more than one sub-architecture, R
CMD check now uses a separate directory examples_arch for each
sub-architecture, and leaves the output in file
pkgname-Ex_arch.Rout. Some packages expect their examples to be
run in a clean directory ....
BUG FIXES:
o stack() now gives an error if no vector column is selected,
rather than returning a 1-column data frame (contrary to its
documentation).
o summary.mlm() did not handle objects where the formula had been
specified by an expression. (Reported by Helios de Rosario
Martinez).
o tools::deparseLatex(dropBraces=TRUE) could drop text as well as
braces.
o colormodel = "grey" (new in R 2.14.0)) did not always work in
postscript() and pdf().
o file.append() could return TRUE for failures. (PR#14727)
o gzcon() connections are no longer subject to garbage collection:
it was possible for this to happen when unintended (e.g. when
calling load()).
o nobs() does not count zero-weight observations for glm() fits,
for consistency with lm(). This affects the BIC() values
reported for such glm() fits. (Spotted by Bill Dunlap.)
o options(warn = 0) failed to end a (C-level) context with more
than 50 accumulated warnings. (Spotted by Jeffery Horner.)
o The internal plot.default() code did not do sanity checks on a
cex argument, so invalid input could cause problems. (Reported
by Ben Bolker.)
o anyDuplicated(<array>, MARGIN=0) no longer fails. (Reported by
Herv'e Pag`es.)
o read.dcf() removes trailing blanks: unfortunately on some
platforms this included \xa0 (non-breaking space) which is the
trailing byte of a UTF-8 character. It now only considers ASCII
space and tab to be 'blank'.
o There was a sign error in part of the calculations for the
variance returned by KalmanSmooth(). (PR#14738)
o pbinom(10, 1e6, 0.01, log.p = TRUE) was NaN thanks to the buggy
fix to PR#14320 in R 2.11.0. (PR#14739)
o RweaveLatex() now emulates auto-printing rather than printing, by
calling methods::show() when auto-printing would.
o duplicated() ignored fromLast for a one-column data frame.
(PR#14742)
o source() and related functions did not put the correct timestamp
on the source references; srcfilecopy() has gained a new argument
timestamp to support this fix. (PR#14750)
o LaTeX conversion of Rd files did not correctly handle
preformatted backslashes. (PR#14751)
o HTML conversion of Rd files did not handle markup within tabular
cells properly. (PR#14708)
o source() on an empty file with keep.source = TRUE tried to read
from stdin(), in R 2.14.0 only. (PR#14753)
o The code to check Rd files in packages would abort if duplicate
description sections were present.
CHANGES IN R VERSION 2.14.0:
SIGNIFICANT USER-VISIBLE CHANGES:
......@@ -259,6 +397,10 @@ CHANGES IN R VERSION 2.14.0:
attribute references an in-memory copy of the source file using
the "srcfilecopy" class or the new "srcfilealias" class.
*NB:* This means that functions sourced with keep.source = TRUE
and saved (e.g., by save() or readRDS()) in earlier versions of R
will no longer show the original sources (including comments).
o New items User Manuals and Technical Papers have been added to
the HTML help main page. These link to vignettes in the base and
recommended packages and to a collection of papers about R
......@@ -833,9 +975,6 @@ CHANGES IN R VERSION 2.14.0:
o A late change in R 2.13.2 broke \Sexpr expressions in Rd files.
o The creation of ticks on log axes (including axTicks() sometimes
incorrectly omitted a tick at one end
o The creation of ticks on log axes (including by axTicks())
sometimes incorrectly omitted a tick at one end of the range by
rounding error in a platform-dependent way. This could be seen
......@@ -846,7 +985,7 @@ CHANGES IN R VERSION 2.14.0:
giving NaN. (PR#8528, PR#14710)
o mapply() now gives an explicit error message (rather than an
obscure one) is inputs of zero and positive length are mixed.
obscure one) if inputs of zero and positive length are mixed.
o Setting a Hershey font family followed by string height query
would crash R.
......
No preview for this file type
Revision: 57496
Last Changed Date: 2011-10-31
Revision: 57956
Last Changed Date: 2011-12-22
This diff is collapsed.
