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File _service:extract_file:R-base.changes of Package R-gnu15
------------------------------------------------------------------- Mon Mar 9 10:26:51 UTC 2015 - detlef.steuer@gmx.de - Upstream release 3.1.3 - Most important CHANGES IN R 3.1.3: NEW FEATURES: * The internal method of download.file() can now handle files larger than 2GB on 32-bit builds which support such files (tested on 32-bit R running on 64-bit Windows). * kruskal.test() warns on more types of suspicious input. * The as.dendrogram() method for "hclust" objects gains a check argument protecting against memory explosion for invalid inputs. * capabilities() has a new item long.double which indicates if the build uses a long double type which is longer than double. * nlm() no longer modifies the callback argument in place (a new vector is allocated for each invocation, which mimics the implicit duplication that occurred in R < 3.1.0); note that this is a change from the previously documented behavior. (PR#15958) * icuSetCollate() now accepts locale = "ASCII" which uses the basic C function strcmp and so collates strings byte-by-byte in numerical order. * sessionInfo() tries to report the OS version in use (not just that compiled under, and including details of Linux distributions). * model.frame() (used by lm() and many other modelling functions) now warns when it drops contrasts from factors. (Wish of PR#16119) * install.packages() and friends now accept the value type = "binary" as a synonym for the native binary type on the platform (if it has one). * Single source or binary files can be supplied for install.packages(type = "both") and the appropriate type and repos = NULL will be inferred. * New function pcre_config() to report on some of the configuration options of the version of PCRE in use. In particular, this reports if regular expressions using \p{xx} are supported. * (Windows.) download.file(cacheOK = FALSE) is now supported when internet2.dll is used. * browseURL() has been updated to work with Firefox 36.0 which has dropped support for the -remote interface. INSTALLATION and INCLUDED SOFTWARE: * The included version of PCRE has been updated to 8.36. * configure accepts MAKEINFO=texi2any as another way to ensure texinfo 5.x is used when both 5.x and 4.x are installed. UTILITIES: * R CMD check now checks the packages used in \donttest sections of the examples are specified in the DESCRIPTION file. (These are needed to run the examples interactively.) * R CMD check checks for the undeclared use of GNU extensions in Makefiles, and for Makefiles with a missing final linefeed. R CMD build will correct line endings in all Makefiles, not just those in the src directory. * R CMD check notes uses of library() and require() in package code: see the section 'Suggested packages' of 'Writing R Extensions' for good practice. DEPRECATED AND DEFUNCT: * The configure option --with-valgrind-instrumentation=3 is deprecated and will be removed in R 3.2.0. BUG FIXES: * (Windows.) Rscript.exe was missing a manifest specifying the modern style for common controls (e.g., the download progress bar). * If a package had extra documentation files but no vignette, the HTML help system produced an empty index page. * The parser now gives an error if a null character is included in a string using Unicode escapes. (PR#16046) * qr.Q() failed on complex arguments due to pre-3.0(!) typo. (PR#16054) * abs() failed with named arguments when the argument was complex. (PR#16047) * "noquote" objects may now be used as columns in dataframes. (PR#15997) * Some values with extremely long names were printed incorrectly. (PR#15999) * Extremely large exponents on zero expressed in scientific notation (e.g. 0.0e50000) could give NaN. (PR#15976) * download.file() reported downloaded sizes as 0KB if less than 1MB, only for R 3.1.2 and only on big-endian platforms. * prompt() did not escape percent signs in the automatically generated usage section of help files. * drop.terms() dropped some of the attributes of the object it was working with. (PR#16029) * (Windows.) The command completion in Rgui.exe messed up the console. (PR#15791) * (Windows.) The choose.files() command returned a blank string when the user asked for a single file but cancelled the request. (PR#16074) * Math2 S4 group generics failed to correctly dispatch "structure"- and "nonStructure"-derived classes. * loadNamespace() imposed undocumented restrictions on the versionCheck parameter. (Reported by Geoff Lee.) * Rare over-runs detected by AddressSanitizer in substr() and its replacement version have been avoided. _Inter alia_ that fix gives the documented behaviour for substr(x, 1, 2) <- "" (subsequently reported as PR#16214). * Loading packages incorrectly defining an S4 generic followed by a function of the same name caused an erroneous cyclic namespace dependency error. * Declared vignette encodings are now always passed to the vignette engine. * Port Tomas Kalibera's fix from R-devel that restores the loadMethod() fast path, effectively doubling the speed of S4 dispatch. * power.t.test() and power.prop.test() now make use of the extendInt option of uniroot() and hence