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From pd.mes at cbs.dk Thu Mar 10 10:45:50 2016
From: pd.mes at cbs.dk (Peter Dalgaard)
Date: Thu, 10 Mar 2016 09:45:50 +0000
Subject: R 3.2.4 is released
Message-ID: <[email protected]>
The build system rolled up R-3.2.4.tar.gz (codename "Very Secure Dishes") this morning.
The list below details the changes in this release.
You can get the source code from
http://cran.r-project.org/src/base/R-3/R-3.2.4.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you.
Binaries for various platforms will appear in due course.
For the R Core Team,
Peter Dalgaard
These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:
MD5 (AUTHORS) = eb97a5cd38acb1cfc6408988bffef765
MD5 (COPYING) = eb723b61539feef013de476e68b5c50a
MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343
MD5 (FAQ) = d2e93152b963acbb53027c355dda539a
MD5 (INSTALL) = 3964b9119adeaab9ceb633773fc94aac
MD5 (NEWS) = 087f64ddfe922d2a565ff64bb8543039
MD5 (NEWS.0) = bfcd7c147251b5474d96848c6f57e5a8
MD5 (NEWS.1) = eb78c4d053ec9c32b815cf0c2ebea801
MD5 (NEWS.2) = 8e2f4d1d5228663ae598a09bf1e2bc6b
MD5 (R-latest.tar.gz) = 5953104583ed93dc2085a6c80e884e4a
MD5 (README) = aece1dfbd18c1760128c3787f5456af6
MD5 (RESOURCES) = 529223fd3ffef95731d0a87353108435
MD5 (THANKS) = ba00f6cc68a823e1741cfa6011f40ccb
MD5 (VERSION-INFO.dcf) = 71584fcd5c399b40750fcd7113521636
MD5 (R-3/R-3.2.4.tar.gz) = 5953104583ed93dc2085a6c80e884e4a
This is the relevant part of the NEWS file
CHANGES IN R 3.2.4:
NEW FEATURES:
* install.packages() and related functions now give a more
informative warning when an attempt is made to install a base
package.
* summary(x) now prints with less rounding when x contains infinite
values. (Request of PR#16620.)
* provideDimnames() gets an optional unique argument.
* shQuote() gains type = "cmd2" for quoting in cmd.exe in Windows.
(Response to PR#16636.)
* The data.frame method of rbind() gains an optional argument
stringsAsFactors (instead of only depending on
getOption("stringsAsFactors")).
* smooth(x, *) now also works for long vectors.
* tools::texi2dvi() has a workaround for problems with the texi2dvi
script supplied by texinfo 6.1.
It extracts more error messages from the LaTeX logs when in
emulation mode.
UTILITIES:
* R CMD check will leave a log file build_vignettes.log from the
re-building of vignettes in the .Rcheck directory if there is a
problem, and always if environment variable
_R_CHECK_ALWAYS_LOG_VIGNETTE_OUTPUT_ is set to a true value.
DEPRECATED AND DEFUNCT:
* Use of SUPPORT_OPENMP from header Rconfig.h is deprecated in
favour of the standard OpenMP define _OPENMP.
(This has been the recommendation in the manual for a while now.)
* The make macro AWK which is long unused by R itself but recorded
in file etc/Makeconf is deprecated and will be removed in R
3.3.0.
* The C header file S.h is no longer documented: its use should be
replaced by R.h.
BUG FIXES:
* kmeans(x, centers = <1-row>) now works. (PR#16623)
* Vectorize() now checks for clashes in argument names. (PR#16577)
* file.copy(overwrite = FALSE) would signal a successful copy when
none had taken place. (PR#16576)
* ngettext() now uses the same default domain as gettext().
(PR#14605)
* array(.., dimnames = *) now warns about non-list dimnames and,
from R 3.3.0, will signal the same error for invalid dimnames as
matrix() has always done.
* addmargins() now adds dimnames for the extended margins in all
cases, as always documented.
* heatmap() evaluated its add.expr argument in the wrong
environment. (PR#16583)
* require() etc now give the correct entry of lib.loc in the
warning about an old version of a package masking a newer
required one.
* The internal deparser did not add parentheses when necessary,
e.g. before [] or [[]]. (Reported by Lukas Stadler; additional
fixes included as well).
* as.data.frame.vector(*, row.names=*) no longer produces
'corrupted' data frames from row names of incorrect length, but
rather warns about them. This will become an error.
* url connections with method = "libcurl" are destroyed properly.
(PR#16681)
* withCallingHandler() now (again) handles warnings even during S4
generic's argument evaluation. (PR#16111)
* deparse(..., control = "quoteExpressions") incorrectly quoted
empty expressions. (PR#16686)
* format()ting datetime objects ("POSIX[cl]?t") could segfault or
recycle wrongly. (PR#16685)
* plot.ts(<matrix>, las = 1) now does use las.
* saveRDS(*, compress = "gzip") now works as documented.
(PR#16653)
* (Windows only) The Rgui front end did not always initialize the
console properly, and could cause R to crash. (PR#16998)
* dummy.coef.lm() now works in more cases, thanks to a proposal by
Werner Stahel (PR#16665). In addition, it now works for
multivariate linear models ("mlm", manova) thanks to a proposal
by Daniel Wollschlaeger.
* The as.hclust() method for "dendrogram"s failed often when there
were ties in the heights.
* reorder() and midcache.dendrogram() now are non-recursive and
hence applicable to somewhat deeply nested dendrograms, thanks to
a proposal by Suharto Anggono in PR#16424.
* cor.test() now calculates very small p values more accurately
(affecting the result only in extreme not statistically relevant
cases). (PR#16704)
* smooth(*, do.ends=TRUE) did not always work correctly in R
versions between 3.0.0 and 3.2.3.
* pretty(D) for date-time objects D now also works well if range(D)
is (much) smaller than a second. In the case of only one unique
value in D, the pretty range now is more symmetric around that
value than previously.
Similarly, pretty(dt) no longer returns a length 5 vector with
duplicated entries for Date objects dt which span only a few
days.
* The figures in help pages such as ?points were accidentally
damaged, and did not appear in R 3.2.3. (PR#16708)
* available.packages() sometimes deleted the wrong file when
cleaning up temporary files. (PR#16712)
* The X11() device sometimes froze on Red Hat Enterprise Linux 6.
It now waits for MapNotify events instead of Expose events,
thanks to Siteshwar Vashisht. (PR#16497)
* [dpqr]nbinom(*, size=Inf, mu=.) now works as limit case, for
'dpq' as the Poisson. (PR#16727)
pnbinom() no longer loops infinitely in border cases.
* approxfun(*, method="constant") and hence ecdf() which calls the
former now correctly "predict" NaN values as NaN.
* summary.data.frame() now displays NAs in Date columns in all
cases. (PR#16709)
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
|
R 3.2.4 is released
|
Peter Dalgaard
| 119
|
|
From jcadima at isa.utl.pt Wed Jul 3 13:42:35 2002
From: jcadima at isa.utl.pt (Jorge Cadima)
Date: Wed, 03 Jul 2002 12:42:35 +0100
Subject: No subject
Message-ID: <E17PiWq-0000bf-00@DMjcadima>
A new version (0.2) of package 'subselect' has been uploaded to CRAN.
Package 'subselect' provides functions to carry out local search
algorithms for k-variable subsets that are optimal, as surrogates for
the full (p-variable, p > k) data sets, under three different criteria.
The functions 'rm.coef', 'rv.coef' and 'gcd.coef' assess the quality
of given k-subsets of variables under the following three
criteria: RM (McCabe's second criterion for Principal Variables, which
measures the quality of the subset as a linear predictor of all the
variables), RV (based on Escoufier's RV-criterion, which measures the
similarity of the n point configurations defined by the original p variables
and the n point configuration resulting from the regression of all variables
on a k-subset of the variables) and GCD (based on Yanai's GCD, and which
measures the similarity of the subspaces spanned by a k-variable subset, and
a subset of g Principal Components of the full data set).
Three additional functions, 'anneal', 'genetic' and 'improve', search for
optimal k-variable subsets under those criteria, using three different
algorithms: a simulated annealing algorithm, a genetic algorithm and a
restricted local improvement algorithm. For computational efficiency, the
basic code implementing these algorithms is written in Fortran (with calls
to Lapack subroutines), but the R functions provide a user-friendly
interface where many parameters associated with the algorithms can be
specified. Among the options, the user can control the number of
iterations, initial temperature, cooling factors
and cooling frequency in simulated annealing, and the number of generations,
population size, admissibility of clones and presence and frequency of
mutations in the
genetic algorithm. For all algorithms, it is possible to specify the number
of solutions required in one or more cardinalities, to specify the initial
solutions and to force the solutions to include and/or to exclude given
subsets of variables. The results of these functions are lists of R objects
detailing the resulting subsets and values of criteria, which can be
manipulated in R.
There is a CHANGELOG file in subdirectory 'inst' documenting changes
from Version 0.1.
Here is the DESCRIPTION file for the package:
Package: subselect
Version: 0.2-0
Date: 2002/06/20
Title: Selecting variable subsets.
Author: Jorge Orestes Cerdeira <orestes at isa.utl.pt>
Jorge Cadima <jcadima at isa.utl.pt>
Manuel Minhoto <minhoto at uevora.pt>
Maintainer: Jorge Cadima <jcadima at isa.utl.pt>
Description: A collection of functions which assess the quality of
variable subsets as surrogates for a full data set using three
different criteria (Yanais' GCD, Escoufier's RV and McCabe's RM), and
search for subsets which are optimal under those criteria, using a
simulated annealing algorithm, a genetic algorithm, or a restricted
local improvement algorithm.
License: GPL
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
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|
No subject
|
<E17PiWq-0000bf-00@DMjcadima>
|
Jorge Cadima
| 53
|
From p.dalgaard at biostat.ku.dk Fri Jan 10 18:13:02 2003
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard BSA)
Date: Fri Jan 10 18:13:02 2003
Subject: [R] R-1.6.2 is released
In-Reply-To: <[email protected]>
References: <[email protected]>
<[email protected]>
Message-ID: <[email protected]>
Paul Gilbert <pgilbert at bank-banque-canada.ca> writes:
> Peter
>
> When I the URL in your message I am getting:
>
> <H1>Not Found</H1>
> The requested URL /pub/CRAN/src/base/R-1.6.2.tgz was not found on this
> server.<P>
> <HR>
> <ADDRESS>Apache/1.3.26 Server at franz.stat.wisc.edu Port 80</ADDRESS>
>
Something got changed, it seems. Try
http://cran.us.r-project.org/src/base/R-1.6.2.tgz
-p
--
O__ ---- Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
|
[R] R-1.6.2 is released
|
Peter Dalgaard BSA
| 151
|
|
From pd.mes at cbs.dk Fri Jul 8 12:16:40 2011
From: pd.mes at cbs.dk (Peter Dalgaard)
Date: Fri, 8 Jul 2011 12:16:40 +0200
Subject: R 2.13.1 is released
Message-ID: <[email protected]>
I've rolled up R-2.13.1.tar.gz a short while ago. This is a maintenance release to consolidate various minor fixes to 2.13.0.
The Licencing change to GPL-2 | GPL-3 may be of interest to some.
You can get it from
http://cran.r-project.org/src/base/R-2/R-2.13.1.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you.
Binaries for various platforms will appear in due course.
For the R Core Team
Peter Dalgaard
These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:
MD5 (AUTHORS) = ac9746b4845ae866661f51cfc99262f5
MD5 (COPYING) = eb723b61539feef013de476e68b5c50a
MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343
MD5 (FAQ) = a6f58169fec241d4fa4ab283d8cb12de
MD5 (INSTALL) = 70447ae7f2c35233d3065b004aa4f331
MD5 (NEWS) = 8347135398220ba817bbf1c97586ec53
MD5 (ONEWS) = 0c3e10eef74439786e5fceddd06dac71
MD5 (OONEWS) = b0d650eba25fc5664980528c147a20db
MD5 (R-latest.tar.gz) = 28dd0d68ac3a0eab93fe7035565a1c30
MD5 (README) = 296871fcf14f49787910c57b92655c76
MD5 (RESOURCES) = 020479f381d5f9038dcb18708997f5da
MD5 (THANKS) = 03d783ff71270c77d497fd573d711fd8
MD5 (R-2/R-2.13.1.tar.gz) = 28dd0d68ac3a0eab93fe7035565a1c30
This is the relevant part of the NEWS file:
R News
CHANGES IN R VERSION 2.13.1:
NEW FEATURES:
? iconv() no longer translates NA strings as "NA".
? persp(box = TRUE) now warns if the surface extends outside the
box (since occlusion for the box and axes is computed assuming
the box is a bounding box). (PR#202.)
? RShowDoc() can now display the licences shipped with R, e.g.
RShowDoc("GPL-3").
? New wrapper function showNonASCIIfile() in package tools.
? nobs() now has a "mle" method in package stats4.
? trace() now deals correctly with S4 reference classes and
corresponding reference methods (e.g., $trace()) have been added.
? xz has been updated to 5.0.3 (very minor bugfix release).
? tools::compactPDF() gets more compression (usually a little,
sometimes a lot) by using the compressed object streams of PDF
1.5.
? cairo_ps(onefile = TRUE) generates encapsulated EPS on platforms
with cairo >= 1.6.
? Binary reads (e.g. by readChar() and readBin()) are now supported
on clipboard connections. (Wish of PR#14593.)
? as.POSIXlt.factor() now passes ... to the character method
(suggestion of Joshua Ulrich). [Intended for R 2.13.0 but
accidentally removed before release.]
? vector() and its wrappers such as integer() and double() now warn
if called with a length argument of more than one element. This
helps track down user errors such as calling double(x) instead of
as.double(x).
INSTALLATION:
? Building the vignette PDFs in packages grid and utils is now part
of running make from an SVN checkout on a Unix-alike: a separate
make vignettes step is no longer required.
These vignettes are now made with keep.source = TRUE and hence
will be laid out differently.
? make install-strip failed under some configuration options.
? Packages can customize non-standard installation of compiled code
via a src/install.libs.R script. This allows packages that have
architecture-specific binaries (beyond the package's shared
objects/DLLs) to be installed in a multi-architecture setting.
SWEAVE & VIGNETTES:
? Sweave() and Stangle() gain an encoding argument to specify the
encoding of the vignette sources if the latter do not contain a
\usepackage[]{inputenc} statement specifying a single input
encoding.
? There is a new Sweave option figs.only = TRUE to run each figure
chunk only for each selected graphics device, and not first using
the default graphics device. This will become the default in R
2.14.0.
? Sweave custom graphics devices can have a custom function
foo.off() to shut them down.
? Warnings are issued when non-portable filenames are found for
graphics files (and chunks if split = TRUE). Portable names are
regarded as alphanumeric plus hyphen, underscore, plus and hash
(periods cause problems with recognizing file extensions).
? The Rtangle() driver has a new option show.line.nos which is by
default false; if true it annotates code chunks with a comment
giving the line number of the first line in the sources (the
behaviour of R >= 2.12.0).
? Package installation tangles the vignette sources: this step now
converts the vignette sources from the vignette/package encoding
to the current encoding, and records the encoding (if not ASCII)
in a comment line at the top of the installed .R file.
LICENCE:
? No parts of R are now licensed solely under GPL-2. The licences
for packages rpart and survival have been changed, which means
that the licence terms for R as distributed are GPL-2 | GPL-3.
DEPRECATED AND DEFUNCT:
? The internal functions .readRDS() and .saveRDS() are now
deprecated in favour of the public functions readRDS() and
saveRDS() introduced in R 2.13.0.
? Switching off lazy-loading of code _via_ the LazyLoad field of
the DESCRIPTION file is now deprecated. In future all packages
will be lazy-loaded.
? The off-line help() types "postscript" and "ps" are deprecated.
UTILITIES:
? R CMD check on a multi-architecture installation now skips the
user's .Renviron file for the architecture-specific tests (which
do read the architecture-specific Renviron.site files). This is
consistent with single-architecture checks, which use
--no-environ.
? R CMD build now looks for DESCRIPTION fields BuildResaveData and
BuildKeepEmpty for per-package overrides. See ?Writing R
Extensions?.
BUG FIXES:
? plot.lm(which = 5) was intended to order factor levels in
increasing order of mean standardized residual. It ordered the
factor labels correctly, but could plot the wrong group of
residuals against the label. (PR#14545)
? mosaicplot() could clip the factor labels, and could overlap them
with the cells if a non-default value of cex.axis was used.
(Related to PR#14550.)
? dataframe[[row,col]] now dispatches on [[ methods for the
selected column (spotted by Bill Dunlap).
? sort.int() would strip the class of an object, but leave its
object bit set. (Reported by Bill Dunlap.)
? pbirthday() and qbirthday() did not implement the algorithm
exactly as given in their reference and so were unnecessarily
inaccurate.
pbirthday() now solves the approximate formula analytically
rather than using uniroot() on a discontinuous function.
The description of the problem was inaccurate: the probability is
a tail probablity (?2 _or more_ people share a birthday?)
? Complex arithmetic sometimes warned incorrectly about producing
NAs when there were NaNs in the input.
? seek(origin = "current") incorrectly reported it was not
implemented for a gzfile() connection.
? c(), unlist(), cbind() and rbind() could silently overflow the
maximum vector length and cause a segfault. (PR#14571)
? The fonts argument to X11(type = "Xlib") was being ignored.
? Reading (e.g. with readBin()) from a raw connection was not
advancing the pointer, so successive reads would read the same
value. (Spotted by Bill Dunlap.)
? Parsed text containing embedded newlines was printed incorrectly
by as.character.srcref(). (Reported by Hadley Wickham.)
? decompose() used with a series of a non-integer number of periods
returned a seasonal component shorter than the original series.
(Reported by Rob Hyndman.)
? fields = list() failed for setRefClass(). (Reported by Michael
Lawrence.)
? Reference classes could not redefine an inherited field which had
class "ANY". (Reported by Janko Thyson.)
? Methods that override previously loaded versions will now be
installed and called. (Reported by Iago Mosqueira.)
? addmargins() called numeric(apos) rather than
numeric(length(apos)).
? The HTML help search sometimes produced bad links. (PR#14608)
? Command completion will no longer be broken if tail.default() is
redefined by the user. (Problem reported by Henrik Bengtsson.)
? LaTeX rendering of markup in titles of help pages has been
improved; in particular, \eqn{} may be used there.
? isClass() used its own namespace as the default of the where
argument inadvertently.
? Rd conversion to latex mis-handled multi-line titles (including
cases where there was a blank line in the \title section).
--
Peter Dalgaard
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
|
R 2.13.1 is released
|
Peter Dalgaard
| 403
|
|
From francois.husson at agrocampus-ouest.fr Thu Apr 30 13:33:02 2009
From: francois.husson at agrocampus-ouest.fr (Francois Husson)
Date: Thu, 30 Apr 2009 11:33:02 +0000
Subject: useR! 2009 program available
Message-ID: <[email protected]>
Dear members of the R user community,
I am pleased to inform you that the program of the useR! 2009 conference
(Rennes, France, July 8 to 10, 2009) is available online:
http://www.agrocampus-ouest.fr/math/useR-2009/program.html
You can register from the link below:
http://www.agrocampus-ouest.fr/math/useR-2009/formulaires/registration.php
The conference web page:
http://www.agrocampus-ouest.fr/math/useR-2009/accomodation.html
gives a list of hotels and some student rooms (200) are also available
on the campus (Rennes will be very busy at the conference time because
the cultural event `Festival Les tomb?es de la nuit' will take place at
the same time, so we recommend to book as soon as possible).
We hope to meet you in Rennes!
F. Husson
--
Francois Husson
Applied Mathematics Department
Agrocampus
65 rue de Saint-Brieuc - CS 84215 - 35042 RENNES
Tel : 33 (0) 2 23 48 58 86
Fax : 33 (0) 2 23 48 58 71
m?l : husson at agrocampus-ouest.fr
http://www.agrocampus-ouest.fr/math/husson
useR!2009 : http://www.agrocampus-ouest.fr/math/useR-2009
|
useR! 2009 program available
|
Francois Husson
| 652
|
|
From martyn.plummer at r-project.org Thu Oct 22 15:06:34 2015
From: martyn.plummer at r-project.org (Martyn Plummer)
Date: Thu, 22 Oct 2015 15:06:34 +0200
Subject: Codes of Conduct at R Conferences
Message-ID: <[email protected]>
The useR! conferences in 2014 and 2015 both had codes of conduct in
order to ensure an experience free from harassment for all participants.
After a request from some members of the R community, the R Foundation
has decided to endorse this practice. Future conferences supported by
the R Foundation must have a code of conduct. We encourage other R
meetings not affiliated with the R Foundation to adopt the same policy.
A code of conduct serves two important purposes. Firstly, it sends a
clear message to those outside the community that an R conference is a
professional and comfortable working environment for all participants.
Secondly, it provides a mechanism for reporting and monitoring any
incidents of harassment that may occur.
We have decided not to require a particular formulation for the code of
conduct, but suggest that conference organizers use the model of the
useR! 2015 meeting ( http://user2015.math.aau.dk/behaviouR ). This will
allow the code to be adapted to local circumstances and to evolve in the
future. Conference organizers should ensure that any sanctions laid out
in the code of conduct are legally and practically enforceable.
Vigorous debate and lively exchange are important features of R
conferences. We expect this to continue within the boundaries set by the
code of conduct.
For the R Foundation
Martyn Plummer, Co-President
-----------------------------------------------------------------------
This message and its attachments are strictly confidenti...{{dropped:8}}
|
Codes of Conduct at R Conferences
|
Martyn Plummer
| 207
|
|
From pgilbert at bank-banque-canada.ca Thu Jun 25 21:00:17 1998
From: pgilbert at bank-banque-canada.ca (Paul Gilbert)
Date: Thu, 25 Jun 1998 15:00:17 -0400
Subject: DSE package
Message-ID: <[email protected]>
There is now an "alpha" version of my DSE time series library available at
<http://www.bank-banque-canada.ca/pgilbert>. The main changes between this and
the version in the development area of CRAN are for installing under R 0.62.1.
There are also a few bug fixes.
I have so far only tested on Solaris, but hope to test on Linux in the next few
days. If anyone installs the package and runs the tests on other operating
systems, I would appreciate having reports. I will submit the new version to
CRAN once I am relatively sure everything is working fairly well on other
platforms.
Paul Gilbert
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
DSE package
|
Paul Gilbert
| 541
|
|
From maechler at stat.math.ethz.ch Tue Jun 1 10:47:27 1999
From: maechler at stat.math.ethz.ch (Martin Maechler)
Date: Tue, 1 Jun 1999 10:47:27 +0200 (MET DST)
Subject: libraries and repeated measurements code
Message-ID: <[email protected]>
I have placed an alpha version 0.5 of the source code for my libraries
on my home page at
www.luc.ac.be/~jlindsey/rcode.html
The data and R code for the second edition of my Models for Repeated
Measurements (which requires these new libraries) can be found at
www.luc.ac.be/~jlindsey/books.html
Comments and corrections welcome!
Jim
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
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Send "info", "help", or "[un]subscribe"
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|
libraries and repeated measurements code
|
Martin Maechler
| 483
|
|
From p.dalgaard at biostat.ku.dk Mon Jan 11 14:56:59 1999
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard BSA)
Date: 11 Jan 1999 14:56:59 +0100
Subject: R-0.63.2 is released
Message-ID: <[email protected]>
I've put up R-0.63.2.tgz up for FTP from Auckland some minutes ago.
As usual, don't get it from there unless you are desperate, but wait
for it to be mirrored at a CRAN site near you within a day or two.
For those who *are* desperate, I've left a copy in
ftp://blueberry.kubism.ku.dk/pub/R-devel/R-0.63.2.tgz
(Be gentle, that's my desktop PC!)
There's also a version split in two for floppies and a patch file if
you prefer that.
This version is mainly to fix a messup with attributes on dataframe
variables that caused trouble for survival4. Completeness in
bug-fixing is not attempted.
Here is the relevant part of the NEWS file:
CHANGES IN R VERSION 0.63.2
NEW FEATURES
o sink() has new `append' argument.
o new function rle().
o plot(.) and curve(.) also accept a function as first argument.
new `plot.function'.
o new function loglin().
o pretty() has new arguments and now better "obeys" its `n' arg.
Internal GPretty() [implicitly used by axis(.., at = NULL,..)
now uses pretty.
o new generic function aggregate() with methods for data frames
and time series.
o data set `euro' with Euro conversion rates.
o new function jitter() [slightly wmore useful than S's].
BUG FIXES
o model.frame(,subset=) no longer loses contrasts
o `make install' copied the R shell script a second time without
getting RHOME right (thus also breaking R CMD check). Fixed.
o help() after help.start() did not work if topic was not equal
to filename (e.g. rnorm is found in Normal.html)
o fix the 0.63.1 fix for abbreviate(.); improved doc.
o predict.mlm(.) couldn't have worked with `newdata'.
o model.frame/na.omit bug for matrices and Surv objects.
o mean( <data.frame> ) now doesn't return sum(.) anymore.
o str(.) doesn't give extraneous "..." in rare cases anymore.
o Added documentation for group methods ("Math", "Ops","Summary").
o R_PAPERSIZE is used for Rd2dvi and at configure time for the
`make dvi' parts.
o hist(i) now also works for e.g., i = -1, 0, or 1.
o range() now works on dataframes (uses c(..., recursive=T))
o pretty(.) does not loop infinitely anymore in very extreme cases.
o math functions should work better on dataframes now
o plot(.., type = 'h', log = 'y') now works ...
o plot.factor(x, y, ...) of two factors now makes
barplot(table(y,x), ...)
o use object$prior.weights in add1.glm, drop1.glm (Brian Ripley)
o rnorm(1,mean=m,sd=0) returns m, not NaN (Ben Bolker)
o runif(n, a,a) now returns rep(a,n) instead of NaNs.
--
O__ ---- Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
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|
R-0.63.2 is released
|
Peter Dalgaard BSA
| 465
|
|
From p.dalgaard at biostat.ku.dk Sun Jun 14 22:18:49 1998
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard BSA)
Date: 14 Jun 1998 22:18:49 +0200
Subject: R-beta: R-0.62 is released *WATCH THE RETURN ADDRESS*
In-Reply-To: Egon Schmid's message of Sun, 14 Jun 1998 21:37:35 +0200 (MET DST)
References: <Pine.NEB.3.95.980614212003.21844A-100000@delos.stuttgart.netsurf.de>
Message-ID: <[email protected]>
Before this gets out of hand:
Please make sure that responses to the announcement goes somewhere
else than to R-announce, which is reserved for people who
want to minimise their email traffic by avoiding the discussion part.
--
O__ ---- Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
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|
R-beta: R-0.62 is released *WATCH THE RETURN ADDRESS*
|
Peter Dalgaard BSA
| 534
|
|
From p.dalgaard at biostat.ku.dk Wed Jan 30 14:07:32 2002
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard BSA)
Date: 30 Jan 2002 14:07:32 +0100
Subject: R version 1.4.1 is released
Message-ID: <[email protected]>
I've rolled up R-1.4.1.tgz a short while ago. This is a patch upgrade,
fixing the most important bugs that cropped up after the 1.4.0 release.
A set of recommended packages which have been tested with R-1.4.1 has
been bundled up. Binary distributions are expected to include these
packages.
You can get the files from the developer site
ftp://cvs.r-project.org/pub/CRAN/src/base/R-1.4.1.tgz
ftp://cvs.r-project.org/pub/CRAN/src/base/R-1.4.1-recommended.tgz
or
http://cran.us.r-project.org/src/base/R-1.4.1.tgz
http://cran.us.r-project.org/src/base/R-1.4.1-recommended.tgz
or wait for them to be mirrored at a CRAN site near you. This may not
happen right away due to circumstances in Vienna. Binaries for various
platforms will appear in due course.
There are also versions split for floppies and a patch file against 1.4.0.
For the R Core Team,
Peter D.
Here's the relevant part of the NEWS file:
CHANGES IN R VERSION 1.4.1
BUG FIXES
o scan(multi.line = FALSE) now always gives an immediate error
message if a line is incomplete. (As requested in PR#1210)
o read.table() is no longer very slow in processing comments:
moved to C code and fewer lines checked.
o type.convert() could give stack imbalance warnings if used
with as.is = TRUE.
o predict.mlm ignored newdata (PR#1226) and also offsets.
o demo(tkttest) was inadvertently changed in 1.4.0 so that it would
evaluate the requested test, but not display the result.
o stars(scale = TRUE) (the default) now works as documented (and
as S does). Previously it only scaled the maximum to 1. (PR#1230)
o d0 <- data.frame(a = 0); data.matrix(d0[0, 0]) and
data.matrix(d0[, 0]) now work.
o plot(multiple time series, plot.type = "single") was computing
`ylim' from the first series only.
o plot.acf() has a new `xpd = par("xpd")' argument which by default
*does* clipping (of the horizontal lines) as desired (xpd = NA was
used before, erronously in most cases).
o predict(smooth.spline(.), deriv = 1) now works.
o identify() failed when x is a structure/matrix. (PR#1238)
o getMethod() returns NULL when optional=TRUE as promised in the
documentation.
o setMethod() allows "..." to be one of the arguments omitted in
the method definition (but so far no check for ... being missing)
o Allow round() to work again on very large numbers (introduced
in fixing PR#1138). (PR#1254)
o Rinternals.h is now accepted by a C++ compiler.
o type.convert() was failing to detect integer overflow.
o piechart() was defaulting to foreground colour (black) fills
rather than background (as used in 1.3.1 and earlier). Now
background is used, but be aware that as from 1.4.0 this may
be transparent.
o La.eigen(*, only.values=TRUE) does not segfault anymore in one
branch (PR#1262).
o cut() now produces correct default labels even when
include.lowest = TRUE (PR#1263).
o reformulate() works properly with a response.
o cmdscale(*, k = 1) now works properly.
o Options by = "month" and "year" to seq.POSIXt() will always
take account of changes to/from daylight savings time: this
was not working on some platforms.
o glm.fit.null() now accepts all the arguments of glm.fit() (it
could be called from glm.fit with arguments it did not
accept), and is now documented.
o cov.wt(cbind(1), cor = TRUE) now works.
o predict(glm.object, se.fit = TRUE) was failing if the fit
involved an offset.
o detach() on package:base would crash R. (PR#1271)
o print or summary on a manova() object with no terms, no names on
the response and intercept = FALSE (which is not sensible)
would give an error.
o seek() on file connections was ignoring the `origin' argument.
o Fixed new environment handling in library() to avoid forcing
promises created by delay()
o arima0() could leak memory: now released via on.exit().
o qr.coef(qr,*) now keeps the names of qr$qr.
o read.00Index() no longer fails on data indexes not generated by
Rdindex (PR#1274).
--
O__ ---- Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
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|
R version 1.4.1 is released
|
Peter Dalgaard BSA
| 8
|
|
From ripley at stats.ox.ac.uk Mon Nov 16 19:07:54 1998
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Mon, 16 Nov 1998 18:07:54 +0000 (GMT)
Subject: VR and tree libraries for 0.63
Message-ID: <[email protected]>
These are now at CRAN (at least in Vienna).
Please note that VR_5.3pl030-1.tar.gz really does need 0.63: there
are problems with 0.62.x and 0.63 reading .rda files written by the
other. The earlier VR_5.3pl027-1.tar.gz for 0.62.3/4 remains on CRAN
in directory Old/0.62.
tree_0.3-1 adds tree.screens and tile.tree (needs 0.63), and support
for formulae like use ~ . - estperf - names.
--
Brian D. Ripley, ripley at stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272860 (secr)
Oxford OX1 3TG, UK Fax: +44 1865 272595
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|
VR and tree libraries for 0.63
|
Prof Brian Ripley
| 558
|
|
From fharrell at virginia.edu Mon May 20 17:07:18 2002
From: fharrell at virginia.edu (Frank E Harrell Jr)
Date: Mon, 20 May 2002 11:07:18 -0400
Subject: Hmisc and Design Packages
Message-ID: <[email protected]>
Thanks to Xiao Gang Fan new versions of the Hmisc and Design libraries are now available for Windows users at http://hesweb1.med.virginia.edu/biostat/s/library/r
The libraries have also been updated for Linux/Unix/MacOSX users. Hmisc now passes R CMD CHECK except for some warnings about help files. Many bugs have been fixed and all help file examples now run. It will soon be submitted to CRAN. Design will be at that point in about 3 weeks hopefully.
--
Frank E Harrell Jr Prof. of Biostatistics & Statistics
Div. of Biostatistics & Epidem. Dept. of Health Evaluation Sciences
U. Virginia School of Medicine http://hesweb1.med.virginia.edu/biostat
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|
Hmisc and Design Packages
|
Frank E Harrell Jr
| 36
|
|
From Achim.Zeileis at wu-wien.ac.at Mon May 29 20:46:35 2006
From: Achim.Zeileis at wu-wien.ac.at (Achim Zeileis)
Date: Mon, 29 May 2006 20:46:35 +0200
Subject: useR! 2006: final program
Message-ID: <[email protected]>
Dear useRs,
the final scientific program for "useR! 2006", the second R user
conference taking place in Vienna June 15-17, is now available online at
http://www.R-project.org/useR-2006/
The registration is open until May 31, so you still have two days to
register for this exciting event where you can meet 400 other useRs,
attend 160 presentations and participate in some of the pre-conference
tutorials given by prominent members of the R community.
We look forward to meeting you in Vienna!
The organizing team
Torsten, Achim, David, Bettina, Fritz and Kurt.
|
useR! 2006: final program
|
Achim Zeileis
| 452
|
|
From Roger.Bivand at nhh.no Fri Jun 30 15:25:55 2017
From: Roger.Bivand at nhh.no (Roger Bivand)
Date: Fri, 30 Jun 2017 15:25:55 +0200
Subject: The R Journal, Volume 9, Issue 1
Message-ID: <[email protected]>
Dear all,
The latest issue of The R Journal is now available at:
https://journal.r-project.org/archive/2017-1/.
Many thanks to all contributors - especially reviewers and authors.
Regards,
Bettina
--
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; e-mail: Roger.Bivand at nhh.no
Editor-in-Chief of The R Journal, https://journal.r-project.org/index.html
http://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
|
The R Journal, Volume 9, Issue 1
|
Roger Bivand
| 139
|
|
From mikalzet at libero.it Thu Jun 28 01:26:29 2001
From: mikalzet at libero.it (mikalzet at libero.it)
Date: Thu, 28 Jun 2001 01:26:29 +0200 (CEST)
Subject: second version of R-1.3.0 RPM for Mandrake 8.0
Message-ID: <[email protected]>
A new version of the RPM of R-1.3.0 for Mandrake 8.0
will be available on CRAN shortly: R-1.3.0-1.2mdk.i586.rpm.
The first version (R-1.3.0-1.1mdk.i586.rpm) unhappily was
broken, please do not install it.
--
Michele Alzetta
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|
second version of R-1.3.0 RPM for Mandrake 8.0
|
mikalzet at libero.it
| 253
|
|
From keitt at nceas.ucsb.edu Wed Feb 9 20:03:54 2000
From: keitt at nceas.ucsb.edu (Timothy H. Keitt)
Date: Wed, 09 Feb 2000 11:03:54 -0800
Subject: RPgSQL and RPMS for 0.99
Message-ID: <[email protected]>
The latest version of RPgSQL and RPMS for R version 0.99 can be found at
http://www.nceas.ucsb.edu/~keitt/R/
Cheers,
Tim
--
Timothy H. Keitt
National Center for Ecological Analysis and Synthesis
735 State Street, Suite 300, Santa Barbara, CA 93101
Phone: 805-892-2519, FAX: 805-892-2510
http://www.nceas.ucsb.edu/~keitt/
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|
RPgSQL and RPMS for 0.99
|
Timothy H. Keitt
| 303
|
|
From p.dalgaard at biostat.ku.dk Mon Aug 25 11:57:29 2008
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard)
Date: Mon, 25 Aug 2008 11:57:29 +0200
Subject: R 2.7.2 is released
Message-ID: <[email protected]>
I've rolled up R-2.7.2.tar.gz a short while ago.
This is intended as a wrap-up release containing all known fixes to issues with the 2.7.x series.
See the full list of changes below.
You can get it (in a short while) from
http://cran.r-project.org/src/base/R-2/R-2.7.2.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you. Binaries
for various platforms will appear in due course.
For the R Core Team
Peter Dalgaard
These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:
70447ae7f2c35233d3065b004aa4f331 INSTALL
433182754c05c2cf7a04ad0da474a1d0 README
4f004de59e24a52d0f500063b4603bcb OONEWS
ff4bd9073ef440b1eb43b1428ce96872 ONEWS
2335719fbb03eb98954abf14b340e46f NEWS
1ad28cbc84485ccdf4ce5721b34ed645 THANKS
070cca21d9f8a6af15f992edb47a24d5 AUTHORS
a6f89e2100d9b6cdffcea4f398e37343 COPYING.LIB
eb723b61539feef013de476e68b5c50a COPYING
020479f381d5f9038dcb18708997f5da RESOURCES
620f0b60f7f14bcb3f8adcbecd590768 FAQ
6122945e9301825b97a506151b3cefde R-2.7.2.tar.gz
6122945e9301825b97a506151b3cefde R-latest.tar.gz
Here is the relevant bit of the NEWS file:
CHANGES IN R VERSION 2.7.2
NEW FEATURES
o sprintf() returns elements of the result in UTF-8 when the
format or any character input has a corresponding element
declared as UTF-8. Similarly for paste(), elements of the
result are in UTF-8 when any input to that element is declared
as UTF-8.
o axis() has new arguments 'col.ticks' and 'lwd.ticks' to allow
the colour and line width of ticks to be set separately from
that of the line (e.g. to set one or the other to transparent
or zero width).
o legend() has a new argument 'box.col' to set the colour of the
enclosing box.
o legend() gains a 'xpd' argument to make it easier to place a
legend in the margins or outer margins.
o stripchart() now passes '...' to title() (as well as to
plot.default() and axis()). (Wish of PR#12202)
o help.search() has new argument 'searchEngine' to go
directly to the search form: this is needed by users of
Firefox 3 to workaround a bug in interpreting the search
results pages.
BUG FIXES
o Plotmath computed the glyph metrics for the wrong character (and
perhaps for a non-existent one) if this was a single-byte
character with the top bit set. An example was symbol("\300").
o sink() and cat() could divert output to a non-writable connection.
o phyper(x, 0,0,0) no longer hangs for huge x and gives 1 for x >= 0.
(PR#11813)
o plnorm(x, ..., log.p=TRUE) is now correct for x <= 0. (PR#11867)
o <data.frame>[, ch] gives an error (again!) when ch is a string not
exactly matching the column names, thanks to an oral bug report by
Matthew Dowle.
o data.frame(x=1:2, y=3:4, row.names=c("a","NA"))[c(2,NA),] has
correct row names c("NA,"NA.1") again.
o The GUI data editor for dataframes did not handle escape
characters in entries properly. (PR#11897)
o PCRE has been updated to 7.7 (bugfix release).
o package.skeleton() wrongly warned about invalid code_files names
when these were not in the current directory.
o shapiro.test(c(0,0,1)) now has P value >= 0 (instead of barely
negative).
o assign() now warns if given a character vector of length > 1,
rather than silently taking the first element.
o rcond(<exactly singular matrix>) now gives 0 instead of an error.
o There was a memory leak in C function ucstoutf8 used by some
graphics devices.
o Plots of profile.mle() objects (package 'stats4') were
misbehaving when the 'which' argument had been used in their
calculation.
o dnbinom(x, size, mu=*, ..) is now more accurate for very large
'size'. The same applies to pnbinom() and rnbinom().
o axis() was ignoring par() mgp[3] if mgp was set in-line.
o Closing an X11 View() or dataentry window via its frame's
close control now works better on some window managers.
o Calling lapply() was not handling method dispatch correctly for
is.numeric(), is.matrix(), is.array(), log() and the Math2
group. This affected data.matrix() which incorrectly regarded
"Date" and "POSIXct" objects as numeric, and has been adjusted
to do so as exceptions.
o package.skeleton() was not looking for non-function objects in
its 'environment' argument.
o nls() was only finding its 'weights' argument in the case when
all the variables in the formula were of the same length and
hence that model.frame() could be used.
It was silently ignoring 'subset' and 'na.action' except in
that case. Now they are ignored only if 'data' is a list and
variables taken from 'data' are not all of the same length,
in which case a warning is given.
o The 'mle' confint() method now takes 'level' into account when
setting 'alpha' for the profile.
o within() was not handling correctly expressions that produced
NULL columns. (PR#11131)
o dev.print() and dev.copy2{eps,pdf}() now ensure that the current
device is restored as the active device even if an error
occurs. (PR#9801)
o as.Date() could fail to convert character strings representing
days on which midnight did not exist in the current timezone
(as happened in parts of Africa on 1960-01-01).
o The automatic placement of legend() with 'title' and a
reversed 'x' axis was incorrect. (PR#12019)
o The use of multiple packages in 'LinkingTo' works again, and
now works when the dependent packages are in the library to be
installed to (but not in the library path seen by R --vanilla).
o bxp() (and hence boxplot) now respects in-line graphical
parameters 'xaxp'/'yaxp' as appropriate. (PR#11463)
o barplot(log = "y") failed if there were NAs in the 'height'
argument. (PR#11585)
o pbeta() is more accurate in some cases with extreme values of
'ncp'. (PR#11277).
o edit.data.frame() no longer fails if called on a 0-column
data frame and no column is created.
o pchisq(x, df=0) was always one even for x < 0; similarly for
pgamma(x, alpha=0).
o add1() and drop1() now return a P-value of NaN in cases with
df=0 for test="Chisq" (they gave NaN until pchisq was altered
in R 2.6.2).
o The default methods of drop1() and add1() now re-evaluate in the
object's formula environment, rather than simply in the parent
(informal bug report by Werner Stahel).
o The undocumented limit of 8191 bytes on comments (from # to
the end of the line) in R code has been removed.
o qgamma() warns if used with shape < 1e-10, when it may be
unreliable. (PR#12324)
o Installing a source package was not using the package's declared
encoding (if any) as a default encoding for the help.search()
database in Meta/hsearch.rds. This could cause packages with
a default encoding to have some of their entries rejected by
help.search() in a multi-byte locale (such as a UTF-8 locale).
o duplicated() and unique() now handle 'incomparables' better,
and avoid occasional segfaults (PR#12551).
o data.frame(row.names=NULL) once again behaves differently from
the default (as documented).
o plot(isoreg(x,y)) now plots the points correctly, also when 'x'
is not sorted.
--
O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
|
R 2.7.2 is released
|
Peter Dalgaard
| 603
|
|
From clive at bell-labs.com Tue Mar 17 13:44:40 1998
From: clive at bell-labs.com (Clive Loader)
Date: Tue, 17 Mar 1998 07:44:40 -0500
Subject: locfit -> CRAN
Message-ID: <[email protected]>
The locfit library is now available through CRAN, in the
Contributed R Code directory. Locfit fits local regression,
likelihood and density estimation models, in the spirit
of loess but with many additional features. To install,
unpack the locfit_19980309.tar.gz file, and
R INSTALL locfit
Most of the functionality and examples on my home page
http://cm.bell-labs.com/stat/project/locfit/ should work
in R, with the exception of trellis displays.
Thanks to Kurt Hornik for helping with the port and testing.
Sincerely,
Clive Loader
clive at bell-labs.com
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|
locfit -> CRAN
|
Clive Loader
| 523
|
|
From Heather.Turner at warwick.ac.uk Tue Aug 10 13:12:27 2010
From: Heather.Turner at warwick.ac.uk (Heather Turner)
Date: Tue, 10 Aug 2010 12:12:27 +0100
Subject: useR! 2011: announcement and call for tutorials
Message-ID: <[email protected]>
We are pleased to announce that the R user conference
useR! 2011
is scheduled for August 16-18, 2011, and will take place at the
University of Warwick, Coventry, UK.
As for the predecessor conferences, the program will consist of two
parts: invited lectures and user-contributed sessions (abstract
submission will be available online later this year). Prior to the
conference, there will be tutorials on R (proposals for tutorials should
be sent before October 29, 2010, see below).
INVITED SPEAKERS
Adrian Bowman, Lee Edlefsen, Ulrike Gr?mping, Wolfgang Huber, Brian
Ripley, Jonathan Rougier, Simon Urbanek, and Brandon Whitcher.
USER-CONTRIBUTED SESSIONS
The conference will feature both talks and posters illustrating the use
of R in practice. Contributions are welcome that introduce recent
developments in the R Project (including CRAN packages), demonstrate
applications of R in areas of current interest, or otherwise engage and
inspire participants in their use of R.
PRE-CONFERENCE TUTORIALS
Before the official program, half-day tutorials will be offered on
Monday, August 15.
We invite R users to submit proposals for three hour tutorials on
special topics regarding R. The proposals should give a brief
description of the tutorial, including goals, detailed outline,
justification of why the tutorial is important, background knowledge
required and potential attendees. The proposals should be sent before
October 29, 2010 to useR-2011_at_R-project.org.
A web page offering more information on the `useR!' conference is
available at
http://www.R-project.org/useR-2011
We hope to see you in Coventry!
The organizing committee:
John Aston, Julia Brettschneider, David Firth, Ashley Ford, Ioannis
Kosmidis, Tom Nichols, Elke Th?nnes and Heather Turner
|
useR! 2011: announcement and call for tutorials
|
Heather Turner
| 368
|
|
From andy_liaw at merck.com Wed Aug 28 17:15:34 2002
From: andy_liaw at merck.com (Liaw, Andy)
Date: Wed, 28 Aug 2002 11:15:34 -0400
Subject: new version of the randomForest package
Message-ID: <[email protected]>
I have just uploaded to CRAN the new version of the randomForest package.
Those who had used the previous version will absolutely want to upgrade, as
the new version fixes a few serious bugs (some giving wrong results w/o
warning or error). This version matches version 3.3 of the classification
code and version 1.0 of the regression code on Prof. Breiman's web site.