......@@ -145,7 +145,9 @@ case "${host_os}" in
## Not all distros use this: some choose to march out of step
case "${host_cpu}" in
x86_64|mips64|ppc64|powerpc64|sparc64|s390x)
libnn=lib64
if test -d /usr/lib64; then
libnn=lib64
fi
;;
esac
;;
......@@ -2718,9 +2720,6 @@ R is now configured for ${host}
if test -n "${warn_f77_cc_double_complex}"; then
AC_MSG_WARN([${warn_f77_cc_double_complex}])
fi
if test -n "${warn_xcompile_sizeof_int}"; then
AC_MSG_WARN([${warn_xcompile_sizeof_int}])
fi
if test -n "${warn_xcompile_sizeof_long}"; then
AC_MSG_WARN([${warn_xcompile_sizeof_long}])
fi
......@@ -2739,15 +2738,9 @@ fi
if test -n "${warn_fcpicflags}"; then
AC_MSG_WARN([${warn_fcpicflags}])
fi
if test -n "${warn_libglade_version}"; then
AC_MSG_WARN([${warn_libglade_version}])
fi
if test -n "${warn_tcltk_version}"; then
AC_MSG_WARN([${warn_tcltk_version}])
fi
if test -n "${warn_perl5}"; then
AC_MSG_WARN([${warn_perl5}])
fi
if test -n "${warn_dvi1}"; then
AC_MSG_WARN([${warn_dvi1}])
fi
......@@ -2763,6 +2756,9 @@ fi
if test -n "${warn_pdf2}"; then
AC_MSG_WARN([${warn_pdf2}])
fi
if test -n "${warn_pdf3}"; then
AC_MSG_WARN([${warn_pdf3}])
fi
if test -n "${warn_pager}"; then
AC_MSG_WARN([${warn_pager}])
fi
......
......@@ -19,7 +19,6 @@ Chile,Chile,Santiago,http://dirichlet.mat.puc.cl/,"Pontificia Universidad Catoli
"China (Beijing 2)",China,Bejing,http://cran.csdb.cn/,"Computer Network Information Center, CAS, Beijing","Hull # cnic.cn",1,cn
"China (Beijing 3)",China,Bejing,http://mirror.bjtu.edu.cn/cran,"Beijing Jiaotong University, Beijing","idealities # gmail.com",1,cn
"China (Hefei)",China,Hefei,http://mirrors.ustc.edu.cn/CRAN/,"University of Science and Technology of China","mirrors # Ustc.edu.cn",1,cn
"China (Hong Kong)",China,"Hong Kong",http://mirrors.geoexpat.com/cran/,GeoExpat.Com,"shri # geoexpat.com",1,cn
"China (Xiamen)",China,Xiamen,http://mirrors.xmu.edu.cn/CRAN/,"Xiamen University","admin # Xdmc.org",1,cn
"Colombia (Bogota)",Colombia,Bogota,http://www.laqee.unal.edu.co/CRAN/,"National University of Colombia","Ernesto Parra Rincon <eparrar # unal.edu.co>",1,co
"Colombia (Cali)",Colombia,Cali,http://www.icesi.edu.co/CRAN/,"Icesi University","adminred # Icesi.edu.co",1,co
......@@ -32,6 +31,7 @@ Denmark,Denmark,Aalborg,http://mirrors.dotsrc.org/cran/,"dotsrc.org, Aalborg","m
"Germany (Muenchen)",Germany,Muenchen,http://cran.rakanu.com/,"Rakanu.com, Muenchen","Carsten Zedler <info # rakanu.com>",1,de
"Germany (Wiesbaden)",Germany,Wiesbaden,http://ftp.yalwa.org/cran/,"Yalwa GmbH, Wiesbaden","webmaster # yalwa.com",1,de
Greece,Greece,Crete,http://cran.cc.uoc.gr/,"University of Crete","mirrors # Cc.uoc.gr",1,gr
India,India,Chennai,http://ftp.iitm.ac.in/cran/,"Indian Institute of Technology Madras","sriram # iitm.ac.in",1,in
"Indonesia (Jakarta 1)",Indonesia,Jakarta,http://cran.cermin.lipi.go.id/,"Indonesian Institute of Sciences","mirror # Teori.fisika.lipi.go.id",1,id
"Indonesia (Jakarta 2)",Indonesia,Jakarta,http://cran.repo.bppt.go.id/,"Agency for The Application and Assessment of Technology","Imam Cartealy <icx # biotek.bppt.go.id>",1,id
Iran,Iran,Mashhad,http://cran.um.ac.ir/,"Ferdowsi University of Mashhad","Majid Sarmad <sarmad # um.ac.ir>",1,ir
......@@ -41,7 +41,9 @@ Ireland,Ireland,Dublin,http://ftp.heanet.ie/mirrors/cran.r-project.org/,"HEAnet,
"Italy (Palermo)",Italy,Palermo,http://dssm.unipa.it/CRAN/,"Universita degli Studi di Palermo","elio.mineo # dssm.unipa.it, alf # dssm.unipa.it",1,it
