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File R-base.changes of Package R-base
------------------------------------------------------------------- Thu Feb 29 09:49:16 UTC 2024 - Detlef Steuer <detlef.steuer@gmx.de> - CHANGES IN R 4.3.3: NEW FEATURES: * iconv() now fixes up variant encoding names such as "utf8" case-insensitively. DEPRECATED AND DEFUNCT: * The legacy encoding = "MacRoman" is deprecated in pdf() and postscript(): support was incomplete in earlier versions of R. BUG FIXES: * Arguments are now properly forwarded to methods on S4 generics with ... in the middle of their formal arguments. This was broken for the case when a method introduced an argument but did not include ... in its own formals. Thanks to Herv'e Pag`es for the report PR#18538. * Some invalid file arguments to pictex(), postscript() and xfig() opened a file called NA rather than throw an error. These included postscript(NULL) (which some people expected to work like pdf(NULL)). * Passing filename = NA to svg(), cairo_pdf(), cairo_ps() or the Cairo-based bitmap devices opened a file called NA: it now throws an error. * quartz(file = NA) opened a file called NA, including when used as a Quartz-based bitmap device. It now gives an error. * rank(<long vector>) now works, fixing PR#18617, thanks to Ilia Kats. * seq.int() did not adequately check its length.out argument. * match(<POSIXct>, .) is correct again for differing time zones, ditto for "POSIXlt", fixing PR#18618 reported by Bastian Klein. * drop.terms(*, dropx = <0-length>) now works, fixing PR#18563 as proposed by Mikael Jagan. * drop.terms(*) keeps + offset(.) terms when it should, PR#18565, and drop.terms() no longer makes up a response, PR#18566, fixing both bugs thanks to Mikael Jagan. * getS3method("t", "test") no longer finds the t.test() function, fixing PR#18627. * pdf() and postscript() support for the documented Adobe encodings "Greek" and "Cyrilllic" was missing (although the corresponding Windows' codepages could be used). * Computations of glyph metric information for pdf() and postscript() did not take into account that transliteration could replace one character by two or more (only seen on macOS 14) and typically warned that the information was not known. * rank(x) no longer overflows during integer addition, when computing rank average for largish but not-yet long vector x, fixing PR#18630, thanks to Ilia Kats. * list.files() on Windows now returns also files with names longer that 260 bytes (the Windows limit is 260 characters). Previously, some file names particularly with 'East Asian' characters were omitted. * cov2cor(<0 x 0>) now works, fixing PR#18423 thanks to Mikael Jagan and Elin Waring. * cov2cor(<negative diagonal>) and similar now give one warning instead of two, with better wording, fixing PR#18424 thanks to Mikael Jagan. * tools:: startDynamicHelp() now ensures port is in proper range, fixing PR#18645. * pbeta(x, a,b) is correct now for x=0 or 1 in the boundary cases where a or b or both are 0, fixing PR#18672 thanks to Michael Fay. * pmatch(x, table) for large table, also called for data frame row selection, dfrm[nm, ], is now interruptible, fixing PR#18656. * predict(<rank-deficient lm>, newdata=*) fix computing of nbasis, see Russ Lenth's comment 29 in PR#16158. * Added a work-around for a bug in macOS 14.3.1 and higher which prevents R plots in the Quartz Cocoa device from updating on screen. ------------------------------------------------------------------- Fri Nov 3 09:49:06 UTC 2023 - Detlef Steuer <detlef.steuer@gmx.de> - CHANGES IN R 4.3.2: NEW FEATURES: * The default initialization of the "repos" option from the repositories file at startup can be skipped by setting environment variable R_REPOSITORIES to NULL such that getOption("repos") is empty if not set elsewhere. * qr.X() is now an implicit S4 generic in methods. * iconv(to = "ASCII//TRANSLIT") is emulated using substitution on platforms which do not support it (notably Alpine Linux). This should give a human-readable conversion in ASCII on all platforms (rather than NA_character_). * trans3d() gains options continuous and verbose addressing the problem of possible "wrap around" when projecting too long curves, as reported by Achim Zeileis in PR#18537. * tools::showNonASCII() has been rewritten to work better on macOS 14 (which has a changed implementation of iconv()). * tiff(type = "quartz") (the default on macOS) now warns if compression is specified: it continues to be ignored. INSTALLATION on a UNIX-ALIKE: * There is some support for building with Intel's LLVM-based compilers on x86_64 Linux, such as (C) icx, (C++) ipcx and (Fortran) ifx from oneAPI 2023.x.y. * There is support for using LLVM's flang-new as the Fortran compiler from LLVM 16.0.x (preferably 17.0.0 or later). UTILITIES: * R CMD check reports the use of the Fortran 90 random number generator RANDOM_NUMBER() and the subroutines to initialize it. 'Writing R Extensions' has example code to use R's RNGs from Fortran. BUG FIXES: * substr(x, n, L) <- cc now works (more) correctly for multibyte UTF-8 strings x when L > nchar(x), thanks to a report and patch by 'Architect 95'. * contrib.url(character()) now returns 0-length character() as documented, which also avoids spurious warnings from available.packages() et al. in the edge case of an empty vector of repository URLs. * readChar(., 4e8) no longer fails, thanks to Kodi Arfer's report (PR#18557). * lapply(<list>, as.data.frame) no longer warns falsely for some base vector components. * Communication between parent and child processes in the multicore part of parallel could fail on platforms that do not support an arbitrarily large payload in system functions read()/write() on pipes (seen on macOS where a restriction to INT_MAX bytes is documented, without doing a partial read unlike Linux). The payload is now split into 1Gb chunks to avoid that problem. (PR#18571) * qqplot(x,y, conf.level=.) gives better confidence bounds when length(x) != length(y), thanks to Alexander Ploner's report and patch proposal (PR#18557). * norm(<0-length>, "2") now gives zero instead of an error, as all the other norm types, thanks to Mikael Jagan's PR#18542. * Build-stage Rd macros \packageAuthor and \packageMaintainer now process Authors@R, fixing NA results when the package DESCRIPTION omits Author and Maintainer fields. * Formatting and printing complex numbers could give things like 0.1683-0i because of rounding error: -0i is now replaced by +0i. * postscript() refused to accept a title comment containing the letter "W" (PR#18599). * isoreg(c(1,Inf)) signals an error instead of segfaulting, fixing PR#18603. * tiff(type = "Xlib") was only outputting the last page of multi-page plots. * tools::latexToUtf8() again knows about \~{n} and other letters with tilde, fixing a regression in R 4.3.0, and about \^{i} as an alternative to \^{\i} (similarly with other accents). Furthermore, LaTeX codes for accented I letters are now correctly converted, also fixing related mistakes in tools::encoded_text_to_latex(). * tar(*, tar = "internal") no longer creates out-of-spec tar files in the very rare case of user or group names longer than 32 bytes, fixing PR#17871 with thanks to Ivan Krylov. * When using the "internal" timezone datetime code, adding a fraction of a second no longer adds one second, fixing PR#16856 from a patch by Ivan Krylov. * tools::checkRd() no longer produces spurious notes about "unnecessary braces" from multi-line Rd results of \Sexpr macros. ------------------------------------------------------------------- Fri Jun 16 10:46:51 UTC 2023 - Detlef Steuer <detlef.steuer@gmx.de> - CHANGES IN R 4.3.1: C-LEVEL FACILITIES: * The C-level API version of R's integrate(), Rdqags() in Applic.h, now returns the correct number of integrand evaluations neval, fixing PR#18515 reported and diagnosed by Stephen Wade. * The C prototypes for LAPACK calls dspgv and dtptrs in R_exts/Lapack.h had one too many and one too few character length arguments - but this has not caused any known issues. To get the corrected prototypes, include #include <Rconfig.h> // for PR18534fixed #ifdef PR18534fixed # define usePR18534fix 1 #endif #include <R_exts/Lapack.h> in your C/C++ code (PR#18534). INSTALLATION: * Many of the checks of esoteric Internet operations and those using unreliable external sites have been moved to a new target that is not run by default and primarily intended for the core developers. To run them use cd tests; make test-Internet-dev BUG FIXES: * .S3methods(), typically called from methods(), again marks methods from package base as visible. Also, the visibility of non-base methods is again determined by the method's presence in search(). * tools::Rdiff() is now more robust against invalid strings, fixing installation tests on Windows without Rtools installed (PR#18530). * Fix (new) bug in hcl.colors(2, *), by Achim Zeileis (PR#18523). * head(., <illegal>) and tail(..) now produce more useful "Error in ...." error messages, fixing PR#18362. * Package code syntax on Windows is checked in UTF-8 when UTF-8 is the native encoding. * na.contiguous(x) now also returns the first run, when it is at the beginning and there is a later one of the same length; reported to R-devel, including a fix, by Georgi Boshnakov. Further, by default, it modifies only an existing attr(*,"tsp") but otherwise no longer sets one. * chol(<not pos.def>, pivot = <T|F>) now gives a correct error or warning message (depending on pivot), thanks to Mikael Jagan's (PR#18541). ------------------------------------------------------------------- Fri Apr 21 17:43:15 UTC 2023 - Detlef Steuer <detlef.steuer@gmx.de> - CHANGES IN R 4.3.0: SIGNIFICANT USER-VISIBLE CHANGES: * Calling && or || with LHS or (if evaluated) RHS of length greater than one is now always an error, with a report of the form 'length = 4' in coercion to 'logical(1)' Environment variable _R_CHECK_LENGTH_1_LOGIC2_ no longer has any effect. NEW FEATURES: * The included BLAS sources have been updated to those shipped with LAPACK version 3.10.1. (This caused some platform-dependent changes to package check output.) And then to the sources from LAPACK version 3.11.0 (with changes only to double complex subroutines). * The included LAPACK sources have been updated to include the four Fortran 90 routines rather than their Fortran 77 predecessors. This may give some different signs in SVDs or eigendecompositions.. (This completes the transition to LAPACK 3.10.x begun in R 4.2.0.) * The LAPACK sources have been updated to version 3.11.0. (No new subroutines have been added, so this almost entirely bug fixes: Those fixes do affect some computations with NaNs, including R's NA.) * The parser now signals _classed_ errors, notably in case of the pipe operator |>. The error object and message now give line and column numbers, mostly as proposed and provided by Duncan Murdoch in PR#18328. * toeplitz() is now generalized for asymmetric cases, with a toeplitz2() variant. * xy.coords() and xyz.coords() and consequently, e.g., plot(x,y, log = "y") now signal a _classed_ warning about negative values of y (where log(.) is NA). Such a warning can be specifically suppressed or caught otherwise. * Regular expression functions now check more thoroughly whether their inputs are valid strings (in their encoding, e.g. in UTF-8). * The performance of grep(), sub(), gsub() and strsplit() has been improved, particularly with perl = TRUE and fixed = TRUE. Use of useBytes = TRUE for performance reasons should no longer be needed and is discouraged: it may lead to incorrect results. * apropos() gains an argument dot_internals which is