work in more extreme cases. (PR#15792) * If a package was updated and attached when its namespace was already loaded, it could end up with parts from one version and parts from the other. (PR#16120) * tools:::.Rdconv() didn't accept --encoding= due to a typo. (PR#16121) * Unix-alike builds without a suitable makeinfo were documented to link the missing HTML manuals to CRAN, but did not. * save(*, ascii=TRUE) and load() now correctly deal with NaN's. (PR#16137) * split.Date() retains fractional representations while avoiding incomplete class propagation. * R_ext/Lapack.h had not been updated for changes made by LAPACK to the argument lists of its (largely internal) functions dlaed2 and dlaed3. (PR#16157) * RShowDoc("NEWS", "txt") had not been updated for the layout changes of R 3.1.0. * The xtfrm() method for class "Surv" has been corrected and its description expanded. * mode(x) <- y would incorrectly evaluate x before changing its mode. (PR#16215) * besselJ(1, 2^64) and besselY(..) now signal a warning, returning NaN instead of typically segfaulting. (Issue 3 of PR#15554) * HTML conversion of \href markup in .Rd files did not remove the backslash from \% and so gave an invalid URL. In a related change, the \ escape is now required in such URLs. ------------------------------------------------------------------- Fri Dec 12 13:16:25 UTC 2014 - sbahling@suse.com - Remove tex(inconsolata.sty) BuildRequires for SLE_12 builds (like older SLE releases). ------------------------------------------------------------------- Fri Oct 31 11:59:25 UTC 2014 - detlef.steuer@gmx.de - Upstream release 3.1.2 - Most important CHANGES IN R 3.1.2: NEW FEATURES: * embedFonts() now defaults to format = "ps2write" for .ps and .eps files. This is available in Ghostscript 9.x (since 2010) whereas the previous default, format = "pswrite", was removed in Ghostscript 9.10. * For consistency with [dpqr]norm(), [dp]lnorm(sdlog = 0) model a point mass at exp(mulog) rather than return NaN (for an error). * capabilities() now reports if ICU is compiled in for use for collation (it is only actually used if a suitable locale is set for collation, and never for a C locale). * (OS X only.) Package tcltk checks when loaded if it is linked against the CRAN X11-based Tcl/Tk and if so that the Tcl/Tk component and the X11 libraries are installed. This allows more informative error messages to be given advising the installation of the missing component or of XQuartz. The X11() device and X11-based versions of the data editor and viewer (invoked by edit() and View() for data frames and matrices from command-line R) check that the X11 libraries are installed and if not advises installing XQuartz. * icuSetCollate() allows locale = "default", and locale = "none" to use OS services rather than ICU for collation. Environment variable R_ICU_LOCALE can be used to set the default ICU locale, in case the one derived from the OS locale is inappropriate (this is currently necessary on Windows). * New function icuGetCollate() to report on the ICU collation locale in use (if any). * utils::URLencode() was updated to use unreserved and reserved characters from RFC 3986, <URL: http://tools.ietf.org/html/rfc3986>, instead of RFC 1738. * unique(warnings()) and c(warnings()) are now supported. * The Bioconductor 'version' used by setRepositories() now defaults to 3.0. (It can be set at runtime _via_ environment variable R_BIOC_VERSION.) INSTALLATION and INCLUDED SOFTWARE: * The configure script reports on the more important capabilities/options which will not be compiled in. More types of external BLAS are recognized by name in that report. * When building R as a shared library, the -L${R_HOME}/lib${R_ARCH} flag is placed earlier in the link commands used during installation and when packages are installed: this helps ensure that the current build has priority if an R shared library has already been installed by e.g. install-libR in a library mentioned in LDFLAGS (and not in 'your system's library directory' as documented). (Wish of PR#15790.) * LaTeX package upquote is no longer required for R's use of inconsolata. * (Windows only) If both 32 and 64 bit versions of R are installed, the bin/R.exe and bin/Rscript.exe executables now run 64 bit R. (To run 32 bit R, overwrite these files with copies of bin/i386/Rfe.exe.) UTILITIES: * Running R CMD check with _R_CHECK_DEPENDS_ONLY_ true now makes the VignetteBuilder packages available even if they are listed in Suggests, since they are needed to recognise and process non-Sweave vignettes. * R CMD check now reports empty importFrom declarations in a NAMESPACE file, as these are common errors (writing importFrom(Pkg) where import(Pkg) was intended). * R CMD check now by default checks code usage directly on the package namespace without loading and attaching the package and its suggests and enhances. For good practice with packages in the Suggests field, see SS1.1.3.1 of 'Writing R Extensions'. For use of lazy-data objects in the package's own code, see ?data. BUG FIXES: * dmultinom() did not handle non-finite probabilities correctly. * prettyNum(x, zero.print=*) now also works when x contains NAs. * A longstanding bug exhibited by