"Japan (Hyogo)",Japan,Hyogo,http://essrc.hyogo-u.ac.jp/cran/,"Hyogo University of Teacher Education","essrc-cran # hyogo-u.ac.jp",1,jp
"Japan (Tsukuba)",Japan,Tsukuba,http://cran.md.tsukuba.ac.jp/,"University of Tsukuba",,1,jp
Korea,Korea,Seoul,http://statlab.korea.ac.kr/R/,"Korea University","hanansh # Korea.ac.kr",1,kr
"Japan (Tokyo)",Japan,Tokyo,http://cran.ism.ac.jp/,"Institute of Statistical Mathematics, Tokyo","Junji Nakano <nakanoj # ism.ac.jp>",1,jp
Korea,Korea,Seoul,http://statlab.korea.ac.kr/R/,"Korea University","hanansh # Korea.ac.kr",0,kr
Korea,Korea,Seoul,http://cran.nexr.com/,"NexR Cortporation, Seoul","mining # nexr.com",1,kr
"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
"Netherlands (Amsterdam)",Netherlands,Amsterdam,http://cran.xl-mirror.nl/,"XL-Data, Amsterdam","werner # xl-mirror.nl",1,nl
......@@ -49,7 +51,6 @@ Korea,Korea,Seoul,http://statlab.korea.ac.kr/R/,"Korea University","hanansh # Ko
"New Zealand","New Zealand",Auckland,http://cran.stat.auckland.ac.nz/,"University of Auckland","w.schmidt # auckland.ac.nz",1,nz
Norway,Norway,Bergen,http://cran.uib.no/,"University of Bergen","sundrift # It.uib.no",1,no
Philippines,Philippines,"Quezon City",http://cran.stat.upd.edu.ph/,"University of the Philippines and PREGINET","edward.p.santos # Up.edu.ph",1,ph
"Poland (Gdansk)",Poland,Gdansk,http://cran.privatejetscharter.net/,"Privatejetscharter.net, Gdansk","info # Privatejetscharter.net",1,pl
"Poland (Oswiecim)",Poland,Oswiecim,http://piotrkosoft.net/pub/mirrors/CRAN/,"Piotrkosoft - Data Storage Center","Piotr Maluty <piotr.maluty # gmail.com>",1,pl
"Poland (Wroclaw)",Poland,Wroclaw,http://r.meteo.uni.wroc.pl/,"University of Wroclaw","Paweł Netzel <netzel # meteo.uni.wroc.pl>",1,pl
Russia,Russia,Moscow,http://cran.gis-lab.info/,GIS-Lab.info,"sim # gis-lab.info",1,ru
......@@ -62,7 +63,7 @@ Sweden,Sweden,Uppsala,http://ftp.sunet.se/pub/lang/CRAN/,"Swedish University Com
Switzerland,Switzerland,Zuerich,http://stat.ethz.ch/CRAN/,"ETH Zuerich","Martin.Maechler # R-project.org",1,ch
"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
"Taiwan (Taipei 2)",Taiwan,Taipei,http://cran.stat.tku.edu.tw/,"Tamkang University, Taipei","steve # stat.tku.edu.tw",0,tw
Thailand,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
......@@ -71,8 +72,9 @@ Thailand,Thailand,Hatyai,http://mirrors.psu.ac.th/pub/cran/,"Prince of Songkla U
"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 (IA)",USA,Ames,http://streaming.stat.iastate.edu/CRAN/,"Iowa State University, Ames, IA","Ted Peterson <cpterson # iastate.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 (MA)",USA,Cambridge,http://software.rc.fas.harvard.edu/mirrors/R/,"Harvard University, Cambridge, MA","Chris Walker <cwalker # fas.harvard.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>",0,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 (MI)",USA,Houghton,http://cran.mtu.edu/,"Michigan Technological University, Houghton, MI","Robert Froese <froese # mtu.edu>",1,us
"USA (MO)",USA,"St. Louis",http://cran.wustl.edu/,"Washington University, St. Louis, MO","admartin # wustl.edu",1,us
"USA (NC)",USA,"Chapel Hill",http://www.ibiblio.org/pub/languages/R/CRAN/,"University of North Carolina, Chapel Hill, NC","""Nancy C. Wilson"" <nancy # metalab.unc.edu>",0,us
