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2005-01-12Move buildlink3.mk files ahead of targets as per example Makefile.jlam1-11/+12
2005-01-12Fix up the comment to note that we still need to unwrap some files atjlam1-13/+12
post-configure time, even after the switch from buildlink2 to buildlink3. Also, use SUBST_CLASSES instead of the custom post-configure target, and take advantage of the fact that the "unwrap" SUBST_CLASS already does mostly the right thing.
2005-01-12Nuke USE_FORTRAN and bring the f2c handling within the mk/compilerjlam1-2/+1
framework. The list of changes include: * Modify compiler.mk so that "c" is always prepended to USE_LANGUAGES, so we no longer need to say it in package Makefiles. Packages should now append to USE_LANGUAGES instead of setting it. * Create mk/compiler/f2c.mk which implements another pseudo-compiler "f2c" that may be used with any C compiler backend, e.g. PKGSRC_COMPILER= f2c ccache gcc * Teach the various "real" compiler files, e.g., sunpro.mk, mipspro.mk, etc., to use f2c if the native Fortran compiler isn't present. Packages that use Fortran should now simply include the line: USE_LANGUAGES+= fortran in the package Makefile.
2004-11-24Make bulk build happy by fixing up the rpath. Not actually an issue inmarkd2-1/+15
normal operation as the binary is always called from a wrapper script that sets LD_LIBRARY_PATH.
2004-11-18Update R to 2.0.1markd5-67/+34
Changes 2.0.1: This is a maintenance version mainly to fix a number of minor bugs and issues. Some rather nasty bugs were Windows-specific. Changes 2.0.0: Many things have changed since 1.0. The R language has acquired namespaces, exception handling constructs, formal methods and classes, much improved garbage collection, generalized I/O via connection objects, and considerable improvements in the graphics area. The user workspace has been reorganized, and so has the set of packages that ship with R. Several "recommended packages" deemed indispensable in a statistical system are bundled. In addition, there has been a large number of more specific new functions, tweaks, and bugfixes.
2004-11-13USE_BUILDLINK3 is a yes/no variable.jlam1-2/+2
2004-10-03Libtool fix for PR pkg/26633, and other issues. Update libtool to 1.5.10tv1-1/+2
in the process. (More information on tech-pkg.) Bump PKGREVISION and BUILDLINK_DEPENDS of all packages using libtool and installing .la files. Bump PKGREVISION (only) of all packages depending directly on the above via a buildlink3 include.
2004-07-06Annotate a comment:wiz1-1/+2
# XXX: following comment still true for buildlink3? # R does ugly things in the configure to get the default list of arguments # for linking Fortran, which exposes the buildlink2 tricks so clean up # afterwards
2004-06-24Update R to 1.9.1markd2-5/+5
CHANGES IN R VERSION 1.9.1 NEW FEATURES o as.Date() now has a method for "POSIXlt" objects. o mean() has a method for "difftime" objects and so summary() works for such objects. o legend() has a new argument 'pt.cex'. o plot.ts() has more arguments, particularly 'yax.flip'. o heatmap() has a new 'keep.dendro' argument. o The default barplot method now handles vectors and 1-d arrays (e.g., obtained by table()) the same, and uses grey instead of heat color palettes in these cases. (Also fixes PR#6776.) o nls() now looks for variables and functions in its formula in the environment of the formula before the search path, in the same way lm() etc look for variables in their formulae. DEPRECATED & DEFUNCT o Support for non-IEEE-754 arithmetic (which has been untested for some time) will be removed in the next full release. o Direct use of R INSTALL|REMOVE|BATCH|COMPILE|SHLIB is deprecated: use R CMD instead. o The gnome/GNOME graphics device is deprecated and will be removed in the next full release. Plus Bug Fixes.
2004-05-18Enable pkgviews installation.uebayasi1-1/+3
2004-05-07R assumes it can append to the DESCRIPTION files of each R package whilemarkd17-332/+6
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.
2004-04-27Convert to buildlink3.snj2-27/+19
2004-04-27Update R to 1.9.0 and buildlink3ifymarkd14-135/+148
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.
2004-03-30Fix build against newest X11. for some obscure reason, ↵jwise2-1/+10
src/modules/x11/dataentry.c explicitly unset NeedFunctionPrototypes, which can no longer safely be done in recent X11 sources (as _Xconst is only defined if this is set, yet is used everywhere).
2004-03-11Switch to using tk8.4markd1-3/+3
bump PKGREVISION
2004-03-08Enable tk84 and replace x11/tk with x11/tk83. Packages compatibleminskim1-2/+2
with 8.4 will be updated to depend on x11/tk after Tk update.
