52
62
NEWS
• select.list() gains a graphics argument to allow Windows/Mac users to choose
the text interface. This changes the behaviour of new.packages(ask=TRUE) to be
like update.packages(ask=TRUE) on those platforms in using a text menu: use
ask="graphics" for a graphical menu.
• New function chooseBioCmirror() to set the "BioC_mirror" option.
• The R grammar now prevents using the argument name in signatures of S4 methods
for $ and $<-, since they will always be called with a character string value for name.
The implicit S4 generic functions have been changed to re
ect this: packages which
included name in the signature of their methods need to be updated and re-installed.
• The handling of the method argument of glm() has been rened following suggestions
by Ioannis Kosmidis and Heather Turner.
• str() gainsa new argument list.len withdefault 99, limiting the number of list()
items (per level), thanks to suggestions from David Winsenius.
• Having formal arguments of an S4 method in a dierent order from the generic is now
an error (the warning having been ignored by some package maintainers for a long
time).
• New functions enc2native() andenc2utf8() convert character vectorswith possibly
marked encodings to the current locale and UTF-8 respectively.
• Unrecognized escapes and embedded nuls in character strings are now an error, not
just a warning. Thus option "warnEscapes" is no longer needed. rawToChar() now
removes trailing nuls silently, but other embedded nuls become errors.
• Informational messages about masked objects displayed when a package is attached
are now more compact, using strwrap() instead of one object per line.
• print.rle() gains argument prefix.
• download.file() gains a "curl" method, mainly for use on platforms which have
curl but not wget, but also for some hard-to-access URLs.
• In Rd, ‘\eqn’ and ‘\deqn’ will render in HTML (and convert to text) upper- and
lower-case Greek letters (entered as ‘\alpha’ ...), ‘...’, ‘...’, ‘\ge’ and ‘\le’.
• utf8ToInt() and intToUtf8() now map NA inputs to NA outputs.
• file() has a new argument raw which may help if it is used with something other
than a regular le, e.g. a character device.
• New function strtoi(), a wrapper for the C function strtol.
• as.octmode() and as.hexmode() now allow inputs of length other than one.
The format() and print() methods for "octmode" now preserve names and dimen-
sions (as those for "hexmode" did).
The format() methodsfor classes "octmode" and "hexmode" gain a width argument.
• seq.int() returns an integer result in some further cases where seq() does,
e.g. seq.int(1L, 9L, by = 2L).
• Added ‘\subsection{}{}’ macro to Rd syntax, for subsections within sections.
• n-dimensional arrays with dimension names can now be indexed by an n-column
character matrix. The indices are matched against the dimension names. NA indices
are propagated to the result. Unmatched values and "" are not allowed and result in
an error.
• interaction(drop=TRUE) uses less memory (related toPR#14121).
• summary() methods have been added to the "srcref" and "srcfile" classes, and
various encoding issues have been cleaned up.
• If option "checkPackageLicense" is set to TRUE (not currently the default), users
will be asked to agree to non-known-to-be-FOSS package licences at rst use.
• Checking setAs(a, b) methods only gives a message instead of a warning, when one
of a or b is unknown.
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53
NEWS
63
• New function norm() to compute a matrix norm. norm() and also backsolve() and
sample() have implicit S4 generics.
• Files ‘Renviron.site’ and ‘Rprofile.site’ can have architecture-specic versions
on systems with sub-architectures.
• R CMD check now (by default) also checks Rd les for auto-generated content in need
of editing, and missing argument descriptions.
• aggregate() gains a formula method thanks to a contribution by Arni Magnusson.
The data frame method now allows summary functions to return arbitrarily many
values.
• path.expand() now propagates NA values rather than converting them to "NA".
• file.show() now disallows NA values for le names, headers, and pager.
• The ‘fuzz’ used by seq() and seq.int() hasbeen reduced from 1e-7 to 1e-10, which
should be ample for the double-precision calculations used in R. It ensures that the
fuzz never comes into play with sequences of integers (wish ofPR#14169).
• The default value of RSiteSearch(restrict=) has beenchanged to include vignettes
but to exclude R-help. The R-help archives available have been split, with a new
option of "Rhelp10" for those from 2010.
• New function rasterImage() in the graphics package for drawing raster images.