......@@ -80,7 +82,8 @@ Thailand,Thailand,Hatyai,http://mirrors.psu.ac.th/pub/cran/,"Prince of Songkla U
"USA (OR)",USA,Corvallis,http://ftp.osuosl.org/pub/cran/,"Oregon State University","support # Osuosl.org",1,us
"USA (PA 1)",USA,Pittsburgh,http://lib.stat.cmu.edu/R/CRAN/,"Statlib, Carnegie Mellon University, Pittsburgh, PA",,1,us
"USA (PA 2)",USA,Pittsburgh,http://cran.mirrors.hoobly.com,"Hoobly Classifieds, Pittsburgh, PA","Peter Grigor <pgrigor # hoobly.com>",1,us
"USA (TX 1)",USA,"San Antonio",http://www.revolution-computing.com/cran/,"Revolution Computing, San Antonio, TX","David Smith <david # revolution-computing.com>",1,us
"USA (TN)",USA,"Oak Ridge",http://mirrors.nics.utk.edu/cran/,"National Institute for Computational Sciences, Oak Ridge, TN","help # nics.utk.edu",1,us
"USA (TX 1)",USA,Dallas,http://cran.revolutionanalytics.com,"Revolution Analytics, Dallas, TX","David Smith <david # revolutionanalytics.com>",1,us
"USA (TX 2)",USA,Houston,http://cran.sixsigmaonline.org/,"sixsigmaonline.org, Houston, TX","gosixsigma # gmail.com",1,us
"USA (WA 1)",USA,Seattle,http://cran.fhcrc.org/,"Fred Hutchinson Cancer Research Center, Seattle, WA","sfalcon # fhcrc.org",1,us
"USA (WA 2)",USA,Bellingham,http://cran.cs.wwu.edu/,"Western Washington University, Bellingham, WA","CS.Support # Wwu.edu",1,us
R FAQ
Frequently Asked Questions on R
Version 2.14.2011-10-24
Version 2.14.2011-12-16
ISBN 3-900051-08-9
Kurt Hornik
......@@ -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 2.14.0. Based on this
The current released version is 2.14.1. 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
......@@ -1310,9 +1310,21 @@ similar to the use of the *brew* (http://CRAN.R-project.org/package=brew)
package with Rapache (http://rapache.net/) with the advantage of
cross-platform support and easy installation.
Finally, the *Rook* (http://CRAN.R-project.org/package=Rook) package by
Jeffrey Horner provides a web server server interface borrowing heavily
from Ruby's Rack project.
The *Rook* (http://CRAN.R-project.org/package=Rook) package by Jeffrey
Horner provides a web server interface borrowing heavily from Ruby's Rack
project.
Finally, Concerto (http://code.google.com/p/concerto-platform/) is a
user friendly open-source Web Interface to R developed at the Psychometrics
Centre of Cambridge University. It was designed as an online platform to
design and run Computerized Adaptive Tests, but can be also used as a
general-purpose R Web Interface. It allows R users with no programming or
web designing background to quickly develop flexible and powerful online
applications, websites, and psychometrics tests. To maximize its
reliability, security, and performance, Concerto relies on the popular and
reliable open-source elements such as MySQL server (exchange and storage of
the data), Rstudio (http://rstudio.org/) (R code designing and testing,
file management), CKEditor (HTML Layer design), and PHP.
5 R Add-On Packages
*******************
......@@ -1373,7 +1385,8 @@ The R distribution comes with the following packages:
former *base* was split into the four packages *base*, *graphics*, *stats*,
and *utils*. Packages *ctest*, *eda*, *modreg*, *mva*, *nls*, *stepfun* and
*ts* were merged into *stats*, package *lqs* returned to the recommended
package *MASS*, and package *mle* moved to *stats4*.
package *MASS* (http://CRAN.R-project.org/package=MASS), and package *mle*
moved to *stats4*.