The package provides an R interface to Prof. Breiman's code for regression
and classification by the random forest algorithm. Details about the
algorithm (and the original Fortran code) can be found on
http://oz.berkeley.edu/users/breiman
New features and bug fixes include:
o Random forest for regression problems now incorporated into the package.
o Factor (categorical) predictors are now handled correctly, especially
through the formula interface. (The previous version wrongly expands
factors into contrasts.)
o Ordered factor predictors are now correctly handled.
o For classification problem, there is an new option for the predict method
to calculate proximity measure for the test data.
o Calls to R's random number generator from Fortran have been made more
portable. I believe this was causing segmentation faults on some platforms
in the previous version.
o The Example section of the help page for randomForest now show some of
the extra things that can be done with the randomForest object.
o The call to the underlying C/Fortran code no longer copy data (i.e.,
.C(..., DUP=FALSE) is used). This should reduce memory requirement quite a
bit, especially for large data sets. This should be fairly safe since data
pass to C/Fortran are copies made at the R level anyway.
o The version number of the package now tracks the version number of Prof.
Breiman's classification code (i.e., currently 3.3).
o The spelling of my co-author's name has been corrected!
Because of the limited amount of time I was able to spend on this package,
the code are not the most elegant. I would appreciate any
comments/suggestions/bugs/patches.
Regards,
Andy
Andy I. Liaw, PhD
Biometrics Research Phone: (732) 594-0820
Merck & Co., Inc. Fax: (732) 594-1565
P.O. Box 2000, RY84-16 Rahway, NJ 07065
mailto:andy_liaw at merck.com
------------------------------------------------------------------------------
Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (Whitehouse Station, New Jersey, USA) that may be confidential, proprietary copyrighted and/or legally privileged, and is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please immediately return this by e-mail and then delete it.
==============================================================================
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|
new version of the randomForest package
|
Liaw, Andy
| 59
|
|
From philippe.grosjean at ifremer.fr Mon Dec 2 11:48:05 2002
From: philippe.grosjean at ifremer.fr (Philippe Grosjean)
Date: Mon Dec 2 11:48:05 2002
Subject: R GUI development mailing list
Message-ID: <[email protected]>
We would like to announce the existence of a Special Interest Group in GUI
development for R (R-SIG-GUI). This mailing list discusses issues concerning
the development of graphical user interfaces for R, especially platform
independent ones. It is a complementary tool to the R GUI web pages
(http://www.r-project.org/GUI) that exist since July 2002.
Best Regards,
Philippe Grosjean
...........]<(({?<...............<?}))><...............................
( ( ( ( (
) ) ) ) ) Philippe Grosjean
( ( ( ( (
) ) ) ) ) IFREMER Nantes - DEL/AO
( ( ( ( ( rue de l'Ile d'Yeu, BP 21105, 44311 Nantes Cedex 3
) ) ) ) ) tel: (33) 02.40.37.42.29, fax: (33) 02.40.37.42.41
( ( ( ( (
) ) ) ) ) SciViews project coordinator (http://www.sciviews.org)
( ( ( ( ( e-mail: phgrosjean at sciviews.org
) ) ) ) )
( ( ( ( ( "I'm 100% confident that p is between 0 and 1"
) ) ) ) ) L. Gonick & W. Smith (1993)
.......................................................................
|
R GUI development mailing list
|
Philippe Grosjean
| 111
|
|
From plummer at iarc.fr Fri Jun 4 09:41:13 1999
From: plummer at iarc.fr (Martyn Plummer)
Date: Fri, 04 Jun 1999 09:41:13 +0200 (CEST)
Subject: Red Hat Linux/Intel 6.0 RPMS for R
Message-ID: <[email protected]>
RPMs of R-0.64.1 are now available for Red Hat Linux/Intel 6.0.
They should be mirrored to a CRAN site near you over the weekend.
If you are desperate you can get them now from:
ftp://ftp-fis.iarc.fr/pub/R/RedHat/6.0/i386
GNOME SUPPORT
-------------
If you have GNOME installed, then use the "R-base-gnome" package.
Otherwise just use the "R-base" package. This is change from the
previous arrangement in which GNOME support for R was distributed
as a separate add-on package.
Don't install both R-base and R-base-gnome.
PGP
---
This is a good opportunity to tell you, if you haven't noticed already,
that the RPM packages are PGP signed. You can pick up my public key
from
http://developer.redhat.com/rhcn/browse/conventional/memberinfo.php3?member=plum
mer at iarc.fr
Thank you for your patience.
Martyn
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|
Red Hat Linux/Intel 6.0 RPMS for R
|
Martyn Plummer
| 485
|
|
From guido at hal.stat.unipd.it Fri Oct 8 11:34:53 1999
From: guido at hal.stat.unipd.it (Guido Masarotto)
Date: Fri, 8 Oct 1999 10:34:53 +0100
Subject: R-0.65.1 for WinNT/9X
Message-ID: <[email protected]>
A binary distribution of R-0.64.2 for Windows is available at
<CRAN>/bin/windows/windows-NT (at least at Wien).
Enjoy it.
guido masarotto
Windows News (since R0.64.2)
rw0651
======
New function savePlot() to save plots to wmf, gif or ps.
There is now support for help via compiled HTML files (as used by the
latest Microsoft products): set options(chmhelp=TRUE) to use this.
You will probably need Internet Explorer 4 or later installed to use
this, or you can install hhupd.exe from the windows/windows-NT/base/etc
directory on CRAN.
There is support for building Windows help files (as in Windows 95).
Set options(winhelp=TRUE) to make this your preferred help system.
Both compiled HTML files and Windows help are available for the
standard packages.
The new function update.packages() is supported if you have wget.exe
(a copy is in the windows/windows-NT/base/etc/wget.zip on CRAN) or
lynx.exe, from http://www.fdisk.com/doslynx/lynxport.htm.
On NT only, CPU times are returned by proc.time() (using a call to
GetProcessTimes).
Rotated text on a windows / win.* device is placed more accurately,
especially for non-multiples of 90 degrees.
A windows() device reports itself as `windows' not `X11'.
getenv() now returns all the environmental variables.
unlink() can now remove (empty) directories (but not using wildcard
specifications).
The complex LINPACK routines which were not included in the Unix
versions of R are now omitted here.
There is more support for (support of) ActiveX Automation via the
Rproxy.dll: see the file front-ends/readme.
As under Unix, .Renviron is first searched for in the working directory,
then in the home directory. (See README for how the home directory is
decided.)
The sockets code is definitely working in this version, enough to support
source.url and friends.
options(pager="console") is set as the default if --ess is used (as it
works better with Emacs).
The rounding code has been re-written to be more accurate and to round
to even as documented.
The rw-FAQ is linked into the HTML help system.
We believe the problems with re-sizing windows (especially on Windows 9x)
have been solved.
rw0650
======
[ Because Guido Masarotto was ill for several weeks, rw0650 was only ever
pre-released. ]
There are many changes `under the skin' which are not reflected in
user-visible changes, but either improve performance or will allow
future enhancements.
The environment variables have been changed: R_HOME is now R's home
directory and R_USER is the HOME for the user which will be used by R
(and defaults to HOME, if set, then to ${HOMEDRIVE}${HOMEPATH}, if that
is set, then the working directory). (There are many other such
changes in R: for example RLIBS becomes R_LIBS, although for the time
being RLIBS is also recognised.)
Saving a plot as postscript from the device menu will produce a
portrait plot irrespective of the setting of ps.options().
Saving a plot as a metafile should be more reliable on machines which
report incorrect information on the size of the screen.
The new flag --no-environ suppresses reading .Renviron and is implied by
--vanilla.
When rterm is used non-interactively either --save or --no-save must be
specified: these is no longer a default of --no-save (for consistency
with Unix).
More support for building R into other applications: see the examples
in the front-ends directory of the source distribution.
Interrupting by Esc or Ctrl-Break is handled internally by signals, so
the `User Break' response will no longer appear, but in rterm ^C will
be echoed.
There is limited support for `tilde-expansion': file paths such as
~/rest will be expanded to ${HOME}\rest if HOME is set, or to
${HOMEDRIVE}${HOMEPATH}\rest if those variables are set.
Using rterm either interactively or with --ess will be more responsive and
use much less CPU time when waiting for input. Interruptions by Ctrl-Break
or (under --ess, for use by ESS) Ctrl-C should happen immediately and be
handled correctly. [On NT: problems with Win 98 were corrected for rw0651.]
The installer can now install correctly in a top-level directory (e.g.
C:\), fixing a bug in the unzip code used.
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
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|
R-0.65.1 for WinNT/9X
|
Guido Masarotto
| 499
|
|
From pd@|gd @end|ng |rom gm@||@com Fri Jun 10 14:01:41 2022
From: pd@|gd @end|ng |rom gm@||@com (peter dalgaard)
Date: Fri, 10 Jun 2022 14:01:41 +0200
Subject: [Rd] R 4.2.1 scheduled for June 23
Message-ID: <[email protected]>
Full schedule available on developer.r-project.org in a short while.
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
|
[Rd] R 4.2.1 scheduled for June 23
|
peter dalgaard
| 591
|
|
From Friedrich.Leisch at ci.tuwien.ac.at Mon Jul 9 12:00:58 2001
From: Friedrich.Leisch at ci.tuwien.ac.at (Friedrich Leisch)
Date: Mon, 9 Jul 2001 12:00:58 +0200
Subject: R News Volume 1/2 published
Message-ID: <[email protected]>
We have just published the second volume of R News on
http://cran.R-project.org/doc/Rnews
where you can download the newsletter as PDF or postscript file. It
will propagate to the CRAN mirrors within a day or two..
Contents:
Changes in R
Changes on CRAN
Date-Time Classes
Installing R under Windows
Spatial Statistics in R
geoR: A Package for Geostatistical Analysis
Simulation and Analysis of RAndom Fields
mgcv: GAMs and Generalized Ridge Regression for R
What's the Point of `tensor'?
On Multivariate t and Gau? Probabilities in R
Programmer's Niche
Recent Events
which makes a total of 32 pages of features, applications and riddles
about our favourite data analysis environment.
Enjoy reading!
For the editorial board,
Fritz Leisch
--
-------------------------------------------------------------------
Friedrich Leisch
Institut f?r Statistik Tel: (+43 1) 58801 10715
Technische Universit?t Wien Fax: (+43 1) 58801 10798
Wiedner Hauptstra?e 8-10/1071 Friedrich.Leisch at ci.tuwien.ac.at
A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch
-------------------------------------------------------------------
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Send "info", "help", or "[un]subscribe"
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|
R News Volume 1/2 published
|
Friedrich Leisch
| 262
|
|
From Friedrich.Leisch at ci.tuwien.ac.at Tue Dec 9 19:21:16 1997
From: Friedrich.Leisch at ci.tuwien.ac.at (Friedrich Leisch)
Date: Tue, 9 Dec 1997 19:21:16 +0100
Subject: R-beta: R FAQ v0.60
In-Reply-To: <[email protected]>
References: <[email protected]>
<[email protected]>
Message-ID: <[email protected]>
>>>>> On 09 Dec 1997 19:11:28 +0100,
>>>>> Peter Dalgaard BSA (PDB) wrote:
PDB> Kurt Hornik <Kurt.Hornik at ci.tuwien.ac.at> writes:
>> code CVS archive. The group currently consists of Peter Dalgaard,
>> Robert Gentleman, Kurt Hornik, Ross Ihaka, Thomas Lumley, Martin
>> Maechler, Paul Murrell, Heiner Schwarte, and Luke Tierney.
PDB> aaaand Beetlebum... (old Spike Jones number)
PDB> It seem Friedrich Leisch fell off the list - again!
Well, I'm just sitting next door to Kurt, so I'm easy to forget ... :-)
fritz
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|
R-beta: R FAQ v0.60
|
Friedrich Leisch
| 580
|
|
From bwheeler at echip.com Mon Dec 31 16:46:03 2001
From: bwheeler at echip.com (Bob Wheeler)
Date: Mon, 31 Dec 2001 10:46:03 -0500
Subject: Johnson system
Message-ID: <[email protected]>
With R 1.4.0 the JohnsonFit() function in
SuppDists has been modified to accept a vector of
the first four central moments. Previously the
only obvious option was to input a set of
observations. The most common need for this seems
to be by those who have no data in hand, but want
random values from non standard distributions.
--
Bob Wheeler --- (Reply to: bwheeler at echip.com)
ECHIP, Inc. --- (302) 239-6620, voice FAX
724 Yorklyn Rd., Hockessin, DE 19707
Randomness comes in bunches
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|
Johnson system
|
Bob Wheeler
| 297
|
|
From luke at stat.uiowa.edu Fri Apr 13 20:21:07 2007
From: luke at stat.uiowa.edu (Luke Tierney)
Date: Fri, 13 Apr 2007 13:21:07 -0500
Subject: Subject: useR! 2007 --- programming competition
Message-ID: <[email protected]>
R Users and Developers,
The first North American useR! to be held at Iowa State University,
Ames, Iowa, August 8-10, 2007, will include a programming
competition. The challenge:
Develop a package useful for the analysis of large data sets.
Your package could augment an existing package like biglm, for
example, by providing graphical or numerical diagnostic tools, or by
adding support methods for transparently handling data from a
database. Alternatively, you could develop a package for fitting
linear or generalized linear models to large data sets that takes an
entirely different approach.
The winning team will receive a cash prize. The submission deadline is
June 30, 2007. Further details are available at the conference website
at http://www.user2007.org/.
As a reminder, we are also calling for papers for presentation at the
meeting. Papers are encouraged in all areas, but particular emphasis
is given to work describing newly created or improved R
packages. Papers will be refereed and a best paper/presentation award
is likely.
Also, if you wish to apply for financial support, please send an
application to user2007 at iastate.edu by April 23 (include a brief CV
and a statement that demonstrates your eligibility, your need for
support, and an amount of support required - students should include
the name of their supervisor).
useR! Program Committee
user2007 at iastate.edu
|
Subject: useR! 2007 --- programming competition
|
Luke Tierney
| 414
|
|
From bates at stat.wisc.edu Fri Jan 10 17:52:04 2003
From: bates at stat.wisc.edu (Douglas Bates)
Date: Fri Jan 10 17:52:04 2003
Subject: R-1.6.2 is available via rsync
In-Reply-To: <[email protected]>
References: <[email protected]>
Message-ID: <[email protected]>
Sources for R-1.6.2 are now available via rsync at rsync.r-project.org
$ rsync rsync.r-project.org::
r-release R-1.6.2 sources (current released version - approx 30 MB)
r-patched R sources (patched released version - approx 30 MB)
r-devel R sources (development version)
r-manuals Development sources for manuals for R
r-recommended Sources for recommended R packages
xlispstat xlispstat sources (development version) CVS tree (approx 12 MB)
CRAN Complete CRAN ftp area
Bioc-release Bioconductor sources (current release version)
Bioc-devel Bioconductor sources (development version)
GGobi GGobi sources (devel version)
omega-cvs Omega Project for Statistical Computing CVS tree
r-project-web Web pages for www.r-project.org and mirrors
Omegahat Complete ftp archive for Omegahat
|
R-1.6.2 is available via rsync
|
Douglas Bates
| 150
|
|
From pdalgd at gmail.com Thu Aug 22 08:29:53 2013
From: pdalgd at gmail.com (peter dalgaard)
Date: Thu, 22 Aug 2013 08:29:53 +0200
Subject: R-3.0.2 on September 25
Message-ID: <[email protected]>
Just a quick note, mainly to warn off maintainers of the recommended packages, that we intend to release R-3.0.2 on Wednesday, September 25.
We'll be following the usual schedule from
http://developer.r-project.org/release-checklist.html
Notice in particular that new versions of recommended packages should be finalized 14 days before release.
For the R Core Team
Peter Dalgaard
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
|
R-3.0.2 on September 25
|
peter dalgaard
| 433
|
|
From pd.mes at cbs.dk Tue May 29 13:40:44 2012
From: pd.mes at cbs.dk (Peter Dalgaard)
Date: Tue, 29 May 2012 13:40:44 +0200
Subject: Release plans: R-2.15.1 on June 22
Message-ID: <[email protected]>
Just a note, mainly to people who maintain larger R installations, that we intend to have a patch release version on June 22. The nickname will be "Roasted Marshmallows".
This is somewhat later than previous .1 releases, but we are also now aiming for an annual rather than biannual release scheme. There have been very few issues with 2.15.0, but some people may be waiting superstitiously for a .1 release (or expecting one come along any day now) and need to be informed about the plans.
--
Peter Dalgaard, Professor
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
|
Release plans: R-2.15.1 on June 22
|
Peter Dalgaard
| 440
|
|
From bates at stat.wisc.edu Fri Aug 31 16:44:22 2001
From: bates at stat.wisc.edu (Douglas Bates)
Date: 31 Aug 2001 09:44:22 -0500
Subject: rsync repository updated to R-1.3.1
Message-ID: <[email protected]>
The rsync repository at rsync.r-project.org has been updated to
R-1.3.1
For example you can create a local directory R-1.3.1 and populate it
with the source tree by
rsync -avC rsycn.r-project.org::r-release ./R-1.3.1
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r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
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|
rsync repository updated to R-1.3.1
|
Douglas Bates
| 266
|
|
From p.dalgaard at biostat.ku.dk Sun Aug 10 21:48:58 2008
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard)
Date: Sun, 10 Aug 2008 21:48:58 +0200
Subject: R 2,7.2 is scheduled for August 25
Message-ID: <[email protected]>
This is to announce that we plan to release R version 2.7.2 on Monday,
August 25, 2008.
Release procedures start Friday August 15 (when we get back from useR).
The source tarballs will be made available daily (barring build
troubles) and the tarballs can be picked up at
http://cran.r-project.org/src/base-prerelease/
a little later.
Binary builds are expected to appear starting Monday 18 at the latest.
For the Core Team
Peter Dalgaard
--
O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
|
R 2,7.2 is scheduled for August 25
|
Peter Dalgaard
| 601
|
|
From pd.mes at cbs.dk Mon Mar 22 11:38:23 2010
From: pd.mes at cbs.dk (Peter Dalgaard)
Date: Mon, 22 Mar 2010 11:38:23 +0100
Subject: R 2.11.0 Scheduled for April 22, 2010
Message-ID: <[email protected]>
This is to announce that we plan to release R version 2.11.0 on Thursday,
April 22, 2010.
Those directly involved should review the generic schedule at
http://developer.r-project.org/release-checklist.html
The source tarballs will be made available daily (barring build
troubles) via
http://cran.r-project.org/src/base-prerelease/
For the R Core Team
Peter Dalgaard
--
O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
--
Peter Dalgaard
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
|
R 2.11.0 Scheduled for April 22, 2010
|
Peter Dalgaard
| 359
|
|
From p.dalgaard at biostat.ku.dk Mon Dec 22 10:24:27 2008
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard)
Date: Mon, 22 Dec 2008 10:24:27 +0100
Subject: R 2.8.1 is released
Message-ID: <[email protected]>
I've rolled up R-2.8.1.tar.gz a short while ago.
This is a maintenance release and fixes a number of mostly minor bugs
and platform issues.
See the full list of changes below.
You can get it (in a short while) from
http://cran.r-project.org/src/base/R-2/R-2.8.1.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you. Binaries
for various platforms will appear in due course.
For the R Core Team
Peter Dalgaard
These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:
70447ae7f2c35233d3065b004aa4f331 INSTALL
433182754c05c2cf7a04ad0da474a1d0 README
4f004de59e24a52d0f500063b4603bcb OONEWS
ff4bd9073ef440b1eb43b1428ce96872 ONEWS
4eff8b4937a55a2c3ece8b0a31772b62 NEWS
1ad28cbc84485ccdf4ce5721b34ed645 THANKS
070cca21d9f8a6af15f992edb47a24d5 AUTHORS
a6f89e2100d9b6cdffcea4f398e37343 COPYING.LIB
eb723b61539feef013de476e68b5c50a COPYING
020479f381d5f9038dcb18708997f5da RESOURCES
5d443029346cbad2f2df7c62a0ea8e0f FAQ
acd40621b8942a2464daa2f9cef3273d R-2.8.1.tar.gz
acd40621b8942a2464daa2f9cef3273d R-latest.tar.gz
Here is the relevant part of the NEWS file:
CHANGES IN R VERSION 2.8.1
NEW FEATURES
o sum() now has a method for "difftime" objects (via the Summary
group).
max(), min() and range() applied to "difftime" object(s) now
return a result in the common units of the objects, if there
is one.
o installed.packages() is now tolerant of malformed DESCRIPTION
files in installed packages (it ignores them, with a warning).
o qt() now works for 0 < df < 1.
o For consistency with matrix() and array(), dimnames(x) <-
list() removes the dimnames (as assigning NULL would do).
It was previously an error.
o nlminb() copies names from 'start' to the parameter vector
used (for consistency with optim()).
o legend() gains a 'title.col' argument: the title colour was
previously set from the first element of 'text.col' (which
remains the default).
o In an Rd file, use of top-level \itemize{} inside a \value{}
block is unnecessary and almost always gave a faulty
conversion. Most cases are now detected and corrected, but
give a warning as such code will not work correctly in earlier
versins of R.
Also, use of \code{} inside a code block such as \examples{}
will give a erroneous conversion that is now detected and
warned against.
o Autoflushing of stdout is turned on when Rd processing, so
warnings/error are likely to appear in the right place in
redirected output (such as that from R CMD check).
UTILITIES
o R_PDFLATEXCMD is added to the environment variables set by
'R CMD' and is used by R CMD Rd2dvi.
R_LATEXCMD, R_PDFLATEXCMD, R_MAKEINDEXCMD and R_DVIPSCMD
default to 'latex', 'pdflatex', 'makeindex' and 'dvips'
respectively if no suitable executable was found at configure
time (since they might well be available at run time,
particularly for binary installations of R). This affects
R CMD Rd2dvi and help(offline=TRUE).
R CMD Rd2dvi now gives an explicit error message if latex (or
pdflatex) fails.
R CMD Rd2dvi gains a --no-index argument: processing some
special characters on PDF indices gave errors which used to be
ignored.
DEPRECATED & DEFUNCT
o R CMD INSTALL --with-package-versions is deprecated (and
support has always been incomplete on Windows).
So is install.packages(installWithVers = TRUE).
o Rd conversion to Sd and Ssgm is now deprecated as we no longer
have any means to check the results (and Sd is long obsolete).
BUG FIXES
o add1.glm() no longer warns if applied to a binomial glm with a
factor response.
o aggregate.data.frame() now does something sensible with a
zero-column 'x' rather than failing with an obscure error
message. It gives an explicit error message if called with a
zero-row 'x'.
o integrate() now accepts integer results from f(): as documented,
but only double was accepted.
o contrib.url() produced an incorrect URL for the type
"mac.binary".
o pairwise.wilcox.test() did not pass on the 'paired' argument
(caught by Matthias Kohl)
o bmp(), jpeg(), and png() on unix with type="cairo" would segfault
on closure if the output file could not be opened.
o tiff() on unix would not write the output file for the first page
when multiple pages were plotted.
o str(1 + structure(1, class = "test")) no longer recurses
indefinitely.
o pf(x, .., ncp, lower.tail=FALSE, log=TRUE) is much more accurate
for large x now.
o dev2bitmap() failed in 2.8.0 if 'taa' and 'gaa' were both NA.
o Under rare circumstances equality tests for character strings
could fail to report equality in 2.8.0 in the same way as
2.7.2. (This needed a current encoding of Latin-1 or UTF-8,
one string whose encoding was marked as that encoding and one
that was marked as "unknown". In that circumstance the two
strings are not actually known to be equal, but earlier
versions of R assumed that "unknown" meant the current
encoding, and this is done once again.)
o R CMD config could echo messages from GNU make if called from
within a Makefile (as e.g. package Rcpp did), especially from
within a parallel make run.
o Rounding error could affect window(extend=TRUE) when applied
to monthly series. (PR#13272)
o Offline help on a Unix-alike now works even if options
"latexcmd" and "dvipscmd" contain spaces
(e.g. "dvips -Pmy_printer").
Informative error messages are given if running latex or dvips
fail.
o Using plot.lm() on a "glm" object since 2.7.1 with which=5
caused the Pearson rather than deviance residuals to be used
in which=2 or 3 (including in the default case). (Thanks to
Effie Greathouse and Greg Snow.)
plot.lm() did not report on omitting observations with
leverage one if they also had residual exactly zero. This was
seen in example(occupationalStatus).
o deparse(nlines=) no longer pads short results with blank
lines. (PR#13299)
o legend(xpd=) now restores 'xpd' correctly. (PR#12756)
o The "formula" method for lines() now works if 'subset' is
supplied and no 'data' argument (as that for points() did).
o Sweave() now takes the defaults for the options 'pdf.version'
and 'pdf.encoding' of its RweaveLatex driver from pdf.options().
o prettyNum(x, drop0trailing=TRUE) treated "1.1e20" as "1.1e2"
and hence str() did as well, in 2.8.0 only.
o dchisq(x, df, ncp) no longer hangs for large x and ncp > 0,
and is more accurate in some cases (PR#13309).
o installed.packages(lib.loc = D, priority="NA") now also works when
D contains a single package. (PR#13332)
o legend(...., merge=TRUE) now warns and has no effect in the
case where no line segments are drawn. (PR#13340)
o transform.data.frame() works better when two or more columns are
added.
o Deparsing argument lists with non-syntactic names (e.g. that for
transform()) now uses backticks rather than double quotes to
produce syntactically valid output.
o matrix() failed to check for 0-length 'dimnames': it now
treats them as NULL (as array did). (PR#13361)
o 0^NA is now NA, not Inf, consistent with x^NA, x != 1.
o anova.mlm() did not work if T had only one row (including
e.g. the case M = ~1).
o axis.POSIXct() mislabelled for some time ranges of a few hours
(reported by Martin Becker).
o mantelhaen.test() with 'exact=FALSE' was not respecting
'alternative'. It now does one-sided tests similarly to
prop.test().
o anova.mlm() had trouble with some designs where near-zero rows of
the tranformation matrix were not removed (caught by Nils Skutara).
o Rd conversion was handling expressions like
'\item{foo}{see \eqn{x}}' (with one argument to \eqn
immediately followed by a right brace) incorrectly, sometimes
giving a spurious warning about 'missing text'.
o R CMD INSTALL used the C locale to install the DESCRIPTION
file, and so escaped non-ASCII characters in packages with a
declared encoding of "latin1" or "UTF-8". (However, the
installed DESCRIPTION file was rarely used since the dumped
metadata are available.)
o xspline() now respects inline par settings.
It and grid.xspline() now handle the special case of only two
control points, and splines with control points that are
located well outside the device (e.g., a zoomed view of a
larger curve). (Both cases were giving the error "reached
MAXNUMPTS").
o In setClass("C", contains="list"); x <- new("C", 1:3), x[2:3] now
remains of class "C". So does rep(x, 2) or rep.int(x, 3).
o median.default() now also works for "numeric"-like vectors.
o The pdf() device can now handle the case where an image uses a
very large number of colours with different levels of
semi-transparency (alpha-values). It used to segfault.
(Also PR#13264.)
o window() failed to apply a fuzz to 'start' or 'end' and so
sometimes warned incorrectly for time series with 'freq' not a
power of two (e.g. 12 or 24).
o unique.default() now preserves the "tzone" attribute on
"POSIXct" objects.
o If all the packages had dependency lists of equal lengths,
occasionally install.packages() would compute an incorrect
sort order.
o col(x, as.factor=TRUE) and row(x, as.factor=TRUE) would fail
if x had no column (row) names. It was documented
incorrectly, and now returns a matrix factor.
o setRepositories() failed if "pkgType" was set to
"mac.binary.leopard".
o formals<-() changed the body of the function if this was a
length-one list.
o body<-() failed if the function had no arguments. It now
warns if discarding elements from a 'value' of type "expression".
o qr.coef() failed in the complex case for non-square systems.
(PR#13305)
o plot.dendrogram(horizontal=TRUE) did not not plot 'edgetext'
at the correct locations. (PR#13313)
o The starting point for plot.acf(ci.type="ma") was lag 0 when it
should have been lag 1. (PR#13071)
o There was an obscure bug with srcrefs, which could put the
parser into a condition giving "Error: bad value" on any input
--
O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
|
R 2.8.1 is released
|
Peter Dalgaard
| 613
|
|
From p.dalgaard at biostat.ku.dk Mon Jun 17 14:37:14 2002
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard BSA)
Date: 17 Jun 2002 14:37:14 +0200
Subject: R-1.5.1 is released
In-Reply-To: <[email protected]>
References: <[email protected]>
Message-ID: <[email protected]>
Peter Dalgaard BSA <p.dalgaard at biostat.ku.dk> writes:
> NOTE: I discovered late in the release process that there is still a
> small problem with the 8.0.x tcl/tk compatibility. A fix is
> forthcoming.
For those who need to know, the fix follows below. Sorry about the
inconvenience.
diff -u -r1.14.2.1 tcltk.c
--- src/library/tcltk/src/tcltk.c 7 Jun 2002 16:37:35 -0000 1.14.2.1
+++ src/library/tcltk/src/tcltk.c 17 Jun 2002 12:23:22 -0000
@@ -239,7 +239,7 @@
PROTECT(ans = allocVector(STRSXP, count));
for (i = 0 ; i < count ; i++)
- SET_STRING_ELT(ans, i, mkChar(Tcl_GetString(elem[i])));
+ SET_STRING_ELT(ans, i, mkChar(Tcl_GetStringFromObj(elem[i], NULL)));
UNPROTECT(1);
return ans;
}
--
O__ ---- Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
R-1.5.1 is released
|
Peter Dalgaard BSA
| 38
|
|
From lawrence.michael at gene.com Wed Sep 7 16:06:20 2016
From: lawrence.michael at gene.com (Michael Lawrence)
Date: Wed, 7 Sep 2016 07:06:20 -0700
Subject: The R Journal, Volume 8, Issue 1
Message-ID: <CAOQ5NydXL7bbvFGMFOPR5wyVm5whZ7S8RNfYXO0MyxP5rBVYiA@mail.gmail.com>
Dear all,
The latest issue of The R Journal is now available at
http://journal.r-project.org/archive/2016-1/
Many thanks to all contributors.
Michael Lawrence
|
The R Journal, Volume 8, Issue 1
|
<CAOQ5NydXL7bbvFGMFOPR5wyVm5whZ7S8RNfYXO0MyxP5rBVYiA@mail.gmail.com>
|
Michael Lawrence
| 127
|
From Torsten.Hothorn at stat.uni-muenchen.de Tue Oct 30 14:04:51 2007
From: Torsten.Hothorn at stat.uni-muenchen.de (Torsten Hothorn)
Date: Tue, 30 Oct 2007 14:04:51 +0100 (CET)
Subject: R News, volume 7, issue 2 is now available (fwd)
Message-ID: <[email protected]>
Dear useRs,
The October 2007 issue of R News is now available on CRAN under the
Documentation/Newsletter link.
Torsten
(on behalf of the R News Editorial Board)
|
R News, volume 7, issue 2 is now available (fwd)
|
Torsten Hothorn
| 423
|
|
From P.Dalgaard at biostat.ku.dk Tue Apr 24 12:34:31 2007
From: P.Dalgaard at biostat.ku.dk (Peter Dalgaard)
Date: Tue, 24 Apr 2007 12:34:31 +0200
Subject: R 2.5.0 is released
Message-ID: <[email protected]>
I've rolled up R-2.5.0.tar.gz a short while ago. This is a development
release which contains a number of new features. In particular:
- Object name completion by integration of package 'rcompletion' by
Deepayan Sarkar
- New recommended package 'codetools' by Luke Tierney
- New Rscript front-end, which enables shell-like R scripting
also, a number of mostly minor bugs have been fixed. See the full list
of changes below.
You can get it (some time this evening) from
http://cran.r-project.org/src/base/R-2/R-2.5.0.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you. In case of
impatience, try http://www.biostat.ku.dk/~pd/R-release
Binaries for various platforms will appear in due course.
For the R Core Team
Peter Dalgaard
These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:
a8efde35b940278de19730d326f58449 AUTHORS
eb723b61539feef013de476e68b5c50a COPYING
a6f89e2100d9b6cdffcea4f398e37343 COPYING.LIB
aa6d06dd154bbde39b4d35f26068675d FAQ
70447ae7f2c35233d3065b004aa4f331 INSTALL
b12ff4c900a49f0d7786d80e249934c9 NEWS
88bbd6781faedc788a1cbd434194480c ONEWS
4f004de59e24a52d0f500063b4603bcb OONEWS
b9088663fc539c059acfaf19d6d90a69 R-2.5.0.tar.gz
b9088663fc539c059acfaf19d6d90a69 R-latest.tar.gz
433182754c05c2cf7a04ad0da474a1d0 README
020479f381d5f9038dcb18708997f5da RESOURCES
4eaf8a3e428694523edc16feb0140206 THANKS
This is the relevant part of the NEWS file:
CHANGES IN R VERSION 2.5.0
USER-VISIBLE CHANGES
o apropos(x) and find(x) now both only work for character 'x',
and hence drop all non-standard evaluation behaviour.
o Data frames can have 'automatic' row names which are not
converted to dimnames by as.matrix(). (Consequently, e.g.,
t(.) for such data frames has NULL column names.) This
change leads to memory reductions in several places, but can
break code which assumes character dimnames for data frames
derived from matrices.
No existing R object is regarded as having 'automatic' row
names, and it may be beneficial to recreate such objects via
read.table() or data.frame().
o Using $ on an atomic vector now raises a warning, as does use
on an S4 class for which a method has not been defined.
o The Unix-alike readline terminal interface now does
command-completion for R objects, incorporating the
functionality formerly in package 'rcompletion' by Deepayan
Sarkar. This can be disabled by setting the environment
variable R_COMPLETION=FALSE when starting R (e.g. in
~/.Renviron). (Note that when this is enabled, filename
completion no longer works for file paths containing R
operators such as '+' and '-'.)
NEW FEATURES
o abbreviate() no longer has an 8191 byte limit on the size of
strings it can handle.
o abs(x) now returns integer for integer or logical arguments.
o apropos() has a new argument 'ignore.case' which defaults to
TRUE, potentially matching more than previously, thanks to a
suggestion by Seth Falcon.
o args(), str() and print() now give the argument lists of primitive
functions.
o as.matrix() gains the '...' argument that several packages have
assumed it always had (and S-PLUS has).
o Manipulation of integers as roman numerals via as.roman() in
package utils.
o attr() no longer treats name = NA_character_ as meaning
name = "NA".
o binom.test() now allows a 'fuzz' for calculated integer values
in its x and n arguments.
o boxplot(*, notch = TRUE) now warns when notches are outside
hinges; related to PR#7690.
o New function callCC() providing a downward-only version of
Scheme's call with current continuation.
o capabilities() now has a "profmem" entry indicating whether
R has been compiled with memory profiling.
o colnames<-() and rownames<-() now handle data frames explicitly,
so calling colnames<- on a data frame no longer alters the
representation of the row names.
o commandArgs() has a new 'trailingOnly' argument to be used in
conjunction with --args.
o contour() now passes graphical parameters in '...' to axis()
and box().
o New data set 'crimtab' on Student(1908)'s 3000 criminals.
o cut.default() has a new argument 'ordered_result'.
o .deparseOpts() has two new options: "keepNA" to ensure that
different types (logical, integer, double, character and
complex) of NAs are distinguished, and "S_compatible" to
suppress the use of R-specific features such as 123L and to
deparse integer values of a double vector with a trailing
decimal point.
The 'keepInteger' option now uses the suffix 'L' rather than
as.integer() where possible (unless all entries are NA or
"S_compatible" is also set).
Other deparse options can now be added to "all" (which has not
for some time actually switched on all options).
Integer sequences m:n are now deparsed in that form.
o deparse() and dput() now include "keepInteger" and "keepNA" in
their defaults for the 'control' argument.
o detach() now takes another argument, unload, which indicates
whether or not to unload the package and then only cleans
up the S4 methods if the package successfully unloads.
o There are new constants NA_integer_, NA_real_, NA_complex_ and
NA_character_ to denote NAs of those types, and they will be
used in deparsing in place of as.integer(NA) etc unless
.deparseOpts() includes "S_compatible".
o dev.print() now recognizes 'screen devices' as all those with
an enabled display list, rather than a hard-coded set.
o Objects of class "difftime" are now handled more flexibly. The
units of such objects can now be accessed via a units()
function, which also has a replacement form, and there are
conversion methods to and from numeric, which also allow the
specification of units. Objects of this class can also be
stored in data frames now. A format() method has been added,
and the print method was revised.
o New function environmentName() to give the print name of
environments such as "namespace:base".
This is now used by str().
o New function env.profile() provides R level access to summary
statistics on environments. In a related patch, new.env()
now allows the user to specify an initial size for a hashed
environment.
o file() can read the X11 clipboard selection as "X11_clipboard"
on suitable X11-using systems.
o file("stdin") is now recognized, and refers to the process's
'stdin' file stream whereas stdin() refers to the console.
These may differ, for example for a GUI console, an embedded
application of R or if --file= has been used.
o file_test() is now also available in package utils.
(It is now private in package tools.)
o file.show() gains an 'encoding' argument.
o New functions formatUL() and formatOL() in package utils for
formatting unordered (itemize) and ordered (enumerate) lists.
o The statistics reported when gcinfo(TRUE) are now of the amounts
used (in Mb) and not of the amounts free (which are not really
relevant when there are no hard limits, only gc trigger points).
o New function get_all_vars() to retrieve all the
(untransformed) variables that the default method of
model.frame() would use to create the model frame.
o interaction() has a new argument 'lex.order'.
o initialize() (in methods) now tries to be smarter about
updating the new instance in place, thereby reducing
copying.
o install.packages(dependencies = NA) is a new default, which is
to install essential dependencies when installing from
repositories to a single library. As a result of this change,
update.packages() will install any new dependencies of the
packages it is updating (alongside the package in the same
library tree).
If 'lib' is not specified or is specified of length one and
the chosen location is not a writable directory,
install.packages() offers to create a personal library
directory for you if one does not already exist, and to
install there.
o is.atomic, is.call, is.character, is.complex, is.double (== is.real),
is.environment, is.expression, is.function, is.integer,
is.list, is.logical, is.null, is.object, is.pairlist,
is.recursive, is.single and is.symbol (== is.name) are no
longer internally S3 generic, nor can S4 methods be written
for them.
The "factor" methods of is.integer and is.numeric have been
replaced by internal code.
o Added is.raw() for completeness.
o l10n_info() also reports if the current locale is Latin-1.
o levels<-(), names() and names<-() now dispatch internally for
efficiency and so no longer have S3 default methods.
o .libPaths() now does both tilde and glob expansion.
o Functions lm(), glm() loess(), xtabs() and the default method
of model.frame() coerce their 'formula' argument (if supplied)
to a formula.
o max(), min() and range() now work with character vectors.
o message() has a new argument 'appendLF' to handle messages
with and without newlines. There is a new message class
packageStartupMessage() that can be suppressed separately.
o A new function, method.skeleton() writes a skeleton version of
a call to setMethod() to a file, with correct arguments and
format, given the name of the function and the method signature.
o mode<- and storage.mode<- do slightly less copying.
o nls.control(* , printEval = FALSE, warnOnly = FALSE) are two new
options to help better analyze (non-)convergence of nls(),
thanks to Kate Mullen.
nls() and summary(nls()) now contain more information and also
print information about convergence.
o options(device = ) now accepts a function object as well as
the name of a function.
o pdf() supports new values for 'paper' of "US" (same as
"letter"), "a4r" and "USr" (the latter two meaning rotated to
landscape). postscript() also accepts paper = "US".
o persp() now respects the graphical pars 'cex.axis', 'cex.lab',
'font.axis' and 'font.lab'.
o New faster internal functions pmax.int() and pmin.int() for
inputs which are atomic vectors without classes (called by
pmax/pmin where applicable).
pmin/pmax are now more likely to work with classed objects:
they work with POSIXlt datetimes, for example.
o postscript() now by default writes grey colors (including black
and white) via 'setgray', which gives more widely acceptable
output. There are options to write pure RGB, CMYK or gray via
the new argument 'colormodel'.
o rbind.data.frame() now ignores all zero-row inputs, as well as
zero-column inputs (which it used to do, undocumented). This
is because read.table() can create zero-row data frames with
NULL columns, and those cannot be extended.
o readChar() and writeChar() can now work with a raw vector.
o read.table(), write.table() and allies have been moved to package
utils.
o rgb() now accepts the red, green and blue components in a
single matrix or data frame.
o New utility function RShowDoc() in package 'utils' to find and
display manuals and other documentation files.
o New .row_names_info() utility function finds the number of rows
efficiently for data frames; consequently, dim.data.frame()
has become very fast for large data frames with 'automatic'
row names.
o RSiteSearch() now also allows to search postings of the 'R-devel'
mailing list.
o screeplot() is now (S3) generic with a default method, thanks
to a patch from Gavin Simpson.
o Experimental 'verbose' argument for selectMethod(). Might be
replaced later by a better interface for method selection
inspection.
o Added links to source files to the parsing routines, so that
source() can now echo the original source and comments (rather
than deparsing). This affects example() and Sweave() as well.
o stack() and unstack() have been moved to package utils.
o strptime() now sets the "tzone" attribute on the result if
tz != "".
o str.default() typically prints fewer entries of logical vectors.
o The RweaveLatex driver for Sweave() now supports two new
options: expand=FALSE, to show chunk references in the output,
and concordance=TRUE, to output the concordance between input
and output lines.
o system() now takes the same set of arguments on all platforms,
with those which are not applicable being ignored with a
warning. Unix-alikes gain 'input' and 'wait', and Windows
gains 'ignore.stderr'.
o system.time() and proc.time() now return an object of class
"proc_time" with a print() method that returns a POSIX-like
format with names.
o Sys.getenv() has a new argument 'unset' to allow unset and set
to "" to be distinguished (if the OS does). The results of
Sys.getenv() are now sorted (by name).
o New function Sys.glob(), a wrapper for the POSIX.2 function
glob(3) to do wildcard expansion (on systems which have it,
plus an emulation on Windows).
o Sys.setenv() is a new (and preferred) synonym for Sys.putenv().
The internal C code uses the POSIX-preferred 'setenv' rather
than 'putenv' where the former is available.
o New function Sys.unsetenv() to remove environment variables
(on systems where unsetenv is implemented or putenv can remove
variables, such as on Windows).
o text(), mtext(), strheight(), strwidth(), legend(), axis(),
title(), pie(), grid.text() and textGrob() all attempt to
coerce non-language annotation objects (in the sense of is.object)
to character vectors. This is principally intended to cover
factors and POSIXt and Date objects, and is done via the
new utility function as.graphicsAnnot() in package grDevices.
o tcltk:tk_select.list() now chooses the width to fit the widest item.
o {re,un}tracemem() are now primitives for efficiency and so
migrate from 'utils' to 'base'.
o union(), interect(), setdiff() and setequal() now coerce their
arguments to be vectors (and they were documented only to
apply to vectors).
o uniroot() now works if the zero occurs at one of the ends of
the interval (suggestion of Tamas Papp).
o There is a new function View() for viewing matrix-like
objects in a spreadsheet, which can be left up whilst R is
running.
o New function withVisible() allows R level access to the
visibility flag.
o zip.file.extract() has been moved to package utils.
o A few more cases of subassignment work, e.g. <raw>[] <- <list>
and <vector>[] <- <expression>, with suitable coercion of the LHS.
o There is a warning if \ is used unnecessarily in a string when
being parsed, e.g. "\." where probably "\\." was intended.
("\." is valid, but the same as ".".) Thanks to Bill Dunlap
for the suggestion.
o Introduced the suffix L for integer literals to create
integer rather than numeric values, e.g. 100L, 0x10L, 1e2L.
o Set the parser to give verbose error messages in case of
syntax errors.
o The class "LinearMethodsList" has been extended and will be
used to create list versions of methods, derived from the
methods tables (environments). The older recursive
"MethodsList" class will be deprecated (by the release of
2.5.0 if possible).
o There are more flexible ways to specify the default library
search path. In addition to R_LIBS and .Library, there are
.Library.site (defaults to R_HOME/site-library) and
R_LIBS_USER (defaults to a platform- and version-specific
directory in ~/R). See ?.libPaths for details.
o LAPACK has been updated to version 3.1.0. This should cause
only small changes to the output, but do remember that the sign
of eigenvectors (and principal components) is indeterminate.
o PCRE has been updated to version 7.0.
o Several functions handle row names more efficiently:
- read.table() and read.DIF() make use of integer row names
where appropriate, and avoid at least one copy in assigning
them.
- data.frame() and the standard as.data.frame() methods avoid
generating long dummy row names and then discarding them.
- expand.grid() and merge() generate compact 'automatic' row
names.
- data.matrix() and as.matrix.data.frame() have a new argument
'rownames.force' that by default drops 'automatic' row names.
o <data frame>[i, j] is substantially more memory-efficient when
only a small part of the data frame is selected, especially
when (part of) a single column is selected.
o Command-line R (and Rterm.exe under Windows) accepts the options
'-f filename', '--file=filename' and '-e expression' to follow
other script interpreters. These imply --no-save unless
--save is specified.
o Invalid bytes in character strings in an MBCS now deparse/print
in the form "\xc1" rather than "<c1>", which means they can be
parsed/scanned.
o Printing functions (without source attributes) and expressions
now preserves integers (using the L suffix) and NAs (using
NA_real_ etc where necessary).
o The 'internal' objects .helpForCall, .tryHelp and topicName are
no longer exported from 'utils'.
o The internal regex code has been upgraded to glibc 2.5 (from 2.3.6).
o Text help now attempts to display files which have an \encoding
section in the specified encoding via file.show().
o R now attempts to keep track of character strings which are
known to be in Latin-1 or UTF-8 and print or plot them
appropriately in other locales. This is primarily intended
to make it possible to use data in Western European languages
in both Latin-1 and UTF-8 locales. Currently scan(),
read.table(), readLines(), parse() and source() allow
encodings to be declared, and console input in suitable
locales is also recognized.
New function Encoding() can read or set the declared encodings
for a character vector.
o There have been numerous performance improvements to the data
editor on both Windows and X11. In particular, resizing the
window works much better on X11.
DEPRECATED & DEFUNCT
o symbol.C() and symbol.For() are defunct, and have been replaced
by wrappers that give a warning.
o Calling a builtin function with an empty argument is now always
an error.
o The autoloading of ts() is defunct.
o The undocumented reserved word GLOBAL.ENV has been removed.
(It was yet another way to get the value of the symbol
.GlobalEnv.)
o The deprecated behaviour of structure() in adding a class when
specifying with "tsp" or "levels" attributes is now defunct.
o unix() is now finally defunct, having been deprecated for
at least seven years.
o Sys.putenv() is now deprecated in favour of Sys.setenv(),
following the POSIX recommendation.
o Building R with --without-iconv is deprecated.
o Using $ on an atomic vector is deprecated (it was previously
valid and documented to return NULL).
o The use of storage.mode<- for other than standard types (and
in particular for value "single") is deprecated: use mode<-
instead.