• stats:::extractAIC.coxph() now omits aliased terms when computing the degrees
of freedom (suggestion of Terry Therneau).
• cor() and cov() now test for misuse with non-numeric arguments, such as the non-
bug reportPR#14207.
• pchisq(ncp =, log.p = TRUE) is more accurate for probabilities near one.
E.g., pchisq(80, 4, ncp=1,
log.p=TRUE). (Maybe what was meant in
PR#14216.)
• maintainer() hasbeen added, togive convenient accessto the name of the maintainer
of a package (contributed by David Scott).
• sample() and sample.int() allow zero itemsto be sampled from a zero-length input.
sample.int() gains a default value size=n to be more similar to sample().
• switch() returned NULL on error (not previously documented on the help page): it
now does so invisibly, analogously to if-without-else.
It is now primitive: this means that argument EXPR is always matched to the rst
argument and there is no danger of partial matching to later named arguments.
• Primitive functions UseMethod(), attr(), attr<-(), on.exit(), retracemem() and
substitute() now use standard argument matching (rather than positional match-
ing). This means that all multi-argument primitives which are not internal now use
standard argument matching except where positional matching is desirable (as for
switch(), call(), .C() ...).
• All the one-argument primitives now check that any name supplied for their rst
argument is a partial match to the argument name as documented on the help page:
this also applies to replacement functions of two arguments.
• base::which() uses a new .Internal function when arr.ind is FALSE resulting in
a10x speedup. Thanks to Patrick Aboyoun for implementation suggestions.
• Help conversion to text now uses the rst part of ‘\enc{}{}’ markup if it is repre-
sentable in the current output encoding. On the other hand, conversion to LaTeX
with the default outputEncoding = "ASCII" uses the second part.
• A new class "listOfMethods" has been introduced to represent the methods in a
methods table, to replace the deprecated class "MethodsList".
• any() and all() return early if possible. This may speed up operations on long
vectors.
49
64
NEWS
• strptime() now accepts "%z" (for the oset from UTC in the RFC822 format of
+/-hhmm).
• The PCRE library has been updated to version 8.02, a bug-x release which also
updates tables to Unicode 5.02.
• Functions which may use a graphical select.list() (including menu() and
install.packages()) now check on a Unix-alike that Tk can be started (and not
just capabilities("tcltk") && capabilities("X11")).
• The parser no longer marks strings containing octal or hex escapes as being in UTF-8
when entered in a UTF-8 locale.
• On platforms with cairo but not Pango (notably Mac OS X) the initial default X11()
type is set to "Xlib": this avoids several problems with font selection when done by
cairo rather than Pango (at least on Mac OS X).
• New function arrayInd() such that which(x,
arr.ind = TRUE) for an array
’x’ is now equivalent to arrayInd(which(x), dim(x), dimnames(x)).
DEPRECATED & DEFUNCT:
• Bundles of packages are defunct.
• stats::clearNames() is defunct: use unname().
• Basic regular expressions are defunct, and strsplit(), grep(), grepl(), sub(),
gsub(), regexpr() and gregexpr() no longer have an extended argument.
• methods::trySilent() is defunct.
• index.search() (which was deprecated in 2.10.0) is no longer exported and has a
dierent argument list.
• Use of multiple arguments to return() is now defunct.
• The use of UseMethod() with more than two arguments is now defunct.
• In the methods package, the "MethodsList" metadata objects which had been su-
perseded by hash tables (environments) since R 2.8.0 are being phased out. Objects
of this class are no longer assigned or used as metadata by the package.
getMethods() is now deprecated, with its internal use replaced by findMethods()
and other changes. Creating objectsfrom the "MethodsList" class is also deprecated.
• Parsing strings containing both octal/hex and Unicode escapes now gives a warning
and will become an error in R 2.12.0.
INSTALLATION:
• UTF-8 is now used for the reference manual and package manuals. This requires
LaTeX ‘2005/12/01’ or later.
• configure looksfor a POSIX compliant tr, Solaris’s /usr/ucb/tr having been found
to cause Rdiff to malfunction.
• configure is now generated with autoconf 2.65, which works better on recent sys-
tems and on Mac OS X.
PACKAGE INSTALLATION:
• CharactersinR source whichare not translatabletothe current locale are now handled
more tolerantly: these will be converted to hex codeswith a warning. Such characters
are only really portable if they appear in comments.
