CVS commit: pkgsrc/math/R

["Wen Heping" <wen%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   wen
Date:           Mon Dec 17 09:08:47 UTC 2012

Modified Files:
        pkgsrc/math/R: Makefile PLIST distinfo
        pkgsrc/math/R/patches: patch-ac patch-ad patch-src_main_format.c

Log Message:
Update to 2.15.1
Approved by wiz@

Upstream changes:
CHANGES IN R VERSION 2.15.1:

  NEW FEATURES:

    o source() now uses withVisible() rather than
      .Internal(eval.with.vis).  This sometimes alters tracebacks
      slightly.

    o install.packages("pkg_version.tgz") on Mac OS X now has sanity
      checks that this is actually a binary package (as people have
      tried it with incorrectly named source packages).

    o splineDesign() and spline.des() in package splines have a new
      option sparse which can be used for efficient construction of a
      sparse B-spline design matrix (_via_ Matrix).

    o norm() now allows type = "2" (the 'spectral' or 2-norm) as well,
      mainly for didactical completeness.

    o pmin() and pmax()) now also work when one of the inputs is of
      length zero and others are not, returning a zero-length vector,
      analogously to, say, +.

    o colorRamp() (and hence colorRampPalette()) now also works for the
      boundary case of just one color when the ramp is flat.

    o qqline() has new optional arguments distribution, probs and
      qtype, following the example of lattice's panel.qqmathline().

    o .C() gains some protection against the misuse of character vector
      arguments.  (An all too common error is to pass character(N),
      which initializes the elements to "", and then attempt to edit
      the strings in-place, sometimes forgetting to terminate them.)

    o Calls to the new function globalVariables() in package utils
      declare that functions and other objects in a package should be
      treated as globally defined, so that CMD check will not note
      them.

    o print(packageDescription(*)) trims the Collate field by default.

    o The included copy of zlib has been updated to version 1.2.7.

    o A new option "show.error.locations" has been added.  When set to
      TRUE, error messages will contain the location of the most recent
      call containing source reference information. (Other values are
      supported as well; see ?options.)
   o The NA warning messages from e.g. pchisq() now report the call to
      the closure and not that of the .Internal.

    o Added Polish translations by <c5><81>ukasz Daniel.

  PERFORMANCE IMPROVEMENTS:

    o In package parallel, makeForkCluster() and the multicore-based
      functions use native byte-order for serialization (deferred from
      2.15.0).

    o lm.fit(), lm.wfit(), glm.fit() and lsfit() do less copying of
      objects, mainly by using .Call() rather than .Fortran().

    o .C() and .Fortran() do less copying: arguments which are raw,
      logical, integer, real or complex vectors and are unnamed are not
      copied before the call, and (named or not) are not copied after
      the call.  Lists are no longer copied (they are supposed to be
      used read-only in the C code).

    o tabulate() makes use of .C(DUP = FALSE) and hence does not copy
      bin.  (Suggested by Tim Hesterberg.)  It also avoids making a
      copy of a factor argument bin.

    o Other functions (often or always) doing less copying include
      cut(), dist(), the complex case of eigen(), hclust(), image(),
      kmeans(), loess(), stl() and svd(LINPACK = TRUE).

    o There is less copying when using primitive replacement functions
      such as names(), attr() and attributes().

  DEPRECATED AND DEFUNCT:

    o The converters for use with .C() (see ?getCConverterDescriptions)
      are deprecated: use the .Call() interface instead.  There are no
      known examples (they were never fully documented).

  UTILITIES:

    o For R CMD check, a few people have reported problems with
      junctions on Windows (although they were tested on Windows 7, XP
      and Server 2008 machines and it is unknown under what
      circumstances the problems occur).  Setting the environment
      variable R_WIN_NO_JUNCTIONS to a non-empty value (e.g. in
      ~/.R/check.Renviron) will force copies to be used instead.

  INSTALLATION:
    o R CMD INSTALL with _R_CHECK_INSTALL_DEPENDS_ set to a true value
      (as done by R CMD check --as-cran) now restricts the packages
      available when lazy-loading as well as when test-loading (since
      packages such as ETLUtils and agsemisc had top-level calls to
      library() for undeclared packages).

