R-stats4-3.5.0-lp151.6.53 >  A \G/=„2e2zvAt l2Z' h3_ϵgDf'B043u%*g[jST Pl+$haUyMTw*q%gW _%̎^%؞_ne28 e>N;=T~i6m9!Bw7c+FAd͖XV c}ɂ4 >لk]nh!Tn$adb9a97a7fe0c02386a78ea9811a448cd7b5adcbed09fed376f9ada88617f6046ed1eedbd986d178ef50bc55eca8d2c21756cc90ԉ\G/=„4];"<&<ѠaDaMB H#aQ?Z1J h@zpC>, NffY>zdʮAp?i"{ 0ja%C{rN崽 0o]e(P^ԭ8_fmi (;H5pEMEFёwȐm,_{W}s՚uAhnZjl?W8PBޚMF+SeG>p;@?@d   7pt|  $$ $ 8$ $  $  h$ $ $ ` $  , @ ( 8 )9x):)F7G7$H8d$I8$X98Y9@\9d$]9$^;]b>xc?!d?~e?f?l?u?$v@,z@\@l@p@v@CR-stats43.5.0lp151.6.53Package providing R-stats4This package provides R-stats4, one of R-core packages.\ʮlamb07openSUSE Leap 15.1openSUSEGPL-2.0-only OR GPL-3.0-onlyhttps://bugs.opensuse.orgDevelopment/Libraries/Otherhttp://www.r-project.org/linuxx86_64Z"6,D,`]wisJA큤A큤AA큤A큤\ʗ\ʗ\ʗ\ʠ\ʗ\ʠ\ʗ\ʗ\ʗ\ʗ\ʗ\ʠ\ʠ\ʗ\ʗ\ʗ\ʗ\ʗ\ʗ\ʗ\ʗ\ʠ\ʗ\ʠ\ʗ\ʗ\ʗ\ʗ\ʗ\ʗ\ʗ\ʗ\ʗ\ʗ\ʗ\ʗ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../../KernSmooth/Meta/features.rds../../KernSmooth/R/KernSmooth../../../doc/html/R.cssrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootR-base-3.5.0-lp151.6.53.src.rpmR-stats4R-stats4(x86-64)    R-baserpmlib(CompressedFileNames)rpmlib(FileDigests)rpmlib(PayloadFilesHavePrefix)rpmlib(PayloadIsXz)3.5.03.0.4-14.6.0-14.0-15.2-14.14.1ZZZZ`@ZkZY5YyYV=@X@XXXXXO@X2@Wv[@Wi,@W n. The "quoteExpressions" option, also part of "all", no longer quote()s formulas as that may not re-parse identically. (PR#17378) * If the option setWidthOnResize is set and TRUE, R run in a terminal using a recent readline library will set the width option when the terminal is resized. Suggested by Ralf Goertz. * If multiple on.exit() expressions are set using add = TRUE then all expressions will now be run even if one signals an error. * mclapply() gets an option affinity.list which allows more efficient execution with heterogeneous processors, thanks to Helena Kotthaus. * The character methods for as.Date() and as.POSIXlt() are more flexible _via_ new arguments tryFormats and optional: see their help pages. * on.exit() gains an optional argument after with default TRUE. Using after = FALSE with add = TRUE adds an exit expression before any existing ones. This way the expressions are run in a first-in last-out fashion. (From Lionel Henry.) * On Windows, file.rename() internally retries the operation in case of error to attempt to recover from possible anti-virus interference. * Command line completion on :: now also includes lazy-loaded data. * If the TZ environment variable is set when date-time functions are first used, it is recorded as the session default and so will be used rather than the default deduced from the OS if TZ is subsequently unset. * There is now a [ method for class "DLLInfoList". * glm() and glm.fit get the same singular.ok = TRUE argument that lm() has had forever. As a consequence, in glm(*, method = ), user specified methods need to accept a singular.ok argument as well. * aspell() gains a filter for Markdown (.md and .Rmd) files. * intToUtf8(multiple = FALSE) gains an argument to allow surrogate pairs to be interpreted. * The maximum number of DLLs that can be loaded into R e.g. _via_ dyn.load() has been increased up to 614 when the OS limit on the number of open files allows. * Sys.timezone() on a Unix-alike caches the value at first use in a session: _inter alia_ this means that setting TZ later in the session affects only the _current_ time zone and not the _system_ one. Sys.timezone() is now used to find the system timezone to pass to the code used when R is configured with --with-internal-tzcode. * When tar() is used with an external command which is detected to be GNU tar or libarchive tar (aka bsdtar), a different command-line is generated to circumvent line-length limits in the shell. * system(*, intern = FALSE), system2() (when not capturing output), file.edit() and file.show() now issue a warning when the external command cannot be executed. * The "default" ("lm" etc) methods of vcov() have gained new optional argument complete = TRUE which makes the vcov() methods more consistent with the coef() methods in the case of singular designs. The former (back-compatible) behavior is given by vcov(*, complete = FALSE). * coef() methods (for lm etc) also gain a complete = TRUE optional argument for consistency with vcov(). For "aov", both coef() and vcov() methods remain back-compatibly consistent, using the _other_ default, complete = FALSE. * attach(*, pos = 1) is now an error instead of a warning. * New function getDefaultCluster() in package parallel to get the default cluster set via setDefaultCluster(). * str(x) for atomic objects x now treats both cases of is.vector(x) similarly, and hence much less often prints "atomic". This is a slight non-back-compatible change producing typically both more informative and shorter output. * write.dcf() gets optional argument useBytes. * New, partly experimental packageDate() which tries to get a valid "Date" object from a package DESCRIPTION file, thanks to suggestions in PR#17324. * tools::resaveRdaFiles() gains a version argument, for use when packages should remain compatible with earlier versions of R. * ar.yw(x) and hence by default ar(x) now work when x has NAs, mostly thanks to a patch by Pavel Krivitsky in PR#17366. The ar.yw.default()'s AIC computations have become more efficient by using determinant(). * New warnErrList() utility (from package nlme, improved). * By default the (arbitrary) signs of the loadings from princomp() are chosen so the first element is non-negative. * If --default-packages is not used, then Rscript now checks the environment variable R_SCRIPT_DEFAULT_PACKAGES. If this is set, then it takes precedence over R_DEFAULT_PACKAGES. If default packages are not specified on the command line or by one of these environment variables, then Rscript now uses the same default packages as R. For now, the previous behavior of not including methods can be restored by setting the environment variable R_SCRIPT_LEGACY to yes. * When a package is found more than once, the warning from find.package(*, verbose=TRUE) lists all library locations. * POSIXt objects can now also be rounded or truncated to month or year. * stopifnot() can be used alternatively via new argument exprs which is nicer and useful when testing several expressions in one call. * The environment variable R_MAX_VSIZE can now be used to specify the maximal vector heap size. On macOS, unless specified by this environment variable, the maximal vector heap size is set to the maximum of 16GB and the available physical memory. This is to avoid having the R process killed when macOS over-commits memory. * sum(x) and sum(x1,x2,..,x) with many or long logical or integer vectors no longer overflows (and returns NA with a warning), but returns double numbers in such cases. * Single components of "POSIXlt" objects can now be extracted and replaced via [ indexing with 2 indices. * S3 method lookup now searches the namespace registry after the top level environment of the calling environment. * Arithmetic sequences created by 1:n, seq_along, and the like now use compact internal representations via the ALTREP framework. Coercing integer and numeric vectors to character also now uses the ALTREP framework to defer the actual conversion until first use. * Finalizers are now run with interrupts suspended. * merge() gains new option no.dups and by default suffixes the second of two duplicated column names, thanks to a proposal by Scott Ritchie (and Gabe Becker). * scale.default(x, center, scale) now also allows center or scale to be "numeric-alike", i.e., such that as.numeric(.) coerces them correctly. This also eliminates a wrong error message in such cases. * par*apply and par*applyLB gain an optional argument chunk.size which allows to specify the granularity of scheduling. * Some as.data.frame() methods, notably the matrix one, are now more careful in not accepting duplicated or NA row names, and by default produce unique non-NA row names. This is based on new function .rowNamesDF(x, make.names = *) <- rNms where the logical argument make.names allows to specify _how_ invalid row names rNms are handled. .rowNamesDF() is a "workaround" compatible default. * R has new serialization format (version 3) which supports custom serialization of ALTREP framework objects. These objects can still be serialized in format 2, but less efficiently. Serialization format 3 also records the current native encoding of unflagged strings and converts them when de-serialized in R running under different native encoding. Format 3 comes with new serialization magic numbers (RDA3, RDB3, RDX3). Format 3 can be selected by version = 3 in save(), serialize() and saveRDS(), but format 2 remains the default for all serialization and saving of the workspace. Serialized data in format 3 cannot be read by versions of R prior to version 3.5.0. * The "Date" and "date-time" classes "POSIXlt" and "POSIXct" now have a working `length<-` method, as wished in PR#17387. * optim(*, control = list(warn.1d.NelderMead = FALSE)) allows to turn off the warning when applying the default "Nelder-Mead" method to 1-dimensional problems. * matplot(.., panel.first = .) etc now work, as log becomes explicit argument and ... is passed to plot() unevaluated, as suggested by Sebastian Meyer in PR#17386. * Interrupts can be suspended while evaluating an expression using suspendInterrupts. Subexpression can be evaluated with interrupts enabled using