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53 commits

Author SHA1 Message Date
markd
6ae7673bf6 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.
2004-05-07 22:47:26 +00:00
markd
01318928ff 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.
2004-04-27 11:24:31 +00:00
markd
1e542beb23 Switch to using tk8.4
bump PKGREVISION
2004-03-11 21:04:47 +00:00
minskim
2827f5b2d8 Enable tk84 and replace x11/tk with x11/tk83. Packages compatible
with 8.4 will be updated to depend on x11/tk after Tk update.
2004-03-08 20:27:13 +00:00
markd
ed34a1ec1f USE_LANGUAGES= c fortran 2004-03-01 11:42:13 +00:00
grant
f1ab3f4ed4 replace deprecated USE_GMAKE with USE_GNU_TOOLS+=make. 2004-01-24 13:51:13 +00:00
markd
56811f2ffc Reintroduce reordering tests for termcap vs termlib vs ncurses and
make dependency on libbz2 explicit

Fixes build on Solaris 8.
2004-01-05 12:20:57 +00:00
adam
4af341792b Now uses shared blas library from math/blas 2003-12-04 13:42:37 +00:00
markd
6ea261acc7 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.
2003-12-03 12:05:18 +00:00
grant
0155927c43 s/netbsd.org/NetBSD.org/ 2003-07-17 21:41:05 +00:00
jmc
b1abe34ac9 Make this relay on blas 1.0nb1 and use libblas_pic.a instead of libblas.a so
proper PIC objects get pulled into the .so's
2003-03-11 02:30:24 +00:00
markd
20f98877bd Update to R-1.6.2
CHANGES IN R VERSION 1.6.2

BUG FIXES

    o   plot.stepfun() now obeys a `ylim=.' specification.

    o   removeClass() does a better job of removing inheritance
        information.

    o   setIs() will not allow mismatched representations between two
        classes (without an explicit coerce method).

    o   The code underlying polygon drawing contained a memory leak.
        This showed up in persp, but did not affect other graphics
        functions.  It is now possible to draw big DEMs.

    o   logLik.nls() gave wrong df.

    o   rbind() with a mixture of data frames and matrices treated the
        matrices as vectors.

    o   stripchart(method="stack") was not handling missing values.

    o   Arithmetic functions such as log() lost the object bit from
        classed objects if coercion was needed.

    o   exp_rand would go into an infinite loop if unif_rand returned 0.

    o   formatC(x, format="fg") could return exponential format if
        rounding pushed x over a positive power of 10.

    o   attr(x, foo) used partial matching for `foo' (even though not
        documented to do so), and failed to find `foo' if there were
        two or more partial matches before the exact match in the list
        of attributes.

    o   Rdconv now creates direct HTML hyperlinks when linking to
        documentation in the same package.  The code now ensures that
        links which can be resolved within the package are so resolved,
        even when there are possible resolutions in other packages.

    o   If readBin(what=character()) is used incorrectly on a file which
        does not contain C-style character strings, warnings (usually
        many) are now given.

    o   Building libR.so with the zlib in the R sources was not
        finding the local zlib headers.

    o   system(intern=TRUE) has an undocumented line length limit of
        119 chars both on Unix and Windows.  The limit is now 8096 and
        documented.  On Unix (only) every 120th character used to be
        discarded.

    o   plot.POSIX[cl]t were not passing graphics parameters on to
        axis.POSIXct.

    o   On some HP-UX systems, installed scripts were not executable
        when using the BSD-compatible install system program found by
        configure.  We now always use install-sh on HP-UX.

    o   c() was converting NA names to "NA": now proper NA strings are
        used wherever possible.

    o   A typo was causing segfaults when using data.entry under SuSE.
2003-01-23 21:24:58 +00:00
markd
3a017607d7 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 Oehlschl<E4>gel).

