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CVS log for pkgsrc/math/R/Makefile.extension

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Default branch: MAIN

Revision 1.26 / (download) - annotate - [select for diffs], Sat Nov 2 16:16:18 2019 UTC (3 months, 2 weeks ago) by rillig
Branch: MAIN
CVS Tags: pkgsrc-2019Q4-base, pkgsrc-2019Q4, HEAD
Changes since 1.25: +8 -8 lines
Diff to previous 1.25 (colored)

math: align variable assignments

pkglint -Wall -F --only aligned -r

Manual correction in R/Makefile.extension for the MASTER_SITES
continuation line.

Revision 1.25 / (download) - annotate - [select for diffs], Sun Oct 13 12:21:23 2019 UTC (4 months, 1 week ago) by rillig
Branch: MAIN
Changes since 1.24: +18 -4 lines
Diff to previous 1.24 (colored)

math/R: add test code for R packages

Revision 1.24 / (download) - annotate - [select for diffs], Wed Aug 7 21:54:34 2019 UTC (6 months, 2 weeks ago) by brook
Branch: MAIN
CVS Tags: pkgsrc-2019Q3-base, pkgsrc-2019Q3
Changes since 1.23: +2 -2 lines
Diff to previous 1.23 (colored)

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

Revision 1.23 / (download) - annotate - [select for diffs], Sat Jul 28 14:53:46 2018 UTC (18 months, 3 weeks ago) by brook
Branch: MAIN
CVS Tags: pkgsrc-2019Q2-base, pkgsrc-2019Q2, pkgsrc-2019Q1-base, pkgsrc-2019Q1, pkgsrc-2018Q4-base, pkgsrc-2018Q4, pkgsrc-2018Q3-base, pkgsrc-2018Q3
Changes since 1.22: +3 -2 lines
Diff to previous 1.22 (colored)

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.

Revision 1.22 / (download) - annotate - [select for diffs], Thu Apr 12 15:40:18 2018 UTC (22 months, 1 week ago) by minskim
Branch: MAIN
CVS Tags: pkgsrc-2018Q2-base, pkgsrc-2018Q2
Changes since 1.21: +6 -1 lines
Diff to previous 1.21 (colored)

math/R: Derive R_PKGNAME and R_PKGVER from DISTNAME

This reduces # of variables to define in an R extension package.

Revision 1.21 / (download) - annotate - [select for diffs], Mon Apr 9 21:57:46 2018 UTC (22 months, 1 week ago) by minskim
Branch: MAIN
Changes since 1.20: +2 -1 lines
Diff to previous 1.20 (colored)

Set default HOMEPAGE for R packages

Revision 1.20 / (download) - annotate - [select for diffs], Mon Feb 29 20:05:00 2016 UTC (3 years, 11 months ago) by jperkin
Branch: MAIN
CVS Tags: pkgsrc-2018Q1-base, pkgsrc-2018Q1, pkgsrc-2017Q4-base, pkgsrc-2017Q4, pkgsrc-2017Q3-base, pkgsrc-2017Q3, pkgsrc-2017Q2-base, pkgsrc-2017Q2, pkgsrc-2017Q1-base, pkgsrc-2017Q1, pkgsrc-2016Q4-base, pkgsrc-2016Q4, pkgsrc-2016Q3-base, pkgsrc-2016Q3, pkgsrc-2016Q2-base, pkgsrc-2016Q2, pkgsrc-2016Q1-base, pkgsrc-2016Q1
Changes since 1.19: +14 -1 lines
Diff to previous 1.19 (colored)

Apply Darwin install_name fix to R extensions.

Revision 1.19 / (download) - annotate - [select for diffs], Thu Oct 9 14:06:41 2014 UTC (5 years, 4 months ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2015Q4-base, pkgsrc-2015Q4, pkgsrc-2015Q3-base, pkgsrc-2015Q3, pkgsrc-2015Q2-base, pkgsrc-2015Q2, pkgsrc-2015Q1-base, pkgsrc-2015Q1, pkgsrc-2014Q4-base, pkgsrc-2014Q4
Changes since 1.18: +1 -3 lines
Diff to previous 1.18 (colored)

Remove pkgviews: don't set PKG_INSTALLATION_TYPES in Makefiles.