used by the completion (help(rcompgen)) engine to also see base internals such as .POSIXct(). * Support in tools::Rdiff() for comparing uncompressed PDF files is further reduced - see its help page. * qqplot(x, y, ...) gains conf.level and conf.args arguments for computing and plotting a confidence band for the treatment function transforming the distribution of x into the distribution of y (Switzer, 1976, _Biometrika_). Contributed by Torsten Hothorn. * Performance of package_dependencies() has been improved for cases when the number of dependencies is large. * Strings newly created by gsub(), sub() and strsplit(), when any of the inputs is marked as "bytes", are also marked as "bytes". This reduces the risk of creating invalid strings and accidental substitution of bytes deemed invalid. * Support for readLines(encoding = "bytes") has been added to allow processing special text files byte-by-byte, without creating invalid strings. * iconv(from = "") now takes into account any declared encoding of the input elements and uses it in preference to the native encoding. This reduces the risk of accidental creation of invalid strings, particularly when different elements of the input have different encoding (including "bytes"). * Package repositories in getOption("repos") are now initialized from the repositories file when utils is loaded (if not already set, e.g., in .Rprofile). (From a report and patch proposal by Gabriel Becker in PR#18405.) * compactPDF() gets a verbose option. * type.convert() and hence read.table() get new option tryLogical = TRUE with back compatible default. When set to false, converts "F" or "T" columns to character. * Added new unit prefixes "R" and "Q" for abbreviating (unrealistically large) sizes beyond 10^{27} in standard = "SI", thanks to Henrik Bengtsson's PR#18435. * as.data.frame()'s default method now also works fine with atomic objects inheriting from classes such as "roman", "octmode" and "hexmode", such fulfilling the wish of PR#18421, by Benjamin Feakins. * The as.data.frame.vector() utility now errors for wrong-length row.names. It warned for almost six years, with "Will be an error!". * sessionInfo() now also contains La_version() and reports codepage and timezone when relevant, in both print() and toLatex() methods which also get new option tzone for displaying timezone information when locale = FALSE. * New function R_compiled_by() reports the C and Fortran compilers used to build R, if known. * predict(<lm>, newdata = *) no longer unnecessarily creates an offset of all 0s. * solve() for complex inputs now uses argument tol and by default checks for 'computational singularity' (as it long has done for numeric inputs). * predict(<rank-deficient lm>, newdata=*) now obeys a new argument rankdeficient, with new default "warnif", warning only if there are non-estimable cases in newdata. Other options include rankdeficient = "NA", predicting NA for non-estimable newdata cases. This addresses PR#15072 by Russ Lenth and is based on his original proposal and discussions in PR#16158 also by David Firth and Elin Waring. Still somewhat experimental. * Rgui console implementation now works better with the NVDA screen reader when the full blinking cursor is selected. The underlying improvements in cursor handling may help also other screen readers on Windows. * The drop-field control in GraphApp can now be left with the TAB key and all controls can be navigated in the reverse order using the Shift+TAB key, improving accessibility of the Rgui configuration editor. * qnorm(<very large negative>, log.p=TRUE) is now fully accurate (instead of to "only" minimally five digits). * demo(error.catching) now also shows off withWarnings() and tryCatchWEMs(). * As an experimental feature the placeholder _ can now also be used in the rhs of a forward pipe |> expression as the first argument in an extraction call, such as _$coef. More generally, it can be used as the head of a chain of extractions, such as _$coef[[2]]. * Spaces in the environment variable used to choose the R session's temporary directory (TMPDIR, TMP and TEMP are tried in turn) are now fatal. (On Windows the 'short path' version of the path is tried and used if that does not contain a space.) * all.equal.numeric() gets a new optional switch giveErr to return the numeric error as attribute. Relatedly, stopifnot(all.equal<some>(a, b, ..)) is as "smart" now, as stopifnot(all.equal(....)) has been already, thus allowing customized all.equal<Some>() wrappers. * R on Windows is now able to work with path names longer than 260 characters when these are enabled in the system (requires at least Windows 10 version 1607). Packages should be updated to work with long paths as well, instead of assuming PATH_MAX to be the maximum length. Custom front-ends and applications embedding R need to update their manifests if they wish to allow this feature. See <https://blog.r-project.org/2023/03/07/path-length-limit-on-windows> for more information. * 'Object not found' and 'Missing argument' errors now give a more accurate error context. Patch provided by Lionel Henry in PR#18241. * The @ operator is now an S3 generic. Based on contributions by Tomasz Kalinowski in PR#18482. * New generic chooseOpsMethod() provides a mechanism for objects to resolve cases where two suitable methods are found for an Ops Group Generic. This supports experimenting with alternative object systems. Based on contributions by Tomasz Kalinowski in PR#18484. * inherits(x, what) now accepts values other than a simple character vector for argument what. A new generic, nameOfClass(), is called to resolve the class name from what. This supports experimenting with alternative object systems. Based on contributions by Tomasz Kalinowski in PR#18485. * Detection of BLAS/LAPACK in use (sessionInfo()) with FlexiBLAS now reports the current backend. * The "data.frame" method for subset() now warns about extraneous arguments, typically catching the use of = instead of == in the subset expression. * Calling a:b when numeric a or b is longer than one may now be made into an error by setting environment variable _R_CHECK_LENGTH_COLON_ to a true value, along the proposal in PR#18419 by Henrik Bengtsson. * density(x, weights = *) now warns if automatic bandwidth selection happens without using weights; new optional warnWbw may suppress the warning. Prompted by Christoph Dalitz' PR#18490 and its discussants. * rm(list = *) is faster and more readable thanks to Kevin Ushey's PR#18492. * The plot.lm() function no longer produces a normal Q-Q plot for GLMs. Instead it plots a half-normal Q-Q plot of the absolute value of the standardized deviance residuals. * The print() method for class "summary.glm" no longer shows summary statistics for the deviance residuals by default. Its optional argument show.residuals can be used to show them if required. * The tapply() function now accepts a data frame as its X argument, and allows INDEX to be a formula in that case. by.data.frame() similarly allows INDICES to be a formula. * The performance of df[j] <- value (including for missing j) and write.table(df) has been improved for data frames df with a large number of columns. (Thanks to Gabriel Becker's PR#18500, PR#18503 and discussants, prompted by a report from Toby Dylan Hocking on the R-devel mailing list.) * The matrix multiply operator %*% is now an S3 generic, belonging to new group generic matrixOps. From Tomasz Kalinowski's contribution in PR#18483. * New function array2DF() to convert arrays to data frames, particularly useful for the list arrays created by tapply(). DATES and TIMES: * On platforms where (non-UTC) datetimes before 1902 (or before 1900 as with system functions on recent macOS) are guessed by extrapolating time zones from 1902-2037, there is a warning at the first use of extrapolation in a session. (As all time zones post 2037 are extrapolation, we do not warn on those.) * (Platforms using --with-internal-tzone, including Windows and by default macOS). How years are printed in dates or date-times can be controlled by environment variable R_PAD_YEARS_BY_ZERO. The default remains to pad to 4 digits by zeroes, but setting value no gives no padding (as used by default by glibc). * strftime() tries harder to determine the offset for the "%z" format, and succeeds on the mainstream R platforms. * strftime() has a limit of 2048 bytes on the string produced - attempting to exceed this is an error. (Previously it silently truncated at 255 bytes.) * sessionInfo() records (and by default prints) the system time zone as part of the locale information. Also, the source (system/internal) of the date-time conversion and printing functions. * Objects of class "POSIXlt" created in this version of R always have 11 components: component zone is always set, and component gmtoff is set for times in UTC and usually set on the (almost all) platforms which have C-level support, otherwise is NA. * There are comprehensive validity checks on the structure of objects of class "POSIXlt" when converting (including formatting and printing). (This avoids mis-conversions of hand-crafted objects.) * There is some support for using the native date-time routines on macOS: this is only viable on recent versions (e.g. 12.6 and 13) and does get wrong some historical changes (before 1900, during WWII). Use of --with-internal-tzone remains the default. * as.POSIXct(<numeric>) and as.POSIXlt(.) (without specifying origin) now work. So does as.Date(<numeric>). * as.Date.POSIXct(., tz) now treats several tz values, notably "GMT" as equivalent to "UTC", proposed and improved by Michael Chirico and Joshua Ulrich in PR#17674. * Experimental balancePOSIXlt() utility allows using "ragged" and or out-of-range "POSIXlt" objects more correctly, e.g., in subsetting and subassignments. Such objects are now documented. More experimentally, a "POSIXlt" object may have an attribute "balanced" indicating if it is known to be filled or fully balanced. * Functions axis.Date() and axis.POSIXct() are rewritten to gain better default tick locations and better default formats by using prettyDate(). Thanks to Swetlana Herbrandt. * The mapping of Windows' names for time zones to IANA's 'Olson' names has been updated. When ICU is available (it is by default), it is used to get a mapping for the current region set in Windows. This can be overridden by setting environment variable TZ to the desired Olson name - see OlsonNames() for those currently available. GRAPHICS: * The graphics engine version, R_GE_version, has been bumped to 16 and so packages that provide graphics devices should be reinstalled. * The grDevices and grid packages have new functions for rendering typeset glyphs, primarily: grDevices::glyphInfo() and grid::grid.glyph(). Rendering of typeset glyphs is only supported so far on the Cairo-based graphics devices and on the pdf() and quartz() devices. * The defined behaviour for "clear" and "source" compositing operators (via grid::grid.group()) has been changed (to align better with simple interpretation of original Porter-Duff definitions). * Support for gradients, patterns, clipping paths, masks, groups, compositing operators, and affine transformations has been added to the quartz() device. INSTALLATION on a UNIX-ALIKE: * A system installation of generic LAPACK 3.10.0 or later will be preferred to the version in the R sources. configure option --with-lapack=no (equivalently --without-lapack) forces compilation of the internal LAPACK sources. If --with-lapack is not specified, a system liblapack is looked for and used if it reports version 3.10.0 or later and does not contain BLAS