Changelog for R-nlme-3.1.125-5.1.x86_64.rpm :

* Fri Apr 15 2016 detlef.steuerAATTgmx.de- CHANGES IN R 3.2.5: BUG FIXES: • format.POSIXlt() behaved incorrectly in R 3.2.4. E.g. the output of format(as.POSIXlt(paste0(1940:2000,\"-01-01\"), tz = \"CET\"), usetz = TRUE) ended in two \"CEST\" time formats. • A typo in the Makefile for src/extra/xz prevented builds of liblzma.a. (Notice that this will become unbundled in 3.3.0.)
* Thu Mar 17 2016 detlef.steuerAATTgmx.de- upstrem releases minorst bug fix release NEWS: The 3.2.4 release had two annoyances which we would rather not have in an \"ultra-stable\" release, designed to hang around for the duration of the 3.3 series. One was a relatively minor Makefile issue affecting system using R\'s bundled lzma library. The other, rather more serious, affected printing and formatting of POSIXlt objects, which would unpredictably get the Daylight Savings Time wrong.
* Fri Mar 11 2016 detlef.steuerAATTgmx.de- Some version numbers of recommended packages corrected
* Fri Mar 11 2016 detlef.steuerAATTgmx.de- Release numbers for sub-packages improved
* Fri Mar 11 2016 detlef.steuerAATTgmx.de- added MakefileTypo.patch to enable building for 12.2 was a one charcter show stopper
* Thu Mar 10 2016 detlef.steuerAATTgmx.de- upstream release 3.2.4, only minor improvements CHANGES IN R 3.2.4: NEW FEATURES: • install.packages() and related functions now give a more informative warning when an attempt is made to install a base package. • summary(x) now prints with less rounding when x contains infinite values. (Request of PR#16620.) • provideDimnames() gets an optional unique argument. • shQuote() gains type = \"cmd2\" for quoting in cmd.exe in Windows. (Response to PR#16636.) • The data.frame method of rbind() gains an optional argument stringsAsFactors (instead of only depending on getOption(\"stringsAsFactors\")). • smooth(x,
*) now also works for long vectors. • tools::texi2dvi() has a workaround for problems with the texi2dvi script supplied by texinfo 6.1. It extracts more error messages from the LaTeX logs when in emulation mode. UTILITIES: • R CMD check will leave a log file build_vignettes.log from the re-building of vignettes in the .Rcheck directory if there is a problem, and always if environment variable _R_CHECK_ALWAYS_LOG_VIGNETTE_OUTPUT_ is set to a true value. DEPRECATED AND DEFUNCT: • Use of SUPPORT_OPENMP from header Rconfig.h is deprecated in favour of the standard OpenMP define _OPENMP. (This has been the recommendation in the manual for a while now.) • The make macro AWK which is long unused by R itself but recorded in file etc/Makeconf is deprecated and will be removed in R 3.3.0. • The C header file S.h is no longer documented: its use should be replaced by R.h.
* Mon Mar 07 2016 detlef.steuerAATTgmx.de- The big split up. What was a monolithic R-base
*rpm now is divided over 30 something packages, with the following layout. R-base-3.2.3: dummy packages, contains all of R Use R-base, if you don´t have a good understandig what it means to install only parts of it! R-base-devel-3.2.3: dummy, contains R-core-devel R-core-3.2.3: R core, no packages at all R-core-devel-3.2.3: devel files R-core-libs-3.2.3: contains Rlib R-core-doc-3.2.3: all the documentation of R-core R-core-packages-3.2.3: dummy package to load all core packages, that are R-compiler-3.2.3, R-datasets-3.2.3, R-grDevices-3.2.3, R-graphics-3.2.3, R-grid-3.2.3, R-methods-3.2.3, R-parallel-3.2.3, R-splines-3.2.3, R-stats-3.2.3, R-stats4-3.2.3, R-tcltk-3.2.3, R-tools-3.2.3, R-utils-3.2.3. Each of these packages may be installed alone. R-recommended-packages-3.2.3: dummy package to load all recommeded packages, that are R-boot-1.3.17, R-class-7.3.14, R-cluster-2.0.3, R-codetools-0.2.14, R-foreign-0.8.66, R-KernSmooth-2.23.15, R-lattice-0.20.33, R-MASS-7.3.45, R-Matrix-1.2.3, R-Matrix-devel-1.2.3, R-mgcv-1.8.9, R-nlme-3.1.122, R-nnet-7.3.11, R-rpart-4.1.10, R-spatial-7.3.11, R-survival-2.38.3. Each of these packages may be installed alone.
* Fri Dec 11 2015 detlef.steuerAATTgmx.de- Upstream release R-3.2.3 CHANGES IN R 3.2.3: NEW FEATURES:
* Some recently-added Windows time zone names have been added to the conversion table used to convert these to Olson names. (Including those relating to changes for Russia in Oct 2014, as in PR#16503.)
* (Windows) Compatibility information has been added to the manifests for Rgui.exe, Rterm.exe and Rscript.exe. This should allow win.version() and Sys.info() to report the actual Windows version up to Windows 10.
* Windows \"wininet\" FTP first tries EPSV / PASV mode rather than only using active mode (reported by Dan Tenenbaum).
* which.min(x) and which.max(x) may be much faster for logical and integer x and now also work for long vectors.
* The \'emulation\' part of tools::texi2dvi() has been somewhat enhanced, including supporting quiet = TRUE. It can be selected by texi2dvi = \"emulation\". (Windows) MiKTeX removed its texi2dvi.exe command in Sept 2015: tools::texi2dvi() tries texify.exe if it is not found.
* (Windows only) Shortcuts for printing and saving have been added to menus in Rgui.exe. (Request of PR#16572.)