    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 <smyth@wehi.edu.au>.

    o   stars() now has add and plot arguments.

and lots of bug fixes.
2002-12-10 11:58:10 +00:00
jlam
940372217e BUILDLINK_X11PKG_DIR is no more. 2002-10-31 23:30:36 +00:00
markd
34fd0ce4df INSTALL_DIRS -> R_INSTALL_DIRS to not conflict with the variable introduced
in bsd.pkg.mk revision 1.1045.  Fixes pkg/18332
2002-09-26 05:36:48 +00:00
markd
bf511b48c1 find ... -or ... -> find ... -o ... for more portability. 2002-09-23 13:41:15 +00:00
markd
64e555d68e Update R to 1.5.1, switch to buildlink2, change maintainer.
User-Visible Changes

    o XDR support is now guaranteed to be available, so the default
        save format will always be XDR binary files, and it is safe to
        distribute data in that format. (We are unaware of any
        platform that did not support XDR in recent versions of R.)

        gzfile() is guaranteed to be available, so the preferred
        method to distribute sizeable data objects is now via
        save(compress = TRUE).

    o pie() replaces piechart() and defaults to using pastel colours.

    o formatC has new arguments (see below) and formatC(*, d = <dig>)
        is no longer valid and must be written as formatC(*, digits = <dig>).

    o Missingness of character strings is treated much more
        consistently, and the character string "NA" can be used as a
        non-missing value.

    o summary.factor() now uses a stable sort, so the output will
        change where there are ties in the frequencies.


Plus lots of new features and many bug fixes.
2002-09-09 00:59:00 +00:00
markd
85b39d0110 Give path for -lblas so modules such as R-KernSmooth can find it when
they try to link it.
2002-07-17 13:12:54 +00:00
dmcmahill
e9bca5e160 don't key off of `alpha' to decide to do OSF specific things (-fpe3 flag
to the fortran compiler).  Also mark as not for older netbsd-alpha systems
as this is an IEEE-754 infected program (hi ross!).
2002-06-16 02:56:50 +00:00
markd
3aafc4760f Reorder PLIST so pkg_delete works cleanly 2002-05-24 13:24:36 +00:00
markd
ba3781530e Add etc/Makeconf to REPLACE_BUILDLINK. Fixes pkg/16620 2002-05-03 12:34:39 +00:00
markd
09d64d9c0c Change MASTER_SITES to use the CRAN list.
Add support for building R extension packages as pkgsrc packages.
Bump PKGREVISION so extension packages can depend on a version of R with
this support.

Discussed with Johnny Lam.
2002-04-23 01:14:49 +00:00
fredb
b48eba1112 Give all packages which depend on "png" a version bump, and update
all dependencies on packages depending on "png" which contain shared
libraries, all for the (imminent) update to the "png" package.
[List courtesy of John Darrow, courtesy of "bulk-build".]
2002-03-13 17:36:35 +00:00
markd
2b2f1f68c7 Update to version 1.4.1 from PR pkg/15757 by Ray Brownrigg with minor mods
by me.

Changes and bug fixes from 1.3.1 are numerous.  See the NEWS file in
the distribution for details.
2002-03-01 10:46:53 +00:00
jlam
3268e058ac Include a patch for the generated configure script so that we don't have
to depend on auto* tools at build-time.  This fixes pkg/14916 by Brook
Milligan <brook@biology.nmsu.edu>.
2001-12-11 22:35:07 +00:00
jlam
a4bc16d30c I am a triple idiot. The only relevant variable that x11.buildlink.mk
redefines about which buildlink.mk files would care is BUILDLINK_X11_DIR,
which points to the location of the X11R6 hierarchy used during building.
If x11.buildlink.mk isn't included, then BUILDLINK_X11_DIR defaults to
${X11BASE} (set in bsd.pkg.mk), so its value is always safe to use.  Remove
the ifdefs surrounding the use of BUILDLINK_X11_DIR in tk/buildlink.mk and
revert changes to move x11.buildlink.mk before the other buildlink.mk files.
2001-10-24 22:10:43 +00:00
tron
a68a277b43 Use wildcard dependence on "autoconf" package. 2001-08-27 14:35:04 +00:00
agc
a9e9fb246c Add back COMMENT definition which got lost. 2001-08-13 10:25:03 +00:00
jlam
cbee525ae7 Update R to 1.3.0. This is a two-generation upgrade from the previous 1.1.1
version in pkgsrc.  There are many, many bugfixes, better compliance with
S3/S4, and many additional statistical analysis functions added to the
base library.  There is also an improved (faster) garbage collector and
support for dynamically sizing the memory used by R.  The full summary of
changes may be found on the R Project website.
2001-07-23 13:14:44 +00:00
jlam
328a35f96f LIBS is automatically added to CONFIGURE_ENV by bsd.pkg.mk if
GNU_CONFIGURE is defined, so simply set LIBS to the appropriate value.
2001-06-12 20:33:00 +00:00
jlam
c4e71c5e7a CPPFLAGS is now passed to MAKE_ENV and CONFIGURE_ENV by bsd.pkg.mk, so
adapt by moving CPPFLAGS settings to top-level, and removing explicit
inclusion of CPPFLAGS into MAKE_ENV and CONFIGURE_ENV.
2001-06-11 06:34:17 +00:00
wiz
26c40c61dd Update dependency on png to >=1.0.11 because of the shlib major bump.
Noted by Frederick Bruckman.
2001-05-22 09:32:18 +00:00
hubertf
e32afb6fea Change BUILD_DEPENDS semantics:
first component is now a package name+version/pattern, no more
executable/patchname/whatnot.