INSTALLATION
o A suitable iconv (e.g. from glibc or GNU libiconv) is
required. For 2.5.x only you can build R without it by
configuring using --without-iconv.
o There is support again for building on AIX (tested on 5.2 and 5.3)
thanks to Ei-ji Nakama.
o Autoconf 2.60 or later is used to create 'configure'. This
makes a number of small changes, and incorporates the changes
to the detection of a C99-compliant C compiler backported for
2.4.1.
o Detection of a Java development environment was added such that
packages don't need to provide their own Java detection. Newly
added make variables are JAVAC, JAVAH, JAR and JAVA_CPPFLAGS.
R CMD javareconf was updated to look for the corresponding
Java tools as well.
In addition, Java detection honors user-supplied environment
variables JAVA_CPPFLAGS, JAVA_LIBS and JAVA_LD_LIBRARY_PATH.
o Added workaround for reported non-POSIX sh on OSF1. (PR#9375)
o 'make install-strip' now works, stripping the executables and
also the shared libraries and modules on platforms where
'libtool' knows how to do so.
o Building R as a shared library and standalone nmath now
installs pkg-config files 'libR.pc' and 'libRmath.pc' respectively.
o Added test for insufficiently complete implementation of sigaction.
C-LEVEL FACILITIES
o Functions str2type, type2char and type2str are now available in
Rinternals.h.
o Added support for Objective C in R and packages (if available).
o R_ParseVector() has a new 4th argument 'SEXP srcfile' allowing
source references to be attached to the returned expression list.
o Added ptr_R_WriteConsoleEx callback which allows consoles to
distinguish between regular output and errors/warnings.
To ensure backward compatibility it is only used if
ptr_R_WriteConsole is set to NULL.
UTILITIES
o Additional Sweave() internal functions are exported to help
writing new drivers, and RweaveLatexRuncode() is now created
using a helper function (all from a patch submitted by Seth
Falcon).
o The following additional flags are accessible from R CMD config:
OBJC, OBJCFLAGS, JAR, JAVA, JAVAC, JAVAH, JAVA_HOME, JAVA_LIBS
and JAVA_CPPFLAGS.
o R CMD build now takes the package name from the DESCRIPTION
file and not from the directory. (PR#9266)
o checkS3methods() (and hence R CMD check) now checks agreement
with primitive internal generics, and checks for additional
arguments in methods where the generic does not have a '...'
argument.
codoc() now knows the argument lists of primitive functions.
o R CMD INSTALL and R CMD REMOVE now use as the default library
(if -l is not specified) the first library that would be used
if R were run in the current environment (and they run R to
find it).
o There is a new front-end Rscript which can be used for #!
scripts and similar tasks. See help("Rscript") and 'An
Introduction to R' for further details.
o R CMD BATCH (not Windows) no longer prepends
'invisible(options(echo = TRUE))' to the input script. This
was the default unless --slave is specified and the latter is
no longer overridden.
On all OSes it makes use of the -f argument to R, so
file("stdin") can be used from BATCH scripts.
On all OSes it reports proc.time() at the end of the script
unless q() is called with options to inhibit this.
o R CMD INSTALL now prepends the installation directory (if
specified) to the library search path.
o Package installation now re-encodes R files and the NAMESPACE
file if the DESCRIPTION file specifies an encoding, and sets
the encoding used for reading files in preparing for
LazyData. This will help if a package needs to be used in
(say) both latin1 and UTF-8 locales on different systems.
o R CMD check now reports on non-ASCII strings in datasets.
(These are a portability issue, which can be alleviated by
marking their encoding: see 'Writing R Extensions'.)
o Rdiff now converts CRLF endings in the target file, and
converts UTF-8 single quotes in either to ASCII quotes.
o New recommended package 'codetools' by Luke Tierney provides
code-analysis tools. This can optionally be used by 'R CMD
check' to detect problems, especially symbols which are not
visible.
o R CMD config now knows about LIBnn .
o New recommended package 'rcompgen' by Deepayan Sarkar
provides support for command-line completion under the Unix
terminal interface (provided readline is enabled) and the
Windows Rgui and Rterm front ends.
BUG FIXES
o gc() can now report quantities of 'Vcells' in excess of 16Gb on
64-bit systems (rather than reporting NA).
o Assigning class "factor" to an object now requires it has
integer (and not say double) codes.
o structure() ensures that objects with added class "factor" have
integer codes.
o The "formula" and "outer" attributes of datasets 'ChickWeight',
'CO2', 'DNase', 'Indometh', 'Loblolly', 'Orange' and 'Theoph'
now have an empty environment and not the environment used to
dump the datasets in the package.
o Dataset 'Seatbelts' now correctly has class c("mts", "ts").
o str() now labels classes on data frames more coherently.
o Several 'special' primitives and .Internals could return
invisibly if the evaluation of an argument led to the
visibility flag being turned off. These included
as.character(), as.vector(), call(), dim(), dimnames(),
lapply(), rep(), seq() and seq_along(). Others (e.g. dput()
and print.default()) could return visibly when this was not
intended.
o Several primitives such as dim() were not checking the number
of arguments supplied before method dispatch.
o Tracing of primitive functions has been corrected. It should
now be the case that tracing either works or is not allowed
for all primitive functions. (Problems remain if you make a
primitive into a generic when it is being traced. To be fixed
later.)
o max.col() now omits infinite values in determining the
relative tolerance.
o R CMD Sweave and R CMD Stangle now respond to --help and --version
like other utilities.
o .libPaths() adds only existing directories (as it was
documented to, but could add non-directories).
o setIs() and setClassUnion() failed to find some existing
subclasses and produced spurious warnings, now fixed.
o data.frame() ignored 'row.names' for 0-column data frames, and
no longer treats an explicit row.names=NULL differently from
the default value.
o identical() looked at the internal structure of the
'row.names' attribute, and not the value visible at R level.
o abline(reg) now also correctly works with intercept-only lm
models, and abline() warns more when it's called illogically.
o warning() was truncating messages at
getOption("warning.length") - 1 (not as documented), with no
indication. It now appends '[... truncated]'.
o Stangle/Sweave were throwing spurious warnings if options
'result' or 'strip.white' were unset.
o all.equal() was ignoring 'check.attributes' for list and
expression targets, and checking only attributes on raw vectors.
Logical vectors were being compared as if they were numeric,
(with a mean difference being quoted).
o Calculating the number of significant digits in a number was
itself subject to rounding errors for digits >= 16. The
calculation has been changed to err on the side of slightly
too few significant digits (but still at least 15) rather than
far too many. (An example is print(1.001, digits=16).)
o unlink() on Unix-alikes failed for paths containing spaces.
o substr() and friends treated NA 'start' or 'stop' incorrectly.
o merge(x, y, all.y = TRUE) would sometimes incorrectly return
logical columns for columns only in y when there were no
common rows.
o read.table(fn, col.names=) on an empty file returned NULL
columns, rather than logical(0) columns (which is what results
from reading a file with just a header).
o grid.[xy]axis(label=logical(0)) failed.
o expression() was unnecessarily duplicating arguments.
o as.expression(<list>) returned a single-element expression
vector, which was not compatible with S: it now copies lists
element-by-element.
o supsmu(periodic = TRUE) could segfault. (PR#9502, detection
and patch by Bill Dunlap.)
o pmax/pmin called with only logical arguments did not coerce to
numeric, although they were documented to do so (as max/min
do).
o methods() did not know that cbind() and rbind() are internally
generic.
o dim(x) <- NULL removed the names of x, but this was always
undocumented. It is not clear that it is desirable but it is
S-compatible and relied on, so is now documented.
o which(x, arr.ind = TRUE) did not return a matrix (as
documented) if 'x' was an array of length 0.
o C-level duplicate() truncated CHARSXPs with embedded nuls.
o Partial matching of attributes was not working as documented
in some cases if there were more than two partial matches or
if "names" was involved.
o data(package=character(0)) was not looking in ./data as
documented.
o summary.mlm() failed if some response names were "" (as can
easily happen if cbind() is used).
o The postscript() and pdf() drivers shared an encoding list
but used slightly different formats. This caused problems if
both were used with the same non-default encoding in the same
session. (PR#9517)
o The data editor was not allowing Inf, NA and NaN to be entered
in numerical columns. It was intended to differentiate
between empty cells and NAs, but did not do so: it now does
so for strings.
o supsmu() could segfault if all cases had non-finite values.
(PR#9519)
o plnorm(x, lower.tail=FALSE) was returning the wrong tail for
x <= 0. (PR#9520)
o which.min() would not report a minimum of +Inf, and
analogously for which.max(). (PR#9522)
o 'R CMD check' could fail with an unhelpful error when checking
Rd files for errors if there was only one file and that had a
serious error. (PR#9459)
o try() has been reimplemented using tryCatch() to solve two
problems with the original implementation: (i) try() would run
non-NULL options("error") expressions for errors within a try, and
(ii) try() would catch user interrupts.
o str(obj) could fail when obj contained a dendrogram.
o Using <data frame>[, <last column>] <- NULL failed (PR#9565)
o choose(n, k) could return non-integer values for integer n and
small k on some platforms.
o nclass.scott(x) and nclass.FD(x) no longer return NaN when var(x)
or IQR(x) (respectively) is zero.
hist() now allows breaks = 1 (which the above patch will
return), but not breaks = Inf (which gave an obscure error).
o strptime("%j") now also works for the first days of Feb-Dec.
(PR#9577)
o write.table() now recovers better if 'file' is an unopened
connection. (It used to open it for both the column names and
the data.)
o Fixed bug in mosaicplot(sort=) introduced by undocumented
change in R 2.4.1 (changeset r39655).
o contr.treatment(n=0) failed with a spurious error message.
(It remains an error.)
o as.numeric() was incorrectly documented: it is identical to
as.double.
o jitter(rep(-1, 3)) gave NaNs. (PR#9580)
o max.col() was not random for a row of zeroes. (PR#9542)
o ansari.test(conf.int=TRUE, exact=FALSE) failed.
o trace() now works on S3 registered methods, by modifying the
version in the S3 methods table.
o rep(length=1, each=0) segfaulted.
o postscript() could overflow a buffer if used with a long
'command' argument.
o The internal computations to copy complete attribute lists did
not copy the flag marking S4 objects, so the copies no longer
behaved like S4 objects.
o The C code of nlminb() was altering a variable without
duplicating it. (This did not affect nlminb() but would have
if the code was called from a different wrapper.)
o smooth(kind = "3RS3R") (the current default) used .C(DUP =
FALSE) but altered its input argument. (This was masked by
duplication in as.double.)
o The signature for the predefined S4 method for as.character()
was missing '...' .
o readBin(<raw vector>) could read beyond the end of the vector
when size-changing was involved.
o The C entry point PrintValue (designed to emulate auto-printing)
would not find show() for use on S4 objects, and did not have
the same search path (for show(), print() and print() methods)
as auto-printing. Also, auto-printing and print() of S4
objects would fail to find 'show' if the methods namespace was
loaded but the package was not attached (or otherwise not in
the search path).
o print() (and auto-printing) now recognize S4 objects even when
'methods' is not loaded, and print a short summary rather than
dump the internal structure.
o Sweave and Stangle had problems due to partial matching of code
chunk names when run with split=TRUE.
o install.packages() on a source package now ensures that
R CMD INSTALL sees the same library search path as
install.packages() did when computing dependencies.
o density() now ensures its 'y' values are non-negative. (PR#8876)
o is.finite() and is.infinite() (and many other primitives)
are not internally generic and so do not support S4 methods,
which can no longer be set. (PR#7951)
o nls(algorithm = "port") now accepts a list 'start' argument,
as for the other methods (and as documented).
o Standard errors from the "ar" method of predict() could be
wrong for the last p predictions for models near
non-stationarity. (PR#9614)
--
O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
|
R 2.5.0 is released
|
Peter Dalgaard
| 416
|
|
From p.dalgaard at biostat.ku.dk Tue Feb 29 10:51:27 2000
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard BSA)
Date: 29 Feb 2000 10:51:27 +0100
Subject: R-1.0.0 is released
Message-ID: <[email protected]>
I've rolled up R-1.0.0.tgz a short while ago.
You can get it from
ftp://cvs.r-project.org/pub/CRAN/src/base/R-1.0.0.tgz
or
http://cvs.r-project.org/pub/CRAN/src/base/R-1.0.0.tgz
or wait for it to be mirrored at a CRAN site near you within a day or
two. It should get to the CRAN master site within a few hours.
There's also a version split in three for floppies if you prefer
that.
Since this is a major release, we've made a formal release
statement this time. Below is an excerpt; full text is available at
http://developer.r-project.org/R-release-1.0.0.txt
"The release of a current major version indicates that we believe that
R has reached a level of stability and maturity that makes it suitable
for production use. Also, the release of 1.0.0 marks that the base
language and the API for extension writers will remain stable for the
foreseeable future. In addition we have taken the opportunity to tie
up as many loose ends as we could."
For the R Core Team,
Peter D.
Here's the relevant bit of the NEWS file:
CHANGES IN R VERSION 1.0.0
NEW FEATURES
o The entry points [dpq]norm no longer exist: the header file
R_ext/Mathlib.h must be used and such code re-compiled.
o Header files in R_ext must be given explicitly as e.g.
"R_ext/Mathlib.h".
o New function log1p(x) := log(1 + x) , accurate for |x| << 1.
o HTML searches can now select between any combination of
titles, keywords and object names. The keyword list of
SearchEngine.html is automatically built from KEYWORDS.db.
Missing links are now resolved using the search engine.
o A data subdirectory of the working directory will be
searched for data, by default after all the loaded packages
(including base).
o Data directories can now be zipped as Rdata.zip, provided a
list of contents is provided in file `filelist'.
o New function try(expr) which provides a user-friendly wrapper
to restart().
o New function geterrmessage() to retrieve the last error
message, for use in try() and user's error handlers, and new
option "show.error.messages" to control the printing of error
messages.
o persp() now labels its axes.
o ?plotmath documents the plotting expressions facility much
more comprehensively, with tables in the examples.
o New functions dump.frames() and debugger() allow post-mortem
debugging. See the help on debugger.
o New functions by() and merge() to split and join data frames.
o Generic methods now do "match before dispatch", so
plot(pch=2, y ~ x) invokes plot.formula. Notice that this will
break user code if it has renamed the dispatch argument and
uses the original name for a different argument.
o Long-named command-line options also allow `--name VALUE'.
o arima0() now uses optim() rather than nlm(), and is thereby
normally faster and gives more accurate solutions. Perhaps
more importantly, it fails to converge much less often.
o Enhanced pairs() function allowing separate upper, lower and
diagonal panel functions and control of diagonal labels.
(Much of this was contributed by Jens Oehlschlaegel-Akiyoshi.)
o Links to R objects in other packages in help files can now be
specified explicitly as \link[pkg]{topic} or
\link[pkg:maintopic]{topic}
o optim() has a new simulated annealing method contributed by
Adrian Trapletti.
o Hershey vector fonts are available in text() and contour().
Documentation for Hershey vector fonts is in help(Hershey).
o The HTML function indices (for packages and for all installed
functions) and the index to the reference manual now omit
methods for generic functions if they would immediately follow
the generic and refer to the same file. This reduces the
clutter considerably.
o New functions points.formula() and lines.formula() to supplement
plot.formula(). The latter has been enhanced so that all
arguments are now evaluated in the supplied data frame and all
subsettable arguments are subsetted. Notice that the data=
argument can no longer be given as a positional argument but
must be given in keyword form.
o The behaviour of pmatch() has been changed to be S-compatible:
in particular the meaning of duplicates.ok=TRUE has changed.
The help for pmatch and charmatch now gives more precise
descriptions, including of their differences.
o print.hclust(), hclust() and dist() now store the method
that has been used.
o If there are unmatched function argument(s), the first found
is named in the message, for example
`unused argument(s) (xlabel ...)'.
o Conversion from Rd to raw nroff is no longer available.
o text() now accepts vector "col", "cex" and "font" arguments.
o "default" is now a valid argument to RNGkind().
o nlm() and optim() will now give up immediately they try to
step to a non-finite value: nlm at least would go into an
infinite loop.
o "mostattributes(obj) <- value" utility useful for careful
attributes' inheritance; e.g. for fixing pmax/pmin (see below).
BUG FIXES
o (0.99.0a) The internal code for strsplit no longer destroys
other internal structures, e.g. postscript file output on
Linux.
o (0.99.0a) nlm() no longer segfaults with Hessian specified.
o (0.99.0a) Gnome version plotmath works, kind of
o (0.99.0a) edit.data.frame() now handles character vectors
better, provided they were generated with I().
o (0.99.0a) Attempt to special-case print-buffer allocation
with just a format argument was abandoned, since there is
no portable way of doing it and it caused compile problem
on Alpha.
o tempfile("") now works on all Unix platforms, and
tempfile("a b c") returns a single name (with spaces in).
The file names are now unique across processes (Unix), are
guaranteed not to exist and very likely to be unique within
an R session.
o The search semantics of data(), example() and help() have changed
(see their help pages). In particular, they will normally
look in the package which was loaded, even if it is not in
one of the libraries given in .lib.loc. Autoloads are no
longer included in the search (as they searched whole packages,
not just the autoloaded objects).
o The documentation for .Rd files said & must be entered as \&
but only the unescaped form was processed correctly. Now both
are accepted but & is preferred.
o list.files now skips non-existent/unreadable directories with
a warning, rather that failing with an error.
o Lots of help examples now tidy up the files they created, and
detach data frames and libraries they attach.
o library(help=foo) lists only contents of first version if
multiple matches are found on lib.loc.
o round(2.345e-99, 100) now works (not giving 0).
C functions fprec() and fround() [= R's signif() and round()],
now use R_pow_di(10.0, n) which is clean and more efficient.
This changes some results in the least significant bits.
o rpois sometimes had problems with mu=0, now special-cased
o Rare memory overrun in rpois fixed.
o --nsize and --vsize arguments to R CMD check now work.
o plot.stepfun had renamed the dispatch argument and used the
original name "x" for a different argument which broke on the
new `match & dispatch' code. Changed to "xval".
o The return value for par() was incorrectly documented, and in
consequence cpgram() was not re-setting "pty".
o package.dependencies() printed unnecessary debugging messages
(version comparison): these have been removed.
o backslashes in examples in help files are now converted
correctly to latex.
o qchisq with non-centrality parameter now does something.
o Greek symbols are now converted correctly in HTML help (but
only rendered correctly on a few browsers).
o rbind(x, y) works when x has no columns.
o \tabular in Rd files is rendered better in latex, and long
tabular material is now acceptable (and split over pages).
o evaluation depth wasn't properly reset by "next"
o Old (pre-0.63.1) .Random.seed would cause problems if used.
o Row indexing of data.frames by characters (e.g. y["ab", ])
was wrong, as pmatch was not S-compatible.
o Contour labels used to be rounded to integers.
o Calling rbinom() repeatedly with the same p but different n
gave incorrect results.
o Rd2contents assumed the \name field was the file name, so
searches could lead to non-existent links.
o Assigning functions to list elements is not longer disallowed.
o Unified usage statement to R CMD xxx for all commands
o Using duplicated new string indices in [<- caused a crash on
some platforms, e.g. x <- 1:2; x[c("3", "3")] <- 3; x.
o rle() can now handle character vectors, as documented.
o print.default failed to reset its settings, so, e.g. na.print
could persist when printing a list.
o [cr]bind could sometimes return an invisible value.
o axis() and rug() sometimes extended the axis line too far.
rug() always clipped x values to the plot region, but now
admits to doing so with a warning.
o plot() and axis() got into trouble with very small relative
ranges: these are now required to be at least 100x the machine
precision.
o split.screen(, erase=TRUE) failed to create a new plot, so
failed if it was used on a postscript device before other plots.
o plotting with lwd = 0 also set the dash length to 0: now
dash lengths are scaled up for lwd > 1 but not reduced for
0 <= lwd < 1.
o plotting a " " vertically caused an X11 error with some fonts,
(notably URW fonts on RedHat) causing plot.lm to crash R
o F distributions with huge DF now behave more sensibly
o Crashes could occur if there was an error in inline
parameters, because the call was not being recorded. It is
now.
o Title field of DESCRIPTION now overrides TITLE file.
o R now reports `50 or more warnings', not just 50, as it only
displays the first 50.
o Resetting the RNG state resets the state of the Box-Muller
generator too.
o Pointer protection bug in load() code.
o Assignment with unknown string index caused memory corruption
when used on matrices.
o It is now possible to call Fortran routines d1mach and 11mach
on platforms which do not append underscores.
o Additions to plots by identify() and locator() were not being
recorded, and so did not appear when a plot was copied or
printed.
o The defaults for `na.action' arguments were inconsistently
documented. In R the default is taken from the
options(na.action) setting, and that defaults to `na.omit'.
If there is no `na.action' setting, the default is `na.fail'.
For consistency, the default for replications() has been
changed.
o Fix cases with lambda==0 in Poisson distribution
o demo(is.things) had been broken by the introduction of is.element.
o palette() didn't check for overflow and was limited to 256
colors, so palette(colors()) would segfault. Limit increased
to 1024 and check inserted.
o C functions fprec() and fround() [= R's signif() and round()],
now use R_pow_di(10., n) which is clean and more efficient.
This changes some results in the least significant bits.
o pmin(c(a=1), 2:3) now works {and pmax(.) too}.
--
O__ ---- Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
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Send "info", "help", or "[un]subscribe"
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|
R-1.0.0 is released
|
Peter Dalgaard BSA
| 307
|
|
From pd.mes at cbs.dk Mon Mar 9 10:04:28 2015
From: pd.mes at cbs.dk (Peter Dalgaard)
Date: Mon, 9 Mar 2015 10:04:28 +0100
Subject: R 3.1.3 is released
Message-ID: <[email protected]>
The build system rolled up R-3.1.3.tar.gz (codename "Smooth Sidewalk") this morning.
The list below details the changes in this release.
You can get the source code from
http://cran.r-project.org/src/base/R-3/R-3.1.3.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you.
Binaries for various platforms will appear in due course.
For the R Core Team
Peter Dalgaard
These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:
MD5 (AUTHORS) = cebbdd1eb8cd620bf2a6ac84c9e731c2
MD5 (COPYING) = eb723b61539feef013de476e68b5c50a
MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343
MD5 (FAQ) = a699fa0eeef280b78134f0abe0b1c1b0
MD5 (INSTALL) = 3964b9119adeaab9ceb633773fc94aac
MD5 (NEWS) = 8790db3a8000910f0bf00fb1ee039634
MD5 (NEWS.0) = bfcd7c147251b5474d96848c6f57e5a8
MD5 (NEWS.1) = eb78c4d053ec9c32b815cf0c2ebea801
MD5 (NEWS.2) = 8e2f4d1d5228663ae598a09bf1e2bc6b
MD5 (R-latest.tar.gz) = 53a85b884925aa6b5811dfc361d73fc4
MD5 (R.css) = 444535b9cb76ddff1bab1e1865a3fb14
MD5 (README) = aece1dfbd18c1760128c3787f5456af6
MD5 (RESOURCES) = a59076c1ac7e9bab0f0a38b3f57a3914
MD5 (THANKS) = 1989ce89fb3891420c9964dc418ab71c
MD5 (R-3/R-3.1.3.tar.gz) = 53a85b884925aa6b5811dfc361d73fc4
This is the relevant part of the NEWS file
CHANGES IN R 3.1.3:
NEW FEATURES:
* The internal method of download.file() can now handle files
larger than 2GB on 32-bit builds which support such files (tested
on 32-bit R running on 64-bit Windows).
* kruskal.test() warns on more types of suspicious input.
* The as.dendrogram() method for "hclust" objects gains a check
argument protecting against memory explosion for invalid inputs.
* capabilities() has a new item long.double which indicates if the
build uses a long double type which is longer than double.
* nlm() no longer modifies the callback argument in place (a new
vector is allocated for each invocation, which mimics the
implicit duplication that occurred in R < 3.1.0); note that this
is a change from the previously documented behavior. (PR#15958)
* icuSetCollate() now accepts locale = "ASCII" which uses the basic
C function strcmp and so collates strings byte-by-byte in
numerical order.
* sessionInfo() tries to report the OS version in use (not just
that compiled under, and including details of Linux
distributions).
* model.frame() (used by lm() and many other modelling functions)
now warns when it drops contrasts from factors. (Wish of
PR#16119)
* install.packages() and friends now accept the value type =
"binary" as a synonym for the native binary type on the platform
(if it has one).
* Single source or binary files can be supplied for
install.packages(type = "both") and the appropriate type and
repos = NULL will be inferred.
* New function pcre_config() to report on some of the configuration
options of the version of PCRE in use. In particular, this
reports if regular expressions using \p{xx} are supported.
* (Windows.) download.file(cacheOK = FALSE) is now supported when
internet2.dll is used.
* browseURL() has been updated to work with Firefox 36.0 which has
dropped support for the -remote interface.
INSTALLATION and INCLUDED SOFTWARE:
* The included version of PCRE has been updated to 8.36.
* configure accepts MAKEINFO=texi2any as another way to ensure
texinfo 5.x is used when both 5.x and 4.x are installed.
UTILITIES:
* R CMD check now checks the packages used in \donttest sections of
the examples are specified in the DESCRIPTION file. (These are
needed to run the examples interactively.)
* R CMD check checks for the undeclared use of GNU extensions in
Makefiles, and for Makefiles with a missing final linefeed.
R CMD build will correct line endings in all Makefiles, not just
those in the src directory.
* R CMD check notes uses of library() and require() in package
code: see the section 'Suggested packages' of 'Writing R
Extensions' for good practice.
DEPRECATED AND DEFUNCT:
* The configure option --with-valgrind-instrumentation=3 is
deprecated and will be removed in R 3.2.0.
BUG FIXES:
* (Windows.) Rscript.exe was missing a manifest specifying the
modern style for common controls (e.g., the download progress
bar).
* If a package had extra documentation files but no vignette, the
HTML help system produced an empty index page.
* The parser now gives an error if a null character is included in
a string using Unicode escapes. (PR#16046)
* qr.Q() failed on complex arguments due to pre-3.0(!) typo.
(PR#16054)
* abs() failed with named arguments when the argument was complex.
(PR#16047)
* "noquote" objects may now be used as columns in dataframes.
(PR#15997)
* Some values with extremely long names were printed incorrectly.
(PR#15999)
* Extremely large exponents on zero expressed in scientific
notation (e.g. 0.0e50000) could give NaN. (PR#15976)
* download.file() reported downloaded sizes as 0KB if less than
1MB, only for R 3.1.2 and only on big-endian platforms.
* prompt() did not escape percent signs in the automatically
generated usage section of help files.
* drop.terms() dropped some of the attributes of the object it was
working with. (PR#16029)
* (Windows.) The command completion in Rgui.exe messed up the
console. (PR#15791)
* (Windows.) The choose.files() command returned a blank string
when the user asked for a single file but cancelled the request.
(PR#16074)
* Math2 S4 group generics failed to correctly dispatch "structure"-
and "nonStructure"-derived classes.
* loadNamespace() imposed undocumented restrictions on the
versionCheck parameter. (Reported by Geoff Lee.)
* Rare over-runs detected by AddressSanitizer in substr() and its
replacement version have been avoided.
_Inter alia_ that fix gives the documented behaviour for
substr(x, 1, 2) <- "" (subsequently reported as PR#16214).
* Loading packages incorrectly defining an S4 generic followed by a
function of the same name caused an erroneous cyclic namespace
dependency error.
* Declared vignette encodings are now always passed to the vignette
engine.
* Port Tomas Kalibera's fix from R-devel that restores the
loadMethod() fast path, effectively doubling the speed of S4
dispatch.
* power.t.test() and power.prop.test() now make use of the
extendInt option of uniroot() and hence work in more extreme
cases. (PR#15792)
* If a package was updated and attached when its namespace was
already loaded, it could end up with parts from one version and
parts from the other. (PR#16120)
* tools:::.Rdconv() didn't accept --encoding= due to a typo.
(PR#16121)
* Unix-alike builds without a suitable makeinfo were documented to
link the missing HTML manuals to CRAN, but did not.
* save(*, ascii=TRUE) and load() now correctly deal with NaN's.
(PR#16137)
* split.Date() retains fractional representations while avoiding
incomplete class propagation.
* R_ext/Lapack.h had not been updated for changes made by LAPACK to
the argument lists of its (largely internal) functions dlaed2 and
dlaed3. (PR#16157)
* RShowDoc("NEWS", "txt") had not been updated for the layout
changes of R 3.1.0.
* The xtfrm() method for class "Surv" has been corrected and its
description expanded.
* mode(x) <- y would incorrectly evaluate x before changing its
mode. (PR#16215)
* besselJ(1, 2^64) and besselY(..) now signal a warning, returning
NaN instead of typically segfaulting. (Issue 3 of PR#15554)
* HTML conversion of \href markup in .Rd files did not remove the
backslash from \% and so gave an invalid URL. In a related
change, the \ escape is now required in such URLs.
--
Peter Dalgaard, Professor
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
|
R 3.1.3 is released
|
Peter Dalgaard
| 198
|
|
From pd.mes at cbs.dk Fri Jun 13 16:18:23 2014
From: pd.mes at cbs.dk (Peter Dalgaard)
Date: Fri, 13 Jun 2014 16:18:23 +0200
Subject: Release of R 3.1.1 scheduled for July 10
Message-ID: <[email protected]>
Just a quick notice that we intend to have a patch release on July 10. Nickname is still undecided.
Due to calendar conflicts, the binaries for some platforms may be delayed by a week or so.
-pd
--
Peter Dalgaard, Professor
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
|
Release of R 3.1.1 scheduled for July 10
|
Peter Dalgaard
| 351
|
|
From Friedrich.Leisch at ci.tuwien.ac.at Tue Jul 6 13:29:32 1999
From: Friedrich.Leisch at ci.tuwien.ac.at (Friedrich Leisch)
Date: Tue, 6 Jul 1999 13:29:32 +0200 (CEST)
Subject: R 0.64.2 at CRAN
Message-ID: <[email protected]>
Hi,
due to some FTP problems in Auckland and me not being in office
yesterday R 0.64.2 took some time to travel from Denmark to New
Zealand and then back to Europe ... but now it is finally available at
the CRAN master site
http://www.ci.tuwien.ac.at/R
here in Vienna and it should propagate to the
various miroors within the next 24 hours or so.
Best,
Fritz
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
R 0.64.2 at CRAN
|
Friedrich Leisch
| 490
|
|
From fharrell at virginia.edu Wed Jan 1 20:33:05 2003
From: fharrell at virginia.edu (Frank E Harrell Jr)
Date: Wed Jan 1 20:33:05 2003
Subject: Updates to Hmisc and Design Libraries
Message-ID: <[email protected]>
The Hmisc and Design libraries have been updated respectively to versions 1.4-2 and 1.1-1. New versions for Linux/Unix/Windows may be obtained from http://hesweb1.med.virginia.edu/biostat/s/library/r . Web sites for the libraries are http://hesweb1.med.virginia.edu/biostat/s/Hmisc.html and http://hesweb1.med.virginia.edu/biostat/s/Design.html .
Thanks to Xiao Gang Fan for porting the libraries to Windows once again.
I still have not had time to fix details in the documentation that will allow R CMD check to be passed, which would allow me to submit the libraries to CRAN.
Change logs may be obtained from http://hesweb1.med.virginia.edu/biostat/s/library/common
Several bugs have been fixed, and new features added. In Hmisc, better use as been made of "units" attributes of variables, and units are incorporated into tables and plots produced by summary.formula. For plots, plotmath is used, especially for annotating plots with test statistics produced by summary(..., test=TRUE). A "matrix tapply" function (mApply) has been added. A new LaTeX table formatting option, ctable, has been added to latex.default. A new function getHdata makes it easy to download and import datasets and their descriptions from our web site. latex functions were changed to allow file="" to be specified, for inline inclusion of LaTeX code in Sweave. Problems with sas.get and [.factor have been fixed. fit.mult.impute was enhanced to compute Rubin's degrees of freedom for t-statistics for scalar parameter tests, as well as to compute a missing information index.
In Design, glmD works much more reliably. plotmath is now used by plot.Design. Bill Pikounis' <v_bill_pikounis at merck.com> improvements have been incorporated in bootcov to allow both cluster and group to be specified. offsets now work in lrm when NAs are present, and predict.Design now works with offsets. bootcov now works with glmD, and summary and print work for glmD (thanks: Fredrik Lundgren <fredrik.lundgren at norrkoping.mail.telia.com>). validate.tree had a bug fix.
Extended documentation for the libraries, and an introduction to the S language have been updated also (http://hesweb1.med.virginia.edu/biostat/s/doc/splus.pdf) and now include more R-specific information.
Thanks to those who have reported bugs and fixes, and Happy New Year to all.
----
Frank E Harrell Jr Prof. of Biostatistics & Statistics
Div. of Biostatistics & Epidem. Dept. of Health Evaluation Sciences
U. Virginia School of Medicine http://hesweb1.med.virginia.edu/biostat
|
Updates to Hmisc and Design Libraries
|
Frank E Harrell Jr
| 146
|
|
From Torsten.Hothorn at rzmail.uni-erlangen.de Tue Apr 11 20:01:13 2006
From: Torsten.Hothorn at rzmail.uni-erlangen.de (Torsten Hothorn)
Date: Tue, 11 Apr 2006 20:01:13 +0200 (CEST)
Subject: useR! 2006: April 15 regular registration deadline
Message-ID: <Pine.LNX.4.64.0604111959580.13078@artemis.imbe.med.uni-erlangen.de>
Dear useRs,
we would like to inform you that we are approaching the regular
registration deadline (2006-04-15) of useR! 2006, the second R
user conference taking place in Vienna on June 15-17. So if you
plan to join the conference, this is the perfect time to register!
The pre-conference tutorials, on June 14, already attracted a lot
of interest, so make sure to book _now_ if you are planning to
attend one or two of the tutorials given by prominent members of
the R community.
The scientific program, including all abstracts, is available from the
conference Web page at
http://www.R-project.org/useR-2006/
We are looking forward to meeting you in Vienna,
The useR! 2006 organizing team.
|
useR! 2006: April 15 regular registration deadline
|
<Pine.LNX.4.64.0604111959580.13078@artemis.imbe.med.uni-erlangen.de>
|
Torsten Hothorn
| 450
|
From pd@|gd @end|ng |rom gm@||@com Sun Oct 3 18:58:08 2021
From: pd@|gd @end|ng |rom gm@||@com (peter dalgaard)
Date: Sun, 3 Oct 2021 18:58:08 +0200
Subject: [Rd] R 4.1.2 scheduled for November 1
In-Reply-To: <[email protected]>
References: <[email protected]>
Message-ID: <[email protected]>
Schedule should appear on developer.r-project.org when it gets updated from SVN.
> On 3 Oct 2021, at 18:40 , peter dalgaard <pdalgd at gmail.com> wrote:
>
> (Just a quick heads-up for developers.)
>
> Full schedule to be made available soon.
>
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
|
[Rd] R 4.1.2 scheduled for November 1
|
peter dalgaard
| 641
|
|
From Friedrich.Leisch at ci.tuwien.ac.at Fri Jan 16 15:31:43 1998
From: Friedrich.Leisch at ci.tuwien.ac.at (Friedrich Leisch)
Date: Fri, 16 Jan 1998 15:31:43 +0100
Subject: New version of e1071 package at CRAN
Message-ID: <[email protected]>
I have put a new version of our e1071 package onto CRAN. New features
are support for reading/writing pgm images.
Contents:
hamming.distance Hamming Distance of Vectors
hamming.window Coefficients of a Hamming window
hanning.window Coefficients of a Hanning window
kmeans k-Means Clustering
kurtosis Kurtosis
moment Statistical Moment
plot.cluster Plot Clustered Data
plot.pgm Plot a PGM image
plot.stft Plots Results of a STFT
predict.cluster Assign Clusters to New Data
rbridge Simulation of Brownian Bridge
read.octave Read Octave Data File
read.pgm Read a PGM image file
rectangle.window Coefficients of a Rectangle window
rwiener Simulation of Wiener Process
skewness Skewness
stft Short Time Fourier Transform
write.pgm Write a PGM image file
write.table Data Output
--
-------------------------------------------------------------------
Friedrich Leisch
Institut f?r Statistik Tel: (+43 1) 58801 4541
Technische Universit?t Wien Fax: (+43 1) 504 14 98
Wiedner Hauptstra?e 8-10/1071 Friedrich.Leisch at ci.tuwien.ac.at
A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch
PGP public key http://www.ci.tuwien.ac.at/~leisch/pgp.key
-------------------------------------------------------------------
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r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
New version of e1071 package at CRAN
|
Friedrich Leisch
| 519
|
|
From Uwe.Ligges at r-project.org Fri Aug 3 14:48:47 2007
From: Uwe.Ligges at r-project.org (Uwe Ligges)
Date: Fri, 03 Aug 2007 14:48:47 +0200
Subject: useR! 2008
Message-ID: <[email protected]>
We are happy to announce that the R user conference
useR! 2008
is scheduled for August 12-14, 2008, and will take place at the
University of Dortmund.
As for the predecessor conferences, the program will consist of two parts:
invited lectures and user-contributed sessions (abstract submission will
be available online starting from December 2007). Prior to the
conference, there will be tutorials on R (proposals for tutorials should
be sent before 2007-10-31).
INVITED LECTURES
Invited speakers will include
Peter B?hlmann, John Fox, Kurt Hornik, Gary King, Duncan Murdoch,
Jean Thioulouse, Graham J. Williams, and Keith Worsley.
USER-CONTRIBUTED SESSIONS
The sessions will be a platform to bring together R users, contributors,
package maintainers and developers in the S spirit that `users are
developers'. People from different fields will show us how they solve
problems with R in fascinating applications.
The sessions are organized by members of the program committee, including
Micah Altman, Roger Bivand, Peter Dalgaard, Jan de Leeuw,
Ram?n D?az-Uriarte, Spencer Graves, Leonhard Held, Torsten Hothorn,
Fran?ois Husson, Christian Kleiber, Friedrich Leisch, Andy Liaw,
Martin M?chler, Kate Mullen, Ei-ji Nakama, Thomas Petzold,
Martin Theus, and Heather Turner.
The program will cover topics such as
* Applied Statistics & Biostatistics
* Bayesian Statistics
* Bioinformatics
* Chemometrics and Computational Physics
* Data Mining
* Econometrics & Finance
* Environmetrics & Ecological Modeling
* High Performance Computing
* Machine Learning
* Marketing & Business Analytics
* Psychometrics
* Robust Statistics
* Sensometrics
* Spatial Statistics
* Statistics in the Social and Political Sciences
* Teaching
* Visualization & Graphics
* and many more.
PRE-CONFERENCE TUTORIALS
Before the official program, half-day tutorials will be offered
on Monday, August 11th.
We invite R users to submit proposals for three hour tutorials on
special topics on R. The proposals should give a brief description of
the tutorial, including goals, detailed outline, justification why the
tutorial is important, background knowledge required and potential
attendees. The proposals should be sent before 2007-10-31 to
useR-2008 at R-project.org.
A web page offering more information on the `useR!' conference is
available at
http://www.R-project.org/useR-2008
ABOUT DORTMUND
In the past, Dortmund was famous for coal, steel and the beer industry -
quite typical for a city in the Ruhrgebiet. Today, Dortmund evolves to a
city with high tech industry, exhibitions and service companies.
Dortmund's football (i.e. soccer) club is world famous and attracts
roughly 80000 people on a regular basis.
IMPORTANT DATES
2007-10-31: submission deadline of tutorial proposals
2007-12-01: start of registration
2007-12-01: start of online abstract submission
2008-03-31: early registration deadline:
2008-03-31: submission deadline of abstracts
2008-05-15: notification of acceptance
2008-05-31: regular registration deadline
2008-07-25: registration deadline
We hope to meet you in Dortmund!
The conference committee:
Uwe Ligges (conference), Achim Zeileis (program), Claus Weihs,
Gerd Kopp (local organization), Friedrich Leisch, Torsten Hothorn
|
useR! 2008
|
Uwe Ligges
| 419
|
|
From plummerM at iarc.fr Wed Jul 11 09:57:26 2012
From: plummerM at iarc.fr (Martyn Plummer)
Date: Wed, 11 Jul 2012 09:57:26 +0200
Subject: The R Journal, Vol. 4 Issue 1
Message-ID: <[email protected]>
Dear All,
The first issue of the fourth volume of The R Journal is now available
at http://journal.r-project.org/current.html
Thanks to everyone involved.
Martyn Plummer
Editor-in-Chief
-----------------------------------------------------------------------
This message and its attachments are strictly confidenti...{{dropped:8}}
|
The R Journal, Vol. 4 Issue 1
|
Martyn Plummer
| 442
|
|
From chr|@@prener @end|ng |rom @|u@edu Wed Feb 26 22:41:21 2020
From: chr|@@prener @end|ng |rom @|u@edu (Chris Prener)
Date: Wed, 26 Feb 2020 21:41:21 +0000
Subject: useR! 2020 - Registration Open!
References: <5128b37f-7f71-4b36-8928-f78059250a3c@Spark>
Message-ID: <a69925d7-fa86-4658-9e4a-e25d4ce2221d@Spark>
Registration for the useR! 2020 conference in St. Louis, Missouri, U.S.A is now open. The conference will run from July 7th through July 10th, with a pre-conference day with some events on July 6th, tutorials on July 7th, and keynotes/break-outs July 8th-10th. You can view a draft, high-level agenda on our website<https://user2020.r-project.org/program/agenda/>.
Early bird registration will run through April 1st, 2020. Early bird prices for attendance are as follows:
Student - $190
Academic (Faculty/Staff) - $390
Industry and all others - $590
Each tutorial is $75, and the Wednesday Gala Dinner and City Museum event is $60 per ticket.
Registration instructions and links to both the registration platform and our hotel partner can be found on our website<https://user2020.r-project.org/registration/instructions/>.
If you have questions, please feel free to reach out to me (chris.prener at slu.edu) or my colleague and co-lead organizer Jenine Harris (harrisj at wustl.edu).
Best,
Chris
Christopher Prener, PhD
useR! 2020 Co-Lead
Assistant Professor of Sociology
Department of Sociology and Anthropology
Saint Louis University
St. Louis, MO
https://chris-prener.github.io
[[alternative HTML version deleted]]
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useR! 2020 - Registration Open!
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<a69925d7-fa86-4658-9e4a-e25d4ce2221d@Spark>
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Chris Prener
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From rpeng at stat.ucla.edu Wed Jan 8 17:48:05 2003
From: rpeng at stat.ucla.edu (Roger Peng)
Date: Wed Jan 8 17:48:05 2003
Subject: New package: gpclib
Message-ID: <[email protected]>
I have just uploaded a package to CRAN called `gpclib' for clipping large
and complex polygons. This package provides an R interface to Alan
Murta's very fast General Polygon Clipper library (written in C), which
has an optimized version of the Vatti algorithm. Not all features of
Murta's library are implemented -- right now you can do intersections,
differences, and unions. There are also functions for reading/writing
from/to files and coercing between various data types.
For some more details about the package see
http://department.stat.ucla.edu/~rpeng/R/gpclib.
Please send any comments, complaints, and bug reports to
rpeng at stat.ucla.edu.
Here is the DESCRIPTION file for the package:
Package: gpclib
Version: 1.0
Date: 1/6/2003
Depends: R (>= 1.6.1)
Title: General Polygon Clipping Library for R
Author: R interface by Roger D. Peng <rpeng at stat.ucla.edu>; GPC library
by Alan Murta
Maintainer: Roger D. Peng <rpeng at stat.ucla.edu>
Description: General polygon clipping routines for R based on Alan
Murta's C library
License: Code written by R. D. Peng is available under the LGPL; the C
code for the GPC library is free for non-commercial use (see the
files `gpc.c' and `gpc.h' for details)
URL: http://department.stat.ucla.edu/~rpeng/R/gpclib;
http://www.cs.man.ac.uk/aig/staff/alan/software
Happy clipping!
-roger
_______________________________
UCLA Department of Statistics
rpeng at stat.ucla.edu
http://www.stat.ucla.edu/~rpeng
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New package: gpclib
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Roger Peng
| 147
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From ripley at stats.ox.ac.uk Mon Jul 20 18:06:50 1998
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Mon, 20 Jul 1998 17:06:50 +0100 (BST)
Subject: V&R libraries, tree for 0.62.2, R Complements for V&R
Message-ID: <[email protected]>
Versions of the V&R libraries, VR_5.3pl025-1.tar.gz, and of
tree_0.2-2.tar.gz (giving most of the functionality of S's tree system
including all that I have ever used) are now available on CRAN's Vienna
node, and will propagate.
There is an early draft of an R user's complements on Venables & Ripley
available from
http://www.stats.ox.ac.uk/pub/MASS2/Compl.shtml
This is unlikely to be completed until 0.62.3 or perhaps 0.63 is
released.
--
Brian D. Ripley, ripley at stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272860 (secr)
Oxford OX1 3TG, UK Fax: +44 1865 272595
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
V&R libraries, tree for 0.62.2, R Complements for V&R
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Prof Brian Ripley
| 543
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From pd.mes at cbs.dk Thu Apr 10 12:05:40 2014
From: pd.mes at cbs.dk (Peter Dalgaard)
Date: Thu, 10 Apr 2014 12:05:40 +0200
Subject: [R] R 3.0.3 is released
Message-ID: <[email protected]>
The build system rolled up R-3.1.0.tar.gz (codename "Spring Dance") this morning.
The list below details the changes in this release.
You can get the source code from
http://cran.r-project.org/src/base/R-3/R-3.1.0.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you.
Binaries for various platforms will appear in due course.
(There seems to be a minor mishap with the NEWS file not getting copied to CRAN. I'll attend to that shortly.)