* loess(..., iterTrace=TRUE) now provides diagnostics for robustness iterations, and the print() method for summary() shows slightly more.
* The included version of PCRE has been updated to 8.38, a bug-fix release.
* View() now displays nested data frames in a more friendly way. (Request with patch in PR#15915.) INSTALLATION and INCLUDED SOFTWARE:
* The included configuration code for libintl has been updated to that from gettext version 0.19.5.1 - this should only affect how an external library is detected (and the only known instance is under OpenBSD). (Wish of PR#16464.)
* configure has a new argument --disable-java to disable the checks for Java.
* The configure default for MAIN_LDFLAGS has been changed for the FreeBSD, NetBSD and Hurd OSes to one more likely to work with compilers other than gcc (FreeBSD 10 defaults to clang).
* configure now supports the OpenMP flags -fopenmp=libomp (clang) and -qopenmp (Intel C).
* Various macros can be set to override the default behaviour of configure when detecting OpenMP: see file config.site.
* Source installation on Windows has been modified to allow for MiKTeX installations without texi2dvi.exe. See file MkRules.dist. BUG FIXES:
* regexpr(pat, x, perl = TRUE) with Python-style named capture did not work correctly when x contained NA strings. (PR#16484)
* The description of dataset ToothGrowth has been improved/corrected. (PR#15953)
* model.tables(type = \"means\") and hence TukeyHSD() now support \"aov\" fits without an intercept term. (PR#16437)
* close() now reports the status of a pipe() connection opened with an explicit open argument. (PR#16481)
* Coercing a list without names to a data frame is faster if the elements are very long. (PR#16467)
* (Unix-only) Under some rare circumstances piping the output from Rscript or R -f could result in attempting to close the input file twice, possibly crashing the process. (PR#16500)
* (Windows) Sys.info() was out of step with win.version() and did not report Windows 8.
* topenv(baseenv()) returns baseenv() again as in R 3.1.0 and earlier. This also fixes compilerJIT(3) when used in .Rprofile.
* detach()ing the methods package keeps .isMethodsDispatchOn() true, as long as the methods namespace is not unloaded.
* Removed some spurious warnings from configure about the preprocessor not finding header files. (PR#15989)
* rchisq(
*, df=0, ncp=0) now returns 0 instead of NaN, and dchisq(
*, df=0, ncp=
*) also no longer returns NaN in limit cases (where the limit is unique). (PR#16521)
* pchisq(
*, df=0, ncp > 0, log.p=TRUE) no longer underflows (for ncp > ~60).
* nchar(x, \"w\") returned -1 for characters it did not know about (e.g. zero-width spaces): it now assumes 1. It now knows about most zero-width characters and a few more double-width characters.
* Help for which.min() is now more precise about behavior with logical arguments. (PR#16532)
* The print width of character strings marked as \"latin1\" or \"bytes\" was in some cases computed incorrectly.
* abbreviate() did not give names to the return value if minlength was zero, unlike when it was positive.
* (Windows only) dir.create() did not always warn when it failed to create a directory. (PR#16537)
* When operating in a non-UTF-8 multibyte locale (e.g. an East Asian locale on Windows), grep() and related functions did not handle UTF-8 strings properly. (PR#16264)
* read.dcf() sometimes misread lines longer than 8191 characters. (Reported by Herv\'e Pag`es with a patch.)
* within(df, ..) no longer drops columns whose name start with a \".\".
* The built-in HTTP server converted entire Content-Type to lowercase including parameters which can cause issues for multi-part form boundaries (PR#16541).
* Modifying slots of S4 objects could fail when the methods package was not attached. (PR#16545)
* splineDesign(
*, outer.ok=TRUE) (splines) is better now (PR#16549), and interpSpline() now allows sparse=TRUE for speedup with non-small sizes.
* If the expression in the traceback was too long, traceback() did not report the source line number. (Patch by Kirill M\"uller.)
* The browser did not truncate the display of the function when exiting with options(\"deparse.max.lines\") set. (PR#16581)
* When bs(
*, Boundary.knots=) had boundary knots inside the data range, extrapolation was somewhat off. (Patch by Trevor Hastie.)
* var() and hence sd() warn about factor arguments which are deprecated now. (PR#16564)
* loess(
*, weights =
*) stored wrong weights and hence gave slightly wrong predictions for newdata. (PR#16587)
* aperm(a,
*) now preserves names(dim(a)).
* poly(x, ..) now works when either raw=TRUE or coef is specified. (PR#16597)
* data(package=
*) is more careful in determining the path.
* prettyNum(
*, decimal.mark, big.mark): fixed bug introduced when fixing PR#16411.
