Commit bf46e866 authored by Dirk Eddelbuettel's avatar Dirk Eddelbuettel

Import Upstream version 3.2.2

parent ec5c0e12
Revision: 68531
Last Changed Date: 2015-06-18
Revision: 69053
Last Changed Date: 2015-08-14
World-Famous Astronaut
Fire Safety
This diff is collapsed.
......@@ -2343,7 +2343,7 @@ int main()
{
#ifdef LIBCURL_VERSION_MAJOR
#if LIBCURL_VERSION_MAJOR > 7
exit(1);
exit(0);
#elif LIBCURL_VERSION_MAJOR == 7 && LIBCURL_VERSION_MINOR >= 28
exit(0);
#else
......
Name,Country,City,URL,Host,Maintainer,OK,CountryCode
0-Bioconductor (World-wide),0-Bioconductor,World-wide,http://bioconductor.org/,"Bioconductor, automatic redirection to servers worldwide",Bioconductor Maintainer <maintainer # bioconductor.org>,1,us
0-Bioconductor (World-wide) [https],0-Bioconductor,World-wide,https://bioconductor.org/,"Bioconductor, automatic redirection to servers worldwide",Bioconductor Maintainer <maintainer # bioconductor.org>,1,us
United States (Rockville),United States,Rockville,http://watson.nci.nih.gov/bioc_mirror/,"National Cancer Institute, National Institutes of Health",Sean Davis <sdavis2 # mail.nih.gov>,1,us
Brazil/Latin America (Ribeirão Preto),Brazil/Latin America,Ribeirão Preto,http://bioconductor.fmrp.usp.br/,"Department of Genetics, Medical School of Ribeirão Preto, University of São Paulo",Houtan Noushmehr <houtan # usp.br>,1,br
Germany (Dortmund),Germany,Dortmund,http://bioconductor.statistik.tu-dortmund.de/,"Department of Statistics, TU Dortmund",Uwe Ligges <ligges # statistik.tu-dortmund.de>,1,de
Germany (Dortmund) [https],Germany,Dortmund,https://bioconductor.statistik.tu-dortmund.de/,"Department of Statistics, TU Dortmund",Uwe Ligges <ligges # statistik.tu-dortmund.de>,1,de
Belgium (Antwerp),Belgium,Antwerp,http://bioc.openanalytics.eu/,OpenAnalytics,Willem Ligtenberg <willem.ligtenberg # openanalytics.eu>,0,be
United Kingdom (Hinxton),United Kingdom,Hinxton,http://mirrors.ebi.ac.uk/bioconductor/,European Bioinformatics Institute,Andrew Tikhonov <andrew # ebi.ac.uk>,1,uk
United Kingdom (Hinxton) [https],United Kingdom,Hinxton,https://mirrors.ebi.ac.uk/bioconductor/,European Bioinformatics Institute,Andrew Tikhonov <andrew # ebi.ac.uk>,1,uk
Japan (Tachikawa),Japan,Tachikawa,http://bioc.ism.ac.jp/,The Institute of Statistical Mathematics,Keisuke Honda <khonda # ism.ac.jp>,1,jp
Japan (Wako),Japan,Wako,http://bioconductor.riken.jp/,RIKEN Advanced Center for Computing and Communication,"Itoshi NIKAIDO, Ph.D. <dritoshi # gmail.com>",1,jp
Japan (Wako) [https],Japan,Wako,https://bioconductor.riken.jp/,RIKEN Advanced Center for Computing and Communication,"Itoshi NIKAIDO, Ph.D. <dritoshi # gmail.com>",1,jp
China (Anhui),China,Anhui,http://mirrors.ustc.edu.cn/bioc/,University of Science and Technology of China,Mirror Maintainer <mirrors # ustc.edu.cn>,1,cn
China (Anhui) [https],China,Anhui,https://mirrors.ustc.edu.cn/bioc/,University of Science and Technology of China,Mirror Maintainer <mirrors # ustc.edu.cn>,1,cn
Australia (Sydney),Australia,Sydney,http://mirror.aarnet.edu.au/pub/bioconductor/,Australia's Academic and Research Network,Alex Dodson <alex.dodson # aarnet.edu.au>,1,au
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......@@ -11,7 +11,7 @@ subdir = doc
include $(top_builddir)/Makeconf
distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
INSTFILES = AUTHORS COPYING COPYRIGHTS CRAN_mirrors.csv \
INSTFILES = AUTHORS COPYING COPYRIGHTS CRAN_mirrors.csv BioC_mirrors.csv \
KEYWORDS KEYWORDS.db THANKS NEWS.0 NEWS.1 NEWS.2
DISTFILES = Makefile.in Makefile.win $(INSTFILES) R.aux Rscript.1 \
NEWS.Rd NEWS.2.Rd
......