nlminb() on Windows was traced to a compiler bug in gcc 4.6.3; a workaround has been put in place. (PR#15244 and PR#15914). * Rendering of \command in HTML versions of help pages has been improved: this is particularly evident on the help page for INSTALL. * as.hexmode(x) and as.octmode(x) now behave correctly for some numeric x, e.g., c(NA, 1) or c(1, pi). * drop1() failed if the scope argument had no variables to drop. (PR#15935) * edit() (and hence fix()) failed if an object had a non-character attribute named "source" (an attribute that had been used in R prior to version 2.14.0). * callGeneric() could fail if the generic had ... as a formal argument. (PR#15937). * Forking in package parallel called C entry point exit in the child. This was unsafe (_exit should have been called), and could flush stdin of the main R process (seen most often on Solaris). As good practice, stdout is now flushed before forking a child. * R objects such as list(`a\b` = 1) now print correctly. * getAnywhere("C_pbinom") now returns correctly a single object (rather than unlisting it). * The confint() method for nls() fits failed it these has specified parameter limits despite using an algorithm other than "port". (PR#15960) * Subclassing an S4 class failed if the class required arguments to the generator, through its initialize() method. * removeSource() did not properly handle expressions containing arguments that were supplied as missing, e.g. x[i,]. (PR#15957) * as.environment(list()) now works, and as.list() of such an environment is now the same as list(). * Several tcltk functions failed when run in unusual environments. (PR#15970) * options(list()) now works (trivially). (PR#15979) * merge(<dendrogram>, ..) now works correctly for two `independent' dendrograms (PR#15648), and still compatibly via adjust = "auto" e.g. for two branches of an existing dendrogram. * The plot method for "hclust" objects gets an optional argument check; When that is true (the default) it checks more carefully for valid input. * (Windows only) If a user chose to install 64 bit R but not 32 bit R, the bin/R and bin/Rscript executables failed to run. (PR#15981) * Various possible buffer overruns have been prevented, and missed memory protection added. (PR#15990) * Rscript no longer passes --args to R when there are no extra ("user") arguments. * objects like getClass("refClass")@prototype now print() and str() without error. * identical() now also looks at the S4 bit. * hist(x, breaks) is more robust in adding a small fuzz to few breaks when some are very large. (PR#15988) * sub() and gsub() did not handle regular expressions like "\s{2,}" properly if the text contained NA or non-ascii elements in a UTF-8 locale. Part of this was due to a bug in the TRE library. (PR#16009) * RShowDoc("NEWS") now displays the PDF version. * Matrices and arrays with last dimension zero did not print at all or incompletely. (PR#16012) * plot.histogram() and hence hist() now respect the xaxs, yaxs and lab graphics parameters. (PR#16021) * bw.SJ(x) and other bw.*() no longer segfault when x contains non-finite values. (PR#16024) * R CMD Rd2pdf unintentionally ignored its --os option. * The internal method of download.file() was not reporting file sizes and progress correctly on files larger than 2GB (inherited from libxml2). This is corrected for 64-bit builds (32-bit platforms may not support such files, but where possible will be supported in future versions of R). * Work around a bug in OS X Yosemite where key environment variables may be duplicated causing issues in subprocesses. The duplicates are now removed on R startup (via Rprofile). (PR#16042) * Adjust X11 auto-launch detection in DISPLAY on OS X to recognize latest XQuartz. ------------------------------------------------------------------- Thu Jul 10 12:35:42 UTC 2014 - detlef.steuer@gmx.de - Added Provides: R-parallel - Upstream release 3.1.1 - Most impotant CHANGES IN R 3.1.1: CHANGES IN R 3.1.1: NEW FEATURES: * When attach() reports conflicts, it does so compatibly with library() by using message(). * R CMD Sweave no longer cleans any files by default, compatibly with versions of R prior to 3.1.0. There are new options --clean, --clean=default and --clean=keepOuts. * tools::buildVignette() and tools::buildVignettes() with clean = FALSE no longer remove any created files. buildvignette() gains a keep argument for more cleaning customization. * The Bioconductor 'version' used by setRepositories() can now be set by environment variable R_BIOC_VERSION at runtime, not just when R is installed. (It has been stated that Bioconductor will switch from 'version' 2.14 to 'version' 3.0 during the lifetime of the R 3.1 series.) * Error messages from bugs in embedded Sexpr code in Sweave documents now report the source location. * type.convert(), read.table() and similar read.