head 1.10; access; symbols pkgsrc-2013Q2:1.10.0.38 pkgsrc-2013Q2-base:1.10 pkgsrc-2012Q4:1.10.0.36 pkgsrc-2012Q4-base:1.10 pkgsrc-2011Q4:1.10.0.34 pkgsrc-2011Q4-base:1.10 pkgsrc-2011Q2:1.10.0.32 pkgsrc-2011Q2-base:1.10 pkgsrc-2009Q4:1.10.0.30 pkgsrc-2009Q4-base:1.10 pkgsrc-2008Q4:1.10.0.28 pkgsrc-2008Q4-base:1.10 pkgsrc-2008Q3:1.10.0.26 pkgsrc-2008Q3-base:1.10 cube-native-xorg:1.10.0.24 cube-native-xorg-base:1.10 pkgsrc-2008Q2:1.10.0.22 pkgsrc-2008Q2-base:1.10 pkgsrc-2008Q1:1.10.0.20 pkgsrc-2008Q1-base:1.10 pkgsrc-2007Q4:1.10.0.18 pkgsrc-2007Q4-base:1.10 pkgsrc-2007Q3:1.10.0.16 pkgsrc-2007Q3-base:1.10 pkgsrc-2007Q2:1.10.0.14 pkgsrc-2007Q2-base:1.10 pkgsrc-2007Q1:1.10.0.12 pkgsrc-2007Q1-base:1.10 pkgsrc-2006Q4:1.10.0.10 pkgsrc-2006Q4-base:1.10 pkgsrc-2006Q3:1.10.0.8 pkgsrc-2006Q3-base:1.10 pkgsrc-2006Q2:1.10.0.6 pkgsrc-2006Q2-base:1.10 pkgsrc-2006Q1:1.10.0.4 pkgsrc-2006Q1-base:1.10 pkgsrc-2005Q4:1.10.0.2 pkgsrc-2005Q4-base:1.10 pkgsrc-2005Q3:1.8.0.12 pkgsrc-2005Q3-base:1.8 pkgsrc-2005Q2:1.8.0.10 pkgsrc-2005Q2-base:1.8 pkgsrc-2005Q1:1.8.0.8 pkgsrc-2005Q1-base:1.8 pkgsrc-2004Q4:1.8.0.6 pkgsrc-2004Q4-base:1.8 pkgsrc-2004Q3:1.8.0.4 pkgsrc-2004Q3-base:1.8 pkgsrc-2004Q2:1.8.0.2 pkgsrc-2004Q2-base:1.8 pkgsrc-2004Q1:1.6.0.2 pkgsrc-2004Q1-base:1.6 pkgsrc-2003Q4:1.5.0.4 pkgsrc-2003Q4-base:1.5 netbsd-1-6-1:1.5.0.2 netbsd-1-6-1-base:1.5 buildlink2-base:1.4 netbsd-1-4-PATCH002:1.3 comdex-fall-1999:1.2 netbsd-1-4-PATCH001:1.1; locks; strict; comment @# @; 1.10 date 2005.12.11.14.37.12; author markd; state dead; branches; next 1.9; 1.9 date 2005.12.01.23.11.27; author joerg; state Exp; branches; next 1.8; 1.8 date 2004.05.07.22.47.26; author markd; state dead; branches; next 1.7; 1.7 date 2004.04.27.11.24.31; author markd; state Exp; branches; next 1.6; 1.6 date 2003.12.03.12.05.19; author markd; state Exp; branches; next 1.5; 1.5 date 2002.12.10.11.58.12; author markd; state Exp; branches; next 1.4; 1.4 date 2000.04.19.15.30.07; author jlam; state dead; branches; next 1.3; 1.3 date 2000.01.12.22.05.33; author rh; state Exp; branches; next 1.2; 1.2 date 99.08.26.23.52.22; author jlam; state Exp; branches; next 1.1; 1.1 date 99.05.25.23.51.12; author jlam; state Exp; branches; next ; desc @@ 1.10 log @Update R to 2.2.0 Changes: This version contains several changes and additions, mostly incremental. @ text @$NetBSD: patch-af,v 1.9 2005/12/01 23:11:27 joerg Exp $ --- src/main/printarray.c.orig 2005-12-01 22:45:25.000000000 +0000 +++ src/main/printarray.c @@@@ -45,7 +45,7 @@@@ #ifdef HAVE_ALLOCA_H #include #endif -#if !HAVE_DECL_ALLOCA && !defined(__FreeBSD__) +#if !HAVE_DECL_ALLOCA && !defined(__FreeBSD__) && !defined(__DragonFly__) extern char *alloca(size_t); #endif @ 1.9 log @- correctly depend on devel/gettext-lib, bump revision for this - this uses libtool, tell the framework so - don't declare alloca on DragonFly, it conflicts with system headers - patch libtool.m4 fragment for DrgaonFly @ text @d1 1 a1 1 $NetBSD$ @ 1.8 log @R assumes it can append to the DESCRIPTION files of each R package while building even though it uses INSTALL_DATA on them so set SHAREMODE=644 rather than have to patch an ever increasing number of files. Idea from Julio M. Merino Vidal. @ text @d1 1 a1 1 $NetBSD: patch-af,v 1.7 2004/04/27 11:24:31 markd Exp $ d3 10 a12 17 --- src/library/ctest/Makefile.in.orig 2004-02-19 08:06:09.000000000 +1300 +++ src/library/ctest/Makefile.in @@@@ -23,14 +23,14 @@@@ all: Makefile DESCRIPTION $(SHELL) $(top_srcdir)/tools/move-if-change $${f} \ $(top_builddir)/library/$(pkg)/R/$(pkg)) @@if test -f DESCRIPTION; then \ - $(INSTALL_DATA) DESCRIPTION $(top_builddir)/library/$(pkg); \ (tmp="Built: R $(VERSION); "; \ if test -d $(srcdir)/src; then \ tmp="$${tmp}$(R_PLATFORM)"; \ fi; \ tmp="$${tmp}; `date`; $(R_OSTYPE)"; \ echo "$${tmp}") \ - >> $(top_builddir)/library/$(pkg)/DESCRIPTION; \ + >> DESCRIPTION; \ + $(INSTALL_DATA) DESCRIPTION $(top_builddir)/library/$(pkg); \ fi a13 1 Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status @ 1.7 log @Update R to 1.9.0 and buildlink3ify USER-VISIBLE CHANGES o Underscore '_' is now allowed in syntactically valid names, and make.names() no longer changes underscores. Very old code that makes use of underscore for assignment may now give confusing error messages. o Package 'base' has been split into packages 'base', 'graphics', 'stats' and 'utils'. All four are loaded in a default installation, but the separation allows a 'lean and mean' version of R to be used for tasks such as building indices. Packages ctest, eda, modreg, mva, nls, stepfun and ts have been merged into stats, and lqs has been returned to MASS. In all cases a stub has been left that will issue a warning and ensure that the appropriate new home is loaded. All the time series datasets have been moved to package stats. Sweave has been moved to utils. Package mle has been moved to stats4 which will become the central place for statistical S4 classes and methods distributed with base R. Package mle remains as a stub. Users may notice that code in .Rprofile is run with only the new base loaded and so functions may now not be found. For example, ps.options(horizontal = TRUE) should be preceded by library(graphics) or called as graphics::ps.options or, better, set as a hook -- see ?setHook. o There has been a concerted effort to speed up the startup of an R session: it now takes about 2/3rds of the time of 1.8.1. o A warning is issued at startup in a UTF-8 locale, as currently R only supports single-byte encodings. plus many new features and bug fixes. @ text @d1 1 a1 1 $NetBSD$ @ 1.6 log @Update R to 1.8.1. Changes since 1.6.2 Many new features. Language changes. Additional standard package 'mle'. Some old features deprecated or defunct. Many many bug fixes. Update to 1.8.0 from Ray Brownrigg in private communication, cleaned up and updated to 1.8.1 by me. @ text @d3 1 a3 1 --- src/library/ctest/Makefile.in.orig 2003-09-21 20:13:04.000000000 +1200 d5 3 a7 3 @@@@ -29,14 +29,14 @@@@ all: Makefile DESCRIPTION fi; \ done d18 1 a18 1 + $(INSTALL_DATA) DESCRIPTION $(top_builddir)/library/$(pkg); \ d20 2 a21 2 @@if test -d $(srcdir)/data; then \ $(MKINSTALLDIRS) $(top_builddir)/library/$(pkg)/data; \ @ 1.5 log @Update R to version 1.6.1. Pkgsrc changes: Now builds the libR.so and provides a buildlink2.mk for packages that want to use it. From suggestions from Kent Polk. Recommended library set is now included in the base package. Changes: CHANGES IN R VERSION 1.6.1 NEW FEATURES o Added a few "trivial and obviously missing" functions to tcltk: tkchooseDirectory, tkpopup, tkdialog, tkread o barplot() has a new argument `axis.lty', which if set to 1 allows the pre-1.6.0 behaviour of plotting the axis and tick marks for the categorical axis. (This was apparently not intentional, but axis() used to ignore lty=0.) The argument `border' is no longer ".NotYetUsed". CHANGES IN R VERSION 1.6.0 USER-VISIBLE CHANGES o The default colour palette now has "grey" instead of "white" in location 8. See palette(). o