• R CMD INSTALL now teststhat the installed package canbe loaded (and backs out the
installation if it cannot): this can be suppressed by ‘--no-test-load’. This avoids
installing/updating a package that cannot be used: common causes of failures to load
are missing/incompatible external software and missing/broken dependent packages.
51
NEWS
65
• Package installation on Windows for a package with a ‘src’ directory now checks if
aDLL is created unless there is a ‘src/Makefile.win’ le: this helps catch broken
installations where the toolchain has not reported problems in building the DLL.
(Note: this can be any DLL, not just one named ‘<pkg-name>.dll’.)
BUG FIXES:
• Using with(), eval() etc with a list with some unnamed elements now works.
(PR#14035)
• The "quick" dispatch of S4 methods for primitive functions was not happening,
forcing a search each time. (Dispatch for closures was not aected.) A side eect is
that default values for arguments in a method that do not have defaults in the generic
will now be ignored.
• Trying to dispatch S4 methods for primitives during the search for inherited methods
slows that search down and potentially could cause an innite recursion. An internal
switch was added to turn o all such methods from findInheritedMethods().
• R framework installation (on Mac OS X) would not work properly if a rogue
Resources directory was present at the top level. Such a non-symlink will now be re-
named to Resources.old (and anything previously named Resources.old removed)
as part of the framework installation process.
• The checks for conforming S4 method arguments could fail when the signature of the
generic function omitted some of the formal arguments (in addition to ...). Argu-
ments omitted from the method denition but conforming (per the documentation)
should now be ignored (treated as "ANY") in dispatching.
• The computations for S4 method evaluation when ... was in the signature could
fail, treating ... as an ordinary symbol. This has been xed, for the known cases.
• Various ar() tting methods have more protection for singular ts.
• callNextMethod now works again with the drop= argument in ‘[’
• parse() and parse_Rd() miscounted columnswhenmultibyte UTF-8characterswere
present.
• Formatting of help pages has had minor improvements: extra blank lines have been
removed from the text format, and empty package labels removed from HTML.
• cor(A, B) where A is n1 and B a 1-dimensional array segfaulted or gave an internal
error. (The case cor(B, A) wasPR#7116.)
• cut.POSIXt() applied to a start value after the DST transition on a DST-change
day could give the wrong time for argument breaks in units of days or longer.
(PR#14208)
• do_par() UNPROTECTed too early (PR#14214)
• Subassignment x[[....]] <- y didn’t check for a zero-length right hand side, and
inserted a rubbish value. (PR#14217)
• fisher.test() no longer gives a P-value very slightly > 1, in some borderline cases.
• Internal function matchArgs() no longer modies the general purpose bits of the
SEXPs that make upthe formalslist of R functions. This xes an invaliderror message
that would occur when a garbage collection triggered a second call to matchArgs for
the same function via a nalizer.
• gsub() in 2.10.x could fail from stack over
ow for extremely long strings due to
temporary data being allocated on the stack. Also, gsub() with fixed=TRUE is in
some circumstances considerably faster.
• Several primitives, including attributes(), attr<-() interactive(), nargs() and
proc.time(), did not check that they were called with the correct number of argu-
ments.
58
66
NEWS
• A potential race condition in list.files() when other processes are operating on
the directory has been xed; the code now dynamically allocates memory for le
listings in a single pass instead of making an initial count pass.
• mean(x, trim=, na.rm = FALSE) failed to return NA if x contained missing values.
(Reported by Bill Dunlap.)
• Extreme
tail
behavior
of,
pbeta()
fand
hence
pf()g,
e.g.,
pbeta(x, 3, 2200, lower.tail=FALSE,
log.p=TRUE) now
returns -
nite values instead of jumping to -Inf too early. (PR#14230).
• parse(text=x) misbehaved for objects x that were not coerced internally to charac-
ter, notably symbols. (Reported to R-devel by Bill Dunlap.)
• The internal C function coerceSymbol now handles coercion to character, and warns
if coercion fails (rather than silently returning NULL). This allows a name to be given
where a character vector is required in functions which coerce internally.
• The interpretation by strptime() of "%c" was non-standard (not that it is ever
advisable to use locale- and system-specic input formats).
• capabilities("X11") now works the same way on Mac OS X as on other platforms (and
as documented: it was always true for R built with ‘--with-aqua’, as the CRAN
builds are).