For the R Core Team
Peter Dalgaard
These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:
MD5 (AUTHORS) = cbf6da8f886ccd8d0dda0cc7ffd1b8ec
MD5 (COPYING) = eb723b61539feef013de476e68b5c50a
MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343
MD5 (FAQ) = 2978039f3d69bde1d31c5a3699dbe88a
MD5 (INSTALL) = 3964b9119adeaab9ceb633773fc94aac
MD5 (NEWS.html) = d88192d6e47eec39df1fe6ba3d673ae0
MD5 (R-latest.tar.gz) = a1ee52446bee81820409661e6d114ab1
MD5 (README) = e259ae5dd943b8547f0b7719664e815b
MD5 (RESOURCES) = c7cb32499ebbf85deb064aab282f93a4
MD5 (THANKS) = d4b45e302b7cad0fc4bb50d2cfe69649
MD5 (R-3/R-3.1.0.tar.gz) = a1ee52446bee81820409661e6d114ab1
This is the relevant part of the NEWS file
CHANGES IN R 3.1.0:
NEW FEATURES:
* type.convert() (and hence by default read.table()) returns a
character vector or factor when representing a numeric input as a
double would lose accuracy. Similarly for complex inputs.
If a file contains numeric data with unrepresentable numbers of
decimal places that are intended to be read as numeric, specify
colClasses in read.table() to be "numeric".
* tools::Rdiff(useDiff = FALSE) is closer to the POSIX definition
of diff -b (as distinct from the description in the man pages of
most systems).
* New function anyNA(), a version of any(is.na(.)) which is fast
for atomic vectors, based on a proposal by Tim Hesterberg. (Wish
of PR#15239.)
* arrayInd(*, useNames = TRUE) and, analogously, which(*, arr.ind =
TRUE) now make use of names(.dimnames) when available.
* is.unsorted() now also works for raw vectors.
* The "table" method for as.data.frame() (also useful as
as.data.frame.table()) now passes sep and base arguments to
provideDimnames().
* uniroot() gets new optional arguments, notably extendInt,
allowing to auto-extend the search interval when needed. The
return value has an extra component, init.it.
* switch(f, ...) now warns when f is a factor, as this typically
happens accidentally where the useR meant to pass a character
string, but f is treated as integer (as always documented).
* The parser has been modified to use less memory.
* The way the unary operators (+ - !) handle attributes is now more
consistent. If there is no coercion, all attributes (including
class) are copied from the input to the result: otherwise only
names, dims and dimnames are.
* colorRamp() and colorRampPalette() now allow non-opaque colours
and a ramp in opacity via the new argument alpha = TRUE.
(Suggested by Alberto Krone-Martins, but optionally as there are
existing uses which expect only RGB values.)
* grid.show.layout() and grid.show.viewport() get an optional vp.ex
argument.
* There is a new function find_gs_cmd() in the tools package to
locate a GhostScript executable. (This is an enhanced version of
a previously internal function there.)
* object.size() gains a format() method.
* There is a new family, "ArialMT", for the pdf() and postscript()
devices. This will only be rendered correctly on viewers which
have access to Monotype TrueType fonts (which are sometimes
requested by journals).
* The text and PDF news files, including NEWS and NEWS.2, have been
moved to the doc directory.
* combn(x, simplify = TRUE) now gives a factor result for factor
input x (previously user error). (Related to PR#15442.)
* Added utils::fileSnapshot() and utils::changedFiles() functions
to allow snapshots and comparison of directories of files.
* make.names(names, unique=TRUE) now tries to preserve existing
names. (Suggestion of PR#15452.)
* New functions cospi(x), sinpi(x), and tanpi(x), for more accurate
computation of cos(pi*x), etc, both in R and the C API. Using
these gains accuracy in some cases, e.g., inside lgamma() or
besselI(). (Suggested by Morten Welinder in PR#15529.)
* print.table(x, zero.print = ".") now also has an effect when x is
not integer-valued.
* There is more support to explore the system's idea of time-zone
names. Sys.timezone() tries to give the current system setting
by name (and succeeds at least on Linux, OS X, Solaris and
Windows), and OlsonNames() lists the names in the system's Olson
database. Sys.timezone(location = FALSE) gives the previous
behaviour.
* Platforms with a 64-bit time_t type are allowed to handle
conversions between the "POSIXct" and "POSIXlt" classes for
date-times outside the 32-bit range (before 1902 or after 2037):
the existing workarounds are used on other platforms. (Note that
time-zone information for post-2037 is speculative at best, and
the OS services are tested for known errors and so not used on OS
X.)
Currently time_t is usually long and hence 64-bit on Unix-alike
64-bit platforms: however it several cases the time-zone database
is 32-bit. On R for Windows it is 64-bit (for both architectures
as from this version).
* The "save.defaults" option can include a value for
compression_level. (Wish of PR#15579.)
* colSums() and friends now have support for arrays and data-frame
columns with 2^31 or more elements.
* as.factor() is faster when f is an unclassed integer vector (for
example, when called from tapply()).
* fft() now works with longer inputs, from the 12 million
previously supported up to 2 billion. (PR#15593)
* Complex svd() now uses LAPACK subroutine ZGESDD, the complex
analogue of the routine used for the real case.
* Sweave now outputs .tex files in UTF-8 if the input encoding is
declared to be UTF-8, regardless of the local encoding. The
UTF-8 encoding may now be declared using a LaTeX comment
containing the string %\SweaveUTF8 on a line by itself.
* file.copy() gains a copy.date argument.
* Printing of date-times will make use of the time-zone
abbreviation in use at the time, if known. For example, for
Paris pre-1940 this could be LMT, PMT, WET or WEST. To enable
this, the "POSIXlt" class has an optional component "zone"
recording the abbreviation for each element.
For platforms which support it, there is also a component
"gmtoff" recording the offset from GMT where known.
* (On Windows, by default on OS X and optionally elsewhere.) The
system C function strftime has been replaced by a more
comprehensive version with closer conformance to the POSIX 2008
standard.
* dnorm(x, log = FALSE) is more accurate (but somewhat slower) for
|x| > 5; as suggested in PR#15620.
* Some versions of the tiff() device have further compression
options.
* read.table(), readLines() and scan() have a new argument to
influence the treatment of embedded nuls.
* Avoid duplicating the right hand side values in complex
assignments when possible. This reduces copying of replacement
values in expressions such as Z$a <- a0 and ans[[i]] <- tmp: some
package code has relied on there being copies.
Also, a number of other changes to reduce copying of objects; all
contributed by or based on suggestions by Michael Lawrence.
* The fast argument of KalmanLike(), KalmanRun() and
KalmanForecast() has been replaced by update, which instead of
updating mod in place, optionally returns the updated model in an
attribute "mod" of the return value.
* arima() and makeARIMA() get a new optional argument SSinit,
allowing the choice of a different *s*tate *s*pace initialization
which has been observed to be more reliable close to
non-stationarity: see PR#14682.
* warning() has a new argument noBreaks., to simplify
post-processing of output with options(warn = 1).
* pushBack() gains an argument encoding, to support reading of
UTF-8 characters using scan(), read.table() and related functions
in a non-UTF-8 locale.
* all.equal.list() gets a new argument use.names which by default
labels differing components by names (if they match) rather than
by integer index. Saved R output in packages may need to be
updated.
* The methods for all.equal() and attr.all.equal() now have
argument check.attributes after ... so it cannot be partially nor
positionally matched (as it has been, unintentionally).
A side effect is that some previously undetected errors of
passing empty arguments (no object between commas) to all.equal()
are detected and reported.
There are explicit checks that check.attributes is logical,
tolerance is numeric and scale is NULL or numeric. This catches
some unintended positional matching.
The message for all.equal.numeric() reports a "scaled difference"
only for scale != 1.
* all.equal() now has a "POSIXt" method replacing the "POSIXct"
method.
* The "Date" and "POSIXt" methods of seq() allows by = "quarter"
for completeness (by = "3 months" always worked).
* file.path() removes any trailing separator on Windows, where they
are invalid (although sometimes accepted). This is intended to
enhance the portability of code written by those using POSIX file
systems (where a trailing / can be used to confine path matching
to directories).
* New function agrepl() which like grepl() returns a logical
vector.
* fifo() is now supported on Windows. (PR#15600)
* sort.list(method = "radix") now allows negative integers (wish of
PR#15644).
* Some functionality of print.ts() is now available in
.preformat.ts() for more modularity.
* mcparallel() gains an option detach = TRUE which allows execution
of code independently of the current session. It is based on a
new estranged = TRUE argument to mcfork() which forks child
processes such that they become independent of the parent
process.
* The pdf() device omits circles and text at extremely small sizes,
since some viewers were failing on such files.
* The rightmost break for the "months", "quarters" and "years"
cases of hist.POSIXlt() has been increased by a day. (Inter
alia, fixes PR#15717.)
* The handling of DF[i,] <- a where i is of length 0 is improved.
(Inter alia, fixes PR#15718.)
* hclust() gains a new method "ward.D2" which implements Ward's
method correctly. The previous "ward" method is "ward.D" now,
with the old name still working. Thanks to research and
proposals by Pierre Legendre.
* The sunspot.month dataset has been amended and updated from the
official source, whereas the sunspots and sunspot.year datasets
will remain immutable. The documentation and source links have
been updated correspondingly.
* The summary() method for "lm" fits warns if the fit is
essentially perfect, as most of the summary may be computed
inaccurately (and with platform-dependent values).
Programmers who use summary() in order to extract just a
component which will be reliable (e.g. $cov.unscaled) should wrap
their calls in suppressWarnings().
INSTALLATION and INCLUDED SOFTWARE:
* The included version of LAPACK has been updated to 3.5.0.
* There is some support for parallel testing of an installation, by
setting TEST_MC_CORES to an integer greater than one to indicate
the maximum number of cores to be used in parallel. (It is worth
specifying at least 8 cores if available.) Most of these require
a make program (such as GNU make and dmake) which supports the
$MAKE -j nproc syntax.
Except on Windows: the tests of standard package examples in make
check are done in parallel. This also applies to running
tools::testInstalledPackages().
The more time-consuming regression tests are done in parallel.
The package checks in make check-devel and make check-recommended
are done in parallel.
* More of make check will work if recommended packages are not
installed: but recommended packages remain needed for thorough
checking of an R build.
* The version of tzcode included in src/extra/tzone has been
updated. (Formerly used only on Windows.)
* The included (64-bit) time-zone conversion code and Olson
time-zone database can be used instead of the system version: use
configure option --with-internal-tzcode. This is the default on
Windows and OS X. (Note that this does not currently work if a
non-default rsharedir configure variable is used.)
(It might be necessary to set environment variable TZ on OSes
where this is not already set, although the system timezone is
deduced correctly on at least Linux, OS X and Windows.)
This option also switches to the version of strftime included in
directory src/extra/tzone.
* configure now tests for a C++11-compliant compiler by testing
some basic features. This by default tries flags for the
compiler specified by CXX, but an alternative compiler, options
and standard can be specified by variables CXX1X, CXX1XFLAGS and
CXX1XSTD (e.g. -std=gnu++11).
* R can now optionally be compiled to use reference counting
instead of the NAMED mechanism by defining SWITCH_TO_REFCNT in
Rinternals.h. This may become the default in the future.
* There is a new option --use-system-tre to use a suitable system
tre library: at present this means a version from their git
repository, after corrections. (Wish of PR#15660.)
PACKAGE INSTALLATION:
* The CRANextra repository is no longer a default repository on
Windows: all the binary versions of packages from CRAN are now on
CRAN, although CRANextra contains packages from Omegahat and
elsewhere used by CRAN packages.
* Only vignettes sources in directory vignettes are considered to
be vignettes and hence indexed as such.
* In the DESCRIPTION file,
License: X11
is no longer recognized as valid. Use MIT or BSD_2_clause
instead, both of which need + file LICENSE.
* For consistency, entries in .Rinstignore are now matched
case-insensitively on all platforms.
* Help for S4 methods with very long signatures now tries harder to
split the description in the Usage field to no more than 80
characters per line (some packages had over 120 characters).
* R CMD INSTALL --build (not Windows) now defaults to the internal
tar() unless R_INSTALL_TAR is set.
* There is support for compiling C++11 code in packages on suitable
platforms: see 'Writing R Extensions'.
* Fake installs now install the contents of directory inst: some
packages use this to install e.g. C++ headers for use by other
packages that are independent of the package itself. Option
--no-inst can be used to get the previous behaviour.
DEBUGGING:
* The behaviour of the code browser has been made more consistent,
in part following the suggestions in PR#14985.
* Calls to browser() are now consistent with calls to the browser
triggered by debug(), in that Enter will default to n rather than
c.
* A new browser command s has been added, to "step into" function
calls.
* A new browser command f has been added, to "finish" the current
loop or function.
* Within the browser, the command help will display a short list of
available commands.
UTILITIES:
* Only vignettes sources in directory vignettes are considered to
be vignettes by R CMD check. That has been the preferred
location since R 2.14.0 and is now obligatory.
* For consistency, R CMD build now matches entries in .Rbuildignore
and vignettes/.install_extras case-insensitively on all platforms
(not just on Windows).
* checkFF() (called by R CMD check by default) can optionally check
foreign function calls for consistency with the registered type
and argument count. This is the default for R CMD check
--as-cran or can be enabled by setting environment variable
_R_CHECK_FF_CALLS_ to registration (but is in any case suppressed
by --install=no). Because this checks calls in which .NAME is an
R object and not just a literal character string, some other
problems are detected for such calls.
Functions suppressForeignCheck() and dontCheck() have been added
to allow package authors to suppress false positive reports.
* R CMD check --as-cran warns about a false value of the
DESCRIPTION field BuildVignettes for Open Source packages, and
ignores it. (An Open Source package needs to have complete
sources for its vignettes which should be usable on a suitably
well-equipped system).
* R CMD check --no-rebuild-vignettes is defunct:
R CMD check --no-build-vignettes has been preferred since R
3.0.0.
* R CMD build --no-vignettes is defunct:
R CMD build --no-build-vignettes has been preferred since R
3.0.0.
* R CMD Sweave and R CMD Stangle now process both Sweave and
non-Sweave vignettes. The tools::buildVignette() function has
been added to do the same tasks from within R.
* The flags returned by R CMD config --ldflags and (where
installed) pkg-config --libs libR are now those needed to link a
front-end against the (shared or static) R library.
* Sweave.sty has a new option [inconsolata].
* R CMD check customizations such as _R_CHECK_DEPENDS_ONLY_ make
available packages only in LinkingTo only for installation, and
not for loading/runtime tests.
* tools::checkFF() reports on .C and .Fortran calls with DUP =
FALSE if argument check_DUP is true. This is selected by R CMD
check by default.
* R CMD check --use-gct can be tuned to garbage-collect less
frequently using gctorture2() _via_ the setting of environment
variable _R_CHECK_GCT_N_.
* Where supported, tools::texi2dvi() limits the number of passes
tried to 20.
C-LEVEL FACILITIES:
* (Windows only) A function R_WaitEvent() has been added (with
declaration in headerR.h) to block execution until the next event
is received by R.
* Remapping in the Rmath.h header can be suppressed by defining
R_NO_REMAP_RMATH.
* The remapping of rround() in header Rmath.h has been removed: use
fround() instead.
* ftrunc() in header Rmath.h is now a wrapper for the C99 function
trunc(), which might as well be used in C code: ftrunc() is still
needed for portable C++ code.
* The never-documented remapping of prec() to fprec() in header
Rmath.h has been removed.
* The included LAPACK subset now contains ZGESDD and ZGELSD.
* The function LENGTH() now checks that it is only applied to
vector arguments. However, in packages length() should be used.
(In R itself LENGTH() is a macro without the function overhead of
length().)
* Calls to SET_VECTOR_ELT() and SET_STRING_ELT() are now checked
for indices which are in-range: several packages were writing one
element beyond the allocated length.
* allocVector3 has been added which allows custom allocators to be
used for individual vector allocations.
DEPRECATED AND DEFUNCT:
* chol(pivot = TRUE, LINPACK = TRUE) is defunct.
Arguments EISPACK for eigen() and LINPACK for chol(), chol2inv(),
solve() and svd() are ignored: LAPACK is always used.
* .find.package() and .path.package() are defunct: only the
versions without the initial dot introduced in R 2.13.0 have ever
been in the API.
* Partial matching when using the $ operator _on data frames_ now
throws a warning and may become defunct in the future. If partial
matching is intended, replace foo$bar by foo[["bar", exact =
FALSE]].
* The long-deprecated use of \synopsis in the Usage section of .Rd
files has been removed: such sections are now ignored (with a
warning).
* package.skeleton()'s deprecated argument namespace has been
removed.
* Many methods are no longer exported by package stats. They are
all registered on their generic, which should be called rather
than calling a method directly.
* Functions readNEWS() and checkNEWS() in package tools are
defunct.
* download.file(method = "lynx") is deprecated.
* .C(DUP = FALSE) and .Fortran(DUP = FALSE) are now deprecated, and
may be disabled in future versions of R. As their help has long
said, .Call() is much preferred.
R CMD check notes such usages (by default).
* The workaround of setting R_OSX_VALGRIND has been removed: it is
not needed in current valgrind.
BUG FIXES:
* Calling lm.wfit() with no non-zero weights gave an array-overrun
in the Fortran code and a not very sensible answer. It is now
special-cased with a simpler answer (no qr component).
* Error messages involving non-syntactic names (e.g. as produced by
`\r` when that object does not exist) now encode the control
characters. (Reported by Hadley Wickham.)
* getGraphicsEvent() caused 100% usage of one CPU in Windows.
(PR#15500)
* nls() with no start argument may now work inside another function
(scoping issue).
* pbeta() and similar work better for very large (billions) ncp.
* Where time zones have changed abbreviations over the years, the
software tries to more consistently use the abbreviation
appropriate to the time or if that is unknown, the current
abbreviation. On some platforms where the C function localtime
changed the tzname variables the reported abbreviation could have
been that of the last time converted.
* all.equal(list(1), identity) now works.
* Bug fix for pushing viewports in grid (reported by JJ Allaire and
Kevin Ushey).
NOTE for anyone poking around within the graphics engine display
list (despite the warnings not to) that this changes what is
recorded by grid on the graphics engine display list.
* Extra checks have been added for unit resolution and conversion
in grid, to catch instances of division-by-zero. This may
introduce error messages in existing code and/or produce a
different result in existing code (but only where a non-finite
location or dimension may now become zero).
* Some bugs in TRE have been corrected by updating from the git
repository. This allows R to be installed on some platforms for
which this was a blocker (PR#15087 suggests Linux on ARM and
HP-UX).
* ? applied to a call to an S4 generic failed in several cases.
(PR#15680)
which this was a blocker (PR#15087 suggests Linux on ARM and
HP-UX).
* ? applied to a call to an S4 generic failed in several cases.
(PR#15680)
* The implicit S4 generics for primitives with ... in their
argument list were incorrect. (PR#15690)
* Bug fixes to methods::callGeneric(). (PR#15691)
* The bug fix to aggregrate() in PR#15004 introduced a new bug in
the case of no grouping variables. (PR#15699)
* In rare cases printing deeply nested lists overran a buffer by
one byte and on a few platforms segfaulted. (PR#15679)
* The dendrogram method of as.dendrogram() was hidden accidentally,
(PR#15703), and order.dendrogram(d) gave too much for a leaf d.
(PR#15702)
* R would try to kill processes on exit that have pids ever used by
a child process spawned by mcparallel even though the current
process with that pid was not actually its child.
* cophenetic() applied to a "dendrogram" object sometimes
incorrectly returned a "Labels" attribute with dimensions.
(PR#15706)
* printCoefmat() called from quite a few print() methods now obeys
small getOption("width") settings, line wrapping the "signif.
codes" legend appropriately. (PR#15708)
* model.matrix() assumed that the stored dimnames for a matrix was
NULL or length 2, but length 1 occurred.
* The clipping region for a device was sometimes used in base
graphics before it was set.
--
Peter Dalgaard, Professor
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
|
[R] R 3.0.3 is released
|
Peter Dalgaard
| 348
|
|
From p.murrell at auckland.ac.nz Fri Dec 1 23:15:05 2006
From: p.murrell at auckland.ac.nz (p.murrell at auckland.ac.nz)
Date: Sat, 2 Dec 2006 11:15:05 +1300 (NZDT)
Subject: R News, volume 6, issue 5 is now available
Message-ID: <[email protected]>
Hi
The December 2006 issue of R News is now available on CRAN under the
Documentation/Newsletter link.
Paul
(on behalf of the R News Editorial Board)
--
Dr Paul Murrell
Department of Statistics
The University of Auckland
Private Bag 92019
Auckland
New Zealand
64 9 3737599 x85392
paul at stat.auckland.ac.nz
http://www.stat.auckland.ac.nz/~paul/
|
R News, volume 6, issue 5 is now available
|
p.murrell at auckland.ac.nz
| 463
|
|
From torlasz at xenia.sote.hu Mon Jul 3 09:51:22 2000
From: torlasz at xenia.sote.hu (Tornoci Laszlo)
Date: Mon, 3 Jul 2000 09:51:22 +0200 (CEST)
Subject: A new mirror site in Hungary
In-Reply-To: <[email protected]>
Message-ID: <[email protected]>
Hi,
I have set up a mirror of CRAN at xenia.sote.hu (193.6.210.44).
It is accessible by:
ftp://cran.hu.r-project.org/pub/mirrors/CRAN
rsync://cran.hu.r-project.org/CRAN
http://cran.hu.r-project.org
The mirror gets updated daily. If you have any problems accessing it,
please inform me: <Laszlo Tornoci> torlasz at xenia.sote.hu
Yours: Laszlo
----------------------------------------------------------------------
Laszlo L Tornoci Inst Pathophysiology
E-mail: torlasz at xenia.sote.hu Semmelweis Univ Med School
torlasz at net.sote.hu Nagyvarad ter 4.
fax: (36-1)-210-4409 Budapest, H-1089, Hungary
----------------------------------------------------------------------
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
A new mirror site in Hungary
|
Tornoci Laszlo
| 325
|
|
From bates at stat.wisc.edu Thu Oct 9 15:07:30 2003
From: bates at stat.wisc.edu (Douglas Bates)
Date: Thu, 09 Oct 2003 13:07:30 -0000
Subject: anonymous access to the R CVS archive
Message-ID: <[email protected]>
Thanks to John Eaton of the Octave project we now have anonymous CVS
access to (a copy of) the R archive. See http://anoncvs.r-project.org/
|
anonymous access to the R CVS archive
|
Douglas Bates
| 186
|
|
From pd.mes at cbs.dk Thu Apr 14 18:39:06 2016
From: pd.mes at cbs.dk (Peter Dalgaard)
Date: Thu, 14 Apr 2016 16:39:06 +0000
Subject: R 3.2.5 is released
Message-ID: <[email protected]>
The 3.2.4-revised version turned out to give trouble for some of CRAN's subsystems.
Accordingly, a rebadged version 3.2.5 is now released; it only differs in the version number and a few clean-up items. If you have a working install of 3.2.4-revised there should be no reason to upgrade it.
You can get the source code from
http://cran.r-project.org/src/base/R-3/R-3.2.5.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you.
For the R Core Team,
Peter Dalgaard
New md5 sums are
MD5 (AUTHORS) = eb97a5cd38acb1cfc6408988bffef765
MD5 (COPYING) = eb723b61539feef013de476e68b5c50a
MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343
MD5 (FAQ) = cd7bfa946b8650cb87807e94e46984c6
MD5 (INSTALL) = 3964b9119adeaab9ceb633773fc94aac
MD5 (NEWS) = 42d76ce7f8e80977d5043bca4234f4c9
MD5 (NEWS.0) = bfcd7c147251b5474d96848c6f57e5a8
MD5 (NEWS.1) = eb78c4d053ec9c32b815cf0c2ebea801
MD5 (NEWS.2) = e840d32b7ef7a7603455d30d6d54fda7
MD5 (R-latest.tar.gz) = 7b23ee70cfb383be3bd4360e3c71d8c3
MD5 (README) = aece1dfbd18c1760128c3787f5456af6
MD5 (RESOURCES) = 529223fd3ffef95731d0a87353108435
MD5 (THANKS) = ba00f6cc68a823e1741cfa6011f40ccb
MD5 (VERSION-INFO.dcf) = 661c20647b9f0b9fa980297c53438609
MD5 (R-3/R-3.2.5.tar.gz) = 7b23ee70cfb383be3bd4360e3c71d8c3
The relevant NEWS file entries (relative to 3.2.4) are
CHANGES IN R 3.2.5:
BUG FIXES:
? format.POSIXlt() behaved incorrectly in R 3.2.4. E.g. the output
of format(as.POSIXlt(paste0(1940:2000,"-01-01"), tz = "CET"),
usetz = TRUE) ended in two "CEST" time formats.
? A typo in the Makefile for src/extra/xz prevented builds of
liblzma.a. (Notice that this will become unbundled in 3.3.0.)
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
|
R 3.2.5 is released
|
Peter Dalgaard
| 123
|
|
From pd@|gd @end|ng |rom gm@||@com Fri Feb 18 11:33:11 2022
From: pd@|gd @end|ng |rom gm@||@com (peter dalgaard)
Date: Fri, 18 Feb 2022 11:33:11 +0100
Subject: [Rd] R 4.1.3 scheduled for March 10
In-Reply-To: <[email protected]>
References: <[email protected]>
Message-ID: <[email protected]>
Schedule will appear on developer.r-project.org when it gets updated from SVN.
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
|
[Rd] R 4.1.3 scheduled for March 10
|
peter dalgaard
| 586
|
|
From Friedrich.Leisch at ci.tuwien.ac.at Mon Nov 25 19:28:37 2002
From: Friedrich.Leisch at ci.tuwien.ac.at (Friedrich.Leisch at ci.tuwien.ac.at)
Date: Mon, 25 Nov 2002 19:28:37 +0100
Subject: Final CFP: DSC 2003
Message-ID: <[email protected]>
This is a short reminder that the submission deadline for the workshop
Distributed Statistical Computing DSC 2003 is approaching rapidly. If
you want to give a talk to the conference please submit a paper or
extended abstract (1-2 pages) by the end of this week. Details on the
workshop can be found at
http://www.ci.tuwien.ac.at/Conferences/DSC-2003/
Best,
--
-------------------------------------------------------------------
Friedrich Leisch
Institut f?r Statistik Tel: (+43 1) 58801 10715
Technische Universit?t Wien Fax: (+43 1) 58801 10798
Wiedner Hauptstra?e 8-10/1071 Friedrich.Leisch at ci.tuwien.ac.at
A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch
-------------------------------------------------------------------
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
Final CFP: DSC 2003
|
Friedrich.Leisch at ci.tuwien.ac.at
| 96
|
|
From plummerm at iarc.fr Wed Oct 4 17:33:21 2017
From: plummerm at iarc.fr (Martyn Plummer)
Date: Wed, 4 Oct 2017 15:33:21 +0000
Subject: Help wanted - R contributed documentation
Message-ID: <[email protected]>
The R Foundation is looking for a volunteer to organize the collection
of contributed documentation for the R project. The collection is
currently hosted on CRAN at https://cran.r-project.org/other-docs.html
We want to move it off the CRAN web site.
We think that this task would be suitable for someone whose primary
interest is in library and information science. Ideally the collection
would be reorganized as an R-project.org epub archive, based on re-
using available open source software which features the following:
* export to .bib
* support for multiple revisions
* support for supplementary material (such as code and data).
If you are interested then please reply privately to me. The R
Foundation board will discuss this at the next meeting. You can, of
course, put together a team of people but we really want a single
person to act as point of reference.
Martyn Plummer
Co-president, The R Foundation
|
Help wanted - R contributed documentation
|
Martyn Plummer
| 143
|
|
From stefano.iacus at unimi.it Sat Apr 28 17:24:55 2001
From: stefano.iacus at unimi.it (Stefano Iacus)
Date: Sat, 28 Apr 2001 17:24:55 +0200
Subject: R 1.2.3 for MacOS/X available
Message-ID: <[email protected]>
From release 1.2.3, R can run different Macintosh platforms.
Two versions are currently available that are non concurrent.
One version runs on MacOS Systems from 8.6 to 9.1 and MacOSX using the
standard MacOS/MacOSX interface, that means that is behaves like any
usual Macintosh application. (This is mantained by Stefano M. Iacus)
The other version is a Darwin/X11 that means a Unix-like version taking
advantages of the X11 server (to be installed separately) and of the BSD
kernel of MacOS X. (This version is mantained by Jan de Leeuw).
About the Carbon version
This new version of R fixes may bugs of the previous Macintosh release
and adopt Apple's Carbon technology to let R run natively under both
MacOS 8.6 to 9.1 and MacOS X. This means that under MacOS X when you
double click on the R icon, the System no longer launches the Classic
Compatibility environment. Under MacOS X the Carbon R take advantages of
the new Aqua look/interface and memory management.
More informations on this version can be found at:
http://www.eco-dip.unimi.it/R/rmac-FAQ.html
You can download the carbon distribution at:
http://cran.r-project.org/bin/macos
About the Darwin/X11 version
There are two builds for Mac OS X, more precisely for Darwin/X11, of the
R-patched and R-devel distributions of 04/14/01.
They were build using the native cc compiler, with help from f2c,
dlcompat, libjpeg, libpng, libz, OS X versions of tcl/tk., and Tenon's
Xtools distribution.
The dynamic libraries you need are included, except for the X11
libraries, which you have to install anyway along with an X11 server.
In order to install one of these builds, su root, move to /, and unpack.
Everything installs in /usr/local/lib, except for the R driver which
goes to /usr/local/bin. The R-devel tarball contains most of the
contributed R packages.
You can find this distribution on Jan's page :
http://www.stat.ucla.edu/~deleeuw/R
For more information read the following r-announce msg
http://www.r-project.org/nocvs/mail/r-announce/latest/0026.html
Stefano
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Stefano Iacus
| 239
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From p.dalgaard at biostat.ku.dk Tue Dec 20 12:01:38 2005
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard)
Date: 20 Dec 2005 12:01:38 +0100
Subject: R 2.2.1 is released
Message-ID: <[email protected]>
I've rolled up R-2.2.1.tar.gz a short while ago. This is a maintenance
release containing mainly bugfixes.
See the full list of changes below.
You can get it from
http://cran.r-project.org/src/base/R-2/R-2.2.1.tar.gz
(give it some time to arrive there) or wait for it to be mirrored at a
CRAN site nearer to you. If you're *really* impatient,
http://www.biostat.ku.dk/~pd/R-release should work too. Binaries for
various platforms will appear in due course.
There is also a version split for floppies.
For the R Core Team
Peter Dalgaard
These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:
94d55d512a9ba36caa9b7df079bae19f COPYING
fad9b3332be894bab9bc501572864b29 COPYING.LIB
de541086db1146c1595d5be1d94a1b94 FAQ
70447ae7f2c35233d3065b004aa4f331 INSTALL
2c832b91154f663c0f07930d5e2a3dee NEWS
88bbd6781faedc788a1cbd434194480c ONEWS
4f004de59e24a52d0f500063b4603bcb OONEWS
42542290c6d1585af7ded330f811385c R-2.2.1.tar.gz
a9126622c51bef60e3febb41b2e737e5 R-2.2.1.tar.gz-split.aa
e89b51f6dbc1ddffd646a3f1f203f4f1 R-2.2.1.tar.gz-split.ab
15d93b1b5c38b6178ddcf9485dbd8cf1 R-2.2.1.tar.gz-split.ac
282bbbdd00c0066b6042ce16844036be R-2.2.1.tar.gz-split.ad
6d00347225140283e6c93f253cb7c180 R-2.2.1.tar.gz-split.ae
2441c58fc24a69dd5cc65517a0b5e285 R-2.2.1.tar.gz-split.af
4ddcd13639debd984e3664a6b0681bd4 R-2.2.1.tar.gz-split.ag
4a042d73ec00d7d46be1cc704063dc39 R-2.2.1.tar.gz-split.ah
0d5d54a78ab994bacb12a98bece1306f R-2.2.1.tar.gz-split.ai
69b38c655e4c1b7c36cb0abaa4890253 R-2.2.1.tar.gz-split.aj
42542290c6d1585af7ded330f811385c R-latest.tar.gz
56a780cdec835c5c598f8dfc0738f7f3 README
020479f381d5f9038dcb18708997f5da RESOURCES
Here is the relevant part of the NEWS file:
USER-VISIBLE CHANGES
o options("expressions") has been reduced to 1000: the limit
of 5000 introduced in 2.1.0 was liable to give crashes from C
stack overflow.
NEW FEATURES
o Use of 'pch' (e.g. in points) in the symbol font 5 is now
interpreted in the single-byte encoding used by that font.
Similarly, strwidth now recognizes that font 5 has a different
encoding from that of the locale. (These are likely to affect
the answer only in MBCS locales such as UTF-8.)
o The URW font metrics have been updated to versions from late
2002 which cover more glyphs, including Cyrillic.
o New postscript encodings for CP1250 (Windows East European),
ISO Latin-7 (8859-13, Latvian, Lithuanian and Maori), Cyrillic
(8859-5), KOI8-R, KOI8-U and CP1251.
o configure has more support for the Intel and Portland Group
compilers on ix86 and x86_64 Linux.
o R CMD INSTALL will clean up if interrupted (e.g. by ctrl-C from
the keyboard).
o There is now a comprehensive French translation of the messages,
thanks to Philippe Grosjean.
DEPRECATED & DEFUNCT
o The undocumented use of atan() with two arguments is deprecated:
instead use atan2() (as documented).
o The 'vfont' argument of axis() and mtext() is deprecated
(it currently warns and does nothing).
o The function mauchley.test() is deprecated (was a misspelling)
and replaced by mauchly.test()
BUG FIXES
o The malloc's of AIX and OSF/1 which return NULL for size 0
are now catered for in src/main/regex.c.
o Names of list elements which are missing are now printed as
$<NA> and not $"NA" (which is how the non-missing name "NA" is
printed). (Brought up in discussion of PR#8161.)
o help.start() was not linking R.css for use by its front page and
immediate links (2.2.0 only).
o Indexing by character NA matched the name "NA".
o The arith-true test used random inputs and did not set the seed, so
it could fail very occasionally.
o arima() with 'fixed' supplied and p=0 for the non-seasonal
part could give spurious warnings about 'some AR parameters
were fixed'.
o summary.matrix() could give an infinite recursion on some
classed objects (e.g. those of class "Surv").
o The 255th character in an 8-bit character set was not handled
correctly as a letter on some platforms where C char is
signed: for example it was printed as \377 and not allowed in
variable names. (Spotted by Alexey Shipunov in Russian
encodings.)
o Conversion from POSIXct to POSIXlt is done more accurately
around the change of DST in years not supported by the OS
(pre-1970 on Windows and some others, and in the far past or
future).
o chisq.test(cbind(1:0, c(7,16)), simulate.p = TRUE) gave wrong
P-values on some platforms. (PR#8224)
o pdf() was not writing details of the encoding to the file
correctly. (Spotted by Alexey Shipunov in Russian encodings.)
o image() was failing with an error when plotting a matrix
of all NA values. (PR#8228)
image() could fail if called with add=FALSE (the default) and
length(x)=1 for either x or y, as it uses the plot coordinates of
the previous plot (if any).
o tools::checkMD5sums was not accepting file names with spaces in.
o The plot() method for TukeyHSD() needed updating after adding
adjusted p-values. (PR#8229)
o read.fwf() did not work for header = TRUE. (PR#8226)
o diag() failed when its argument had NA values in its dimnames.
o [g]sub(pcre=TRUE) did not work correctly with \U and \L in a
UTF-8 locale, even on the example on the help page.
o promptMethods() was failing if the "methods" argument was supplied.
o is.loaded() now finds Fortran symbols whether or not the
registration mechanism has been used.
o ISODateTime() mistakenly corrected non-existent times (when
DST was being started) in the current time zone.
o Some replacement operations on data frames gave incorrect
answers, e.g. DF[3:4, "y"] if column "y" did not exist or was
a matrix.
o getGraphicsEvent() would cause memory corruption if passed an
empty prompt.
o qr() and chol() now pivot the colnames of the result when
pivoting is used. (PR#8258)
o example(points) omitted pch=0, although it was valid and
said in the text to be illustrated.
o plot.default() had an unused 'lab' argument, thereby preventing
the 'lab' graphics parameter being passed through '...' .
o Although polygon(col = NA) was the stated default, specifying
NA was not equivalent to omitting the argument (but col=NULL
was equivalent).
o Im(-1) was pi. (PR#8272, a side effect from all previous
versions of R returning the same value for Im and Arg of
non-complex numbers.)
o symbols(fg) defaulted to colour 1, not par("col") as documented.
It does now defaults to par("col").
o par("family") did not check the length of the value (up to 49
bytes) and so could segfault.
o aggregate.ts() did not allow for rounding in frequencies such
as 1/5.
o prcomp(tol=) was not dropping the sdev's corresponding to
dropped columns.
o Subassignment of a vector which increased the length of the
vector _and_ had the wrong length of replacement could
occasionally segfault. (This has been there since at least
mid 1997.)
o The registration of .Fortran symbols was broken: these could
only be looked up if there were also .Call symbols registered!
o R CMD build was incorrectly rejecting the recommended form of
name for a translation package, 'Translation-ll'. (PR#8314)
o numericDeriv() gave nonsense results unless the variables were
real, which was not checked.
o predict.prcomp() would sometimes give an error when predicting
a single observation. (PR#8324)
o mapply() could segfault if MoreArgs was not a list. (PR#8332)
o The arith-true test used identical() on floating-point results,
and this allowed a failure when the relative difference was
less than .Machine$double.eps but non-zero.
o qbinom() was not accepting p = -Inf when log.p = TRUE, although
it is a legitimate value.
o write.csv[2] only accepted logical constants for 'row.names', and
now accepts variables.
o Conversion of .Rd files did not correctly match braces
enclosing a whole argument, e.g. \eqn{{\bf a}}{a}.
o The C function pythag (used if hypot was not available) would
infinite-loop on systems with effective optimizing compilers.
o Writing long formats (more than 1000 bytes) with connections
that use dummy_vfprintf could fail on some systems. The limit
has been changed to 100000 bytes pending a more complete fix in R
2.3.0.
o Making in src/nmath/standalone without making R was not
making Rmath.h.
o Both the R front-end and INSTALL could find the attempted
temporary directory name already in use on platforms without
mktemp (and a genuine Bourne shell /bin/sh, not bash). Now
both the process ID and a timestamp are used to create the
directory name.
o [dpqr]gamma now return NaN for an invalid 'shape' parameter
(rather than throw an error), for consistency with other
distribution functions.
o t() now longer drops dimnames 'list(NULL,NULL)' or 'list(NULL)'.
o Influence measures such as rstandard() and cooks.distance()
could return infinite values rather than NaN for a case which
was fitted exactly. Similarly, plot.lm() could fail on such
examples. plot.lm(which = 5) had to be modified to only plot
cases with hat < 1. (PR#8367)
lm.influence() was incorrectly reporting 'coefficients' and
'sigma' as NaN for cases with hat = 1, and on some platforms
not detecting hat = 1 correctly.
o Rmath.h for standalone Rmath was not recording HAVE_WORKING_LOG,
so R_log was not available on platforms defining it.
o HoltWinters() was using a slightly incorrect formula in the C code.
o dir.create() could be confused by a trailing slash on the
path, and by paths containing drives on Windows.
o The search for tcl/tkConfig.sh looked in 'lib' before 'lib64'
directories (and not at all in /usr/local/lib64) and so might
prefer 32- to 64-bit versions if both are available.
o nlminb() used an uninitialized variable unless bounds were supplied,
and so failed on 64-bit Solaris.
--
O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
|
R 2.2.1 is released
|
Peter Dalgaard
| 394
|
|
From guido at hal.stat.unipd.it Thu Mar 18 08:49:14 1999
From: guido at hal.stat.unipd.it (Guido Masarotto)
Date: Thu, 18 Mar 1999 08:49:14 +0100
Subject: R0.63.3 for Win9X/NT available at CRAN
Message-ID: <[email protected]>
Windows binaries and source at CRAN (bin/windows/Windows-NT/base) have
been updated to R-0.63.3 (now at Wien, in one/two days to the
other mirrors).
WINDOWS NEWS:
============
The beginnings of a FAQ (RHOME/rw-faq).
Programs can be launched from all shells: the full path to the
executable is not needed.
Configurable fonts in the graphics devices by the file Rdevga (?Rdevga).
Workspaces are saved in XDR format, and so can be shared with most
Unix implementations of R.
Printer and metafile graphics devices (?win.print and ?win.metafile).
Consistent handling of start directory for dialogs and the working
directory across versions of R. Improved handling of R directories
via the new environmental variable R_HOME (look to the README).
An improved and enhanced system() function (?system and ?shell).
Windows-specific help files where necessary.
Better support for ESS.
Better support for the installation of pre-compiled packages
(?link.html.help)
=================================================================
Pre-compiled packages for this version of R are provided by
Brian D. Ripley and available CRAN/binaries/Windows-NT/contrib.
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
R0.63.3 for Win9X/NT available at CRAN
|
Guido Masarotto
| 469
|
|
From maechler at stat.math.ethz.ch Wed Mar 4 23:13:14 2015
From: maechler at stat.math.ethz.ch (Martin Maechler)
Date: Wed, 4 Mar 2015 23:13:14 +0100
Subject: format( "www.R-project.org" , year = 2015)
Message-ID: <CAPRP4-e0OjY9EFJdmSp99amsSy8NYewwimo5QUeseYNY+Aq_Eg@mail.gmail.com>
The R Foundation is pleased to announce that our website
http://www.r-project.org/ has under gone a nice retouch (and
thus arrived in the 21st century :-)
Thanks to a working group of Dirk Eddelbuettel, Simon Urbanek and
Hadley Wickham.,
the current page sources are in markdown, and the html is auto
produced using pandoc
(and IT infrastructure in Vienna and Zurich).
Martin Maechler,
as secretary of the R Foundation
|
format( "www.R-project.org" , year = 2015)
|
<CAPRP4-e0OjY9EFJdmSp99amsSy8NYewwimo5QUeseYNY+Aq_Eg@mail.gmail.com>
|
Martin Maechler
| 197
|
From maechler at stat.math.ethz.ch Tue Nov 26 18:39:45 2002
From: maechler at stat.math.ethz.ch (Martin Maechler)
Date: Tue, 26 Nov 2002 18:39:45 +0100
Subject: R-announce moved from majordomo to [procmail+mailman]
Message-ID: <[email protected]>
I have moved the R-announce mailing list from the Majordomo
software to a combination of procmail & mailman an hour or so ago.
You find a link in the footer of this message giving an URL
where you can modify your subscription, look at the archives
(everything from the beginning in 1997) and more.
CHANGE: Postings to R-announce are now moderated, ie.
they have to be approved by a list maintainer
unless they come from one of a small set of R developers.
Note that *everyone* subscribed to R-help also gets R-announce
messages without a need to subscribe.
Notice that the "Sender:" field of these e-mails has changed
from owner-r-announce to r-announce-admin. Those who use
mail-filtering rules may wish to adapt.
We expect faster mail delivery and an easier user (and
maintainer!) interface. Feedback welcome, to me privately or R-help.
The R-help mailing list (and its "digest") version will move to
mailman too.
Martin Maechler <maechler at stat.math.ethz.ch> http://stat.ethz.ch/~maechler/
Seminar fuer Statistik, ETH-Zentrum LEO C16 Leonhardstr. 27
ETH (Federal Inst. Technology) 8092 Zurich SWITZERLAND
phone: x-41-1-632-3408 fax: ...-1228 <><
|
R-announce moved from majordomo to [procmail+mailman]
|
Martin Maechler
| 97
|
|
From pd.mes at cbs.dk Fri Oct 15 11:15:50 2010
From: pd.mes at cbs.dk (Peter Dalgaard)
Date: Fri, 15 Oct 2010 11:15:50 +0200
Subject: R 2.12.0 is released
Message-ID: <[email protected]>
I've rolled up R-2.12.0.tar.gz a short while ago. This is a development
release which contains a number of new features.
Also, a number of mostly minor bugs have been fixed. See the full list
of changes below.
You can get it from
http://cran.r-project.org/src/base/R-2/R-2.12.0.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you.
Binaries for various platforms will appear in due course.
For the R Core Team
Peter Dalgaard
These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:
MD5 (AUTHORS) = ac9746b4845ae866661f51cfc99262f5
MD5 (COPYING) = eb723b61539feef013de476e68b5c50a
MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343
MD5 (FAQ) = dbdfe3f2451a4394b4f982e45ba4395c
MD5 (INSTALL) = 70447ae7f2c35233d3065b004aa4f331
MD5 (NEWS) = 8431585f21ee3e9a1cb83e1eb552d0e5
MD5 (ONEWS) = 0c3e10eef74439786e5fceddd06dac71
MD5 (OONEWS) = 58d5b3b614888a6e366ff0c60073584f
MD5 (R-latest.tar.gz) = aa003654d238d70bf5bc7433b8257aac
MD5 (README) = 296871fcf14f49787910c57b92655c76
MD5 (RESOURCES) = 020479f381d5f9038dcb18708997f5da
MD5 (THANKS) = f2ccf22f3e20ebaa86f8ee5cc6b0f655
MD5 (R-2/R-2.12.0.tar.gz) = aa003654d238d70bf5bc7433b8257aac
This is the relevant part of the NEWS file (hoping that the new format survives email...)
R News
CHANGES IN R VERSION 2.12.0:
NEW FEATURES:
? Reading a packages'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.
? difftime() now defaults to the "tzone" attribute of "POSIXlt"
objects rather than to the current timezone as set by the default
for the tz argument. (Wish of PR#14182.)
? pretty() is now generic, with new methods for "Date" and "POSIXt"
classes (based on code contributed by Felix Andrews).
? unique() and match() are now faster on character vectors where
all elements are in the global CHARSXP cache and have unmarked
encoding (ASCII). Thanks to Matthew Dowle for suggesting
improvements to the way the hash code is generated in unique.c.
? The enquote() utility, in use internally, is exported now.
? .C() and .Fortran() now map non-zero return values (other than
NA_LOGICAL) for logical vectors to TRUE: it has been an implicit
assumption that they are treated as true.
? The print() methods for "glm" and "lm" objects now insert
linebreaks in long calls in the same way that the print() methods
for "summary.[g]lm" objects have long done. This does change the
layout of the examples for a number of packages, e.g. MASS.
(PR#14250)
? constrOptim() can now be used with method "SANN". (PR#14245)
It gains an argument hessian to be passed to optim(), which
allows all the ... arguments to be intended for f() and grad().
(PR#14071)
? curve() now allows expr to be an object of mode "expression" as
well as "call" and "function".
? The "POSIX[cl]t" methods for Axis() have been replaced by a
single method for "POSIXt".