*() functions get a new numerals argument, specifying how numeric input is converted when its conversion to double precision loses accuracy. The default value, "allow.loss" allows accuracy loss, as in R versions before 3.1.0. * For some compilers, integer addition could overflow without a warning. R's internal code for both integer addition and subtraction is more robust now. (PR#15774) * The function determining the default number of knots for smooth.spline() is now exported, as .nknots.smspl(). * dbeta(, a,b), pbeta(), qbeta() and rbeta() are now defined also for a = 0, b = 0, or infinite a and b (where they typically returned NaN before). * Many package authors report that the RStudio graphics device does not work correctly with their package's use of dev.new(). The new option dev.new(noRStudioGD = TRUE) replaces the RStudio override by the default device as selected by R itself, still respecting environment variables R_INTERACTIVE_DEVICE and R_DEFAULT_DEVICE. * readRDS() now returns visibly. * Modifying internal logical scalar constants now results in an error instead of a warning. * install.packages(repos = NULL) now accepts http:// or ftp:// URLs of package archives as well as file paths, and will download as required. In most cases repos = NULL can be deduced from the extension of the URL. * The warning when using partial matching with the $ operator on data frames is now only given when options("warnPartialMatchDollar") is TRUE. * Package help requests like package?foo now try the package foo whether loaded or not. * General help requests now default to trying all loaded packages, not just those on the search path. * Added a new function promptImport(), to generate a help page for a function that was imported from another package (and presumably re-exported, or help would not be needed). INSTALLATION and INCLUDED SOFTWARE: * configure option --with-internal-tzcode can now be used with variable rsharedir. * The included version of PCRE has been updated to 8.35. * There is a new target make uninstall-libR to remove an installed shared/static libR. make install-libR now works if a sub-architecture is used, although the user will need to specify libdir differently for different sub-architectures. * There is more extensive advice on which LaTeX packages are required to install R or to make package manuals (as done by R CMD check) in the 'Writing R Extensions' manual. * Compilers/linkers were handling the visibility controls in src/extra/xz inconsistently (and apparently in some cases incorrectly), so it has been simplified. (PR#15327) * (Windows) There is updated support for the use of ICU for collation: see the 'R Installation and Administration Manual'. BUG FIXES: * dbinom(x, n), pbinom(), dpois(), etc, are slightly less restrictive in checking if n is integer-valued. (Wish of PR#15734.) * pchisq(x, df, ncp, log.p = TRUE) is more accurate and no longer underflows for small x and ncp < 80, e.g, for pchisq(1e-5, df = 100, ncp = 1, log = TRUE). (Based on PR#15635 and a suggestion by Roby Joehanes.) * The s ("step into") command in the debugger would cause R to step into expressions evaluated there, not just into functions being debugged. (PR#15770) * The C code used by strptime() rejected time-zone offsets of more than +1200 (+1245, +1300 and +1400 can occur). (PR#15768) * (Windows only.) png(type = "cairo", antialias = "gray") was not accepted. (PR#15760) * Use of save(..., envir=) with named objects could fail. (PR#15758) * Sweave() mis-parsed Sexpr expressions that contained backslashes. (PR#15779) * The return value from options(foo = NULL) was not the previous value of the option. (PR#15781) * enc2utf8() and enc2native() did not always mark the encoding of the return values when it was known. * dnbinom(x, size = <large>, mu, log = TRUE) no longer underflows to -Inf for large mu, thanks to a suggestion from Alessandro Mammana (MPI MolGen, Berlin). * pbeta(x, a, b, log = TRUE) no longer behaves discontinuously (in a small x-region) because of denormalized numbers. Also, pbeta(1-1e-12, 1e30, 1.001, log=TRUE) now terminates "in real time". * The "CRAN" filter (see available.packages()) no longer removes duplicates other than of packages on CRAN, and does not fail if there is no CRAN repository in getOption("repos"). * The device listing from dev2bitmap() and bitmap() was truncated to 1000 characters: modern versions of GhostScript on most platforms have many more devices. * (Windows.) Commands such as Sys.which() and pipe() which needed to find the full path to a command could segfault if the 'long' path name was much longer than the 'short' path name (which Sys.which() returns), as the behaviour of the Windows API call had changed. * R CMD build will fail with an error if one of the packages specified in the VignetteBuilder field is not installed. (Without loading those packages it cannot be ascertained which files are intended to be vignettes. This means that the VignetteBuilder packages have to be installed for package checking too.) (Wish of PR#15775.) * Misguided attempts to use chull() with non-finite points now give an error (related to PR#15777). * For a formula with exactly 32 variables the 32nd variable was aliased to the intercept in some C-level computations of terms, so that for example attempting to remove it would remove the intercept instead (and leave a corrupt internal structure). (PR#15735) * anyDuplicated() silently returned wrong values when the first duplicate was at an index which was too large to be stored in an integer vector (although a