allowInterrupts. These functions can be used to make sure cleanup handlers cannot be interrupted. * R 3.5.0 includes a framework that allows packages to provide alternate representations of basic R objects (ALTREP). The framework is still experimental and may undergo changes in future R releases as more experience is gained. For now, documentation is provided in . UTILITIES: * install.packages() for source packages now has the possibility to set a 'timeout' (elapsed-time limit). For serial installs this uses the timeout argument of system2(): for parallel installs it requires the timeout utility command from GNU coreutils. * It is now possible to set 'timeouts' (elapsed-time limits) for most parts of R CMD check _via_ environment variables documented in the 'R Internals' manual. * The 'BioC extra' repository which was dropped from Bioconductor 3.6 and later has been removed from setRepositories(). This changes the mapping for 6-8 used by setRepositories(ind=). * R CMD check now also applies the settings of environment variables _R_CHECK_SUGGESTS_ONLY_ and _R_CHECK_DEPENDS_ONLY_ to the re-building of vignettes. * R CMD check with environment variable _R_CHECK_DEPENDS_ONLY_ set to a true value makes test-suite-management packages available and (for the time being) works around a common omission of rmarkdown from the VignetteBuilder field. INSTALLATION on a UNIX-ALIKE: * Support for a system Java on macOS has been removed - install a fairly recent Oracle Java (see 'R Installation and Administration' SSC.3.2). * configure works harder to set additional flags in SAFE_FFLAGS only where necessary, and to use flags which have little or no effect on performance. In rare circumstances it may be necessary to override the setting of SAFE_FFLAGS. * C99 functions expm1, hypot, log1p and nearbyint are now required. * configure sets a -std flag for the C++ compiler for all supported C++ standards (e.g., -std=gnu++11 for the C++11 compiler). Previously this was not done in a few cases where the default standard passed the tests made (e.g. clang 6.0.0 for C++11). C-LEVEL FACILITIES: * 'Writing R Extensions' documents macros MAYBE_REFERENCED, MAYBE_SHARED and MARK_NOT_MUTABLE that should be used by package C code instead NAMED or SET_NAMED. * The object header layout has been changed to support merging the ALTREP branch. This requires re-installing packages that use compiled code. * 'Writing R Extensions' now documents the R_tryCatch, R_tryCatchError, and R_UnwindProtect functions. * NAMEDMAX has been raised to 3 to allow protection of intermediate results from (usually ill-advised) assignments in arguments to BUILTIN functions. Package C code using SET_NAMED may need to be revised. DEPRECATED AND DEFUNCT: * Sys.timezone(location = FALSE) is defunct, and is ignored (with a warning). * methods:::bind_activation() is defunct now; it typically has been unneeded for years. The undocumented 'hidden' objects .__H__.cbind and .__H__.rbind in package base are deprecated (in favour of cbind and rbind). * The declaration of pythag() in Rmath.h has been removed - the entry point has not been provided since R 2.14.0. BUG FIXES: * printCoefmat() now also works without column names. * The S4 methods on Ops() for the "structure" class no longer cause infinite recursion when the structure is not an S4 object. * nlm(f, ..) for the case where f() has a "hessian" attribute now computes LL' = H + uI correctly. (PR#17249). * An S4 method that "rematches" to its generic and overrides the default value of a generic formal argument to NULL no longer drops the argument from its formals. * Rscript can now accept more than one argument given on the #! line of a script. Previously, one could only pass a single argument on the #! line in Linux. * Connections are now written correctly with encoding "UTF-16LE". (PR#16737). * Evaluation of ..0 now signals an error. When ..1 is used and ... is empty, the error message is more appropriate. * (Windows mainly.) Unicode code points which require surrogate pairs in UTF-16 are now handled. All systems should properly handle surrogate pairs, even those systems that do not need to make use of them. (PR#16098) * stopifnot(e, e2, ...) now evaluates the expressions sequentially and in case of an error or warning shows the relevant expression instead of the full stopifnot(..) call. * path.expand() on Windows now accepts paths specified as UTF-8-encoded character strings even if not representable in the current locale. (PR#17120) * line(x, y) now correctly computes the medians of the left and right group's x-values and in all cases reproduces straight lines. * Extending S4 classes with slots corresponding to special attributes like dim and dimnames now works. * Fix for legend() when fill has multiple values the first of which is NA (all colours used to default to par(fg)). (PR#17288) * installed.packages() did not remove the cached value for a library tree that had been emptied (but would not use the old value, just waste time checking it). * The documentation for installed.packages(noCache = TRUE) incorrectly claimed it would refresh the cache. * aggregate() no longer uses spurious names in some cases. (PR#17283) * object.size() now also works for long vectors. * packageDescription() tries harder to solve re-encoding issues, notably seen in some Windows locales. This fixes the citation() issue in PR#17291. * poly(, 3) now works, thanks to prompting by Marc Schwartz. * readLines() no longer segfaults on very large files with embedded '\0' (aka 'nul') characters. (PR#17311) * ns() (package splines) now also works for a single observation. interpSpline() gives a more friendly error message when the number of points is less than four. * dist(x, method = "canberra") now uses the correct definition; the result may only differ when x contains values of differing signs, e.g. not for 0-1 data. * methods:::cbind() and methods:::rbind() avoid deep recursion, thanks to Suharto Anggono via PR#17300. * Arithmetic with zero-column data frames now works more consistently; issue raised by Bill Dunlap. Arithmetic with data frames gives a data frame for ^ (which previously gave a numeric matrix). * pretty(x, n) for large n or large diff(range(x)) now works better (though it was never meant for large n); internally it uses the same rounding fuzz (1e-10) as seq.default() - as it did up to 2010-02-03 when both were 1e-7. * Internal C-level R_check_class_and_super() and hence R_check_class_etc() now also consider non-direct super classes and hence return a match in more cases. This e.g., fixes behaviour of derived classes in package Matrix. * Reverted unintended change in behavior of return calls in on.exit expressions introduced by stack unwinding changes in R 3.3.0. * Attributes on symbols are now detected and prevented; attempt to add an attribute to a symbol results in an error. * fisher.test(*, workspace = ) now may also increase the internal stack size which allows larger problem to be solved, fixing PR#1662. * The methods package no longer directly copies slots (attributes) into a prototype that is of an "abnormal" (reference) type, like a symbol. * The methods package no longer attempts to call length<-() on NULL (during the bootstrap process). * The methods package correctly shows methods when there are multiple methods with the same signature for the same generic (still not fully supported, but at least the user can see them). * sys.on.exit() is now always evaluated in the right frame. (From Lionel Henry.) * seq.POSIXt(*, by = " DSTdays") now should work correctly in all cases and is faster. (PR#17342) * .C() when returning a logical vector now always maps values other than FALSE and NA to TRUE (as documented). * Subassignment with zero length vectors now coerces as documented (PR#17344). Further, x <- numeric(); x[1] <- character() now signals an error 'replacement has length zero' (or a translation of that) instead of doing nothing. * (Package parallel.) mclapply(), pvec() and mcparallel() (when mccollect() is used to collect results) no longer leave zombie processes behind. * R CMD INSTALL now produces the intended error message when, e.g., the LazyData field is invalid. * as.matrix(dd) now works when the data frame dd contains a column which is a data frame or matrix, including a 0-column matrix/d.f. . * mclapply(X, mc.cores) now follows its documentation and calls lapply() in case mc.cores = 1 also in the case mc.preschedule is false. (PR#17373) * aggregate(, drop=FALSE) no longer calls the function on parts but sets corresponding results to NA. (Thanks to Suharto Anggono's patches in PR#17280). * The duplicated() method for data frames is now based on the list method (instead of string coercion). Consequently unique() is better distinguishing data frame rows, fixing PR#17369 and PR#17381. The methods for matrices and arrays are changed accordingly. * Calling names() on an S4 object derived from "environment" behaves (by default) like calling names() on an ordinary environment. * read.table() with a non-default separator now supports quotes following a non-whitespace character, matching the behavior of scan(). * parLapplyLB and parSapplyLB have been fixed to do load balancing (dynamic scheduling). This also means that results of computations depending on random number generators will now really be non-reproducible, as documented. * Indexing a list using dollar and empty string (l$"") returns NULL. * Using \usage{ data(, package="") } no longer produces R CMD check warnings. * match.arg() more carefully chooses the environment for constructing default choices, fixing PR#17401 as proposed by Duncan Murdoch. * Deparsing of consecutive ! calls is now consistent with deparsing unary - and + calls and creates code that can be reparsed exactly; thanks to a patch by Lionel Henry in PR#17397. (As a side effect, this uses fewer parentheses in some other deparsing involving ! calls.)