pkgsrc/math/R, branch pkgsrc-2014Q2

FreeBSD 10 is not FreeBSD 1.

2014-06-26T20:34:02Z

Bump for perl-5.20.0.

2014-05-29T23:35:13Z

Do it for all packages that * mention perl, or * have a directory name starting with p5-*, or * depend on a package starting with p5- like last time, for 5.18, where this didn't lead to complaints. Let me know if you have any this time.

Recursive revbump from x11/pixman

2014-05-05T00:47:34Z

Fix PR pkg/48777

Update to R 3.1.0

2014-05-03T22:29:42Z

NEW FEATURES: * type.convert() (and hence by default read.table()) returns a character vector or factor when representing a numeric input as a double would lose accuracy. Similarly for complex inputs. If a file contains numeric data with unrepresentable numbers of decimal places that are intended to be read as numeric, specify colClasses in read.table() to be "numeric". * tools::Rdiff(useDiff = FALSE) is closer to the POSIX definition of diff -b (as distinct from the description in the man pages of most systems). * New function anyNA(), a version of any(is.na(.)) which is fast for atomic vectors, based on a proposal by Tim Hesterberg. * arrayInd(*, useNames = TRUE) and, analogously, which(*, arr.ind = TRUE) now make use of names(.dimnames) when available. * is.unsorted() now also works for raw vectors. * The "table" method for as.data.frame() (also useful as as.data.frame.table()) now passes sep and base arguments to provideDimnames(). * uniroot() gets new optional arguments, notably extendInt, allowing to auto-extend the search interval when needed. The return value has an extra component, init.it. * switch(f, ...) now warns when f is a factor, as this typically happens accidentally where the useR meant to pass a character string, but f is treated as integer (as always documented). * The parser has been modified to use less memory. * The way the unary operators (+ - !) handle attributes is now more consistent. If there is no coercion, all attributes (including class) are copied from the input to the result: otherwise only names, dims and dimnames are. * colorRamp() and colorRampPalette() now allow non-opaque colours and a ramp in opacity via the new argument alpha = TRUE. (Suggested by Alberto Krone-Martins, but optionally as there are existing uses which expect only RGB values.) * grid.show.layout() and grid.show.viewport() get an optional vp.ex argument. * There is a new function find_gs_cmd() in the tools package to locate a GhostScript executable. (This is an enhanced version of a previously internal function there.) * object.size() gains a format() method. * There is a new family, "ArialMT", for the pdf() and postscript() devices. This will only be rendered correctly on viewers which have access to Monotype TrueType fonts (which are sometimes requested by journals). * The text and PDF news files, including NEWS and NEWS.2, have been moved to the doc directory. * combn(x, simplify = TRUE) now gives a factor result for factor input x (previously user error). * Added utils::fileSnapshot() and utils::changedFiles() functions to allow snapshots and comparison of directories of files. * make.names(names, unique=TRUE) now tries to preserve existing names. * New functions cospi(x), sinpi(x), and tanpi(x), for more accurate computation of cos(pi*x), etc, both in R and the C API. Using these gains accuracy in some cases, e.g., inside lgamma() or besselI(). * print.table(x, zero.print = ".") now also has an effect when x is not integer-valued. * There is more support to explore the system's idea of time-zone names. Sys.timezone() tries to give the current system setting by name (and succeeds at least on Linux, OS X, Solaris and Windows), and OlsonNames() lists the names in the system's Olson database. Sys.timezone(location = FALSE) gives the previous behaviour. * Platforms with a 64-bit time_t type are allowed to handle conversions between the "POSIXct" and "POSIXlt" classes for date-times outside the 32-bit range (before 1902 or after 2037): the existing workarounds are used on other platforms. (Note that time-zone information for post-2037 is speculative at best, and the OS services are tested for known errors and so not used on OS X.) Currently time_t is usually long and hence 64-bit on Unix-alike 64-bit platforms: however it several cases the time-zone database is 32-bit. On R for Windows it is 64-bit (for both architectures as from this version). * The "save.defaults" option can include a value for compression_level. * colSums() and friends now have support for arrays and data-frame columns with 2^31 or more elements. * as.factor() is faster when f is an unclassed integer vector (for example, when called from tapply()). * fft() now works with longer inputs, from the 12 million previously supported up to 2 billion. * Complex svd() now uses LAPACK subroutine ZGESDD, the complex analogue of the routine used for the real case. * Sweave now outputs .tex files in UTF-8 if the input encoding is declared to be UTF-8, regardless of the local encoding. The UTF-8 encoding may now be declared using a LaTeX comment containing the string %\SweaveUTF8 on a line by itself. * file.copy() gains a copy.date argument. * Printing of date-times will make use of the time-zone abbreviation in use at the time, if known. For example, for Paris pre-1940 this could be LMT, PMT, WET or WEST. To enable this, the "POSIXlt" class has an optional component "zone" recording the abbreviation for each element. For platforms which support it, there is also a component "gmtoff" recording the offset from GMT where known. * (On Windows, by default on OS X and optionally elsewhere.) The system C function strftime has been replaced by a more comprehensive version with closer conformance to the POSIX 2008 standard. * dnorm(x, log = FALSE) is more accurate (but somewhat slower) for |x| > 5. * Some versions of the tiff() device have further compression options. * read.table(), readLines() and scan() have a new argument to influence the treatment of embedded nuls. * Avoid duplicating the right hand side values in complex assignments when possible. This reduces copying of replacement values in expressions such as Z$a <- a0 and ans[[i]] <- tmp: some package code has relied on there being copies. Also, a number of other changes to reduce copying of objects; all contributed by or based on suggestions by Michael Lawrence. * The fast argument of KalmanLike(), KalmanRun() and KalmanForecast() has been replaced by update, which instead of updating mod in place, optionally returns the updated model in an attribute "mod" of the return value. * arima() and makeARIMA() get a new optional argument SSinit, allowing the choice of a different *s*tate *s*pace initialization which has been observed to be more reliable close to non-stationarity. * warning() has a new argument noBreaks., to simplify post-processing of output with options(warn = 1). * pushBack() gains an argument encoding, to support reading of UTF-8 characters using scan(), read.table() and related functions in a non-UTF-8 locale. * all.equal.list() gets a new argument use.names which by default labels differing components by names (if they match) rather than by integer index. Saved R output in packages may need to be updated. * The methods for all.equal() and attr.all.equal() now have argument check.attributes after ... so it cannot be partially nor positionally matched (as it has been, unintentionally). A side effect is that some previously undetected errors of passing empty arguments (no object between commas) to all.equal() are detected and reported. There are explicit checks that check.attributes is logical, tolerance is numeric and scale is NULL or numeric. This catches some unintended positional matching. The message for all.equal.numeric() reports a "scaled difference" only for scale != 1. * all.equal() now has a "POSIXt" method replacing the "POSIXct" method. * The "Date" and "POSIXt" methods of seq() allows by = "quarter" for completeness (by = "3 months" always worked). * file.path() removes any trailing separator on Windows, where they are invalid (although sometimes accepted). This is intended to enhance the portability of code written by those using POSIX file systems (where a trailing / can be used to confine path matching to directories). * New function agrepl() which like grepl() returns a logical vector. * fifo() is now supported on Windows. * sort.list(method = "radix") now allows negative integers * Some functionality of print.ts() is now available in .preformat.ts() for more modularity. * mcparallel() gains an option detach = TRUE which allows execution of code independently of the current session. It is based on a new estranged = TRUE argument to mcfork() which forks child processes such that they become independent of the parent process. * The pdf() device omits circles and text at extremely small sizes, since some viewers were failing on such files. * The rightmost break for the "months", "quarters" and "years" cases of hist.POSIXlt() has been increased by a day. * The handling of DF[i,] <- a where i is of length 0 is improved. * hclust() gains a new method "ward.D2" which implements Ward's method correctly. The previous "ward" method is "ward.D" now, with the old name still working. Thanks to research and proposals by Pierre Legendre. * The sunspot.month dataset has been amended and updated from the official source, whereas the sunspots and sunspot.year datasets will remain immutable. The documentation and source links have been updated correspondingly. * The summary() method for "lm" fits warns if the fit is essentially perfect, as most of the summary may be computed inaccurately (and with platform-dependent values). Programmers who use summary() in order to extract just a component which will be reliable (e.g. $cov.unscaled) should wrap their calls in suppressWarnings().

