R 1.9.0 is release

From: Peter Dalgaard <p.dalgaard_at_biostat.ku.dk>
Date: Mon 12 Apr 2004 - 12:05:25 GMT


I've rolled up R-1.9.0.tgz a short while ago. This is a new version with a number of new features, most notably a substantial reorganization of the standard packages, a major update of the grid package, and the fact that underscore can now be used as a regular character in variable names. See below for further changes.

Because of the disturbances at the machine that hosted the CVS archives, you will now have to wait for the file to show up on the CRAN master site. You can then get it from

http://cran.r-project.org/src/base/R-1.9.0.tgz

or wait for it to be mirrored at a CRAN site nearer to you. Binaries for various platforms will appear in due course.  

There is also a version split for floppies.

These are the md5sums for the freshly created files, in case you wish to check that they are uncorrupted:

79ae9d20a7bed94d7c92504c8c130310  R-1.9.0.tgz
de40f2e366d3ed9e2b3e8813fb8bba6c  R-1.9.0.tgz-split.aa
a963d3ac009ff6c5f321391e26cb0892  R-1.9.0.tgz-split.ab
0e8f55216051057dfafdabc5f578e68e  R-1.9.0.tgz-split.ac
7add0d9b6dbd8cdbc36608b7166b910b  R-1.9.0.tgz-split.ad
667222d63ce7e19bf869ea20439d0867  R-1.9.0.tgz-split.ae
42dcd15c23b07decb43a65f937942489  R-1.9.0.tgz-split.af
136279c8d59def0a5221e20ba763c997  R-1.9.0.tgz-split.ag

Here is the relevant bit of the NEWS file:

                CHANGES IN R VERSION 1.9.0 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.


NEW FEATURES

    o	$, $<-, [[, [[<- can be applied to environments. Only character
	arguments are allowed and no partial matching is done.	The
	semantics are basically that of get/assign to the environment with
	inherits=FALSE.

    o	There are now print() and [ methods for "acf" objects.

    o	aov() will now handle singular Error() models, with a warning.

    o	arima() allows models with no free parameters to be fitted (to
	find log-likelihood and AIC values, thanks to Rob Hyndman).

    o	array() and matrix() now allow 0-length `data' arguments for
	compatibility with S.

    o	as.data.frame() now has a method for arrays.

    o	as.matrix.data.frame() now coerces an all-logical data frame
	to a logical matrix.

    o	New function assignInNamespace() parallelling fixInNamespace.

    o	There is a new function contourLines() to produce contour
	lines (but not draw anything).	This makes the CRAN package
	clines (with its clines() function) redundant.

