R 1.9.0 の新機能・変更点

R の新バージョンが公開されました。結構大がかりな変更があったようですので、r-help に投稿された変更サマリーを和訳したいと思います。例により、勝手にボランティアお願いします。結構訳しにくいので、誤訳気味でも英語よりはましという人向きです。(2004.4.12)
MS Windows 版 R 固有の変更点も r-help 記事より付け加えました。(2004.4.13)


ユーザーの目に見える変更

↑

新しい機能

	--- Renamed push/pop.viewport() to push/popViewport().
	--- Added upViewport(), downViewport(), and seekViewport() to
	  allow creation and navigation of viewport tree
	  (rather than just viewport stack).
	--- Added id and id.lengths arguments to grid.polygon() to allow
	  multiple polygons within single grid.polygon() call.
	--- Added vpList(), vpStack(), vpTree(), and current.vpTree()
	  to allow creation of viewport "bundles" that may be pushed
	  at once (lists are pushed in parallel, stacks in series).
	  current.vpTree() returns the current viewport tree.
	--- Added vpPath() to allow specification of viewport path
	  in downViewport() and seekViewport().
	  See ?viewports for an example of its use.
	  NOTE: it is also possible to specify a path directly,
	  e.g., something like "vp1::vp2", but this is only
	  advised for interactive use (in case I decide to change the
	  separator :: in later versions).
	--- Added "just" argument to grid.layout() to allow justification
	  of layout relative to parent viewport *IF* the layout is not
	  the same size as the viewport.  There's an example in
	  help(grid.layout).
	--- Allowed the "vp" slot in a grob to be a viewport name or a
	  vpPath.  The interpretation of these new alternatives is to
	  call downViewport() with the name or vpPath before drawing the
	  grob and upViewport() the appropriate amount after drawing the
	  grob.	 Here's an example of the possible usage:
	      pushViewport(viewport(w=.5, h=.5, name="A"))
	      grid.rect()
	      pushViewport(viewport(w=.5, h=.5, name="B"))
	      grid.rect(gp=gpar(col="grey"))
	      upViewport(2)
	      grid.rect(vp="A", gp=gpar(fill="red"))
	      grid.rect(vp=vpPath("A", "B"), gp=gpar(fill="blue"))
	--- Added engine.display.list() function.
         This allows the user to
	  tell grid NOT to use the graphics engine display list and to handle
	  ALL redraws using its own display list (including redraws after
	  device resizes and copies).
	  This provides a way to avoid some of the problems with resizing
	  a device when you have used grid.convert(), or the gridBase package,
	  or even base functions such as legend().
	  There is a document discussing the use of display lists in grid
	  on the grid web site
	  (http://www.stat.auckland.ac.nz/~paul/grid/grid.html)
	--- Changed the implementation of grob objects.  They are no longer
	  implemented as external references.  They are now regular R objects
	  which copy-by-value.	This means that they can be saved/loaded
	  like normal R objects.  In order to retain some existing grob
	  behaviour, the following changes were necessary:
	  + grobs all now have a "name" slot.  The grob name is used to
	    uniquely identify a "drawn" grob (i.e., a grob on the display
	    list).
	  + grid.edit() and grid.pack() now take a grob name as the first
	    argument instead of a grob.	 (Actually, they take a gPath -
	    see below)
	  + the "grobwidth" and "grobheight" units take either a grob
	    OR a grob name (actually a gPath - see below).  Only in the
	    latter case will the unit be updated if the grob "pointed to"
	    is modified.
	  In addition, the following features are now possible with grobs:
	  + grobs now save()/load() like any normal R object.
	  + many grid.*() functions now have a *Grob() counterpart.  The
	    grid.*() version is used for its side-effect of drawing
	    something or modifying something which has been drawn;  the
	    *Grob() version is used for its return value, which is a grob.
	    This makes it more convenient to just work with grob
	    objects without producing any graphical output
	    (by using the *Grob() functions).
	  + there is a gTree object (derived from grob), which is a grob
	    that can have children.  A gTree also has a "childrenvp" slot
	    which is a viewport which is pushed and then "up"ed before the
	    children are drawn;	 this allows the children of a gTree to
	    place themselves somewhere in the viewports specified in the
	    childrenvp by having a vpPath in their vp slot.
	  + there is a gPath object, which is essentially a concatenation
	    of grob names.  This is used to specify the child of
	    (a child of ...) a gTree.
	  + there is a new API for creating/accessing/modifying grob objects:
	    grid.add(), grid.remove(), grid.edit(), grid.get() (and their
	    *Grob() counterparts can be used to add, remove, edit, or extract
	    a grob or the child of a gTree.  NOTE: the new grid.edit() API
	    is incompatible with the previous version.
	--- Added stringWidth(), stringHeight(), grobWidth(), and grobHeight()
	  convenience functions (they produce "strwidth", "strheight",
	  "grobwidth", and "grobheight" unit objects, respectively).
	--- Allowed viewports to turn off clipping altogether.
	  Possible settings for viewport clip arg are now:
	    "on"      = clip to the viewport (was TRUE)
	    "inherit" = clip to whatever parent says (was FALSE)
	    "off"     = turn off clipping
	  Still accept logical values (and NA maps to "off")
↑