Update to R 3.0.3. update from wen heping.

2014-03-14T20:15:38Z

CHANGES IN R 3.0.3: NEW FEATURES: * On Windows there is support for making .texi manuals using texinfo 5.0 or later: the setting is in file src/gnuwin32/MkRules.dist. A packaging of the Perl script and modules for texinfo 5.2 has been made available at . * write.table() now handles matrices of 2^31 or more elements, for those with large amounts of patience and disc space. * There is a new function, La_version(), to report the version of LAPACK in use. * The HTML version of 'An Introduction to R' now has links to PNG versions of the figures. * There is some support to produce manuals in ebook formats. (See doc/manual/Makefile. Suggested by Mauro Cavalcanti.) * On a Unix-alike Sys.timezone() returns NA if the environment variable TZ is unset, to distinguish it from an empty string which on some OSes means the UTC time zone. * The backtick may now be escaped in strings, to allow names containing them to be constructed, e.g. `\``. * read.table(), readLines() and scan() now warn when an embedded nul is found in the input. * KalmanForecast(fast = FALSE) is now the default, and the help contains an example of how fast = TRUE can be used in this version. (The usage will change in 3.1.0.) * strptime() now checks the locale only when locale-specific formats are used and caches the locale in use: this can halve the time taken on OSes with slow system functions (e.g. OS X). * strptime() and the format() methods for classes "POSIXct", "POSIXlt" and "Date" recognize strings with marked encodings: this allows, for example, UTF-8 French month names to be read on (French) Windows. * iconv(to = "utf8") is now accepted on all platforms (some implementations did already, but GNU libiconv did not: however converted strings were not marked as being in UTF-8). The official name, "UTF-8" is still preferred. * available.packages() is better protected against corrupt metadata files. * Finalizers are marked to be run at garbage collection, but run only at a somewhat safer later time (when interrupts are checked). This circumvents some problems with finalizers running arbitrary code during garbage collection (the known instances being running options() and (C-level) path.expand() re-entrantly).