    o	D(), deriv(), etc now also differentiate asin(), acos(), atan(),

(thanks to a contribution of Kasper Kristensen).
o The `package' argument to data() is no longer allowed to be a
(unquoted) name and so can be a variable name or a quoted
character string. o There is a new class "Date" to represent dates (without times) plus many utility functions similar to those for date-times. See ?Date. o Deparsing (including using dump() and dput()) an integer vector now wraps it in as.integer() so it will be source()d correctly. (Related to PR#4361.) o .Deprecated() has a new argument `package' which is used in the warning message for non-base packages. o The print() method for "difftime" objects now handles arrays. o dir.create() is now an internal function (rather than a call to mkdir) on Unix as well as on Windows. There is now an option to suppress warnings from mkdir, which may or may not have been wanted. o dist() has a new method to calculate Minkowski distances. o expand.grid() returns appropriate array dimensions and dimnames in the attribute "out.attrs", and this is used by the predict() method for loess to return a suitable array. o factanal(), loess() and princomp() now explicitly check for numerical inputs; they might have silently coded factor variables in formulae. o New functions factorial(x) defined as gamma(x+1) and for S-PLUS compatibility, lfactorial(x) defined as lgamma(x+1). o findInterval(x, v) now allows +/-Inf values, and NAs in x. o formula.default() now looks for a "terms" component before a 'formula' argument in the saved call: the component will have `.' expanded and probably will have the original environment set as its environment. And what it does is now documented. o glm() arguments `etastart' and `mustart' are now evaluated via the model frame in the same way as `subset' and `weights'. o Functions grep(), regexpr(), sub() and gsub() now coerce their arguments to character, rather than give an error. The perl=TRUE argument now uses character tables prepared for the locale currently in use each time it is used, rather than those of the C locale. o New functions head() and tail() in package `utils'.
(Based on a contribution by Patrick Burns.)
o legend() has a new argument 'text.col'. o methods(class=) now checks for a matching generic, and so no longer returns methods for non-visible generics (and eliminates various mismatches). o A new function mget() will retrieve multiple values from an environment. o model.frame() methods, for example those for "lm" and "glm", pass relevant parts of ... onto the default method. (This has long been documented but not done.) The default method is now able to cope with model classes such as "lqs" and "ppr". o nls() and ppr() have a `model' argument to allow the model frame to be returned as part of the fitted object. o "POSIXct" objects can now have a "tzone" attribute that determines how they will be converted and printed. This means that date-time objects which have a timezone specified will generally be regarded as in their original time zone. o postscript() device output has been modified to work around rounding errors in low-precision calculations in gs >= 8.11.
(PR#5285, which is not a bug in R.)
It is now documented how to use other Computer Modern fonts, for example italic rather than slanted. o ppr() now fully supports categorical explanatory variables, ppr() is now interruptible at suitable places in the underlying FORTRAN code. o princomp() now warns if both `x' and `covmat' are supplied, and returns scores only if the centring used is known. o psigamma(x, deriv=0), a new function generalizes, digamma() etc. All these (psigamma, digamma, trigamma,...) now also work for x < 0. o pchisq(*, ncp > 0) and hence qchisq() now work with much higher values of ncp; it has become much more accurate in the left tail. o read.table() now allows embedded newlines in quoted fields. (PR#4555) o rep.default(0-length-vector, length.out=n) now gives a vector of length n and not length 0, for compatibility with S. If both `each' and `length.out' have been specified, it now recycles rather than fills with NAs for S compatibility. If both `times' and `length.out' have been specified, `times' is now ignored for S compatibility. (Previously padding with NAs was used.) The "POSIXct" and "POSIXlt" methods for rep() now pass ... on to the default method (as expected by PR#5818). o rgb2hsv() is new, an R interface the C API function with the same name. o User hooks can be set for onLoad, library, detach and onUnload of packages/namespaces: see ?setHook. o save() default arguments can now be set using option "save.defaults", which is also used by save.image() if option "save.image.defaults" is not present. o New function shQuote() to quote strings to be passed to OS shells. o sink() now has a split= argument to direct output to both the sink and the current output connection. o split.screen() now works for multiple devices at once. o On some OSes (including Windows and those using glibc) strptime() did not validate dates correctly, so we have added extra code to do so. However, this cannot correct scanning errors in the OS's strptime (although we have been able to work around these on Windows). Some examples are now tested for during configuration. o strsplit() now has `fixed' and `perl' arguments and split="" is optimized. o subset() now allows a `drop' argument to remove unused factor levels. The default is still to keep them. o termplot() has an option to smooth the partial residuals. o varimax() and promax() add class "loadings" to their loadings component. o Model fits now add a "dataClasses" attribute to the terms, which can be used to check that the variables supplied for prediction are of the same type as those used for fitting.
(It is currently used by predict() methods for classes "lm",
"mlm", "glm" and "ppr", as well as methods in packages MASS, rpart and tree.) o New command-line argument --max-ppsize allows the size of the pointer protection stack to be set higher than the previous limit of 10000. o The fonts on an X11() device (also jpeg() and png() on Unix) can be specified by a new argument `fonts' defaulting to the value of a new option "X11fonts". o New functions in the tools package: pkgDepends, getDepList and installFoundDepends. These provide functionality for assessing dependencies and the availability of them (either locally or from on-line repositories). o The parsed contents of a NAMESPACE file are now stored at installation and if available used to speed loading the package, so packages with namespaces should be reinstalled. o Argument `asp' although not a graphics parameter is accepted in the ... of graphics functions without a warning. It now works as expected in contour(). o Package stats4 exports S4 generics for AIC() and BIC(). o The Mac OS X version now produces an R framework for easier linking of R into other programs. As a result, R.app is now relocatable. o Added experimental support for conditionals in NAMESPACE files. o Added as.list.environment to coerce environments to lists
(efficiently).
o New function addmargins() in the stats package to add marginal summaries to tables, e.g. row and column totals. (Based on a contribution by Bendix Carstensen.) o dendrogam edge and node labels can now be expressions (to be plotted via stats:::plotNode called from plot.dendrogram). The diamond frames around edge labels are more nicely scaled horizontally. o Methods defined in the methods package can now include default expressions for arguments. If these arguments are missing in the call, the defaults in the selected method will override a default in the generic. See ?setMethod. o Changes to package 'grid': - 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")