routines. Packages using LAPACK will need to be reinstalled if this changes to using an external library. * On aarch64 Linux platforms using GCC, configure now defaults to -fPIC (instead of -fpic), as desired in PR#18326. * configure now checks conversion of datetimes between POSIXlt and POSIXct around year 2020. Failure (which has been seen on platforms missing tzdata) is fatal. * If configure option --with-valgrind-instrumentation is given value 1 or 2, option --with-system-valgrind-headers is now the default and ignored (with a warning). It is highly recommended that the system headers are installed alongside valgrind: they are part of its packaging on some Linux distributions and packaged separately (e.g. in the valgrind-devel RPM) on others. configure will give a warning if they are not found. The system headers will be required in a future release of R to build with valgrind instrumentation. * libcurl 8.x is now accepted by configure: despite a change in major version number it changes neither API nor ABI. INSTALLATION on WINDOWS: * The makefiles and installer scripts for Windows have been tailored to Rtools43, an update of the Rtools42 toolchain. It is based on gcc 12 and newer versions of MinGW-W64, binutils and libraries. At this time R-devel can still be built using Rtools42 without changes, but when R-devel is installed via the installer, it will by default look for Rtools43. * Old make targets rsync-extsoft and 32-bit ones that are no longer needed have been removed. * Default builds (including for packages) no longer select C99. Thus the C standard used is the default for the compiler, which for the toolchain in Rtools43 is C17. (This is consistent with Unix builds.) PACKAGE INSTALLATION: * The default C++ standard has been changed to C++17 where available (which it is on all currently checked platforms): if not C++14 or C++11 is used if available otherwise C++ is not supported. * USE_FC_LEN_T is the default: this uses the correct (compiler-dependent) prototypes for Fortran BLAS/LAPACK routines called from C/C++, and requires adjustment of many such calls - see 'Writing R Extensions' SS6.6.1. * There is initial support for C++23 as several compilers are now supporting -std=c++23 or -std=c++2b or similar. As for C++20, there no additional configure checks for C++23 features beyond a check that the compiler reports a __cplusplus value greater than that in the C++20 standard. C++ feature tests should be used. * There is support for a package to indicate the version of the C standard which should be used to compile it, and for the installing user to specify this. In most cases R defaults to the C compiler's default standard which is C17 (a `bug-fix' of C11) - earlier versions of R or compilers may have defaulted to C99. Current options are: USE_C17 Use a standard that is at most C17. The intention is to allow legacy packages to still be installed when later C standards become the default, including packages using new keywords as identifiers or with K&R-style function declarations. This will use C17 if available, falling back to C11. USE_C90 Use the C90 (aka C89) standard. (As that standard did not require compilers to identify that version, all we can verify is that the compiler does not claim to be using a later standard. It may accept C99 features - for example clang accepts // to make comments.) USE_C99 Use the C99 standard. This should be rarely needed - it avoids the few new features of C11/C17 which can be useful if a package assumes them if C17 is specified and they are not implemented. USE_C23 Use C23 (or in future, later). Compiler/library support for C23 is still being implemented, but LLVM clang from 15.0.0 and the upcoming GCC 13 have quite extensive support. These can be specified as part of the SystemRequirements field in the package's DESCRIPTION file or _via_ options --use-C17 and so on of R CMD INSTALL and R CMD SHLIB. For further details see "Writing R Extensions" SS1.2.5. * (Windows) A src/Makefile.ucrt or src/Makefile.win file is now included after R_HOME/etcR_ARCH/Makeconf and so no longer needs to include that file itself. Installation of a package with such a file now uses a site Makevars file in the same way as a package with a src/Makevars.win file would. * configure is now passed crucial variables such as CC and CFLAGS in its environment, as many packages were not setting them (as documented in 'Writing R Extensions' SS1.2). This has most effect where configure is used to compile parts of the package - most often by cmake or libtool which obfuscate the actual compile commands used. Also used for configure.win and configure.ucrt on Windows. FORTRAN FLAGS: * The flag -fno-optimize-sibling-calls is no longer forced for gfortran 7 and later. It should no longer be needed now using 'hidden' character-length arguments when calling BLAS/LAPACK routines from C/C++ is the default even for packages. (Unless perhaps packages call Fortran code from C/C++ without using R's headers and without allowing for these arguments.) C-LEVEL FACILITIES: * The deprecated S-compatibility macros DOUBLE_* in R_ext/Constants.h (included by R.h) have been removed. * The deprecated legacy typedefs of Sint and Sfloat in header R.h are no longer defined, and that header no longer includes header limits.h from C nor climits from C++. * New macro CAD5R() is provided in Rinternals.h and used in a few places in the R sources. * ALTREP now supports VECSXP vectors. Contributed by Gabor Csardi in PR#17620. * The Rcomplex definition (in header R_ext/Complex.h) has been extended to prevent possible mis-compilation when interfacing with Fortran (PR#18430). The new definition causes compiler warnings with static initializers such as {1, 2}, which can be changed to {.r=1, .i=2}. Using the new definition from C++ depends on compiler extensions supporting C features that have not been incorporated into the C++ standards but are available in g++ and clang++: this may result in C++ compiler warnings but these have been worked around for recent versions of common compilers (GCC, Apple/LLVM clang, Intel). It is intended to change the inclusion of header R_ext/Complex.h by other R headers, so C/C++ code files which make use of Rcomplex should include that header explicitly. UTILITIES: * R CMD check does more checking of package .Rd files, warning about invalid email addresses and (some) invalid URIs and noting empty \item labels in description lists. * R CMD check now also reports problems when reading package news in md (file NEWS.md) and (optionally) plain text (file NEWS) formats. * _R_CHECK_TIMINGS_ defaults to a value from the environment even for R CMD check --as-cran; this allows for exceptionally fast or slow platforms. It now applies to checking PDF and HTML versions of the manuals, and 'checking CRAN incoming feasibility'. * R CMD check can optionally (but included in --as-cran) check whether HTML math rendering _via_ KaTeX works for the package .Rd files. * Non-interactive debugger invocations can be trapped by setting the environment variable _R_CHECK_BROWSER_NONINTERACTIVE_ to a true value. This is enabled by R CMD check --as-cran to detect the use of leftover browser() statements in the package. * The use of sprintf and vsprintf from C/C++ has been deprecated in macOS 13 and is a known security risk. R CMD check now reports (on all platforms) if their use is found in compiled code: replace by snprintf or vsnprintf respectively. [*NB:* whether such calls get compiled into the package is platform-dependent.] * Where recorded at installation, R CMD check reports the C and Fortran compilers used to build R. It reports the OS in use (if known, as given by osVersion) as well as that R was built for. It notes if a C++ standard was specified which is older than the current default: many packages have used C++11 to mean 'not C++98' - as C++11 is the minimum supported since R 4.0.0, that specification can probably be removed. * R CMD INSTALL reports the compilers (and on macOS, the SDK) used, and this is copied to the output of R CMD check. Where a C++ standard is specified, it is reported. * R CMD check's 'checking compilation flags in Makevars' has been relaxed to accept the use of flags such as -std=f2008 in PKG_FFLAGS. * tools::buildVignettes() has a new argument skip, which is used by R CMD check to skip (and note) vignettes with unavailable \VignetteDepends (PR#18318). * New generic .AtNames() added to enable class-specific completions after @. The formerly internal function findMatches() is now exported, mainly for use in methods for .DollarNames() and .AtNames(). DEPRECATED AND DEFUNCT: * default.stringsAsFactors() is defunct. * Calling as.data.frame.<class>() directly (for 12 atomic classes) is going to be formally deprecated, currently activated by setting the environment variable _R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_ to non-empty, which also happens in R CMD check --as-cran. BUG FIXES: * Hashed environments with sizes less than 5 can now grow. (Reported to R-devel by Duncan Garmonsway.) * as.character(<Rd>, deparse = TRUE) failed to re-escape curly braces in LaTeX-like text. (Reported by Hadley Wickham in PR#18324.) * library() now passes its lib.loc argument when requiring Depends packages; reported (with fix) in PR#18331 by Mikael Jagan. * R CMD Stangle: improved message about 'Output' files. * head(x, n) and tail(x, n) now signal an error if n is not numeric, instead of incidentally "working" sometimes returning all of x. Reported and discussed by Colin Fay, in PR#18357. * The "lm" method for summary() now gives the correct F-statistic when the model contains an offset. Reported in PR#18008. * C() and `contrasts<-`() now preserve factor level names when given a function object (as opposed a function name which did preserve names). Reported in PR#17616. * c(a = 1, 2)[[]] no longer matches 2 but rather signals a _classed_ error. Reported and analysed by Davis Vaughan in PR#18367, a duplicate of PR#18004, by Jan Meis et al. For consistency, NULL[[]] is also erroneous now. x[[]] <- v gives an error of the same class "MissingSubscriptError". * The relist() function of utils now supports NULL elements in the skeleton (PR#15854). * ordered(levels = *) (missing x) now works analogously to factor(, ordered=TRUE); reported (with fix) by Achim Zeileis in PR#18389. * User-defined Rd macro definitions can now span multiple lines, thanks to a patch from Duncan Murdoch. Previously, the Rd parser silently ignored everything after the first line. * Plain-text help (tools::Rd2txt()) now preserves an initial blank line for text following description list items. * tools::Rd2HTML() and tools::Rd2latex() no longer split \arguments and \value lists at Rd comments. * tools::Rd2latex() now correctly handles optional text outside \items of argument lists as well as bracketed text at the beginning of sections, e.g., \value{[NULL]}. * as.character(<POSIXt>) now behaves more in line with the methods for atomic vectors such as numbers, and is no longer influenced by options(). Ditto for as.character(<Date>). The as.character() method gets arguments digits and OutDec with defaults _not_ depending on options(). Use of as.character(*, format = .) now warns. * Similarly, the as.character.hexmode() and *.octmode() methods also behave as good citizen methods and back compatibility option keepStr = TRUE. * The as.POSIXlt(<POSIXlt>) and as.POSIXct(<POSIXct>) default methods now do obey their tz argument, also in this case. * as.POSIXlt(<Date>) now does apply a tz (time zone) argument, as does as.POSIXct(); partly suggested by Roland Fuss on the R-devel mailing list. * as.Date.POSIXlt(x) now