      This check is now also available on Windows.

  C-LEVEL FACILITIES:

    o C entry points mkChar and mkCharCE now check that the length of
      the string they are passed does not exceed 2^31-1 bytes: they
      used to overflow with unpredictable consequences.

    o C entry points R_GetCurrentSrcref and R_GetSrcFilename have been
      added to the API to allow debuggers access to the source
      references on the stack.

  WINDOWS-SPECIFIC CHANGES:

    o Windows-specific changes will now be announced in this file
      (NEWS).  Changes up and including R 2.15.0 remain in the CHANGES
      file.

    o There are two new environment variables which control the
      defaults for command-line options.

      If R_WIN_INTERNET2 is set to a non-empty value, it is as if
      --internet2 was used.

      If R_MAX_MEM_SIZE is set, it gives the default memory limit if
      --max-mem-size is not specified: invalid values being ignored.

  BUG FIXES:

    o lsfit() lost the names from the residuals.

    o More cases in which merge() could create a data frame with
      duplicate column names now give warnings.  Cases where names
      specified in by match multiple columns are errors.

    o Nonsense uses such as seq(1:50, by = 5) (from package plotrix)
      and seq.int(1:50, by = 5) are now errors.

    o The residuals in the 5-number summary printed by summary() on an
      "lm" object are now explicitly labelled as weighted residuals
      when non-constant weights are present.  (Wish of PR#14840.)

    o tracemem() reported that all objects were copied by .C() or
      .Fortran() whereas only some object types were ever copied.

      It also reported and marked as copies _some_ transformations such
      as rexp(n, x): it no longer does so.

    o The plot() method for class "stepfun" only used the optional xval
      argument to compute xlim and not the points at which to plot (as
      documented).  (PR#14864)

    o Names containing characters which need to be escaped were not
      deparsed properly.  (PR#14846)

    o Trying to update (recommended) packages in R_HOME/library without
      write access is now dealt with more gracefully.  Further, such
      package updates may be skipped (with a warning), when a newer
      installed version is already going to be used from .libPaths().
      (PR#14866)

    o hclust() is now fast again (as up to end of 2003), with a
      different fix for the "median"/"centroid" problem.  (PR#4195).

    o get_all_vars() failed when the data came entirely from vectors in
      the global environment. (PR#14847)

    o R CMD check with _R_CHECK_NO_RECOMMENDED_ set to a true value (as
      done by the --as-cran option) could issue false errors if there
      was an indirect dependency on a recommended package.

    o formatC() uses the C entry point str_signif which could write
      beyond the length allocated for the output string.

    o Missing default argument added to implicit S4 generic for
      backsolve(). (PR#14883)

    o Some bugs have been fixed in handling load actions that could
      fail to export assigned items or generate spurious warnings in
      CMD check on loading.

    o For tiff(type = "windows"), the numbering of per-page files
      except the last was off by one.

    o On Windows, loading package stats (which is done for a default
      session) would switch line endings on stdout and stderr from CRLF
      to LF.  This affected Rterm and R CMD BATCH.

    o On Windows, the compatibility function x11() had not kept up with
      changes to windows(), and issued warnings about bad parameters.
      (PR#14880)

    o On Windows, the Sys.glob() function did not handle UNC paths as
      it was designed to try to do. (PR#14884)

    o In package parallel, clusterApply() and similar failed to handle
      a (pretty pointless) length-1 argument. (PR#14898)

    o Quartz Cocoa display reacted asynchronously to dev.flush() which
      means that the redraw could be performed after the plot has been
      already modified by subsequent code. The redraw is now done
      synchronously in dev.flush() to allow animations without sleep
      cycles.

    o Source locations reported in traceback() were incorrect when
      byte-compiled code was on the stack.

    o plogis(x, lower = FALSE, log.p = TRUE) no longer underflows early
      for large x (e.g. 800).

    o ?Arithmetic's "1 ^ y and y ^ 0 are 1, _always_" now also applies
      for integer vectors y.

    o X11-based pixmap devices like png(type = "Xlib") were trying to
      set the cursor style, which triggered some warnings and hangs.