There are no longer separate plot() methods for "POSIX[cl]t" and
"Date": the default method has been able to handle those classes
for a long time. This _inter alia_ allows a single date-time
object to be supplied, the wish of PR#14016.
The methods had a different default ("") for xlab.
? Classes "POSIXct", "POSIXlt" and "difftime" have generators
.POSIXct(), .POSIXlt() and .difftime(). Package authors are
advised to make use of them (they are available from R 2.11.0) to
proof against planned future changes to the classes.
The ordering of the classes has been changed, so "POSIXt" is now
the second class. See the document ?Updating packages for
changes in R 2.12.x? on <URL: http://developer.r-project.org> for
the consequences for a handful of CRAN packages.
? The "POSIXct" method of as.Date() allows a timezone to be
specified (but still defaults to UTC).
? New list2env() utility function as an inverse of
as.list(<environment>) and for fast multi-assign() to existing
environment. as.environment() is now generic and uses list2env()
as list method.
? 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().
? Special names such as "dim", "names", etc, are now allowed as
slot names of S4 classes, with "class" the only remaining
exception.
? File .Renviron can have architecture-specific versions such as
.Renviron.i386 on systems with sub-architectures.
? installed.packages() has a new argument subarch to filter on
sub-architecture.
? The summary() method for packageStatus() now has a separate
print() method.
? The default summary() method returns an object inheriting from
class "summaryDefault" which has a separate print() method that
calls zapsmall() for numeric/complex values.
? The startup message now includes the platform and if used,
sub-architecture: this is useful where different
(sub-)architectures run on the same OS.
? The getGraphicsEvent() mechanism now allows multiple windows to
return graphics events, through the new functions
setGraphicsEventHandlers(), setGraphicsEventEnv(), and
getGraphicsEventEnv(). (Currently implemented in the windows()
and X11() devices.)
? tools::texi2dvi() gains an index argument, mainly for use by R
CMD Rd2pdf.
It avoids the use of texindy by texinfo's texi2dvi >= 1.157,
since that does not emulate 'makeindex' well enough to avoid
problems with special characters (such as (, {, !) in indices.
? The ability of readLines() and scan() to re-encode inputs to
marked UTF-8 strings on Windows since R 2.7.0 is extended to
non-UTF-8 locales on other OSes.
? scan() gains a fileEncoding argument to match read.table().
? points() and lines() gain "table" methods to match plot(). (Wish
of PR#10472.)
? Sys.chmod() allows argument mode to be a vector, recycled along
paths.
? There are |, & and xor() methods for classes "octmode" and
"hexmode", which work bitwise.
? Environment variables R_DVIPSCMD, R_LATEXCMD, R_MAKEINDEXCMD,
R_PDFLATEXCMD are no longer used nor set in an R session. (With
the move to tools::texi2dvi(), the conventional environment
variables LATEX, MAKEINDEX and PDFLATEX will be used.
options("dvipscmd") defaults to the value of DVIPS, then to
"dvips".)
? New function isatty() to see if terminal connections are
redirected.
? summaryRprof() returns the sampling interval in component
sample.interval and only returns in by.self data for functions
with non-zero self times.
? print(x) and str(x) now indicate if an empty list x is named.
? install.packages() and remove.packages() with lib unspecified and
multiple libraries in .libPaths() inform the user of the library
location used with a message rather than a warning.
? There is limited support for multiple compressed streams on a
file: all of [bgx]zfile() allow streams to be appended to an
existing file, but bzfile() reads only the first stream.
? Function person() in package utils now uses a given/family scheme
in preference to first/middle/last, is vectorized to handle an
arbitrary number of persons, and gains a role argument to specify
person roles using a controlled vocabulary (the MARC relator
terms).
? Package utils adds a new "bibentry" class for representing and
manipulating bibliographic information in enhanced BibTeX style,
unifying and enhancing the previously existing mechanisms.
? A bibstyle() function has been added to the tools package with
default JSS style for rendering "bibentry" objects, and a
mechanism for registering other rendering styles.
? Several aspects of the display of text help are now customizable
using the new Rd2txt_options() function.
options("help_text_width") is no longer used.
? Added \href tag to the Rd format, to allow hyperlinks to URLs
without displaying the full URL.
? Added \newcommand and \renewcommand tags to the Rd format, to
allow user-defined macros.
? New toRd() generic in the tools package to convert objects to
fragments of Rd code, and added "fragment" argument to Rd2txt(),
Rd2HTML(), and Rd2latex() to support it.
? Directory R_HOME/share/texmf now follows the TDS conventions, so
can be set as a texmf tree (?root directory? in MiKTeX parlance).
? S3 generic functions now use correct S4 inheritance when
dispatching on an S4 object. See ?Methods, section on ?Methods
for S3 Generic Functions? for recommendations and details.
? format.pval() gains a ... argument to pass arguments such as
nsmall to format(). (Wish of PR#9574)
? legend() supports title.adj. (Wish of PR#13415)
? Added support for subsetting "raster" objects, plus assigning to
a subset, conversion to a matrix (of colour strings), and
comparisons (== and !=).
? Added a new parseLatex() function (and related functions
deparseLatex() and latexToUtf8()) to support conversion of
bibliographic entries for display in R.
? Text rendering of \itemize in help uses a Unicode bullet in UTF-8
and most single-byte Windows locales.
? Added support for polygons with holes to the graphics engine.
This is implemented for the pdf(), postscript(),
x11(type="cairo"), windows(), and quartz() devices (and
associated raster formats), but not for x11(type="Xlib") or
xfig() or pictex(). The user-level interface is the polypath()
function in graphics and grid.path() in grid.
? File NEWS is now generated at installation with a slightly
different format: it will be in UTF-8 on platforms using UTF-8,
and otherwise in ASCII. There is also a PDF version, NEWS.pdf,
installed at the top-level of the R distribution.
? kmeans(x, 1) now works. Further, kmeans now returns between and
total sum of squares.
? arrayInd() and which() gain an argument useNames. For arrayInd,
the default is now false, for speed reasons.
? As is done for closures, the default print method for the formula
class now displays the associated environment if it is not the
global environment.
? A new facility has been added for inserting code into a package
without re-installing it, to facilitate testing changes which can
be selectively added and backed out. See ?insertSource.
? New function readRenviron to (re-)read files in the format of
~/.Renviron and Renviron.site.
? require() will now return FALSE (and not fail) if loading the
package or one of its dependencies fails.
? aperm() now allows argument perm to be a character vector when
the array has named dimnames (as the results of table() calls
do). Similarly, array() allows MARGIN to be a character vector.
(Based on suggestions of Michael Lachmann.)
? Package utils now exports and documents functions
aspell_package_Rd_files() and aspell_package_vignettes() for
spell checking package Rd files and vignettes using Aspell,
Ispell or Hunspell.
? Package news can now be given in Rd format, and news() prefers
these inst/NEWS.Rd files to old-style plain text NEWS or
inst/NEWS files.
? New simple function packageVersion().
? The PCRE library has been updated to version 8.10.
? The standard Unix-alike terminal interface declares its name to
readline as 'R', so that can be used for conditional sections in
~/.inputrc files.
? ?Writing R Extensions? now stresses that the standard sections in
.Rd files (other than \alias, \keyword and \note) are intended to
be unique, and the conversion tools now drop duplicates with a
warning.
The .Rd conversion tools also warn about an unrecognized type in
a \docType section.
? ecdf() objects now have a quantile() method.
? format() methods for date-time objects now attempt to make use of
a "tzone" attribute with "%Z" and "%z" formats, but it is not
always possible. (Wish of PR#14358.)
? tools::texi2dvi(file, clean = TRUE) now works in more cases (e.g.
where emulation is used and when file is not in the current
directory).
? New function droplevels() to remove unused factor levels.
? system(command, intern = TRUE) now gives an error on a Unix-alike
(as well as on Windows) if command cannot be run. It reports a
non-success exit status from running command as a warning.
On a Unix-alike an attempt is made to return the actual exit
status of the command in system(intern = FALSE): previously this
had been system-dependent but on POSIX-compliant systems the
value return was 256 times the status.
? system() has a new argument ignore.stdout which can be used to
(portably) ignore standard output.
? system(intern = TRUE) and pipe() connections are guaranteed to be
avaliable on all builds of R.
? Sys.which() has been altered to return "" if the command is not
found (even on Solaris).
? A facility for defining reference-based S4 classes (in the OOP
style of Java, C++, etc.) has been added experimentally to
package methods; see ?ReferenceClasses.
? The predict method for "loess" fits gains an na.action argument
which defaults to na.pass rather than the previous default of
na.omit.
Predictions from "loess" fits are now named from the row names of
newdata.
? Parsing errors detected during Sweave() processing will now be
reported referencing their original location in the source file.
? New adjustcolor() utility, e.g., for simple translucent color
schemes.
? qr() now has a trivial lm method with a simple (fast) validity
check.
? An experimental new programming model has been added to package
methods for reference (OOP-style) classes and methods. See
?ReferenceClasses.
? bzip2 has been updated to version 1.0.6 (bug-fix release).
--with-system-bzlib now requires at least version 1.0.6.
? R now provides jss.cls and jss.bst (the class and bib style file
for the Journal of Statistical Software) as well as RJournal.bib
and Rnews.bib, and R CMD ensures that the .bst and .bib files are
found by BibTeX.
? Functions using the TAR environment variable no longer quote the
value when making system calls. This allows values such as tar
--force-local, but does require additional quotes in, e.g., TAR =
"'/path with spaces/mytar'".
DEPRECATED & DEFUNCT:
? Supplying the parser with a character string containing both
octal/hex and Unicode escapes is now an error.
? File extension .C for C++ code files in packages is now defunct.
? R CMD check no longer supports configuration files containing
Perl configuration variables: use the environment variables
documented in ?R Internals? instead.
? The save argument of require() now defaults to FALSE and save =
TRUE is now deprecated. (This facility is very rarely actually
used, and was superseded by the Depends field of the DESCRIPTION
file long ago.)
? R CMD check --no-latex is deprecated in favour of --no-manual.
? R CMD Sd2Rd is formally deprecated and will be removed in R
2.13.0.
PACKAGE INSTALLATION:
? install.packages() has a new argument libs_only to optionally
pass --libs-only to R CMD INSTALL and works analogously for
Windows binary installs (to add support for 64- or 32-bit
Windows).
? When sub-architectures are in use, the installed architectures
are recorded in the Archs field of the DESCRIPTION file. There
is a new default filter, "subarch", in available.packages() to
make use of this.
Code is compiled in a copy of the src directory when a package is
installed for more than one sub-architecture: this avoid problems
with cleaning the sources between building sub-architectures.
? R CMD INSTALL --libs-only no longer overrides the setting of
locking, so a previous version of the package will be restored
unless --no-lock is specified.
UTILITIES:
? R CMD Rprof|build|check are now based on R rather than Perl
scripts. The only remaining Perl scripts are the deprecated R
CMD Sd2Rd and install-info.pl (used only if install-info is not
found) as well as some maintainer-mode-only scripts.
*NB:* because these have been completely rewritten, users should
not expect undocumented details of previous implementations to
have been duplicated.
R CMD no longer manipulates the environment variables PERL5LIB
and PERLLIB.
? R CMD check has a new argument --extra-arch to confine tests to
those needed to check an additional sub-architecture.
Its check for ?Subdirectory 'inst' contains no files? is more
thorough: it looks for files, and warns if there are only empty
directories.
Environment variables such as R_LIBS and those used for
customization can be set for the duration of checking _via_ a
file ~/.R/check.Renviron (in the format used by .Renviron, and
with sub-architecture specific versions such as
~/.R/check.Renviron.i386 taking precedence).
There are new options --multiarch to check the package under all
of the installed sub-architectures and --no-multiarch to confine
checking to the sub-architecture under which check is invoked.
If neither option is supplied, a test is done of installed
sub-architectures and all those which can be run on the current
OS are used.
Unless multiple sub-architectures are selected, the install done
by check for testing purposes is only of the current
sub-architecture (_via_ R CMD INSTALL --no-multiarch).
It will skip the check for non-ascii characters in code or data
if the environment variables _R_CHECK_ASCII_CODE_ or
_R_CHECK_ASCII_DATA_ are respectively set to FALSE. (Suggestion
of Vince Carey.)
? R CMD build no longer creates an INDEX file (R CMD INSTALL does
so), and --force removes (rather than overwrites) an existing
INDEX file.
It supports a file ~/.R/build.Renviron analogously to check.
It now runs build-time \Sexpr expressions in help files.
? R CMD Rd2dvi makes use of tools::texi2dvi() to process the
package manual. It is now implemented entirely in R (rather than
partially as a shell script).
? R CMD Rprof now uses utils::summaryRprof() rather than Perl. It
has new arguments to select one of the tables and to limit the
number of entries printed.
? R CMD Sweave now runs R with --vanilla so the environment setting
of R_LIBS will always be used.
C-LEVEL FACILITIES:
? lang5() and lang6() (in addition to pre-existing lang[1-4]())
convenience functions for easier construction of eval() calls.
If you have your own definition, do wrap it inside #ifndef lang5
.... #endif to keep it working with old and new R.
? Header R.h now includes only the C headers it itself needs, hence
no longer includes errno.h. (This helps avoid problems when it
is included from C++ source files.)
? Headers Rinternals.h and R_ext/Print.h include the C++ versions
of stdio.h and stdarg.h respectively if included from a C++
source file.
INSTALLATION:
? A C99 compiler is now required, and more C99 language features
will be used in the R sources.
? Tcl/Tk >= 8.4 is now required (increased from 8.3).
? System functions access, chdir and getcwd are now essential to
configure R. (In practice they have been required for some
time.)
? make check compares the output of the examples from several of
the base packages to reference output rather than the previous
output (if any). Expect some differences due to differences in
floating-point computations between platforms.
? File NEWS is no longer in the sources, but generated as part of
the installation. The primary source for changes is now
doc/NEWS.Rd.
? The popen system call is now required to build R. This ensures
the availability of system(intern = TRUE), pipe() connections and
printing from postscript().
? The pkg-config file libR.pc now also works when R is installed
using a sub-architecture.
? R has always required a BLAS that conforms to IE60559 arithmetic,
but after discovery of more real-world problems caused by a BLAS
that did not, this is tested more thoroughly in this version.
BUG FIXES:
? Calls to selectMethod() by default no longer cache inherited
methods. This could previously corrupt methods used by as().
? The densities of non-central chi-squared are now more accurate in
some cases in the extreme tails, e.g. dchisq(2000, 2, 1000), as a
series expansion was truncated too early. (PR#14105)
? pt() is more accurate in the left tail for ncp large, e.g.
pt(-1000, 3, 200). (PR#14069)
? The default C function (R_binary) for binary ops now sets the S4
bit in the result if either argument is an S4 object. (PR#13209)
? source(echo=TRUE) failed to echo comments that followed the last
statement in a file.
? S4 classes that contained one of "matrix", "array" or "ts" and
also another class now accept superclass objects in new(). Also
fixes failure to call validObject() for these classes.
? Conditional inheritance defined by argument test in
methods::setIs() will no longer be used in S4 method selection
(caching these methods could give incorrect results). See
?setIs.
? The signature of an implicit generic is now used by setGeneric()
when that does not use a definition nor explicitly set a
signature.
? A bug in callNextMethod() for some examples with "..." in the
arguments has been fixed. See file
src/library/methods/tests/nextWithDots.R in the sources.
? match(x, table) (and hence %in%) now treat "POSIXlt" consistently
with, e.g., "POSIXct".
? Built-in code dealing with environments (get(), assign(),
parent.env(), is.environment() and others) now behave
consistently to recognize S4 subclasses; is.name() also
recognizes subclasses.
? The abs.tol control parameter to nlminb() now defaults to 0.0 to
avoid false declarations of convergence in objective functions
that may go negative.
? The standard Unix-alike termination dialog to ask whether to save
the workspace takes a EOF response as n to avoid problems with a
damaged terminal connection. (PR#14332)
? Added warn.unused argument to hist.default() to allow suppression
of spurious warnings about graphical parameters used with
plot=FALSE. (PR#14341)
? predict.lm(), summary.lm(), and indeed lm() itself had issues
with residual DF in zero-weighted cases (the latter two only in
connection with empty models). (Thanks to Bill Dunlap for
spotting the predict() case.)
? aperm() treated resize = NA as resize = TRUE.
? constrOptim() now has an improved convergence criterion, notably
for cases where the minimum was (very close to) zero; further,
other tweaks inspired from code proposals by Ravi Varadhan.
? Rendering of S3 and S4 methods in man pages has been corrected
and made consistent across output formats.
? Simple markup is now allowed in \title sections in .Rd files.
? The behaviour of as.logical() on factors (to use the levels) was
lost in R 2.6.0 and has been restored.
? prompt() did not backquote some default arguments in the \usage
section. (Reported by Claudia Beleites.)
? writeBin() disallows attempts to write 2GB or more in a single
call. (PR#14362)
? new() and getClass() will now work if Class is a subclass of
"classRepresentation" and should also be faster in typical calls.
? The summary() method for data frames makes a better job of names
containing characters invalid in the current locale.
? [[ sub-assignment for factors could create an invalid factor
(reported by Bill Dunlap).
? Negate(f) would not evaluate argument f until first use of
returned function (reported by Olaf Mersmann).
? quietly=FALSE is now also an optional argument of library(), and
consequently, quietly is now propagated also for loading
dependent packages, e.g., in require(*, quietly=TRUE).
? If the loop variable in a for loop was deleted, it would be
recreated as a global variable. (Reported by Radford Neal; the
fix includes his optimizations as well.)
? Task callbacks could report the wrong expression when the task
involved parsing new code. (PR#14368)
? getNamespaceVersion() failed; this was an accidental change in
2.11.0. (PR#14374)
? identical() returned FALSE for external pointer objects even when
the pointer addresses were the same.
? L$a at x[] <- val did not duplicate in a case it should have.
? tempfile() now always gives a random file name (even if the
directory is specified) when called directly after startup and
before the R RNG had been used. (PR#14381)
? quantile(type=6) behaved inconsistently. (PR#14383)
? backSpline(.) behaved incorrectly when the knot sequence was
decreasing. (PR#14386)
? The reference BLAS included in R was assuming that 0*x and x*0
were always zero (whereas they could be NA or NaN in IEC 60559
arithmetic). This was seen in results from tcrossprod, and for
example that log(0) %*% 0 gave 0.
? The calculation of whether text was completely outside the device
region (in which case, you draw nothing) was wrong for screen
devices (which have [0, 0] at top-left). The symptom was (long)
text disappearing when resizing a screen window (to make it
smaller). (PR#14391)
? model.frame(drop.unused.levels = TRUE) did not take into account
NA values of factors when deciding to drop levels. (PR#14393)
? library.dynam.unload required an absolute path for libpath.
(PR#14385)
Both library() and loadNamespace() now record absolute paths for
use by searchpaths() and getNamespaceInfo(ns, "path").
? The self-starting model NLSstClosestX failed if some deviation
was exactly zero. (PR#14384)
? X11(type = "cairo") (and other devices such as png using
cairographics) and which use Pango font selection now work around
a bug in Pango when very small fonts (those with sizes between 0
and 1 in Pango's internal units) are requested. (PR#14369)
? Added workaround for the font problem with X11(type = "cairo")
and similar on Mac OS X whereby italic and bold styles were
interchanged. (PR#13463 amongst many other reports.)
? source(chdir = TRUE) failed to reset the working directory if it
could not be determined - that is now an error.
? Fix for crash of example(rasterImage) on x11(type="Xlib").
? Force Quartz to bring the on-screen display up-to-date
immediately before the snapshot is taken by grid.cap() in the
Cocoa implementation. (PR#14260)
? model.frame had an unstated 500 byte limit on variable names.
(Example reported by Terry Therneau.)
? The 256-byte limit on names is now documented.
? Subassignment by [, [[ or $ on an expression object with value
NULL coerced the object to a list.
--
Peter Dalgaard
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
|
R 2.12.0 is released
|
Peter Dalgaard
| 371
|
|
From hornik at ci.tuwien.ac.at Wed Jun 28 23:13:32 2000
From: hornik at ci.tuwien.ac.at (Kurt Hornik)
Date: Wed, 28 Jun 2000 23:13:32 +0200
Subject: New version of chron
Message-ID: <[email protected]>
A new version of the chron add-on package is now available from CRAN.
The previous version introduced code to ensure that chron would work
correctly in the 21st century. Of course, the main issue is how to deal
with 2-digit dates. To this end, the original author of chron, David
James, indicated that the `y' format specifier was always meant to
specify the year without the century (i.e., the year modulo 100), as in
strftime(3)'s `%y'. Hence, there should be an error when using a number
outside the [0, 99] range, such as 1999 or 2000, with the `y' format
specifier.
Several users have expressed their dislike of the new behavior and that
using `y' with 4-digit years used to work, sort of. Hence, the new
versions has changed the default behavior as follows. 2-digit years are
expanded using 30 as century cutoff, i.e.
00 -> 29 21st century
30 -> 99 20th century
All other values are left alone.
In the next version, I want to introduce strftime(3) formatting specs,
similar to the new timeDate class in S-PLUS 5. Most likely, ISO 8601
format (yyyy-mm-dd hh:mm:ss) will be used as default.
-kh
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
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|
New version of chron
|
Kurt Hornik
| 324
|
|
From brahm at alum.mit.edu Mon Dec 3 17:25:02 2001
From: brahm at alum.mit.edu (David Brahm)
Date: Mon, 3 Dec 2001 11:25:02 -0500
Subject: New package: g.data
Message-ID: <[email protected]>
A new package "g.data" is available on CRAN, to create and maintain databases
that work more like the S-Plus model.
Here's the official Description for g.data (v1.2):
Create and maintain delayed-data packages (DDP's). Data stored in
a DDP are available on demand, but do not take up memory until requested.
You attach a DDP with g.data.attach(), then read from it and assign to it in
a manner similar to S-Plus, except that you must run g.data.save() to
actually commit to disk.
Here's a very abbreviated (Unix) example:
g.data.attach("/tmp/mydir") # Open package:mydir in pos=2
assign("x1", matrix(1, 1000, 1000), 2) # Put data there
g.data.save() # Commit to disk
detach(2) # Detach package:mydir
g.data.attach("/tmp/mydir") # Re-attach it, no resources used
dim(x1) # x1 is loaded only when needed!
find("x1") # It still lives in package:mydir
g.data is the end result of my post "Reading and writing to S-like databases",
sent to R-help on Sep 28, 2001. Thanks to all who responded, especially
Dr. Agustin Lobo <alobo at ija.csic.es> and (by reference) Ray Brownrigg
<Ray.Brownrigg at mcs.vuw.ac.nz>, who suggested using delay(); Martin Maechler
<maechler at stat.math.ethz.ch>, Thomas Lumley <tlumley at u.washington.edu>, Brian
D. Ripley <ripley at stats.ox.ac.uk>, and Peter Dalgaard
<p.dalgaard at biostat.ku.dk>, who helped me with platform independence issues;
and Kurt Hornik <Kurt.Hornik at ci.tuwien.ac.at>, who cleaned it up for CRAN.
I have one concern: g.data relies heavily on delay(), whose documentation says:
This is an experimental feature and its addition is purely for
evaluation purposes.
Is there any plan to deprecate delay()?
Feedback is welcome!
--
-- David Brahm (brahm at alum.mit.edu)
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
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|
New package: g.data
|
David Brahm
| 279
|
|
From stefano.iacus at unimi.it Sat Dec 22 12:51:34 2001
From: stefano.iacus at unimi.it (Stefano Iacus)
Date: Sat, 22 Dec 2001 12:51:34 +0100
Subject: R 1.4.0 for Apple Machines (both Carbon and Darwin)
Message-ID: <[email protected]>
I have just uplodaed on CRAN both versions of R 1.4.0.
So starting from Dec 23rd, you'll find the builds for Carbon and Darwin
directly on CRAN respectively at
http://cran.r-project.org/bin/macos : Carbon R (8.6 -> 9.2 and OSX)
http://cran.r-project.org/bin/macosx : Darwin/X11 R (thanks to Jan!)
specific updates and bug fixing for the Carbon release can be found in
http://cran.r-project.org/bin/macos/base/CHANGES
along with the Carbon FAQ
http://cran.r-project.org/bin/macos/rmac-FAQ.html
Contributed packages for rm140 will come in 2002 !
stefano
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Send "info", "help", or "[un]subscribe"
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|
R 1.4.0 for Apple Machines (both Carbon and Darwin)
|
Stefano Iacus
| 293
|
|
From stefano.iacus at unimi.it Thu Jun 28 11:24:41 2001
From: stefano.iacus at unimi.it (Stefano Iacus)
Date: Thu, 28 Jun 2001 11:24:41 +0200
Subject: R 1.3.0 for MacOS 8.6 -> X
Message-ID: <[email protected]>
A binary distribution of R-1.3.0 to run on Macintosh PowerPC machines
with System 8.6 to OS X is available at
http://cran.r-project.org/bin/macos
Stefano M. Iacus
(for the R-core team)
Macintosh-specific changes to R
* Fixed a bug when saving from menus
* Added module support
* Fixed a bug that crashes R under System 8.6 due to a calling
to a non-existent function under 8.6
* Stack and memory settings changed to work on System 8.6
* R main project file and packages project files have been changed
* Added back the "Save" menu
* file.choose() works correctly now
* Now R takes track of file names associated to each window
* Fixed a bug with printer dialog
* Now R can handle "user breaks" in evaluation and printing loops
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
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|
R 1.3.0 for MacOS 8.6 -> X
|
Stefano Iacus
| 254
|
|
From pd.mes at cbs.dk Wed Apr 13 11:03:39 2011
From: pd.mes at cbs.dk (Peter Dalgaard)
Date: Wed, 13 Apr 2011 11:03:39 +0200
Subject: R 2.13.0 is released
Message-ID: <[email protected]>
I've rolled up R-2.13.0.tar.gz a short while ago. This is a development
release which contains a number of new features.
Also, a number of mostly minor bugs have been fixed (but notice that serious build issues were fixed in 2.12.2). See the full list
of changes below.
You can get it from
http://cran.r-project.org/src/base/R-2/R-2.13.0.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you.
Binaries for various platforms will appear in due course.
For the R Core Team
Peter Dalgaard
These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:
MD5 (AUTHORS) = ac9746b4845ae866661f51cfc99262f5
MD5 (COPYING) = eb723b61539feef013de476e68b5c50a
MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343
MD5 (FAQ) = 3cbcd5d33708d03431cd13f695d1bcb0
MD5 (INSTALL) = 70447ae7f2c35233d3065b004aa4f331
MD5 (NEWS) = de39d09adf2c02e573722507c610d0f6
MD5 (ONEWS) = 0c3e10eef74439786e5fceddd06dac71
MD5 (OONEWS) = b0d650eba25fc5664980528c147a20db
MD5 (R-latest.tar.gz) = ecfb928067cfd932e75135f8b8bba3e7
MD5 (README) = 296871fcf14f49787910c57b92655c76
MD5 (RESOURCES) = 020479f381d5f9038dcb18708997f5da
MD5 (THANKS) = 03d783ff71270c77d497fd573d711fd8
MD5 (R-2/R-2.13.0.tar.gz) = ecfb928067cfd932e75135f8b8bba3e7
This is the relevant part of the NEWS file:
R News
CHANGES IN R VERSION 2.13.0:
SIGNIFICANT USER-VISIBLE CHANGES:
? replicate() (by default) and vapply() (always) now return a
higher-dimensional array instead of a matrix in the case where
the inner function value is an array of dimension >= 2.
? Printing and formatting of floating point numbers is now using
the correct number of digits, where it previously rarely differed
by a few digits. (See ?scientific? entry below.) This affects
_many_ *.Rout.save checks in packages.
NEW FEATURES:
? normalizePath() has been moved to the base package (from utils):
this is so it can be used by library() and friends.
It now does tilde expansion.
It gains new arguments winslash (to select the separator on
Windows) and mustWork to control the action if a canonical path
cannot be found.
? The previously barely documented limit of 256 bytes on a symbol
name has been raised to 10,000 bytes (a sanity check). Long
symbol names can sometimes occur when deparsing expressions (for
example, in model.frame).
? reformulate() gains a intercept argument.
? cmdscale(add = FALSE) now uses the more common definition that
there is a representation in n-1 or less dimensions, and only
dimensions corresponding to positive eigenvalues are used.
(Avoids confusion such as PR#14397.)
? Names used by c(), unlist(), cbind() and rbind() are marked with
an encoding when this can be ascertained.
? R colours are now defined to refer to the sRGB color space.
The PDF, PostScript, and Quartz graphics devices record this
fact. X11 (and Cairo) and Windows just assume that your screen
conforms.
? system.file() gains a mustWork argument (suggestion of Bill
Dunlap).
? new.env(hash = TRUE) is now the default.
? list2env(envir = NULL) defaults to hashing (with a suitably sized
environment) for lists of more than 100 elements.
? text() gains a formula method.
? IQR() now has a type argument which is passed to quantile().
? as.vector(), as.double() etc duplicate less when they leave the
mode unchanged but remove attributes.
as.vector(mode = "any") no longer duplicates when it does not
remove attributes. This helps memory usage in matrix() and
array().
matrix() duplicates less if data is an atomic vector with
attributes such as names (but no class).
dim(x) <- NULL duplicates less if x has neither dimensions nor
names (since this operation removes names and dimnames).
? setRepositories() gains an addURLs argument.
? chisq.test() now also returns a stdres component, for
standardized residuals (which have unit variance, unlike the
Pearson residuals).
? write.table() and friends gain a fileEncoding argument, to
simplify writing files for use on other OSes (e.g. a spreadsheet
intended for Windows or Mac OS X Excel).
? Assignment expressions of the form foo::bar(x) <- y and
foo:::bar(x) <- y now work; the replacement functions used are
foo::`bar<-` and foo:::`bar<-`.
? Sys.getenv() gains a names argument so Sys.getenv(x, names =
FALSE) can replace the common idiom of as.vector(Sys.getenv()).
The default has been changed to not name a length-one result.
? Lazy loading of environments now preserves attributes and locked
status. (The locked status of bindings and active bindings are
still not preserved; this may be addressed in the future).
? options("install.lock") may be set to FALSE so that
install.packages() defaults to --no-lock installs, or (on
Windows) to TRUE so that binary installs implement locking.
? sort(partial = p) for large p now tries Shellsort if quicksort is
not appropriate and so works for non-numeric atomic vectors.
? sapply() gets a new option simplify = "array" which returns a
?higher rank? array instead of just a matrix when FUN() returns a
dim() length of two or more.
replicate() has this option set by default, and vapply() now
behaves that way internally.
? aperm() becomes S3 generic and gets a table method which
preserves the class.
? merge() and as.hclust() methods for objects of class "dendrogram"
are now provided.
? as.POSIXlt.factor() now passes ... to the character method
(suggestion of Joshua Ulrich).
? The character method of as.POSIXlt() now tries to find a format
that works for all non-NA inputs, not just the first one.
? str() now has a method for class "Date" analogous to that for
class "POSIXt".
? New function file.link() to create hard links on those file
systems (POSIX, NTFS but not FAT) that support them.
? New Summary() group method for class "ordered" implements min(),
max() and range() for ordered factors.
? mostattributes<-() now consults the "dim" attribute and not the
dim() function, making it more useful for objects (such as data
frames) from classes with methods for dim(). It also uses
attr<-() in preference to the generics name<-(), dim<-() and
dimnames<-(). (Related to PR#14469.)
? There is a new option "browserNLdisabled" to disable the use of
an empty (e.g. via the ?Return? key) as a synonym for c in
browser() or n under debug(). (Wish of PR#14472.)
? example() gains optional new arguments character.only and
give.lines enabling programmatic exploration.
? serialize() and unserialize() are no longer described as
?experimental?. The interface is now regarded as stable,
although the serialization format may well change in future
releases. (serialize() has a new argument version which would
allow the current format to be written if that happens.)
New functions saveRDS() and readRDS() are public versions of the
?internal? functions .saveRDS() and .readRDS() made available for
general use. The dot-name versions remain available as several
package authors have made use of them, despite the documentation.
saveRDS() supports compress = "xz".
? Many functions when called with a not-open connection will now
ensure that the connection is left not-open in the event of
error. These include read.dcf(), dput(), dump(), load(),
parse(), readBin(), readChar(), readLines(), save(), writeBin(),
writeChar(), writeLines(), .readRDS(), .saveRDS() and
tools::parse_Rd(), as well as functions calling these.
? Public functions find.package() and path.package() replace the
internal dot-name versions.
? The default method for terms() now looks for a "terms" attribute
if it does not find a "terms" component, and so works for model
frames.
? httpd() handlers receive an additional argument containing the
full request headers as a raw vector (this can be used to parse
cookies, multi-part forms etc.). The recommended full signature
for handlers is therefore function(url, query, body, headers,
...).
? file.edit() gains a fileEncoding argument to specify the encoding
of the file(s).
? The format of the HTML package listings has changed. If there is
more than one library tree , a table of links to libraries is
provided at the top and bottom of the page. Where a library
contains more than 100 packages, an alphabetic index is given at
the top of the section for that library. (As a consequence,
package names are now sorted case-insensitively whatever the
locale.)
? isSeekable() now returns FALSE on connections which have
non-default encoding. Although documented to record if ?in
principle? the connection supports seeking, it seems safer to
report FALSE when it may not work.
? R CMD REMOVE and remove.packages() now remove file R.css when
removing all remaining packages in a library tree. (Related to
the wish of PR#14475: note that this file is no longer
installed.)
? unzip() now has a unzip argument like zip.file.extract(). This
allows an external unzip program to be used, which can be useful
to access features supported by Info-ZIP's unzip version 6 which
is now becoming more widely available.
? There is a simple zip() function, as wrapper for an external zip
command.
? bzfile() connections can now read from concatenated bzip2 files
(including files written with bzfile(open = "a")) and files
created by some other compressors (such as the example of
PR#14479).
? The primitive function c() is now of type BUILTIN.
? plot(<dendrogram>, .., nodePar=*) now obeys an optional xpd
specification (allowing clipping to be turned off completely).
? nls(algorithm="port") now shares more code with nlminb(), and is
more consistent with the other nls() algorithms in its return
value.
? xz has been updated to 5.0.1 (very minor bugfix release).
? image() has gained a logical useRaster argument allowing it to
use a bitmap raster for plotting a regular grid instead of
polygons. This can be more efficient, but may not be supported by
all devices. The default is FALSE.
? list.files()/dir() gains a new argument include.dirs() to include
directories in the listing when recursive = TRUE.
? New function list.dirs() lists all directories, (even empty
ones).
? file.copy() now (by default) copies read/write/execute
permissions on files, moderated by the current setting of
Sys.umask().
? Sys.umask() now accepts mode = NA and returns the current umask
value (visibly) without changing it.
? There is a ! method for classes "octmode" and "hexmode": this
allows xor(a, b) to work if both a and b are from one of those
classes.
? as.raster() no longer fails for vectors or matrices containing
NAs.
? New hook "before.new.plot" allows functions to be run just before
advancing the frame in plot.new, which is potentially useful for
custom figure layout implementations.
? Package tools has a new function compactPDF() to try to reduce
the size of PDF files _via_ qpdf or gs.
? tar() has a new argument extra_flags.
? dotchart() accepts more general objects x such as 1D tables which
can be coerced by as.numeric() to a numeric vector, with a
warning since that might not be appropriate.
? The previously internal function create.post() is now exported
from utils, and the documentation for bug.report() and
help.request() now refer to that for create.post().
It has a new method = "mailto" on Unix-alikes similar to that on
Windows: it invokes a default mailer via open (Mac OS X) or
xdg-open or the default browser (elsewhere).
The default for ccaddress is now getOption("ccaddress") which is
by default unset: using the username as a mailing address
nowadays rarely works as expected.
? The default for options("mailer") is now "mailto" on all
platforms.
? unlink() now does tilde-expansion (like most other file
functions).
? file.rename() now allows vector arguments (of the same length).
? The "glm" method for logLik() now returns an "nobs" attribute
(which stats4::BIC() assumed it did).
The "nls" method for logLik() gave incorrect results for zero
weights.
? There is a new generic function nobs() in package stats, to
extract from model objects a suitable value for use in BIC
calculations. An S4 generic derived from it is defined in
package stats4.
? Code for S4 reference-class methods is now examined for possible
errors in non-local assignments.
? findClasses, getGeneric, findMethods and hasMethods are revised
to deal consistently with the package= argument and be consistent
with soft namespace policy for finding objects.
? tools::Rdiff() now has the option to return not only the status
but a character vector of observed differences (which are still
by default sent to stdout).
? The startup environment variables R_ENVIRON_USER, R_ENVIRON,
R_PROFILE_USER and R_PROFILE are now treated more consistently.
In all cases an empty value is considered to be set and will stop
the default being used, and for the last two tilde expansion is
performed on the file name. (Note that setting an empty value is
probably impossible on Windows.)
? Using R --no-environ CMD, R --no-site-file CMD or R
--no-init-file CMD sets environment variables so these settings
are passed on to child R processes, notably those run by INSTALL,
check and build. R --vanilla CMD sets these three options (but
not --no-restore).
? smooth.spline() is somewhat faster. With cv=NA it allows some
leverage computations to be skipped,
? The internal (C) function scientific(), at the heart of R's
format.info(x), format(x), print(x), etc, for numeric x, has been
re-written in order to provide slightly more correct results,
fixing PR#14491, notably in border cases including when digits >=
16, thanks to substantial contributions (code and experiments)
from Petr Savicky. This affects a noticable amount of numeric
output from R.
? A new function grepRaw() has been introduced for finding subsets
of raw vectors. It supports both literal searches and regular
expressions.
? Package compiler is now provided as a standard package. See
?compiler::compile for information on how to use the compiler.
This package implements a byte code compiler for R: by default
the compiler is not used in this release. See the ?R
Installation and Administration Manual? for how to compile the
base and recommended packages.
? Providing an exportPattern directive in a NAMESPACE file now
causes classes to be exported according to the same pattern, for
example the default from package.skeleton() to specify all names
starting with a letter. An explicit directive to
exportClassPattern will still over-ride.
? There is an additional marked encoding "bytes" for character
strings. This is intended to be used for non-ASCII strings which
should be treated as a set of bytes, and never re-encoded as if
they were in the encoding of the currrent locale: useBytes = TRUE
is autmatically selected in functions such as writeBin(),
writeLines(), grep() and strsplit().
Only a few character operations are supported (such as substr()).
Printing, format() and cat() will represent non-ASCII bytes in
such strings by a \xab escape.
? The new function removeSource() removes the internally stored
source from a function.
? "srcref" attributes now include two additional line number
values, recording the line numbers in the order they were parsed.
? New functions have been added for source reference access:
getSrcFilename(), getSrcDirectory(), getSrcLocation() and
getSrcref().
? Sys.chmod() has an extra argument use_umask which defaults to
true and restricts the file mode by the current setting of umask.
This means that all the R functions which manipulate
file/directory permissions by default respect umask, notably R
CMD INSTALL.
? tempfile() has an extra argument fileext to create a temporary
filename with a specified extension. (Suggestion and initial
implementation by Dirk Eddelbuettel.)
There are improvements in the way Sweave() and Stangle() handle
non-ASCII vignette sources, especially in a UTF-8 locale: see
?Writing R Extensions? which now has a subsection on this topic.
? factanal() now returns the rotation matrix if a rotation such as
"promax" is used, and hence factor correlations are displayed.
(Wish of PR#12754.)
? The gctorture2() function provides a more refined interface to
the GC torture process. Environment variables R_GCTORTURE,
R_GCTORTURE_WAIT, and R_GCTORTURE_INHIBIT_RELEASE can also be
used to control the GC torture process.
? file.copy(from, to) no longer regards it as an error to supply a
zero-length from: it now simply does nothing.
? rstandard.glm gains a type argument which can be used to request
standardized Pearson residuals.
? A start on a Turkish translation, thanks to Murat Alkan.
? .libPaths() calls normalizePath(winslash = "/") on the paths:
this helps (usually) present them in a user-friendly form and
should detect duplicate paths accessed via different symbolic
links.
SWEAVE CHANGES:
? Sweave() has options to produce PNG and JPEG figures, and to use
a custom function to open a graphics device (see ?RweaveLatex).
(Based in part on the contribution of PR#14418.)
? The default for Sweave() is to produce only PDF figures (rather
than both EPS and PDF).
? Environment variable SWEAVE_OPTIONS can be used to supply
defaults for existing or new options to be applied after the
Sweave driver setup has been run.
? The Sweave manual is now included as a vignette in the utils
package.
? Sweave() handles keep.source=TRUE much better: it could duplicate
some lines and omit comments. (Reported by John Maindonald and
others.)
C-LEVEL FACILITIES:
? Because they use a C99 interface which a C++ compiler is not
required to support, Rvprintf and REvprintf are only defined by
R_ext/Print.h in C++ code if the macro R_USE_C99_IN_CXX is
defined when it is included.
? pythag duplicated the C99 function hypot. It is no longer
provided, but is used as a substitute for hypot in the very
unlikely event that the latter is not available.
? R_inspect(obj) and R_inspect3(obj, deep, pvec) are (hidden)
C-level entry points to the internal inspect function and can be
used for C-level debugging (e.g., in conjunction with the p
command in gdb).
? Compiling R with --enable-strict-barrier now also enables
additional checking for use of unprotected objects. In
combination with gctorture() or gctorture2() and a C-level
debugger this can be useful for tracking down memory protection
issues.
UTILITIES:
? R CMD Rdiff is now implemented in R on Unix-alikes (as it has
been on Windows since R 2.12.0).
? R CMD build no longer does any cleaning in the supplied package
directory: all the cleaning is done in the copy.
It has a new option --install-args to pass arguments to R CMD
INSTALL for --build (but not when installing to rebuild
vignettes).
There is new option, --resave-data, to call
tools::resaveRdaFiles() on the data directory, to compress
tabular files (.tab, .csv etc) and to convert .R files to .rda
files. The default, --resave-data=gzip, is to do so in a way
compatible even with years-old versions of R, but better
compression is given by --resave-data=best, requiring R >=
2.10.0.
It now adds a datalist file for data directories of more than
1Mb.
Patterns in .Rbuildignore are now also matched against all
directory names (including those of empty directories).
There is a new option, --compact-vignettes, to try reducing the
size of PDF files in the inst/doc directory. Currently this
tries qpdf: other options may be used in future.
When re-building vignettes and a inst/doc/Makefile file is found,
make clean is run if the makefile has a clean: target.
After re-building vignettes the default clean-up operation will
remove any directories (and not just files) created during the
process: e.g. one package created a .R_cache directory.
Empty directories are now removed unless the option
--keep-empty-dirs is given (and a few packages do deliberately
include empty directories).
If there is a field BuildVignettes in the package DESCRIPTION
file with a false value, re-building the vignettes is skipped.
? R CMD check now also checks for filenames that are
case-insensitive matches to Windows' reserved file names with
extensions, such as nul.Rd, as these have caused problems on some
Windows systems.
It checks for inefficiently saved data/*.rda and data/*.RData
files, and reports on those large than 100Kb. A more complete
check (including of the type of compression, but potentially much
slower) can be switched on by setting environment variable
_R_CHECK_COMPACT_DATA2_ to TRUE.
The types of files in the data directory are now checked, as
packages are _still_ misusing it for non-R data files.
It now extracts and runs the R code for each vignette in a
separate directory and R process: this is done in the package's
declared encoding. Rather than call tools::checkVignettes(), it
calls tool::buildVignettes() to see if the vignettes can be
re-built as they would be by R CMD build. Option --use-valgrind
now applies only to these runs, and not when running code to
rebuild the vignettes. This version does a much better job of
suppressing output from successful vignette tests.
The 00check.log file is a more complete record of what is output
to stdout: in particular contains more details of the tests.
It now check all syntactically valid Rd usage entries, and warns
about assignments (unless these give the usage of replacement
functions).
.tar.xz compressed tarballs are now allowed, if tar supports them
(and setting environment variable TAR to internal ensures so on
all platforms).
? R CMD check now warns if it finds inst/doc/makefile, and R CMD
build renames such a file to inst/doc/Makefile.
INSTALLATION:
? Installing R no longer tries to find perl, and R CMD no longer
tries to substitute a full path for awk nor perl - this was a
legacy from the days when they were used by R itself. Because a
couple of packages do use awk, it is set as the make (rather than
environment) variable AWK.
? make check will now fail if there are differences from the
reference output when testing package examples and if environment
variable R_STRICT_PACKAGE_CHECK is set to a true value.
? The C99 double complex type is now required.
The C99 complex trigonometric functions (such as csin) are not
currently required (FreeBSD lacks most of them): substitutes are
used if they are missing.
? The C99 system call va_copy is now required.
? If environment variable R_LD_LIBRARY_PATH is set during
configuration (for example in config.site) it is used unchanged
in file etc/ldpaths rather than being appended to.
? configure looks for support for OpenMP and if found compiles R
with appropriate flags and also makes them available for use in
packages: see ?Writing R Extensions?.
This is currently experimental, and is only used in R with a
single thread for colSums() and colMeans(). Expect it to be more
widely used in later versions of R.
This can be disabled by the --disable-openmp flag.
PACKAGE INSTALLATION:
? R CMD INSTALL --clean now removes copies of a src directory which
are created when multiple sub-architectures are in use.
(Following a comment from Berwin Turlach.)
? File R.css is now installed on a per-package basis (in the
package's html directory) rather than in each library tree, and
this is used for all the HTML pages in the package. This helps
when installing packages with static HTML pages for use on a
webserver. It will also allow future versions of R to use
different stylesheets for the packages they install.
? A top-level file .Rinstignore in the package sources can list (in
the same way as .Rbuildignore) files under inst that should not
be installed. (Why should there be any such files? Because all
the files needed to re-build vignettes need to be under inst/doc,
but they may not need to be installed.)
? R CMD INSTALL has a new option --compact-docs to compact any PDFs
under the inst/doc directory. Currently this uses qpdf, which
must be installed (see ?Writing R Extensions?).
? There is a new option --lock which can be used to cancel the
effect of --no-lock or --pkglock earlier on the command line.
? Option --pkglock can now be used with more than one package, and
is now the default if only one package is specified.
? Argument lock of install.packages() can now be use for Mac binary
installs as well as for Windows ones. The value "pkglock" is now
accepted, as well as TRUE and FALSE (the default).
