Commit 221a6fc7 authored by Radford Neal's avatar Radford Neal

First version released on github

parent e0e1a4c8
configure
NEWS
NEWS.pdf
This file records modifications in pqR that are of little interest to
users, such as cleanups of source code.
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pqR - a "pretty quick" implementation of the R programming language
THE BASIC R README
This directory contains the source code (plus documentation) for an
implementation of the R programming language, including some R
packages. This implementation is a modification of R-2.15.0,
distributed by the R Core Team, and found at www.r-project.org.
The modifications in pqR substantially improve the speed of R. Some
extensions to R are also implemented. These modifications were
written by Radford M. Neal, radfordneal@gmail.com.
A git repository for this source code that include modification
history is at github.com/radfordneal/pqR.
This implementation of R is distributed under the GNU General Public
Licence, version 2 or version 3. See the files COPYING and
doc/COPYRIGHTS for details.
See INSTALL, NEWS, MODS, and the files in the doc sub-directory for
more information.
-----------------------------------------------------------------------------
THE BASIC R README
(from R-2.15.0, distributed 2012-03-30)
(See "doc/FAQ" and "doc/RESOURCES" for more detailed information
......
Revision: 58871
Last Changed Date: 2012-03-30
Last Changed Date: 2013-05-31
This diff is collapsed.
......@@ -30,7 +30,7 @@ m4_define([R_VERSION],
m4_bpatsubst(m4_esyscmd([cat VERSION]),
[\([0-9.]*\)\(\w\|\W\)*],
[\1]))
AC_INIT([R],[R_VERSION],[http://bugs.r-project.org],[R],[http://www.r-project.org])
AC_INIT([R],[R_VERSION],[http://github.com/radfordneal/pqR/issues],[R],[http://github.com/radfordneal/pqR/])
AC_CONFIG_SRCDIR([src/include/Defn.h])
AC_CONFIG_AUX_DIR([tools])
......
Authors of R.
pqR is a modification of R-2.15.0, containing numerous efficiency
improvements, and other changes. These modifications were done by
Radford Neal. Radford Neal also contributed some efficiency
improvements to R incorporated into R-2.12.0 and later versions.
Radford Neal can be contacted at radfordneal@gmail.com. The pqR source
code repository is at githup.com/radfordneal/pqR.
--------------------------------------------------------------------------
R-2.15.0 credits authors as follows:
R was initially written by Robert Gentleman and Ross Ihaka of the
Statistics Department of the University of Auckland.
......
COPYRIGHT STATUS OF pqR.
The modifications made to the source of R-2.15.0 to create pqR are
Copyright (C) 2013 by Radford M. Neal.
COPYRIGHT STATUS
COPYRIGHT STATUS of R-2.15.0 (taken from this file in R-2.15.0)
The bulk of this code is copyright by members of or all of the R
Development Core Team.
......
......@@ -147,14 +147,19 @@ $(texinputs_RECOMMENDED): FORCE
| LC_ALL=C $(R_EXE) ; \
fi)
version.texi: Makefile $(top_srcdir)/VERSION $(SVN_REV)
version.texi: Makefile $(top_srcdir)/VERSION $(SVN_REV) \
$(top_srcdir)/pqR-BASE-VERSION $(top_srcdir)/pqR-BASE-DATE
@$(ECHO) "creating $(subdir)/$@"
@(vv=`sed 's/ *(.*//' $(top_srcdir)/VERSION`;v=`echo $${vv}| sed 's/\([^ ]*\).*/\1/'`; \
$(ECHO) "@set VERSIONno $${v}" > $@; \
$(ECHO) "@set pqRVERSIONno $${v}" > $@; \
v="$${vv} (`sed -e 1d -e 's/^Last Changed Date: //' $(SVN_REV)`)"; \
$(ECHO) "@set VERSION $${v}" >> $@; \
$(ECHO) "@set pqRVERSION $${v}" >> $@; \
$(ECHO) "@set pqRYEAR" `echo $${v} | sed s/.\*\(// | sed s/-.\*//` >> $@; \
rwv=`$(R_EXE) -f $(top_srcdir)/src/gnuwin32/fixed/rwver.R`; \
$(ECHO) "@set RWVERSION $${rwv}" >> $@ )
$(ECHO) "@set RWVERSION $${rwv}" >> $@; \
$(ECHO) "@set VERSIONno" `cat $(top_srcdir)/pqR-BASE-VERSION` >>$@;\
$(ECHO) "@set VERSION" `cat $(top_srcdir)/pqR-BASE-VERSION` \
\(`cat $(top_srcdir)/pqR-BASE-DATE`\) >> $@ )
@if test "$(R_PAPERSIZE)" = "a4"; then \
$(ECHO) "@afourpaper" >> $@ ; \
fi
......