R News
CHANGES IN R 3.2.2:
SIGNIFICANT USER-VISIBLE CHANGES:
* It is now easier to use secure downloads from https:// URLs on
builds which support them: no longer do non-default options need
to be selected to do so. In particular, packages can be
installed from repositories which offer https:// URLs, and those
listed by setRepositories() now do so (for some of their
mirrors).
Support for https:// URLs is available on Windows, and on other
platforms if support for libcurl was compiled in and if that
supports the https protocol (system installations can be expected
to do). So https:// support can be expected except on rather old
OSes (an example being OS X 'Snow Leopard', where a non-system
version of libcurl can be used).
(Windows only) The default method for accessing URLs _via_
download.file() and url() has been changed to be "wininet" using
Windows API calls. This changes the way proxies need to be set
and security settings made: there have been some reports of sites
being inaccessible under the new default method (but the previous
methods remain available).
NEW FEATURES:
* cmdscale() gets new option list. for increased flexibility when a
list should be returned.
* configure now supports texinfo version 6.0, which (unlike the
change from 4.x to 5.0) is a minor update. (Wish of PR#16456.)
* (Non-Windows only) download.file() with default method = "auto"
now chooses "libcurl" if that is available and a https:// or
ftps:// URL is used.
* (Windows only) setInternet2(TRUE) is now the default. The
command-line option --internet2 and environment variable
R_WIN_INTERNET2 are now ignored.
Thus by default the "internal" method for download.file() and
url() uses the "wininet" method: to revert to the previous
default use setInternet2(FALSE).
This means that https:// can be read by default by
download.file() (they have been readable by file() and url()
since R 3.2.0).
There are implications for how proxies need to be set (see
?download.file): also, cacheOK = FALSE is not supported.
* chooseCRANmirror() and chooseBioCmirror() now offer HTTPS mirrors
in preference to HTTP mirrors. This changes the interpretation
of their ind arguments: see their help pages.
* capture.output() gets optional arguments type and split to pass
to sink(), and hence can be used to capture messages.
C-LEVEL FACILITIES:
* Header Rconfig.h now defines HAVE_ALLOCA_H if the platform has
the alloca.h header (it is needed to define alloca on Solaris and
AIX, at least: see 'Writing R Extensions' for how to use it).
INSTALLATION and INCLUDED SOFTWARE:
* The libtool script generated by configure has been modified to
support FreeBSD >= 10 (PR#16410).
BUG FIXES:
* The HTML help page links to demo code failed due to a change in R
3.2.0. (PR#16432)
* If the na.action argument was used in model.frame(), the original
data could be modified. (PR#16436)
* getGraphicsEvent() could cause a crash if a graphics window was
closed while it was in use. (PR#16438)
* matrix(x, nr, nc, byrow = TRUE) failed if x was an object of type
"expression".
* strptime() could overflow the allocated storage on the C stack
when the timezone had a non-standard format much longer than the
standard formats. (Part of PR#16328.)
* options(OutDec = s) now signals a warning (which will become an
error in the future) when s is not a string with exactly one
character, as that has been a documented requirement.
* prettyNum() gains a new option input.d.mark which together with
other changes, e.g., the default for decimal.mark, fixes some
format()ting variants with non-default getOption("OutDec") such
as in PR#16411.