* Thu Dec 10 2015 detlef.steuerAATTgmx.de- Reverse the whole split. Back to the big package. Had user reports of broken installations. R-base, R-base-devel and R-base-libs are provided for now. The big split will come for 3.3.0
* Wed Dec 09 2015 detlef.steuerAATTgmx.de- R-base was changed from a giant monolith to thirty-some packages. There were requests to use the libs without the interpreter. Furthermore it is now possible to use a frugal installation of R. The following binaries are built now: R-base-3.2.2-5.1.x86_64.rpm : A Meta-package. Use this, and it looks just like it looked the last 10 years. Requires base and recommended packages. R-base-devel-3.2.2-5.1.x86_64.rpm: Just for backward compatibility. R-core-3.2.2-5.1.x86_64.rpm R-core-libs-3.2.2-5.1.x86_64.rpm R-core-devel-3.2.2-5.1.x86_64.rpm : The R-core packages install a bare-bones R. No packages inculded. R-grid-3.2.2-5.1.x86_64.rpm R-graphics-3.2.2-5.1.x86_64.rpm R-grDevices-3.2.2-5.1.x86_64.rpm R-datasets-3.2.2-5.1.x86_64.rpm R-stats4-3.2.2-5.1.x86_64.rpm R-methods-3.2.2-5.1.x86_64.rpm R-tcltk-3.2.2-5.1.x86_64.rpm R-compiler-3.2.2-5.1.x86_64.rpm R-parallel-3.2.2-5.1.x86_64.rpm R-splines-3.2.2-5.1.x86_64.rpm R-stats-3.2.2-5.1.x86_64.rpm R-utils-3.2.2-5.1.x86_64.rpm R-tools-3.2.2-5.1.x86_64.rpm : All the base packages. R-recommended-3.2.2-5.1.x86_64.rpm : A meta-package including all recommended packages. R-cluster-2.0.3-5.1.x86_64.rpm R-nlme-3.1.121-5.1.x86_64.rpm R-lattice-0.20.33-5.1.x86_64.rpm R-class-7.3.13-5.1.x86_64.rpm R-Matrix-devel-1.2.2-5.1.x86_64.rpm R-codetools-0.2.14-5.1.x86_64.rpm R-survival-2.38.3-5.1.x86_64.rpm R-rpart-4.1.10-5.1.x86_64.rpm R-MASS-7.3.43-5.1.x86_64.rpm R-mgcv-1.8.7-5.1.x86_64.rpm R-foreign-0.8.65-5.1.x86_64.rpm R-nnet-7.3.10-5.1.x86_64.rpm R-Matrix-1.2.2-5.1.x86_64.rpm R-boot-1.3.17-5.1.x86_64.rpm R-KernSmooth-2.23.15-5.1.x86_64.rpm R-spatial-7.3.10-5.1.x86_64.rpm : All recommended packaged. Note: They now have their own version numbers, so it should be much easier to use newer Versions of the recommended packages. And the source RPM for all the above. R-base-3.2.2-5.1.src.rpm
* Wed Aug 19 2015 badshah400AATTgmail.com- Disable building man files for openSUSE:42.
* Mon Aug 17 2015 detlef.steuerAATTgmx.de- Upstream release 3.2.2- Most important CHANGES IN R 3.2.2: SIGNIFICANT USER-VISIBLE CHANGES:
* It is now easier to use secure downloads from https:// URLs on builds which support them: no longer do non-default options need to be selected to do so. In particular, packages can be installed from repositories which offer https:// URLs, and those listed by setRepositories() now do so (for some of their mirrors). Support for https:// URLs is available on Windows, and on other platforms if support for libcurl was compiled in and if that supports the https protocol (system installations can be expected to do). So https:// support can be expected except on rather old OSes (an example being OS X \'Snow Leopard\', where a non-system version of libcurl can be used). (Windows only) The default method for accessing URLs _via_ download.file() and url() has been changed to be \"wininet\" using Windows API calls. This changes the way proxies need to be set and security settings made: there have been some reports of sites being inaccessible under the new default method (but the previous methods remain available). NEW FEATURES:
* cmdscale() gets new option list. for increased flexibility when a list should be returned.
* configure now supports texinfo version 6.0, which (unlike the change from 4.x to 5.0) is a minor update. (Wish of PR#16456.)
* (Non-Windows only) download.file() with default method = \"auto\" now chooses \"libcurl\" if that is available and a https:// or ftps:// URL is used.
* (Windows only) setInternet2(TRUE) is now the default. The command-line option --internet2 and environment variable R_WIN_INTERNET2 are now ignored. Thus by default the \"internal\" method for download.file() and url() uses the \"wininet\" method: to revert to the previous default use setInternet2(FALSE). This means that https:// can be read by default by download.file() (they have been readable by file() and url() since R 3.2.0). There are implications for how proxies need to be set (see ?download.file): also, cacheOK = FALSE is not supported.
* chooseCRANmirror() and chooseBioCmirror() now offer HTTPS mirrors in preference to HTTP mirrors. This changes the interpretation of their ind arguments: see their help pages.
* capture.output() gets optional arguments type and split to pass to sink(), and hence can be used to capture messages. C-LEVEL FACILITIES:
* Header Rconfig.h now defines HAVE_ALLOCA_H if the platform has the alloca.h header (it is needed to define alloca on Solaris and AIX, at least: see \'Writing R Extensions\' for how to use it). INSTALLATION and INCLUDED SOFTWARE:
* The libtool script generated by configure has been modified to support FreeBSD >= 10 (PR#16410). BUG FIXES:
* The HTML help page links to demo code failed due to a change in R 3.2.0. (PR#16432)
* If the na.action argument was used in model.frame(), the original data could be modified. (PR#16436)
* getGraphicsEvent() could cause a crash if a graphics window was closed while it was in use. (PR#16438)
* matrix(x, nr, nc, byrow = TRUE) failed if x was an object of type \"expression\".
* strptime() could overflow the allocated storage on the C stack when the timezone had a non-standard format much longer than the standard formats. (Part of PR#16328.)
* options(OutDec = s) now signals a warning (which will become an error in the future) when s is not a string with exactly one character, as that has been a documented requirement.
* prettyNum() gains a new option input.d.mark which together with other changes, e.g., the default for decimal.mark, fixes some format()ting variants with non-default getOption(\"OutDec\") such as in PR#16411.
* download.packages() failed for type equal to either \"both\" or \"binary\". (Reported by Dan Tenenbaum.)
* The dendrogram method of labels() is much more efficient for large dendrograms, now using rapply(). (Comment #15 of PR#15215)
* The \"port\" algorithm of nls() could give spurious errors. (Reported by Radford Neal.)