ユーティリティー

↑

C-レベルの機能

↑

削除された機能

↑

インストール法の変更

	The included zlib sources have been updated to 1.2.1, and this
	is now required if --with-zlib is used.
↑

バグフィックス

   o	When lm.{w}fit() disregarded arguments in ... they reported
	the values and not the names.
   o	lm(singular.ok = FALSE) was looking for 0 rank, not rank < p.
   o	The substitution code for strptime in the sources no longer
	follows glibc in silently `correcting' invalid inputs.
   o	find(simple.words=TRUE) (the default) was still using regular
	expressions for e.g. "+" and "*".  Also, it checked the mode
	only of the first object matching a regular expression found
	in a package.
   o	Memory leaks in [dpq]wilcox and [dqr]signrank have been plugged.
	These only occurred when multiple values of m or n > 50 were
	used in a single call. (PR#5314, plus another potential leak.)
   o	Non-finite input values to eigen(), La.eigen(), svd() and
	La.svd() are now errors: they often caused infinite
	looping.  (PR#5406, PR#4366, PR#3723: the fix for 3723/4366
	returned a vector of NAs, not a matrix, for the eigenvectors.)
   o	stepfun(x,y) now gives an error when `x' has length 0 instead
	of an invalid result (that could lead to a segmentation
	fault).
   o	buildVignettes() uses file.remove() instead of unlink() to
	remove temporary files.
   o	methods(class = "lqs") does not produce extraneous entries anymore.
   o	Directly calling a method that uses NextMethod() no longer
	produces the erroneous error message 'function is not a
	closure'.
   o	cutree(a, h=h) silently gave wrong results when 'a' was an
	agnes object; now gives an error and reminds of as.hclust().
   o	postscript() could crash if given a font value outside the
	valid range 1...5.
   o	qchisq(1-e, .., ncp=.) did not terminate for small e.
	(PR#6421 (PR#875))
   o	contrasts() turns a logical variable into a factor.  This now
	always has levels c("FALSE", "TRUE") even if only one (or
	none) of these occur in the variable.
   o	model.frame()'s lm and glm methods had 'data' and 'na.action'
	arguments which they ignored and have been removed.
   o	The defaults data=list() in lm() and glm() could never be
	used and have been removed.  glm had na.action=na.fail, again
	never used.
   o	tools:::.getInternalS3generics() was omitting all the members
	of the S3 group generics, which also accept methods for members.
   o	Some BLASes were returning NA %*% 0 as 0 and some as NA.  Now
	slower but more careful code is used if NAs are present. (PR#4582)
   o	package.skeleton() no longer generates invalid filenames for
	code and help files.  Also, care is taken not to generate
	filenames that differ only by case.
   o	pairs() now respects axis graphical parameters such as
	cex.main, font.main and las.
   o	Saving images of packages with namespaces (such as mle) was
	not compressing the image.
   o	When formula.default() returned a terms object, it returned a
	result of class c("terms", "formula") with different
	subsetting rules from an object of class "formula".
   o	The standalone Rmath library did not build correctly on systems
	with inaccurate log1p.
   o	Specifying asp is now respected in calls like plot(1, 10, asp=1)
	with zero range on both axes.
   o	outer() called rep() with an argument the generic does not
	have, and discarded the class of the answer.
   o	object.size() now returns a real (not integer) answer and so
	can cope with objects occupying more than 2Gb.
   o	Lookups base:: and ::: were not confining their search to the
	named package/namespace.
   o	qbinom() was returning NaN for prob = 0 or 1 or size = 0 even