lot of RAM and patience would have been needed to encounter this). * tools::Rd2ex(commentDontrun = FALSE) failed if the block had only one line. * Hexadecimal constants such as 0x110p-5L which were incorrectly qualified by L were parsed incorrectly since R 3.0.0, with a slightly garbled warning. (PR#15753) * system() returned success on some platforms even if the system was unable to launch a process. (PR#15796) * (Windows Rgui console.) Unbuffered output was sometimes not output immediately if the prompt was not on the last line of the console. * The built-in help server did not declare the encoding for the DESCRIPTION or other text files to be the package encoding, so non-ASCII characters could be displayed incorrectly. * R is now trying harder to not cleanup child processes that were not spawned by mcparallel() on platforms that provide information about the source process of the SIGCHLD signal. This allows 3rd party libraries to manage the exit status of children that they spawn without R interfering. * mcmapply() was only parallelizing if the number of jobs was bigger than the number of cores. It now parallelizes if the number of jobs is more than one. * Auto-printing would re-evaluate its argument when trying to dispatch to a print method. This is now avoided when possible. * Unserializing (including load() and readRDS()) could silently return incorrect numeric values from ASCII saves if there was a read error. * getParseData() could return incorrect values for the parents of some elements. (Reported by Andrew Redd.) * Attempting to use data frames of 2^31 or more rows with merge() or to create a merged data frame of that size now gives a clearer error message. * parse() did not check its file argument was a connection if it was not a character string, so e.g. parse(FALSE) attempted to read from stdin. Nor did dump() and dput(). * The "help.try.all.packages" option was ignored when the shortcut syntax for help was used, e.g. ?foo. * A potential segfault in string allocation has been fixed. (Found by Radford Neal.) * Potential memory protection errors in sort() and D() have been fixed. (Found by Radford Neal.) * Fixed a lack of error checking in graphics event functions. (Found by Radford Neal; a different patch used here than the one in pqR.) * numericDeriv() sometimes miscalculated the gradient. (PR#15849, reported originally by Radford Neal) ------------------------------------------------------------------- Fri Jun 20 18:26:23 UTC 2014 - darin@darins.net - added parallel provides ------------------------------------------------------------------- Fri May 9 18:18:25 UTC 2014 - detlef.steuer@gmx.de - Removed / commented out symlink to %{_bindir}/r new package 'littler' should be used instead for packages that need /usr/bin/r ------------------------------------------------------------------- Thu May 1 15:29:30 UTC 2014 - darin@darins.net - Add make dependency for Rcmd ------------------------------------------------------------------- Tue Apr 29 15:31:15 UTC 2014 - darin@darins.net - Created symlink to %{_bindir}/r Many CRAN packages ship with scripts which call %{_bindir}/r, which creates a dependency on it, this fixes that. ------------------------------------------------------------------- Thu Apr 10 10:58:30 UTC 2014 - detlef.steuer@gmx.de - Upstream release 3.1.0 - Most impotant CHANGES IN R 3.1.0: 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. (Wish of PR#15239.) * 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). (Related to PR#15442.) * 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. (Suggestion of PR#15452.) * 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(). (Suggested by Morten Welinder in PR#15529.) * 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. (Wish of PR#15579.) * 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. (PR#15593) * 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; as suggested in PR#15620. * 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: see PR#14682. * 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. (PR#15600) * sort.list(method = "radix") now allows negative integers (wish of PR#15644). * 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. (Inter alia, fixes PR#15717.) * The handling of DF[i,] <- a where i is of length 0 is improved. (Inter alia, fixes PR#15718.) * 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(). INSTALLATION and INCLUDED SOFTWARE: * The included version of LAPACK has been updated to 3.5.0. * There is some support for parallel testing of an installation, by setting TEST_MC_CORES to an integer greater than one to indicate the maximum number of cores to be used in parallel. (It is worth specifying at least 8 cores if available.) Most of these require a make program (such as GNU make and dmake) which supports the $MAKE -j nproc syntax. Except on Windows: the tests of standard package examples in make check are done in parallel. This also applies to running tools::testInstalledPackages(). The more time-consuming regression tests are done in parallel. The package checks in make check-devel and make check-recommended are done in parallel. * More of make check will work if recommended packages are not