- added gcc-c++ build dependency- Setting correctly R_UNZIPCMD Corrects this bug: http://bugzilla.suse.com/show_bug.cgi?id=1083075- upstrem updated to 3.4.4 CHANGES IN R 3.4.4: NEW FEATURES: * Sys.timezone() tries more heuristics on Unix-alikes and so is more likely to succeed (especially on Linux). For the slowest method, a warning is given recommending that TZ is set to avoid the search. * The version of LAPACK included in the sources has been updated to 3.8.0 (for the routines used by R, a very minor bug-fix change). * parallel::detectCores(logical = FALSE) is ignored on Linux systems, since the information is not available with virtualized OSes. INSTALLATION on a UNIX-ALIKE: * configure will use pkg-config to find the flags to link to jpeg if available (as it should be for the recently-released jpeg-9c and libjpeg-turbo). (This amends the code added in R 3.3.0 as the module name in jpeg-9c is not what that tested for.) DEPRECATED AND DEFUNCT: * Sys.timezone(location = FALSE) (which was a stop-gap measure for Windows long ago) is deprecated. It no longer returns the value of environment variable TZ (usually a location). * Legacy support of make macros such as CXX1X is formally deprecated: use the CXX11 forms instead. BUG FIXES: * power.prop.test() now warns when it cannot solve the problem, typically because of impossible constraints. (PR#17345) * removeSource() no longer erroneously removes NULL in certain cases, thanks to D'enes T'oth. * nls(`NO [mol/l]` ~ f(t)) and nls(y ~ a) now work. (Partly from PR#17367) * R CMD build checks for GNU cp rather than assuming Linux has it. (PR#17370 says 'Alpine Linux' does not.) * Non-UTF-8 multibyte character handling fixed more permanently (PR#16732). * sum(, ) is more consistent. (PR#17372) * rf() and rbeta() now also work correctly when ncp is not scalar, notably when (partly) NA. (PR#17375) * R CMD INSTALL now correctly sets C++ compiler flags when all source files are in sub-directories of src.- Do not buildrequire xorg-x11-devel but individual x libs.- upstream updated to 3.4.3 CHANGES IN R 3.4.3: INSTALLATION on a UNIX-ALIKE: * A workaround has been added for the changes in location of time-zone files in macOS 10.13 'High Sierra' and again in 10.13.1, so the default time zone is deduced correctly from the system setting when R is configured with --with-internal-tzcode (the default on macOS). * R CMD javareconf has been updated to recognize the use of a Java 9 SDK on macOS. BUG FIXES: * raw(0) & raw(0) and raw(0) | raw(0) again return raw(0) (rather than logical(0)). * intToUtf8() converts integers corresponding to surrogate code points to NA rather than invalid UTF-8, as well as values larger than the current Unicode maximum of 0x10FFFF. (This aligns with the current RFC3629.) * Fix calling of methods on S4 generics that dispatch on ... when the call contains .... * Following Unicode 'Corrigendum 9', the UTF-8 representations of U+FFFE and U+FFFF are now regarded as valid by utf8ToInt(). * range(c(TRUE, NA), finite = TRUE) and similar no longer return NA. (Reported by Lukas Stadler.) * The self starting function attr(SSlogis, "initial") now also works when the y values have exact minimum zero and is slightly changed in general, behaving symmetrically in the y range. * The printing of named raw vectors is now formatted nicely as for other such atomic vectors, thanks to Lukas Stadler.- upstream update to 3.4.2 CHANGES IN R 3.4.2: NEW FEATURES: * Setting the LC_ALL category in Sys.setlocale() invalidates any cached locale-specific day/month names and the AM/PM indicator for strptime() (as setting LC_TIME has since R 3.1.0). * The version of LAPACK included in the sources has been updated to 3.7.1, a bug-fix release. * The default for tools::write_PACKAGES(rds_compress=) has been changed to "xz" to match the compression used by CRAN. * c() and unlist() are now more efficient in constructing the names(.) of their return value, thanks to a proposal by Suharto Anggono. (PR#17284) UTILITIES: * R CMD check checks for and R CMD build corrects CRLF line endings in shell scripts configure and cleanup (even on Windows). INSTALLATION on a UNIX-ALIKE: * The order of selection of OpenMP flags has been changed: Oracle Developer Studio 12.5 accepts -fopenmp and -xopenmp but only the latter enables OpenMP so it is now tried first. BUG FIXES: * within(List, rm(x1, x2)) works correctly again, including when List[["x2"]] is NULL. * regexec(pattern, text, *) now applies as.character(.) to its first two arguments, as documented. * write.table() and related functions, writeLines(), and perhaps other functions writing text to connections did not signal errors when the writes failed, e.g. due to a disk being full. Errors will now be signalled if detected during the write, warnings if detected when the connection is closed. (PR#17243) * rt() assumed the ncp parameter was a scalar. (PR#17306) * menu(choices) with more than 10 choices which easily fit into one getOption("width")-line no longer erroneously repeats choices. (PR#17312) * length()<- on a pairlist succeeds. () * Language objects such as quote(("\n")) or R functions are correctly printed again, where R 3.4.1 accidentally duplicated the backslashes. * Construction of names() for very large objects in c() and unlist() now works, thanks to Suharto Anggono's patch proposals in PR#17292. * Resource leaks (and similar) reported by Steve Grubb fixed. (PR#17314, PR#17316, PR#17317, PR#17318, PR#17319, PR#17320) * model.matrix(~1, mf) now gets the row names from mf also when they differ from 1:nrow(mf), fixing PR#14992 thanks to the suggestion by Sebastian Meyer. * sigma(fm) now takes the correct denominator degrees of freedom for a fitted model with NA coefficients. (PR#17313) * hist(x, "FD") no longer "dies" with a somewhat cryptic error message when x has extreme outliers or IQR() zero: nclass.FD(x) tries harder to find a robust bin width h in the latter case, and hist.default(*, breaks) now checks and corrects a too large breaks number. (PR#17274) * callNextMethod() works for ... methods. * qr.coef(qd, y) now has correct names also when qd is a complex QR or stems from qr(*, LAPACK=TRUE). * Setting options(device = *) to an invalid function no longer segfaults when plotting is initiated. (PR#15883) * encodeString() no longer segfaults. (PR#15885) * It is again possible to use configure --enable-maintainer-mode without having installed notangle (it was required in R 3.4.[01]). * S4 method dispatch on ... calls the method by name instead of .Method (for consistency with default dispatch), and only attempts to pass non-missing arguments from the generic. * readRDS(textConnection(.)) works again. (PR#17325) * (1:n)[-n] no longer segfaults for n <- 2.2e9 (on a platform with enough RAM). * x <- 1:2; tapply(x, list(x, x), function(x) "")[1,2] now correctly returns NA. (PR#17333) * Running of finalizers after explicit GC request moved from the R interface do_gc to the C interface R_gc. This helps with reclaiming inaccessible connections. * help.search(topic) and ??topic matching topics in vignettes with multiple file name extensions (e.g., *.md.rsp but not *.Rmd) failed with an error when using options(help_type = "html"). * The X11 device no longer uses the Xlib backing store (PR#16497). * array(character(), 1) now gives (a 1D array with) NA as has been documented for a long time as in the other cases of zero-length array initialization and also compatibly with matrix(character(), * ). As mentioned there, this also fixes PR#17333. * splineDesign(.., derivs = 4) no longer segfaults. * fisher.test(*, hybrid=TRUE) now (again) will use the hybrid method when Cochran's conditions are met, fixing PR#16654.- Corrected "bug" "https://bugzilla.suse.com/show_bug.cgi?id=1049503 R now installs zip and unzip, what in turn eases the installation of packages directly from github via devtools.