	though the result is well-defined.  (In part, PR#5900.)
   o	par(mgp)[2] was being interpreted as relative to par(mgp)[3].
	(PR#6045)
   o	Versioned install was broken both with and without namespaces:
	no R code was loaded.
   o	methods(), getS3method() and the registration of S3 methods in
	namespaces were broken if the S3 generic was converted into an
	S4 generic by setting an S4 method.
   o	Title and copyright holder of the reference manual are now in
	sync with the citation() command.
   o	The validation code for POSIXlt dates and hence
	seq(, by="DSTdays") now works for large mday values (not
	just those in -1000...1000).  (PR#6212)
   o	The print() method for data frames now copes with data frames
	containing arrays (other than matrices).
   o	texi2dvi() and buildVignettes() use clean=FALSE as default
	because the option is not supported on some Solaris
	machines. For buildVignettes() this makes no difference as it
	uses an internal cleanup mechanism.
   o	The biplot() method for "prcomp" was not registered nor exported.
	(PR#6425)
   o	Latex conversion of .Rd files was missing newline before
	\end{Section} etc which occasionally gave problems, as fixed for
	some other \end{Foo} in 1.8.1.	(PR#5645)
   o	Work around a glibc bug to make the %Z format usable in strftime().
   o	The glm method for rstandard() was wrongly scaled for cases where
	summary(model)$dispersion != 1.
   o	Calling princomp() with a covariance matrix (rather than a
	list) failed to predict scores rather than predict NA as
	intended.  (PR#6452)
   o	termplot() is more tolerant of variables not in the data= argument.
	(PR#6327)
   o	isoreg() could segfault on monotone input sequences.  (PR#6494)
   o	Rdconv detected \link{\url{}} only very slowly.	 (PR#6496)
   o	aov() with Error() term and no intercept incorrectly assigned
	terms to strata. (PR#6510)
   o	ftable() incorrectly handled arguments named "x".  (PR#6541)
   o	vector(), matrix(), array() and their internal equivalents
	report correctly that the number of elements specified was too
	large (rather than reporting it as negative).
   o	Minor copy-paste error in example(names).  (PR#6594)
   o	length<-() now works correctly on factors (and is now generic
	with a method for factors).
   o	x <- 232; x:(x+3) no longer generates an error (but gives a
	result of type "double").
   o	pgamma(30, 100, lower=FALSE, log=TRUE) is not quite 0, now.
	pgamma(x, alph) now only uses a normal approximation for
	alph > 1e5 instead of alph > 1000.  This also improves the accuracy
	of ppois().
   o	qgamma() now does one or more final Newton steps, increasing
	accuracy from around 2e-8 to 3e-16 in some cases.  (PR#2214).
	It allows values p close to 1 not returning Inf, with accuracy for
	'lower=FALSE', and values close to 0 not returning 0 for
	'log=TRUE'.  These also apply to qchisq(), e.g.,
	qchisq(1e-13, 4, lower=FALSE) is now finite and
	qchisq(1e-101, 1) is positive.
   o	gamma(-n) now gives NaN for all negative integers -n.
   o	The Unix version of browseURL() now protects the URL from the
	shell, for example allowing & and $ to occur in the URL.
	It was incorrectly attempting to use -remote "openURL()" for
	unknown browsers.
   o	extractAIC.coxph() works around an inconsistency in the
	$loglik output from coxph.  (PR#6646)
   o	stem() was running into integer overflows with nearly-constant
	inputs, and scaling badly for constant ones.  (Partly PR#6645)
   o	system() under Unix was losing the 8095th char if the output
	was split.  (PR#6624)
   o	plot.lm() gave incorrect results if there were zero weights.