? There is a new option --no-clean-on-error for R CMD INSTALL to
retain a partially installed package for forensic analysis.
? Packages with names ending in . are not portable since Windows
does not work correctly with such directory names. This is now
warned about in R CMD check, and will not be allowed in R 2.14.x.
? The vignette indices are more comprehensive (in the style of
browseVignetttes()).
DEPRECATED & DEFUNCT:
? require(save = TRUE) is defunct, and use of the save argument is
deprecated.
? R CMD check --no-latex is defunct: use --no-manual instead.
? R CMD Sd2Rd is defunct.
? The gamma argument to hsv(), rainbow(), and rgb2hsv() is
deprecated and no longer has any effect.
? The previous options for R CMD build --binary (--auto-zip,
--use-zip-data and --no-docs) are deprecated (or defunct): use
the new option --install-args instead.
? When a character value is used for the EXPR argument in switch(),
only a single unnamed alternative value is now allowed.
? The wrapper utils::link.html.help() is no longer available.
? Zip-ing data sets in packages (and hence R CMD INSTALL options
--use-zip-data and --auto-zip, as well as the ZipData: yes field
in a DESCRIPTION file) is defunct.
Installed packages with zip-ed data sets can still be used, but a
warning that they should be re-installed will be given.
? The ?experimental? alternative specification of a name space via
.Export() etc is now defunct.
? The option --unsafe to R CMD INSTALL is deprecated: use the
identical option --no-lock instead.
? The entry point pythag in Rmath.h is deprecated in favour of the
C99 function hypot. A wrapper for hypot is provided for R 2.13.x
only.
? Direct access to the "source" attribute of functions is
deprecated; use deparse(fn, control="useSource") to access it,
and removeSource(fn) to remove it.
? R CMD build --binary is now formally deprecated: R CMD INSTALL
--build has long been the preferred alternative.
? Single-character package names are deprecated (and R is already
disallowed to avoid confusion in Depends: fields).
BUG FIXES:
? drop.terms and the [ method for class "terms" no longer add back
an intercept. (Reported by Niels Hansen.)
? aggregate preserves the class of a column (e.g. a date) under
some circumstances where it discarded the class previously.
? p.adjust() now always returns a vector result, as documented. In
previous versions it copied attributes (such as dimensions) from
the p argument: now it only copies names.
? On PDF and PostScript devices, a line width of zero was recorded
verbatim and this caused problems for some viewers (a very thin
line combined with a non-solid line dash pattern could also cause
a problem). On these devices, the line width is now limited at
0.01 and for very thin lines with complex dash patterns the
device may force the line dash pattern to be solid. (Reported by
Jari Oksanen.)
? The str() method for class "POSIXt" now gives sensible output for
0-length input.
? The one- and two-argument complex maths functions failed to warn
if NAs were generated (as their numeric analogues do).
? Added .requireCachedGenerics to the dont.mind list for library()
to avoid warnings about duplicates.
? $<-.data.frame messed with the class attribute, breaking any S4
subclass. The S4 data.frame class now has its own $<- method,
and turns dispatch on for this primitive.
? Map() did not look up a character argument f in the correct
frame, thanks to lazy evaluation. (PR#14495)
? file.copy() did not tilde-expand from and to when to was a
directory. (PR#14507)
? It was possible (but very rare) for the loading test in R CMD
INSTALL to crash a child R process and so leave around a lock
directory and a partially installed package. That test is now
done in a separate process.
? plot(<formula>, data=<matrix>,..) now works in more cases;
similarly for points(), lines() and text().
? edit.default() contained a manual dispatch for matrices (the
"matrix" class didn't really exist when it was written). This
caused an infinite recursion in the no-GUI case and has now been
removed.
? data.frame(check.rows = TRUE) sometimes worked when it should
have detected an error. (PR#14530)
? scan(sep= , strip.white=TRUE) sometimes stripped trailing spaces
from within quoted strings. (The real bug in PR#14522.)
? The rank-correlation methods for cor() and cov() with use =
"complete.obs" computed the ranks before removing missing values,
whereas the documentation implied incomplete cases were removed
first. (PR#14488)
They also failed for 1-row matrices.
? The perpendicular adjustment used in placing text and expressions
in the margins of plots was not scaled by par("mex"). (Part of
PR#14532.)
? Quartz Cocoa device now catches any Cocoa exceptions that occur
during the creation of the device window to prevent crashes. It
also imposes a limit of 144 ft^2 on the area used by a window to
catch user errors (unit misinterpretation) early.
? The browser (invoked by debug(), browser() or otherwise) would
display attributes such as "wholeSrcref" that were intended for
internal use only.
? R's internal filename completion now properly handles filenames
with spaces in them even when the readline library is used. This
resolves PR#14452 provided the internal filename completion is
used (e.g., by setting rc.settings(files = TRUE)).
? Inside uniroot(f, ...), -Inf function values are now replaced by
a maximally *negative* value.
? rowsum() could silently over/underflow on integer inputs
(reported by Bill Dunlap).
? as.matrix() did not handle "dist" objects with zero rows.
CHANGES IN R VERSION 2.12.2 patched:
NEW FEATURES:
? max() and min() work harder to ensure that NA has precedence over
NaN, so e.g. min(NaN, NA) is NA. (This was not previously
documented except for within a single numeric vector, where
compiler optimizations often defeated the code.)
BUG FIXES:
? A change to the C function R_tryEval had broken error messages in
S4 method selection; the error message is now printed.
? PDF output with a non-RGB color model used RGB for the line
stroke color. (PR#14511)
? stats4::BIC() assumed without checking that an object of class
"logLik" has an "nobs" attribute: glm() fits did not and so BIC()
failed for them.
? In some circumstances a one-sided mantelhaen.test() reported the
p-value for the wrong tail. (PR#14514)
? Passing the invalid value lty = NULL to axis() sent an invalid
value to the graphics device, and might cause the device to
segfault.
? Sweave() with concordance=TRUE could lead to invalid PDF files;
Sweave.sty has been updated to avoid this.
? Non-ASCII characters in the titles of help pages were not
rendered properly in some locales, and could cause errors or
warnings.
? checkRd() gave a spurious error if the \href macro was used.
--
Peter Dalgaard
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
|
R 2.13.0 is released
|
Peter Dalgaard
| 400
|
|
From murdoch.duncan at gmail.com Mon Apr 4 20:05:05 2016
From: murdoch.duncan at gmail.com (Duncan Murdoch)
Date: Mon, 4 Apr 2016 14:05:05 -0400
Subject: [R] Extending the beta period for R 3.3.0 till April 25, Final
release on May 3
In-Reply-To: <[email protected]>
References: <[email protected]>
Message-ID: <[email protected]>
On 02/04/2016 11:58 AM, Peter Dalgaard wrote:
> Due to delays in implementing an updated Windows toolchain for CRAN, R Core has found it unsafe to go with our usual 1-week beta testing period. Combined with other scheduling issues, we have decided to postpone the transition to 3.3.0 RC until April 26, with the final release happening on May 3.
>
> Apologies for any inconvenience, but it is really rather important to get this right before the release of 3.3.0. One cannot mix and match binaries from different toolchains - CRAN packages binaries for 3.3.x must be all of the same kind. Accordingly, if we have too little time to fix issues discovered in the beta period, we might have to back out and be stuck with the old tools for another year.
>
> Web site updates will happen shortly.
I have finally added a public link to the binary build of the 3.3.0
beta. (It may take a few hours before it makes it to the visible
machines on CRAN.) It will work with binary builds of many packages,
but definitely not with those that use C++ unless they were built with
the same toolchain.
In case you want to get it before the link is visible, here it is on one
mirror:
http://cran.rstudio.com/bin/windows/base/rtest.html
Duncan Murdoch
|
[R] Extending the beta period for R 3.3.0 till April 25, Final release on May 3
|
Duncan Murdoch
| 122
|
|
From maechler at stat.math.ethz.ch Mon Sep 15 17:07:09 2003
From: maechler at stat.math.ethz.ch (Martin Maechler)
Date: Mon, 15 Sep 2003 17:07:09 +0200
Subject: Fourth R Mailing List : "R-packages"
Message-ID: <[email protected]>
We (mainly the R core team) have been discussing the creation of another
R mailing list, with the goal to fill the gap between
R-help very high volume, with its great merits, but....
and
R-announce only for R important announcements (mostly R-core)
hence __MODERATED__ and *very* low volume, and hence
highly recommended for almost all users of R.
*** all messages are forwarded to R-help ***
In the past, several CRAN package authors have rightly felt that
they would like the announcement of a major update of a package
be a bit more prominent than the flood of messages on R-help but
(most of the time) they still weren't supposed nor granted to
use R-announce for this. This has been one main motivation for
this new mailing list:
R-packages o all messages forwarded to R-help
o moderated (i.e. not accepting posts by anyone),
but CRAN package authors (and others,
similarly qualified) can freely post without
moderator interaction {unless there's abuse}.
The corresponding (new) web page,
http://www.stat.math.ethz.ch/mailman/listinfo/r-packages/
now has
TITLE: R Packages & Extensions Announcements
DESCRIPTION :
A moderated board for announcements about contributed R packages
and similar R project extensions.
All messages are forwarded to R-help automatically, so please do
not subscribe to this list if you are subscribed to R-help.
For major announcements on the R project, see the R-announce
mailing list, instead.
And R-project.org's "Mailing Lists" web page will describe it
from tomorrow as
>> R-packages
>>
>> This list is for announcements as well, usually on the
>> availability of new or enhanced contributed packages (on CRAN, typically).
>>
>> Note that the list is moderated. However, CRAN package
>> authors (and others, similarly qualified) can freely post.
>>
>> As with R-announce, all messages to R-packages are
>> automatically forwarded to the main R-help mailing list;
>> hence you should only subscribe to R-packages if you do not
>> to R-help.
>>
>> Use the web interface for information, subscription, archives, etc.
Amount of mail to expect: Of course, we don't know yet, but
I'd expect to see only a few messages per week.
Finally, just re-iterating the obvious:
o This is *NOT* a list for discussion, just announcements of extensions to R.
o Do only subscribe if you are *NOT* subscribed to R-help,
(but then, strongly consider doing it)!
For more info, subscription, etc, please use the URL above
Your R mailing list maintainer,
Martin Maechler <maechler at stat.math.ethz.ch> http://stat.ethz.ch/~maechler/
Seminar fuer Statistik, ETH-Zentrum LEO C16 Leonhardstr. 27
ETH (Federal Inst. Technology) 8092 Zurich SWITZERLAND
phone: x-41-1-632-3408 fax: ...-1228 <><
|
Fourth R Mailing List : "R-packages"
|
Martin Maechler
| 183
|
|
From pd.mes at cbs.dk Thu Jun 18 11:04:58 2015
From: pd.mes at cbs.dk (Peter Dalgaard)
Date: Thu, 18 Jun 2015 11:04:58 +0200
Subject: R 3.2.1 liftoff
Message-ID: <[email protected]>
The build system sent R-3.2.1.tar.gz (codename "World-Famous Astronaut") in orbit this morning.
The list below details the changes in this release.
You can get the source code from
http://cran.r-project.org/src/base/R-3/R-3.2.1.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you.
Binaries for various platforms will appear in due course.
For the R Core Team,
Peter Dalgaard
These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:
MD5 (AUTHORS) = eb97a5cd38acb1cfc6408988bffef765
MD5 (COPYING) = eb723b61539feef013de476e68b5c50a
MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343
MD5 (FAQ) = 181370b39076e34f64b842257076cd5c
MD5 (INSTALL) = 3964b9119adeaab9ceb633773fc94aac
MD5 (NEWS) = 6342bc1164e9f8e17713f47cff1910b4
MD5 (NEWS.0) = bfcd7c147251b5474d96848c6f57e5a8
MD5 (NEWS.1) = eb78c4d053ec9c32b815cf0c2ebea801
MD5 (NEWS.2) = 8e2f4d1d5228663ae598a09bf1e2bc6b
MD5 (R-latest.tar.gz) = c2aac8b40f84e08e7f8c9068de9239a3
MD5 (README) = aece1dfbd18c1760128c3787f5456af6
MD5 (RESOURCES) = a59076c1ac7e9bab0f0a38b3f57a3914
MD5 (THANKS) = ba00f6cc68a823e1741cfa6011f40ccb
MD5 (R-3/R-3.2.1.tar.gz) = c2aac8b40f84e08e7f8c9068de9239a3
This is the relevant part of the NEWS file
CHANGES IN R 3.2.1:
NEW FEATURES:
* utf8ToInt() now checks that its input is valid UTF-8 and returns
NA if it is not.
* install.packages() now allows type = "both" with repos = NULL if
it can infer the type of file.
* nchar(x, *) and nzchar(x) gain a new argument keepNA which
governs how the result for NAs in x is determined. For the R
3.2.x series, the default remains FALSE which is fully back
compatible. From R 3.3.0, the default will change to keepNA = NA
and you are advised to consider this for code portability.
* news() more flexibly extracts dates from package NEWS.Rd files.
* lengths(x) now also works (trivially) for atomic x and hence can
be used more generally as an efficient replacement of sapply(x,
length) and similar.
* The included version of PCRE has been updated to 8.37, a bug-fix
release.
* diag() no longer duplicates a matrix when extracting its
diagonal.
* as.character.srcref() gains an argument to allow characters
corresponding to a range of source references to be extracted.
BUG FIXES:
* acf() and ccf() now guarantee values strictly in [-1,1] (instead
of sometimes very slightly outside). PR#15832.
* as.integer("111111111111") now gives NA (with a warning) as it
does for the corresponding numeric or negative number coercions.
Further, as.integer(M + 0.1) now gives M (instead of NA) when M
is the maximal representable integer.
* On some platforms nchar(x, "c") and nchar(x, "w") would return
values (possibly NA) for inputs which were declared to be UTF-8
but were not, or for invalid strings without a marked encoding in
a multi-byte locale, rather than give an error. Additional
checks have been added to mitigate this.
* apply(a, M, function(u) c(X = ., Y = .)) again has dimnames
containing "X" and "Y" (as in R < 3.2.0).
* (Windows only) In some cases, the --clean option to R CMD INSTALL
could fail. (PR#16178)
* (Windows only) choose.files() would occasionally include
characters from the result of an earlier call in the result of a
later one. (PR#16270)
* A change in RSiteSearch() in R 3.2.0 caused it to submit invalid
URLs. (PR#16329)
* Rscript and command line R silently ignored incomplete statements
at the end of a script; now they are reported as parse errors.
(PR#16350)
* Parse data for very long strings was not stored. (PR#16354)
* plotNode(), the workhorse of the plot method for "dendrogram"s is
no longer recursive, thanks to Suharto Anggono, and hence also
works for deeply nested dendrograms. (PR#15215)
* The parser could overflow internally when given numbers in
scientific format with extremely large exponents. (PR#16358)
* If the CRAN mirror was not set, install.packages(type = "both")
and related functions could repeatedly query the user for it.
(Part of PR#16362)
* The low-level functions .rowSums() etc. did not check the length
of their argument, so could segfault. (PR#16367)
* The quietly argument of library() is now correctly propagated
from .getRequiredPackages2().
* Under some circumstances using the internal PCRE when building R
fron source would cause external libs such as -llzma to be
omitted from the main link.
* The .Primitive default methods of the logic operators, i.e., !, &
and |, now give correct error messages when appropriate, e.g.,
for `&`(TRUE) or `!`(). (PR#16385)
* cummax(x) now correctly propagates NAs also when x is of type
integer and begins with an NA.
* summaryRprof() could fail when the profile contained only two
records. (PR#16395)
* HTML vignettes opened using vignette() did not support links into
the rest of the HTML help system. (Links worked properly when
the vignette was opened using browseVignettes() or from within
the help system.)
* arima(*, xreg = .) (for d >= 1) computes estimated variances
based on a the number of effective observations as in R version
3.0.1 and earlier. (PR#16278)
* slotNames(.) is now correct for "signature" objects (mostly used
internally in methods).
* On some systems, the first string comparison after a locale
change would result in NA.
|
R 3.2.1 liftoff
|
Peter Dalgaard
| 202
|
|
From pd.mes at cbs.dk Fri Mar 30 11:07:41 2012
From: pd.mes at cbs.dk (Peter Dalgaard)
Date: Fri, 30 Mar 2012 11:07:41 +0200
Subject: R 2.15.0 is released
Message-ID: <[email protected]>
The build system rolled up R-2.15.0.tar.gz (codename "Easter Beagle") at 9:00 this morning. This is the first release of the 2.15 series and contains several new features and changes; see the list below for details.
You can get the source code from
http://cran.r-project.org/src/base/R-2/R-2.15.0.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you.
Binaries for various platforms will appear in due course.
For the R Core Team
Peter Dalgaard
These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:
MD5 (AUTHORS) = cbf6da8f886ccd8d0dda0cc7ffd1b8ec
MD5 (COPYING) = eb723b61539feef013de476e68b5c50a
MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343
MD5 (FAQ) = c6cf7cff235e9bd3c823e6a1a3d76cd5
MD5 (INSTALL) = 37adac6d0fbadf25b5a40e3f7535415e
MD5 (NEWS) = 31dee994d35636656c9e254bfb819d7c
MD5 (NEWS.html) = 0551e23b675fa9dc709830d1a4ee738c
MD5 (ONEWS) = 0c3e10eef74439786e5fceddd06dac71
MD5 (OONEWS) = b0d650eba25fc5664980528c147a20db
MD5 (R-latest.tar.gz) = 905f638990492618559202cc1e48a867
MD5 (README) = 296871fcf14f49787910c57b92655c76
MD5 (RESOURCES) = a7a02d98a407c3cb8674d067608f14fc
MD5 (THANKS) = 159efc7bd4ae7b23dda07c1d431657bc
MD5 (R-2/R-2.15.0.tar.gz) = 905f638990492618559202cc1e48a867
This is the relevant part of the NEWS file
CHANGES IN R VERSION 2.15.0:
SIGNIFICANT USER-VISIBLE CHANGES:
o The behaviour of unlink(recursive = TRUE) for a symbolic link to
a directory has changed: it now removes the link rather than the
directory contents (just as rm -r does).
On Windows it no longer follows reparse points (including
junctions and symbolic links).
NEW FEATURES:
o Environment variable RD2DVI_INPUTENC has been renamed to
RD2PDF_INPUTENC.
o .Deprecated() becomes a bit more flexible, getting an old
argument.
o Even data-only packages without R code need a namespace and so
may need to be installed under R 2.14.0 or later.
o assignInNamespace() has further restrictions on use apart from at
top-level, as its help page has warned. Expect it to be disabled
from programmatic use in the future.
o system() and system2() when capturing output report a non-zero
status in the new "status" attribute.
o kronecker() now has an S4 generic in package methods on which
packages can set methods. It will be invoked by X %x% Y if
either X or Y is an S4 object.
o pdf() accepts forms like file = "|lpr" in the same way as
postscript().
o pdf() accepts file = NULL. This means that the device does NOT
create a PDF file (but it can still be queried, e.g., for font
metric info).
o format() (and hence print()) on "bibentry" objects now uses
options("width") to set the output width.
o legend() gains a text.font argument. (Suggested by Tim Paine,
PR#14719.)
o nchar() and nzchar() no longer accept factors (as integer
vectors). (Wish of PR#6899.)
o summary() behaves slightly differently (or more precisely, its
print() method does). For numeric inputs, the number of NAs is
printed as an integer and not a real. For dates and datetimes,
the number of NAs is included in the printed output (the latter
being the wish of PR#14720).
The "data.frame" method is more consistent with the default
method: in particular it now applies zapsmall() to
numeric/complex summaries.
o The number of items retained with options(warn = 0) can be set by
options(nwarnings=).
o There is a new function assignInMyNamespace() which uses the
namespace of the function it is called from.
o attach() allows the default name for an attached file to be
overridden.
o bxp(), the work horse of boxplot(), now uses a more sensible
default xlim in the case where at is specified differently from
1:n, see the discussion on R-devel, <URL:
https://stat.ethz.ch/pipermail/r-devel/2011-November/062586.html>.
o New function paste0(), an efficient version of paste(*, sep=""),
to be used in many places for more concise (and slightly more
efficient) code.
o Function setClass() in package methods now returns, invisibly, a
generator function for the new class, slightly preferred to
calling new(), as explained on the setClass help page.
o The "dendrogram" method of str() now takes its default for
last.str from option str.dendrogram.last.
o New simple fitted() method for "kmeans" objects.
o The traceback() function can now be called with an integer
argument, to display a current stack trace. (Wish of PR#14770.)
o setGeneric() calls can be simplified when creating a new generic
function by supplying the default method as the def argument.
See ?setGeneric.
o serialize() has a new option xdr = FALSE which will use the
native byte-order for binary serializations. In scenarios where
only little-endian machines are involved (these days, close to
universal) and (un)serialization takes an appreciable amount of
time this may speed up noticeably transferring data between
systems.
o The internal (un)serialization code is faster for long vectors,
particularly with XDR on some platforms. (Based on a suggested
patch by Michael Spiegel.)
o For consistency, circles with zero radius are omitted by points()
and grid.circle(). Previously this was device-dependent, but
they were usually invisible.
o NROW(x) and NCOL(x) now work whenever dim(x) looks appropriate,
e.g., also for more generalized matrices.
o PCRE has been updated to version 8.30.
o The internal R_Srcref variable is now updated before the browser
stops on entering a function. (Suggestion of PR#14818.)
o There are 'bare-bones' functions .colSums(), .rowSums(),
.colMeans() and .rowMeans() for use in programming where ultimate
speed is required.
o The formerly internal function .package_dependencies() from
package tools for calculating (recursive) (reverse) dependencies
on package databases has been renamed to package_dependencies()
and is now exported.
o There is a new function optimHess() to compute the (approximate)
Hessian for an optim() solution if hessian = TRUE was forgotten.
o .filled.contour() is a 'bare-bones' function to add a
filled-contour rectangular plot to an already prepared plot
region.
o The stepping in debugging and single-step browsing modes has
changed slightly: now left braces at the start of the body are
stepped over for if statements as well as for for and while
statements. (Wish of PR#14814.)
o library() no longer warns about a conflict with a function from
package:base if the function has the same code as the base one
but with a different environment. (An example is Matrix::det().)
o When deparsing very large language objects, as.character() now
inserts newlines after each line of approximately 500 bytes,
rather than truncating to the first line.
o New function rWishart() generates Wishart-distributed random
matrices.
o Packages may now specify actions to be taken when the package is
loaded (setLoadActions()).
o options(max.print = Inf) and similar now give an error (instead
of warnings later).
o The "difftime" replacement method of units tries harder to
preserve other attributes of the argument. (Wish of PR#14839.)
o poly(raw = TRUE) no longer requires more unique points than the
degree. (Requested by John Fox.)
PACKAGE parallel:
o There is a new function mcmapply(), a parallel version of
mapply(), and a wrapper mcMap(), a parallel version of Map().
o A default cluster can be registered by the new function
setDefaultCluster(): this will be used by default in functions
such as parLapply().
o clusterMap() has a new argument .scheduling to allow the use of
load-balancing.
o There are new load-balancing functions parLapplyLB() and
parSapplyLB().
o makePSOCKCluster() has a new option useXDR = FALSE which can be
used to avoid byte-shuffling for serialization when all the nodes
are known to be little-endian (or all big-endian).
PACKAGE INSTALLATION:
o Non-ASCII vignettes without a declared encoding are no longer
accepted.
o C/C++ code in packages is now compiled with -NDEBUG to mitigate
against the C/C++ function assert being called in production use.
Developers can turn this off during package development with
PKG_CPPFLAGS = -UNDEBUG.
o R CMD INSTALL has a new option --dsym which on Mac OS X (Darwin)
dumps the symbols alongside the .so file: this is helpful when
debugging with valgrind (and especially when installing packages
into R.framework). [This can also be enabled by setting the
undocumented environment variable PKG_MAKE_DSYM, since R 2.12.0.]
o R CMD INSTALL will test loading under all installed
sub-architectures even for packages without compiled code, unless
the flag --no-multiarch is used. (Pure R packages can do things
which are architecture-dependent: in the case which prompted
this, looking for an icon in a Windows R executable.)
o There is a new option install.packages(type = "both") which tries
source packages if binary packages are not available, on those
platforms where the latter is the default.
o The meaning of install.packages(dependencies = TRUE) has changed:
it now means to install the essential dependencies of the named
packages plus the Suggests, but only the essential dependencies
of dependencies. To get the previous behaviour, specify
dependencies as a character vector.
o R CMD INSTALL --merge-multiarch is now supported on OS X and
other Unix-alikes using multiple sub-architectures.
o R CMD INSTALL --libs-only now by default does a test load on
Unix-alikes as well as on Windows: suppress with --no-test-load.
UTILITIES:
o R CMD check now gives a warning rather than a note if it finds
inefficiently compressed datasets. With bzip2 and xz compression
having been available since R 2.10.0, it only exceptionally makes
sense to not use them.
The environment variable _R_CHECK_COMPACT_DATA2_ is no longer
consulted: the check is always done if _R_CHECK_COMPACT_DATA_ has
a true value (its default).
o Where multiple sub-architectures are to be tested, R CMD check
now runs the examples and tests for all the sub-architectures
even if one fails.
o R CMD check can optionally report timings on various parts of the
check: this is controlled by environment variable
_R_CHECK_TIMINGS_ documented in 'Writing R Extensions'. Timings
(in the style of R CMD BATCH) are given at the foot of the output
files from running each test and the R code in each vignette.
o There are new options for more rigorous testing by R CMD check
selected by environment variables - see the 'Writing R
Extensions' manual.
o R CMD check now warns (rather than notes) on undeclared use of
other packages in examples and tests: increasingly people are
using the metadata in the DESCRIPTION file to compute information
about packages, for example reverse dependencies.
o The defaults for some of the options in R CMD check (described in
the 'R Internals' manual) have changed: checks for unsafe and
.Internal() calls and for partial matching of arguments in R
function calls are now done by default.
o R CMD check has more comprehensive facilities for checking
compiled code and so gives fewer reports on entry points linked
into .so/.dll files from libraries (including C++ and Fortran
runtimes).
Checking compiled code is now done on FreeBSD (as well as the
existing supported platforms of Linux, Mac OS X, Solaris and
Windows).
o R CMD build has more options for --compact-vignettes: see R CMD
build --help.
o R CMD build has a new option --md5 to add an MD5 file (as done by
CRAN): this is used by R CMD INSTALL to check the integrity of
the distribution.
If this option is not specified, any existing (and probably
stale) MD5 file is removed.
DEPRECATED AND DEFUNCT:
o R CMD Rd2dvi is now defunct: use R CMD Rd2pdf.
o Options such --max-nsize, --max-vsize and the function
mem.limits() are now defunct. (Options --min-nsize and
--min-vsize remain available.)
o Use of library.dynam() without specifying all the first three
arguments is now disallowed.
Use of an argument chname in library.dynam() including the
extension .so or .dll (which was never allowed according to the
help page) is defunct. This also applies to
library.dynam.unload() and to useDynLib directives in NAMESPACE
files.
o The internal functions .readRDS() and .saveRDS() are now defunct.
o The off-line help() types "postscript" and "ps" are defunct.
o Sys.putenv(), replaced and deprecated in R 2.5.0, is finally
removed.
o Some functions/objects which have been defunct for five or more
years have been removed completely. These include .Alias(),
La.chol(), La.chol2inv(), La.eigen(), Machine(), Platform(),
Version, codes(), delay(), format.char(), getenv(), httpclient(),
loadURL(), machine(), parse.dcf(), printNoClass(), provide(),
read.table.url(), restart(), scan.url(), symbol.C(), symbol.For()
and unix().
o The ENCODING argument to .C() is deprecated. It was intended to
smooth the transition to multi-byte character strings, but can be
replaced by the use of iconv() in the rare cases where it is
still needed.
INSTALLATION:
o Building with a positive value of --with-valgrind-instrumentation
now also instruments logical, complex and raw vectors.
o There is experimental support for _link-time optimization_ with
gcc 4.5.0 or later on platforms which support it.
C-LEVEL FACILITIES:
o Passing R objects other than atomic vectors, functions, lists and
environments to .C() is now deprecated and will give a warning.
Most cases (especially NULL) are actually coding errors. NULL
will be disallowed in future.
.C() now passes a pairlist as a SEXP to the compiled code. This
is as was documented, but pairlists were in reality handled
differently as a legacy from the early days of R.
o call_R and call_S are deprecated. They still exist in the
headers and as entry points, but are no longer documented and
should not be used for new code.
BUG FIXES:
o str(x, width) now obeys its width argument also for function
headers and other objects x where deparse() is applied.
o The convention for x %/% 0L for integer-mode x has been changed
from 0L to NA_integer_. (PR#14754)
o The exportMethods directive in a NAMESPACE file now exports S4
generics as necessary, as the extensions manual said it does.
The manual has also been updated to be a little more informative
on this point.
It is now required that there is an S4 generic (imported or
created in the package) when methods are to be exported.
o Reference methods cannot safely use non-exported entries in the
namespace. We now do not do so, and warn in the documentation.
o The namespace import code was warning when identical S4 generic
functions were imported more than once, but should not (reported
by Brian Ripley, then Martin Morgan).
o merge() is no longer allowed (in some ways) to create a data
frame with duplicate column names (which confused PR#14786).
o Fixes for rendering raster images on X11 and Windows devices when
the x-axis or y-axis scale is reversed.
o getAnywhere() found S3 methods as seen from the utils namespace
and not from the environment from which it was called.
o selectMethod(f, sig) would not return inherited group methods
when caching was off (as it is by default).
o dev.copy2pdf(out.type = "cairo") gave an error. (PR#14827)
o Virtual classes (e.g., class unions) had a NULL prototype even if
that was not a legal subclass. See ?setClassUnion.
o The C prototypes for zdotc and zdotu in R_ext/BLAS.h have been
changed to the more modern style rather than that used by f2c.
(Patch by Berwin Turlach.)
o isGeneric() produced an error for primitives that can not have
methods.
o .C() or .Fortran() had a lack-of-protection error if the
registration information resulted in an argument being coerced to
another type.
o boxplot(x=x, at=at) with non finite elements in x and non integer
at could not generate a warning but failed.
o heatmap(x, symm=TRUE, RowSideColors=*) no longer draws the colors
in reversed order.
o predict(<ar>) was incorrect in the multivariate case, for p >= 2.
o print(x, max=m) is now consistent when x is a "Date"; also the
"reached ... max.print .." messages are now consistently using
single brackets.
o Closed the <li> tag in pages generated by Rd2HTML(). (PR#14841.)
o Axis tick marks could go out of range when a log scale was used.
(PR#14833.)
o Signature objects in methods were not allocated as S4 objects
(caused a problem with trace() reported by Martin Morgan).
--
Peter Dalgaard, Professor
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
|
R 2.15.0 is released
|
Peter Dalgaard
| 438
|
|
From paul at stat.auckland.ac.nz Mon May 21 23:11:34 2001
From: paul at stat.auckland.ac.nz (Paul Murrell)
Date: Tue, 22 May 2001 09:11:34 +1200
Subject: new packages: grid and lattice
Message-ID: <[email protected]>
Hi
Two new packages have just been uploaded to the _DEVEL_ section on CRAN:
1. package "grid"
AUTHOR
Paul Murrell
OVERVIEW
This package provides an altenative graphics system for R.
FEATURES
Very flexible layout facilities (viewports, units, layouts)
Component-based design (graphics can be constructed incrementally and
hierarchically)
Basic support for interaction (graphics functions return "objects")
Highly customisable and extensible
BUGS/UNIMPLEMENTED FEATURES
No clipping
Only single active device
Viewport rotation very fragile
...
2. package "lattice"
AUTHOR
Deepayan Sarkar
OVERVIEW
This package provides graphics functionality similar to the Trellis suite in
S-Plus.
FEATURES
Mutipanel plots of one or two variables conditioned on one or more other
variables.
Formula-style specification of conditioning.
Strips atop the panels to indicate levels of the conditioning variables.
BUGS/UNIMPLEMENTED FEATURES
The "key" argument.
The "font" argument.
The lattice package uses the graphics system provided by grid so you will
need to download both packages in order to use lattice. Furthermore, the
packages are most likely to work only with the latest development release of
R. At the very least they require R 1.2.0 or later.
The packages are in the DEVEL section of CRAN because they are far from
complete and have many bugs and missing features. However, they should
contain sufficient functionality to be of use to some people. We are also
very interested in feedback on things that don't work, things that people
don't like, and even things that people do like :)
Paul Murrell
Deepayan Sarkar
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
new packages: grid and lattice
|
Paul Murrell
| 246
|
|
From dicook at iastate.edu Fri Apr 20 18:33:49 2007
From: dicook at iastate.edu (Dianne Cook)
Date: Fri, 20 Apr 2007 11:33:49 -0500
Subject: useR! 2007 online registration is now available
Message-ID: <[email protected]>
R Users and Developers,
Online registration for useR! 2007 is now available on the conference
web site. The deadline for the early registration discount has been
extended to May 15.
We haven't had many contributed papers as yet, or requests for travel
support from young researchers and graduate students. Please consider
contributing a paper, and encouraging your students and young faculty
to submit a paper and request travel support. The deadline for these
has also been extended to May 15. Contributed papers will be
refereed.
Please also note that we have negotiated airline discounts with both
Northwest and United airlines. They are excellent discounts, there is
some reduction in even the cheapest fares. So do keep this in mind
when you plane your travel. Details are on the web page.
The deadline to submit an abstract for a poster is June 30. These
abstracts will not be refereed. All poster submissions will be
accepted.
Information about the meeting can be found at
http://www.user2007.org/
If you have suggestions for the meeting please email the program
committee at user2007 at iastate.edu.
Douglas Bates, Dianne Cook, Dave Henderson, Heike Hofmann, Olivia Lau,
Michael Lawrence, Luke Tierney, Hadley Wickham
---------------------------
Di Cook
dicook at iastate.edu
|
useR! 2007 online registration is now available
|
Dianne Cook
| 415
|
|
From edd at debian.org Fri Dec 19 20:52:28 2008
From: edd at debian.org (Dirk Eddelbuettel)
Date: Fri, 19 Dec 2008 13:52:28 -0600
Subject: R/Finance 2009: Applied Finance with R -- Call for Papers
Message-ID: <[email protected]>
Call for Papers
The Finance Department of the University of Illinois at Chicago (UIC),
the International Center for Futures and Derivatives at UIC, and
members of the R finance community are pleased to announce
R/Finance 2009: Applied Finance with R
on April 24 and 25, 2009, in Chicago, IL, USA
Confirmed keynote speakers include:
Patrick Burns (Burns Statistics)
David Kane (Kane Capital)
Roger Koenker (U of Illinois at Urbana/Champaign)
David Ruppert (Cornell)
Diethelm Wuertz (ETH Z?rich)
Eric Zivot (U of Washington)
We invite all users of R in Finance to submit one-page abstracts or
complete papers (in txt/pdf/doc format). We encourage papers both on
academic research topics and related to use of R by Finance practitioners.
Presenters are strongly encouraged to provide working R code to accompany
the presentation/paper. Datasets need not be made public.
Please send submissions to committee at RinFinance.com.
The submission deadline is January 31st, 2009.
Submissions will be evaluated and submitters notified via email
on a rolling basis.
Additional details about the conference will be announced as available.
For the program committee:
Gib Bassett, Peter Carl, Dirk Eddelbuettel, John Miller,
Brian Peterson, Dale Rosenthal, Jeffrey Ryan
|
R/Finance 2009: Applied Finance with R -- Call for Papers
|
Dirk Eddelbuettel
| 612
|
|
From pdalgd at gmail.com Wed Oct 5 19:48:47 2016
From: pdalgd at gmail.com (peter dalgaard)
Date: Wed, 5 Oct 2016 19:48:47 +0200
Subject: R-3.3.2 on October 31
Message-ID: <[email protected]>
Just a quick heads-up, mostly for those who want to keep their packages up to date with respect to updates of R: We intend to have a patch release on October 31. Nickname and detailed schedule will be made available on developer.r-project.org in due course.
For the R Core Team
Peter Dalgaard
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
|
R-3.3.2 on October 31
|
peter dalgaard
| 129
|
|
From pd.mes at cbs.dk Thu Jun 30 14:13:18 2011
From: pd.mes at cbs.dk (Peter Dalgaard)
Date: Thu, 30 Jun 2011 14:13:18 +0200
Subject: R 2.13.1 scheduled for July 8
Message-ID: <[email protected]>
This is to announce that we plan to release R version 2.13.1 on Friday,
July 8, 2011.
The 2.13.0 release has been quite solid, but some people expect an x.y.1 to roll out on larger installations for the next academic year. Of course, there have also been a sampling of minor bug fixes.
Those directly involved should review the generic schedule at
http://developer.r-project.org/release-checklist.html
(We are breaking the schedule a little this time because of traveling.)
The source tarballs will be made available daily (barring build
troubles) via
http://cran.r-project.org/src/base-prerelease/
For the R Core Team
Peter Dalgaard
--
Peter Dalgaard
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
|
R 2.13.1 scheduled for July 8
|
Peter Dalgaard
| 402
|
|
From Kurt.Hornik at ci.tuwien.ac.at Tue Dec 9 18:48:20 1997
From: Kurt.Hornik at ci.tuwien.ac.at (Kurt Hornik)
Date: Tue, 9 Dec 1997 18:48:20 +0100
Subject: R FAQ v0.60
Message-ID: <[email protected]>
An updated version of the R FAQ to accompany the new 0.60 release is now
available at the usual site,
http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
A plain text version of the FAQ is appended below.
-kh
****** snip snip snip **************************************************
R FAQ
Kurt Hornik
v0.60-6, 1997/12/08
This document contains answers to some of the most frequently asked
questions about R. Feedback is welcome.
______________________________________________________________________
Table of Contents:
1. Introduction
1.1 Legalese
1.2 Obtaining this Document
1.3 Notation
1.4 Feedback
2. R Basics
2.1 What Is R?
2.2 What Machines Does R Run on?
2.3 What Is the Current Version of R?
2.4 How Can R Be Obtained?
2.5 How Can R Be Installed?
2.5.1 How Can R Be Installed (Unix)
2.5.2 How Can R Be Installed (Windows)
2.5.3 How Can R Be Installed (Macintosh)
2.6 Are there Unix Binaries for R?
2.7 Which Documentation Exists for R?
2.8 Which Mailing Lists Exist for R?
2.9 What is CRAN?
3. R and S
3.1 What Is S?
3.2 What Is S-PLUS?
3.3 What Are the Differences between R and S?
3.3.1 Lexical Scoping
3.3.2 Models
3.3.3 Others
4. R Add-On Packages
4.1 Which Add-on Packages Exist for R?
4.2 How Can Add-on Packages Be Installed?
4.3 How Can Add-on Packages Be Used?
4.4 How Can Add-on Packages Be Removed?
4.5 How Can I Create an R Package?
4.6 How Can I Contribute to R?
5. R and Emacs
5.1 Is there Emacs Support for R?
5.2 Should I Run R from Within Emacs?
6. R Miscellania
6.1 How Can I Read a Large Data Set into R?
6.2 Why Can't R Source a `Correct' File?
6.3 How Can I Set Components of a List to NULL?
6.4 How Can I Save My Workspace?
6.5 How Can I Clean Up My Workspace?
6.6 How Can I Get `eval' and `D' to Work?
6.7 Why Do My Matrices Lose Dimensions?
6.8 How Does Autoloading Work?
6.9 How Should I Set Options?
7. Acknowledgments
______________________________________________________________________
1. Introduction
This document contains answers to some of the most frequently asked
questions about R.
1.1. Legalese
This document is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2, or (at your option)
any later version.
This document is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
General Public License for more details.
A copy of the GNU General Public License is available via WWW at
http://www.gnu.org/copyleft/gpl.html. You can also obtain it by
writing to the Free Software Foundation, Inc., 675 Mass Ave,
Cambridge, MA 02139, USA.
1.2. Obtaining this Document
The latest version of this document is always available from
http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
From there, you can also obtain versions converted to plain ASCII
text, GNU info, DVI, and PostScript, as well as the SGML source used
for creating all these formats using the SGML-Tools (formerly
Linuxdoc-SGML) system.
1.3. Notation
Everything should be pretty standard. `R>' is used for the R prompt,
and a `$' for the shell prompt (where applicable).
1.4. Feedback
Feedback is of course most welcome.
In particular, note that I do not have access to Windows or Mac
systems. If you have information on these systems that you think
should be added to this document, please let me know.
2. R Basics
2.1. What Is R?
R is a system for statistical computation and graphics. It consists
of a language plus a run-time environment with graphics, a debugger,
access to certain system functions, and the ability to run programs
stored in script files.
The design of R has been heavily influenced by two existing languages:
Becker, Chambers & Wilks' S (see question ``What is S?'') and
Sussman's Scheme. Whereas the resulting language is very similar in
appearance to S, the underlying implementation and semantics are
derived from Scheme. See question ``What Are the Differences between
R and S?'' for a discussion of the differences between R and S.
R was initially written by Robert Gentleman and Ross Ihaka, who are
Senior Lecturers at the Department of Statistics of the University of
Auckland in Auckland, New Zealand. In addition, a large group of
individuals has contributed to R by sending code and bug reports.
Since mid-1997 there has been a core group who can modify the R source
code CVS archive. The group currently consists of Peter Dalgaard,
Robert Gentleman, Kurt Hornik, Ross Ihaka, Thomas Lumley, Martin
Maechler, Paul Murrell, Heiner Schwarte, and Luke Tierney.
R has a home page at http://stat.auckland.ac.nz/r/r.html. It is free
software distributed under a GNU-style copyleft, and an official part
of the GNU project (``GNU S'').
2.2. What Machines Does R Run on?
R is being developed for the Unix, Windows and Mac platforms.
R will configure and build under a number of common Unix platforms
including dec-alpha-osf, freebsd, hpux, i386-linux (ELF), sgi-irix,
solaris, and sunos, and according to Jim Lindsey <jlindsey at luc.ac.be>
also on Mac, Amiga and Atari under m68k-linux.
If you know about other platforms, please drop me a note.
2.3. What Is the Current Version of R?
The current Unix version is 0.60, the previous version was 0.50. The
``jump'' is due to both a major reorganization of the directory
structure and the conversion to a new, TeX-like documentation format.
See the file `CHANGES' in the R distribution for more information.
With some good luck, the Windows version will soon catch up with the
Unix version. The version for the Mac is pre-alpha.
2.4. How Can R Be Obtained?
Sources, binaries and documentation for R can be obtained via CRAN,
the ``Comprehensive R Archive Network'' (see question ``What is
CRAN?'').
2.5. How Can R Be Installed?
2.5.1. How Can R Be Installed (Unix)
If binaries are available for your platform (see question ``Are there
Unix Binaries for R?''), you can use these, following the instructions
that come with them.
Otherwise, you can compile and install R yourself, which can be done
very easily under a number of common Unix platforms (see question
``What Machines Does R Run on?''). The file INSTALL that comes with
the R distribution contains instructions.
Choose a place to install the R tree (R is not just a binary, but has
additional data sets, help files, font metrics etc). Let's call this
place RHOME (given appropriate permissions, a natural choice would be
`/usr/local/lib/R'). Untar the source code, and issue the following
commands (at the shell prompt):
$ ./configure
$ make
If these commands execute successfully, the R binary will be copied to
the `$RHOME/bin' directory. In addition, a shell script font-end
called `R' will be created and copied to the same directory. You can
copy this script to a place where users can invoke it, for example to
`/usr/local/bin'. You could also copy the man page `R.1' to a place
where your man reader finds it, such as `/usr/local/man/man1'.
Using
$ make docs
will build preformatted plain text help pages as well as HTML and
LaTeX versions of the documentation (the three kinds can also be gen-
erated separately using make help, make html and make latex). Note
that as of R version 0.60, you need Perl version 5 to build the docu-
mentation. If this is not available on your system, you can obtain
precompiled documentation files via CRAN.
If everything (including docs) built properly (and you do not want to
apply patches in the future), you can safely do rm -rf src to free
disk space.
2.5.2. How Can R Be Installed (Windows)
The file `rsept.zip' from the `bin/ms-windows' directory of a CRAN
site contains a binary Windows 95 distribution for R which should be
about a 0.50a4 release (plus a few features from 0.60). This version
is quite limited in Windows-specific features, although it has been
reported to work rather nicely.
The file `rseptbeta.zip' contains the same version with a few bugs
fixed and some experimental code for dynamic loading of DLL files.
The survival4 packages is included but it currently does not work.
These versions also work on NT4.0, both server and workstation.
The file `rsept31.zip' contains a version compiled for Windows 3.11.
There have been mixed reports regarding this one, some get it going
with a few inconsequential error messages on startup, others seem to
be getting absolutely nowhere with it. It will definitely not run
without a version of Win32s installed, available free of charge from
Microsoft (ftp://ftp.microsoft.com/Softlib/MSLFILES/pw1118.exe). For
reasons related to the lack of long filenames, the HTML help files
cannot work and are not included.
Note that when uncompressing the zip files, the pkunzip program needs
to be invoked with the -D flag to create subdirectories. Also, be
aware that some decompression programs do not preserve long file names
properly.
2.5.3. How Can R Be Installed (Macintosh)
The CRAN `bin/macintosh' directory contains `R.sea.hqx', a binhexed
self-extracting archive, and installation instructions in
`README.MACINTOSH'. Note that the version in it is nowhere near the
quality of the current Unix version.
The Power Macintosh port is temporarily on hold.
2.6. Are there Unix Binaries for R?
Packages ready for installation under the i386 versions of Debian
GNU/Linux and Red Hat Linux, respectively, can be found at CRAN in
`bin/i386-linux'. There are also `tar' distributions for NEXTSTEP on
the i386 and m68k platforms in `bin/i386-nextstep' and `bin/m68k-
nextstep'. No others binary distributions have thus far been made
publically available.
2.7. Which Documentation Exists for R?
Online documentation for most of the functions and variables in R
exists, and can be printed on-screen by typing help(name) (or ?name)
at the R prompt, where name is the name of the topic help is sought
for. (In the case of unary and binary operators and control-flow
special forms, the name may need to be be quoted.)