* Reference classes that inherited from reference classes in another package could invalidate methods of the inherited class. Fixing this requires adding the ability for methods to be \"external\", with the object supplied explicitly as the first argument, named .self. See \"Inter-Package Superclasses\" in the documentation.
* readBin() could fail on the SPARC architecture due to alignment issues. (Reported by Radford Neal.)
* qt(
*, df=Inf, ncp=.) now uses the natural qnorm() limit instead of returning NaN. (PR#16475)
* Auto-printing of S3 and S4 values now searches for print() in the base namespace and show() in the methods namespace instead of searching the global environment.
* polym() gains a coefs = NULL argument and returns class \"poly\" just like poly() which gets a new simple=FALSE option. They now lead to correct predict()ions, e.g., on subsets of the original data.
* rhyper(nn, ) now works correctly. (PR#16489)
* ttkimage() did not (and could not) work so was removed. Ditto for tkimage.cget() and tkimage.configure(). Added two Ttk widgets and missing subcommands for Tk\'s image command: ttkscale(), ttkspinbox(), tkimage.delete(), tkimage.height(), tkimage.inuse(), tkimage.type(), tkimage.types(), tkimage.width(). (PR#15372, PR#16450)
* getClass(\"foo\") now also returns a class definition when it is found in the cache more than once.
* Thu Jun 18 2015 detlef.steuerAATTgmx.de- Upstream release 3.2.1- Improvement of build: include libcurl and texlive-dvips/ texlive-hevetic- Most important CHANGES IN R 3.2.1: NEW FEATURES:
* utf8ToInt() now checks that its input is valid UTF-8 and returns NA if it is not.
* install.packages() now allows type = \"both\" with repos = NULL if it can infer the type of file.
* nchar(x,
*) and nzchar(x) gain a new argument keepNA which governs how the result for NAs in x is determined. For the R 3.2.x series, the default remains FALSE which is fully back compatible. From R 3.3.0, the default will change to keepNA = NA and you are advised to consider this for code portability.
* news() more flexibly extracts dates from package NEWS.Rd files.
* lengths(x) now also works (trivially) for atomic x and hence can be used more generally as an efficient replacement of sapply(x, length) and similar.
* The included version of PCRE has been updated to 8.37, a bug-fix release.
* diag() no longer duplicates a matrix when extracting its diagonal.
* as.character.srcref() gains an argument to allow characters corresponding to a range of source references to be extracted. BUG FIXES:
* acf() and ccf() now guarantee values strictly in [-1,1] (instead of sometimes very slightly outside). PR#15832.
* as.integer(\"111111111111\") now gives NA (with a warning) as it does for the corresponding numeric or negative number coercions. Further, as.integer(M + 0.1) now gives M (instead of NA) when M is the maximal representable integer.
* On some platforms nchar(x, \"c\") and nchar(x, \"w\") would return values (possibly NA) for inputs which were declared to be UTF-8 but were not, or for invalid strings without a marked encoding in a multi-byte locale, rather than give an error. Additional checks have been added to mitigate this.
* apply(a, M, function(u) c(X = ., Y = .)) again has dimnames containing \"X\" and \"Y\" (as in R < 3.2.0).
* (Windows only) In some cases, the --clean option to R CMD INSTALL could fail. (PR#16178)
* (Windows only) choose.files() would occasionally include characters from the result of an earlier call in the result of a later one. (PR#16270)
* A change in RSiteSearch() in R 3.2.0 caused it to submit invalid URLs. (PR#16329)
* Rscript and command line R silently ignored incomplete statements at the end of a script; now they are reported as parse errors. (PR#16350)
* Parse data for very long strings was not stored. (PR#16354)
* plotNode(), the workhorse of the plot method for \"dendrogram\"s is no longer recursive, thanks to Suharto Anggono, and hence also works for deeply nested dendrograms. (PR#15215)
* The parser could overflow internally when given numbers in scientific format with extremely large exponents. (PR#16358)
* If the CRAN mirror was not set, install.packages(type = \"both\") and related functions could repeatedly query the user for it. (Part of PR#16362)
* The low-level functions .rowSums() etc. did not check the length of their argument, so could segfault. (PR#16367)
* The quietly argument of library() is now correctly propagated from .getRequiredPackages2().
* Under some circumstances using the internal PCRE when building R fron source would cause external libs such as -llzma to be omitted from the main link.
* The .Primitive default methods of the logic operators, i.e., !, & and |, now give correct error messages when appropriate, e.g., for `&`(TRUE) or `!`(). (PR#16385)
* cummax(x) now correctly propagates NAs also when x is of type integer and begins with an NA.
* summaryRprof() could fail when the profile contained only two records. (PR#16395)
* HTML vignettes opened using vignette() did not support links into the rest of the HTML help system. (Links worked properly when the vignette was opened using browseVignettes() or from within the help system.)
* arima(
*, xreg = .) (for d >= 1) computes estimated variances based on a the number of effective observations as in R version 3.0.1 and earlier. (PR#16278)
* slotNames(.) is now correct for \"signature\" objects (mostly used internally in methods).
* On some systems, the first string comparison after a locale change would result in NA.
* Thu Apr 16 2015 detlef.steuerAATTgmx.de- Upstream release 3.2.0- Most important CHANGES IN 3.2.0: NEW FEATURES:
* anyNA() gains a recursive argument.
* When x is missing and names is not false (including the default value), Sys.getenv(x, names) returns an object of class \"Dlist\" and hence prints tidily.
* (Windows.) shell() no longer consults the environment variable SHELL: too many systems have been encountered where it was set incorrectly (usually to a path where software was compiled, not where it was installed). R_SHELL, the preferred way to select a non-default shell, can be used instead.
* Some unusual arguments to embedFonts() can now be specified as character vectors, and the defaults have been changed accordingly.