- upstream update to 3.4.1 CHANGES IN R 3.4.1: INSTALLATION on a UNIX-ALIKE: * The deprecated support for PCRE versions older than 8.20 has been removed. BUG FIXES: * getParseData() gave incorrect column information when code contained multi-byte characters. (PR#17254) * Asking for help using expressions like ?stats::cor() did not work. (PR#17250) * readRDS(url(....)) now works. * R CMD Sweave again returns status = 0 on successful completion. * Vignettes listed in .Rbuildignore were not being ignored properly. (PR#17246) * file.mtime() no longer returns NA on Windows when the file or directory is being used by another process. This affected installed.packages(), which is now protected against this. * R CMD INSTALL Windows .zip file obeys --lock and --pkglock flags. * (Windows only) The choose.files() function could return incorrect results when called with multi = FALSE. (PR#17270) * aggregate(, drop = FALSE) now also works in case of near-equal numbers in by. (PR#16918) * fourfoldplot() could encounter integer overflow when calculating the odds ratio. (PR#17286) * parse() no longer gives spurious warnings when extracting srcrefs from a file not encoded in the current locale. This was seen from R CMD check with inst/doc/*.R files, and check has some additional protection for such files. * print.noquote(x) now always returns its argument x (invisibly). * Non-UTF-8 multibyte character sets were not handled properly in source references. (PR#16732)- upstream update to 3.4.0 CHANGES IN R 3.4.0: SIGNIFICANT USER-VISIBLE CHANGES: * (Unix-alike) The default methods for download.file() and url() now choose "libcurl" except for file:// URLs. There will be small changes in the format and wording of messages, including in rare cases if an issue is a warning or an error. For example, when HTTP re-direction occurs, some messages refer to the final URL rather than the specified one. Those who use proxies should check that their settings are compatible (see ?download.file: the most commonly used forms work for both "internal" and "libcurl"). * table() has been amended to be more internally consistent and become back compatible to R <= 2.7.2 again. Consequently, table(1:2, exclude = NULL) no longer contains a zero count for , but useNA = "always" continues to do so. * summary.default() no longer rounds, but its print method does resulting in less extraneous rounding, notably of numbers in the ten thousands. * factor(x, exclude = L) behaves more rationally when x or L are character vectors. Further, exclude = now behaves as documented for long. * Arithmetic, logic (&, |) and comparison (aka 'relational', e.g., <, ==) operations with arrays now behave consistently, notably for arrays of length zero. Arithmetic between length-1 arrays and longer non-arrays had silently dropped the array attributes and recycled. This now gives a warning and will signal an error in the future, as it has always for logic and comparison operations in these cases (e.g., compare matrix(1,1) + 2:3 and matrix(1,1) < 2:3). * The JIT ('Just In Time') byte-code compiler is now enabled by default at its level 3. This means functions will be compiled on first or second use and top-level loops will be compiled and then run. (Thanks to Tomas Kalibera for extensive work to make this possible.) For now, the compiler will not compile code containing explicit calls to browser(): this is to support single stepping from the browser() call. JIT compilation can be disabled for the rest of the session using compiler::enableJIT(0) or by setting environment variable R_ENABLE_JIT to 0. * xtabs() works more consistently with NAs, also in its result no longer setting them to 0. Further, a new logical option addNA allows to count NAs where appropriate. Additionally, for the case sparse = TRUE, the result's dimnames are identical to the default case's. * Matrix products now consistently bypass BLAS when the inputs have NaN/Inf values. Performance of the check of inputs has been improved. Performance when BLAS is used is improved for matrix/vector and vector/matrix multiplication (DGEMV is now used instead of DGEMM). One can now choose from alternative matrix product implementations _via_ options(matprod = ). The "internal" implementation is not optimized for speed but consistent in precision with other summations in R (using long double accumulators where available). "blas" calls BLAS directly for best speed, but usually with undefined behavior for inputs with NaN/Inf. * factor() now uses order() to sort its levels, not sort.list(). This makes factor() support custom vector-like objects if methods for the appropriate generics are defined. This change has the side effect of making factor() succeed on empty or length-one non-atomic vector(-like) types (e.g., list), where it failed before. NEW FEATURES: * User errors such as integrate(f, 0:1, 2) are now caught. * Add signature argument to debug(), debugonce(), undebug() and isdebugged() for more conveniently debugging S3 and S4 methods. (Based on a patch by Gabe Becker.) * Add utils::debugcall() and utils::undebugcall() for debugging the function that would be called by evaluating the given expression. When the call is to an S4 generic or standard S3 generic, debugcall() debugs the method that would be dispatched. A number of internal utilities were added to support this, most notably utils::isS3stdGeneric(). (Based on a patch by Gabe Becker.) * Add utils::strcapture(). Given a character vector and a regular expression containing capture expressions, strcapture() will extract the captured tokens into a tabular data structure, typically a data.frame. * str() and strOptions() get a new option drop.deparse.attr with improved but _changed_ default behaviour for expressions. For expression objects x, str(x) now may remove extraneous white space and truncate long lines. * str() is no longer very slow; inspired by Mikko Korpela's proposal in PR#16527. * str(x)'s default method is more "accurate" and hence somewhat more generous in displaying character vectors; this will occasionally change R outputs (and need changes to some * .Rout(.save) files). For a classed integer vector such as x <- xtabs(~ c(1,9,9,9)), str(x) now shows both the class and "int", instead of only the latter. * isSymmetric(m) is much faster for large asymmetric matrices m _via_ pre-tests and a new option tol1 (with which strict back compatibility is possible but not the default). * The result of eigen() now is of class "eigen" in the default case when eigenvectors are computed. * Zero-length date and date-time objects (of classes "POSIX[cl]?t") now print() "recognizably". * xy.coords() and xyz.coords() get a new setLab option. * The method argument of sort.list(), order() and sort.int() gains an "auto" option (the default) which should behave the same as before when method was not supplied. * stopifnot(E, ..) now reports differences when E is a call to all.equal() and that is not true. * boxplot(, *) gain optional arguments drop, sep, and lex.order to pass to split.default() which itself gains an argument lex.order to pass to interaction() for more flexibility. * The plot() method for ppr() has enhanced default labels (xmin and main). * sample.int() gains an explicit useHash option (with a back compatible default). * identical() gains an ignore.srcref option which drops "srcref" and similar attributes when true (as by default). * diag(x, nrow = n) now preserves typeof(x), also for logical, integer and raw x (and as previously for complex and numeric). * smooth.spline() now allows direct specification of lambda, gets a hatvalues() method and keeps tol in the result, and optionally parts of the internal matrix computations. * addNA() is faster now, e.g. when applied twice. (Part of PR#16895.) * New option rstandard(, type = "predicted") provides the "PRESS"-related leave-one-out cross-validation errors for linear models. * After seven years of deprecation, duplicated factor levels now produce a warning when printed and an error in levels<- instead of a warning. * Invalid factors, e.g., with duplicated levels (invalid but constructable) now give a warning when printed, _via_ new function .valid.factor(). * sessionInfo() has been updated for Apple's change in OS naming as from '10.12' ('macOS Sierra' _vs_ 'OS X El Capitan'). Its toLatex() method now includes the running component. * options(interrupt=) can be used to specify a default action for user interrupts. For now, if this option is not set and the error option is set, then an unhandled user interrupt invokes the error option. (This may be dropped in the future as interrupt conditions are not error conditions.) * In most cases user interrupt handlers will be called with a "resume" restart available. Handlers can invoke this restart to resume computation. At the browser prompt the r command will invoke a "resume" restart if one is available. Some read operations cannot be resumed properly when interrupted and do not provide a "resume" restart. * Radix sort is now chosen by method = "auto" for sort.int() for double vectors (and hence used for sort() for unclassed double vectors), excluding 'long' vectors. sort.int(method = "radix") no longer rounds double vectors. * The default and data.frame methods for stack() preserve the names of empty elements in the levels of the ind column of the return value. Set the new drop argument to TRUE for the previous behavior. * Speedup in simplify2array() and hence sapply() and mapply() (for the case of names and common length > 1), thanks to Suharto Anggono's PR#17118. * table(x, exclude = NULL) now sets useNA = "ifany" (instead of "always"). Together with the bug fixes for this case, this recovers more consistent behaviour compatible to older versions of R. As a consequence, summary() for a logical vector no longer reports (zero) counts for NA when there are no NAs. * dump.frames() gets a new option include.GlobalEnv which allows to also dump the global environment, thanks to Andreas Kersting's proposal in PR#17116. * system.time() now uses message() instead of cat() when terminated early, such that suppressMessages() has an effect; suggested by Ben Bolker. * citation() supports inst/CITATION files from package source trees, with lib.loc pointing to the directory containing the package. * try() gains a new argument outFile with a default that can be modified _via_ options(try.outFile = .), useful notably for Sweave. * The unexported low-level functions in package parallel for passing serialized R objects to and from forked children now support long vectors on 64-bit platforms. This removes some limits on higher-level functions such as mclapply() (but returning gigabyte results from forked processes _via_ serialization should be avoided if at all possible). * Connections now print() without error even if invalid, e.g. after having been destroyed. * apropos() and find(simple.words = FALSE) no longer match object names starting with . which are known to be internal objects (such as .