UTILITIES

    o	R CMD check  now runs the (Rd) examples with default RNGkind

(uniform & normal) and set.seed(1).
example(*, setRNG = TRUE) does the same. o undoc() in package `tools' has a new default of `use.values = NULL' which produces a warning whenever the default values of function arguments differ between documentation and code. Note that this affects "R CMD check" as well. o Testing examples via massage-examples.pl (as used by R CMD check) now restores the search path after every help file. o checkS3methods() in package 'tools' now also looks for generics in the loaded namespaces/packages listed in the Depends fields of the package's DESCRIPTION file when testing an installed package. o The DESCRIPTION file of packages may contain a 'Suggests:' field for packages that are only used in examples or vignettes. o Added an option to package.dependencies() to handle the 'Suggests' levels of dependencies. o Vignette dependencies can now be checked and obtained via vignetteDepends. o Option 'repositories' to list URLs for package repositories added. o package.description() has been replaced by packageDescription(). o R CMD INSTALL/build now skip Subversion's .svn directories as well as CVS directories.

C-LEVEL FACILITIES

    o	arraySubscript and vectorSubscript take a new argument which
	is a function pointer that provides access to character
	strings (such as the names vector) rather than assuming these
	are passed in.

    o	R_CheckUserInterrupt is now described in `Writing R Extensions'
	and there is a new equivalent subroutine rchkusr for calling
	from FORTRAN code.

    o	hsv2rgb and rgb2hsv are newly in the C API.

    o	Salloc and Srealloc are provided in S.h as wrappers for S_alloc
	and S_realloc, since current S versions use these forms.

    o	The type used for vector lengths is now R_len_t rather than
	int, to allow for a future change.

    o	The internal header nmath/dpq.h has slightly improved macros
	R_DT_val() and R_DT_Cval(), a new R_D_LExp() and improved
	R_DT_log() and R_DT_Clog();  this improves accuracy in several
	[dpq]-functions {for "extreme" arguments}.


DEPRECATED & DEFUNCT     o print.coefmat() is defunct, replaced by printCoefmat().

    o codes() and codes<-() are defunct.

    o anovalist.lm (replaced in 1.2.0) is now defunct.

    o glm.fit.null(), lm.fit.null() and lm.wfit.null() are defunct.

    o print.atomic() is defunct.

    o	The command-line arguments --nsize and --vsize are no longer
	recognized as synonyms for --min-nsize and --min-vsize (which
	replaced them in 1.2.0).

    o	Unnecessary methods coef.{g}lm and fitted.{g}lm have been
	removed: they were each identical to the default method.

    o	La.eigen() is deprecated now eigen() uses LAPACK by default.

    o	tetragamma() and pentagamma() are deprecated, since they are
	equivalent to psigamma(, deriv=2) and psigamma(, deriv=3).

    o	LTRUE/LFALSE in Rmath.h have been removed: they were
	deprecated in 1.2.0.

    o	package.contents() has been deprecated.


INSTALLATION CHANGES

    o	The defaults for configure are now --without-zlib
	--without-bzlib --without-pcre.

	The included PCRE sources have been updated to version 4.5 and
	PCRE >= 4.0 is now required if --with-pcre is used.

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

    o	configure no longer lists bzip2 and PCRE as `additional
	capabilities' as all builds of R have had them since 1.7.0.

    o	--with-blas=goto to use K. Goto's optimized BLAS will now work.


BUG FIXES

    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	The cor() function did not remove missing values in the
	non-Pearson case.

    o	[l]choose() use a more accurate formula which also slightly
	improves p- and qhyper(); choose(n, k) now returns 0 instead
	of NaN for k < 0 or > n.

    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	chisq.test(x, simulate.p.value = TRUE) could hang in an infinite
	loop or segfault, as r2dtable() did, when the entries in x where
	large. (PR#5701)

    o	fisher.test(x) could give a P-value of 'Inf' in similar cases which
	now result in an error (PR#4688).  It silently truncated
	non-integer 'x' instead of rounding.

    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 <- 2^32; 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) -- O__ ---- Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard@biostat.ku.dk) FAX: (+45) 35327907 _______________________________________________
R-announce@stat.math.ethz.ch mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-announce Received on Mon Apr 12 22:17:00 2004

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