* Functions in the Summary group duplicate less. (PR#15798)
* (Unix-alikes.) system(cmd, input = ) now uses \'shell-execution-environment\' redirection, which will be more natural if cmd is not a single command (but requires a POSIX-compliant shell). (Wish of PR#15508)
* read.fwf() and read.DIF() gain a fileEncoding argument, for convenience.
* Graphics devices can add attributes to their description in .Device and .Devices. Several of those included with R use a \"filepath\" attribute.
* pmatch() uses hashing in more cases and so is faster at the expense of using more memory. (PR#15697)
* pairs() gains new arguments to select sets of variables to be plotted against each other.
* file.info(, extra_cols = FALSE) allows a minimal set of columns to be computed on Unix-alikes: on some systems without properly-configured caching this can be significantly faster with large file lists.
* New function dir.exists() in package base to test efficiently whether one or more paths exist and are directories.
* dput() and friends gain new controls hexNumeric and digits17 which output double and complex quantities as, respectively, binary fractions (exactly, see sprintf(\"%a\")) and as decimals with up to 17 significant digits.
* save(), saveRDS() and serialize() now support ascii = NA which writes ASCII files using sprintf(\"%a\") for double/complex quantities. This is read-compatible with ascii = TRUE but avoids binary->decimal->binary conversions with potential loss of precision. Unfortunately the Windows C runtime\'s lack of C99 compliance means that the format cannot be read correctly there in R before 3.1.2.
* The default for formatC(decimal.mark =) has been changed to be getOption(\"OutDec\"); this makes it more consistent with format() and suitable for use in print methods, e.g. those for classes \"density\", \"ecdf\", \"stepfun\" and \"summary.lm\". getOption(\"OutDec\") is now consulted by the print method for class \"kmeans\", by cut(), dendrogram(), plot.ts() and quantile() when constructing labels and for the report from legend(trace = TRUE). (In part, wish of PR#15819.)
* printNum() and hence format() and formatC() give a warning if big.mark and decimal.mark are set to the same value (period and comma are not uncommonly used for each, and this is a check that conventions have not got mixed).
* merge() can create a result which uses long vectors on 64-bit platforms.
* dget() gains a new argument keep.source which defaults to FALSE for speed (dput() and dget() are most often used for data objects where this can make dget() many times faster).
* Packages may now use a file of common macro definitions in their help files, and may import definitions from other packages.
* A number of macros have been added in the new share/Rd directory for use in package overview help pages, and promptPackage() now makes use of them.
* tools::parse_Rd() gains a new permissive argument which converts unrecognized macros into text. This is used by utils:::format.bibentry to allow LaTeX markup to be ignored.
* options(OutDec =) can now specify a multi-byte character, e.g., options(OutDec = \"\\u00b7\") in a UTF-8 locale.
* is.recursive(x) is no longer true when x is an external pointer, a weak reference or byte code; the first enables all.equal(x, x) when x <- getClass(.).
* ls() (aka objects()) and as.list.environment() gain a new argument sorted.
* The \"source\" attribute (which has not been added to functions by R since before R version 2.14.0) is no longer treated as special.
* Function returnValue() has been added to give on.exit() code access to a function\'s return value for debugging purposes.
* crossprod(x, y) allows more matrix coercions when x or y are vectors, now equalling t(x) %
*% y in these cases (also reported by Radford Neal). Similarly, tcrossprod(x,y) and %
*% work in more cases with vector arguments.
* Utility function dynGet() useful for detecting cycles, aka infinite recursions.
* The byte-code compiler and interpreter include new instructions that allow many scalar subsetting and assignment and scalar arithmetic operations to be handled more efficiently. This can result in significant performance improvements in scalar numerical code.
* apply(m, 2, identity) is now the same as the matrix m when it has _named_ row names.
* A new function debuggingState() has been added, allowing to temporarily turn off debugging.
* example() gets a new optional argument run.donttest and tools::Rd2ex() a corresponding commentDonttest, with a default such that example(..) in help examples will run \\donttest code only if used interactively (a change in behaviour).
* rbind.data.frame() gains an optional argument make.row.names, for potential speedup.
* New function extSoftVersion() to report on the versions of third-party software in use in this session. Currently reports versions of zlib, bzlib, the liblzma from xz, PCRE, ICU, TRE and the iconv implementation. A similar function grSoftVersion() in package grDevices reports on third-party graphics software. Function tcltk::tclVersion() reports the Tcl/Tk version.
* Calling callGeneric() without arguments now works with primitive generics to some extent.
* vapply(x, FUN, FUN.VALUE) is more efficient notably for large length(FUN.VALUE); as extension of PR#16061.
* as.table() now allows tables with one or more dimensions of length 0 (such as as.table(integer())).
* names(x) <- NULL now clears the names of call and ... objects.
* library() will report a warning when an insufficient dependency version is masking a sufficient one later on the library search path.
* A new plot() method for class \"raster\" has been added.
* New check_packages_in_dir_changes() function in package tools for conveniently analyzing how changing sources impacts the check results of their reverse dependencies.
* Speed-up from Peter Haverty for ls() and methods:::.requirePackage() speeding up package loading. (PR#16133)
* New get0() function, combining exists() and get() in one call, for efficiency.
* match.call() gains an envir argument for specifying the environment from which to retrieve the ... in the call, if any; this environment was wrong (or at least undesirable) when the definition argument was a function.
* topenv() has been made .Internal() for speedup, based on Peter Haverty\'s proposal in PR#16140.
* getOption() no longer calls options() in the main case.
* Optional use of libcurl (version 7.28.0 from Oct 2012 or later) for Internet access:
* capabilities(\"libcurl\") reports if this is available.