installed: but recommended packages remain needed for thorough checking of an R build. * The version of tzcode included in src/extra/tzone has been updated. (Formerly used only on Windows.) * The included (64-bit) time-zone conversion code and Olson time-zone database can be used instead of the system version: use configure option --with-internal-tzcode. This is the default on Windows and OS X. (Note that this does not currently work if a non-default rsharedir configure variable is used.) (It might be necessary to set environment variable TZ on OSes where this is not already set, although the system timezone is deduced correctly on at least Linux, OS X and Windows.) This option also switches to the version of strftime included in directory src/extra/tzone. * configure now tests for a C++11-compliant compiler by testing some basic features. This by default tries flags for the compiler specified by CXX, but an alternative compiler, options and standard can be specified by variables CXX1X, CXX1XFLAGS and CXX1XSTD (e.g. -std=gnu++11). * R can now optionally be compiled to use reference counting instead of the NAMED mechanism by defining SWITCH_TO_REFCNT in Rinternals.h. This may become the default in the future. * There is a new option --use-system-tre to use a suitable system tre library: at present this means a version from their git repository, after corrections. (Wish of PR#15660.) ------------------------------------------------------------------- Thu Mar 6 10:08:59 UTC 2014 - detlef.steuer@gmx.de - Upstream release 3.0.3 - Most important 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 <URL: http://www.stats.ox.ac.uk/pub/Rtools/>. * 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. `\``. (PR#15621) * read.table(), readLines() and scan() now warn when an embedded nul is found in the input. (Related to PR#15625 which was puzzled by the behaviour in this unsupported case.) * (Windows only.) file.symlink() works around the undocumented restriction of the Windows system call to backslashes. (Wish of PR#15631.) * 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. (A recurring problem with Debian package shogun-r: PR#14713.) * 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). ------------------------------------------------------------------- Fri Sep 27 13:20:39 UTC 2013 - detlef.steuer@gmx.de - Removed outdated source file ------------------------------------------------------------------- Wed Sep 25 14:01:26 UTC 2013 - detlef.steuer@gmx.de - Upstream release 3.0.2 - Most important CHANGES IN R 3.0.2: NEW FEATURES: * 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 and single quotes better in several instances, including in \code and \samp expressions. * 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. ------------------------------------------------------------------- Mon Aug 26 14:19:31 UTC 2013 - schwab@suse.de - tre.patch: Fix tre library for aarch64 where wchar_t is unsigned int ------------------------------------------------------------------- Thu May 16 13:17:09 UTC 2013 - detlef.steuer@gmx.de - Improved spec file: R-base-devel requires R-base ------------------------------------------------------------------- Thu May 16 11:21:09 UTC 2013 - detlef.steuer@gmx.de - Upstream release 3.0.1 - Most important CHANGES IN R 3.0.1: NEW FEATURES: o chooseCRANmirror() and chooseBioCmirror() gain an ind argument (like setRepositories()). o mcparallel has a new argument mc.interactive which can modify the interactive flag in the child process. The new default is FALSE which makes child processes non-interactive by default (this prevents lock-ups due to children waiting for interactive input). o scan() now warns when end-of-file occurs within a quoted string. o count.fields() is now consistent with scan() in its handling of newlines in quoted strings. Instead of triggering an error, this results in the current line receiving NA as the field count, with the next line getting the total count of the two lines. o The default method of image() will plot axes of the class of xlim and ylim (and hence of x and y if there is a suitable range() method). Based on a suggestion of Michael Sumner. o load() now has a verbose argument for debugging support, to print the names of objects just before loading them. o When loading a serialized object encounters a reference to a namespace which cannot be loaded, this is replaced by a reference to the global environment, with a warning. o pairs() gains a line.main option for title placement. o The remaining instances in which serialization to a raw vector was limited to 2GB have been unlimited on a 64-bit platform, and in most cases serialization to a vector of more than 1GB will be substantially faster. - Improved spec file. Lots of commented out lines finally removed ------------------------------------------------------------------- Wed Apr 10 07:26:36 UTC 2013 - detlef.steuer@gmx.de - R-base.spec improved: now uses R-%{version}.tar.bz2 explicitly. Mistake when version bumping to 3.0.0 corrected ------------------------------------------------------------------- Wed Apr 3 18:39:35 UTC 2013 - detlef.steuer@gmx.de - Upstream release 3.0.0 - News for package: some new