    o Code executed by the built-in HTTP server no longer allows other
      HTTP clients to re-enter R until the current worker evaluation
      finishes, to prevent cascades.

    o The plot() and Axis() methods for class "table" now respect
      graphical parameters such as cex.axis.  (Reported by Martin
      Becker.)

    o Under some circumstances package.skeleton() would give out
      progress reports that could not be translated and so were
      displayed by question marks.  Now they are always in English.
      (This was seen for CJK locales on Windows, but may have occurred
      elsewhere.)

    o The evaluator now keeps track of source references outside of
      functions, e.g. when source() executes a script.

    o The replacement method for window() now works correctly for
      multiple time series of class "mts".  (PR#14925)

    o is.unsorted() gave incorrect results on non-atomic objects such
      as data frames.  (Reported by Matthew Dowle.)

    o The value returned by tools::psnice() for invalid pid values was
      not always NA as documented.

    o Closing an X11() window while locator() was active could abort
      the R process.

    o getMethod(f, sig) produced an incorrect error message in some
      cases when f was not a string).

    o Using a string as a "call" in an error condition with
      options(showErrorCalls=TRUE) could cause a segfault.  (PR#14931)

    o The string "infinity" allowed by C99 was not accepted as a
      numerical string value by e.g. scan() and as.character().
      (PR#14933)

    o In legend(), setting some entries of lwd to NA was inconsistent
      (depending on the graphics device) in whether it would suppress
      those lines; now it consistently does so.  (PR#14926)

    o by() failed for a zero-row data frame.  (Reported by Weiqiang
      Qian)

    o Yates correction in chisq.test() could be bigger than the terms
      it corrected, previously leading to an infinite test statistic in
      some corner cases which are now reported as NaN.

    o xgettext() and related functions sometimes returned items that
      were not strings for translation. (PR#14935)

    o plot(<lm>, which=5) now correctly labels the factor level
      combinations for the special case where all h[i,i] are the same.
      (PR#14837)

CHANGES IN R VERSION 2.15.0:

  SIGNIFICANT USER-VISIBLE CHANGES:

    o The behaviour of unlink(recursive = TRUE) for a symbolic link to
      a directory has changed: it now removes the link rather than the
      directory contents (just as rm -r does).

      On Windows it no longer follows reparse points (including
      junctions and symbolic links).

  NEW FEATURES:

    o Environment variable RD2DVI_INPUTENC has been renamed to
      RD2PDF_INPUTENC.

    o .Deprecated() becomes a bit more flexible, getting an old
      argument.

    o Even data-only packages without R code need a namespace and so
      may need to be installed under R 2.14.0 or later.

    o assignInNamespace() has further restrictions on use apart from at
      top-level, as its help page has warned.  Expect it to be disabled
      from programmatic use in the future.

    o system() and system2() when capturing output report a non-zero
      status in the new "status" attribute.

    o kronecker() now has an S4 generic in package methods on which
      packages can set methods.  It will be invoked by X %x% Y if
      either X or Y is an S4 object.

    o pdf() accepts forms like file = "|lpr" in the same way as
      postscript().

    o pdf() accepts file = NULL.  This means that the device does NOT
      create a PDF file (but it can still be queried, e.g., for font
      metric info).

    o format() (and hence print()) on "bibentry" objects now uses
      options("width") to set the output width.

    o legend() gains a text.font argument. (Suggested by Tim Paine,
      PR#14719.)

    o nchar() and nzchar() no longer accept factors (as integer
      vectors).  (Wish of PR#6899.)

    o summary() behaves slightly differently (or more precisely, its
      print() method does).  For numeric inputs, the number of NAs is
      printed as an integer and not a real.  For dates and datetimes,
      the number of NAs is included in the printed output (the latter
      being the wish of PR#14720).