* libcurlVersion() reports the version in use, and other details of the \"libcurl\" build including which URL schemes it supports.
* curlGetHeaders() retrieves the headers for http://, https://, ftp:// and ftps:// URLs: analysis of these headers can provide insights into the `existence\' of a URL (it might for example be permanently redirected) and is so used in R CMD check --as-cran.
* download.file() has a new optional method \"libcurl\" which will handle more URL schemes, follow redirections, and allows simultaneous downloads of multiple URLs.
* url() has a new method \"libcurl\" which handles more URL schemes and follows redirections. The default method is controlled by a new option url.method, which applies also to the opening of URLs _via_ file() (which happens implicitly in functions such as read.table.)
* When file() or url() is invoked with a https:// or ftps:// URL which the current method cannot handle, it switches to a suitable method if one is available.
* (Windows.) The DLLs internet.dll and internet2.dll have been merged. In this version it is safe to switch (repeatedly) between the internal and Windows internet functions within an R session. The Windows internet functions are still selected by flag - -internet2 or setInternet2(). This can be overridden for an url() connection _via_ its new method argument. download.file() has new method \"wininet\", selected as the default by --internet2 or setInternet2().
* parent.env<- can no longer modify the parent of a locked namespace or namespace imports environment. Contributed by Karl Millar.
* New function isLoadedNamespace() for readability and speed.
* names(env) now returns all the object names of an environment env, equivalently to ls(env, all.names = TRUE, sorted = FALSE) and also to the names of the corresponding list, names(as.list(env, all.names = TRUE)). Note that although names() returns a character vector, the names have no particular ordering.
* The memory manager now grows the heap more aggressively. This reduces the number of garbage collections, in particular while data or code are loaded, at the expense of slightly increasing the memory footprint.
* New function trimws() for removing leading/trailing whitespace.
* cbind() and rbind() now consider S4 inheritance during S3 dispatch and also obey deparse.level.
* cbind() and rbind() will delegate recursively to methods::cbind2 (methods::rbind2) when at least one argument is an S4 object and S3 dispatch fails (due to ambiguity).
* (Windows.) download.file(quiet = FALSE) now uses text rather than Windows progress bars in non-interactive use.
* New function hsearch_db() in package utils for building and retrieving the help search database used by help.search(), along with functions for inspecting the concepts and keywords in the help search database.
* New function .getNamespaceInfo(), a no-check version of getNamespaceInfo() mostly for internal speedups.
* The help search system now takes \\keyword entries in Rd files which are not standard keywords (as given in KEYWORDS in the R documentation directory) as concepts. For standard keyword entries the corresponding descriptions are additionally taken as concepts.
* New lengths() function for getting the lengths of all elements in a list.
* New function toTitleCase() in package tools, tailored to package titles.
* The matrix methods of cbind() and rbind() allow matrices as inputs which have 2^31 or more elements. (For cbind(), wish of PR#16198.)
* The default method of image() has an explicit check for a numeric or logical matrix (which was always required).
* URLencode() will not by default encode further URLs which appear to be already encoded.
* BIC(mod) and BIC(mod, mod2) now give non-NA numbers for arima() fitted models, as nobs(mod) now gives the number of \"used\" observations for such models. This fixes PR#16198, quite differently than proposed there.
* The print() methods for \"htest\", \"pairwise.htest\" and \"power.htest\" objects now have a digits argument defaulting to (a function of) getOption(\"digits\"), and influencing all printed numbers coherently. Unavoidably, this changes the display of such test results in some cases.
* Code completion for namespaces now recognizes all loaded namespaces, rather than only the ones that are also attached.
* The code completion mechanism can now be replaced by a user-specified completer function, for (temporary) situations where the usual code completion is inappropriate.
* unzip() will now warn if it is able to detect truncation when unpacking a file of 4GB or more (related to PR#16243).
* methods() reports S4 in addition to S3 methods; output is simplified when the class argument is used. .S3methods() and methods::.S4methods() report S3 and S4 methods separately.
* Higher order functions such as the apply functions and Reduce() now force arguments to the functions they apply in order to eliminate undesirable interactions between lazy evaluation and variable capture in closures. This resolves PR#16093. INSTALLATION and INCLUDED SOFTWARE:
* The \\donttest sections of R\'s help files can be tested by make check TEST_DONTTEST=TRUE .
* It is possible to request the use of system valgrind headers _via_ configure option --with-system-valgrind-headers: note the possible future incompatibility of such headers discussed in the \'R Installation and Administration\' manual. (Wish of PR#16068.)
* The included version of liblzma has been updated to xz-utils 5.0.7 (minor bug fixes from 5.0.5).
* configure options --with-system-zlib, --with-system-bzlib and - -with-system-pcre are now the default. For the time being there is fallback to the versions included in the R sources if no system versions are found or (unlikely) if they are too old. Linux users should check that the -devel or -dev versions of packages zlib, bzip2/libbz2 and pcre as well as xz-devel/liblzma-dev (or similar names) are installed.
* configure by default looks for the texi2any script from texinfo 5.1 or later, rather than the makeinfo program. (makeinfo is a link to the Perl script texi2any in texinfo 5.x.)
* R CMD INSTALL gains an option --built-timestamp=STAMP allowing 100% reproducible package building, thanks to Dirk Eddelbuettel. UTILITIES:
* There is support for testing the \\dontrun and \\donttest parts of examples in packages. tools::testInstalledPackage() accepts new arguments commentDontrun = FALSE and commentDonttest = FALSE. R CMD check gains options --run-dontrun and --run-donttest.
* The HTML generated by tools::Rd2HTML() and tools::toHTML() methods is now \'XHTML 1.0 Strict\'.