* download.packages() failed for type equal to either "both" or
"binary". (Reported by Dan Tenenbaum.)
* The dendrogram method of labels() is much more efficient for
large dendrograms, now using rapply(). (Comment #15 of PR#15215)
* The "port" algorithm of nls() could give spurious errors.
(Reported by Radford Neal.)
* Reference classes that inherited from reference classes in
another package could invalidate methods of the inherited class.
Fixing this requires adding the ability for methods to be
"external", with the object supplied explicitly as the first
argument, named .self. See "Inter-Package Superclasses" in the
documentation.
* readBin() could fail on the SPARC architecture due to alignment
issues. (Reported by Radford Neal.)
* qt(*, df=Inf, ncp=.) now uses the natural qnorm() limit instead
of returning NaN. (PR#16475)
* Auto-printing of S3 and S4 values now searches for print() in the
base namespace and show() in the methods namespace instead of
searching the global environment.
* polym() gains a coefs = NULL argument and returns class "poly"
just like poly() which gets a new simple=FALSE option. They now
lead to correct predict()ions, e.g., on subsets of the original
data.
* rhyper(nn, <large>) now works correctly. (PR#16489)
* ttkimage() did not (and could not) work so was removed. Ditto for
tkimage.cget() and tkimage.configure(). Added two Ttk widgets and
missing subcommands for Tk's image command: ttkscale(),
ttkspinbox(), tkimage.delete(), tkimage.height(),
tkimage.inuse(), tkimage.type(), tkimage.types(),
tkimage.width(). (PR#15372, PR#16450)
* getClass("foo") now also returns a class definition when it is
found in the cache more than once.
CHANGES IN R 3.2.1:
NEW FEATURES:
......@@ -84,7 +224,7 @@ CHANGES IN R 3.2.1:
from .getRequiredPackages2().
* Under some circumstances using the internal PCRE when building R
fron source would cause external libs such as -llzma to be
from 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., !, &
......
......@@ -5,6 +5,175 @@
\title{R News}
\encoding{UTF-8}
\section{\Rlogo CHANGES IN R 3.2.2}{
\subsection{SIGNIFICANT USER-VISIBLE CHANGES}{
\itemize{
\item It is now easier to use secure downloads from
\samp{https://} URLs on builds which support them: no longer do
non-default options need to be selected to do so. In particular,
packages can be installed from repositories which offer
\samp{https://} URLs, and those listed by \code{setRepositories()}
now do so (for some of their mirrors).
Support for \samp{https://} URLs is available on Windows, and on
other platforms if support for \code{libcurl} was compiled in and
if that supports the \code{https} protocol (system installations
can be expected to do). So \samp{https://} support can be
expected except on rather old OSes (an example being OS X
\sQuote{Snow Leopard}, where a non-system version of
\code{libcurl} can be used).
(Windows only) The default method for accessing URLs \emph{via}
\code{download.file()} and \code{url()} has been changed to be
\code{"wininet"} using Windows API calls. This changes the way
proxies need to be set and security settings made: there have been
some reports of sites being inaccessible under the new default
method (but the previous methods remain available).
}
}
\subsection{NEW FEATURES}{
\itemize{
\item \code{cmdscale()} gets new option \code{list.} for increased
flexibility when a list should be returned.
\item \command{configure} now supports \code{texinfo} version 6.0,
which (unlike the change from 4.x to 5.0) is a minor update.
(Wish of \PR{16456}.)
\item (Non-Windows only) \code{download.file()} with default
\code{method = "auto"} now chooses \code{"libcurl"} if that is
available and a \samp{https://} or \samp{ftps://} URL is used.
\item (Windows only) \code{setInternet2(TRUE)} is now the default.
The command-line option \command{--internet2} and environment
variable \env{R_WIN_INTERNET2} are now ignored.
Thus by default the \code{"internal"} method for
\code{download.file()} and \code{url()} uses the \code{"wininet"}
method: to revert to the previous default use
\code{setInternet2(FALSE)}.