• The X11() device with cairo but not Pango (notably Mac OS X) now checks validity
of text strings in UTF-8 locales (since Pango does but cairo it seems does not).
• read.fwf() misread multi-line records when n was specied. (PR#14241)
• all.equal(tolerance = e) passes the numeric tolerance also to the comparison of
the attributes.
• pgamma(0, 0), a boundary case, now returns 0, its limit from the left, rather than
the limit from the right.
• Issuing POST requests to the internal web server could stall the request under certain
circumstances.
• gzcon( <textConnection> ), an error, no longer damages the connection (in a way
to have it segfault). (PR#14237)
• All the results from hist() now use the nominal breaks not those adjusted by the
numeric ‘fuzz’: in recent versions the nominal breaks were reported but the ’density’
referred to the intervals used in the calculation { which mattered very slightly for one
of the extreme bins. (Based on a report by Martin Becker.)
• If xy[z].coords (used internally by many graphics functions) are given a list as x,
they now check that the list has suitable names and give a more informative error
message. (PR#13936)
CHANGES IN R VERSION 2.10.1 patched
NEW FEATURES:
• The handling of line textures in the postscript() and pdf() devices was set up for
round end caps (the only type which existed at the time): it has now been adjusted
for butt endcaps.
• lchoose(a, k) is now dened as log(abs(choose(a,k))), analogously to
lfactorial().
• Although \eqn{} inRd les is dened as a ‘verbatim’ macro, many packages expected
... and ... to be interpreted there (as was the case in R < 2.10.0), so this is now
done (using an ellipsis in HTML rendering).
51
NEWS
67
• Escaping of braces in quoted strings in R-code sections of Rd les is allowed again.
This had been changed for the new Rd format in R 2.10.0 but was only documented
on the developer site and was handled inconsistently by the converters: text and
example conversion removed the escapes but HTML conversion did not.
• The PCRE library has been updated to version 8.01, a bug-x release.
• tools::readNEWS() now accepts a digit as the rst character of a news section.
BUG FIXES:
• Using read.table(header=TRUE) ona header with an embeddednew line would copy
part of the header into the data. (PR#14103)
• qpois(p = 1, lambda = 0) now gives 0 as for all other p. (PR#14135)
• Functions related to string comparison (e.g., unique(), match()) could cause crashes
when used with strings not in the native encoding, e.g., UTF-8 strings on Windows.
(PR#14114andPR#14125)
• x[ , drop=TRUE] dropped an NA level even if it was in use.
• The dynamic HTML help system reported the wrong MIME type for the style sheet.
• tools::codoc() (used by R CMD check) was missing cases where the function had
no arguments but was documented to have some.
• Help links containing special characters (e.g., "?") were not generated correctly when
rendered in HTML. (PR#14155)
• lchoose(a, k) no longer wrongly gives NaN for negative a.
• ks.test() could give a p-value that waso by one observation due to rounding error.
(PR#14145)
• readBin()/readChar() when reading millions of character strings in a single call
used excessive amounts of memory (which also slowed them down).
• R CMD SHLIB could fail if used with paths that were not alphanumeric, e.g. contained
+. (PR#14168)
• sprintf() was not re-entrant, which potentially caused problems if an
as.character() method called it.
• The quartz() device did not restore the clipping region when lling the background
for a new page. This could be observed in multi-page bitmap output as stale outer
regions of the plot.
• p.adjust(method, n) now works correctly for the rare case n > length(p), also
when method diers from "bonferroni" or "none", thanks to a patch from Gordon
Smyth.
• tools::showNonASCII() failed to detect non-ASCII characters if iconv() (incor-
rectly) converted them to dierent ASCII characters. (Seen on Windows only.)
• tcrossprod() wrongly failed in some cases when one of the arguments was a vector
and the other a matrix.
• [cr]bind(..., deparse.level=2) was not always giving names when documented
to do so. (Discovered whilst investigatingPR#14189.)
• match(incomparables=<non-NULL>) could in rare cases innite-loop.
• poisson.test() needed to pass argument conf.level to binom.test().
(PR#14195)
• The "nls" method for df.residual() gave incorrect results for models tted with
na.action =
na.exclude. (PR#14194)
• A change to options(scipen=) was only implemented when printing next occurred,
even though it should have aected intervening calls to axis(), contour() and
filledcontour().