__S3MethodsTable__.). * Convenience function hasName() has been added; it is intended to replace the common idiom !is.null(x$name) without the usually unintended partial name matching. * strcapture() no longer fixes column names nor coerces strings to factors (suggested by Bill Dunlap). * strcapture() returns NA for non-matching values in x (suggested by Bill Dunlap). * source() gets new optional arguments, notably exprs; this is made use of in the new utility function withAutoprint(). * sys.source() gets a new toplevel.env argument. This argument is useful for frameworks running package tests; contributed by Tomas Kalibera. * Sys.setFileTime() and file.copy(copy.date = TRUE) will set timestamps with fractions of seconds on platforms/filesystems which support this. * (Windows only.) file.info() now returns file timestamps including fractions of seconds; it has done so on other platforms since R 2.14.0. (NB: some filesystems do not record modification and access timestamps to sub-second resolution.) * The license check enabled by options(checkPackageLicense = TRUE) is now done when the package's namespace is first loaded. * ppr() and supsmu() get an optional trace argument, and ppr(.., sm.method = ..spline) is no longer limited to sample size n <= 2500. * The POSIXct method for print() gets optional tz and usetz arguments, thanks to a report from Jennifer S. Lyon. * New function check_packages_in_dir_details() in package tools for analyzing package-check log files to obtain check details. * Package tools now exports function CRAN_package_db() for obtaining information about current packages in the CRAN package repository, and several functions for obtaining the check status of these packages. * The (default) Stangle driver Rtangle allows annotate to be a function and gets a new drop.evalFALSE option. * The default method for quantile(x, prob) should now be monotone in prob, even in border cases, see PR#16672. * bug.report() now tries to extract an email address from a BugReports field, and if there is none, from a Contacts field. * The format() and print() methods for object.size() results get new options standard and digits; notably, standard = "IEC" and standard = "SI" allow more standard (but less common) abbreviations than the default ones, e.g. for kilobytes. (From contributions by Henrik Bengtsson.) * If a reference class has a validity method, validObject will be called automatically from the default initialization method for reference classes. * tapply() gets new option default = NA allowing to change the previously hardcoded value. * read.dcf() now consistently interprets any 'whitespace' to be stripped to include newlines. * The maximum number of DLLs that can be loaded into R e.g. _via_ dyn.load() can now be increased by setting the environment variable R_MAX_NUM_DLLS before starting R. * Assigning to an element of a vector beyond the current length now over-allocates by a small fraction. The new vector is marked internally as growable, and the true length of the new vector is stored in the truelength field. This makes building up a vector result by assigning to the next element beyond the current length more efficient, though pre-allocating is still preferred. The implementation is subject to change and not intended to be used in packages at this time. * Loading the parallel package namespace no longer sets or changes the .Random.seed, even if R_PARALLEL_PORT is unset. NB: This can break reproducibility of output, and did for a CRAN package. * Methods "wget" and "curl" for download.file() now give an R error rather than a non-zero return value when the external command has a non-zero status. * Encoding name "utf8" is mapped to "UTF-8". Many implementations of iconv accept "utf8", but not GNU libiconv (including the late 2016 version 1.15). * sessionInfo() shows the full paths to the library or executable files providing the BLAS/LAPACK implementations currently in use (not available on Windows). * The binning algorithm used by bandwidth selectors bw.ucv(), bw.bcv() and bw.SJ() switches to a version linear in the input size n for n > nb/2. (The calculations are the same, but for larger n/nb it is worth doing the binning in advance.) * There is a new option PCRE_study which controls when grep(perl = TRUE) and friends 'study' the compiled pattern. Previously this was done for 11 or more input strings: it now defaults to 10 or more (but most examples need many more for the difference from studying to be noticeable). * grep(perl = TRUE) and friends can now make use of PCRE's Just-In-Time mechanism, for PCRE >= 8.20 on platforms where JIT is supported. It is used by default whenever the pattern is studied (see the previous item). (Based on a patch from Mikko Korpela.) This is controlled by a new option PCRE_use_JIT. Note that in general this makes little difference to the speed, and may take a little longer: its benefits are most evident on strings of thousands of characters. As a side effect it reduces the chances of C stack overflow in the PCRE library on very long strings (millions of characters, but see next item). Warning: segfaults were seen using PCRE with JIT enabled on 64-bit Sparc builds. * There is a new option PCRE_limit_recursion for grep(perl = TRUE) and friends to set a recursion limit taking into account R's estimate of the remaining C stack space (or 10000 if that is not available). This reduces the chance of C stack overflow, but because it is conservative may report a non-match (with a warning) in examples that matched before. By default it is enabled if any input string has 1000 or more bytes. (PR#16757) * getGraphicsEvent() now works on X11(type = "cairo") devices. Thanks to Frederick Eaton (for reviving an earlier patch). * There is a new argument onIdle for getGraphicsEvent(), which allows an R function to be run whenever there are no pending graphics events. This is currently only supported on X11 devices. Thanks to Frederick Eaton. * The deriv() and similar functions now can compute derivatives of log1p(), sinpi() and similar one-argument functions, thanks to a contribution by Jerry Lewis. * median() gains a formal ... argument, so methods with extra arguments can be provided. * strwrap() reduces indent if it is more than half width rather than giving an error. (Suggested by Bill Dunlap.) * When the condition code in if(.) or while(.) is not of length one, an error instead of a warning may be triggered by setting an environment variable, see the help page. * Formatting and printing of bibliography entries (bibentry) is more flexible and better documented. Apart from setting options(citation.bibtex.max = 99) you can also use print(, bibtex=TRUE) (or format(..)) to get the BibTeX entries in the case of more than one entry. This also affects citation(). Contributions to enable style = "html+bibtex" are welcome. C-LEVEL FACILITIES: * Entry points R_MakeExternalPtrFn and R_ExternalPtrFn are now declared in header Rinternals.h to facilitate creating and retrieving an R external pointer from a C function pointer without ISO C warnings about the conversion of function pointers. * There was an exception for the native Solaris C++ compiler to the dropping (in R 3.3.0) of legacy C++ headers from headers such as R.h and Rmath.h - this has now been removed. That compiler has strict C++98 compliance hence does not include extensions in its (non-legacy) C++ headers: some packages will need to request C++11 or replace non-C++98 calls such as lgamma: see SS1.6.4 of 'Writing R Extensions'. Because it is needed by about 70 CRAN packages, headers R.h and Rmath.h still declare use namespace std; when included on Solaris. * When included from C++, the R headers now use forms such as std::FILE directly rather than including the line using std::FILE; C++ code including these headers might be relying on the latter. * Headers R_ext/BLAS.h and R_ext/Lapack.h have many improved declarations including const for double-precision complex routines. _Inter alia_ this avoids warnings when passing 'string literal' arguments from C++11 code. * Headers for Unix-only facilities R_ext/GetX11Image.h, R_ext/QuartzDevice.h and R_ext/eventloop.h are no longer installed on Windows. * No-longer-installed headers GraphicsBase.h, RGraphics.h, Rmodules/RX11.h and Rmodules/Rlapack.h which had a LGPL license no longer do so. * HAVE_UINTPTR_T is now defined where appropriate by Rconfig.h so that it can be included before Rinterface.h when CSTACK_DEFNS is defined and a C compiler (not C++) is in use. Rinterface.h now includes C header stdint.h or C++11 header cstdint where needed. * Package tools has a new function package_native_routine_registration_skeleton() to assist adding native-symbol registration to a package. See its help and SS5.4.1 of 'Writing R Extensions' for how to use it. (At the time it was added it successfully automated adding