This means that \samp{https://} can be read by default by
\code{download.file()} (they have been readable by \code{file()} and
\code{url()} since \R 3.2.0).
There are implications for how proxies need to be set (see
\code{?download.file}): also, \code{cacheOK = FALSE} is not
supported.
\item \code{chooseCRANmirror()} and \code{chooseBioCmirror()} now
offer HTTPS mirrors in preference to HTTP mirrors. This changes
the interpretation of their \code{ind} arguments: see their help
pages.
\item \code{capture.output()} gets optional arguments \code{type}
and \code{split} to pass to \code{sink()}, and hence can be used to
capture messages.
}
}
\subsection{C-LEVEL FACILITIES}{
\itemize{
\item Header \file{Rconfig.h} now defines \code{HAVE_ALLOCA_H} if
the platform has the \file{alloca.h} header (it is needed to
define \code{alloca} on Solaris and AIX, at least: see
\sQuote{Writing R Extensions} for how to use it).
}
}
\subsection{INSTALLATION and INCLUDED SOFTWARE}{
\itemize{
\item The \command{libtool} script generated by
\command{configure} has been modified to support FreeBSD >= 10
(\PR{16410}).
}
}
\subsection{BUG FIXES}{
\itemize{
\item The HTML help page links to demo code failed due to a change
in \R 3.2.0. (\PR{16432})
\item If the \code{na.action} argument was used in
\code{model.frame()}, the original data could be
modified. (\PR{16436})
\item \code{getGraphicsEvent()} could cause a crash if a graphics
window was closed while it was in use. (\PR{16438})
\item \code{matrix(x, nr, nc, byrow = TRUE)} failed if \code{x}
was an object of type \code{"expression"}.
\item \code{strptime()} could overflow the allocated storage on
the C stack when the timezone had a non-standard format much
longer than the standard formats. (Part of \PR{16328}.)
\item \code{options(OutDec = s)} now signals a warning (which will
become an error in the future) when \code{s} is not a string with
exactly one character, as that has been a documented requirement.
\item \code{prettyNum()} gains a new option \code{input.d.mark}
which together with other changes, e.g., the default for
\code{decimal.mark}, fixes some \code{format()}ting variants with
non-default \code{getOption("OutDec")} such as in \PR{16411}.
\item \code{download.packages()} failed for \code{type} equal to
either \code{"both"} or \code{"binary"}. (Reported by Dan
Tenenbaum.)
\item The \code{dendrogram} method of \code{labels()} is much more
efficient for large dendrograms, now using \code{rapply()}.
(Comment #15 of \PR{15215})
\item The \code{"port"} algorithm of \code{nls()} could give
spurious errors. (Reported by Radford Neal.)
\item Reference classes that inherited from reference classes in
another package could invalidate methods of the inherited
class. Fixing this requires adding the ability for methods to be
\dQuote{external}, with the object supplied explicitly as the first
argument, named \code{.self}. See "Inter-Package Superclasses"
in the documentation.
\item \code{readBin()} could fail on the SPARC architecture
due to alignment issues. (Reported by Radford Neal.)
\item \code{qt(*, df=Inf, ncp=.)} now uses the natural
\code{qnorm()} limit instead of returning \code{NaN}. (\PR{16475})
\item Auto-printing of S3 and S4 values now searches for
\code{print()} in the base namespace and \code{show()} in the
\pkg{methods} namespace instead of searching the global
environment.
\item \code{polym()} gains a \code{coefs = NULL} argument and
returns class \code{"poly"} just like \code{poly()} which gets a
new \code{simple=FALSE} option. They now lead to correct
\code{predict()}ions, e.g., on subsets of the original data.