2004-03-01USE_LANGUAGES= c fortranmarkd1-1/+2
2004-01-24replace deprecated USE_GMAKE with USE_GNU_TOOLS+=make.grant1-2/+2
2004-01-20Move WRKSRC definition away from the first paragraph in a Makefile.agc1-2/+2
2004-01-05Reintroduce reordering tests for termcap vs termlib vs ncurses andmarkd4-7/+163
make dependency on libbz2 explicit Fixes build on Solaris 8.
2003-12-19Fix building when non-root.markd2-1/+23
Closes PR pkg/23760
2003-12-04Now uses shared blas library from math/blasadam1-5/+3
2003-12-03Update R to 1.8.1.markd22-369/+320
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.
2003-07-17s/netbsd.org/NetBSD.org/grant1-2/+2
2003-03-29Place WRKSRC where it belongs, to make pkglint happy; ok'ed by wiz.jmmv1-2/+2
2003-03-14(1) Publicly export the value of _OPSYS_RPATH_NAME as RPATH_FLAG;jlam1-2/+3
Makefiles simply need to use this value often, for better or for worse. (2) Create a new variable FIX_RPATH that lists variables that should be cleansed of -R or -rpath values if ${_USE_RPATH} is "no". By default, FIX_RPATH contains LIBS, X11_LDFLAGS, and LDFLAGS, and additional variables may be appended from package Makefiles.
2003-03-11Make this relay on blas 1.0nb1 and use libblas_pic.a instead of libblas.a sojmc1-2/+5
proper PIC objects get pulled into the .so's
2003-01-23Update to R-1.6.2markd3-25/+30
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.
2002-12-10Update R to version 1.6.1.markd21-48/+328
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.
2002-10-31BUILDLINK_X11PKG_DIR is no more.jlam1-2/+1
2002-09-26INSTALL_DIRS -> R_INSTALL_DIRS to not conflict with the variable introducedmarkd1-4/+4
in bsd.pkg.mk revision 1.1045. Fixes pkg/18332
2002-09-23find ... -or ... -> find ... -o ... for more portability.markd2-4/+4
2002-09-09Update R to 1.5.1, switch to buildlink2, change maintainer.markd5-2668/+311
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.
2002-07-17Give path for -lblas so modules such as R-KernSmooth can find it whenmarkd1-2/+2
they try to link it.
2002-06-16don't key off of `alpha' to decide to do OSF specific things (-fpe3 flagdmcmahill5-65/+2564
to the fortran compiler). Also mark as not for older netbsd-alpha systems as this is an IEEE-754 infected program (hi ross!).
2002-05-24Reorder PLIST so pkg_delete works cleanlymarkd1-3/+3
2002-05-20Fix up distinfo to reflect last change to patches.cjep1-2/+2
2002-05-20Add NetBSD tag. Fix NetBSD tag in patch-ad.cjep2-1/+2
2002-05-03Add etc/Makeconf to REPLACE_BUILDLINK. Fixes pkg/16620markd1-2/+2
2002-04-23Change MASTER_SITES to use the CRAN list.markd2-14/+52
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.
2002-03-13Give all packages which depend on "png" a version bump, and updatefredb1-1/+2
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".]
2002-03-01Make local copy of R's package list writable before trying to appendmarkd2-1/+14
to it. From PR# pkg/15773 from Ray Brownrigg.
2002-03-01Update to version 1.4.1 from PR pkg/15757 by Ray Brownrigg with minor modsmarkd5-48/+86
by me. Changes and bug fixes from 1.3.1 are numerous. See the NEWS file in the distribution for details.
2001-12-11Include a patch for the generated configure script so that we don't havejlam3-7/+159
to depend on auto* tools at build-time. This fixes pkg/14916 by Brook Milligan <brook@biology.nmsu.edu>.
2001-11-01Move pkg/ files into package's toplevel directoryzuntum3-3/+3
2001-10-24I am a triple idiot. The only relevant variable that x11.buildlink.mkjlam1-1/+2
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.
2001-08-27Use wildcard dependence on "autoconf" package.tron1-2/+2
2001-08-13Add back COMMENT definition which got lost.agc1-1/+2
2001-07-23Update R to 1.3.0. This is a two-generation upgrade from the previous 1.1.1jlam4-52/+67
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.
2001-06-12LIBS is automatically added to CONFIGURE_ENV by bsd.pkg.mk ifjlam1-2/+1
GNU_CONFIGURE is defined, so simply set LIBS to the appropriate value.