Revision 1.18 / (download) - annotate - [select for diffs], Thu Jan 17 11:09:44 2013 UTC (7 years, 1 month ago) by mishka
Branch: MAIN
CVS Tags: pkgsrc-2014Q3-base, pkgsrc-2014Q3, pkgsrc-2014Q2-base, pkgsrc-2014Q2, pkgsrc-2014Q1-base, pkgsrc-2014Q1, pkgsrc-2013Q4-base, pkgsrc-2013Q4, pkgsrc-2013Q3-base, pkgsrc-2013Q3, pkgsrc-2013Q2-base, pkgsrc-2013Q2, pkgsrc-2013Q1-base, pkgsrc-2013Q1
Changes since 1.17: +5 -1 lines
Diff to previous 1.17 (colored)

Some R libraries may extensively use GNU configure, so pass
the obvious CONFIGURE_ARGS through.

Revision 1.17 / (download) - annotate - [select for diffs], Tue Sep 11 23:04:16 2012 UTC (7 years, 5 months ago) by asau
Branch: MAIN
CVS Tags: pkgsrc-2012Q4-base, pkgsrc-2012Q4, pkgsrc-2012Q3-base, pkgsrc-2012Q3
Changes since 1.16: +1 -2 lines
Diff to previous 1.16 (colored)

"user-destdir" is default these days

Revision 1.16 / (download) - annotate - [select for diffs], Thu Aug 2 14:35:01 2012 UTC (7 years, 6 months ago) by mishka
Branch: MAIN
Changes since 1.15: +5 -2 lines
Diff to previous 1.15 (colored)

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!

Revision 1.15 / (download) - annotate - [select for diffs], Tue Jul 24 21:26:27 2012 UTC (7 years, 6 months ago) by mishka
Branch: MAIN
Changes since 1.14: +2 -2 lines
Diff to previous 1.14 (colored)

On internationalized environment some locales may fail wich equals
to error during addons installation phase - force all locales to C.

Revision 1.14 / (download) - annotate - [select for diffs], Tue Jun 16 15:25:31 2009 UTC (10 years, 8 months ago) by joerg
Branch: MAIN
CVS Tags: pkgsrc-2012Q2-base, pkgsrc-2012Q2, pkgsrc-2012Q1-base, pkgsrc-2012Q1, pkgsrc-2011Q4-base, pkgsrc-2011Q4, pkgsrc-2011Q3-base, pkgsrc-2011Q3, pkgsrc-2011Q2-base, pkgsrc-2011Q2, pkgsrc-2011Q1-base, pkgsrc-2011Q1, pkgsrc-2010Q4-base, pkgsrc-2010Q4, pkgsrc-2010Q3-base, pkgsrc-2010Q3, pkgsrc-2010Q2-base, pkgsrc-2010Q2, pkgsrc-2010Q1-base, pkgsrc-2010Q1, pkgsrc-2009Q4-base, pkgsrc-2009Q4, pkgsrc-2009Q3-base, pkgsrc-2009Q3, pkgsrc-2009Q2-base, pkgsrc-2009Q2
Changes since 1.13: +2 -2 lines
Diff to previous 1.13 (colored)

Fix a number of GENERATE_PLIST entries to always have a terminating ;

Revision 1.13 / (download) - annotate - [select for diffs], Sun Jun 14 22:58:04 2009 UTC (10 years, 8 months ago) by joerg
Branch: MAIN
Changes since 1.12: +2 -7 lines
Diff to previous 1.12 (colored)

Remove @dirrm related logic.

Revision 1.12 / (download) - annotate - [select for diffs], Mon Oct 13 11:08:31 2008 UTC (11 years, 4 months ago) by markd
Branch: MAIN
CVS Tags: pkgsrc-2009Q1-base, pkgsrc-2009Q1, pkgsrc-2008Q4-base, pkgsrc-2008Q4
Changes since 1.11: +10 -6 lines
Diff to previous 1.11 (colored)

user-destdir support from Masao Uebayashi with minor changes from me.
also update R_HOMEPAGE_BASE

Revision 1.11 / (download) - annotate - [select for diffs], Wed Mar 14 11:50:33 2007 UTC (12 years, 11 months ago) by markd
Branch: MAIN
CVS Tags: pkgsrc-2008Q3-base, pkgsrc-2008Q3, pkgsrc-2008Q2-base, pkgsrc-2008Q2, pkgsrc-2008Q1-base, pkgsrc-2008Q1, pkgsrc-2007Q4-base, pkgsrc-2007Q4, pkgsrc-2007Q3-base, pkgsrc-2007Q3, pkgsrc-2007Q2-base, pkgsrc-2007Q2, pkgsrc-2007Q1-base, pkgsrc-2007Q1, cwrapper, cube-native-xorg-base, cube-native-xorg
Changes since 1.10: +5 -7 lines
Diff to previous 1.10 (colored)

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.