also works when the list components are of unequal length, aka "partially filled" or "ragged". * expand.model.frame() looked up variables in the wrong environment when applied to models fitted without data. Reported in PR#18414. * time() now (also) uses the ts.eps = getOption("ts.eps") argument and thus by default rounds values very close to the start (or end) of a year. Based on a proposal by Andre"i V. Kostyrka on R-help. * Printing of a factanal() result with just one factor and sort = TRUE now works regularly, fixing PR#17863 by Timothy Bates, thanks to the 'R Contributors' working group. * Printing 0-length objects of class "factor", "roman", "hexmode", "octmode", "person", "bibentry", or "citation" now prints something better, one of which fixes PR#18422, reported by Benjamin Feakins. * Sys.timezone() queries timedatectl only if systemd is loaded; addressing a report by Jan Gorecki in PR#17421. * The formula method of cor.test() had scoping problems when environment(formula) was not the calling environment; reported with a patch proposal by Mao Kobayashi in PR#18439. * attach() of an environment with active bindings now preserves the active bindings. Reported by Kevin Ushey in PR#18425. * BLAS detection now works also with system-provided libraries not available as regular files. This fixes detection of the Accelerate framework on macOS since Big Sur. Reported by David Novgorodsky. * download.file() gives a helpful error message in case of an invalid download.file.method option, thanks to Colin Fay's report in PR#18455. * Sporadic crashes of Rterm when using completion have been fixed. * Rprof() is now more reliable. A livelock in thread initialization with too short sampling interval has been fixed on macOS. A deadlock in using the C runtime has been fixed on Windows. A potential deadlock has been prevented on Unix. * Cursor placement in Rgui now works even after a fixed-width font is selected. * Mandatory options (options()) are now set on startup so that saving and restoring them always works (PR#18372). * Package installation, R CMD INSTALL or install.packages(*), now parses each of the <pkg>/R/*.R files individually instead of first concatenating and then parse()ing the large resulting file. This allows parser or syntax errors to be diagnosed with correct file names and line numbers, thanks to Simon Dedman's report and Bill Dunlap's patch in PR#17859. This _does_ require syntactically self contained R source files now, fixing another inadvertent bug. * predict.lm(<model with offset>) now finds the offset in the correct environment, thanks to Andr'e Gillibert's report and patch in PR#18456. * getInitial(<formula>) now finds the selfStart model in the correct environment. (Reported by Ivan Krylov in PR#18368.) * Fix for possible segfault when using recently-added graphics features, such as gradients, clipping paths, masks, and groups with pdf(file=NULL). * class(m) <- class(m) no longer changes a matrix m by adding a class _attribute_. * packageDate(pkg) now only warns once if there is no pkg. * When ts() creates a multivariate time series, "mts", it also inherits from "array" now, and is.mts() is documented _and_ stricter. * Rd2txt() now preserves line breaks of \verb Rd content and from duplicated \cr. The former also fixes the rendering of verbatim output from Rd \Sexpr in plain-text help. * uniroot(f, interval) should no longer wrongly converge _outside_ the interval in some cases where abs(f(x)) == Inf for an x at the interval boundary, thanks to posts by Ben Bolker and Serguei Sokol on R-devel. * Vectorized alpha handling in palette functions such as in gray(), rainbow(), or hcl.colors() works correctly now, thanks to Achim Zeileis' report and patch in PR#18476. * Formatting and print()ing of bibentry objects has dropped the deprecated citation.bibtex.max argument, such that the bibtex argument's default for print.bibentry() depends directly on the citation.bibtex.max option, whereas in format.bibentry() the option no longer applies. * Attempting to use a character string naming a foreign function entry point in a foreign function call in a package will now signal an error if the packages has called R_forceSymbols to specify that symbols must be used. * An error in table() could permanently set options(warn=2) promoting all subsequent warnings to errors. * The sigma() function gave misleading results for binary GLMs. A new method for objects of class "glm" returns the square root of the estimate of the dispersion parameter using the same calculation as summary.glm(). * bs() and ns() in the (typical) case of automatic knot construction, when some of the supposedly inner knots coincide with boundary knots, now moves them inside (with a warning), building on PR#18442 by Ben Bolker. * R CMD on Windows now skips the site profile with --no-site-file and --vanilla even when R_PROFILE is set (PR#18512, from Kevin Ushey). ------------------------------------------------------------------- Mon Apr 10 11:06:06 UTC 2023 - Detlef Steuer <detlef.steuer@gmx.de> - add patch to build with libcurl >= 8 ------------------------------------------------------------------- Wed Mar 15 11:30:49 UTC 2023 - Detlef Steuer <detlef.steuer@gmx.de> - CHANGES IN R 4.2.3: C-LEVEL FACILITIES: * The definition of DL_FUNC in R_ext/Rdynload.h has been changed to be fully C-compliant. This means that functions loaded _via_ for example R_GetCCallable need to be cast to an appropriate type if they have any arguments. * .Machine has a new element sizeof.time_t to identify old systems with a 32-bit type and hence a limited range of date-times (and limited support for dates millions of years from present). PACKAGE INSTALLATION: * (Windows) The default C++ standard had accidentally been left at C++11 when it was changed to C++14 on Unix. BUG FIXES: * As "POSIXlt" objects may be "partially filled" and their list components meant to be recycled, length() now is the length of the longest component. * as.POSIXlt.Date() could underflow for dates in the far past (more than half a million years BCE). * as.Date.POSIXlt(x) would return "1970-01-01" instead of NA in R 4.2.2, e.g., for x <- as.POSIXlt(c("2019-01-30","2001-1-1")) x$mon <- c(0L, NA); as.Date(x) * R CMD check failed to apply enabled _R_CHECK_SUGGESTS_ONLY_ to examples and vignettes (regression in R 4.2.0). * R CMD check did not re-build vignettes in separate processes by default (regression in R 4.2.0). * Running examples from HTML documentation now restores previous knitr settings and options (PR#18420). * Quartz: fonts are now located using Core Graphics API instead of deprecated ATS which is no longer supported in the macOS 13 SDK (PR#18426). This also addresses an issue where the currently used font in the Quartz device context was not correctly retained. * (Windows) Math symbols in text drawing functions are again rendered correctly (PR#18440). This fixes a regression in R 4.2.1 caused by a fix in PR#18382 which uncovered an issue in GraphApp due to which the symbol charset was not used with TT Symbol font face. * (Windows) Installing a package with a src/Makefile.{win,ucrt} file includes ~/.R/Makevars.win64 in the search for user makevars, as documented in "R Installation and Administration" and done for packages with a src/Makevars.{win,ucrt} file. * format(<POSIXlt_w/_unbalanced_sec>, "....%OS<n>") with n > 0 no longer accidentally uses the unbalanced seconds, thanks to Suharto Anggono's report (including patch) in PR#18448. * solve.default(a, b) works around issues with some versions of LAPACK when a contains NA or NaN values. * When UseMethod() cannot dispatch, it no longer segfaults producing the error message in case of a long class(), thanks to Joris Vankerschaver's report (including patch) in PR#18447. * When example(foo, ..) produces graphics on an interactive device it needs to open itself, it now leaves devAskNewPage() unchanged even when it was FALSE, thus fixing a 14 years old '<FIXME>'. * packageDescription() again catches errors from encoding conversions. This also fixes broken packageVersion() in C locale on systems where iconv does not support transliteration. ------------------------------------------------------------------- Mon Oct 31 18:56:44 UTC 2022 - Detlef Steuer <detlef.steuer@gmx.de> - CHANGES IN R 4.2.2: NEW FEATURES: * tools::Rdiff(useDiff = TRUE) checks for the presence of an external diff command and switches to useDiff = FALSE if none is found. This allows R CMD Rdiff to always work. * On Windows, environment variable R_LIBCURL_SSL_REVOKE_BEST_EFFORT can be used to switch to only 'best-effort' SSL certificate revocation checks with the default "libcurl" download method. This reduces security, but may be needed for downloads to work with MITM proxies (PR#18379). * (macOS) The run-time check for libraries from XQuartz for X11 and Tcl/Tk no longer uses otool from the Apple Developer Tools (PR#18400). * The LaTeX style for producing the PDF manuals, Rd.sty, now loads the standard amsmath, amsfonts and amssymb packages for greater coverage of math commands in the Rd \eqn and \deqn macros. The \mathscr LaTeX command is also provided (via the mathrsfs package, if available, or the amsfonts bundle otherwise), fulfilling the wish of PR#18398. * (Windows) The default format of readClipboard() and writeClipboard() has been changed to 13 (CF_UNICODETEXT). INSTALLATION on a UNIX-ALIKE: * The PDF manuals (if built) can be compacted by the new target make compact-pdf (at the top level or in directory doc/manual). * There is now configure support for LLVM clang 15 on Linux, which defaults to position-independent (PIE) executables whereas gfortran does not. * Many small changes to ease compilation (and suppress warnings) with LLVM clang 15. BUG FIXES: * Rscript -e would fail if stdin were closed (Reported by Henrik Bengtsson.) * qt(*, log.p=TRUE) in outer tails no longer produces NaN in its final steps, thus fixing PR#18360. * tools::Rd2latex() now escapes hashes and ampersands when writing URLs, fixing LaTeX errors with such URLs in \tabular. * When isGeneric(f, fdef=*) is used with mismatching names, the warning is better understandable; reported (with fix) in PR#18370 by Gabe Becker. * poly(x, n) now works again (and is now documented) when x is a "Date" or "POSIXct" object, or of another class while fulfilling mode(x) == "numeric". This also enables poly(x, *, raw=TRUE) for such variables. Reported by Michael Chirico to R-devel. * write.table(), write.csv() and write.csv2() restore their numerical precision (internal equivalent of digits = 15) after an interrupt (PR#18384). * One can now read also byte FF from a clipboard connection (PR#18385). * source("") and source(character()) now give more helpful error messages. * R CMD check --as-cran set _R_CHECK_TIMINGS_ too late to have the intended effect. * as.POSIXlt(x) now also works with very large dates x, fixing PR#18401 reported by Hannes M"uhleisen. * Files can now be extracted even from very large zip archives (PR#18390, thanks to Martin Jakt). * Non-finite objects of class "POSIXlt" are now correctly coerced to classes "Date" and "POSIXct"; following up on the extension to format() them correctly. * Added methods for is.finite(), is.infinite() and is.nan() for "POSIXlt" date-time objects. ------------------------------------------------------------------- Thu Jun 23 08:40:01 UTC 2022 - Detlef Steuer <detlef.steuer@gmx.de> - CHANGES IN R 4.2.1: NEW FEATURES: * New function utils::findCRANmirror() to find out if a CRAN mirror has been selected, otherwise fallback to the main site. This behaves in the same way as tools::CRAN_package_db() and is intended