This documentation can also be made available as HTML, and as hardcopy
via LaTeX, see question ``How Can R Be Installed?''. An up-to-date
HTML version is always available for web browsing at
http://www.stat.math.ethz.ch/R/manual/
An R manual (``Notes on R: A Programming Environment for Data
Analysis and Graphics'') is currently being written, based on the
``Notes on S-PLUS'' by Bill Venables <venables at stats.adelaide.edu.au>
and David Smith <D.M.Smith at lancaster.ac.uk>. The current version can
be obtained as `Rnotes.tgz' (LaTeX source) in a CRAN `doc' directory.
Note that the ``conversion'' from S(-PLUS) to R is not complete yet.
Last, but not least, Ross' and Robert's experience in designing and
implementing R is described in:
@Article{,
author = {Ross Ihaka and Robert Gentleman},
title = {R: A Language for Data Analysis and Graphics},
journal = {Journal of Computational and Graphical Statistics},
year = 1996,
volume = 5,
number = 3,
pages = {299--314}
}
This is also the reference for R to use in publications.
2.8. Which Mailing Lists Exist for R?
Thanks to Martin Maechler <maechler at stat.math.ethz.ch>, there are
three mailing lists devoted to R.
r-announce
This list is for announcements about the development of R and
the availability of new code.
r-devel
This list is for discussions about the future of R and pre-
testing of new versions. It is meant for those who maintain an
active position in the development of R.
r-help
The `main' R mailing list, for announcements about the
development of R and the availability of new code, questions and
answers about problems and solutions using R, enhancements and
patches to the source code and documentation of R, comparison
and compatibility with S and S-plus, and for the posting of nice
examples and benchmarks.
Note that the r-announce list is gatewayed into r-help, so you don't
need to subscribe to both of them.
To send a message to everyone on the r-help mailing list, send email
to
r-help at stat.math.ethz.ch
To subscribe (or unsubscribe) to this list send subscribe (or unsub-
scribe) in the BODY of the message (not in the subject!) to r-help-
request at stat.math.ethz.ch. Information about the list can be obtained
by sending an email with info as its contens to r-help-
request at stat.math.ethz.ch.
Subscription and posting to the other lists is done analogously, with
`r-help' replaced by `r-announce' and `r-devel', respectively.
It is recommended that you send mail to r-help rather than only to the
R developers (who are also subscribed to the list, of course). This
may save them precious time they can use for constantly improving R,
and will typically also result in much quicker feedback for yourself.
Of course, in the case of bug reports it would be very helpful to have
code which reliably reproduces the problem. Also, make sure that you
include information on the system and version of R being used.
Archives of the above three mailing lists are made available on the
net in a monthly schedule at ftp://ftp.stat.math.ethz.ch/Mail-
archives/ (which is a directory of mail archive files). Archives of
the r-help mailing list (including the previous r-testers lists back
to March 1996), are also available in HTML format at
http://www.ens.gu.edu.au/robertk/rhelp/about.htm.
The developers of R can be reached for comments and reports at
R at stat.auckland.ac.nz.
2.9. What is CRAN?
The ``Comprehensive R Archive Network'' (CRAN) is a collection of
sites which carry identical material, consisting of the R
distribution(s), the contributed extensions, documentation for R, and
binaries.
The CRAN master site can be found at the URL
http://www.ci.tuwien.ac.at/R/ (Austria)
and is currently being mirrored daily at
http://www.stat.unipg.it/pub/stat/statlib/R/CRAN/ (Italy)
ftp://ftp.u-aizu.ac.jp/pub/lang/R/CRAN/ (Japan)
ftp://ftp.stat.math.ethz.ch/R-CRAN/ (Switzerland)
http://lib.stat.cmu.edu/R/CRAN/ (USA/Pennsylvania)
ftp://ftp.biostat.washington.edu/mirrors/R/CRAN/ (USA/Washington)
ftp://franz.stat.wisc.edu/pub/R/ (USA/Wisconsin)
Please use the CRAN site closest to you to reduce network load.
The structure of the CRAN tree is as follows.
`src/base'
contains the official R distribution as provided by Ross Ihaka
and Robert Gentleman.
`src/contrib'
contains code for extension packages.
`doc'
is for additional documentation and information on R.
`bin'
is for prebuilt R binaries (the base distribution and
extensions), grouped according to platforms. Currently, there
are experimental `.deb' and `.rpm' packages for i386-linux, and
tar files for i386-nextstep and m68k-nextstep. I hope that
`.tar.gz' files with contents relative to an installation tree
(e.g. `bin', `lib/R/', and `man/man1/R.1') can be made available
soon for all major supported Unix platforms.
To ``submit'' something to CRAN, simply upload it to
ftp://ftp.ci.tuwien.ac.at/incoming and send an email to
<wwwadmin at ci.tuwien.ac.at>. Please indicate the copyright situation
(GPL, ...) in your submission.
3. R and S
3.1. What Is S?
S is a very high level language and an environment for data analysis
and graphics. S was written by Richard A. Becker, John M. Chambers,
and Allan R. Wilks of AT&T Bell Laboratories Statistics Research
Department.
The primary references for S are two books by the creators of S.
o Richard A. Becker, John M. Chambers and Allan R. Wilks (1988),
``The New S Language,'' Chapman & Hall, London.
This book is often called the ``Blue Book''.
o John M. Chambers and Trevor J. Hastie (1992), ``Statistical Models
in S,'' Chapman & Hall, London.
This is also called the ``White Book''.
There is a huge amount of user-contributed code for S, available at
the S Repository at CMU.
See the ``Frequently Asked Questions about S''
(http://lib.stat.cmu.edu/S/faq) for further information about S.
3.2. What Is S-PLUS?
S-PLUS is a value-added version of S sold by Statistical Sciences,
Inc. (now a division of Mathsoft, Inc.) S is a subset of S-PLUS, and
hence anything which may be done in S may be done in S-PLUS. In
addition S-PLUS has extended functionality in a wide variety areas,
including robust regression, modern nonparametric regression, time
series, survival analysis, multivariate analysis, classical
statistical tests, quality control, and graphics drivers. Add-on
modules add additional capabilities for wavelet analysis, spatial
statistics, and design of experiments.
See the MathSoft S-PLUS page (http://www.mathsoft.com/splus.html) for
further information.
3.3. What Are the Differences between R and S?
3.3.1. Lexical Scoping
Whereas the developers of R have tried to stick to the S language as
defined in ``The New S Language'' (Blue Book, see question ``What is
S?''), they have adopted the evaluation model of Scheme.
This difference becomes manifest when free variables occur in a
function. Free variables are those which are neither formal
parameters (occurring in the argument list of the function) nor local
variables (created by assigning to them in the body of the function).
Whereas S (like C) by default uses static scoping, R (like Scheme) has
adopted lexical scoping. This means the values of free variables are
determined by a set of global variables in S, but in R by the bindings
that were in effect at the time the function was created.
Consider the following function:
cube <- function(n) {
sq <- function() n * n
n * sq()
}
Under S, sq() does not ``know'' about the variable n unless it is
defined globally:
S> cube(2)
Error in sq(): Object "n" not found
Dumped
S> n <- 3
S> cube(2)
[1] 18
In R, the ``environment'' created when cube() was invoked is also
looked in:
R> cube(2)
[1] 8
The following more `realistic' example illustrating the differences in
scoping is due to Thomas Lumley <thomas at biostat.washington.edu>. The
function
jackknife.lm <- function(lmobj) {
n <- length(resid(lmobj))
jval <- t(apply(as.matrix(1:n), 1,
function(i) coef(update(lmobj, subset = -i))))
(n - 1) * (n - 1) * var(jval) / n
}
does something useful in R, but does not work in S. In order to make
it work in S you need to explicitly pass the linear model object into
the function nested in apply(). If you don't and you are lucky you
will get ``Error: Object "lmobj" not found''. If you are unlucky
enough to have a linear model called lmobj in your global environment
you will get the wrong answer with no warning.
The following version works in S.
jackknife.S.lm <- function(lmobj) {
n <- length(resid(lmobj))
jval <- t(apply(as.matrix(1:n), 1,
function(i, lmobj) coef(update(lmobj, subset = -i)),
lmobj = lmobj))
(n - 1) * (n - 1) * var(jval) / n
}
(The S version was written independently by Thomas and at least three
of his fellow students over the past couple of years, causing liter-
ally hours of confusion on each occasion.)
Similarly, most optimization (or zero-finding) routines need some
arguments to be optimized over and have other parameters that depend
on the data but are fixed with respect to optimization. With R
scoping rules, this is a trivial problem; simply make up the function
with the required definitions in the same environment and scoping
takes care of it. With S, one solution is to add an extra parameter
to the function and to the optimizer to pass in these extras, which
however can only work if the optimizer supports this (and typically,
the builtin ones do not).
Lexical scoping allows using function closures and maintaining local
state. A simple example (taken from Abelson and Sussman) can be found
in the `demos/language' subdirectory of the R distribution. Further
information is provided in the standard R reference ``R: A Language
for Data Analysis and Graphics'' (see question ``Which Documentation
Exists for R?'') and a paper on ``Lexical Scope and Statistical
Computing'' by Robert Gentleman and Ross Ihaka which can be obtained
from the `doc/misc' directory of a CRAN site.
Lexical scoping also implies a further major difference. Whereas S
stores all objects as separate files in a directory somewhere (usually
`.Data' under the current directory), R does not. All objects in R
are stored internally. When R is started up it grabs a very large
piece of memory and uses it to store the objects. R performs its own
memory management of this piece of memory. Having everything in
memory is necessary because it is not really possible to externally
maintain all relevant ``environments'' of symbol/value pairs. This
difference also seems to make R much faster than S.
The down side is that if R crashes you will lose all the work for the
current session. Saving and restoring the memory ``images'' (the
functions and data stored in R's internal memory at any time) can be a
bit slow, especially if they are big. In S this does not happen,
because everything is saved in disk files and if you crash nothing is
likely to happen to them. R is still in a beta stage, and may crash
from time to time. Hence, for important work you should consider
saving often, see question ``How Can I Save My Workspace?'' (other
possibilities are logging your sessions, or have your R commands
stored in text files which can be read in using source()). (Note that
if you run R from within Emacs (see question ``R and Emacs''), you can
save the contents of the interaction buffer to a file and conveniently
manipulate it using ess-transcript-mode, as well as save source copies
of all functions and data used.)
3.3.2. Models
There are some differences in the modeling code, such as
o Whereas in S, you would use lm(y ~ x^3) to regress y on x^3 and
lm(y ~ poly(x, 3)) to perform ``cubic'' regression, in R, you have
to insulate powers of numeric vectors (using I()), i.e., you have
to use lm(y ~ I(x^3)) and lm(y ~ x + I(x^2) + I(x^3)),
respectively.
o The glm family objects are implemented differently in R and S. The
same functionality is available but the components have different
names.
o terms objects are stored differently. In S a terms object is an
expression with attributes, in R it is a formula with attributes.
The attributes have the same names but are mostly stored
differently. The major difference in functionality is that a terms
object is subscriptable in S but not in R. If you can't imagine
why this would matter then you don't need to know.
Also, attr(terms(y~x), "response") give 1 in S and TRUE in R. In S
the attribute indicates which column of the model frame will
contain the response. In R this always column 1.
Finally, in R y~x+0 is an alternative to y~x-1 for specifying a model
with no intercept. Models with no parameters at all can be specified
by y~0.
3.3.3. Others
Apart from lexical scoping and its implications, R follows the S
language definition in the Blue Book as much as possible, and hence
really is an ``implementation'' of S. There are some intentional
differences where the behavior of S is considered ``not clean''. In
general, the rationale is that R should help you detect programming
errors, while at the same time being as compatible as possible with S.
Some known differences are the following.
o In R, if x is a list, then x[sub] <- NULL and x[[sub]] <- NULL
remove the specified elements from x. The first of these is
incompatible with S, where it is a no-op.
o In S, the functions named .First and .Last in the `.Data' directory
can be used for customizing, as they are executed at the very
beginning and end of a session, respectively.
R looks for files called `.Rprofile' in the user's home directory
and the current directory, and sources these. It also loads a
saved image from `.RData' in case there is one. If a .First()
function exists then, it is executed. The .Last mechanism is not
supported yet.
o In R, the .First.lib mechanism when loading add-on packages using
library() is not yet supported.
o In R, dyn.load() can only load shared libraries, as created for
example by `R SHLIB'.
o R presently does not support IEEE Inf and NaN.
o Whereas in S, abs(z) is the same as Mod(z) for complex z, in R you
must use Mod(z), since abs() is a function of real numbers only.
o In R, attach() currently only works for lists and data frames (not
for directories). Also, you cannot attach at position 1.
o Categories do not exist in R, and never will as they are deprecated
now in S. Use factors instead.
o In R, For() loops are not necessary and hence not supported.
o In R, assign() uses the argument envir= rather than where= as in S.
o The random number generators are different, and the seeds have
different length.
o R uses only double precision and so can only pass numeric arguments
to C/FORTRAN subroutines as double * or DOUBLE PRECISION,
respectively.
o R does not allow indexing beyond the end of an array. E.g., if x
is a vector of length 5, both x[6] and x[-6] return an error
(``subscript out of bounds''). This is a feature, as the R
developers feel that indexing beyond array bounds causes bugs in
code that are hard to find and in lots of cases only subtly wrong,
and typically manifest themselves when least needed.
As another example, suppose that DF is a data frame and you want to
add a new variable VAR named x to it. In S, you can do DF[["x"]]
<- VAR. In R, this is not possible; you can use DF$"x" <- VAR or
DF <- cbind(DF, x = VAR).
o R currently does not allow recycling when subscripting with
logicals. E.g., x <- 1:5; x[c(F, T)] currently gives an error.
This is a bug and will be fixed soon.
There are also differences which are not intentional, and result from
missing or incorrect code in R. The developers would appreciate
hearing about any deficiencies you may find (in a written report fully
documenting the difference as you see it). Of course, it would be
useful if you were to implement the change yourself and make sure it
works.
4. R Add-On Packages
4.1. Which Add-on Packages Exist for R?
The R distribution comes with the following extra packages:
eda
Exploratory Data Analysis. Currently only contains functions
for robust line fitting, and median polish and smoothing.
mva
Multivariate Analysis. Currently contains code for principal
components (prcomp), canonical correlations (cancor),
hierarchichal clustering (hclust), and metric multidimensional
scaling (cmdscale). More functions for clustering and scaling,
biplots, profile and star plots, and code for ``real''
discriminant analysis will be added soon.
The following packages are available from the CRAN `src/contrib' area.
Note that R 0.60 has brought a change in both organization of package
sources and documentation format, and that some of the packages below
may not yet have been updated accordingly.
acepack
ace (Alternating Conditional Expectations) and avas (Additivity
and VAriance Stabilization for regression) for selecting
regression transformations.
bootstrap
Software (bootstrap, cross-validation, jackknife), data and
errata for the book ``An Introduction to the Bootstrap'' by B.
Efron and R. Tibshirani, 1993, Chapman and Hall.
class
Functions for classification (k-nearest neighbor and LVQ).
clus
Functions for cluster analysis.
ctest
A collection of classical tests, including the Bartlett, Fisher,
Kruskal-Wallis, Kolmogorov-Smirnov, and Wilcoxon tests.
date
Functions for dealing with dates. The most useful of them
accepts a vector of input dates in any of the forms 8/30/53,
30Aug53, 30 August 1953, ..., August 30 53, or any mixture of
these.
e1071
Miscellaneous functions used at the Department of Statistics at
TU Wien (E1071).
fracdiff
Maximum likelihood estimation of the parameters of a
fractionally differenced ARIMA(p,d,q) model (Haslett and
Raftery, Applied Statistics, 1989).
gee
An implementation of the Liang/Zeger generalized estimating
equation approach to GLMs for dependent data.
integrate
Code for adaptive quadrature.
jpn
A function to plot Japan's coast-line and prefecture boundaries.
leaps
A package which performs an exhaustive search for the best
subsets of a given set of potential regressors, using a branch-
and-bound algorithm, and also performs searches using a number
of less time-consuming techniques.
mlbench
A collection of artificial and real-world machine learning
benchmark problems, including the Boston housing data.
nnet
Software for feed-forward neural networks with a single hidden
layer and for multinomial log-linear models.
oz Functions for plotting Australia's coastline and state
boundaries.
polynom
A collection of functions to implement a class for univariate
polynomial manipulations.
ratetables
US national and state mortality data (requires survival4 and
date).
rational
A few small functions to find numerical rational approximations
using a continued fraction method.
snns
An R interface to the Stuttgart Neural Networks Simulator
(SNNS).
splines
Regression spline functions.
survival4
Functions for survival analysis (requires splines).
wavethresh
Code for doing wavelet transforms and thresholding in 1 and 2D.
xgobi
Interface to the XGobi program for graphical data analysis.
See CRAN `src/contrib/INDEX' for more information.
Paul Gilbert <pgilbert at bank-banque-canada.ca> will make an R version
of his package DSE (Dynamic Systems Estimation) shortly after the 0.60
release. The package provides state-space models and the Kalman
filter, VARMA and cointegration models, and numerical differentiation.
Also, it can do various rational expectation models via an interface
to run Troll (a commercially available product) from R. According to
Paul, the PADI interface from the Bank of Canada also works with minor
changes. PADI can be used to access Fame time series data bases and
potentially other databases, even remotely over the Internet. For
further information see http://www.bank-banque-canada.ca/pgilbert.
Harald Fekjaer <hfe at math.uio.no> has written addreg, a package for
additive hazards regression, which can be obtained from
http://www.med.uio.no/imb/stat/addreg/.
More code has been posted to the r-help mailing list, and can be
obtained from the mailing list archive.
4.2. How Can Add-on Packages Be Installed?
(Unix only.) The add-on packages on CRAN come as gzipped tar files.
``Unpack'' the package (in a directory that you may write to). If you
have GNU tar, you can use tar zxf name, otherwise you can do something
like gunzip -c name | tar xf -. Let pkg be the name of the directory
thus created. To install the package to the default R directory tree
(the `library' subdirectory of `RHOME'), type
$ R INSTALL pkg
at the shell prompt. To install to another tree (e.g., your private
one), use
$ R INSTALL pkg lib
where lib gives the path to the library tree to install to.
You can use several library trees of add-on packages. The easiest way
to tell R to use these is via the environment variable RLIBS which
should be a colon-separated list of directories at which R library
trees are rooted. You do not have to specify the default tree in
RLIBS. E.g., to use a private tree in `$HOME/lib/R' and a public
site-wide tree in `/usr/local/lib/R/site', put
RLIBS="$HOME/lib/R:/usr/local/lib/R/site"; export RLIBS
into your (Bourne) shell profile.
4.3. How Can Add-on Packages Be Used?
To find out which additional packages are available on your system,
type
library()
at the R prompt.
This produces something like
Packages in `/home/me/lib/R':
mystuff My own R functions, nicely packaged and not documented
Packages in `/usr/local/lib/R/library':
acepack ace() and avas() for selecting regression transformations
bootstrap Functions for the book "An Introduction to the Bootstrap"
ctest Classical Tests
date Functions for handling dates
eda Exploratory Data Analysis
fracdiff Fractionally differenced ARIMA(p,d,q) models
gee Generalized Estimating Equation models
mva Classical Multivariate Analysis
splines Regression spline functions
survival4 Survival analysis (needs `splines')
You can ``load'' the installed package name by
library(name)
You can then find out which functions it provides by typing one of
help(package = name)
library(help = name)
You can unload the loaded package name by
detach("package:name")
4.4. How Can Add-on Packages Be Removed?
To remove the package pkg from the default library or the library lib,
do
$ R REMOVE pkg
or
$ R REMOVE pkg lib
respectively.
4.5. How Can I Create an R Package?
A package consists of a subdirectory containing a `TITLE' and `INDEX'
file, and subdirectories `R', `man' and optionally `src', `src-c', and
`data'.
The `TITLE' file contains a line giving the name of the package and a
brief description. `INDEX' contains a line for each sufficiently
interesting object in the package, giving its name and a description
(functions such as print methods not usually called explicitly might
not be included).
The `R' subdirectory contains R code files with names beginning with
lowercase letters. One of these should use library.dynam() to load
any necessary compiled code. The `man' subdirectory should contain R
documentation files for the objects in the package.
Source and a Makefile for the compiled code is in `src', and a pure C
version of the source should be in `src-c'. In the common case when
all the source is in C it may be convenient to make one of these
directories a symbolic link to the other. The `Makefile' will be
passed various machine-dependent compile and link flags, examples of
which can be seen in the `eda' package.
Finally, the `data' subdirectory is for additional data files the
package makes available for loading using data(). Note that (at least
currently) all such files are in fact R code files, and must have the
extension `.R'.
See the documentation for library() for more information.
The web page http://www.biostat.washington.edu/~thomas/Rlib.html
maintained by Thomas Lumley provides information on porting S packages
to R.
4.6. How Can I Contribute to R?
R is currently still in alpha (or pre-alpha) state, so simply using it
and communicating problems is certainly of great value.
One place where functionality is still missing is the modeling
software as described in ``Statistical Models in S'' (see question
``What is S?''). The functions
add1 kappa alias labels drop1 proj
are missing; many of these are interpreted functions so anyone that is
bored and wants to have a go at implementing them it would be appreci-
ated. In addition, only linear and generalized linear models are cur-
rently available, aov, gam, loess, tree, and the nonlinear modelling
code are not there yet.
See also the `PROJECTS' file in the top level R source directory.
Many of the packages available at the Statlib S Repository might be
worth porting to R.
If you are interested in working on any of these projects, please
notify Kurt Hornik.
5. R and Emacs
5.1. Is there Emacs Support for R?
There is an Emacs-Lisp interface for interactive statistical
programming and data analysis called ESS (``Emacs Speaks
Statistics''). Languages supported include: S dialects (S 3/4, S-PLUS
3.x, and R), LispStat dialects (XLispStat, ViSta), and SAS. Stata and
SPSS dialect (SPSS, Fiasco) support is being examined for possible
future implementation (a preliminary Stata mode is distributed).
ESS grew out of the desire for bug fixes and extensions to S-mode-4.8
(which was a GNU Emacs interface to S/S-PLUS version 3 only). In
particular, XEmacs support as well as extensions to incorporate R were
desired. In addition, with new modes being developed for R, Stata,
and SAS, it was felt that providing for a unifying framework would
eliminate differences in the user interface, as well as to provide for
faster development of production tools and statistical analysis. 5.0
has, for its guts, the basic framework from S-mode. However, it has
been cleaned, streamlined, brought closer to conformance as a standard
GNU Emacs package, and redesigned for modularity and reuse.
R support contains code for editing R source code (syntactic
indentation and highlighting of source code, partial evaluations of
code, loading and error-checking of code, and source code revision
maintenance) and documentation (including sending examples to a
running R process and previewing), interacting with an inferior R
process from within Emacs (command-line editing, searchable command
history, command-line completion of R object and file names, quick
access to object and search lists, transcript recording, and an
interface to the help system), and transcript manipulation (in
particular for re-evaluating commands from transcript files).
The latest versions of ESS are always available by WWW from
http://franz.stat.wisc.edu/pub/ESS/
or ftp://franz.stat.wisc.edu/pub/ESS/, or via CRAN. The HTML version
of the documentation can be found at
http://www.stat.math.ethz.ch/ESS/.
ESS comes with detailed installation instructions.
5.2. Should I Run R from Within Emacs?
Yes, definitely. Inferior R mode provides a readline/history
mechanism, object name completion, and syntax-based highlighting of
the interaction buffer using Font Lock mode, as well as a very
convenient interface to the R help system.
Of course, it also integrates nicely with the mechanisms for editing R
source using Emacs. One can write code in one Emacs buffer and send
whole or parts of it for execution to R; this is helpful for both data
analysis and programming. One can also seamlessly integrate with a
revision control system, in order to maintain a log of changes in your
programs and data, as well as to allow for the retrieval of past
versions of the code.
In addition, it allows you to keep a record of your session, which can
also be used for error recovery through the use of the transcript
mode.
6. R Miscellania
6.1. How Can I Read a Large Data Set into R?
R (currently) uses a static memory model. This means that when it
starts up, it asks the operating system to reserve a fixed amount of
memory for it. The size of this chunk cannot be changed subsequently.
Hence, it can happen that not enough memory was allocated.
In these cases, you should restart R with more memory available, using
the command line options -n and -v. To understand these options, one
needs to know that R maintains separate areas for fixed and variable
sized objects. The first of these is allocated as an array of ``cons
cells'' (Lisp programmers will know what they are, others may think of
them as the building blocks of the language itself, parse trees,
etc.), and the second are thrown on a ``heap''. The -n option can be
used to specify the number of cons cells (each occupying 16 bytes)
which R is to use (the default is 200000), and the -v option to
specify the size of the vector heap in megabytes (the default is 2).
Only integers are allowed for both options.
E.g., to read in a table of 5000 observations on 40 numeric variables,
R -v 6 should do.
Note that the information on where to find vectors and strings on the
heap is stored using cons cells. Thus, it may also be necessary to
allocate more space for cons cells in order to perform computations
with very ``large'' variable-size objects.
You can find out the current memory consumption (the proportion of
heap and cons cells used) by typing gc() at the R prompt. This may
help you in finding out whether to increase -v or -n. Note that
following gcinfo(TRUE), automatic garbage collection always prints
memory use statistics.
When using read.table(), the memory requirements are in fact higher
than anticipated, because the file is first read in as one long string
which is then split again. Use scan() if possible in case you run out
of memory when reading in a large table.
6.2. Why Can't R Source a `Correct' File?
R sometimes has problems parsing a file which does not end in a
newline. This can happen for example when Emacs is used for editing
the file and next-line-add-newlines is set to nil. To avoid the
problem, either set require-final-newline to a non-nil value in one of
your Emacs startup files, or make sure R-mode (see question ``Is there
Emacs Support for R?'') is used for editing R source files (which
locally ensures this setting).
Earlier R versions had a similar problem when reading in data files,
but this should have been taken care of now.
6.3. How Can I Set Components of a List to NULL?
You can use
x[i] <- list(NULL)
to set component i of the list x to NULL, similarly for named compo-
nents. Do not set x[i] or x[[i]] to NULL, because this will remove
the corresponding component from the list.
For dropping the row names of a matrix x, it may be easier to use
rownames(x) <- NULL, similarly for column names.
6.4. How Can I Save My Workspace?
The expression
save(list = ls(), file = ".RData")
saves the objects in the currently active environment (typically the
user's .GlobalEnv) to the file `.RData' in the R startup directory.
6.5. How Can I Clean Up My Workspace?
To remove all objects in the currently active environment (typically
the user's .GlobalEnv), you can do
rm(list = ls())
6.6. How Can I Get `eval' and `D' to Work?
Strange things will happen if you use eval(print(x), envir = e) or
D(x^2, "x"). The first one will either tell you that "x" is not
found, or print the value of the wrong x. The other one will likely
return zero if x exists, and an error otherwise.
This is because in both cases, the first argument is evaluated in the
calling environment first. The result (which should be an object of
mode `expression' or `call') is then evaluated or differentiated.
What you (most likely) really want is obtained by ``quoting'' the
first argument upon surrounding it with expression(). For example,
R> D(expression(x^2),"x")
2 * x
Although this behavior may initially seem to be rather strange, is
perfectly logical. The ``intuitive'' behaviour could easily be
implemented, but problems would arise whenever the expression is
contained in a variable, passed as a parameter, or is the result of a
function call. Consider for instance the semantics in cases like
D2 <- function(e, n) D(D(e, n), n)
or
g <- function(y) eval(substitute(y), sys.frame(sys.parent(n = 2)))
g(a * b)
See the help pages for more examples.
6.7. Why Do My Matrices Lose Dimensions?
When a matrix with a single row or column is created by a subscripting
operation, e.g., row <- mat[2, ], it is by default turned into a
vector. In a similar way if an array with dimension, say, 2x3x1x4 is
created by subscripting it will be coerced into a 2x3x4 array, losing
the unnecessary dimension. After much discussion this has been
determined to be a feature.
To prevent this happening, add the option `drop = FALSE' to the
subscripting. For example,
rowmatrix <- mat[2, , drop = F] # creates a row matrix
colmatrix <- mat[, 2, drop = F] # creates a column matrix
a <- b[1, 1, 1, drop = F] # creates a 1x1x1 array
The `drop = F' option should be used defensively when programming.
For example, the statement
somerows <- mat[index, ]
will return a vector rather than a matrix if index happens to have
length 1, causing errors later in the code. It should probably be
rewritten as
somerows <- mat[index, , drop = F]
6.8. How Does Autoloading Work?
R has a special environment called `.AutoloadEnv'. Using
autoload(name, pkg), where name and pkg are strings giving the names
of an object and the package containing it, stores some information in
this environment. When R tries to evaluate name, it loads the
corresponding package pkg and reevaluates name in the new package's
environment.
Using this mechanism makes R behave as if the package was loaded, but
does not occupy memory (yet).
See the help page for autoload() for a very nice example.
6.9. How Should I Set Options?
The function options() allows setting and examining a variety of
global ``options'' which affect the way in which R computes and
displays its results. The variable .Options holds the current values
of these options, but should never directly be assigned to unless you
want to drive yourself crazy---simply pretend that it is a ``read-
only'' variable.
For example, given
test1 <- function(x = pi, dig = 3) {
oo <- options(digits = dig); on.exit(options(oo));
cat(.Options$digits, x, "\n")
}
test2 <- function(x = pi, dig = 3) {
.Options$digits <- dig
cat(.Options$digits, x, "\n")
}
we obtain:
R> test1()
3 3.14
R> test2()
3 3.141593
What is really used is the global value of .Options, and using
options(OPT = VAL) correctly updates it. Local copies of .Options,
either in .GlobalEnv or in a function environment (frame), are just
silently disregarded.
7. Acknowledgments
Of course, many many thanks to Robert and Ross for the R system, and
to the package writers and porters for adding to it.
Special thanks go to Peter Dalgaard, Paul Gilbert, Fritz Leisch, Jim
Lindsey, Thomas Lumley, Martin Maechler, Anthony Rossini, and Andreas
Weingessel for their comments which helped me improve this FAQ.
More to some soon ...
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|
R FAQ v0.60
|
Kurt Hornik
| 579
|
|
From dimi at ci.tuwien.ac.at Tue Jun 16 16:54:58 1998
From: dimi at ci.tuwien.ac.at (Evgenia Dimitriadou)
Date: Tue, 16 Jun 1998 16:54:58 +0200 (CEST)
Subject: New Package
Message-ID: <[email protected]>
I have put a new package called "cclust", that is dealing with Convex
Clustering Methods. More anallyticaly, it is performing the normal Kmeans
clustering, the On-line Update clustering(Hard Competitive Learning) and
the Neural Gas (Soft Competitive) clustering method.
For more details there is a help page in R.
************************************************************************
* Evgenia Dimitriadou *
************************************************************************
* Institut f?r Statistik * Tel: (+43 1) 58801 4592 *
* Technische Universit?t Wien * Fax: (+43 1) 504 14 98 *
* Wiedner Hauptstr. 8-10/1071 * dimi at ci.tuwien.ac.at *
* A-1040 Wien, Austria * *
************************************************************************
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|
New Package
|
Evgenia Dimitriadou
| 538
|
|
From Friedrich.Leisch at ci.tuwien.ac.at Wed Jan 24 11:59:32 2001
From: Friedrich.Leisch at ci.tuwien.ac.at (Friedrich Leisch)
Date: Wed, 24 Jan 2001 11:59:32 +0100
Subject: R News Volume 1/1
Message-ID: <[email protected]>
We are pleased to announce the first volume of R News, the
newsletter of the R project for statistical computing. The newsletter
is available online as PDF file at
http://cran.R-project.org/doc/Rnews
and will propagate to the CRAN mirrors within the next days.
R News will feature short to medium length articles covering topics
that might be of interest to users or developers of R, including
* Changes in R: new features of the latest release
* Changes on CRAN: new add-on packages, manuals, binary distributions,
mirrors, ...
* Add-on packages: short introductions to or reviews of R extension packages
* Programmer's Niche: nifty hints for programming in R (or S)
* Applications: Examples of analyzing data with R
The newsletter as a medium for communication intends to fill the gap
between the R mailing lists and scientific journals: Compared with
emails it is more persistent, one can cite articles in the newsletter
and because the newsletter is edited it has better quality control. On
the other hand, when compared to scientific journals, it is faster,
less formal, and last but not least focused on R.
As all of R, R News is a volunteer project. The editorial board
currently consists of the R core development team plus Bill
Venables.
We really hope you will enjoy reading R News!
For the editorial board,
Fritz Leisch
--
-------------------------------------------------------------------
Friedrich Leisch
Institut f?r Statistik Tel: (+43 1) 58801 10715
Technische Universit?t Wien Fax: (+43 1) 58801 10798
Wiedner Hauptstra?e 8-10/1071 Friedrich.Leisch at ci.tuwien.ac.at
A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch
-------------------------------------------------------------------
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|
R News Volume 1/1
|
Friedrich Leisch
| 219
|
|
From pd@|gd @end|ng |rom gm@||@com Sat Oct 10 10:11:50 2020
From: pd@|gd @end|ng |rom gm@||@com (Peter Dalgaard)
Date: Sat, 10 Oct 2020 10:11:50 +0200
Subject: [Rd] R 4.0.3 is released
Message-ID: <[email protected]>
The build system rolled up R-4.0.3.tar.gz (codename "Bunny-Wunnies Freak Out") this morning.
The list below details the changes in this release.
You can get the source code from
https://cran.r-project.org/src/base/R-4/R-4.0.3.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you.
Binaries for various platforms will appear in due course.
For the R Core Team,
Peter Dalgaard
These are the checksums (md5 and SHA-256) for the freshly created files, in case you wish
to check that they are uncorrupted:
MD5 (AUTHORS) = b9c44f9f78cab3184ad9898bebc854b4
MD5 (COPYING) = eb723b61539feef013de476e68b5c50a
MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343
MD5 (FAQ) = 5be656453b81e9393e2a0c42688b04b8
MD5 (INSTALL) = 7893f754308ca31f1ccf62055090ad7b
MD5 (NEWS) = 71728ef32a09c5b9df36b496b52d5c8e
MD5 (NEWS.0) = bfcd7c147251b5474d96848c6f57e5a8
MD5 (NEWS.1) = eb78c4d053ec9c32b815cf0c2ebea801
MD5 (NEWS.2) = 496062c138e2def06cebccddfb814ac6
MD5 (NEWS.3) = 012e7f4a80cc8ec947bf3f0ff6117ec8
MD5 (R-latest.tar.gz) = 8ecf46afa36c9aff9904aad5ca422c6d
MD5 (README) = f468f281c919665e276a1b691decbbe6
MD5 (RESOURCES) = 529223fd3ffef95731d0a87353108435
MD5 (THANKS) = 251d20510bfc3cc93b82c5a99f7efcc6
MD5 (VERSION-INFO.dcf) = bfbcfb2f4ef4416b635087160f965904
MD5 (R-4/R-4.0.3.tar.gz) = 8ecf46afa36c9aff9904aad5ca422c6d
2cde824a7b18958e5f06b391c801c8288be0f84fa8934b7ddefef23c67e60c09 AUTHORS
e6d6a009505e345fe949e1310334fcb0747f28dae2856759de102ab66b722cb4 COPYING
6095e9ffa777dd22839f7801aa845b31c9ed07f3d6bf8a26dc5d2dec8ccc0ef3 COPYING.LIB
4390543804392e072378b2d75cd3fb0d57e9885f9dc38ddd5a2ff780487b9d97 FAQ
f87461be6cbaecc4dce44ac58e5bd52364b0491ccdadaf846cb9b452e9550f31 INSTALL
895ba3f810fd33d3be63deb6c4588be1f7ba3f5bf80e10ffeafc194221dd5ba9 NEWS
4e21b62f515b749f80997063fceab626d7258c7d650e81a662ba8e0640f12f62 NEWS.0
12b30c724117b1b2b11484673906a6dcd48a361f69fc420b36194f9218692d01 NEWS.1
e80de410c77f05ff2012fa70051b89119845f734a7fa5c55857e61e4ed7d5f6e NEWS.2
7201d139947afa52b5e09d26dc01445edf444506264355b2185122bc1ed3dce0 NEWS.3
09983a8a78d5fb6bc45d27b1c55f9ba5265f78fa54a55c13ae691f87c5bb9e0d R-latest.tar.gz
2fdd3e90f23f32692d4b3a0c0452f2c219a10882033d1774f8cadf25886c3ddc README
408737572ecc6e1135fdb2cf7a9dbb1a6cb27967c757f1771b8c39d1fd2f1ab9 RESOURCES
c9c7cb32308b4e560a22c858819ade9de524a602abd4e92d1c328c89f8037d73 THANKS
cd9666c09064b120655598c1ac792266ad20adb57c36aab4d094dedc7e480fa6 VERSION-INFO.dcf
09983a8a78d5fb6bc45d27b1c55f9ba5265f78fa54a55c13ae691f87c5bb9e0d R-4/R-4.0.3.tar.gz
This is the relevant part of the NEWS file
CHANGES IN R 4.0.3:
NEW FEATURES:
* On platforms using configure option --with-internal-tzcode,
additional values "internal" and (on macOS only) "macOS" are
accepted for the environment variable TZDIR. (See ?TZDIR.)
On macOS, "macOS" is used by default if the system timezone
database is a newer version than that in the R installation.
* When install.packages(type = "source") fails to find a package in
a repository it mentions package versions which are excluded by
their R version requirement and links to hints on why a package
might not be found.
* The default value for options("timeout") can be set from
enviromnent variable R_DEFAULT_INTERNET_TIMEOUT, still defaulting
to 60 (seconds) if that is not set or invalid.
This may be needed when child R processes are doing downloads,
for example during the installation of source packages which
download jars or other forms of data.
LINK-TIME OPTIMIZATION on a UNIX-ALIKE:
* There is now support for parallelized Link-Time Optimization
(LTO) with GCC and for 'thin' LTO with clang _via_ setting the
LTO macro.
* There is support for setting a different LTO flag for the Fortran
compiler, including to empty when mixing clang and gfortran (as
on macOS). See file config.site.
* There is a new LTO_LD macro to set linker options for LTO
compilation, for example to select an alternative linker or to
parallelize thin LTO.
DEPRECATED AND DEFUNCT:
* The LINPACK argument to chol.default(), chol2inv(),
solve.default() and svd() has been defunct since R 3.1.0. Using
it now gives a warning which will become an error in R 4.1.0.
BUG FIXES:
* The code mitigating stack overflow with PCRE regexps on very long
strings is enabled for PCRE2 < 10.30 also when JIT is enabled,
since stack overflows have been seen in that case.
* Fix to correctly show the group labels in dotchart() (which where
lost in the ylab improvement for R 4.0.0).
* addmargins(*, ..) now also works when fn() is a local function,
thanks to bug report and patch PR#17124 from Alex Bertram.
* rank(x) and hence sort(x) now work when x is an object (as per
is.object(x)) of type "raw" _and_ provides a valid `[` method,
e.g., for gmp::as.bigz(.) numbers.
* chisq.test(*, simulate.p.value=TRUE) and r2dtable() now work
correctly for large table entries (in the millions). Reported by
Sebastian Meyer and investigated by more helpers in PR#16184.
* Low-level socket read/write operations have been fixed to
correctly signal communication errors. Previously, such errors
could lead to a segfault due to invalid memory access. Reported
and debugged by Dmitriy Selivanov in PR#17850.
* quantile(x, pr) works more consistently for pr values slightly
outside [0,1], thanks to Suharto Anggono's PR#17891.
Further, quantile(x, prN, names=FALSE) now works even when prN
contains NAs, thanks to Anggono's PR#17892. Ditto for ordered
factors or Date objects when type = 1 or 3, thanks to PR#17899.
* Libcurl-based internet access, including curlGetHeaders(), was
not respecting the "timeout" option. If this causes
unanticipated timeouts, consider increasing the default by
setting R_DEFAULT_INTERNET_TIMEOUT.
* as.Date(<char>) now also works with an initial "", thanks to
Michael Chirico's PR#17909.
* isS3stdGeneric(f) now detects an S3 generic also when it it is
trace()d, thanks to Gabe Becker's PR#17917.
* R_allocLD() has been fixed to return memory aligned for long
double type PR#16534.
* fisher.test() no longer segfaults when called again after its
internal stack has been exceeded PR#17904.
* Accessing a long vector represented by a compact integer sequence
no longer segfaults (reported and debugged by Hugh Parsonage).
* duplicated() now works also for strings with multiple encodings
inside a single vector PR#17809.
* phyper(11, 15, 0, 12, log.p=TRUE) no longer gives NaN; reported
as PR#17271 by Alexey Stukalov.
* Fix incorrect calculation in logLik.nls() PR#16100, patch from
Sebastian Meyer.
* A very old bug could cause a segfault in model.matrix() when
terms involved logical variables. Part of PR#17879.
* model.frame.default() allowed data = 1, leading to involuntary
variable capture (rest of PR#17879).
* tar() no longer skips non-directory files, thanks to a patch by
Sebastian Meyer, fixing the remaining part of PR#16716.
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
______________________________________________
R-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
|
[Rd] R 4.0.3 is released
|
Peter Dalgaard
| 628
|
|
From p.dalgaard at biostat.ku.dk Sat May 2 22:19:07 1998
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard BSA)
Date: 02 May 1998 22:19:07 +0200
Subject: R-0.61.3 released
Message-ID: <[email protected]>
I've just put up R-0.61.3.tgz and R-0.61.2-0.61.3.diff.gz for
anonymous FTP on ftp.stat.auckland.ac.nz.
As usual: Don't get it from there unless you are in a desperate hurry.
It will migrate to the CRAN sites within a day or two. (See the FAQ
for the list of CRAN sites. And see the footer for the FAQ location....)
This release mainly fixes a couple of embarassing bugs in 0.61.2. It
is expected to be the last of the 0.61.x series (unless something
*really* ghastly is discovered), 0.62.0 being scheduled for release
some time in mid-June.
Here is the list of changes:
CHANGES IN R VERSION 0.61.3
NEW FEATURES
o find(.) function [on wish of many...]
BUG FIXES
o Remove "Alpha" revision from opening blurb. Didn't make sense
with our development model
o set SHELL=/bin/sh in Makefile and use $(MAKE). Avoid use of
wildcards in $(MANSRC) for non-gnu "make" (notably Solaris).
o rhyper gave wrong results in degenerate cases
o Using get with pos=length(search()) or envir=NULL was
actually actually starting the search in .GlobalEnv.
o first=0 (or negative) argument to substr() caused trouble.
o 1%o%1 would segfault
o .Dyn.libs would linger in .RData causing code not to be dyn.loaded.
Now removed in .First(), if necessary
o system.time() expression could not access local variables in
functions.
--
O__ ---- Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
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|
R-0.61.3 released
|
Peter Dalgaard BSA
| 526
|
|
From pd@|gd @end|ng |rom gm@||@com Mon Feb 15 10:18:01 2021
From: pd@|gd @end|ng |rom gm@||@com (Peter Dalgaard)
Date: Mon, 15 Feb 2021 10:18:01 +0100
Subject: [Rd] R 4.0.4 is released
Message-ID: <[email protected]>
The build system rolled up R-4.0.4.tar.gz (codename "Lost Library Book") this morning.
The list below details the changes in this release.
You can get the source code from
https://cran.r-project.org/src/base/R-4/R-4.0.4.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you.
Binaries for various platforms will appear in due course.
For the R Core Team,
Peter Dalgaard
These are the checksums (md5 and SHA-256) for the freshly created files, in case you wish
to check that they are uncorrupted:
MD5 (AUTHORS) = b9c44f9f78cab3184ad9898bebc854b4
MD5 (COPYING) = eb723b61539feef013de476e68b5c50a
MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343
MD5 (FAQ) = a5596520508b8749aa18baea2cf8ff80
MD5 (INSTALL) = 7893f754308ca31f1ccf62055090ad7b
MD5 (NEWS) = eeb2d15f39e0a38935de2c419b4263f7
MD5 (NEWS.0) = bfcd7c147251b5474d96848c6f57e5a8
MD5 (NEWS.1) = eb78c4d053ec9c32b815cf0c2ebea801
MD5 (NEWS.2) = 496062c138e2def06cebccddfb814ac6
MD5 (NEWS.3) = 012e7f4a80cc8ec947bf3f0ff6117ec8
MD5 (R-latest.tar.gz) = e205f000947f99eeba0fb6311bd61970
MD5 (README) = f468f281c919665e276a1b691decbbe6
MD5 (RESOURCES) = 529223fd3ffef95731d0a87353108435
MD5 (THANKS) = 251d20510bfc3cc93b82c5a99f7efcc6
MD5 (VERSION-INFO.dcf) = 6a5ad95f3b708ce0dc19bab8bbfc3bc0
MD5 (R-4/R-4.0.4.tar.gz) = e205f000947f99eeba0fb6311bd61970
2cde824a7b18958e5f06b391c801c8288be0f84fa8934b7ddefef23c67e60c09 AUTHORS
e6d6a009505e345fe949e1310334fcb0747f28dae2856759de102ab66b722cb4 COPYING
6095e9ffa777dd22839f7801aa845b31c9ed07f3d6bf8a26dc5d2dec8ccc0ef3 COPYING.LIB
e9783551b3724b368a42c1300a8e5795ae84add34823c4eb9d8054a0e76f592c FAQ
f87461be6cbaecc4dce44ac58e5bd52364b0491ccdadaf846cb9b452e9550f31 INSTALL
2227d48d78c4d70d07c367ecd4c5ba60a04a699ed0391fabac3da6edffdaa5db NEWS
4e21b62f515b749f80997063fceab626d7258c7d650e81a662ba8e0640f12f62 NEWS.0
12b30c724117b1b2b11484673906a6dcd48a361f69fc420b36194f9218692d01 NEWS.1
e80de410c77f05ff2012fa70051b89119845f734a7fa5c55857e61e4ed7d5f6e NEWS.2
7201d139947afa52b5e09d26dc01445edf444506264355b2185122bc1ed3dce0 NEWS.3
523f27d69744a08c8f0bd5e1e6c3d89a4db29ed983388ba70963a3cd3a4a802e R-latest.tar.gz
2fdd3e90f23f32692d4b3a0c0452f2c219a10882033d1774f8cadf25886c3ddc README
408737572ecc6e1135fdb2cf7a9dbb1a6cb27967c757f1771b8c39d1fd2f1ab9 RESOURCES
c9c7cb32308b4e560a22c858819ade9de524a602abd4e92d1c328c89f8037d73 THANKS
6c5117e36f4e69f0cd90f3bab6e7fd47ec90b0047e2aaed145300ad4ece20ede VERSION-INFO.dcf
523f27d69744a08c8f0bd5e1e6c3d89a4db29ed983388ba70963a3cd3a4a802e R-4/R-4.0.4.tar.gz
This is the relevant part of the NEWS file
CHANGES IN R 4.0.4:
NEW FEATURES:
* File share/texmf/tex/latex/jss.cls has been updated to work with
LaTeX versions since Oct 2020.