      The "data.frame" method is more consistent with the default
      method: in particular it now applies zapsmall() to
      numeric/complex summaries.

    o The number of items retained with options(warn = 0) can be set by
      options(nwarnings=).

    o There is a new function assignInMyNamespace() which uses the
      namespace of the function it is called from.

    o attach() allows the default name for an attached file to be
      overridden.

    o bxp(), the work horse of boxplot(), now uses a more sensible
      default xlim in the case where at is specified differently from
      1:n, see the discussion on R-devel, <URL:
      https://stat.ethz.ch/pipermail/r-devel/2011-November/062586.html>.

    o New function paste0(), an efficient version of paste(*, sep=""),
      to be used in many places for more concise (and slightly more
      efficient) code.

    o Function setClass() in package methods now returns, invisibly, a
      generator function for the new class, slightly preferred to
      calling new(), as explained on the setClass help page.

    o The "dendrogram" method of str() now takes its default for
      last.str from option str.dendrogram.last.

    o New simple fitted() method for "kmeans" objects.

    o The traceback() function can now be called with an integer
      argument, to display a current stack trace. (Wish of PR#14770.)

    o setGeneric() calls can be simplified when creating a new generic
      function by supplying the default method as the def argument.
      See ?setGeneric.

    o serialize() has a new option xdr = FALSE which will use the
      native byte-order for binary serializations.  In scenarios where
      only little-endian machines are involved (these days, close to
      universal) and (un)serialization takes an appreciable amount of
      time this may speed up noticeably transferring data between
      systems.

    o The internal (un)serialization code is faster for long vectors,
      particularly with XDR on some platforms.  (Based on a suggested
      patch by Michael Spiegel.)

    o For consistency, circles with zero radius are omitted by points()
      and grid.circle().  Previously this was device-dependent, but
      they were usually invisible.

    o NROW(x) and NCOL(x) now work whenever dim(x) looks appropriate,
      e.g., also for more generalized matrices.

    o PCRE has been updated to version 8.30.

    o The internal R_Srcref variable is now updated before the browser
      stops on entering a function.  (Suggestion of PR#14818.)

    o There are 'bare-bones' functions .colSums(), .rowSums(),
      .colMeans() and .rowMeans() for use in programming where ultimate
      speed is required.

    o The formerly internal function .package_dependencies() from
      package tools for calculating (recursive) (reverse) dependencies
      on package databases has been renamed to package_dependencies()
      and is now exported.

    o There is a new function optimHess() to compute the (approximate)
      Hessian for an optim() solution if hessian = TRUE was forgotten.

    o .filled.contour() is a 'bare-bones' function to add a
      filled-contour rectangular plot to an already prepared plot
      region.

    o The stepping in debugging and single-step browsing modes has
      changed slightly: now left braces at the start of the body are
      stepped over for if statements as well as for for and while
      statements.  (Wish of PR#14814.)

    o library() no longer warns about a conflict with a function from
      package:base if the function has the same code as the base one
      but with a different environment.  (An example is Matrix::det().)

    o When deparsing very large language objects, as.character() now
      inserts newlines after each line of approximately 500 bytes,
      rather than truncating to the first line.

    o New function rWishart() generates Wishart-distributed random
      matrices.

    o Packages may now specify actions to be taken when the package is
      loaded (setLoadActions()).

    o options(max.print = Inf) and similar now give an error (instead
      of warnings later).

    o The "difftime" replacement method of units tries harder to
      preserve other attributes of the argument.  (Wish of PR#14839.)

    o poly(raw = TRUE) no longer requires more unique points than the
      degree.  (Requested by John Fox.)

  PACKAGE parallel:

    o There is a new function mcmapply(), a parallel version of
      mapply(), and a wrapper mcMap(), a parallel version of Map().

    o A default cluster can be registered by the new function
      setDefaultCluster(): this will be used by default in functions
      such as parLapply().

    o clusterMap() has a new argument .scheduling to allow the use of
      load-balancing.

    o There are new load-balancing functions parLapplyLB() and
      parSapplyLB().

    o makePSOCKCluster() has a new option useXDR = FALSE which can be
      used to avoid byte-shuffling for serialization when all the nodes
      are known to be little-endian (or all big-endian).