While there, introduce BUILD_USES_MSGFMT as shorthand to pull in
devel/gettext unless /usr/bin/msgfmt exists (i.e. on post-1.5 -current).

Patch by Alistair Crooks <agc@netbsd.org>
2001-03-27 03:19:43 +00:00
tron
5382bbe7c6 Because the minor number of the PNG library was increased packages compiled
using the newest PNG library won't work on system with an older one. To
prevent such problems with precompiled binary packages require at least
"png-1.0.9nb1" in all dependences.
2001-03-04 09:06:09 +00:00
jlam
3ee88936ba Add NOT_FOR_PLATFORMS=*-*-alpha as R requires IEEE math. Information
gleaned from port-alpha mailing list posting by Paul Mather
<paul@gromit.dlib.vt.edu> in:

	http://mail-index.netbsd.org/port-alpha/2001/02/14/0004.html
2001-02-26 15:01:43 +00:00
wiz
a13ea108bb Update to new COMMENT style: COMMENT var in Makefile instead of pkg/COMMENT. 2001-02-17 17:52:59 +00:00
fredb
46a9e2c3de Make that "autoreconf" -- there is no "autoremake". 2001-02-06 03:16:56 +00:00
tron
f2d262e0be Use full pathname "${LOCALBASE}/bin/auto..." in dependences and make
targets. This includes a fix for PR pkg/12125 by Tomasz Luchowski.
2001-02-05 09:00:54 +00:00
jlam
55962912b3 Homepage has moved. 2000-11-03 01:14:51 +00:00
jlam
32d4c82932 Update R to 1.1.1. This is primarily a bugfix release from version 1.1.0,
particularly fixing the table editor, but also contains a few additions:

    o	data(), example() and help() now search the loaded packages, then
	in their .lib.loc argument, the latter as pre-0.99.0.  See
	their help pages for the precise details.

    o	help() has a new argument `try.all.packages' set by the option
	"help.try.all.packages". If help is not found in the normal
	path and this is TRUE then a search is made of all packages
	for possible matches.

    o   prop.trend.test() - test for trend in proportions.

    o   write.table() has new argument `dec' for setting the decimal
        separator (SPSS/Windows and probably others want commas in
	continental European locales).

    o   Advance warning: save(, oldstyle=TRUE) will no longer be
	available after this release.

    o   Symbols can now be coerced to expressions, making
	as.expression(quote(a)) work
2000-08-16 19:04:42 +00:00
jlam
a3e1ef88eb Update R to 1.1.0. Many additions and bug-fixes from 1.1.0 make this
a more usable replacement for S/S-PLUS.
2000-08-11 23:02:37 +00:00
jlam
9c5f6d504b 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.
2000-04-19 15:30:05 +00:00
rh
168ae0f782 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).
2000-01-12 22:05:30 +00:00
dmcmahill
2ff514e91e add USE_FORTRAN 1999-11-23 17:37:28 +00:00
jlam
fafc727081 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 <file.Rd> 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).
1999-08-26 23:52:21 +00:00
jlam
ac803dafa1 Update readline dependency. 1999-07-13 01:20:11 +00:00
hubertf
6fd57bf638 default R_PAPERSIZE to A4 if PAPERSIZE is not set. 1999-06-09 00:45:08 +00:00
jlam
d85fb58285 Updated R to 0.64.1. Too many changes from 0.62.1 to enumerate.
See NEWS file in distribution.
1999-05-25 23:45:05 +00:00
garbled
3fe7edf239 add USE_X11=yes 1999-04-26 18:56:13 +00:00
hubertf
2a95ad9c6b Fix CONFLICTS (remove redundancy, mostly) 1999-02-20 22:48:24 +00:00