\input texinfo
@c %**start of header
@setfilename R-admin.info
@settitle R Installation and Administration
@settitle R Installation and Administration - with modifications for pqR
@setchapternewpage on
@defcodeindex en
@c %**end of header
......@@ -19,7 +19,7 @@
@include version.texi
@ifinfo
This is a guide to installation and administration for R.
This is a guide to installation and administration for R - modified for pqR
@Rcopyright{2001}
......@@ -36,9 +36,9 @@ notice identical to this one except for the removal of this paragraph
@end ifinfo
@titlepage
@title R Installation and Administration
@subtitle Version @value{VERSION}
@author R Development Core Team
@title R Installation and Administration - with modifications for pqR
@subtitle R Version @value{VERSION}, pqR version @value{pqRVERSION}
@author R Development Core Team, pqR modifications by Radford Neal
@page
@vskip 0pt plus 1filll
@permission{}
......@@ -46,6 +46,9 @@ notice identical to this one except for the removal of this paragraph
@Rcopyright{2001}
@value{ISBN-admin}
Modifications for pqR copyright @copyright{} @value{pqRYEAR} Radford M. Neal
@end titlepage
@c @ifnothtml
......@@ -58,9 +61,12 @@ notice identical to this one except for the removal of this paragraph
This is a guide to installation and administration for R.
The current version of this document is @value{VERSION}.
The current version of this document is for R @value{VERSION}.
@value{ISBN-admin}
Modifications for pqR are for pqR version @value{pqRVERSION}.
@end ifnottex
@menu
......
\input texinfo
@c %**start of header
@setfilename R-exts.info
@settitle Writing R Extensions
@settitle Writing R Extensions - with modifications for pqR
@setchapternewpage on
@c %**end of header
......@@ -21,7 +21,7 @@
@include version.texi
@ifinfo
This is a guide to extending R.
This is a guide to extending R - with modifications for pqR.
@Rcopyright{1999}
......@@ -38,9 +38,9 @@ notice identical to this one except for the removal of this paragraph
@end ifinfo
@titlepage
@title Writing R Extensions
@subtitle Version @value{VERSION}
@author R Development Core Team
@title Writing R Extensions - with modifications for pqR
@subtitle R Version @value{VERSION}, pqR version @value{pqRVERSION}
@author R Development Core Team, pqR modifications by Radford Neal
@page
@vskip 0pt plus 1filll
@permission{}
......@@ -48,6 +48,9 @@ notice identical to this one except for the removal of this paragraph
@Rcopyright{1999}
@value{ISBN-exts}
Modifications for pqR copyright @copyright{} @value{pqRYEAR} Radford M. Neal
@end titlepage
@c @ifnothtml
......@@ -62,9 +65,12 @@ This is a guide to extending @R{}, describing the process of creating
@R{} add-on packages, writing @R{} documentation, @R{}'s system and
foreign language interfaces, and the @R{} @acronym{API}.
The current version of this document is @value{VERSION}.
The current version of this document is for R @value{VERSION}.
@value{ISBN-exts}
Modifications for pqR are for pqR version @value{pqRVERSION}.
@end ifnottex
@menu
......
\input texinfo
@c %**start of header
@setfilename R-ints.info
@settitle R Internals
@settitle R Internals - with modifications for pqR
@setchapternewpage on
@c %**end of header
......@@ -20,7 +20,8 @@
@include version.texi
@ifinfo
This is a guide to R's internal structures.
This is a guide to R's internal structures,
modified to reflect changes in pqR.
@Rcopyright{1999}
......@@ -37,9 +38,9 @@ notice identical to this one except for the removal of this paragraph
@end ifinfo
@titlepage
@title R Internals
@subtitle Version @value{VERSION}
@author R Development Core Team
@title R Internals - with modifications for pqR
@subtitle R Version @value{VERSION}, pqR version @value{pqRVERSION}
@author R Development Core Team, pqR modifications by Radford Neal
@page
@vskip 0pt plus 1filll
@permission{}
......@@ -47,6 +48,9 @@ notice identical to this one except for the removal of this paragraph
@Rcopyright{1999}
@value{ISBN-ints}
Modifications for pqR copyright @copyright{} @value{pqRYEAR} Radford M. Neal
@end titlepage
@c @ifnothtml
......@@ -60,9 +64,12 @@ notice identical to this one except for the removal of this paragraph
This is a guide to the internal structures of @R{} and coding standards for
the core team working on @R{} itself.