%% see https://stat.ethz.ch/pipermail/r-devel/2015-July/071532.html
\item \code{rhyper(nn, <large>)} now works correctly. (\PR{16489})
\item \code{ttkimage()} did not (and could not) work so was
removed. Ditto for \code{tkimage.cget()} and
\code{tkimage.configure()}. Added two Ttk widgets and missing
subcommands for Tk's \code{image} command:
\code{ttkscale()},
\code{ttkspinbox()},
\code{tkimage.delete()},
\code{tkimage.height()},
\code{tkimage.inuse()},
\code{tkimage.type()},
\code{tkimage.types()},
\code{tkimage.width()}. (\PR{15372}, \PR{16450})
\item \code{getClass("foo")} now also returns a class definition when it is
found in the cache more than once.
}
}
}
\section{\Rlogo CHANGES IN R 3.2.1}{
\subsection{NEW FEATURES}{
\itemize{
......@@ -93,7 +262,7 @@
correctly propagated from \code{.getRequiredPackages2()}.
\item Under some circumstances using the internal PCRE when
building \R fron source would cause external libs such as
building \R from source would cause external libs such as
\code{-llzma} to be omitted from the main link.
\item The .Primitive default methods of the logic operators, i.e.,
......@@ -118,7 +287,7 @@
\item \code{slotNames(.)} is now correct for \code{"signature"}
objects (mostly used internally in \pkg{methods}).
\item On some systems, the first string comparison after
a locale change would result in \code{NA}.
}
......@@ -342,8 +511,8 @@
schemes it supports.
\item \code{curlGetHeaders()} retrieves the headers for
\code{http://}, \code{https://}, \code{ftp://} and
\code{ftps://} URLs: analysis of these headers can provide
\samp{http://}, \samp{https://}, \samp{ftp://} and
\samp{ftps://} URLs: analysis of these headers can provide
insights into the `existence' of a URL (it might for example be
permanently redirected) and is so used in \command{R CMD
check --as-cran}.
......@@ -1227,7 +1396,7 @@
an error instead of a warning.
\item \code{install.packages(repos = NULL)} now accepts
\code{http://} or \code{ftp://} URLs of package archives as well
\samp{http://} or \samp{ftp://} URLs of package archives as well
as file paths, and will download as required. In most cases
\code{repos = NULL} can be deduced from the extension of the URL.
......
No preview for this file type
......@@ -8,7 +8,7 @@ A collection of Frequently Asked Questions and their answers is
maintained by Kurt Hornik <Kurt.Hornik@R-project.org> and can be found
at the URL
<http://CRAN.R-project.org/doc/FAQ/R-FAQ.html>
<https://CRAN.R-project.org/doc/FAQ/R-FAQ.html>
A text version is in file 'FAQ' in this directory, and an HTML version
is available as file 'doc/html/faq.html' and via the on-line help (on
......@@ -20,7 +20,7 @@ the index page given by 'help.start()').
Thanks to Martin Maechler <Martin.Maechler@R-project.org> there are a
number of mailing lists which are used by R users and developers. See
<http://www.R-project.org/mail.html>
<https://www.R-project.org/mail.html>
for details.
......@@ -30,10 +30,10 @@ for details.
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, with the
master site at <http://CRAN.R-project.org/> and information on daily
master site at <https://CRAN.R-project.org/> and information on daily
mirrors available from
<http://CRAN.R-project.org/mirrors.html>
<https://CRAN.R-project.org/mirrors.html>
4 Bug-tracking system
*********************
......@@ -41,5 +41,5 @@ mirrors available from
R has a bug-tracking system (or perhaps a bug-filing system is a more
precise description) available on the net at
<http://bugs.R-project.org/>
<https://bugs.R-project.org/>
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......@@ -165,7 +165,7 @@ answers is maintained by <a href="mailto:Kurt.Hornik@R-project.org">Kurt Hornik<
and can be found at the <acronym>URL</acronym>
</p>
<blockquote>
<p><a href="http://CRAN.R-project.org/doc/FAQ/R-FAQ.html">http://CRAN.R-project.org/doc/FAQ/R-FAQ.html</a>
<p><a href="https://CRAN.R-project.org/doc/FAQ/R-FAQ.html">https://CRAN.R-project.org/doc/FAQ/R-FAQ.html</a>
</p></blockquote>
......@@ -179,7 +179,7 @@ are a number of mailing lists which are used by R users and developers.