registration to over 90% of CRAN packages which lacked it. Many of the failures were newly-detected bugs in the packages, e.g. 50 packages called entry points with varying numbers of arguments and 65 packages called entry points not in the package.) INSTALLATION on a UNIX-ALIKE: * readline headers (and not just the library) are required unless configuring with --with-readline=no. * configure now adds a compiler switch for C++11 code, even if the compiler supports C++11 by default. (This ensures that g++ 6.x uses C++11 mode and not its default mode of C++14 with 'GNU extensions'.) The tests for C++11 compliance are now much more comprehensive. For gcc < 4.8, the tests from R 3.3.0 are used in order to maintain the same behaviour on Linux distributions with long-term support. * An alternative compiler for C++11 is now specified with CXX11, not CXX1X. Likewise C++11 flags are specified with CXX11FLAGS and the standard (e.g., -std=gnu++11 is specified with CXX11STD. * configure now tests for a C++14-compliant compiler by testing some basic features. This by default tries flags for the compiler specified by CXX11, but an alternative compiler, options and standard can be specified by variables CXX14, CXX14FLAGS and CXX14STD (e.g., -std=gnu++14). * There is a new macro CXXSTD to help specify the standard for C++ code, e.g. -std=c++98. This makes it easier to work with compilers which default to a later standard: for example, with CXX=g++6 CXXSTD=-std=c++98 configure will select commands for g++ 6.x which conform to C++11 and C++14 where specified but otherwise use C++98. * Support for the defunct IRIX and OSF/1 OSes and Alpha CPU has been removed. * configure checks that the compiler specified by $CXX $CXXFLAGS is able to compile C++ code. * configure checks for the required header sys/select.h (or sys/time.h on legacy systems) and system call select and aborts if they are not found. * If available, the POSIX 2008 system call utimensat will be used by Sys.setFileTime() and file.copy(copy.date = TRUE). This may result in slightly more accurate file times. (It is available on Linux and FreeBSD but not macOS.) * The minimum version requirement for libcurl has been reduced to 7.22.0, although at least 7.28.0 is preferred and earlier versions are little tested. (This is to support Debian 7 'Wheezy' LTS and Ubuntu 'Precise' 12.04 LTS, although the latter is close to end-of-life.) * configure tests for a C++17-compliant compiler. The tests are experimental and subject to change in the future. INCLUDED SOFTWARE: * (Windows only) Tcl/Tk version 8.6.4 is now included in the binary builds. The tcltk*.chm help file is no longer included; please consult the online help at instead. * The version of LAPACK included in the sources has been updated to 3.7.0: no new routines have been added to R. PACKAGE INSTALLATION: * There is support for compiling C++14 or C++17 code in packages on suitable platforms: see 'Writing R Extensions' for how to request this. * The order of flags when LinkingTo other packages has been changed so their include directories come earlier, before those specified in CPPFLAGS. This will only have an effect if non-system include directories are included with -I flags in CPPFLAGS (and so not the default -I/usr/local/include which is treated as a system include directory on most platforms). * Packages which register native routines for .C or .Fortran need to be re-installed for this version (unless installed with R-devel SVN revision r72375 or later). * Make variables with names containing CXX1X are deprecated in favour of those using CXX11, but for the time being are still made available _via_ file etc/Makeconf. Packages using them should be converted to the new forms and made dependent on R (>= 3.4.0).- And again that ldconfig call. Newline was obviously wrong. Hopefully correct now.- Jan Engelhardt asked for reverting the change to the ldconfig call. So be it.- improvements for a) calling /sbin/ldconfig, which no longer gives a warning b) unregistering info-pages in %preun instead of %postun- a change in OBS now requires a BuildRequire: shadow for some openSUSE releases.- upstream release 3.3.3 - Most important changes CHANGES IN R 3.3.3: NEW FEATURES: * Changes when redirection of a http:// URL to a https:// URL is encountered: * The internal methods of download.file() and url() now report that they cannot follow this (rather than failing silently). * (Unix-alike) download.file(method = "auto") (the default) re-tries with method = "libcurl". * (Unix-alike) url(method = "default") with an explicit open argument re-tries with method = "libcurl". This covers many of the usages, e.g. readLines() with a URL argument. INSTALLATION on a UNIX-ALIKE: * The configure check for the zlib version is now robust to versions longer than 5 characters, including 1.2.11. UTILITIES: * Environmental variable _R_CHECK_TESTS_NLINES_ controls how R CMD check reports failing tests (see SS8 of the 'R Internals' manual). DEPRECATED AND DEFUNCT: * (C-level Native routine registration.) The undocumented styles field of the components of R_CMethodDef and R_FortranMethodDef is deprecated. BUG FIXES: * vapply(x, *) now works with long vectors x. (PR#17174) * isS3method("is.na.data.frame") and similar are correct now. (PR#17171) * grepRaw(, , fixed = TRUE) now works, thanks to a patch by Mikko Korpela. (PR#17132) * Package installation into a library where the package exists _via_ symbolic link now should work wherever Sys.readlink() works, resolving PR#16725. * "Cincinnati" was missing an "n" in the precip dataset. * Fix buffer overflow vulnerability in pdf() when loading an encoding file. Reported by Talos (TALOS-2016-0227). * getDLLRegisteredRoutines() now produces its warning correctly when multiple DLLs match, thanks to Matt Dowle's PR#17184. * Sys.timezone() now returns non-NA also on platforms such as Ubuntu 14.04.5 LTS, thanks to Mikko Korpela's PR#17186. * format(x) for an illegal "POSIXlt" object x no longer segfaults. * methods(f) now also works for f "(" or "{". * (Windows only) dir.create() did not check the length of the path to create, and so could overflow a buffer and crash R. (PR#17206) * On some systems, very small hexadecimal numbers in hex notation would underflow to zero. (PR#17199) * pmin() and pmax() now work again for ordered factors and 0-length S3 classed objects, thanks to Suharto Anggono's PR#17195 and PR#17200. * bug.report() did not do any validity checking on a package's BugReports field. It now ignores an empty field, removes leading whitespace and only attempts to open http:// and https:// URLs, falling back to emailing the maintainer. * Bandwidth selectors bw.ucv() and bw.SJ() gave incorrect answers or incorrectly reported an error (because of integer overflow) for inputs longer than 46341. Similarly for bw.bcv() at length 5793. Another possible integer overflow is checked and may result in an error report (rather than an incorrect result) for much longer inputs (millions for a smooth distribution). * findMethod() failed if the active signature had expanded beyond what a particular package used. (Example with packages XR and XRJulia on CRAN.) * qbeta() underflowed too early in some very asymmetric cases. (PR#17178) * R CMD Rd2pdf had problems with packages with non-ASCII titles in .Rd files (usually the titles were omitted).- upstream release 3.3.2 - Most important changes CHANGES IN R 3.3.2: NEW FEATURES: * extSoftVersion() now reports the version (if any) of the readline library in use. * The version of LAPACK included in the sources has been updated to 3.6.1, a bug-fix release including a speedup for the non-symmetric case of eigen(). * Use options(deparse.max.lines=) to limit the number of lines recorded in .Traceback and other deparsing activities. * format() looks more regular, also for non-character atomic matrices. * abbreviate() gains an option named = TRUE. * The online documentation for package methods is extensively rewritten. The goals are to simplify documentation for basic use, to note old features not recommended and to correct out-of-date information. * Calls to setMethod() no longer print a message when creating a generic function in those cases where that is natural: S3 generics and primitives. INSTALLATION and INCLUDED SOFTWARE: * Versions of the readline library >= 6.3 had been changed so that terminal window resizes were not signalled to readline: code has been added using a explicit signal handler to work around that (when R is compiled against readline >= 6.3). (PR#16604) * configure works better with Oracle Developer Studio 12.5. UTILITIES: * R CMD check reports more dubious flags in files src/Makevars[.in], including -w and -g. * R CMD check has been set up to filter important warnings from recent versions of gfortran with -Wall -pedantic: this now reports non-portable GNU extensions such as out-of-order declarations. * R CMD config works better with paths containing spaces, even those of home directories (as reported by Ken Beath). DEPRECATED AND DEFUNCT: * Use of the C/C++ macro NO_C_HEADERS is deprecated (no C headers are included by R headers from C++ as from R 3.3.0, so it should no longer be needed). BUG FIXES: * The check for non-portable flags in R CMD check could be stymied by src/Makevars files which contained targets. * (Windows only) When using certain desktop themes in Windows 7 or higher, Alt-Tab could cause Rterm to