grid(nx) behaves differently (but the same as in R versions <= 0.64). NEW FEATURES o Preparations for name space support: o The objects created in the methods package to represent classes, generic functions, method definitions, and inheritance relations now themselves belong to true classes. In particular, the "classRepresentation" objects follow the description in "Programming with Data" (section 7.6). o Other additions and changes to the methods package: o New methods ([[, print, str) and extended plot() method (incl. logical `horiz') for "dendrogram" class. o sprintf() now checks the agreement between formats and object types, and handles special values (NA, Inf, ...) correctly. o chol() now uses a tolerance for non-positive-definiteness and so should give more consistent results across platforms. o New function agrep() for approximate (fuzzy) string matching. o help.search() can now use both approximate (fuzzy) and regular expression matching. By default, if the pattern to be matched consists of only alphanumeric characters, whitespace or a dash, approximate matching is used. o axis() has three new optional arguments `col', `lty', and `lwd' all for drawing the axis line and tick marks. o Function vcov() (formerly in MASS), a generic function to return the variance-covariance matrix of the parameter estimates of a fitted model. o duplicated() and unique() have methods for matrices and arrays (based on ideas from Jens Oehlschlgel). o Internally memory sizes and counts of cons cells are now stored in unsigned longs. This allows memory limits to be set and objects created in the range 2-4Gb on 32-bit platforms, and allows 64-bit platforms to use much larger amounts of memory. o Command-line flags to set memory can now use the suffix `G' for gigabytes. The setting of maximum vsize is now only limited by the platform's address space. o All warning and error messages are truncated to a length set by options(warning.length=), defaulting to 1000. (Previously most (but not quite all) were truncated at 8192 characters.) o [dpqr]gamma() check for shape parameter > 0. o as.POSIX[cl]t can now convert logical NAs. o All installed packages (even those shipped with R) are given a `Built' field in the DESCRIPTION file. o as.data.frame() now coerces logical matrices into logical columns (rather than factors). o [[<-.data.frame no longer coerces character replacement values to factor. This is consistent with using $ to replace and with S4. o library() attempts to detect improperly installed packages, so as from this version an installed package must have a DESCRIPTION file and that file must have been stamped with a `Built:' line (which was introduced in 1.2.0). Under Unix-alikes, the platform is checked against that used for installation. o print.factor() has new arguments `max.levels' (with a smart default) and `width'. print.ordered() is no longer needed. o RNGkind() has an additional option for normal random generators: "Inversion". o data.frame() recycles factors and "AsIs" objects as well as atomic vectors. o rect() accepts additional graphics parameters through a ... argument (in the same way as polygon). o strwidth/strheight() now coerce their first argument in exactly the same way text() does, so a wider range of inputs is allowed. o prompt()'s default and data.frame methods have a new 3rd argument `name' allowing them to used more easily in scripts and loops. o rgb() has a new `maxColorValue' argument, allowing r,g,b in [0,M], particularly in {0:255}, efficiently