  PACKAGE INSTALLATION:

    o Non-ASCII vignettes without a declared encoding are no longer
      accepted.

    o C/C++ code in packages is now compiled with -NDEBUG to mitigate
      against the C/C++ function assert being called in production use.
      Developers can turn this off during package development with
      PKG_CPPFLAGS = -UNDEBUG.

    o R CMD INSTALL has a new option --dsym which on Mac OS X (Darwin)
      dumps the symbols alongside the .so file: this is helpful when
      debugging with valgrind (and especially when installing packages
      into R.framework).  [This can also be enabled by setting the
      undocumented environment variable PKG_MAKE_DSYM, since R 2.12.0.]

    o R CMD INSTALL will test loading under all installed
      sub-architectures even for packages without compiled code, unless
      the flag --no-multiarch is used.  (Pure R packages can do things
      which are architecture-dependent: in the case which prompted
      this, looking for an icon in a Windows R executable.)

    o There is a new option install.packages(type = "both") which tries
      source packages if binary packages are not available, on those
      platforms where the latter is the default.

    o The meaning of install.packages(dependencies = TRUE) has changed:
      it now means to install the essential dependencies of the named
      packages plus the Suggests, but only the essential dependencies
      of dependencies.  To get the previous behaviour, specify
      dependencies as a character vector.

    o R CMD INSTALL --merge-multiarch is now supported on OS X and
      other Unix-alikes using multiple sub-architectures.

    o R CMD INSTALL --libs-only now by default does a test load on
      Unix-alikes as well as on Windows: suppress with --no-test-load.

  UTILITIES:

    o R CMD check now gives a warning rather than a note if it finds
      inefficiently compressed datasets.  With bzip2 and xz compression
      having been available since R 2.10.0, it only exceptionally makes
      sense to not use them.

      The environment variable _R_CHECK_COMPACT_DATA2_ is no longer
      consulted: the check is always done if _R_CHECK_COMPACT_DATA_ has
      a true value (its default).

    o Where multiple sub-architectures are to be tested, R CMD check
      now runs the examples and tests for all the sub-architectures
      even if one fails.

    o R CMD check can optionally report timings on various parts of the
      check: this is controlled by environment variable
      _R_CHECK_TIMINGS_ documented in 'Writing R Extensions'.  Timings
      (in the style of R CMD BATCH) are given at the foot of the output
      files from running each test and the R code in each vignette.

    o There are new options for more rigorous testing by R CMD check
      selected by environment variables - see the 'Writing R
      Extensions' manual.

    o R CMD check now warns (rather than notes) on undeclared use of
      other packages in examples and tests: increasingly people are
      using the metadata in the DESCRIPTION file to compute information
      about packages, for example reverse dependencies.

    o The defaults for some of the options in R CMD check (described in
      the 'R Internals' manual) have changed: checks for unsafe and
      .Internal() calls and for partial matching of arguments in R
      function calls are now done by default.

    o R CMD check has more comprehensive facilities for checking
      compiled code and so gives fewer reports on entry points linked
      into .so/.dll files from libraries (including C++ and Fortran
      runtimes).

      Checking compiled code is now done on FreeBSD (as well as the
      existing supported platforms of Linux, Mac OS X, Solaris and
      Windows).

    o R CMD build has more options for --compact-vignettes: see R CMD
      build --help.

    o R CMD build has a new option --md5 to add an MD5 file (as done by
      CRAN): this is used by R CMD INSTALL to check the integrity of
      the distribution.

      If this option is not specified, any existing (and probably
      stale) MD5 file is removed.

  DEPRECATED AND DEFUNCT:

    o R CMD Rd2dvi is now defunct: use R CMD Rd2pdf.

    o Options such --max-nsize, --max-vsize and the function
      mem.limits() are now defunct.  (Options --min-nsize and
      --min-vsize remain available.)

    o Use of library.dynam() without specifying all the first three
      arguments is now disallowed.

      Use of an argument chname in library.dynam() including the
      extension .so or .dll (which was never allowed according to the
      help page) is defunct.  This also applies to
      library.dynam.unload() and to useDynLib directives in NAMESPACE
      files.

    o The internal functions .readRDS() and .saveRDS() are now defunct.

    o The off-line help() types "postscript" and "ps" are defunct.

    o Sys.putenv(), replaced and deprecated in R 2.5.0, is finally
      removed.

    o Some functions/objects which have been defunct for five or more
      years have been removed completely.  These include .Alias(),
      La.chol(), La.chol2inv(), La.eigen(), Machine(), Platform(),
      Version, codes(), delay(), format.char(), getenv(), httpclient(),
      loadURL(), machine(), parse.dcf(), printNoClass(), provide(),
      read.table.url(), restart(), scan.url(), symbol.C(), symbol.For()
      and unix().

    o The ENCODING argument to .C() is deprecated.  It was intended to
      smooth the transition to multi-byte character strings, but can be
      replaced by the use of iconv() in the rare cases where it is
      still needed.