	(PR#6640)
   o	Binary operators warned for inconsistent lengths on vector op
	vector operations, but not on vector op matrix ones.  (PR#6633
	and more.)
	Comparison operators did not warn about inconsistent lengths
	for real vectors, but did for integer, logical and character
	vectors.
   o	spec.pgram(x, ..., pad, fast, ...) computed the periodogram with
	a bias (downward) whenever 'pad > 0' (non-default) or 'fast = TRUE'
	(default) and nextn(n) > n where n = length(x); similarly for
	'df' (approximate degrees of freedom for chisq).
   o	dgamma(0, a) now gives Inf for a < 1 (instead of NaN), and
	so does dchisq(0, 2*a, ncp).
   o	pcauchy() is now correct in the extreme tails.
   o	file.copy() did not check that any existing `from' file had
	been truncated before appending the new contents.
   o	The QC files now check that their file operations succeeded.
   o	replicate() worked by making the supplied expression the
	body of an anonymous function(x), leading to a variable
	capture issue. Now, function(...) is used instead.
   o	chisq.test(simulate.p.value = TRUE) was returning slightly
	incorrect p values, notably p = 0 when the data gave the most
	extreme value.
   o	terms.formula(simplify = TRUE) was losing offset terms.
	Multiple offset terms were not being removed correctly if two
	of them appeared first or last in the formula.	(PR#6656)
   o	Rd conversion to latex did not add a new line before
	\end{Section} in more cases than were corrected in 1.8.1.
   o	split.default() dropped NA levels in its internal code but
	returned them as NA in all components in the interpreted code
	for factors.  (PR#6672)
   o	points.formula() had problems if there was a subset argument
	and no data argument.  (PR#6652)
   o	as.dist() does a bit more checking of its first argument and now
	warns when applied to non-square matrices.
   o	mle() gives a more understandable error message when its 'start'
	argument is not ok.
   o	All uses of dir.create() check the return value.
	download.packages() checks that destdir exists and is a directory.
   o	Methods dispatch corrects an error that failed to find
	methods for classes that extend sealed classes (class unions
	that contain basic classes, e.g.).
   o	Sweave no longer wraps the output of code chunks with
	echo=false and results=tex in Schunk environments.
   o	termplot() handles models with missing data better, especially
	with na.action=na.exclude.
   o	1:2 * 1e-100  now prints with correct number of spaces.
   o	Negative subscripts that were out of range or NA were not handled
	correctly.  Mixing negative and NA subscripts is now caught as
	an error: it was not caught on some platforms and segfaulted
	on others.
   o	gzfile() connections had trouble at EOF when used on uncompressed
	file.
   o	The Unix version of dataentry segfaulted if the `Copy' button
	was used.  (PR#6605)
   o	unlist on lists containing expressions now works (PR#5628)
   o	D(), deriv() and deriv3() now also can deal with gamma and lgamma.
   o	The X11 module can now be built against XFree86 4.4.0 headers (still
	with some warnings).
   o	seq.POSIXt(from, to, by="DSTdays") was shorter than expected
	for rare times in the UK time zone.  (PR#4558)
   o	c/rbind() did not support vectors/matrices of mode "list".  (PR#6702)
   o	summary() methods for POSIX[cl]t and Date classes coerced the
	number of NAs to a date on printing.
   o	KalmanSmooth would sometimes return NA values with NA inputs.
	(PR#6738)
   o	fligner.test() worked correctly only if data were already sorted
	by group levels. (PR#6739)
↑