Revision 1.10 / (download) - annotate - [select for diffs], Thu Feb 22 19:26:45 2007 UTC (13 years ago) by wiz
Branch: MAIN
Changes since 1.9: +2 -2 lines
Diff to previous 1.9 (colored)

Whitespace cleanup, courtesy of pkglint.
Patch provided by Sergey Svishchev in private mail.

Revision 1.9 / (download) - annotate - [select for diffs], Sun Jul 2 12:52:43 2006 UTC (13 years, 7 months ago) by markd
Branch: MAIN
CVS Tags: pkgsrc-2006Q4-base, pkgsrc-2006Q4, pkgsrc-2006Q3-base, pkgsrc-2006Q3
Changes since 1.8: +6 -6 lines
Diff to previous 1.8 (colored)

Replace DEPENDS line with appropriate
Also allow passing arguments to the "R CMD INSTALL"

Revision 1.8 / (download) - annotate - [select for diffs], Fri Jun 9 11:15:32 2006 UTC (13 years, 8 months ago) by rillig
Branch: MAIN
CVS Tags: pkgsrc-2006Q2-base, pkgsrc-2006Q2
Changes since 1.7: +12 -12 lines
Diff to previous 1.7 (colored)

Fixed pkglint warnings.

Revision 1.7 / (download) - annotate - [select for diffs], Thu Nov 3 12:00:32 2005 UTC (14 years, 3 months ago) by rillig
Branch: MAIN
CVS Tags: pkgsrc-2006Q1-base, pkgsrc-2006Q1, pkgsrc-2005Q4-base, pkgsrc-2005Q4
Changes since 1.6: +3 -1 lines
Diff to previous 1.6 (colored)

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.

Revision 1.6 / (download) - annotate - [select for diffs], Tue Jan 20 12:20:04 2004 UTC (16 years, 1 month ago) by agc
Branch: MAIN
CVS Tags: pkgsrc-2005Q3-base, pkgsrc-2005Q3, pkgsrc-2005Q2-base, pkgsrc-2005Q2, pkgsrc-2005Q1-base, pkgsrc-2005Q1, pkgsrc-2004Q4-base, pkgsrc-2004Q4, pkgsrc-2004Q3-base, pkgsrc-2004Q3, pkgsrc-2004Q2-base, pkgsrc-2004Q2, pkgsrc-2004Q1-base, pkgsrc-2004Q1
Changes since 1.5: +2 -2 lines
Diff to previous 1.5 (colored)

Move WRKSRC definition away from the first paragraph in a Makefile.

Revision 1.5 / (download) - annotate - [select for diffs], Wed Dec 3 12:05:18 2003 UTC (16 years, 2 months ago) by markd
Branch: MAIN
Changes since 1.4: +2 -2 lines
Diff to previous 1.4 (colored)

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.

Revision 1.4 / (download) - annotate - [select for diffs], Sat Mar 29 12:41:38 2003 UTC (16 years, 10 months ago) by jmmv
Branch: MAIN
CVS Tags: pkgsrc-2003Q4-base, pkgsrc-2003Q4
Changes since 1.3: +2 -2 lines
Diff to previous 1.3 (colored)

Place WRKSRC where it belongs, to make pkglint happy; ok'ed by wiz.

Revision 1.3 / (download) - annotate - [select for diffs], Tue Dec 10 11:58:10 2002 UTC (17 years, 2 months ago) by markd
Branch: MAIN
CVS Tags: netbsd-1-6-1-base, netbsd-1-6-1
Changes since 1.2: +2 -2 lines
Diff to previous 1.2 (colored)

Update R to version 1.6.1.

Pkgsrc changes:
Now builds the and provides a for packages that want
to use it.  From suggestions from Kent Polk.

Recommended library set is now included in the base package.

               CHANGES IN R VERSION 1.6.1


    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


    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).


    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 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 now coerces logical matrices into logical
        columns (rather than factors).

    o   [[< 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

    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:

    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

    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.

Revision 1.2 / (download) - annotate - [select for diffs], Mon Sep 23 13:41:15 2002 UTC (17 years, 5 months ago) by markd
Branch: MAIN
Changes since 1.1: +2 -2 lines
Diff to previous 1.1 (colored)

find ... -or ... -> find ... -o ... for more portability.

Revision 1.1 / (download) - annotate - [select for diffs], Tue Apr 23 01:14:49 2002 UTC (17 years, 10 months ago) by markd
Branch: MAIN
CVS Tags: pkgviews-base, pkgviews, netbsd-1-6-RELEASE-base, netbsd-1-6, buildlink2-base, buildlink2

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.

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