translation files - News upstream: /usr/lib/R/doc/NEWS.html - Most important CHANGES IN R 3.0.0: SIGNIFICANT USER-VISIBLE CHANGES: o Packages need to be (re-)installed under this version (3.0.0) of R. o There is a subtle change in behaviour for numeric index values 2^31 and larger. These never used to be legitimate and so were treated as NA, sometimes with a warning. They are now legal for long vectors so there is no longer a warning, and x[2^31] <- y will now extend the vector on a 64-bit platform and give an error on a 32-bit one. o It is now possible for 64-bit builds to allocate amounts of memory limited only by the OS. It may be wise to use OS facilities (e.g. ulimit in a bash shell, limit in csh), to set limits on overall memory consumption of an R process, particularly in a multi-user environment. A number of packages need a limit of at least 4GB of virtual memory to load. 64-bit Windows builds of R are by default limited in memory usage to the amount of RAM installed: this limit can be changed by command-line option --max-mem-size or setting environment variable R_MAX_MEM_SIZE. o Negative numbers for colours are consistently an error: previously they were sometimes taken as transparent, sometimes mapped into the current palette and sometimes an error. ------------------------------------------------------------------- Mon Mar 18 14:38:57 UTC 2013 - schwab@suse.de - Override LIBnn from %{_lib} ------------------------------------------------------------------- Fri Mar 1 12:15:30 UTC 2013 - detlef.steuer@gmx.de - There were a few new files in foreign and rpart. Fixed now. Builds fine. ------------------------------------------------------------------- Fri Mar 1 10:25:32 UTC 2013 - detlef.steuer@gmx.de - Upstream release 2.15.3 - see, as usual, /usr/lib/R/doc/NEWS.html - This is mostly a bugfix release and the final release for the R-2.x.y series. - Most important additions: NEW FEATURES: o lgamma(x) for very small x (in the denormalized range) is no longer Inf with a warning. o image() now sorts an unsorted breaks vector, with a warning. o The internal methods for tar() and untar() do a slightly more general job for 'ustar'-style handling of paths of more than 100 bytes. o Packages compiler and parallel have been added to the reference index (refman.pdf). o untar(tar = "internal") has some support for pax headers as produced by e.g. gnutar --posix (which seems prevalent on OpenSUSE 12.2) or bsdtar --format pax, including long path and link names. o sQuote() and dQuote() now handle 0-length inputs. (Suggestion of Ben Bolker.) o summaryRprof() returns zero-row data frames rather than throw an error if no events are recorded, for consistency. o The included version of PCRE has been updated to 8.32. o The tcltk namespace can now be re-loaded after unloading. The Tcl/Tk event loop is inhibited in a forked child from package parallel (as in e.g. mclapply()). o parallel::makeCluster() recognizes the value random for the environment variable R_PARALLEL_PORT: this chooses a random value for the port and reduces the chance of conflicts when multiple users start a cluster at the same time. ------------------------------------------------------------------- Fri Oct 26 12:35:44 UTC 2012 - detlef.steuer@gmx.de - Upstream release 2.15.2 - see, as usual, /usr/lib/R/doc/NEWS.html - most relevant change for rpm are some added translation files ------------------------------------------------------------------- Tue Jul 10 08:37:58 UTC 2012 - werner@suse.de - Make it build with latest TeXLive 2012 with new package layout ------------------------------------------------------------------- Fri Jun 22 14:22:25 UTC 2012 - detlef.steuer@gmx.de - Fixed: R-base-2.15.1-48.1.x86_64.rpm: directories not owned by a package: - /usr/lib64/R/share/locale/pl - /usr/lib64/R/share/locale/pl/LC_MESSAGES ------------------------------------------------------------------- Fri Jun 22 13:43:05 UTC 2012 - detlef.steuer@gmx.de - one more forgotten file in polish translation ... ------------------------------------------------------------------- Fri Jun 22 12:38:18 UTC 2012 - detlef.steuer@gmx.de - spec file update to incorporate new polish translation ------------------------------------------------------------------- Fri Jun 22 11:53:39 UTC 2012 - detlef.steuer@gmx.de - Upstream bugfix only release 2.15.1 - see, as usual, /usr/lib/R/doc/NEWS.html ------------------------------------------------------------------- Tue Apr 10 21:51:18 UTC 2012 - gregkh@opensuse.org - make R-base-devel require R-base as some packages think this dependancy is already there (i.e. some KDE packages). ------------------------------------------------------------------- Fri Mar 30 09:26:11 UTC 2012 - detlef.steuer@gmx.de - Upstream updated to 2.15.0 - see, as usual, /usr/lib/R/doc/NEWS.html ------------------------------------------------------------------- Wed Feb 29 18:00:59 UTC 2012 - detlef.steuer@gmx.de - upstream minor version increase to 2.14.2 - see, as usual, /usr/lib/R/doc/NEWS.html for details. ------------------------------------------------------------------- Fri Feb 17 20:53:49 UTC 2012 - detlef.steuer@gmx.de - Minor cleanup for easier automativ building of