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R: Ensure all "-" are converted to "." in PKGVERSION. math/R-robustbase is apparently the first package to use multiple "-" in its R_PKGVER, resulting in 0.99-4-1 being parsed as version "1", and breaking a bunch of DEPENDS matches. Hopefully this fixes bulk builds without causing any regressions.
R: remove superfluous "-Wl," in configure patch Bump PKGREVISION. Fix some pkglint while here.
Conditionally define WRKSRC. Conditionally define WRKSRC so that R packages with an unusual organization can override the default.
math: align variable assignments pkglint -Wall -F --only aligned -r Manual correction in R/Makefile.extension for the MASTER_SITES continuation line.
math/R: add test code for R packages
Add 'R' to the cateogries for R packages. The category 'R' is used to denote R packages, just as 'perl5' and 'python' are used in other cases. To ensure consistency, add that to CATEGORIES in Makefile.extension rather than in each individual R package. This was discussed in http://mail-index.netbsd.org/tech-pkg/2019/08/02/msg021711.html.
Add the CRAN archives to R package MASTER_SITES. Distfiles for older R packges are moved on CRAN from contrib/ to contrib/Archive/${R_PKGNAME}/. As a result, they may be inaccessible to 'make fetch'. Add the additional directory to MASTER_SITES in math/R/Makefile.extension so that older distfiles will be retrieved directly from CRAN. In addition, remove the definition of MASTER_SITES from math/R-prob/Makefile, which is the only package directly referring to the distfile archive. At this point all R packages should rely on math/R/Makefile.extension to define MASTER_SITES; they should not be defining MASTER_SITES directly.
math/R: Derive R_PKGNAME and R_PKGVER from DISTNAME This reduces # of variables to define in an R extension package.
Set default HOMEPAGE for R packages
Apply Darwin install_name fix to R extensions.
Remove pkgviews: don't set PKG_INSTALLATION_TYPES in Makefiles.
Some R libraries may extensively use GNU configure, so pass the obvious CONFIGURE_ARGS through.
"user-destdir" is default these days
The R build/install process should seize all relevant environment variables, and customization should be done via INSTALL_ENV/MAKE_ENV respectively. This also solves the internationalization issue fixed in previous commit properly. Noted by <joerg> on pkgsrc-changes@, many thanks!
On internationalized environment some locales may fail wich equals to error during addons installation phase - force all locales to C.
Fix a number of GENERATE_PLIST entries to always have a terminating ;
Remove @dirrm related logic.
user-destdir support from Masao Uebayashi with minor changes from me. also update R_HOMEPAGE_BASE
Update R to version 2.4.1. pkgsrc changes: no longer automatically generate the PLIST. use (de)install templates for handling updating the index files when adding/removing R packages. Changes 2.4.1 This is a maintenance release and fixes a number of mostly minor bugs. Changes 2.4.0 This release has many new features. One important aspect is that S4 classes now have their own internal type, and S4 method dispatch has been completely revised to using cached generic functions, giving substantial performance improvements. As a consequence, all packages depending on "methods" need to be reinstalled.
Whitespace cleanup, courtesy of pkglint. Patch provided by Sergey Svishchev in private mail.
Replace DEPENDS line with appropriate buildlink3.mk. Also allow passing arguments to the "R CMD INSTALL"
Fixed pkglint warnings.
Added a variable R_HOMEPAGE_BASE that is needed as a replacement for all those packages that currently use ${MASTER_SITE_R_CRAN:=foo} as their HOMEPAGE. As the HOMEPAGE is a single URL, not a list of URLs, the MASTER_SITE variables cannot be used for this.
Move WRKSRC definition away from the first paragraph in a Makefile.
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.
Place WRKSRC where it belongs, to make pkglint happy; ok'ed by wiz.
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.
find ... -or ... -> find ... -o ... for more portability.
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.