The current version of this document is @value{VERSION}.
The current version of this document is for R @value{VERSION}.
@value{ISBN-ints}
Modifications for pqR are for pqR version @value{pqRVERSION}.
@end ifnottex
@menu
......
Changes to display pqR version information, including separating the
pqR version from the version of R that pqR is based on. Also updates
some copyright notices, and changes bug reporting address.
2012-03-30
......@@ -14,7 +14,7 @@ BEGIN
BEGIN
VALUE "FileDescription", "Graphapp DLL for R\0"
VALUE "FileVersion", R_MAJOR "." R_MINOR " " R_STATUS " (" R_YEAR "-" R_MONTH "-" R_DAY ")\0"
VALUE "LegalCopyright", "R Development Core Team 1995-" R_YEAR "\0"
VALUE "LegalCopyright", "R Development Core Team 1995-" R_BASE_YEAR "\0"
VALUE "R Version", R_MAJOR "." R_MINOR " " R_STATUS " (" R_YEAR "-" R_MONTH "-" R_DAY ")\0"
VALUE "Project info", "http://www.r-project.org\0"
END
......
......@@ -14,7 +14,7 @@ BEGIN
BEGIN
VALUE "FileDescription", "R for Windows DLL\0"
VALUE "FileVersion", R_MAJOR "." R_MINOR " " R_STATUS " (" R_YEAR "-" R_MONTH "-" R_DAY ")\0"
VALUE "LegalCopyright", "R Development Core Team 1995-" R_YEAR "\0"
VALUE "LegalCopyright", "R Development Core Team 1995-" R_BASE_YEAR "\0"
VALUE "R Version", R_MAJOR "." R_MINOR " " R_STATUS " (" R_YEAR "-" R_MONTH "-" R_DAY ")\0"
VALUE "Project info", "http://www.r-project.org\0"
END
......
......@@ -20,7 +20,7 @@ BEGIN
BEGIN
VALUE "FileDescription", "R for Windows front-end\0"
VALUE "FileVersion", R_MAJOR "." R_MINOR " " R_STATUS " (" R_YEAR "-" R_MONTH "-" R_DAY ")\0"
VALUE "LegalCopyright", "R Development Core Team 1995-" R_YEAR "\0"
VALUE "LegalCopyright", "R Development Core Team 1995-" R_BASE_YEAR "\0"
VALUE "R Version", R_MAJOR "." R_MINOR " " R_STATUS " (" R_YEAR "-" R_MONTH "-" R_DAY ")\0"
VALUE "Project info", "http://www.r-project.org\0"
END
......
......@@ -22,7 +22,7 @@ BEGIN
BEGIN
VALUE "FileDescription", "R for Windows GUI front-end\0"
VALUE "FileVersion", R_MAJOR "." R_MINOR " " R_STATUS " (" R_YEAR "-" R_MONTH "-" R_DAY ")\0"
VALUE "LegalCopyright", "R Development Core Team 1995-" R_YEAR "\0"
VALUE "LegalCopyright", "R Development Core Team 1995-" R_BASE_YEAR "\0"
VALUE "R Version", R_MAJOR "." R_MINOR " " R_STATUS " (" R_YEAR "-" R_MONTH "-" R_DAY ")\0"
VALUE "Project info", "http://www.r-project.org\0"
END
......
......@@ -22,7 +22,7 @@ BEGIN
BEGIN
VALUE "FileDescription", "R for Windows terminal front-end\0"
VALUE "FileVersion", R_MAJOR "." R_MINOR " " R_STATUS " (" R_YEAR "-" R_MONTH "-" R_DAY ")\0"
VALUE "LegalCopyright", "R Development Core Team 1995-" R_YEAR "\0"
VALUE "LegalCopyright", "R Development Core Team 1995-" R_BASE_YEAR "\0"
VALUE "R Version", R_MAJOR "." R_MINOR " " R_STATUS " (" R_YEAR "-" R_MONTH "-" R_DAY ")\0"
VALUE "Project info", "http://www.r-project.org\0"
END
......