Set USE_GCC_RUNTIME=yes for packages which build shared libraries but do

2014-03-13T11:08:49Z

not use libtool to do so. This is required to correctly depend upon a gcc runtime package (e.g. gcc47-libs) when using USE_PKGSRC_GCC_RUNTIME.

Pass --disable-openmp on Darwin. With changes to g95 and tk, this package

2014-02-17T17:11:07Z

finally builds.

Update to R 3.0.2

2014-02-06T10:57:21Z

* The NEWS files have been re-organized. This file contains news for R >= 3.0.0: news for the 0.x.y, 1.x.y and 2.x.y releases is in files NEWS.0, NEWS.1 and NEWS.2. The latter files are now installed when R is installed. An HTML version of news from 2.10.0 to 2.15.3 is available as doc/html/NEWS.2.html. * sum() for integer arguments now uses an integer accumulator of at least 64 bits and so will be more accurate in the very rare case that a cumulative sum exceeds 2^53 (necessarily summing more than 4 million elements). * The example() and tools::Rd2ex() functions now have parameters to allow them to ignore \dontrun markup in examples. (Suggested by Peter Solymos.) * str(x) is considerably faster for very large lists, or factors with 100,000 levels, the latter as in PR#15337. * col2rgb() now converts factors to character strings not integer codes (suggested by Bryan Hanson). * tail(warnings()) now works, via the new `[` method. * There is now support for the LaTeX style file zi4.sty which has in some distributions replaced inconsolata.sty. * unlist(x) now typically returns all non-list xs unchanged, not just the "vector" ones. Consequently, format(lst) now also works when the list lst has non-vector elements. * The tools::getVignetteInfo() function has been added to give information about installed vignettes. * New assertCondition(), etc. utilities in tools, useful for testing. * Profiling now records non-inlined calls from byte-compiled code to BUILTIN functions. * Various functions in stats and elsewhere that use non-standard evaluation are now more careful to follow the namespace scoping rules. E.g. stats::lm() can now find stats::model.frame() even if stats is not on the search path or if some package defines a function of that name. * If an invalid/corrupt .Random.seed object is encountered in the workspace it is ignored with a warning rather than giving an error. (This allows R itself to rely on a working RNG, e.g. to choose a random port.) * seq() and seq.int() give more explicit error messages if called with invalid (e.g. NaN) inputs. * When parse() finds a syntax error, it now makes partial parse information available up to the location of the error. (Request of Reijo Sund.) * Methods invoked by NextMethod() had a different dynamic parent to the generic. This was causing trouble where S3 methods invoked via lazy evaluation could lose track of their generic. (PR#15267) * Code for the negative binomial distribution now treats the case size == 0 as a one-point distribution at zero. * abbreviate() handles without warning non-ASCII input strings which require no abbreviation. * read.dcf() no longer has a limit of 8191 bytes per line. (Wish of PR#15250.) * formatC(x) no longer copies the class of x to the result, to avoid misuse creating invalid objects as in PR#15303. A warning is given if a class is discarded. * Dataset npk has been copied from MASS to allow more tests to be run without recommended packages being installed. * The initialization of the regression coefficients for non-degenerate differenced models in arima() has been changed and in some examples avoids a local maximum. (PR#15396) * termplot() now has an argument transform.x to control the display of individual terms in the plot. (PR#15329) * format() now supports digits = 0, to display nsmall decimal places. * There is a new read-only par() parameter called "page", which returns a logical value indicating whether the next plot.new() call will start a new page. * Processing Sweave and Rd documents to PDF now renders backticks * utils::modifyList() gets a new argument keep.null allowing NULL components in the replacement to be retained, instead of causing corresponding components to be deleted. * tools::pkgVignettes() gains argument check; if set to TRUE, it will warn when it appears a vignette requests a non-existent vignette engine.

Exclude 64-bit system library paths on SunOS.

2014-01-13T11:25:54Z

Revbump after updating tcl/tk.

2014-01-11T14:42:00Z