for packages wishing to access CRAN for purposes other than installing packages. The need for this was shown by a day when the main CRAN website was offline and a dozen or so packages which had its URL hardcoded failed their checks. INSTALLATION on a UNIX-ALIKE: * The libraries searched for by --with-blas (without a value) now include BLIS (after OpenBLAS but before ATLAS). And on macOS, the Accelerate framework (after ATLAS). (This is patterned after the AX_BLAS macro from the Autoconf Archive.) * The included LAPACK sources have been updated to 3.10.1. UTILITIES: * The (full path to) the command tidy to be used for HTML validation can be set by environment variable R_TIDYCMD. * Setting environment variable _R_CHECK_RD_VALIDATE_RD2HTML_ to a false value will override R CMD check --as-cran and turn off HTML validation. This provides a way to circumvent a problematic tidy. The 2006 version that ships with macOS is always skipped. C-LEVEL FACILITIES: * The undocumented legacy declarations of Sint, Sfloat, SINT_MAX and SINT_MIN in header R.h are deprecated. BUG FIXES: * fisher.test(d) no longer segfaults for "large" d; fixing PR#18336 by preventing/detecting an integer overflow reliably. * tar(., files=*) now produces correctly the warning about invalid uid or gid of files, fixing PR#18344, reported by Martin Morgan. * tk_choose.files() with multi = FALSE misbehaved on paths containing spaces (PR#18334) (regression introduced in R 4.0.0). * sort(x, partial = ind, *) now works correctly notably for the non-default na.last = FALSE or TRUE, fixing PR#18335 reported by James Edwards. * Environment variable _R_CHECK_XREFS_REPOSITORIES_ is only used for checking .Rd cross-references in R CMD check (as documented) and not for other uses looking for a CRAN mirror. * The search for a CRAN mirror when checking packages now uses getOption("repos") if that specifies a CRAN mirror, even when it does not also specify all three Bioconductor repositories (as was previously required). * The HTML code generated by tools::Rd2HTML() has been improved to pass tidy 5.8.0. ------------------------------------------------------------------- Fri Apr 22 12:38:25 UTC 2022 - Detlef Steuer <detlef.steuer@gmx.de> - CHANGES IN R 4.2.0: SIGNIFICANT USER-VISIBLE CHANGES: * The formula method of aggregate() now matches the generic in naming its first argument x (resolving PR#18299 by Thomas Soeiro). This means that calling aggregate() with a formula as a named first argument requires name formula in earlier versions of R and name x now, so portable code should not name the argument (code in many packages did). * Calling && or || with either argument of length greater than one now gives a warning (which it is intended will become an error). * Calling if() or while() with a condition of length greater than one gives an error rather than a warning. Consequently, environment variable _R_CHECK_LENGTH_1_CONDITION_ no longer has any effect. * Windows users should consult the WINDOWS section below for some profound changes including * Support for 32-bit builds has been dropped. * UTF-8 locales are used where available. * The default locations for the R installation and personal library folder have been changed. Thanks to Tomas Kalibera for months of work on the Windows port for this release. NEW FEATURES: * matrix(x, n, m) now warns in more cases where length(x) differs from n * m, as suggested by Abby Spurdle and Wolfgang Huber in Feb 2021 on the R-devel mailing list. This warning can be turned into an error by setting environment variable _R_CHECK_MATRIX_DATA_ to TRUE: R CMD check --as-cran does so unless it is already set. * Function file_test() in package utils gains tests for symlinks, readability and writability. * capabilities("libxml") is now false. The description of capabilities("http/ftp") now reflects that it refers to the default method, no longer the internal one. * simplify2array() gains an except argument for controlling the exceptions used by sapply(). * Environment variables R_LIBS_USER and R_LIBS_SITE are both now set to the R system default if unset or empty, and can be set to NULL to indicate an empty list of user or site library directories. * The warning for axis()(-like) calls in cases of relatively small ranges (typically in log-scale situations) is slightly improved _and_ suppressed from explicit calls to .axisPars() as has always been the intention. * The contrasts setter function `contrasts<-` gains an explicit default how.many = NULL rather than just using missing(how.many). * grid.pretty() gains a new optional argument n = 5. * There is a new function .pretty() with option bounds as a technical-utility version of pretty(). It and pretty() gain a new argument f.min with a better than back-compatible default. * Function grDevices::axisTicks() and related functions such as graphics::axis() work better, notably for the log scale; partly because of the pretty() improvements, but also because care is taken e.g., when ylim is finite but diff(ylim) is infinite. * nclass.FD() gains a digits option. * The R Mathlib internal C function bd0() (called indirectly from a dozen probability density and distribution functions such as dpois(), dbinom(), dgamma(), pgamma() _etc_) has been complemented by a more sophisticated and (mostly) more accurate C function ebd0(), currently called only by internal dpois_raw() improving accuracy for R level dpois() and potentially others calling it such as dnbinom(), dgamma() or pgamma(). (Thanks to Morten Welinder's PR#15628.) * write.ftable() gains sep = " " argument as suggested by Thomas Soeiro. * The names of the locale categories supported by R's Sys.getlocale() and Sys.setlocale() are now provided by variable .LC.categories in the base namespace. * The Date and POSIXt methods for hist() and the histogram method for plot() now also use the new default col = "lightgray" in consistency with the corresponding change to hist()'s default for R 4.0.0. * hist.default() gains new fuzz argument, and the histogram plot method no longer uses fractional axis ticks when displaying counts ("Frequency"). * mapply() and hence Map() now also obey the "max-or-0-if-any" recycling rule, such that, e.g., Map(`+`, 1:3, 1[0]) is valid now. * as.character(<obj>) for "hexmode" or "octmode" objects now fulfils the important basic rule as.character(x)[j] === as.character(x[j]). * The set utility functions, notably intersect() have been tweaked to be more consistent and symmetric in their two set arguments, also preserving a common mode. * substr(ch, start,end) <- new now e.g., preserves names(ch); ditto for substring(), thanks to a patch from Brodie Gaslam. * plot(<lm>) gains a extend.ylim.f argument, in partial response to PR#15285; further PR#17784 is fixed thanks to several contributors and a patch by Elin Waring. The Cook's dist contours get customizable via cook.col and cook.lty with a different default color and their legend is nicer by default and customizable via cook.legendChanges. * Attempting to subset an object that is not subsettable now signals an error of class notSubsettableError. The non-subsettable object is contained in the object field of the error condition. * Subscript-out-of-bounds errors are now signaled as errors of class subscriptOutOfBoundsError. * Stack-overflow errors are now signaled as errors inheriting from class stackOverflowError. See ?stackOverflowError for more details. * New partly experimental Sys.setLanguage() utility, solving the main problem of PR#18055. * gettext() and gettextf() get a new option trim = TRUE which when set to false allows translations for strings such as "Execution halted\n" typical for C code. * An experimental implementation of hash tables is now available. See ?hashtab for more details. * identical() gains a extptr.as.ref argument for requesting that external pointer objects be compared as reference objects. * reorder() gets an argument decreasing which it passes to sort() for level creation; based on the wish and patch by Thomas Soeiro in PR#18243. * as.vector() gains a data.frame method which returns a simple named list, also clearing a long standing 'FIXME' to enable as.vector(<data.frame>, mode="list"). This breaks code relying on as.vector(<data.frame>) to return the unchanged data frame. * legend() is now vectorized for arguments cex, x.intersp, and text.width. The latter can now also be specified as a vector (one element for each column of the legend) or as NA for computing a proper column wise maximum value of strwidth(legend). The argument y.intersp can be specified as a vector with one entry for each row of the legend. legend() also gains new arguments title.cex and title.font. Thanks to Swetlana Herbrandt. * Deparsing no longer remaps attribute names dim, dimnames, levels, names and tsp to historical S-compatible names (which structure() maps back). * sample() and sample.int() have additional sanity checks on their size and n arguments. all.equal.numeric() gains a sanity check on its tolerance argument - calling all.equal(a, b, c) for three numeric vectors is a surprisingly common error. mean(na.rm =), rank(na.last =), barplot(legend.text =), boxplot(), contour(drawlabels =), polygon(border =) and methods::is(class2 =) have more robust sanity checks on their arguments. R CMD Rd2pdf (used by R CMD check) has a more robust sanity check on the format of \alias{} commands. * psigamma(x, deriv) for negative x now also works for deriv = 4 and 5; their underlying C level dpsifn() is documented in 'Writing R Extensions'. * The HTML help system now uses HTML5 (wish of PR#18149). * ks.test() now provides exact p-values also with ties and MC p-values in the two-sample (Smirnov) case. By Torsten Hothorn. * ks.test() gains a formula interface, with y ~ 1 for the one-sample (Kolmogorov) test and y ~ group for the two-sample (Smirnov) test. Contributed by Torsten Hothorn. * The return value from ks.test() now has class c("ks.test", "htest") - packages using try() need to take care to use inherits() and not == on the class. * New functions psmirnov(), qsmirnov() and rsmirnov() in package stats implementing the asymptotic and exact distributions of the two-sample Smirnov statistic. * iconv() now allows sub = "c99" to use C99-style escapes for UTF-8 inputs which cannot be converted to encoding to. * In a forward pipe |> expression it is now possible to use a named argument with the placeholder _ in the rhs call to specify where the lhs is to be inserted. The placeholder can only appear once on the rhs. * The included LAPACK sources have been updated to version 3.10.0, except for the four Fortran 77 routines which 3.10.0 has re-implemented in Fortran 90 (where the older versions have been retained as the R build process does not support Fortran 90). * path.expand() and most other uses of tilde expansion now warn if a path would be too long if expanded. (An exception is file.exists(), which silently returns false.) * trunc(<Date>, *) now supports units = "months" or "years" for consistency with the POSIXt method, thanks to Dirk Eddelbuettel's proposal in PR#18099. * list2DF() now checks that its arguments are of the same length, rather than use recycling. * The HTML help system has several new features: LaTeX-like math can be typeset using either KaTeX or MathJax, usage and example code is highlighted using Prism, and for dynamic help the output of examples and demos can be shown within the browser if the knitr package is installed. These features can be disabled by setting the environment variable _R_HELP_ENABLE_ENHANCED_HTML_ to a false value. GRAPHICS: * The graphics engine version, R_GE_version, has been bumped to 15 and so