......@@ -663,7 +663,7 @@ static void menuabout(control m)
PrintVersionString(s2);
sprintf(s, "%s\n%s %s %s",
s2,
"Copyright (C)", R_YEAR,
"Copyright (C)", R_BASE_YEAR,
"The R Foundation for Statistical Computing");
askok(s);
/* show(RConsole); */
......
Package: base
Version: @VERSION@
Priority: base
Title: The R Base Package
Title: The R Base Package - with modifications for pqR
Author: R Development Core Team and contributors worldwide
Maintainer: R Core Team <R-core@r-project.org>
Description: Base R functions
......
# File src/library/base/R/contributors.R
# Part of the R package, http://www.R-project.org
# Modifications for pqR Copyright (c) 2013 Radford M. Neal.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
......@@ -18,13 +19,7 @@ contributors <- function()
{
outFile <- tempfile()
outConn <- file(outFile, open = "w")
writeLines(paste("R is a project which is attempting to provide a ",
"modern piece of\nstatistical software for the ",
"GNU suite of software.\n\n",
"The current R is the result of a collaborative ",
"effort with\ncontributions from all over the ",
"world.\n\n",
sep = ""), outConn)
writeLines(readLines(file.path(R.home("doc"), "AUTHORS")), outConn)
writeLines("", outConn)
writeLines(readLines(file.path(R.home("doc"), "THANKS")), outConn)
......
......@@ -3,12 +3,12 @@ bibentry("Manual",
author = person("R Development Core Team"),
organization = "R Foundation for Statistical Computing",
address = "Vienna, Austria",
year = version$year,
year = version$pqR.base.year,
note = "{ISBN} 3-900051-07-0",
url = "http://www.R-project.org/",
textVersion =
paste("R Development Core Team (", version$year, "). ",
paste("R Development Core Team (", version$pqR.base.year, "). ",
"R: A language and environment for statistical computing. ",
"R Foundation for Statistical Computing, Vienna, Austria. ",
"ISBN 3-900051-07-0, URL http://www.R-project.org/.",
......
Package: tools
Version: @VERSION@
Priority: base
Title: Tools for Package Development
Title: Tools for Package Development - with modifications for pqR
Author: R Development Core Team
Maintainer: R Core Team <R-core@r-project.org>
Description: Tools for package development, administration and documentation
......
# File src/library/tools/R/testing.R
# Part of the R package, http://www.R-project.org
# Modifications for pqR Copyright (c) 2013 Radford M. Neal.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
......@@ -118,10 +119,14 @@ Rdiff <- function(from, to, useDiff = FALSE, forEx = FALSE, nullPointers=TRUE, L
{
if(!length(txt)) return(txt)
## remove R header
if(length(top <- grep("^(R version|R : Copyright|R Under development)",
txt, perl = TRUE, useBytes = TRUE)) &&
length(bot <- grep("quit R.$", txt, perl = TRUE, useBytes = TRUE)))
if(length(top <-
grep("^(pqR version|R version|R : Copyright|R Under development)",
txt, perl = TRUE, useBytes = TRUE)) > 0
&& length(bot <-
grep("quit R.$", txt, perl = TRUE, useBytes = TRUE)) > 0) {
txt <- txt[-(top[1L]:bot[1L])]
}
## remove BATCH footer
nl <- length(txt)
if(nl > 3L && grepl("^> proc.time()", txt[nl-2L])) txt <- txt[1:(nl-3L)]
......
Package: utils
Version: @VERSION@
Priority: base
Title: The R Utils Package
Title: The R Utils Package - with modifications for pqR
Author: R Development Core Team and contributors worldwide
Maintainer: R Core Team <R-core@r-project.org>
Description: R utility functions
......
# File src/library/utils/R/RShowDoc.R
# Part of the R package, http://www.R-project.org
# Modifications for pqR Copyright (c) 2013 Radford M. Neal.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
......@@ -98,7 +99,7 @@ RShowDoc <- function(what, type=c("pdf", "html", "txt"), package)
writeLines(tmp, tf)
file.show(tf, delete.file = TRUE, encoding = "UTF-8")
return(invisible(path))
} else if(what == "COPYING") {
} else if(what %in% c("COPYING","ONEWS","OONEWS","OOONEWS","MODS")) {
path <- file.path(R.home(), what)
file.show(path)
return(invisible(path))
......