* The compiler package\'s utility function setCompilerOptions() now returns the old values invisibly. The initial optimization level can also be set with the environment variable R_COMPILER_OPTIMIZE.
* R CMD build adds a NeedsCompilation field if one is not already present in the DESCRIPTION file.
* R CMD check gains option --test-dir to specify an alternative set of tests to run.
* R CMD check will now by default continue with testing after many types of errors, and will output a summary count of errors at the end if any have occurred.
* R CMD check now checks that the Title and Description fields are correctly terminated.
* R CMD check --as-cran now:
* checks a README.md file can be processed: this needs pandoc installed.
* checks the existence and accessibility of URLs in the DESCRIPTION, CITATION, NEWS.Rd and README.md files and in the help files (provided the build has libcurl support).
* reports non-ASCII characters in R source files when there is no package encoding declared in the DESCRIPTION file.
* reports (apparent) S3 methods exported but not registered.
* reports overwriting registered S3 methods from base/recommended packages. (Such methods are replaced in the affected package for the rest of the session, even if the replacing namespace is unloaded.)
* reports if the Title field does not appear to be in title case (see \'Writing R Extensions\': there may be false positives, but note that technical words should be single-quoted and will then be accepted). Most of these checks can also be selected by environment variables: see the \'R Internals\' manual. C-LEVEL FACILITIES:
* New C API utility logspace_sum(logx[], n).
* Entry points rbinom_mu, rnbinom_mu and rmultinom are remapped (by default) to Rf_rbinom_mu etc. This requires packages using them to be re-installed.
* .C(DUP = FALSE) and .Fortran(DUP = FALSE) are now ignored, so arguments are duplicated if DUP = TRUE would do so. As their help has long said, .Call() is much preferred.
* New entry point R_allocLD, like R_alloc but guaranteed to have sufficient alignment for long double pointers.
* isPairList() now returns TRUE for DOTSXP. WINDOWS BUILD CHANGES: A number of changes to the Windows build system are in development. The following are currently in place.
* Installation using external binary distributions of zlib, bzip2, liblzma, pcre, libpng, jpeglib and libtiff is now required, and the build instructions have been revised.
* A new make target rsync-extsoft has been added to obtain copies of the external libraries from CRAN.
* Building the manuals now requires texi2any from texinfo 5.1 or later. CRAN binary builds include the manuals, but by default builds from source will not, and they will be accessed from CRAN. See the comments in src/gnuwin32/MkRules.dist for how to specify the location of texi2any.
* (Windows) Changes have been made to support an experimental Windows toolchain based on GCC 4.9.2. The default toolchain continues to be based on GCC 4.6.3, as the new toolchain is not yet stable enough. A change to a new toolchain is expected during the R 3.2.x lifetime. PACKAGE INSTALLATION:
* (Windows) The use of macro ZLIB_LIBS in file src/Makevars.win (which has not been documented for a long time) now requires an external libz.a to be available (it is part of the \'goodies\' used to compile Windows binary packages). It would be simpler to use - lz instead.
* The default for option pkgType on platforms using binary packages is now \"both\", so source packages will be tried if binary versions are not available or not up to date. There are options for what install.packages(type = \"both\") (possibly called _via_ update.packages()) will do if compilation of a source package is desirable: see ?options (under utils). If you intend not to accept updates as source packages, you should use update.packages(type = \"binary\"). DEPRECATED AND DEFUNCT:
* download.file(method = \"lynx\") is defunct.
* Building R using the included versions of zlib, bzip2, xz and PCRE is deprecated: these are frozen (bar essential bug-fixes) and will be removed for R 3.3.0.
* The configure option --with-valgrind-instrumentation=3 has been withdrawn, as it did not work with recent valgrind headers: it is now treated as level 2.
* The MethodsList class in package methods had been deprecated in R 2.11.0 and is defunct now. Functions using it are defunct if they had been deprecated in R 2.11.0, and are deprecated now, otherwise. BUG FIXES:
* Fixed two obscure bugs in pairlist subassignment, reported by Radford Neal as part of pqR issue 16.
* Fixes for bugs in handling empty arguments and argument matching by name in log().
* all.equal() gains methods for environments and refClasses.
* [<- and [[<- gain S4 data.frame methods to avoid corruption of S4 class information by the S3 methods.
* callNextMethod() should now work within a .local call when ... is absent from formals(.local).
* dput(pairlist(x)) generates a call to the pairlist constructor instead of the list constructor.
* Fix missing() when arguments are propagated through ... . (PR#15707)
* eigen(m) now defaults to symmetric = TRUE even when the dimnames are asymmetric if the matrix is otherwise symmetric. (PR#16151)
* Fix issues with forwarding ... through callGeneric() and callNextMethod(). (PR#16141)
* callGeneric() now works after a callNextMethod().
* Subclass information is kept consistent when replacing an ordinary S4 class with an \"old class\" _via_ the S4Class argument to setOldClass(). Thus, for example, a data.frame is valid for a list argument in the signature, and a factor is valid for vector arguments.
* In qbeta() the inversion of pbeta() is much more sophisticated. This works better in corner cases some of which failed completely previously (PR#15755), or were using too many iterations.
* Auto-printing no longer duplicates objects when printing is dispatched to a method.
* kmeans(x, k) would fail when nrow(x) >= 42949673. (Comment 6 of PR#15364)
* \'Abbreviated\' locale-specific day and month names could have been truncated in those rare locales where there are the same as the full names.
* An irrelevant warning message from updating subclass information was silenced (the namespace would not be writable in this case).
* Mon Mar 09 2015 detlef.steuerAATTgmx.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 2014 sbahlingAATTsuse.com- Remove tex(inconsolata.sty) BuildRequires for SLE_12 builds (like older SLE releases).