* Unicode character width tables (as used by nchar(, type = "w"))
have been updated to Unicode 12.1 by Brodie Gaslam (PR#17781),
including many emoji.
* The internal table for iswprint (used on Windows, macOS and AIX)
has been updated to include many recent Unicode characters.
INSTALLATION on a UNIX-ALIKE:
* If an external BLAS is specified by --with-blas=foo or _via_
environment variable BLAS_LIBS is not found, this is now a
configuration error. The previous behaviour was not clear from
the documentation: it was to continue the search as if
--with-blas=yes was specified.
BUG FIXES:
* all.equal(x,y) now "sees" the two different NAs in factors,
thanks to Bill Dunlap and others in PR#17897.
* (~ NULL)[1] and similar formula subsetting now works, thanks to a
report and patch by Henrik Bengtsson in PR#17935. Additionally,
subsetting leaving an empty formula now works too, thanks to
suggestions by Suharto Anggono.
* .traceback(n) keeps source references again, as before R 4.0.0,
fixing a regression; introduced by the PR#17580, reported
including two patch proposals by Brodie Gaslam.
* unlist(plst, recursive=FALSE) no longer drops content for
pairlists with list components, thanks to the report and patch by
Suharto Anggono in PR#17950.
* iconvlist() now also works on MUSL based (Linux) systems, from a
report and patch suggestion by Wesley Chan in PR#17970.
* round() and signif() no longer tolerate wrong argument names,
notably in 1-argument calls; reported by Shane Mueller on R-devel
(mailing list); later reported as PR#17976.
* .Machine has longdouble.* elements only if
capabilities("long.double") is true, as documented. (Previously
they were included if the platform had long double identical to
double, as ARM does.)
* p.adjust(numeric(), n=0) now works, fixing PR#18002.
* identical(x,y) no longer prints "Unknown Type .." for typeof(x)
== "..." objects.
* Fix (auto-)print()ing of named complex vectors, see PR#17868 and
PR#18019.
* all.equal(<language>, <...>) now works, fixing PR#18029.
* as.data.frame.list(L, row.names=NULL) now behaves in line with
data.frame(), disregarding names of components of L, fixing
PR#18034, reported by Kevin Tappe.
* checkRdaFiles(ff)$version is now correct also when ff contains
files of different versions, thanks to a report and patch from
Sebastian Meyer in PR#18041.
* macOS: Quartz device live drawing could fail (no plot is shown)
if the system changes the drawing context after view update
(often the case since macOS Big Sur). System log may show
"CGContextDelegateCreateForContext: invalid context" error.
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
______________________________________________
R-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
|
[Rd] R 4.0.4 is released
|
Peter Dalgaard
| 631
|
|
From Ted.Harding at nessie.mcc.ac.uk Sun Jun 14 20:55:18 1998
From: Ted.Harding at nessie.mcc.ac.uk ( (Ted Harding))
Date: Sun, 14 Jun 1998 19:55:18 +0100 (BST)
Subject: R-beta: R-0.62 is released
In-Reply-To: <[email protected]>
Message-ID: <[email protected]>
On 14-Jun-98 Peter Dalgaard BSA wrote:
> I've put up R-0.62.0.tgz up for FTP from Auckland some minutes ago.
> As usual, don't get it from there unless you are desperate, but wait
> for it to be mirrored at a CRAN site near you within a day or two.
You didn't expect us to be THAT patient, did you?!
Some comments (compiling on S.u.S.E. Linux 5.1):
1. I like to compile in a side-room, /depot/R-0.62 as it happens.
My intended ultimate destination was /usr/local/R-0.62. After setting
prefix, "./configure", "make", and "make install", it wouldn't run properly.
Despite trying every obvious config option, the "R" script had insisted
on setting RHOME as the directory it was compiled from: /depot/R-0.62/R-0.62/
It took some time to suss out that this needed to be edited to read
RHOME=/usr/local/R-0.62/lib/R
After this was done, it seems fine. The above is NOT obvious from the INSTALL
document.
2. The "help" browser seems to be hard-wired to be netscape. This can of course
be changed by editing the function "help.start" in
/usr/local/R-0.62/lib/R/library/base/R
but the knock-on effects are not obvious.
a) I don't have netscape on the machine I run R on;
b) In any case, with KDE on this machine, I like to use the program
/opt/kde/bin/kdehelp
as HTML browser: it's attractive-looking, slim (199428 bytes!) and fast.
I'd welcome informed advice on how to change this function without breaking
anything else that depends on it, and on any consequential changes that may
be needed.
That's it for now. More later, possibly ... !
With thanks, and best wishes to all,
Ted.
--------------------------------------------------------------------
E-Mail: (Ted Harding) <Ted.Harding at nessie.mcc.ac.uk>
Date: 14-Jun-98 Time: 19:55:18
--------------------------------------------------------------------
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r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
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|
R-beta: R-0.62 is released
|
(Ted Harding
| 533
|
|
From p.dalgaard at biostat.ku.dk Mon Nov 15 16:07:05 2004
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard)
Date: 15 Nov 2004 16:07:05 +0100
Subject: R-2.0.1 is released
Message-ID: <[email protected]>
I've rolled up R-2.0.1.tgz a short while ago. This is a maintenance
version mainly to fix a number of minor bugs and issues. (Some rather
nasty ones were Windows-specific - please check the CHANGES file for
those.)
You can get it from
http://cran.r-project.org/src/base/R-2.0.1.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you. Binaries
for various platforms will appear in due course.
There is also a version split for floppies.
These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:
6f75951d61cc321f597ea28ad43a9ada INSTALL
b5519f795224506e7702f74dbbb152b1 NEWS
1a2248b10e3dbf078559705a25b52ca4 ONEWS
fb47b1fdef4323031e24d541a2f36b2b R-2.0.1.tar.gz
4e334bc539e5a2d8cc3e6b8cca4171be R-2.0.1.tar.gz-split.aa
bc7cb22034948998a4eeb18006a53094 R-2.0.1.tar.gz-split.ab
b73f587c39599ce47bba00544f2cd100 R-2.0.1.tar.gz-split.ac
bbec006c26c6a236c6b5e98989a2f0a2 R-2.0.1.tar.gz-split.ad
8d04842319525ba6cead4bff1b259263 R-2.0.1.tar.gz-split.ae
e3d1af261c7ea83820597f6fef9e9449 R-2.0.1.tar.gz-split.af
3595c1939484762a6440a957908023ce R-2.0.1.tar.gz-split.ag
4492e468cc5003e06a2a85c496ff2672 R-2.0.1.tar.gz-split.ah
fb47b1fdef4323031e24d541a2f36b2b R-latest.tgz
b5509d1e6232e66dee66d9644bf65490 README
7a5a7cfe9419affd9574aba3cf525741 RESOURCES
Here is the relevant bit of the NEWS file:
CHANGES IN R VERSION 2.0.1
NEW FEATURES
o Platform equivalence in library() is tested by a new function
testPlatformEquivalence() which ignores the 'vendor' field and
can be customized by cognescenti.
o The assignment form of split() allows recycling of vectors
within the value list. In particular, things like
split(x, g) <- lapply(split(x, g), mean)
now work
DOCUMENTATION
o Manual `Writing R Extensions' has new sections on writing
portable packages and on writing new front-ends for R -- the
latter will be more comprehensive in R 2.1.0 which has new
public header files.
DEPRECATED & DEFUNCT
o The aqua module in MacOS X is deprecated.
o Capabilities "bzip2", "GNOME, "libz" and "PCRE" are deprecated.
o The GNOME GUI on Unix-alikes is deprecated as part of R;
it will be available in another form as from R 2.1.0.
o The undocumented use of UseMethod() with no argument is now
formally deprecated.
INSTALLATION CHANGES
o Building on Alpha OSF/1 no longer forces the C flag -std1,
which appears to be no longer needed. (PR#7257)
o The compiler flag -mieee-fp is no longer used on i386 Linux
(these days it is only passed to the linker and was only
invoked for compilation steps).
o -D__NO_MATH_INLINES is only used on older ix86 glibc-based
systems which need it (tested at configure time). This leads to
small improvements in speed and accuracy on modern systems.
o If makeinfo >= 4.5 is not available, warnings are given that
some of the HTML manuals will be missing, and the index page
given by help.start() will link to CRAN versions of those manuals.
o Files aclocal.m4 and acinclude.m4 used in maintainer builds
are not longer included in the distribution.
C-LEVEL FACILITIES
o It was not clear in 'Writing R Extensions' that some of the
entry points in the 'Utilities' section were not declared in
<R.h> (they were in <R_ext/Applic.h>). Now all the entry
points in that section are declared in <R_ext/Utils.h>,
included by <R.h>.
BUG FIXES
o The grid.grab() function in package grid would throw an error
if there were no viewports pushed (now returns NULL).
o model.frame.default() takes row names from the response
variable if that has suitable names and there is no 'data'
argument. (This follows S but was not previously implemented
in R.)
o write.table() was not respecting the 'dec' argument for complex
numbers.
o write.table() printed a mixture of numeric and complex numbers
as all complex. (PR#7260)
o R CMD INSTALL failed with versioned installs on packages which
save images (only).
o dlogis() gave NaN not 0 for large negative arguments.
o Importing from another namespace was broken for versioned
installs, incorrectly reporting something like
"package 'imported_from' does not have a name space".
o The GNOME interface under Linux/Unix was broken. (PR#7276)
o For the jpeg/png devices under Linux/Unix, under certain rare
circumstances clipping needed to be cleared before starting a
new page. (PR#7270, which has been the case since the devices
were introduced in 1.1.0.)
o First lattice plot (first grid.newpage() call) did not start
a new page IF there had been a previous traditional graphics
plot (on the same device).
o Using install.packages() to install the same package to more
than one library gave an incorrect warning message. (If there
were two or more such packages it might give an error.)
o .packages(all.available=TRUE) returned packages with an invalid
version field in their DESCRIPTION whereas .find.packages() and
packageDescription() did not. Now all do not.
o packageDescription() now correctly reports that a package does
not exist, rather than that its DESCRIPTION file is 'missing
or broken'.
o 'make dist' from builddir != sourcedir was copying not linking
recommended packages to *.tgz.
o Slots in prototype objects can inherit from locally defined
classes (which were not being found correctly before).
o Several fixes to the behavior of as() when there are either
coerce= or replace= methods supplied in a call to
setIs(). Related fixes to setIs() to handle correctly previous
methods, if there were any.
o splinefun(1[0], 1[0])(1) doesn't segfault anymore (PR#7290).
spline() and splinefun() now also work with missing values by
omiting them.
o ecdf() was failing on inputs containing NAs. (Part of PR#7292)
o tools:::.install_package_description was splitting the Built:
field across lines on platforms with very long names.
o capabilities() was wrong for the Aqua GUI on MacOS X.
o Using Rprof() with a non-writable 'file' argument is now a
non-fatal error and does not abort R.
o binom.test() did not deparse its arguments early enough such
that the reported data were ugly if x was a table.
o Systems based on glibc, including those using R's substitute for
strptime, were handling strptime("2001", "%Y") incorrectly, in
some cases crashing. R's substitute code has been corrected
(but problems may remain if glibc is used). See the ?strptime
for what should happen (which is system-specific).
o untrace() after trace() failed if package 'methods' was attached.
(PR#7301)
o summary.stepfun() was reporting for n > 6 summaries of the
knots and levels as the actual values. Both print() and
summary() methods called the constant values "step heights",
although they were not the heights of the steps.
o is.na/is.nan() were giving spurious warnings if applied to a
raw vector.
o is.atomic() gave incorrect result (false) for a raw vector.
o rank() and order() accepted raw and list inputs, but did not
give a sensible answer (always 1:n). Similarly, partial sorts
of a raw vector were accepted but did nothing.
o require() without a version argument tried for an unversioned
load of a package even though a versioned install was already
loaded. This often led to a message that a required package
was being loaded when it was not actually being loaded.
o str(<S4.object>) made use of attributes() instead of slot(),
and hence didn't properly print NULL slots.
o contrib.url() now handles URLs ending in '/' correctly.
o str() removed any class from externalptr objects.
o logLik() and hence AIC() failed or gave incorrect answers
on "lm" fits with na.action = na.exclude (and perhaps other
na.actions's except na.omit and na.fail).
o pmax() and pmin() sometimes used NAs in internal subassignments,
and sometimes these failed.
o Subassigning an expression, e.g. expr[2] <- 1, could leave an
invalid object and so cause a segfault. (PR#7326)
o download/install.packages() would misbehave if there was more
than one version of a package in a repository.
o sort(partial=) silently ignored some other arguments: using
'decreasing' or 'index.return' or supplying a factor are now
errors.
o The ave() function had trouble if the grouping contained
unused levels.
o read.fwf() got confused by skip > 0 and could infinite loop
under some circumstances. (PR#7350)
o upgrade(x, ask = FALSE) was broken for a "packageStatus" object.
o Class "raw" had been omitted from the list of basic classes in
the "methods" package and so could not be used in S4 classes.
o Function getGroupMembers(), part of the definition of S4
classes, had been promised for release 2.0, but slipped through.
--
O__ ---- Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
|
R-2.0.1 is released
|
Peter Dalgaard
| 386
|
|
From pd@me@ @end|ng |rom cb@@dk Mon Mar 11 09:35:49 2019
From: pd@me@ @end|ng |rom cb@@dk (Peter Dalgaard)
Date: Mon, 11 Mar 2019 08:35:49 +0000
Subject: R 3.5.3 is released
Message-ID: <[email protected]>
The build system rolled up R-3.5.3.tar.gz (codename "Great Truth") this morning.
The list below details the changes in this release. This is the wrap-up release for the 3.5.x series, so actually, not much has happened.
You can get the source code from
http://cran.r-project.org/src/base/R-3/R-3.5.3.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you.
Binaries for various platforms will appear in due course.
For the R Core Team,
Peter Dalgaard
These are the checksums (md5 and SHA-256) for the freshly created files, in case you wish
to check that they are uncorrupted:
MD5 (AUTHORS) = b9c44f9f78cab3184ad9898bebc854b4
MD5 (COPYING) = eb723b61539feef013de476e68b5c50a
MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343
MD5 (FAQ) = 3bba37aa1dd06de3f781200a8081302f
MD5 (INSTALL) = 7893f754308ca31f1ccf62055090ad7b
MD5 (NEWS) = ab129f42b1d5ca25122db6b1bda0fcd9
MD5 (NEWS.0) = bfcd7c147251b5474d96848c6f57e5a8
MD5 (NEWS.1) = eb78c4d053ec9c32b815cf0c2ebea801
MD5 (NEWS.2) = 591dcf615162127f904e4e461f330ce9
MD5 (R-latest.tar.gz) = 525e902dd331c387f271692a1537aff8
MD5 (README) = f468f281c919665e276a1b691decbbe6
MD5 (RESOURCES) = 529223fd3ffef95731d0a87353108435
MD5 (THANKS) = 08158353102084599797db8c9ccf8e2a
MD5 (VERSION-INFO.dcf) = cb61b0eb560efcbbec47128abf3fb761
MD5 (R-3/R-3.5.3.tar.gz) = 525e902dd331c387f271692a1537aff8
2cde824a7b18958e5f06b391c801c8288be0f84fa8934b7ddefef23c67e60c09 AUTHORS
e6d6a009505e345fe949e1310334fcb0747f28dae2856759de102ab66b722cb4 COPYING
6095e9ffa777dd22839f7801aa845b31c9ed07f3d6bf8a26dc5d2dec8ccc0ef3 COPYING.LIB
98df47801c33cc4f4a4de98447cb2bd40e09c0920195f540a981ceed874714f2 FAQ
f87461be6cbaecc4dce44ac58e5bd52364b0491ccdadaf846cb9b452e9550f31 INSTALL
4c6eb7cd9d8f4c1858a8f853698d2954d42d5d8b71c5c4d20bc6bd970f034bfe NEWS
4e21b62f515b749f80997063fceab626d7258c7d650e81a662ba8e0640f12f62 NEWS.0
12b30c724117b1b2b11484673906a6dcd48a361f69fc420b36194f9218692d01 NEWS.1
ca04f78ffe54afa326fe3ed40e7e1411aca0000ed2fa5ead97ddf51c6aa5b7bc NEWS.2
2bfa37b7bd709f003d6b8a172ddfb6d03ddd2d672d6096439523039f7a8e678c R-latest.tar.gz
2fdd3e90f23f32692d4b3a0c0452f2c219a10882033d1774f8cadf25886c3ddc README
408737572ecc6e1135fdb2cf7a9dbb1a6cb27967c757f1771b8c39d1fd2f1ab9 RESOURCES
2d2e85e85574c4430951f6b070c08cd5aff1602abfd1bb162bed6d89c436b11f THANKS
1ce83e7a843f95e8b0d5abf6ced7426cc337cc607f9862f99d46a7d05793ac15 VERSION-INFO.dcf
2bfa37b7bd709f003d6b8a172ddfb6d03ddd2d672d6096439523039f7a8e678c R-3/R-3.5.3.tar.gz
This is the relevant part of the NEWS file:
CHANGES IN R 3.5.3:
INSTALLATION on a UNIX-ALIKE:
* Detection of flags for C++98/11/14/17 has been improved: in
particular if CXX??STD is set, it is tried first with no
additional flags.
PACKAGE INSTALLATION:
* New macro F_VISIBILITY as an alternative to F77_VISIBILITY. This
will become the preferred form in R 3.6.0.
BUG FIXES:
* writeLines(readLines(fnam), fnam) now works as expected, thanks
to Peter Meissner's PR#17528.
* setClassUnion() no longer warns, but uses message() for now, when
encountering "non local" subclasses of class members.
* stopifnot(exprs = T) no longer fails.
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
|
R 3.5.3 is released
|
Peter Dalgaard
| 670
|
|
From guido at hal.stat.unipd.it Wed Nov 24 10:31:07 1999
From: guido at hal.stat.unipd.it (Guido Masarotto)
Date: Wed, 24 Nov 1999 10:31:07 +0100
Subject: R 0.90.0 for Windows
Message-ID: <[email protected]>
A binary distribution of R 0.90.0 for Windows is available at
http://cran.r-project.org (in bin/windows/windows-NT/base).
It should run on Windows 9X/NT/2000 systems.
Windows News:
-------------
We made a determined attempt to quote paths which might contain spaces,
and almost all cases work. Be careful with external unzip, pager and editor
programs that these do handle quoted paths.
Rterm can be interrupted by Ctrl-C as well as Ctrl-Break. Fast
typing should not give problems in interactive use.
Better formatting of math expressions in graphics labels, legends, ...
(but only if font is True Type since it seems not possible to get
per-char font metric information for raster fonts).
Support for GIF format bitmaps has been removed, but support for PNG,
JPEG and BMP has been added. This can be done via the File menu on the
graphics window, savePlot() or dev.print to the new devices png(), bmp()
and jpeg(), which can also be used directly.
PDF versions of the (draft) manuals are available in file rw0900d.zip
and install into rw0900/doc/manual. These can be read in Acrobat
Reader from the Manuals sub-menu of the Help menu provided they and
the reader (http://www.adobe.com) are installed.
The installer will install packages in the library directory if the
installation directory path ends in rw0900.
You can install packages by
install.packages("/path/to/mypkg.zip", CRAN=NULL)
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
R 0.90.0 for Windows
|
Guido Masarotto
| 509
|
|
From deleeuw at stat.ucla.edu Fri Aug 31 19:33:32 2001
From: deleeuw at stat.ucla.edu (Jan de Leeuw)
Date: Fri, 31 Aug 2001 10:33:32 -0700
Subject: R-1.3.1 for OS X
Message-ID: <[email protected]>
The full version with 154 packages is on
http://gifi.stat.ucla.edu/R
I dropped the gnome support, and ATLAS is now standard.
Unpack in /usr/local
Once again, if your R complains about missing dynamic
libraries, first look in
http://gifi.stat.ucla.edu/R/dylibs
and if you cannot find what you need drop me an email.
===
Jan de Leeuw; Professor and Chair, UCLA Department of Statistics;
US mail: 9432 Boulter Hall, Box 951554, Los Angeles, CA 90095-1554
phone (310)-825-9550; fax (310)-206-5658; email: deleeuw at stat.ucla.edu
homepage: http://www.stat.ucla.edu/~deleeuw
========================================================
No matter where you go, there you are. --- Buckaroo Banzai
http://www.stat.ucla.edu/~deleeuw/sounds/nomatter.au
========================================================
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|
R-1.3.1 for OS X
|
Jan de Leeuw
| 267
|
|
From pd.mes at cbs.dk Fri Jun 22 11:33:55 2012
From: pd.mes at cbs.dk (Peter Dalgaard)
Date: Fri, 22 Jun 2012 11:33:55 +0200
Subject: R 2.15.1 is released
Message-ID: <[email protected]>
The build system has rolled up R-2.15.1.tar.gz (codename "Roasted Marshmallows") at 9:00 this morning. This is a maintenance release; see the list below for details.
You can get it from
http://cran.r-project.org/src/base/R-2/R-2.15.1.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you.
Binaries for various platforms will appear in due course.
For the R Core Team
Peter Dalgaard
These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:
MD5 (AUTHORS) = cbf6da8f886ccd8d0dda0cc7ffd1b8ec
MD5 (COPYING) = eb723b61539feef013de476e68b5c50a
MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343
MD5 (FAQ) = fa1101eba3c4c01ffa154053a5dcd2d6
MD5 (INSTALL) = 37adac6d0fbadf25b5a40e3f7535415e
MD5 (NEWS) = 8d6a52daa2d18630a8aa7a8e7a58ddf6
MD5 (NEWS.html) = 4a8f2f5824ba44427719e2badc5128d1
MD5 (ONEWS) = 0c3e10eef74439786e5fceddd06dac71
MD5 (OONEWS) = b0d650eba25fc5664980528c147a20db
MD5 (R-latest.tar.gz) = fcdf247e707fdade82b78bcf911a54f1
MD5 (README) = 296871fcf14f49787910c57b92655c76
MD5 (RESOURCES) = a7a02d98a407c3cb8674d067608f14fc
MD5 (THANKS) = 159efc7bd4ae7b23dda07c1d431657bc
MD5 (R-2/R-2.15.1.tar.gz) = fcdf247e707fdade82b78bcf911a54f1
This is the relevant part of the NEWS file:
CHANGES IN R VERSION 2.15.1:
NEW FEATURES:
o source() now uses withVisible() rather than
.Internal(eval.with.vis). This sometimes alters tracebacks
slightly.
o install.packages("pkg_version.tgz") on Mac OS X now has sanity
checks that this is actually a binary package (as people have
tried it with incorrectly named source packages).
o splineDesign() and spline.des() in package splines have a new
option sparse which can be used for efficient construction of a
sparse B-spline design matrix (_via_ Matrix).
o norm() now allows type = "2" (the 'spectral' or 2-norm) as well,
mainly for didactical completeness.
o pmin() and pmax()) now also work when one of the inputs is of
length zero and others are not, returning a zero-length vector,
analogously to, say, +.
o colorRamp() (and hence colorRampPalette()) now also works for the
boundary case of just one color when the ramp is flat.
o qqline() has new optional arguments distribution, probs and
qtype, following the example of lattice's panel.qqmathline().
o .C() gains some protection against the misuse of character vector
arguments. (An all too common error is to pass character(N),
which initializes the elements to "", and then attempt to edit
the strings in-place, sometimes forgetting to terminate them.)
o Calls to the new function globalVariables() in package utils
declare that functions and other objects in a package should be
treated as globally defined, so that CMD check will not note
them.
o print(packageDescription(*)) trims the Collate field by default.
o The included copy of zlib has been updated to version 1.2.7.
o A new option "show.error.locations" has been added. When set to
TRUE, error messages will contain the location of the most recent
call containing source reference information. (Other values are
supported as well; see ?options.)
o The NA warning messages from e.g. pchisq() now report the call to
the closure and not that of the .Internal.
o Added Polish translations by <c5><81>ukasz Daniel.
PERFORMANCE IMPROVEMENTS:
o In package parallel, makeForkCluster() and the multicore-based
functions use native byte-order for serialization (deferred from
2.15.0).
o lm.fit(), lm.wfit(), glm.fit() and lsfit() do less copying of
objects, mainly by using .Call() rather than .Fortran().
o .C() and .Fortran() do less copying: arguments which are raw,
logical, integer, real or complex vectors and are unnamed are not
copied before the call, and (named or not) are not copied after
the call. Lists are no longer copied (they are supposed to be
used read-only in the C code).
o tabulate() makes use of .C(DUP = FALSE) and hence does not copy
bin. (Suggested by Tim Hesterberg.) It also avoids making a
copy of a factor argument bin.
o Other functions (often or always) doing less copying include
cut(), dist(), the complex case of eigen(), hclust(), image(),
kmeans(), loess(), stl() and svd(LINPACK = TRUE).
o There is less copying when using primitive replacement functions
such as names(), attr() and attributes().
DEPRECATED AND DEFUNCT:
o The converters for use with .C() (see ?getCConverterDescriptions)
are deprecated: use the .Call() interface instead. There are no
known examples (they were never fully documented).
UTILITIES:
o For R CMD check, a few people have reported problems with
junctions on Windows (although they were tested on Windows 7, XP
and Server 2008 machines and it is unknown under what
circumstances the problems occur). Setting the environment
variable R_WIN_NO_JUNCTIONS to a non-empty value (e.g. in
~/.R/check.Renviron) will force copies to be used instead.
INSTALLATION:
o R CMD INSTALL with _R_CHECK_INSTALL_DEPENDS_ set to a true value
(as done by R CMD check --as-cran) now restricts the packages
available when lazy-loading as well as when test-loading (since
packages such as ETLUtils and agsemisc had top-level calls to
library() for undeclared packages).
This check is now also available on Windows.
C-LEVEL FACILITIES:
o C entry points mkChar and mkCharCE now check that the length of
the string they are passed does not exceed 2^31-1 bytes: they
used to overflow with unpredictable consequences.
o C entry points R_GetCurrentSrcref and R_GetSrcFilename have been
added to the API to allow debuggers access to the source
references on the stack.
WINDOWS-SPECIFIC CHANGES:
o Windows-specific changes will now be announced in this file
(NEWS). Changes up and including R 2.15.0 remain in the CHANGES
file.
o There are two new environment variables which control the
defaults for command-line options.
If R_WIN_INTERNET2 is set to a non-empty value, it is as if
--internet2 was used.
If R_MAX_MEM_SIZE is set, it gives the default memory limit if
--max-mem-size is not specified: invalid values being ignored.
BUG FIXES:
o lsfit() lost the names from the residuals.
o More cases in which merge() could create a data frame with
duplicate column names now give warnings. Cases where names
specified in by match multiple columns are errors.
o Nonsense uses such as seq(1:50, by = 5) (from package plotrix)
and seq.int(1:50, by = 5) are now errors.
o The residuals in the 5-number summary printed by summary() on an
"lm" object are now explicitly labelled as weighted residuals
when non-constant weights are present. (Wish of PR#14840.)
o tracemem() reported that all objects were copied by .C() or
.Fortran() whereas only some object types were ever copied.
It also reported and marked as copies _some_ transformations such
as rexp(n, x): it no longer does so.
o The plot() method for class "stepfun" only used the optional xval
argument to compute xlim and not the points at which to plot (as
documented). (PR#14864)
o Names containing characters which need to be escaped were not
deparsed properly. (PR#14846)
o Trying to update (recommended) packages in R_HOME/library without
write access is now dealt with more gracefully. Further, such
package updates may be skipped (with a warning), when a newer
installed version is already going to be used from .libPaths().
(PR#14866)
o hclust() is now fast again (as up to end of 2003), with a
different fix for the "median"/"centroid" problem. (PR#4195).
o get_all_vars() failed when the data came entirely from vectors in
the global environment. (PR#14847)
o R CMD check with _R_CHECK_NO_RECOMMENDED_ set to a true value (as
done by the --as-cran option) could issue false errors if there
was an indirect dependency on a recommended package.
o formatC() uses the C entry point str_signif which could write
beyond the length allocated for the output string.
o Missing default argument added to implicit S4 generic for
backsolve(). (PR#14883)
o Some bugs have been fixed in handling load actions that could
fail to export assigned items or generate spurious warnings in
CMD check on loading.
o For tiff(type = "windows"), the numbering of per-page files
except the last was off by one.
o On Windows, loading package stats (which is done for a default
session) would switch line endings on stdout and stderr from CRLF
to LF. This affected Rterm and R CMD BATCH.
o On Windows, the compatibility function x11() had not kept up with
changes to windows(), and issued warnings about bad parameters.
(PR#14880)
o On Windows, the Sys.glob() function did not handle UNC paths as
it was designed to try to do. (PR#14884)
o In package parallel, clusterApply() and similar failed to handle
a (pretty pointless) length-1 argument. (PR#14898)
o Quartz Cocoa display reacted asynchronously to dev.flush() which
means that the redraw could be performed after the plot has been
already modified by subsequent code. The redraw is now done
synchronously in dev.flush() to allow animations without sleep
cycles.
o Source locations reported in traceback() were incorrect when
byte-compiled code was on the stack.
o plogis(x, lower = FALSE, log.p = TRUE) no longer underflows early
for large x (e.g. 800).
o ?Arithmetic's "1 ^ y and y ^ 0 are 1, _always_" now also applies
for integer vectors y.
o X11-based pixmap devices like png(type = "Xlib") were trying to
set the cursor style, which triggered some warnings and hangs.
o Code executed by the built-in HTTP server no longer allows other
HTTP clients to re-enter R until the current worker evaluation
finishes, to prevent cascades.
o The plot() and Axis() methods for class "table" now respect
graphical parameters such as cex.axis. (Reported by Martin
Becker.)
o Under some circumstances package.skeleton() would give out
progress reports that could not be translated and so were
displayed by question marks. Now they are always in English.
(This was seen for CJK locales on Windows, but may have occurred
elsewhere.)
o The evaluator now keeps track of source references outside of
functions, e.g. when source() executes a script.
o The replacement method for window() now works correctly for
multiple time series of class "mts". (PR#14925)
o is.unsorted() gave incorrect results on non-atomic objects such
as data frames. (Reported by Matthew Dowle.)
o The value returned by tools::psnice() for invalid pid values was
not always NA as documented.
o Closing an X11() window while locator() was active could abort
the R process.
o getMethod(f, sig) produced an incorrect error message in some
cases when f was not a string).
o Using a string as a "call" in an error condition with
options(showErrorCalls=TRUE) could cause a segfault. (PR#14931)
o The string "infinity" allowed by C99 was not accepted as a
numerical string value by e.g. scan() and as.character().
(PR#14933)
o In legend(), setting some entries of lwd to NA was inconsistent
(depending on the graphics device) in whether it would suppress
those lines; now it consistently does so. (PR#14926)
o by() failed for a zero-row data frame. (Reported by Weiqiang
Qian)
o Yates correction in chisq.test() could be bigger than the terms
it corrected, previously leading to an infinite test statistic in
some corner cases which are now reported as NaN.
o xgettext() and related functions sometimes returned items that
were not strings for translation. (PR#14935)
o plot(<lm>, which=5) now correctly labels the factor level
combinations for the special case where all h[i,i] are the same.
(PR#14837)
--
Peter Dalgaard, Professor
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
|
R 2.15.1 is released
|
Peter Dalgaard
| 441
|
|
From p.dalgaard at biostat.ku.dk Fri Aug 27 15:06:46 1999
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard BSA)
Date: 27 Aug 1999 15:06:46 +0200
Subject: R-0.65.0 is released
Message-ID: <[email protected]>
I've rolled up R-0.65.0.tgz a moment ago.
You shouldn't get it from Auckland, but wait for it to be mirrored at
a CRAN site near you within a day or two. With the current transfer
speed from Auckland, you probably don't need a deterrent anyway...
For those who are too curious to wait, I'll put a copy in
ftp://blueberry.kubism.ku.dk/pub/R-devel/R-0.65.0.tgz
There's also a version split in two for floppies if you prefer that.
For the R Core Team,
Peter D.
The relevant part of the NEWS file follows below. In addition, GNOME
support, although still experimental, has been considerably improved.
You'll need a substantial amount of support libraries, see the INSTALL
file for details.
NEW FEATURES
o A first step in improving performance has been made.
Attached objects, libraries etc are now hashed; performance
gains will be particularly apparent if large packages are in use.
o First version of package ts for time-series analysis.
This has fairly complete S-PLUS compatibility, but more features
are planned. See library(help=ts) for details.
o warnings can be collected (options(warn=0), the default), printed
immediately (options(warn=1)) or turned into errors (options(warn=2)).
As a consequence, all warnings and errors now are printed followed
by a newline, if one is not supplied. (This should improve the
S compatibility of the use of PROBLEM ... in compiled code.)
o All R environment variables are now of the form `R_xxx'. In
particular, `RHOME', `RLIBS' and `RPROFILE' are now called
`R_HOME', `R_LIBS', and `R_PROFILE'.
o The handling of q()/quit()/EOF has been changed, with a new option
"default". In interactive use this asks unless --save or --no-save
has been specified: if these are specified they set the default.
o Limited capability for tilde expansion of file names even without
readline (on Unix, and on Windows).
o New environment variables `R_HISTFILE' and `R_HISTSIZE' for the
name and size of the history file.
o Attempting to restore (at startup) too large a .RData is now
a fatal error.
o The loading of shared library on Unix now uses RTLD_NOW not
RTLD_LAZY. This means that all symbols must be resolvable
when the library is loaded, and R will not terminate later
when a missing symbol is called. Code which had missing symbols
(including some packages) will need to be re-compiled.
o New generic function all.equal();
most useful for numerical comparisons `up to rounding errors'.
o New function boxplot.formula() as a formula interface to boxplots.
o New functions getwd() and setwd() for getting and setting the R
working directory, basename() and dirname() for manipulating paths.
o Function locator(, type=) is implemented to plot points or
draw lines interactively.
o Functions new.env() to create empty environment and local() to
allow local evaluation of expressions, with various useful
idiomatic uses.
o Convenience functions parent.frame() and eval.parent().
o A new scheme for keeping source code with user-defined
functions has been implemented. In particular, comments
will no longer move about or disappear. The flip side of the
coin is that you can no longer rely on R to indent your
code for you. The stored-source facility can be turned
off with options(keep.source=FALSE), and for an individual
function by deleting the "source" attribute.
If the source attribute is absent, the function will be
deparsed for editing or printing, but any comments will be
lost.
o expressions have gained semantics that are closer to
those of S. They don't get evaluated except when explicitly
specified. Example:
e <- expression(x); e[[1]] <- expression(123); eval(e)
now gives expression(123), not 123. This fixes some problems
with expressions in the list argument to do.call().
o contrast() no longer drops colnames for 1DF contrasts.
Consequentially, the labels of regression coefficients for binary
factors contain level names (again ...).
o na.omit() and na.fail() are now generic.
o plot.lm() has more options and now does 4 plots by default, should
also be okay for "glm" object; all thanks to John Maindonald.
o If the dimnames of a table are themselves named, then their names
are used to label the respective dimensions in tabular output.
o chisq.test() now optionally computes the p-value by Monte Carlo
simulation (in the standard case of a 2-d contigency table).
o source() has a new argument `chdir' for changing the working
directory to that of the file being sourced when evaluating.
o If data() loads an R source file, it now changes the working
directory (to that containing the file) when evaluating.
o Interpret strings NaN and Inf in character to numeric conversions
(and thereby in read.table)
o The presence of an object `.conflicts.OK' in a package suppresses
conflict checking in library() for that package.
o uniroot() can now be used recursively.
o hdf5{read|write} now allow more kinds of attributes and add support
for HDF5 version 1.2 (or newer) thanks to Marcus G. Daniels.
Configure checks for HDF5 1.2 availability, older versions will
no longer work.
BUG FIXES
o x ^ y gives proper results when x or y are infinite.
o The semantics of <<- have been corrected. The search for
a variable binding to modify now begins one level "up" from
the current one. Thus S and R semantics in "non-closure"
functions will be identical.
o .Last() is called when terminating with q() (not just with EOF).
o abline() now understands the "lwd" graphics parameter if it
is supplied as an inline argument.
o axis() now sorts `labels' when it sorts `at'.
o Some small changes have made in the axis drawing code to
ensure that tick-mark label alignment is correct for
non-default values of the "las" parameter.
o Improved error message from check.options().
o cm.colors(n) now doesn't append silly "v=1"; works for n=0, n=1.
o cooks.distance() now also works for "glm" objects;
deviance.lm() now ok for the case of weights.
o date() doesn't return a final "\n" (again ...).
o diag() and diag<- now handle correctly matrices with zero rows or cols.
o help([<-.factor) (etc) work again.
o is.recursive(list(.)) is now TRUE [PR#221].
o log(0) gives -Inf on all architectures.
o When persp() was the first graphics command given to R it gave
the error "plot.new() has not been called yet". This no
longer happens.
o pgamma() gave 0 or 1 for extreme arguments too soon.
o plot(<function>, log="x") doesn't give a silly warning any more.
o The internals of postscript() have been changed so that line
textures (dotted dashed etc) look better. The use of the
PostScript "initclip" operator has been removed so that we
can(?) really claim eps compliance.
o revsort() misbehaved if n<=1, causing sample(1,1,,1) to
segfault
o seq(along = v) { and seq(v) when length(v) > 1 } now returns
a result of mode "integer".
o split.default() now uses subscripting for x with a non-null
class, this preserves, e.g., the class of factors
o substr/substring(), deparse(), dput(), dump(), print()
will work for arbitrarily long strings.
o which(x) failed when x had names and contained NAs.
o Default editor files (e.g. from fix()) are now removed at termination.
o Typos in NegBinomial.Rd (Negative Binomial distrib), thanks to Ch. Gu.
o a clipping problem for plots when there non-zero outer margins
has been fixed. This problem used to affect coplot() and pairs().
o get("zzz", mode="xxx") missed promise objects.
o match.fun failed when a data frame was attached containing a
"length" variable (e.g.)
--
O__ ---- Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
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|
R-0.65.0 is released
|
Peter Dalgaard BSA
| 496
|
|
From gregory_r_warnes at groton.pfizer.com Wed Dec 4 13:49:05 2002
From: gregory_r_warnes at groton.pfizer.com (Warnes, Gregory R)
Date: Wed Dec 4 13:49:05 2002
Subject: Initial release of RSOAP - a simple interface to R via SOAP
Message-ID: <[email protected]>
Announcing the initial public release of RSOAP at
http://software.biostat.washington.edu/statsoft/snake/RSOAP.
Description:
RSOAP provides a SOAP interface for the open-source statistical
package R. It permits software to take advantage of the advanced
statistical analysis techniques provided by R---running either
locally or on a remote machine---using the simple and widely
accepted SOAP protocol.
RSOAP provides a simple API for managing and communicating with
multiple concurrent R processes. Using SOAP as the communications
protocol avoids direct handling of binary data while preserving
the underlying data structures, and makes R easily accessible
from a variety of applications and programming languages.
Availability:
More information and the source code for RSOAP is available at
http://software.biostat.washington.edu/statsoft/snake/RSOAP/manage.
-Greg
LEGAL NOTICE
Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this E-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents of this E-mail or any action taken (or not taken) in reliance on it is unauthorized and may be unlawful. If you are not an addressee, please inform the sender immediately.
|
Initial release of RSOAP - a simple interface to R via SOAP
|
Warnes, Gregory R
| 112
|
|
From deleeuw at stat.ucla.edu Sun Apr 22 17:54:51 2001
From: deleeuw at stat.ucla.edu (Jan de Leeuw)
Date: Sun, 22 Apr 2001 08:54:51 -0700
Subject: new Darwin/X11 builds
Message-ID: <[email protected]>
New MacOS X (Darwin with X11R6) builds are at
http://www.stat.ucla.edu/~deleeuw/R
These include some dylibs that were missing from previous
builds. One is of R-1.2.2 (patched), the other of R-devel
(with many add-on libraries included).
You do need some version of X11 (I use Xtools, they tell me
Xfree also works) installed.
If something does not work for you, drop me an email.
===
Jan de Leeuw; Professor and Chair, UCLA Department of Statistics;
US mail: 9432 Boulter Hall, Box 951554, Los Angeles, CA 90095-1554
phone (310)-825-9550; fax (310)-206-5658; email: deleeuw at stat.ucla.edu
http://www.stat.ucla.edu/~deleeuw and http://home1.gte.net/datamine/
========================================================
No matter where you go, there you are. --- Buckaroo Banzai
http://www.stat.ucla.edu/sounds/nomatter.au
========================================================
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
|
new Darwin/X11 builds
|
Jan de Leeuw
| 232
|
|
From francois.husson at agrocampus-ouest.fr Tue Feb 3 16:02:29 2009
From: francois.husson at agrocampus-ouest.fr (Francois Husson)
Date: Tue, 03 Feb 2009 15:02:29 +0000
Subject: Abstract submission deadline for useR! 2009
Message-ID: <[email protected]>
Dear members of the R user community,
the submission deadline for useR! 2009 (Rennes, France, July 8 to 10,
2009) is approaching:
Submission deadline: 2009-02-27
(and along with that the early registration deadline).
We encourage you to give a presentation at the conference and submit an
abstract or a poster on topics presenting innovations or exciting
applications of R. You can use the conference Web page at
http://www.R-project.org/useR-2009/
Invited speakers will include: Adele Cutler, Peter Dalgaard, Jerome H.
Friedman, Michael Greenacre, Trevor Hastie, John Storey, Martin Theus.
July 7, 2009, half-day tutorials are presented by R experts prior to the
conference.
The conference web page:
http://www.agrocampus-ouest.fr/math/useR-2009/accomodation.html
gives a list of hotels and some student rooms (200) are also available
on the campus (Rennes will be very busy at the conference time because
the cultural event `Festival Les tomb?es de la nuit' will take place at
the same time, so we recommend to book as soon as possible).
We hope to meet you in Rennes!
F. Husson
for the organizing committee.
|
Abstract submission deadline for useR! 2009
|
Francois Husson
| 645
|
|
From pd.mes at cbs.dk Thu Dec 16 10:35:01 2010
From: pd.mes at cbs.dk (Peter Dalgaard)
Date: Thu, 16 Dec 2010 10:35:01 +0100
Subject: [R] R 2.12.1 is released
Message-ID: <[email protected]>
I've rolled up R-2.12.1.tar.gz a short while ago. This is an update release, which fixes a number of mostly minor issues, and some consolidation within the area of reference classes. The most serious issues were probably that we were not catching misspelled NAMESPACE directives and not catching accidentally unnamed switch() arguments (notice that fixing either will likely uncover errors in preexisting code)
You can get it from
http://cran.r-project.org/src/base/R-2/R-2.12.1.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you.
Binaries for various platforms will appear in due course.
For the R Core Team
Peter Dalgaard
These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:
MD5 (AUTHORS) = ac9746b4845ae866661f51cfc99262f5
MD5 (COPYING) = eb723b61539feef013de476e68b5c50a
MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343
MD5 (FAQ) = 49b596b26b3e5c082dfde8bacfdffcb0
MD5 (INSTALL) = 70447ae7f2c35233d3065b004aa4f331
MD5 (NEWS) = 453317871e758763aa9bf385b545bdc6
MD5 (ONEWS) = 0c3e10eef74439786e5fceddd06dac71
MD5 (OONEWS) = 58d5b3b614888a6e366ff0c60073584f
MD5 (R-latest.tar.gz) = 078e8d1179fc9a762e326e6da2725468
MD5 (README) = 296871fcf14f49787910c57b92655c76
MD5 (RESOURCES) = 020479f381d5f9038dcb18708997f5da
MD5 (THANKS) = f2ccf22f3e20ebaa86f8ee5cc6b0f655
MD5 (R-2/R-2.12.1.tar.gz) = 078e8d1179fc9a762e326e6da2725468
This is the relevant part of the NEWS file:
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.
--
Peter Dalgaard
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
|
[R] R 2.12.1 is released
|
Peter Dalgaard
| 373
|
|
From didier at fmrib.ox.ac.uk Tue Apr 24 12:36:45 2001
From: didier at fmrib.ox.ac.uk (Didier Leibovici)
Date: Tue, 24 Apr 2001 11:36:45 +0100
Subject: New Package Released: PTAk
Message-ID: <[email protected]>
PTAk_1.1-1 ( Principal Tensor Analysis on k modes) has been released on
CRAN
A multiway method to decompose a tensor (array) of any
order,
as a generalisation of SVD also supporting non-identity
metrics and penalisations.
2-way SVD with these extensions is also available. The
package includes also some other multiway
methods: PCAn (Tucker-n) and PARAFAC/CANDECOMP with these
extensions.
please send comments
+ looking for nice not too big multi-arrays for the next release demos
Didier
--
Didier G. Leibovici didier at fmrib.ox.ac.uk +44 (0)1865 222 739
Image Analysis Group fax:+44 (0)1865 222 717
Oxford University, Centre For Functional Magnetic Resonance Imaging of
the Brain (FMRIB), John Radcliffe Hospital, Headington, Oxford OX3 9DU,
U.K
http://www.fmrib.ox.ac.uk/~didier/
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
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|
New Package Released: PTAk
|
Didier Leibovici
| 233
|
|
From Andreas.Weingessel at ci.tuwien.ac.at Wed Aug 19 14:01:54 1998
From: Andreas.Weingessel at ci.tuwien.ac.at (Andreas Weingessel)
Date: Wed, 19 Aug 1998 14:01:54 +0200 (CEST)
Subject: CRAN incoming
In-Reply-To: <Pine.SUN.3.95.980811152337.509H-100000@beast>
References: <Pine.SUN.3.95.980811152337.509H-100000@beast>
Message-ID: <[email protected]>
>>>>> On Tue, 11 Aug 1998 15:24:43 -0700 (PDT),
>>>>> Thomas Lumley wrote:
> updated version of integrate package
> integrate_1.1-1.tar.gz
> now in /incoming.
> -thomas
I moved the new version to CRAN.
Andreas
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch
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|
CRAN incoming
|
Andreas Weingessel
| 547
|
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