# Modifications for pqR Copyright (c) 2013 Radford M. Neal.
## What a silly name ...
.is_not_nonempty_text <-
function(x)
......@@ -894,6 +896,18 @@ function(file, meta = NULL)
citation <-
function(package = "base", lib.loc = NULL, auto = NULL)
{
## Preliminary citation for pqR to use for "base" package.
if (package=="base" && is.null(auto))
pqR.rval <- bibentry ("Misc",
author = "R. M. Neal",
title = "pqR - a pretty quick version of R",
year = 2012,
note = "source repository at github.com/radfordneal/pqR",
textVersion = "Neal, RM (2012) pqR - a pretty quick version of R, source repository at github.com/radfordneal/pqR")
else
pqR.rval <- NULL
## Allow citation(auto = meta) in CITATION files to include
## auto-generated package citation.
if(inherits(auto, "packageDescription")) {
......@@ -912,9 +926,19 @@ function(package = "base", lib.loc = NULL, auto = NULL)
## available.
citfile <- file.path(dir, "CITATION")
if(is.null(auto)) auto <- !file_test("-f", citfile)
## if CITATION is available
if(!auto) {
return(readCitationFile(citfile, meta))
rval <- readCitationFile(citfile, meta)
if (!is.null(pqR.rval)) {
rval <- .citation (c (pqR.rval, rval))
attr(rval,"mheader") <-
"pqR is based on R-2.15.0. These contributions may be referenced as follows:"
attr(rval,"mfooter") <-
"Please cite as appropriate. See 'citation(\"pkgname\")' for citing packages."
}
return (rval)
} else if(package == "base") {
## Avoid infinite recursion for broken installation.
stop("broken installation, no CITATION file in the base package.")
......@@ -1019,6 +1043,7 @@ function(package = "base", lib.loc = NULL, auto = NULL)
footer = footer,
other = z
)
.citation(rval)
}
......
% File src/library/utils/man/news.Rd
% Part of the R package, http://www.R-project.org
% Copyright 1995-2011 R Core Development Team
% Modifications for pqR Copyright (c) 2013 Radford M. Neal.
% Distributed under GPL 2 or later
\name{news}
......@@ -29,12 +30,18 @@ news(query, package = "R", lib.loc = NULL, format = NULL,
}
\details{
If \code{package} is \code{"R"} (default), a news db is built with the
news since the 2.10.0 release of R (corresponding to R's top-level
news since the first release of pqR (corresponding to pqR's top-level
\file{NEWS} file). Otherwise, if the given add-on package can be
found in the given libraries, it is attempted to read its news in
structured form from files \file{inst/NEWS.Rd}, \file{NEWS} or
\file{inst/NEWS} (in that order).
News on versions of R distributed by the R Core Team up to the
version pqR was based on may be perused using RShowDoc("ONEWS"),
RShowDoc("OONEWS"), and RShowDoc("OOONEWS"). RShowDoc("MODS")
will show some mods in pqR that are not in NEWS, since they are
of little interest to users.
File \file{inst/NEWS.Rd} should be an Rd file given the entries as Rd
\verb{\itemize} lists, grouped according to version using
\verb{section} elements with names starting with a suitable prefix
......
......@@ -27,7 +27,7 @@
void attribute_hidden PrintGreeting(void)
{
char buf[384];
char buf[2000];
Rprintf("\n");
PrintVersion_part_1(buf);
......@@ -47,11 +47,12 @@ Type 'q()' to quit R.\n\n"));
SEXP attribute_hidden do_version(SEXP call, SEXP op, SEXP args, SEXP env)
{
SEXP value, names;
char buf[128];
char buf[200];
checkArity(op, args);
PROTECT(value = allocVector(VECSXP,14));
PROTECT(names = allocVector(STRSXP,14));
PROTECT(value = allocVector(VECSXP,17));
PROTECT(names = allocVector(STRSXP,17));
SET_STRING_ELT(names, 0, mkChar("platform"));
SET_VECTOR_ELT(value, 0, mkString(R_PLATFORM));
......@@ -87,6 +88,13 @@ SEXP attribute_hidden do_version(SEXP call, SEXP op, SEXP args, SEXP env)
SET_STRING_ELT(names, 13, mkChar("nickname"));
SET_VECTOR_ELT(value, 13, mkString(R_NICK));
SET_STRING_ELT(names, 14, mkChar("pqR.base.version"));