packages that provide graphics devices should be reinstalled. * The grid package now allows the user to specify a "vector" of pattern fills. The fill argument to gpar() accepts a list of gradients and/or patterns and the functions linearGradient(), radialGradient(), and pattern() have a new group argument. Points grobs (data symbols) can now also have a pattern fill. The grobCoords() function now returns a more informative and complex result. * The grid package has new functions for drawing isolated groups: grid.group(), grid.define(), and grid.use(). These functions add compositing operators and affine transformations to R's graphics capabilities. The grid package also has new functions for stroking and filling paths: grid.stroke(), grid.fill(), and grid.fillStroke(). A new function as.path() allows the user to specify the fill rule for a path that is to be used for clipping, stroking, or filling; available options are "winding" and "evenodd". A new function as.mask() allows the user to specify the type of a mask; available options are "alpha" and "luminance". These new features are only supported so far (at most) on the Cairo-based graphics devices and on the pdf() device. * dev.capabilities() reports on device support for the new features. * par() now warns about unnamed non-character arguments to prevent misuse such as {usr <- par("usr"); par(usr)}. INSTALLATION: * Facilities for accessing ftp:// sites are no longer tested (except _pro tem_ for curlGetHeaders()) as modern browsers have removed support. * R can now be built with DEFS = -DSTRICT_R_HEADERS . PACKAGE INSTALLATION: * R CMD INSTALL no longer tangles vignettes. This completes an R CMD build change in R 3.0.0 and affects packages built before R 3.0.2. Such packages should be re-made with R CMD build to have the tangled R code of vignettes shipped with the tarball. * USE_FC_LEN_T will become the default: this uses the correct prototypes for Fortran BLAS/LAPACK routines called from C/C++, and requires adjustment of most such calls - see 'Writing R Extensions' SS6.6.2. (This has been supported since R 3.6.2.) * Package installation speed for packages installed with keep.source has been improved. This resolve the issue reported by Ofek Shilon in PR#18236. UTILITIES: * R CMD check can optionally report files/directories left behind in home, /tmp (even though TMPDIR is set) and other directories. See the "R Internals" manual for details. * R CMD check now reports byte-compilation errors during installation. These are not usually fatal but may result in parts of the package not being byte-compiled. * _R_CHECK_DEPENDS_ONLY_ can be applied selectively to examples, tests and/or vignettes in R CMD check: see the "R Internals" manual. * _R_CHECK_SRC_MINUS_W_IMPLICIT_ now defaults to true: recent versions of Apple clang on macOS have made implicit function declarations in C into a compilation error. * R CMD check --as-cran makes use of the environment variable AUTORECONF. See the "R Internals" manual SS8 for further details. * R CMD check --use-valgrind also uses valgrind when re-building vignettes as some non-Sweave vignettes unhelpfully comment out all their code when R CMD check runs vignettes. * Errors in re-building vignettes (unless there are LaTeX errors) are reported by R CMD check as ERROR rather than WARNING when running vignettes has been skipped (as it frequently is in CRAN checks and by --as-cran). * R CMD Rd2pdf gains a --quiet option that is used by R CMD build when building the PDF package manual. * R CMD Rd2pdf now always runs LaTeX in batch mode, consistent with Texinfo >= 6.7. The --batch option is ignored. * R CMD build and R CMD check now include the Rd file name and line numbers in the error message of an \Sexpr evaluation failure. * For packages using the \doi Rd macro (now an install-time \Sexpr) but no other dynamic Rd content, R CMD build now produces a smaller tarball and is considerably faster - skipping temporary package installation. C-LEVEL FACILITIES: * The non-API header R_ext/R-ftp-http.h is no longer provided, as the entry points it covered are now all defunct. * A number of non-API declarations and macro definitions have been moved from the installed header Rinternals.h to the internal header Defn.h. Packages that only use entry points and definitions documented to be part of the API as specified in 'Writing R Extensions' SS6 should not be affected. * The macro USE_RINTERNALS no longer has any effect when compiling package code. Packages which also use R_NO_REMAP will need to ensure that the remapped names are used for calls to API functions that were formerly also made available as macros. * The deprecated legacy S-compatibility macros PROBLEM, MESSAGE, ERROR, WARN, WARNING, RECOVER, ... are no longer defined in R_exts/RS.h (included by R.h). Replace these by calls to Rf_error and Rf_warning (defined in header R_ext/Error.h included by R.h). Header R_ext/RS.h no longer includes R_ext/Error.h. * Header R_ext/Constants.h (included by R.h) when included from C++ now includes the C++ header cfloat rather than the C header float.h (now possible as C++11 is required). * The legacy S-compatibility macros DOUBLE_* in R_ext/Constants.h (included by R.h) are deprecated. * The deprecated S-compatibility macros SINGLE_* in R_ext/Constants.h (included by R.h) have been removed. * R_Calloc, R_Free and R_Realloc are preferred to their unprefixed forms and error messages now use the prefix. These forms were introduced in R 3.4.0 and are available even when STRICT_R_HEADERS is defined. * rmultinom has been documented in 'Writing R Extensions' SS6 so is now part of the R API. * Similarly, Rtanpi, called from R level tanpi() is now part of the R API. * The long-deprecated, undocumented and non-API entry point call_R is no longer declared in R_ext/RS.h (included by R.h). * The header S.h which has been unsupported since Jan 2016 has been removed. Use R.h instead. DEPRECATED AND DEFUNCT: * The (non-default and deprecated) method = "internal" for download.file() and url() no longer supports http:// nor ftp:// URIs. (It is used only for file:// URIs.) On Windows, download.file(method = "wininet") no longer supports ftp:// URIs. (It is no longer the default method, which is "libcurl" and does.) On Windows, the deprecated method = "wininet" now gives a warning for http:// and https:// URIs for both download.file() and url(). (It is no longer the default method.) * On Windows, the command-line option --max-mem-size and environment variable R_MAX_MEM_SIZE are defunct. The memory allocation limit was important for 32-bit builds, but these are no longer supported. * default.stringsAsFactors() is now formally deprecated, where that was only mentioned on its regular help page, previously. So it now gives a warning if called. * unix.time() is defunct now; it had been deprecated since R 3.4.0. BUG FIXES: * Setting digits = 0 in format(), print.default() (and hence typically print()) or options() is again invalid. Its behaviour was platform-dependent, and it is unclear what "zero significant digits" should mean (PR#18098). * Messages from C code in the cairo section of package grDevices are now also offered for translation, thanks to Michael Chirico's PR#18123. * mean(x) with finite x now is finite also without "long.double" capability. * R CMD Rd2pdf no longer leaves an empty build directory behind when it aborts due to an already existing output file. (Thanks to Sebastian Meyer's PR#18141.) * density(x, weights = w, na.rm = TRUE) when anyNA(x) is true, now removes weights "in parallel" to x, fixing PR#18151, reported by Matthias Gondan. Additionally, it gets a subdensity option. * Conversion of \Sexpr[]{<expR>} to LaTeX or HTML no longer produces long blocks of empty lines when <expR> itself contains several lines all producing empty output. Thanks to a report and patch by Ivan Krylov posted to R-devel. * R CMD build no longer fails if a package vignette uses child documents and inst/doc exists. (Thanks to Sebastian Meyer's PR#18156.) * When an R documentation ('help' source) file man/foo.Rd in a package has \donttest{..} examples with a syntax error, it is now signalled as ERROR and with correct line numbers relating to the *-Ex.R file, thanks to Duncan Murdoch and Sebastian Meyer's reports and patch proposals in PR#17501. * Improved determination of the correct translation domain in non-base packages, addressing the combination of PR#18092 and PR#17998 (#c6) with reports and _augmented_ patch #2904 by Suharto Anggono. Note that "R-base" is no longer the default domain e.g., for top-level calls to gettext(); rather translation needs explicit domain = * specification in such cases. * identical(attrib.as.set=FALSE) now works correctly with data frames with default row names (Thanks to Charlie Gao's PR#18179). * txtProgressBar() now enforces a non-zero width for argument char, without which no progress can be visible. * dimnames(table(d)) is more consistent in the case where d is a list with a single component, thanks to Thomas Soeiro's report to R-devel. Further, table(d1, d2) now gives an error when d1 and d2 are data frames as suggested by Thomas in PR#18224. * Fix for drawing semi-transparent lines and fills on the native Windows graphics device (PR#18219 and PR#16694). Thanks to Nick Ray for helpful diagnosis on Bugzilla. * The deparser now wraps sub-expressions such as if(A) .. with parentheses when needed; thanks to Duncan Murdoch's PR#18232 and Lionel Henry's patches there. * remove.packages() no longer tries to uninstall Priority: base packages, thanks to a report and suggestions by Colin Fay in PR#18227. * win.metafile() now has xpinch and ypinch arguments so that the user can override Windows' (potentially wrong) guess at device dimensions. * x[i] and x[[i]] for non-integer i should now behave in all cases as always documented: the index used is equivalent to as.integer(i) unless that would overflow where trunc(i) is used instead; thanks to Suharto Anggono's report and patch proposals in PR#17977. * asOneSidedFormula() now associates the resulting formula with the global environment rather than the evaluation environment created for the call. * <bibentry>$name now matches the field name case-insensitively, consistent with bibentry() creation and the replacement method. * cbind() failed to detect some length mismatches with a mixture of time-series and non-time-series inputs. * The default LaTeX style file Sweave.sty used by the RweaveLatex driver no longer loads the obsolete ae package; thanks to a report by Thomas Soeiro in PR#18271. Furthermore, it now skips \usepackage[T1]{fontenc} for engines other than pdfTeX (if detected) or if the new [nofontenc] option is used. * smooth.spline() now stores its logical cv argument more safely, fixing a rare bug when printing, and also stores n. * smooth.spline(x,y,*) now computes the cv.crit statistic correctly, also when is.unsorted(x), fixing PR#18294. * The data.frame method of rbind() now warns when binding not-wholly-recycling vectors, by analogy to the default method (for matrices). * setAs() finds the correct class for name to when multiple packages define a class with that name. Thanks to Gabor Csardi for the report. * Fix for detaching a package when two classes of the same name are present in method signatures for the same generic. Thanks to Gabor Csardi for the report. * match.arg("", c("", "a", "B")) gives a better error message, in part from PR#17959, thanks to Elin Waring. * R CMD Sweave --clean no longer removes pre-existing files or subdirectories (PR#18242). * The quartz() device no longer splits polylines into subpaths. That has caused narrowly-spaced lines with many points to always look solid even when dashed line type was used due to dash phase restarts. * Deparsing constructs such as quote(1 + `!