R-patched.spec ------------------------------------------------------------------- Wed Feb 15 19:41:43 UTC 2012 - detlef.steuer@gmx.de - changed licence string to "GPL-2.0 or GPL-3.0" ------------------------------------------------------------------- Mon Feb 13 22:39:51 UTC 2012 - detlef.steuer@gmx.de - uninstall rule for R.conf more than useless ... reverted. ------------------------------------------------------------------- Mon Feb 13 21:59:13 UTC 2012 - detlef.steuer@gmx.de - Applications like KDE's Cantor search for the R standard library - using the library search path. However, in openSUSE's package, - libraries are installed to %{_libdir}/R/lib, hence attempts to - load them from these applications will fail. - This revision adds a R.conf file to ld.so.conf.d to enable - searching for libraries where R is installed. Once this change - is in, applications are able to use libR.so. - Thx to einar@heavensinferno.net for spotting this. - Thought had done this for release of 2.14.0. ------------------------------------------------------------------- Thu Dec 22 12:19:10 UTC 2011 - steuer@unibw-hamburg.de - Upstream updated to 2.14.1 - see, as usual, /usr/lib/R/doc/NEWS.html for details. - Only minor bug fixes + workaround for missing inconsolata.sty - on older systems. ------------------------------------------------------------------- Mon Oct 31 12:40:03 UTC 2011 - detlef.steuer@gmx.de - merged change infor Oct 5th into working copy ------------------------------------------------------------------- Mon Oct 31 12:34:30 UTC 2011 - detlef.steuer@gmx.de - corrected subpackge version number in R-base-devel ------------------------------------------------------------------- Mon Oct 31 11:12:24 UTC 2011 - detlef.steuer@gmx.de - Upstream updated to 2.14.0 - see, as usual, /usr/lib/R/doc/NEWS.html for details. - On system side most important, that /etc/ld.so.conf.d/R-base.conf - was added to help third party programs, i.e. rpy2, tp link against - R-base ------------------------------------------------------------------- Wed Oct 5 07:13:03 UTC 2011 - detlef.steuer@gmx.de - corrected version string for Matrix subpackage ------------------------------------------------------------------- Tue Oct 4 14:00:04 UTC 2011 - detlef.steuer@gmx.de - removed 4 warnings about unescaped macros in comments ------------------------------------------------------------------- Tue Oct 4 12:13:18 UTC 2011 - detlef.steuer@gmx.de - explicitly added some locale directories. Worked before implicitly. ------------------------------------------------------------------- Tue Oct 4 11:10:56 UTC 2011 - detlef.steuer@gmx.de - update to upstream version 2.13.2 - see, as usual, /usr/lib/R/doc/NEWS.html for details. ------------------------------------------------------------------- Sat Sep 17 10:18:38 UTC 2011 - jengelh@medozas.de - Remove redundant tags/sections from specfile - Use %_smp_mflags for parallel build ------------------------------------------------------------------- Fri Jul 8 19:32:45 UTC 2011 - detlef.steuer@gmx.de - resolved some conflicts for R-base.spec after osc up -e && osc pull ------------------------------------------------------------------- Fri Jul 8 12:51:05 UTC 2011 - detlef.steuer@gmx.de - corrected version string in R-base.spec ------------------------------------------------------------------- Fri Jul 8 11:51:35 UTC 2011 - detlef.steuer@gmx.de - Upstream updated to 2.13.1. Licence change from GPLv2 to GPLv2 || GPLv3. Packages rpart and survival now GPLed, too. Various minor bugfixes. See /usr/lib/R/doc/NEWS.html for details. ------------------------------------------------------------------- Thu May 12 13:45:43 UTC 2011 - detlef.steuer@gmx.de - Removed possible dangerous links of libraries. R`s internal libraries now are only available in $lib/R/lib . ------------------------------------------------------------------- Fri May 6 07:33:40 UTC 2011 - detlef.steuer@gmx.de - Changed Licence string to GPLv2, taken from opensuse`s list aof allowed licences, as requested from coolo ------------------------------------------------------------------- Wed Apr 13 11:13:38 UTC 2011 - detlef.steuer@gmx.de - Upstream update to 2.13.0; new package 'compiler'; some new language files ------------------------------------------------------------------- Fri Mar 4 12:36:54 UTC 2011 - detlef.steuer@gmx.de - update to 2.12.2 minor bugfixes see /usr/lib/R/doc/html/NEWS.html for details ------------------------------------------------------------------- Mon Jan 10 16:56:55 CET 2011 - detlef.steuer@gmx.de - removed -n parameter from %build/%install - removed %doc from man/info pages in files section ------------------------------------------------------------------- Fri Dec 17 14:05:39 UTC 2010 - detlef.steuer@gmx.de reverting mandir/infodir directiven, didn't build in some releases- ------------------------------------------------------------------- Fri Dec 17 12:40:12 UTC 2010 - detlef.steuer@gmx.de sorted out list of problems shown bei mrueckert- ------------------------------------------------------------------- Mon Nov 29 20:08:31 UTC 2010 - detlef.steuer@gmx.de Version, to be submitted to factory-
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