and non-error-prone. o summaryRprof() provides the functionality of R CMD Rprof in R code, though more slowly. o pdf() now uses PDF not R code for clipping, which ensures that partially visible text strings are (partially) shown. o Each R session uses a per-session temporary directory which is removed at normal termination. The directory name is given by the tempdir() function, and filenames returned by tempfile() will be within that directory. o help.start() on Unix now uses a .R subdirectory of the per-session temporary directory and not ~/.R. A side effect is that ~/.R is now never deleted by R. o cbind/rbind() used to ignore all zero-length vectors, an undocumented quirk for S-compatibility. This caused problems when combining zero-extent matrices and zero-length vectors, and now zero-length vectors are ignored unless the result would have zero rows/columns. o plot.spec(x) now also works for other x than AR and Pgram results. o New functions La.chol() and La.chol2inv() for Cholesky decomposition and inverse of positive definite matrices using Lapack. o Changes to the tcltk package o New function axTicks() returning tick mark locations like axis(). o grid() has a more sensible default behavior. Tick axis alignment only happens when no numbers of grid cells are specified. New arguments lwd and equilogs; nx/ny = NA for not drawing, see ?grid. o installed.packages() has a new argument `priority'. o termplot() uses factor levels rather than 1,2,3... for x-axis. o The trace() function has been robustified and a new function tracingState() added to turn tracing temporarily on and off. o New cophenetic() in "mva" as utility for hierarchical clustering. o p.adjust() has two new methods, 'Hommel' and 'FDR', contributed by Gordon Smyth . o stars() now has add and plot arguments. and lots of bug fixes. @ text @d3 4 a6 4 --- src/library/ctest/Makefile.in.orig Mon Jul 22 00:32:06 2002 +++ src/library/ctest/Makefile.in Mon Dec 9 23:59:27 2002 @@@@ -29,10 +29,10 @@@@ fi; \ d8 11 a18 7 @@if test -f $(top_builddir)/$(subdir)/DESCRIPTION; then \ + echo "Built: R" @@VERSION@@\; @@R_PLATFORM@@\; `date` >> \ + $(top_builddir)/$(subdir)/DESCRIPTION; \ $(INSTALL_DATA) $(top_builddir)/$(subdir)/DESCRIPTION \ $(top_builddir)/library/$(pkg); \ - echo "Built: R" @@VERSION@@\; @@R_PLATFORM@@\; `date` >> \ - $(top_builddir)/library/$(pkg)/DESCRIPTION; \ @ 1.4 log @Update to R-1.0.1. Move R library tree to ${PREFIX}/lib (a la perl5) since it contains loadable shared object files that are platform-specific. Lots of bug-fixes and additions ... it's getting closer to a usable replacement for S-PLUS. @ text @d1 1 a1 1 $NetBSD: patch-af,v 1.3 2000/01/12 22:05:33 rh Exp $ d3 15 a17 19 --- src/scripts/R.sh.in.orig Wed Jan 12 20:12:45 2000 +++ src/scripts/R.sh.in Wed Jan 12 20:15:02 2000 @@@@ -114,14 +114,14 @@@@ fi if test -z "${DBG}"; then - exec ${R_HOME}/bin/${R_BINARY} @@R_BATCHSAVE@@ ${ARGS} + exec @@prefix@@/bin/${R_BINARY} @@R_BATCHSAVE@@ ${ARGS} else if test -n "${ARGS}"; then echo "*** Further command line arguments (\`${ARGS}') disregarded" echo "*** (maybe use \`run ${ARGS}' from *inside* ${DBG})" echo "" fi - exec ${DBG} ${R_HOME}/bin/${R_BINARY} + exec ${DBG} @@prefix@@/bin/${R_BINARY} fi ### Local Variables: *** @ 1.3 log @Update R to 0.90.1. Changes are tons of changes and bugfixes, too numerous to list here (see http://cran.r-project.org/src/base/NEWS for more information). @ text @d1 1 a1 1 $NetBSD$ @ 1.2 log @Update R to 0.64.2. Changes from 0.64.1: NEW FEATURES o