`(2) + 3) works again as before R 3.5.0, thanks to the report and patch in PR#18284 by Suharto Anggono. * as.list(f) for a factor f now keeps names(f), fixing PR#18309. * qbeta(.001, .9, .009) and analogous qf() calls now return a correct value instead of NaN or wrongly 1, all with a warning; thanks to the report by Ludger Goeminne in PR#18302. * plot.lm() failed to produce the plot of residuals vs. factor levels (i.e., which=5 when leverages are constant) for models with character predictors (PR#17840). * interaction.plot(..., xtick = TRUE) misplaced the x-axis line (PR#18305). * Not strictly fixing a bug, format()ing and print()ing of non-finite Date and POSIXt values NaN and +/-Inf no longer show as NA but the respective string, e.g., Inf, for consistency with numeric vector's behaviour, fulfilling the wish of PR#18308. * R CMD check no longer runs test scripts generated from corresponding .Rin files twice and now signals an ERROR if processing an .Rin script fails. * tools::Rd2txt() used for plain-text help pages now renders \hrefs (if tools::Rd2txt_options(showURLs = TRUE)) and \urls with percent-encoding and standards-compliant delimiting style (angle brackets and no URL: prefix). \email is now rendered with a mailto: prefix. ------------------------------------------------------------------- Fri Mar 11 07:54:58 UTC 2022 - Detlef Steuer <detlef.steuer@gmx.de> - CHANGES IN R 4.1.3: NEW FEATURES: * The default version of Bioconductor has been changed to 3.14. (This is used by setRepositories and the menus in GUIs.) UTILITIES: * R CMD check --as-cran has a workaround for a bug in versions of file up to at least 5.41 which mis-identify DBF files last changed in 2022 as executables. C-LEVEL FACILITIES: * The legacy S-compatibility macros SINGLE_* in R_ext/Constants.h (included by R.h) are deprecated and will be removed in R 4.2.0. BUG FIXES: * Initialization of self-starting nls() models with initialization functions following the pre-R-4.1.0 API (without the ... argument) works again for now, with a deprecation warning. * Fixed quoting of ~autodetect~ in Java setting defaults to avoid inadvertent user lookup due to leading ~, reported in PR#18231 by Harold Gutch. * substr(., start, stop) <- v now treats _negative_ stop values correctly. Reported with a patch in PR#18228 by Brodie Gaslam. * Subscripting an array x without dimnames by a length(dim(x))-column character matrix gave "random" non-sense, now an error; reported in PR#18244 by Mikael Jagan. * ...names() now matches names(list(...)) closely, fixing PR#18247. * all.equal(*, scale = s) now works as intended when length(s) > 1, partly thanks to Michael Chirico's PR#18272. * print(x) for long vectors x now also works for named atomic vectors or lists and prints the correct number when reaching the getOption("max.print") limit; partly thanks to a report and proposal by Hugh Parsonage to the R-devel list. * all.equal(<selfStart>, *) no longer signals a deprecation warning. * reformulate(*, response=r) gives a helpful error message now when length(r) > 1, thanks to Bill Dunlap's PR#18281. * Modifying globalCallingHandlers inside withCallingHandlers() now works or fails correctly, thanks to Henrik Bengtsson's PR#18257. * hist(<Date>, breaks = "days") and hist(<POSIXt>, breaks = "secs") no longer fail for inputs of length 1. * qbeta(.001, .9, .009) and similar cases now converge correctly thanks to Ben Bolker's report in PR#17746. * window(x, start, end) no longer wrongly signals "'start' cannot be after 'end'", fixing PR#17527 and PR#18291. * data() now checks that its (rarely used) list argument is a character vector - a couple of packages passed other types and gave incorrect results. * which() now checks its arr.ind argument is TRUE rather coercing to logical and taking the first element - which gave incorrect results in package code. * model.weights() and model.offset() more carefully extract their model components, thanks to Ben Bolker and Tim Taylor's R-devel post. * list.files(recursive = TRUE) now shows all broken symlinks (previously, some of them may have been omitted, PR#18296). ------------------------------------------------------------------- Mon Nov 1 09:24:49 UTC 2021 - Detlef Steuer <detlef.steuer@gmx.de> - CHANGES IN R 4.1.2: C-LEVEL FACILITIES: * The workaround in headers R.h and Rmath.h (using namespace std;) for the Oracle Developer Studio compiler is no longer needed now C++11 is required so has been removed. A couple more usages of log() (which should have been std::log()) with an int argument are reported on Solaris. * The undocumented limit of 4095 bytes on messages from the S-compatibility macros PROBLEM and MESSAGE is now documented and longer messages will be silently truncated rather than potentially causing segfaults. * If the R_NO_SEGV_HANDLER environment variable is non-empty, the signal handler for SEGV/ILL/BUS signals (which offers recovery user interface) is not set. This allows more reliable debugging of crashes that involve the console. DEPRECATED AND DEFUNCT: * The legacy S-compatibility macros PROBLEM, MESSAGE, ERROR, WARN, WARNING, RECOVER, ... are deprecated and will be hidden in R 4.2.0. R's native interface of Rf_error and Rf_warning has long been preferred. BUG FIXES: * .mapply(F, dots, .) no longer segfaults when dots is not a list and uses match.fun(F) as always documented; reported by Andrew Simmons in PR#18164. * hist(<Date>, ...) and hist(<POSIXt>, ...) no longer pass arguments for rect() (such as col and density) to axis(). (Thanks to Sebastian Meyer's PR#18171.) * \Sexpr{ch} now preserves Encoding(ch). (Thanks to report and patch by Jeroen Ooms in PR#18152.) * Setting the RNG to "Marsaglia-Multicarry" e.g., by RNGkind(), now warns in more places, thanks to Andr'e Gillibert's report and patch in PR#18168. * gray(numeric(), alpha=1/2) no longer segfaults, fixing PR#18183, reported by Till Krenz. * Fixed dnbinom(x, size=<very_small>, .., log=TRUE) regression, reported by Martin Morgan. * as.Date.POSIXlt(x) now keeps names(x), thanks to Davis Vaughan's report and patch in PR#18188. * model.response() now strips an "AsIs" class typically, thanks to Duncan Murdoch's report and other discussants in PR#18190. * try() is considerably faster in case of an error and long call, as e.g., from some do.call(). Thanks to Alexander Kaever's suggestion posted to R-devel. * qqline(y = <object>) such as y=I(.), now works, see also PR#18190. * Non-integer mgp par() settings are now handled correctly in axis() and mtext(), thanks to Mikael Jagan and Duncan Murdoch's report and suggestion in PR#18194. * formatC(x) returns length zero character() now, rather than "" when x is of length zero, as documented, thanks to Davis Vaughan's post to R-devel. * removeSource(fn) now retains (other) attributes(fn). ------------------------------------------------------------------- Mon Oct 25 14:09:08 UTC 2021 - Detlef Steuer <detlef.steuer@gmx.de> - repaired https://bugzilla.suse.com/show_bug.cgi?id=1191380 (rpmacros now go to rpmmacrodir) - minor clean-ups in spec file ------------------------------------------------------------------- Tue Aug 10 12:23:48 UTC 2021 - Detlef Steuer <detlef.steuer@gmx.de> - CHANGES IN R 4.1.1: NEW FEATURES: * require(pkg, quietly = TRUE) is quieter and in particular does not warn if the package is not found. DEPRECATED AND DEFUNCT: * Use of ftp:// URIs should be regarded as deprecated, with on-going support confined to method = "libcurl" and not routinely tested. (Nowadays no major browser supports them.) * The non-default method = "internal" is deprecated for http:// and ftp:// URIs for both download.file and url. * On Windows, method = "wininet" is deprecated for http://, https:// and ftp:// URIs for both download.file and url. (A warning is only given for ftp://.) For ftp:// URIs the default method is now "libcurl" if available (which it is on CRAN builds). method = "wininet" remains the default for http:// and https:// URIs but if libcurl is available, using method = "libcurl" is preferred. INSTALLATION: * make check now works also without a LaTeX installation. (Thanks to Sebastian Meyer's PR#18103.) BUG FIXES: * make check-devel works again in an R build configured with --without-recommended-packages. * qnbinom(p, size, mu) for large size/mu is correct now in a range of cases (PR#18095); similarly for the (size, prob) parametrization of the negative binomial. Also qpois() and qbinom() are better and or faster for extreme cases. The underlying C code has been modularized and is common to all four cases of discrete distributions. * gap.axis is now part of the axis() arguments which are passed from bxp(), and hence boxplot(). (Thanks to Martin Smith's report and suggestions in PR#18109.) * .First and .Last can again be set from the site profile. * seq.int(from, to, *) and seq.default(..) now work better in large range cases where from-to is infinite where the two boundaries are finite. * all.equal(x,y) now returns TRUE correctly also when several entries of abs(x) and abs(y) are close to .Machine$double.xmax, the largest finite numeric. * model.frame() now clears the object bit when removing the class attribute of a value via na.action (PR#18100). * charClass() now works with multi-character strings on Windows (PR#18104, fixed by Bill Dunlap). * encodeString() on Solaris now works again in Latin-1 encoding on characters represented differently in UTF-8. Support for surrogate pairs on Solaris has been improved. * file.show() on Windows now works with non-ASCII path names representable in the current native encoding (PR#18132). * Embedded R on Windows can now find R home directory via the registry even when installed only for the current user (PR#18135). * pretty(x) with finite x now returns finite values also in the case where the extreme x values are close in size to the maximal representable number .Machine$double.xmax. Also, it's been tweaked for very small ranges and when a boundary is close (or equal) to zero; e.g., pretty(c(0,1e-317)) no longer has negative numbers, currently still warning about a very small range, and pretty(2^-(1024 - 2^-1/(c(24,10)))) is more accurate. * The error message for not finding vignette files when weaving has correct file sizes now. (Thanks to Sebastian Meyer's PR#18154.) * dnbinom(20, <large>, 1) now correctly gives 0, and similar cases are more accurate with underflow precaution. (Reported by Francisco Vera Alcivar in PR#18072.) ------------------------------------------------------------------- Fri Jun 4 07:21:23 UTC 2021 - Detlef Steuer <detlef.steuer@gmx.de> - The line %{__install} -m 755 -d %{_infodir} no longer works in TW or Factory. But without that line it works everywhere. So this instruction was commented out of the spec file. ------------------------------------------------------------------- Tue May 18 17:01:25 UTC 2021 - Detlef Steuer <detlef.steuer@gmx.de> - CHANGES IN R 4.1.0: FUTURE DIRECTIONS: * It is planned that the 4.1.x series will be the last to support 32-bit Windows, with production of binary packages for that series continuing until early 2023. SIGNIFICANT USER-VISIBLE CHANGES: * Data set esoph in package datasets now provides the correct numbers of controls; previously it had the numbers of cases added to these. (Reported by Alexander Fowler in PR#17964.) NEW FEATURES: * www.omegahat.net is no longer one of the repositories known by default to setRepositories(). (Nowadays it only provides source packages and is often unavailable.) * Function