See
</p>
<blockquote>
<p><a href="http://www.R-project.org/mail.html">http://www.R-project.org/mail.html</a>
<p><a href="https://www.R-project.org/mail.html">https://www.R-project.org/mail.html</a>
</p></blockquote>
<p>for details.
......@@ -192,11 +192,11 @@ See
<p>The Comprehensive R Archive Network (<acronym>CRAN</acronym>) is a collection of
sites which carry identical material, consisting of the R
distribution(s), the contributed extensions, documentation for R, and
binaries, with the master site at <a href="http://CRAN.R-project.org/">http://CRAN.R-project.org/</a> and
binaries, with the master site at <a href="https://CRAN.R-project.org/">https://CRAN.R-project.org/</a> and
information on daily mirrors available from
</p>
<blockquote>
<p><a href="http://CRAN.R-project.org/mirrors.html">http://CRAN.R-project.org/mirrors.html</a>
<p><a href="https://CRAN.R-project.org/mirrors.html">https://CRAN.R-project.org/mirrors.html</a>
</p></blockquote>
<hr>
......@@ -208,7 +208,7 @@ information on daily mirrors available from
precise description) available on the net at
</p>
<blockquote>
<p><a href="http://bugs.R-project.org/">http://bugs.R-project.org/</a>
<p><a href="https://bugs.R-project.org/">https://bugs.R-project.org/</a>
</p></blockquote>
<hr>
......
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......@@ -226,7 +226,7 @@ Modern Unix-alike systems, including OS X, are likely to produce
UTF-8 files. Windows may produce what it calls `Unicode' files
(@code{UCS-2LE} or just possibly @code{UTF-16LE}@footnote{the
distinction is subtle,
@uref{http://en.wikipedia.org/@/wiki/@/UTF-16/UCS-2}, and the use of
@uref{https://en.wikipedia.org/@/wiki/@/UTF-16/UCS-2}, and the use of
surrogate pairs is very rare.}). Otherwise most files will be in a
8-bit encoding unless from a Chinese/Japanese/Korean locale (which have
a wide range of encodings in common use). It is not possible to
......@@ -236,7 +236,7 @@ example above), so you may simply have to ask the originator for some
clues (e.g.@: `Russian on Windows').
`BOMs' (Byte Order Marks,
@uref{http://en.wikipedia.org/wiki/Byte_order_mark}) cause problems for
@uref{https://en.wikipedia.org/wiki/Byte_order_mark}) cause problems for
Unicode files. In the Unix world BOMs are rarely used, whereas in the
Windows world they almost always are for UCS-2/UTF-16 files, and often
are for UTF-8 files. The @command{file} utility will not even recognize
......@@ -322,7 +322,7 @@ locales the comma is used as the decimal point (set this in
semicolon as the field separator: use @code{write.csv2} for appropriate
defaults. There is an IETF standard for CSV files (which mandates
commas and CRLF line endings, for which use @code{eol = "\r\n"}), RFC4180
(see @uref{http://tools.ietf.org/html/rfc4180}), but what is more
(see @uref{https://tools.ietf.org/html/rfc4180}), but what is more
important in practice is that the file is readable by the application it
is targeted at.
......@@ -1164,19 +1164,19 @@ from a database for separate analysis.
Increasingly OSes are themselves making use of DBMSs for these reasons,
so it is nowadays likely that one will be already installed on your
(non-Windows) OS. @uref{http://en.wikipedia.org/wiki/Akonadi, Akonadi}
(non-Windows) OS. @uref{https://en.wikipedia.org/wiki/Akonadi, Akonadi}
is used by KDE4 to store personal information. Several OS X
applications, including Mail and Address Book, use SQLite.