new target for R installation testing : make strict-tests. o symnum(x) now nicely codes logical x. o convolve() has a new type = c("circular", "open", "filter") argument allowing more than the only circular convolution. o par(xpd) now has three settings: FALSE (clip to plot region), TRUE (clip to figure region), or NA (clip to device region). o zapsmall(x) works for complex x. o new global variable R.version.string (for plots & reports). Deprecated version & Version for new R.version & R.Version. o R CMD Rd2dvi has builtin "Usage" help and works for multiple files. Useful for automatic reference manual of a package. (doc/manual/lib2tex is more efficient for installed packages, however). BUG FIXES o power() is now fully implemented and documented. o A couple of problems with group generic operations. o A bug which meant that it was not possible to add elements to zero length lists in the obvious way has been fixed. x <- list(); x[[1]] <- 10 x <- list(); x[["a"]] <- 11 both now work. o save.image() ignored dot-names. (esp. .First()) o lab= argument to plot() misinterpreted by axis() via ... passing o NULL labels in text() caused segfault o matrix(f,...) with f a factor now coerces to character o documentation errors for substitute and is.vector, minor fixups for trig and nlm o Background colours are set properly on X11 devices with colortype="pseudo": sometimes they were not allocated separately. o C() works (again?) for a single argument. o is.na() didn't work properly for "list" arguments. o symnum() sometimes failed with arrays of rank >= 3. o in some cases one could get nonblack color instead of black on 2nd x11() window. o influence.measures(.) $ is.influential was wrong on the cooks.distance. o printing of complex NaN/Inf was wrong as well. o printing of complex named vectors had a wrong initial space. o allow trailing space in character->numeric coercion o library() gave wrong "masked" warnings in some cases. o par(xpd) semantics were not compatible with S. o rect() output was not clipped in PostScript. o par(pin=c(width, height)) was behaving as par(pin=c(width, width)). o Non-blank separated data files didn't have their 1st field handled properly. o "aux" directory moved to "tools" to avoid difficulties on Windows. o structure() clobbered factors with missing levels. o pmatch() misbehaved on duplicate matches. o R CMD Rd2dvi works again. o logical binops tried to set time series parameters before dimensions. o upped the BUFSIZE in model.c (NOT proper long-term solution). o dput(), dump() and deparse() now always use DBL_DIG (=15) digits for numeric formatting. o chull() now works for vertical borders, such as in chull(c(1,1,2),3:1). @ text @d3 16 a18 14 --- src/scripts/R.sh.in.orig Wed May 12 03:12:32 1999 +++ src/scripts/R.sh.in Thu Aug 26 18:44:22 1999 @@@@ -47,7 +47,7 @@@@ echo "*** (maybe use \`run ${args}' from *inside* ${deb}" echo "" fi - exec ${deb} ${RHOME}/bin/${R_BINARY} ;; + exec ${deb} @@prefix@@/bin/${R_BINARY} ;; --no-environ) USE_R_ENVIRON=false ;; --vanilla) @@@@ -107,7 +107,7 @@@@ if ${USE_R_ENVIRON}; then [ -r ${HOME}/.Renviron ] && . ${HOME}/.Renviron a19 2 -exec ${RHOME}/bin/${R_BINARY} @@R_BATCHSAVE@@ ${ARGS} +exec @@prefix@@/bin/${R_BINARY} @@R_BATCHSAVE@@ ${ARGS} a21 1 ### mode: sh *** @ 1.1 log @Oops...still learning CVS. Forgot to add these files before the commit. @ text @d3 2 a4 2 --- src/scripts/R.sh.in.orig Thu May 6 04:32:27 1999 +++ src/scripts/R.sh.in Mon May 24 19:26:06 1999 d14 1 a14 1 @@@@ -106,7 +106,7 @@@@ @