  INSTALLATION:

    o Building with a positive value of --with-valgrind-instrumentation
      now also instruments logical, complex and raw vectors.

  C-LEVEL FACILITIES:

    o Passing R objects other than atomic vectors, functions, lists and
      environments to .C() is now deprecated and will give a warning.
      Most cases (especially NULL) are actually coding errors.  NULL
      will be disallowed in future.

      .C() now passes a pairlist as a SEXP to the compiled code.  This
      is as was documented, but pairlists were in reality handled
      differently as a legacy from the early days of R.

    o call_R and call_S are deprecated.  They still exist in the
      headers and as entry points, but are no longer documented and
      should not be used for new code.

  BUG FIXES:

    o str(x, width) now obeys its width argument also for function
      headers and other objects x where deparse() is applied.

    o The convention for x %/% 0L for integer-mode x has been changed
      from 0L to NA_integer_.  (PR#14754)

    o The exportMethods directive in a NAMESPACE file now exports S4
      generics as necessary, as the extensions manual said it does.
      The manual has also been updated to be a little more informative
      on this point.

      It is now required that there is an S4 generic (imported or
      created in the package) when methods are to be exported.

    o Reference methods cannot safely use non-exported entries in the
      namespace.  We now do not do so, and warn in the documentation.

    o The namespace import code was warning when identical S4 generic
      functions were imported more than once, but should not (reported
      by Brian Ripley, then Martin Morgan).

    o merge() is no longer allowed (in some ways) to create a data
      frame with duplicate column names (which confused PR#14786).

    o Fixes for rendering raster images on X11 and Windows devices when
      the x-axis or y-axis scale is reversed.

    o getAnywhere() found S3 methods as seen from the utils namespace
      and not from the environment from which it was called.

    o selectMethod(f, sig) would not return inherited group methods
      when caching was off (as it is by default).

    o dev.copy2pdf(out.type = "cairo") gave an error.  (PR#14827)

    o Virtual classes (e.g., class unions) had a NULL prototype even if
      that was not a legal subclass.  See ?setClassUnion.

    o The C prototypes for zdotc and zdotu in R_ext/BLAS.h have been
      changed to the more modern style rather than that used by f2c.
      (Patch by Berwin Turlach.)

    o isGeneric() produced an error for primitives that can not have
      methods.

    o .C() or .Fortran() had a lack-of-protection error if the
      registration information resulted in an argument being coerced to
      another type.

    o boxplot(x=x, at=at) with non finite elements in x and non integer
      at could not generate a warning but failed.

    o heatmap(x, symm=TRUE, RowSideColors=*) no longer draws the colors
      in reversed order.

    o predict(<ar>) was incorrect in the multivariate case, for p >= 2.

    o print(x, max=m) is now consistent when x is a "Date"; also the
      "reached ... max.print .." messages are now consistently using
      single brackets.

    o Closed the <li> tag in pages generated by Rd2HTML(). (PR#14841.)

    o Axis tick marks could go out of range when a log scale was used.
      (PR#14833.)

    o Signature objects in methods were not allocated as S4 objects
      (caused a problem with trace() reported by Martin Morgan).


To generate a diff of this commit:
cvs rdiff -u -r1.132 -r1.133 pkgsrc/math/R/Makefile
cvs rdiff -u -r1.14 -r1.15 pkgsrc/math/R/PLIST
cvs rdiff -u -r1.49 -r1.50 pkgsrc/math/R/distinfo
cvs rdiff -u -r1.27 -r1.28 pkgsrc/math/R/patches/patch-ac
cvs rdiff -u -r1.14 -r1.15 pkgsrc/math/R/patches/patch-ad
cvs rdiff -u -r1.2 -r1.3 pkgsrc/math/R/patches/patch-src_main_format.c

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.