5.1.2 Add-on packages from CRAN
-------------------------------
......@@ -1921,9 +1934,10 @@ task at hand (as `as.numeric()' or `unclass()' give the internal codes).
7.11 Are Trellis displays implemented in R?
===========================================
The recommended package *lattice* (which is based on another recommended
package, *grid*) provides graphical functionality that is compatible with
most Trellis commands.
The recommended package *lattice*
(http://CRAN.R-project.org/package=lattice) (which is based on base package
*grid*) provides graphical functionality that is compatible with most
Trellis commands.
You could also look at `coplot()' and `dotchart()' which might do at
least some of what you want. Note also that the R version of `pairs()' is
......@@ -2052,11 +2066,12 @@ Package *gam* (http://CRAN.R-project.org/package=gam) from CRAN implements
all the Generalized Additive Models (GAM) functionality as described in the
GAM chapter of the White Book. In particular, it implements backfitting
with both local regression and smoothing splines, and is extendable. There
is a `gam()' function for GAMs in package *mgcv*, but it is not an exact
clone of what is described in the White Book (no `lo()' for example).
Package *gss* (http://CRAN.R-project.org/package=gss) can fit spline-based
GAMs too. And if you can accept regression splines you can use `glm()'.
For Gaussian GAMs you can use `bruto()' from package *mda*
is a `gam()' function for GAMs in package *mgcv*
(http://CRAN.R-project.org/package=mgcv), but it is not an exact clone of
what is described in the White Book (no `lo()' for example). Package *gss*
(http://CRAN.R-project.org/package=gss) can fit spline-based GAMs too. And
if you can accept regression splines you can use `glm()'. For Gaussian
GAMs you can use `bruto()' from package *mda*
(http://CRAN.R-project.org/package=mda).
7.16 Why is the output not printed when I source() a file?
......@@ -2524,8 +2539,8 @@ quietly interpreted as just `p'. Current versions of R emit a warning.
Some functions will display a particular kind of plot with error bars, such
as the `bar.err()' function in the *agricolae*
(http://CRAN.R-project.org/package=agricolae) package, the `plotCI()'
function in the *gplots* (http://CRAN.R-project.org/package=gplots)
package, the `plotCI()' and `brkdn.plot()' functions in the *plotrix*
function in the *gplots* (http://CRAN.R-project.org/package=gplots) package,
the `plotCI()' and `brkdn.plot()' functions in the *plotrix*
(http://CRAN.R-project.org/package=plotrix) package and the `error.bars()',
`error.crosses()' and `error.bars.by()' functions in the *psych*
(http://CRAN.R-project.org/package=psych) package. Within these types of
......
This diff is collapsed.
......@@ -8,6 +8,223 @@
<h2> R News</h2>
<h3><img src="../help/figures/../../html/logo.jpg" alt="../../html/logo.jpg" /> CHANGES IN R VERSION 2.14.0 patched</h3>
<h4>NEW FEATURES</h4>
<ul>
<li> <p><code>parallel::detectCores()</code> is now able to find the
number of physical cores (rather than CPUs) on Sparc Solaris.
</p>
<p>It can also do so on most versions of Windows; however the default
remains <code>detectCores(logical = TRUE)</code> on that platform.
</p>
</li>
<li><p> Reference classes now keep a record of which fields are
locked. <code>$lock()</code> with no arguments returns the names
of the locked fields.
</p>
</li>
<li> <p><code>HoltWinters()</code> reports a warning rather than an error
for some optimization failures (where the answer might be a
reasonable one).
</p>
</li>
<li> <p><code>tools::dependsOnPkg()</code> now accepts the shorthand
<code>dependencies = "all"</code>.
</p>
</li>
<li> <p><code>parallel::clusterExport()</code> now allows specification of
an environment from which to export.
</p>
</li>
<li><p> The <code>quartz()</code> device now does tilde expansion on its
<code>file</code> argument.