@c http://www.actualtechnologies.com/sqlite_applications.php
@c https://www.actualtech.com/sqlite_applications.php
@node Overview of RDBMSs, R interface packages, Why use a database?, Relational databases
@section Overview of RDBMSs
Traditionally there had been large (and expensive) commercial RDBMSs
(@uref{http://www.informix.com, Informix}; @uref{http://www.oracle.com,
(@uref{http://www.informix.com, Informix}; @uref{https://www.oracle.com,
Oracle}; @uref{http://www.sybase.com, Sybase};
@uref{http://www.ibm.com/db2, IBM's DB2};
@uref{http://www.microsoft.com/SQL/default.mspx, Microsoft @acronym{SQL}
@uref{https://www.microsoft.com/SQL/default.mspx, Microsoft @acronym{SQL}
Server} on Windows) and academic and small-system databases (such as
MySQL@footnote{and forks, notably MariaDB.}, PostgreSQL, Microsoft
Access, @dots{}), the former marked out by much greater emphasis on data
......@@ -1190,7 +1190,7 @@ There are other commonly used data sources, including spreadsheets,
non-relational databases and even text files (possibly compressed).
Open Database Connectivity (@acronym{ODBC}) is a standard to use all of
these data sources. It originated on Windows (see
@uref{http://msdn.microsoft.com/@/en-us/@/library/@/ms710252%28v=vs.85%29.aspx})
@uref{https://msdn.microsoft.com/@/en-us/@/library/@/ms710252%28v=vs.85%29.aspx})
but is also implemented on Linux/Unix/OS X.
All of the packages described later in this chapter provide clients to
......@@ -1330,11 +1330,11 @@ data frame or in pieces (usually as groups of rows).
All except @CRANpkg{RODBC} are tied to one DBMS, but there has been a
proposal for a unified `front-end' package @CRANpkg{DBI}
(@uref{http://developer.r-project.org/db}) in conjunction with a
(@uref{https://developer.r-project.org/db}) in conjunction with a
`back-end', the most developed of which is @CRANpkg{RMySQL}. Also on
@acronym{CRAN} are the back-ends @CRANpkg{ROracle}, @CRANpkg{RPostgreSQL} and
@CRANpkg{RSQLite} (which works with the bundled DBMS @code{SQLite},
@uref{http://www.sqlite.org}), @CRANpkg{RJDBC} (which uses Java and can
@uref{https://www.sqlite.org}), @CRANpkg{RJDBC} (which uses Java and can
connect to any DBMS that has a JDBC driver) and @CRANpkg{RpgSQL} (a
specialist interface to PostgreSQL built on top of @CRANpkg{RJDBC}).
......@@ -1346,7 +1346,7 @@ The BioConductor project has updated @pkg{RdbiPgSQL} (formerly on
PostgreSQL.
Package @CRANpkg{RMongo} provides an @R{} interface to a Java client for
`MongoDB' (@uref{http://en.wikipedia.org/wiki/MongoDB}) databases, which
`MongoDB' (@uref{https://en.wikipedia.org/wiki/MongoDB}) databases, which
are queried using JavaScript rather than SQL. Package @CRANpkg{rmongodb} is
another client using @pkg{mongodb}'s C driver.
......@@ -1362,8 +1362,9 @@ another client using @pkg{mongodb}'s C driver.
@cindex MySQL database system
Package @CRANpkg{RMySQL} on @acronym{CRAN} provides an interface to the
MySQL database system (see @uref{http://www.mysql.com} and Dubois,
2000). The description here applies to version @code{0.5-0}: earlier
MySQL database system (see @uref{https://www.mysql.com} and Dubois,
2000) or its fork MariaDB (see @uref{https://mariadb.org/}). The
description here applies to versions @code{0.5-0} and later: earlier
versions had a substantially different interface. The current version
requires the @CRANpkg{DBI} package, and this description will apply with
minor changes to all the other back-ends to @CRANpkg{DBI}.
......@@ -1477,15 +1478,16 @@ database system.
Windows provides drivers not just for DBMSs but also for Excel
(@file{.xls}) spreadsheets, DBase (@file{.dbf}) files and even text
files. (The named applications do @emph{