* Fri Oct 31 2014 detlef.steuerAATTgmx.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, , 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(, ..) 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\")AATTprototype 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 2014 detlef.steuerAATTgmx.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 = , 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 2014 darinAATTdarins.net- added parallel provides
* Fri May 09 2014 detlef.steuerAATTgmx.de- Removed / commented out symlink to %{_bindir}/r new package \'littler\' should be used instead for packages that need /usr/bin/r
* Thu May 01 2014 darinAATTdarins.net- Add make dependency for Rcmd
* Tue Apr 29 2014 darinAATTdarins.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 2014 detlef.steuerAATTgmx.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 06 2014 detlef.steuerAATTgmx.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 .
* 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 2013 detlef.steuerAATTgmx.de- Removed outdated source file
* Wed Sep 25 2013 detlef.steuerAATTgmx.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 2013 schwabAATTsuse.de- tre.patch: Fix tre library for aarch64 where wchar_t is unsigned int
* Thu May 16 2013 detlef.steuerAATTgmx.de- Improved spec file: R-base-devel requires R-base
* Thu May 16 2013 detlef.steuerAATTgmx.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 2013 detlef.steuerAATTgmx.de- R-base.spec improved: now uses R-%{version}.tar.bz2 explicitly. Mistake when version bumping to 3.0.0 corrected
* Wed Apr 03 2013 detlef.steuerAATTgmx.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 2013 schwabAATTsuse.de- Override LIBnn from %{_lib}
* Fri Mar 01 2013 detlef.steuerAATTgmx.de- There were a few new files in foreign and rpart. Fixed now. Builds fine.
* Fri Mar 01 2013 detlef.steuerAATTgmx.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 2012 detlef.steuerAATTgmx.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 2012 wernerAATTsuse.de- Make it build with latest TeXLive 2012 with new package layout
* Fri Jun 22 2012 detlef.steuerAATTgmx.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 2012 detlef.steuerAATTgmx.de- one more forgotten file in polish translation ...
* Fri Jun 22 2012 detlef.steuerAATTgmx.de- spec file update to incorporate new polish translation
* Fri Jun 22 2012 detlef.steuerAATTgmx.de- Upstream bugfix only release 2.15.1- see, as usual, /usr/lib/R/doc/NEWS.html
* Tue Apr 10 2012 gregkhAATTopensuse.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 2012 detlef.steuerAATTgmx.de- Upstream updated to 2.15.0- see, as usual, /usr/lib/R/doc/NEWS.html
* Wed Feb 29 2012 detlef.steuerAATTgmx.de- upstream minor version increase to 2.14.2- see, as usual, /usr/lib/R/doc/NEWS.html for details.
* Fri Feb 17 2012 detlef.steuerAATTgmx.de- Minor cleanup for easier automativ building of R-patched.spec
* Wed Feb 15 2012 detlef.steuerAATTgmx.de- changed licence string to \"GPL-2.0 or GPL-3.0\"
* Mon Feb 13 2012 detlef.steuerAATTgmx.de- uninstall rule for R.conf more than useless ... reverted.
* Mon Feb 13 2012 detlef.steuerAATTgmx.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 einarAATTheavensinferno.net for spotting this.- Thought had done this for release of 2.14.0.
* Thu Dec 22 2011 steuerAATTunibw-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 2011 detlef.steuerAATTgmx.de- merged change infor Oct 5th into working copy
* Mon Oct 31 2011 detlef.steuerAATTgmx.de- corrected subpackge version number in R-base-devel
* Mon Oct 31 2011 detlef.steuerAATTgmx.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 05 2011 detlef.steuerAATTgmx.de- corrected version string for Matrix subpackage
* Tue Oct 04 2011 detlef.steuerAATTgmx.de- removed 4 warnings about unescaped macros in comments
* Tue Oct 04 2011 detlef.steuerAATTgmx.de- explicitly added some locale directories. Worked before implicitly.
* Tue Oct 04 2011 detlef.steuerAATTgmx.de- update to upstream version 2.13.2- see, as usual, /usr/lib/R/doc/NEWS.html for details.
* Sat Sep 17 2011 jengelhAATTmedozas.de- Remove redundant tags/sections from specfile- Use %_smp_mflags for parallel build
* Fri Jul 08 2011 detlef.steuerAATTgmx.de- resolved some conflicts for R-base.spec after osc up -e && osc pull
* Fri Jul 08 2011 detlef.steuerAATTgmx.de- corrected version string in R-base.spec
* Fri Jul 08 2011 detlef.steuerAATTgmx.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 2011 detlef.steuerAATTgmx.de- Removed possible dangerous links of libraries. R`s internal libraries now are only available in $lib/R/lib .
* Fri May 06 2011 detlef.steuerAATTgmx.de- Changed Licence string to GPLv2, taken from opensuse`s list aof allowed licences, as requested from coolo
* Wed Apr 13 2011 detlef.steuerAATTgmx.de- Upstream update to 2.13.0; new package \'compiler\'; some new language files
* Fri Mar 04 2011 detlef.steuerAATTgmx.de- update to 2.12.2 minor bugfixes see /usr/lib/R/doc/html/NEWS.html for details
* Mon Jan 10 2011 detlef.steuerAATTgmx.de- removed -n parameter from %build/%install- removed %doc from man/info pages in files section
* Fri Dec 17 2010 detlef.steuerAATTgmx.dereverting mandir/infodir directiven, didn\'t build in some releases-
* Fri Dec 17 2010 detlef.steuerAATTgmx.desorted out list of problems shown bei mrueckert-
* Mon Nov 29 2010 detlef.steuerAATTgmx.deVersion, to be submitted to factory-