stop accepting input. (PR#14406; patch submitted by Jan Gleixner.) * pretty(d, ..) behaves better for date-time d (PR#16923). * When an S4 class name matches multiple classes in the S4 cache, perform a dynamic search in order to obey namespace imports. This should eliminate annoying messages about multiple hits in the class cache. Also, pass along the package from the ClassExtends object when looking up superclasses in the cache. * sample(NA_real_) now works. * Packages using non-ASCII encodings in their code did not install data properly on systems using different encodings. * merge(df1, df2) now also works for data frames with column names "na.last", "decreasing", or "method". (PR#17119) * contour() caused a segfault if the labels argument had length zero. (Reported by Bill Dunlap.) * unique(warnings()) works more correctly, thanks to a new duplicated.warnings() method. * findInterval(x, vec = numeric(), all.inside = TRUE) now returns 0s as documented. (Reported by Bill Dunlap.) * (Windows only) R CMD SHLIB failed when a symbol in the resulting library had the same name as a keyword in the .def file. (PR#17130) * pmax() and pmin() now work with (more ?) classed objects, such as "Matrix" from the Matrix package, as documented for a long time. * axis(side, x = D) and hence Axis() and plot() now work correctly for "Date" and time objects D, even when "time goes backward", e.g., with decreasing xlim. (Reported by William May.) * str(I(matrix(..))) now looks as always intended. * plot.ts(), the plot() method for time series, now respects cex, lwd and lty. (Reported by Greg Werbin.) * parallel::mccollect() now returns a named list (as documented) when called with wait = FALSE. (Reported by Michel Lang.) * If a package added a class to a class union in another package, loading the first package gave erroneous warnings about "undefined subclass". * c()'s argument use.names is documented now, as belonging to the (C internal) default method. In "parallel", argument recursive is also moved from the generic to the default method, such that the formal argument list of base generic c() is just (...). * rbeta(4, NA) and similarly rgamma() and rnbinom() now return NaN's with a warning, as other r(), and as documented. (PR#17155) * Using options(checkPackageLicense = TRUE) no longer requires acceptance of the licence for non-default standard packages such as compiler. (Reported by Mikko Korpela.) * split(, *) now works even when the split off parts are long. (PR#17139) * min() and max() now also work correctly when the argument list starts with character(0). (PR#17160) * Subsetting very large matrices (prod(dim(.)) >= 2^31) now works thanks to Michael Schubmehl's PR#17158. * bartlett.test() used residual sums of squares instead of variances, when the argument was a list of lm objects. (Reported by Jens Ledet Jensen). * plot(, which = *) now correctly labels the contour lines for the standardized residuals for which = 6. It also takes the correct p in case of singularities (also for which = 5). (PR#17161) * xtabs(~ exclude) no longer fails from wrong scope, thanks to Suharto Anggono's PR#17147. * Reference class calls to methods() did not re-analyse previously defined methods, meaning that calls to methods defined later would fail. (Reported by Charles Tilford). * findInterval(x, vec, left.open = TRUE) misbehaved in some cases. (Reported by Dmitriy Chernykh.)- Fix typo in Group tag.- upstream release 3.3.1 - Most important changes CHANGES IN R 3.3.1: BUG FIXES: * R CMD INSTALL and hence install.packages() gave an internal error installing a package called description from a tarball on a case-insensitive file system. * match(x, t) (and hence x %in% t) failed when x was of length one, and either character and x and t only differed in their Encoding or when x and t where complex with NAs or NaNs. (PR#16885.) * unloadNamespace(ns) also works again when ns is a 'namespace', as from getNamespace(). * rgamma(1,Inf) or rgamma(1, 0,0) no longer give NaN but the correct limit. * length(baseenv()) is correct now. * pretty(d, ..) for date-time d rarely failed when "halfmonth" time steps were tried (PR#16923) and on 'inaccurate' platforms such as 32-bit windows or a configuration with --disable-long-double; see comment #15 of PR#16761. * In text.default(x, y, labels), the rarely(?) used default for labels is now correct also for the case of a 2-column matrix x and missing y. * as.factor(c(a = 1L)) preserves names() again as in R < 3.1.0. * strtrim(""[0], 0[0]) now works. * Use of Ctrl-C to terminate a reverse incremental search started by Ctrl-R in the readline-based Unix terminal interface is now supported for readline >= 6.3 (Ctrl-G always worked). (PR#16603) * diff() now keeps the "units" attribute, as subtraction already did, PR#16940.- further cleanup of spec file. Removed unneeded explicit Requires for libcairo2/libfreetype6/liblzma5/libreadline6 Removed removal of backup file that was meanwhile removed upstream.- clean up of spec file after comments from Jan Engelhardt in https://build.opensuse.org/request/show/393426 Some unneeded explicit BuildRequires removed.- tre.patch was removed.- and libbz2-devel needed, too.- added BuildRequires: bzip2 for i586.- upstream release 3.3.0 CHANGES IN R 3.3.0: SIGNIFICANT USER-VISIBLE CHANGES: * nchar(x, *)'s argument keepNA governing how the result for NAs in x is determined, gets a new default keepNA = NA which returns NA where x is NA, except for type = "width" which still returns 2, the formatting / printing width of NA. * All builds have support for https: URLs in the default methods for download.file(), url() and code making use of them. Unfortunately that cannot guarantee that any particular https: URL can be accessed. For example, server and client have to successfully negotiate a cryptographic protocol (TLS/SSL, ...) and the server's identity has to be verifiable _via_ the available certificates. Different access methods may allow different protocols or use private certificate bundles: we encountered a https: CRAN mirror which could be accessed by one browser but not by another nor by download.file() on the same Linux machine. NEW FEATURES: * The print method for methods() gains a byclass argument. * New functions validEnc() and validUTF8() to give access to the validity checks for inputs used by grep() and friends. * Experimental new functionality for S3 method checking, notably isS3method(). Also, the names of the R 'language elements' are exported as character vector tools::langElts. * str(x) now displays "Time-Series" also for matrix (multivariate) time-series, i.e. when is.ts(x) is true. * (Windows only) The GUI menu item to install local packages now accepts *.tar.gz files as well as *.zip files (but defaults to the latter). * New programmeR's utility function chkDots(). * D() now signals an error when given invalid input, rather than silently returning NA. (Request of John Nash.) * formula objects are slightly more "first class": e.g., formula() or new("formula", y ~ x) are now valid. Similarly, for "table", "ordered" and "summary.table". Packages defining S4 classes with the above S3/S4 classes as slots should be reinstalled. * New function strrep() for repeating the elements of a character vector. * rapply() preserves attributes on the list when how = "replace". * New S3 generic function sigma() with methods for extracting the estimated standard deviation aka "residual standard deviation" from a fitted model. * news() now displays R and package news files within the HTML help system if it is available. If no news file is found, a visible NULL is returned to the console. * as.raster(x) now also accepts raw arrays x assuming values in 0:255. * Subscripting of matrix/array objects of type "expression" is now supported. * type.convert("i") now returns a factor instead of a complex value with zero real part and missing imaginary part. * Graphics devices cairo_pdf() and cairo_ps() now allow non-default values of the cairographics 'fallback resolution' to be set. This now defaults to 300 on all platforms: that is the default documented by cairographics, but apparently was not used by all system installations. * file() gains an explicit method argument rather than implicitly using getOption("url.method", "default"). * Thanks to a patch from Tomas Kalibera, x[x != 0] is now typically faster than x[which(x != 0)] (in the case where x has no NAs, the two are equivalent). * read.table() now always uses the names for a named colClasses argument (previously names were only used when colClasses was too short). (In part, wish of PR#16478.) * (Windows only) download.file() with default method = "auto" and a ftps:// URL chooses "libcurl" if that is available. * The out-of-the box Bioconductor mirror has been changed to one using https://: use chooseBioCmirror() to choose a http:// mirror if required. * The data frame and formula methods for aggregate() gain a drop argument. * available.packages() gains a repos argument. * The undocumented switching of methods for url() on https: and ftps: URLs is confined to method = "default" (and documented). * smoothScatter() gains a ret.selection argument. * qr() no longer has a ... argument to pass additional arguments to methods. * [ has a method for class "table". * It is now possible (again) to replayPlot() a display list snapshot that was created by recordPlot() in a different R session. It is still