</p>
</li>
<li> <p><code>tempfile()</code> on a Unix-alike now takes the process ID
into account. This is needed with <span class="pkg">multicore</span> (and as part of
<span class="pkg">parallel</span>) because the parent and all the children share a
session temporary directory, and they can share the C random
number stream used to produce the uniaue part. Further, two
children can call <code>tempfile()</code> simultaneously.
</p>
</li>
<li><p> Option <code>print</code> in Sweave's <code>RweaveLatex()</code> driver
now emulates auto-printing rather than printing (which can differ
for an S4 object by calling <code>show()</code> rather than
<code>print()</code>).
</p>
</li>
<li> <p><code>filled.contour()</code> now accepts infinite values:
previously it might have generated invalid graphics files
(e.g. containing NaN values).
</p>
</ul>
<h4>INSTALLATION</h4>
<ul>
<li><p> On 64-bit Linux systems, <CODE>configure</CODE> now only sets
<span class="samp">LIBnn</span> to <code>lib64</code> if &lsquo;<span class="file">/usr/lib64</span>&rsquo; exists. This
may obviate setting <span class="samp">LIBnn</span> explicitly on Debian-derived
systems.
</p>
<p>It is still necessary to set <span class="samp">LIBnn = lib</span> (or
<span class="samp">lib32</span>) for 32-bit builds of <font face="Courier New,Courier" color="#666666"><b>R</b></font> on a 64-bit OS on those Linux
distributions capable for supporting that concept.
</p>
</li>
<li> <p><CODE>configure</CODE> looks for &lsquo;<span class="file">inconsolata.sty</span>&rsquo;, and if
not found adjusts the default <span class="env">R_RD4PDF</span> to not use it (with a
warning, since it is needed for high-quality rendering of manuals).
</p>
</ul>
<h4>PACKAGE INSTALLATION</h4>
<ul>
<li> <p><CODE>R CMD INSTALL</CODE> will now do a test load for all
sub-architectures for which code was compiled (rather than just
the primary sub-architecture).
</p>
</ul>
<h4>UTILITIES</h4>
<ul>
<li><p> When checking examples under more than one sub-architecture,
<CODE>R CMD check</CODE> now uses a separate directory
&lsquo;<span class="file">examples_arch</span>&rsquo; for each sub-architecture, and leaves the
output in file &lsquo;<span class="file">pkgname-Ex_arch.Rout</span>&rsquo;. Some packages
expect their examples to be run in a clean directory ....
</p>
</ul>
<h4>BUG FIXES</h4>
<ul>
<li> <p><code>stack()</code> now gives an error if no vector column is
selected, rather than returning a 1-column data frame (contrary to
its documentation).
</p>
</li>
<li> <p><code>summary.mlm()</code> did not handle objects where the
formula had been specified by an expression. (Reported by
Helios de Rosario Martinez).
</p>
</li>
<li> <p><code>tools::deparseLatex(dropBraces=TRUE)</code> could drop
text as well as braces.
</p>
</li>
<li> <p><code>colormodel = "grey"</code> (new in <font face="Courier New,Courier" color="#666666"><b>R</b></font> 2.14.0))
did not always work in <code>postscript()</code> and <code>pdf()</code>.
</p>
</li>
<li> <p><code>file.append()</code> could return <code>TRUE</code> for failures.
(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14727">PR#14727</a>)
</p>
</li>
<li> <p><code>gzcon()</code> connections are no longer subject to garbage
collection: it was possible for this to happen when unintended
(e.g. when calling <code>load()</code>).
</p>
</li>
<li> <p><code>nobs()</code> does not count zero-weight observations for
<code>glm()</code> fits, for consistency with <code>lm()</code>. This affects
the <code>BIC()</code> values reported for such <code>glm()</code> fits.
(Spotted by Bill Dunlap.)
</p>
</li>
<li> <p><code>options(warn = 0)</code> failed to end a (C-level) context
with more than 50 accumulated warnings. (Spotted by Jeffery
Horner.)
</p>
</li>
<li><p> The internal <code>plot.default()</code> code did not do sanity
checks on a <code>cex</code> argument, so invalid input could cause
problems. (Reported by Ben Bolker.)
</p>
</li>
<li> <p><code>anyDuplicated(&lt;array&gt;, MARGIN=0)</code> no longer fails.
(Reported by Hervé Pagès.)