45
68
NEWS
• prettyNum(drop0trailing=TRUE) did not handle signs of imaginary partsof complex
numbers correctly (and this was used by str():PR#14201).
• system.time() had the sys.child component wrong (copied user.child instead)
on systems with HAVE_GETRUSAGE. (PR#14210)
• Changing both line texture and line cap (end) resulted in the latter to be omitted
form the PDF code. In addition, line cap (end) and join are now set explicitly in
PDF output to ensure correct defaults.
• The suppression of auto-rotation in bitmap() and dev2bitmap() with the
"pdfwrite" device was not working correctly.
• plot(ecdf(), log="x") no longer gives an incorrect warning.
• read.fwf() works again when argument file is a connection.
• Startup les will now be found if their paths exceed 255 bytes. (PR#14228)
• contrasts<- (in the stats package) no longer has an undeclared dependence on meth-
ods (introduced in 2.10.0).
CHANGES IN R VERSION 2.10.1
NEW FEATURES:
• The PCRE library has been updated to version 8.00.
• R CMD INSTALL has new options ‘--no-R’, ‘--no-libs’, ‘--no-data’, ‘--no-help’,
‘--no-demo’, ‘--no-exec’, and ‘--no-inst’ to suppress installation of the specied
part of the package. These are intendedfor special purposes (e.g., building a database
of help pages without fully installing all packages).
• The documented line-length limit of 4095 bytes when reading from the console now
also applies also to parse(file="") (which previously had a limit of around 1024
bytes).
• A Bioconductor mirror can be set for use by setRepositories() via
the option "BioC_mirror", e.g. the European mirror can be selected by
options(BioC_mirror="http://bioconductor.statistik.tu-dortmund.de").
• Double-clicking in a tk_select.list() list box now selects the item and closes the
list box (as happens on the Windows select.list() widget).
INSTALLATION:
• configure will be able to nd a usable libtiff in some rare circumstances where it
did not previously (where libtiff needed to be linked explicitly against -ljpeg).
• Making refman.pdf works around a problem with the indexing with hyperref 6.79d
and later.
DEPRECATED & DEFUNCT:
• The extended argument is deprecated in strsplit(), grep(), grepl(), sub(),
gsub(), regexpr() and gregexpr() (not just the value extended = FALSE) and
will be removed in R 2.11.0.
BUG FIXES:
• trigamma(x) and other psigamma(x, n) callsare now accurate for very large abs(x).
(PR#14020)
• [g]sub(perl=FALSE, fixed=FALSE) could use excessive stack space when used with
avery long vector containing some non-ASCII strings.
54
NEWS
69
• The default method of weighted.mean(na.rm = TRUE) did not omit weights for NA
observations in 2.10.0. (PR#14032)
• [g]regexpr(pattern, fixed = TRUE) returned match positions in bytes (not char-
acters) in an MBCS locale if pattern was a single byte.
[g]sub(fixed = TRUE) with a single-byte pattern could conceivably have matched
part of a multibyte character in a non-UTF-8 MBCS.
• findLineNum() and setBreakpoint() would sometimes fail if the specied le was
not in the current directory.
• Package tcltk’s demo(tkdensity) was broken in 2.9.0 when demo() was changed to
set par(ask = TRUE).
• gsub() with backrefs could fail on extremely long strings (hundreds of thousands of
characters) due to integer over
ow in a length calculation.
• abline(untf=TRUE) now
uses a better x-grid in log-scale, e.g., for
plot(c(1,300), c(1,300), log="xy"); abline(4,1, untf=TRUE).
• detach()/unloadNamespace() arrange to
ush the package’s lazyload cache of R
objects once the package/namespace is no longer needed.
• There have been small xes to the rendering of help, e.g. \command is now rendered
verbatim (so e.g. -- is not interpreted,PR#14045).
Also, there are many small changes to help les where the new converters were not
rendering them in the same way as before.
• available.packages() would fail whenrunona repository withno packages meeting
the ltering conditions. (PR#14042)
• rep(x, times, each = 2) gave invalid results when the times argument was a vec-
tor longer than x. Reported by Bill Dunlap.
• An error when unloadNamespace() attempted to run the .onUnload() function gave
an error in the reporting function and so was not reported properly.