MS Windows 固有の変更点

↑

トピックス

↑

rw1090

新規ウィンドウがMDIクライアント領域に収まるように windows() が修正された。

ユーザメニューを調べるための関数 winMenuNames() と winMenuItems() が追加された。

ヘルプメニューに www.r-project.org と CRAN の項目が追加された。 (Wishlist PR#6492)

Added "R" command to be similar to Unix invocation of scripts, e.g. "R CMD INSTALL" is the same as "Rcmd INSTALL". Rcmd still exists for backwards compatibility (and to avoid conflicts over the name `R'). All of R, R CMD and Rcmd now accept --help.

Rcmd Rd2dvi.sh でなく Rcmd Rd2dvi と指定できるようになった。

Rguiコンソールの編集メニュー、ポップアップメニューに "Paste commands only" を追加。 出力のブロックをコピーする際、 再実行のためコンソールにはコマンドのみを張り付ける。 (Code contributed by Tony Plate.)

↑

インストール

並列 make (make -j2など) が使えるようになったが、最低384MBのメモリを持つ デュアルプロセッサ（もしかしたらhyperthreading対応）マシンでのみ便利と言えるだろう。

Installing now sorts in the C locale to ensure that a consistent sort order is used. (Some aspects of sorting used to be done in the locale of the host machine, but Perl and the cygwin-based tools used the ASCII collation order.)

長らくテストされていなかった、Windowsの .hlp ファイル作成への対応が放棄された。

K. Gotoによる高速BLASへの対応が行われた。 2.6GHz Pentium 4、1GB RAMという環境で1000 x 1000行列Aに対し以下の結果を得た。

	R BLAS	ATLAS	Goto

A %*% A 3.7 0.65 0.56 svd(A) 16.2 7.77 6.83

高速BLASは統計処理で多く出てくる小さな行列に対してはずっと非効率的であることに注意。

指数関数に速いアセンブラコードが使われるようになった。

R自身のクロスコンパイルが再び機能するようになった。 （1.8.0 以降で壊れていた）

↑

パッケージの構築とインストール法

R CMD INSTALL/build/check が空白を含むパス名をMS-DOSの8.3形式に変換するようになった。

R CMD INSTALL が --with-package-versions によってヴァージョンを意識したインストールに対応するようになった。

（バイナリ）パッケージバンドルのインストールにおいて、パッケージと同様にMD5をチェックして報告するようになった。

INSTALL ログの末尾に "* DONE" を追加したので、 CHECK へのオプション --install が機能するようになった。 (This is a repository maintainer option; see src/scripts/check.in for docs).

↑

内部機能の変更

R 1.8.0 で導入された高速 bmp/png/jpeg 処理コードが256色表示にも使われるようになった (as we have now been able to test it on such).

R内部の malloc 等の関数が Rm_malloc 等に変更され、 Rのオブジェクト、Wilcoxon検定他いくつかのメモリに敏感な処理のためのメモリ割り当てのみに使われるようになった。

Doug Lea の手になる改良型 malloc ルーチン（David Tellerの示唆による）のおかげで、 大きなメモリ領域（特に、OSがサポートすれば、2GB超えのメモリ）を効率的に扱えるようになった。 最初に要求されたメモリは保たれなくなったが、 この malloc ルーチンは非連続なメモリ領域も扱えるので、問題ない。

インストーラがLZMA圧縮を使うようになり、Inno Setupのヴァージョンが 4.1.5 以降である必要がある。

バイナリビルドではlibpngのヴァージョン 1.2.5 を使うようになった。

↑

バグフィックス

list.files() が "C:" 等のパスを正しく扱うよう修正。

Unixでの一貫性のため unlink() がファイルの空リストを受け付けるよう修正。

Rd2dvi.sh で DESCRIPTION ファイルの処理における空白文字の扱いの修正。

コマンドライン引数 "--max-mem-size" の処理の文法エラーを修正

RGui で、 ctrl-T が行の第1、2番目の文字を入れ換えることができなかった。 (PR#5593)

pipe() の先頭にあったゴミ文字を修正。 (PR#5053)

R CMD SHLIB がコマンドラインで指定されたものに限らず全てのCファイルに対する依存性を求めており、 またDLLをディレクトリ内の全ての *.o ファイルから作っていた。

メタファイルのピクセル単位のサイズがしばしば要求より1大きくなっていて、背景が塗りつくされないことがあった。 よって多めに塗るようにした。

Rproxy.dll が大きいデータを扱うときにクラッシュすることがあった。

「1970-01-01 00:00:00 (UTC) 以前の日付データは無効」とするMicrosoft社の奇妙な方針に対する応急処置 （時計がUTCより早い地域で as.POSIXct("1970-01-01 00:00:00") がエラーになっていた）

browseURL() に264文字以上のURLを渡すと起きるかも知れないセグメンテーションフォルトの回避 (確実に直ったとはまだ言えないが)。

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