</p>
</li>
<li> <p><code>read.dcf()</code> removes trailing blanks: unfortunately
on some platforms this included <code>\xa0</code> (non-breaking space)
which is the trailing byte of a UTF-8 character. It now only
considers ASCII space and tab to be &lsquo;blank&rsquo;.
</p>
</li>
<li><p> There was a sign error in part of the calculations for the
variance returned by <code>KalmanSmooth()</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14738">PR#14738</a>)
</p>
</li>
<li> <p><code>pbinom(10, 1e6, 0.01, log.p = TRUE)</code> was <code>NaN</code>
thanks to the buggy fix to <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14320">PR#14320</a> in <font face="Courier New,Courier" color="#666666"><b>R</b></font> 2.11.0. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14739">PR#14739</a>)
</p>
</li>
<li> <p><code>RweaveLatex()</code> now emulates auto-printing rather than
printing, by calling <code>methods::show()</code> when auto-printing
would.
</p>
</li>
<li> <p><code>duplicated()</code> ignored <code>fromLast</code> for a
one-column data frame. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14742">PR#14742</a>)
</p>
</li>
<li> <p><code>source()</code> and related functions did not put the correct
timestamp on the source references; <code>srcfilecopy()</code> has gained
a new argument <code>timestamp</code> to support this fix. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14750">PR#14750</a>)
</p>
</li>
<li><p> LaTeX conversion of Rd files did not correctly handle
preformatted backslashes. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14751">PR#14751</a>)
</p>
</li>
<li><p> HTML conversion of Rd files did not handle markup within
tabular cells properly. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14708">PR#14708</a>)
</p>
</li>
<li> <p><code>source()</code> on an empty file with <code>keep.source =
TRUE</code> tried to read from <code>stdin()</code>, in <font face="Courier New,Courier" color="#666666"><b>R</b></font> 2.14.0 only.
(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14753">PR#14753</a>)
</p>
</li>
<li><p> The code to check Rd files in packages would abort if
duplicate description sections were present.
</p>
</ul>
<h3><img src="../help/figures/../../html/logo.jpg" alt="../../html/logo.jpg" /> CHANGES IN R VERSION 2.14.0</h3>
......@@ -364,6 +581,11 @@ attribute. The <code>"srcref"</code> attribute references an in-memory
copy of the source file using the <code>"srcfilecopy"</code> class or
the new <code>"srcfilealias"</code> class.
</p>
<p><STRONG>NB:</STRONG> This means that functions sourced with
<code>keep.source = TRUE</code> and saved (e.g., by <code>save()</code> or
<code>readRDS()</code>) in earlier versions of <font face="Courier New,Courier" color="#666666"><b>R</b></font> will no longer show
the original sources (including comments).
</p>
</li>
<li><p> New items <a href="UserManuals.html">User Manuals</a> and
<a href="http://developer.r-project.org/TechDocs">Technical Papers</a>
......@@ -1180,10 +1402,6 @@ help pages with names containing e.g. spaces and slashes.
in Rd files.
</p>
</li>
<li><p> The creation of ticks on log axes (including
<code>axTicks()</code> sometimes incorrectly omitted a tick at one end
</p>
</li>
<li><p> The creation of ticks on log axes (including by
<code>axTicks()</code>) sometimes incorrectly omitted a tick at one end
of the range by rounding error in a platform-dependent way. This
......@@ -1198,7 +1416,7 @@ sometimes omitted.
</p>
</li>
<li> <p><code>mapply()</code> now gives an explicit error message (rather
than an obscure one) is inputs of zero and positive length are
than an obscure one) if inputs of zero and positive length are
mixed.
</p>
</li>
......
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......@@ -666,7 +666,7 @@ but in a UTF-8 locale on a Unix-alike is likely to need
@example
con <- file("intro.dat", "r")
seek(con, 3) # step over the 3 initial bytes, the BOM
foo <- read.table("intro.dat")
foo <- read.table(con)
close(con)
@end example
......@@ -1349,9 +1349,10 @@ The BioConductor project has updated @pkg{RdbiPgSQL} (formerly on
@code{http://@/www.joeconway.com/@/plr/}}) is a project to embed R into
PostgreSQL.
Package @pkg{RMongo} provides an @R{} inteface to a Java client for
`MongoDB'(@uref{http://en.wikipedia.org/wiki/MongoDB}) databases, which
are queried using JavaScript rather than SQL.