not a good idea to use snapshots as a persistent storage format for R plots, but it is now not completely silly to use a snapshot as a format for transferring an R plot between two R sessions. The underlying changes mean that packages providing graphics devices (e.g., Cairo, RSvgDevice, cairoDevice, tikzDevice) will need to be reinstalled. Code for restoring snapshots was contributed by Jeroen Ooms and JJ Allaire. Some testing code is available at . * tools::undoc(dir = D) and codoc(dir = D) now also work when D is a directory whose normalizePath()ed version does not end in the package name, e.g. from a symlink. * abbreviate() has more support for multi-byte character sets - it no longer removes bytes within characters and knows about Latin vowels with accents. It is still only really suitable for (most) European languages, and still warns on non-ASCII input. abbreviate(use.classes = FALSE) is now implemented, and that is more suitable for non-European languages. * match(x, table) is faster (sometimes by an order of magnitude) when x is of length one and incomparables is unchanged, thanks to Peter Haverty (PR#16491). * More consistent, partly not back-compatible behavior of NA and NaN coercion to complex numbers, operations less often resulting in complex NA (NA_complex_). * lengths() considers methods for length and [[ on x, so it should work automatically on any objects for which appropriate methods on those generics are defined. * The logic for selecting the default screen device on OS X has been simplified: it is now quartz() if that is available even if environment variable DISPLAY has been set by the user. The choice can easily be overridden _via_ environment variable R_INTERACTIVE_DEVICE. * On Unix-like platforms which support the getline C library function, system(*,intern = TRUE) no longer truncates (output) lines longer than 8192 characters, thanks to Karl Millar. (PR#16544) * rank() gains a ties.method = "last" option, for convenience (and symmetry). * regmatches(invert = NA) can now be used to extract both non-matched and matched substrings. * data.frame() gains argument fix.empty.names; as.data.frame.list() gets new cut.names, col.names and fix.empty.names. * plot(x ~ x, *) now warns that it is the same as plot(x ~ 1, *). * recordPlot() has new arguments load and attach to allow package names to be stored as part of a recorded plot. replayPlot() has new argument reloadPkgs to load/attach any package names that were stored as part of a recorded plot. * S4 dispatch works within calls to .Internal(). This means explicit S4 generics are no longer needed for unlist() and as.vector(). * Only font family names starting with "Hershey" (and not "Her" as before) are given special treatment by the graphics engine. * S4 values are automatically coerced to vector (via as.vector) when subassigned into atomic vectors. * findInterval() gets a left.open option. * The version of LAPACK included in the sources has been updated to 3.6.0, including those 'deprecated' routines which were previously included. _Ca_ 40 double-complex routines have been added at the request of a package maintainer. As before, the details of what is included are in src/modules/lapack/README and this now gives information on earlier additions. * tapply() has been made considerably more efficient without changing functionality, thanks to proposals from Peter Haverty and Suharto Anggono. (PR#16640) * match.arg(arg) (the one-argument case) is faster; so is sort.int(). (PR#16640) * The format method for object_size objects now also accepts "binary" units such as "KiB" and e.g., "Tb". (Partly from PR#16649.) * Profiling now records calls of the form foo::bar and some similar cases directly rather than as calls to . Contributed by Winston Chang. * New string utilities startsWith(x, prefix) and endsWith(x, suffix). Also provide speedups for some grepl("^...",*) uses (related to proposals in PR#16490). * Reference class finalizers run at exit, as well as on garbage collection. * Avoid parallel dependency on stats for port choice and random number seeds. (PR#16668) * The radix sort algorithm and implementation from data.table (forder) replaces the previous radix (counting) sort and adds a new method for order(). Contributed by Matt Dowle and Arun Srinivasan, the new algorithm supports logical, integer (even with large values), real, and character vectors. It outperforms all other methods, but there are some caveats (see ?sort). * The order() function gains a method argument for choosing between "shell" and "radix". * New function grouping() returns a permutation that stably rearranges data so that identical values are adjacent. The return value includes extra partitioning information on the groups. The implementation came included with the new radix sort. * rhyper(nn, m, n, k) no longer returns NA when one of the three parameters exceeds the maximal integer. * switch() now warns when no alternatives are provided. * parallel::detectCores() now has default logical = TRUE on all platforms - as this was the default on Windows, this change only affects Sparc Solaris. Option logical = FALSE is now supported on Linux and recent versions of OS X (for the latter, thanks to a suggestion of Kyaw Sint). * hist() for "Date" or "POSIXt" objects would sometimes give misleading labels on the breaks, as they were set to the day before the start of the period being displayed. The display format has been changed, and the shift of the start day has been made conditional on right = TRUE (the default). (PR#16679) * R now uses a new version of the logo (donated to the R Foundation by RStudio). It is defined in .svg format, so will resize without unnecessary degradation when displayed on HTML pages-there is also a vector PDF version. Thanks to Dirk Eddelbuettel for producing the corresponding X11 icon. * New function .traceback() returns the stack trace which traceback() prints. * lengths() dispatches internally. * dotchart() gains a pt.cex argument to control the size of points separately from the size of plot labels. Thanks to Michael Friendly and Milan Bouchet-Valat for ideas and patches. * as.roman(ch) now correctly deals with more diverse character vectors ch; also arithmetic with the resulting roman numbers works in more cases. (PR#16779) * prcomp() gains a new option rank. allowing to directly aim for less than min(n,p) PC's. The summary() and its print() method have been amended, notably for this case. * gzcon() gains a new option text, which marks the connection as text-oriented (so e.g. pushBack() works). It is still always opened in binary mode. * The import() namespace directive now accepts an argument except which names symbols to exclude from the imports. The except expression should evaluate to a character vector (after substituting symbols for strings). See Writing R Extensions. * New convenience function Rcmd() in package tools for invoking R CMD tools from within R. * New functions makevars_user() and makevars_site() in package tools to determine the location of the user and site specific Makevars files for customizing package compilation.- 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.)- 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.- Some version numbers of recommended packages corrected- Release numbers for sub-packages improved- added MakefileTypo.patch to enable building for 12.2 was a one charcter show stopper- 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.- 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.- 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.- 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- 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- Disable building man files for openSUSE:42.- 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.- 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.- 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).- 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.- Remove tex(inconsolata.sty) BuildRequires for SLE_12 builds (like older SLE releases).- 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")@prototype now print() and str() without error. * identical() now also looks at the S4 bit. * hist(x, breaks) is more robust in adding a small fuzz to few breaks when some are very large. (PR#15988) * sub() and gsub() did not handle regular expressions like "\s{2,}" properly if the text contained NA or non-ascii elements in a UTF-8 locale. Part of this was due to a bug in the TRE library. (PR#16009) * RShowDoc("NEWS") now displays the PDF version. * Matrices and arrays with last dimension zero did not print at all or incompletely. (PR#16012) * plot.histogram() and hence hist() now respect the xaxs, yaxs and lab graphics parameters. (PR#16021) * bw.SJ(x) and other bw.*() no longer segfault when x contains non-finite values. (PR#16024) * R CMD Rd2pdf unintentionally ignored its --os option. * The internal method of download.file() was not reporting file sizes and progress correctly on files larger than 2GB (inherited from libxml2). This is corrected for 64-bit builds (32-bit platforms may not support such files, but where possible will be supported in future versions of R). * Work around a bug in OS X Yosemite where key environment variables may be duplicated causing issues in subprocesses. The duplicates are now removed on R startup (via Rprofile). 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