• Text help rendering did not handle very long input lines properly.
• promptMethods() generated signature documentation improperly.
• pgamma(x, a, lower.tail=FALSE) and qgamma(...) are now considerably more
accurate in some regions for very small a. qgamma() now correctly returns 0 instead
of NaN in similar extreme cases, and qgamma() no longer warns in the case of small
a, see (PR#12324).
• unname() now also removes names from a zero length vector.
• Printing results from ls.str() no longer evaluates unevaluated calls.
• complete.cases() failed on a 0-column data frame argument.
(Underlies
PR#14066.)
It could return nonsensical results if no input determined the number of cases (seen
in the no-segfault tests).
• An error in nls() with a long formula could cause a segfault. (PR#14059)
• qchisq(p, df, ncp, lower.tail = FALSE) with ncp >= 80 was inaccurate for
small p (as the help page said): it is now less inaccurate. (In part,PR#13999.)
For ncp less than but close to 80, pchisq() and qchisq() are more accurate for
probabilities very close to 1 (a series expansion was truncated slightly too early).
pchisq(x, df, ncp) can no longer return values just larger than one for large values
of ncp.
• intToUtf8() could fail when asked to produce 10Mb or more strings, something it
was never intended to do: unfortunately Windows crashed R (other OSes reported a
lack of resources). (PR#14068)
• chisq.test() could fail when given argument x or y which deparsed to more than
one line. (Reported by Laurent Gauthier.)
48
70
NEWS
• S4 methods are uncached whenever the namespace containing them is unloaded (by
unloadNamespace() as well as by detach(unload = TRUE)).
• The internal record-keeping by dyn.load/dyn.unload was incomplete, which could
crash R if a DLL that registered .External routines had earlier been unloaded.
• bessel[JY](x, nu) with nu a negative integer (a singular case) is now correct, anal-
ogously to besselI(), seePR#13556.
• tools::file_path_as_absolute() doubled the le separator when applied to a le
such as ‘"/vmunix"’ or (on Windows) ‘"d:/afile"’ in a directory for which getwd()
would return a path with a trailing separator (largely cosmetic, as reasonable le
systems handle such a path correctly). (Perhaps what was meant byPR#14078.)
• unsplit(drop = TRUE) applied to a data frame failed to pass drop to the computa-
tion of row names. (PR#14084)
• The "difftime" method of mean() ignored its na.rm argument.
• tcltk::tk_select.list() isnow more likely toremove the widget immediately after
selection is complete.
• Adding/subtracting a "difftime" object to/from a "POSIXt" or "Date" object works
again (it was broken by the addition of Ops.difftime).
• Conversion to latex of an Rd le with no aliases failed.
• wilcox.test(conf.int=TRUE) has achieved.level corrected and, for exact=FALSE,
now returns a estimate component which does not depend on the alternative used.
• help.search() failed when the package argument was specied. (PR#14113)
• switch(EXPR = "A") now returns NULL, as does switch(1) (which used to signal an
error).
CHANGES IN R VERSION 2.10.0
SIGNIFICANT USER-VISIBLE CHANGES:
• Package help is now converted from Rd by the R-based converters that were rst
introduced in 2.9.0. This means
{ Packages that were installed by R-devel after 2009-08-09 should not be used with
earlier versions of R, and most aspects of package help (including the runnable
examples) will be missing if they are so used.
{ Text, HTML and latex help and examples for packages installed under the new
system are convertedon-demand from stored parsed Rd les. (Conversions stored
in packages installed under R < 2.10.0 are used if no parsed Rd les are found.
It is recommended that such packages be re-installed.)
• HTML help is now generated dynamically using an HTTP server running in the R
process and listening on the loopback interface.
{ Those worriedabout security implications of sucha server can disable it by setting
the environment variable R_DISABLE_HTTPD to a non-empty value. This disables
help.start() and HTML help (so text help is shown instead).
{ The Java/Javascript search engine has been replaced by an HTML interface to
help.search(). help.start() no longer has an argument searchEngine as it
is no longer needed.
{ The HTML help can now locate cross-references of the form \link[pkg]{foo}
and \link[pkg:foo]{bar} where foo is an alias in the package, rather than the
documented (basename of a) lename (since the documentation has been much
ignored).
Documents you may be interested
Documents you may be interested