package_dependencies() (in package tools) can now use different dependency types for direct and recursive dependencies. * The checking of the size of tarball in R CMD check --as-cran <pkg> may be tweaked via the new environment variable _R_CHECK_CRAN_INCOMING_TARBALL_THRESHOLD_, as suggested in PR#17777 by Jan Gorecki. * Using c() to combine a factor with other factors now gives a factor, an ordered factor when combining ordered factors with identical levels. * apply() gains a simplify argument to allow disabling of simplification of results. * The format() method for class "ftable" gets a new option justify. (Suggested by Thomas Soeiro.) * New ...names() utility. (Proposed by Neal Fultz in PR#17705.) * type.convert() now warns when its as.is argument is not specified, as the help file always said it _should_. In that case, the default is changed to TRUE in line with its change in read.table() (related to stringsAsFactor) in R 4.0.0. * When printing list arrays, classed objects are now shown _via_ their format() value if this is a short enough character string, or by giving the first elements of their class vector and their length. * capabilities() gets new entry "Rprof" which is TRUE when R has been configured with the equivalent of --enable-R-profiling (as it is by default). (Related to Michael Orlitzky's report PR#17836.) * str(xS4) now also shows extraneous attributes of an S4 object xS4. * Rudimentary support for vi-style tags in rtags() and R CMD rtags has been added. (Based on a patch from Neal Fultz in PR#17214.) * checkRdContents() is now exported from tools; it and also checkDocFiles() have a new option chkInternal allowing to check Rd files marked with keyword "internal" as well. The latter can be activated for R CMD check via environment variable _R_CHECK_RD_INTERNAL_TOO_. * New functions numToBits() and numToInts() extend the raw conversion utilities to (double precision) numeric. * Functions URLencode() and URLdecode() in package utils now work on vectors of URIs. (Based on patch from Bob Rudis submitted with PR#17873.) * path.expand() can expand ~user on most Unix-alikes even when readline is not in use. It tries harder to expand ~, for example should environment variable HOME be unset. * For HTML help (both dynamic and static), Rd file links to help pages in external packages are now treated as references to topics rather than file names, and fall back to a file link only if the topic is not found in the target package. The earlier rule which prioritized file names over topics can be restored by setting the environment variable _R_HELP_LINKS_TO_TOPICS_ to a false value. * c() now removes NULL arguments before dispatching to methods, thus simplifying the implementation of c() methods, _but_ for back compatibility keeps NULL when it is the first argument. (From a report and patch proposal by Lionel Henry in PR#17900.) * Vectorize()'s result function's environment no longer keeps unneeded objects. * Function ...elt() now propagates visibility consistently with ..n. (Thanks to Lionel Henry's PR#17905.) * capture.output() no longer uses non-standard evaluation to evaluate its arguments. This makes evaluation of functions like parent.frame() more consistent. (Thanks to Lionel Henry's PR#17907.) * packBits(bits, type="double") now works as inverse of numToBits(). (Thanks to Bill Dunlap's proposal in PR#17914.) * curlGetHeaders() has two new arguments, timeout to specify the timeout for that call (overriding getOption("timeout")) and TLS to specify the minimum TLS protocol version to be used for https:// URIs (_inter alia_ providing a means to check for sites using deprecated TLS versions 1.0 and 1.1). * For nls(), an optional constant scaleOffset may be added to the denominator of the relative offset convergence test for cases where the fit of a model is expected to be exact, thanks to a proposal by John Nash. nls(*, trace=TRUE) now also shows the convergence criterion. * Numeric differentiation _via_ numericDeriv() gets new optional arguments eps and central, the latter for taking central divided differences. The latter can be activated for nls() via nls.control(nDcentral = TRUE). * nls() now passes the trace and control arguments to getInitial(), notably for all self-starting models, so these can also be fit in zero-noise situations via a scaleOffset. For this reason, the initial function of a selfStart model must now have ... in its argument list. * bquote(splice = TRUE) can now splice expression vectors with attributes: this makes it possible to splice the result of parse(keep.source = TRUE). (Report and patch provided by Lionel Henry in PR#17869.) * textConnection() gets an optional name argument. * get(), exists(), and get0() now signal an error if the first argument has length greater than 1. Previously additional elements were silently ignored. (Suggested by Antoine Fabri on R-devel.) * R now provides a shorthand notation for creating functions, e.g. \(x) x + 1 is parsed as function(x) x + 1. * R now provides a simple native forward pipe syntax |>. The simple form of the forward pipe inserts the left-hand side as the first argument in the right-hand side call. The pipe implementation as a syntax transformation was motivated by suggestions from Jim Hester and Lionel Henry. * all.equal(f, g) for functions now by default also compares their environment(.)s, notably via new all.equal method for class function. Comparison of nls() fits, e.g., may now need all.equal(m1, m2, check.environment = FALSE). * .libPaths() gets a new option include.site, allowing to _not_ include the site library. (Thanks to Dario Strbenac's suggestion and Gabe Becker's PR#18016.) * Lithuanian translations are now available. (Thanks to Rimantas Zakauskas.) * names() now works for DOTSXP objects. On the other hand, in R-lang, the R language manual, we now warn against relying on the structure or even existence of such dot-dot-dot objects. * all.equal() no longer gives an error on DOTSXP objects. * capabilities("cairo") now applies only to the file-based devices as it is now possible (if very unusual) to build R with Cairo support for those but not for X11(). * There is optional support for tracing the progress of loadNamespace() - see its help. * (Not Windows.) l10n_info() reports an additional element, the name of the encoding as reported by the OS (which may differ from the encoding part (if any) of the result from Sys.getlocale("LC_CTYPE"). * New function gregexec() which generalizes regexec() to find _all_ disjoint matches and well as all substrings corresponding to parenthesized subexpressions of the given regular expression. (Contributed by Brodie Gaslam.) * New function charClass() in package utils to query the wide-character classification functions in use (such as iswprint). * The names of quantile()'s result no longer depend on the global getOption("digits"), but quantile() gets a new optional argument digits = 7 instead. * grep(), sub(), regexp and variants work considerably faster for long factors with few levels. (Thanks to Michael Chirico's PR#18063.) * Provide grouping of x11() graphics windows within a window manager such as Gnome or Unity; thanks to a patch by Ivan Krylov posted to R-devel. * The split() method for class data.frame now allows the f argument to be specified as a formula. * sprintf now warns on arguments unused by the format string. * New palettes "Rocket" and "Mako" for hcl.colors() (approximating palettes of the same name from the 'viridisLite' package). Contributed by Achim Zeileis. * The base environment and its namespace are now locked (so one can no longer add bindings to these or remove from these). * Rterm handling of multi-byte characters has been improved, allowing use of such characters when supported by the current locale. * Rterm now accepts ALT+ +xxxxxxxx sequences to enter Unicode characters as hex digits. * Environment variable LC_ALL on Windows now takes precedence over LC_CTYPE and variables for other supported categories, matching the POSIX behaviour. * duplicated() and anyDuplicated() are now optimized for integer and real vectors that are known to be sorted via the ALTREP framework. Contributed by Gabriel Becker via PR#17993. GRAPHICS: * The graphics engine version, R_GE_version, has been bumped to 14 and so packages that provide graphics devices should be reinstalled. * Graphics devices should now specify deviceVersion to indicate what version of the graphics engine they support. * Graphics devices can now specify deviceClip. If TRUE, the graphics engine will never perform any clipping of output itself. The clipping that the graphics engine does perform (for both canClip = TRUE and canClip = FALSE) has been improved to avoid producing unnecessary artifacts in clipped output. * The grid package now allows gpar(fill) to be a linearGradient(), a radialGradient(), or a pattern(). The viewport(clip) can now also be a grob, which defines a clipping path, and there is a new viewport(mask) that can also be a grob, which defines a mask. These new features are only supported so far on the Cairo-based graphics devices and on the pdf() device. * (Not Windows.) A warning is given when a Cairo-based type is specified for a png(), jpeg(), tiff() or bmp() device but Cairo is unsupported (so type = "Xlib" is tried instead). * grSoftVersion() now reports the versions of FreeType and FontConfig if they are used directly (not _via_ Pango), as is most commonly done on macOS. C-LEVEL FACILITIES: * The _standalone_ libRmath math library and R's C API now provide log1pexp() again as documented, and gain log1mexp(). INSTALLATION on a UNIX-ALIKE: * configure checks for a program pkgconf if program pkg-config is not found. These are now only looked for on the path (like almost all other programs) so if needed specify a full path to the command in PKG_CONFIG, for example in file config.site. * C99 function iswblank is required - it was last seen missing ca 2003 so the workaround has been removed. * There are new configure options --with-internal-iswxxxxx, --with-internal-towlower and --with-internal-wcwidth which allows the system functions for wide-character classification, case-switching and width (wcwidth and wcswidth) to be replaced by internal ones. The first has long been used on macOS, AIX (and Windows) but this enables it to be unselected there and selected for other platforms (it is the new default on Solaris). The second is new in this version of R and is selected by default on macOS and Solaris. The third has long been the default and remains so as it contains customizations for East Asian languages. System versions of these functions are often minimally implemented (sometimes only for ASCII characters) and may not cover the full range of Unicode points: for example Solaris (and Windows) only cover the Basic Multilingual Plane. * Cairo installations without X11 are more likely to be detected by configure, when the file-based Cairo graphics devices will be available but not X11(type = "cairo"). * There is a new configure option --with-static-cairo which is the default on macOS. This should be used when only static cairo (and where relevant, Pango) libraries are available. * Cairo-based graphics devices on platforms without Pango but with FreeType/FontConfig will make use of the latter for font selection. LINK-TIME OPTIMIZATION on a UNIX-ALIKE: * Configuring with flag --enable-lto=R now also uses LTO when installing the recommended packages. * R CMD INSTALL and R CMD SHLIB have a new flag --use-LTO to use LTO when compiling code, for use with R configured with --enable-lto=R. For R configured with --enable-lto, they have the new flag --no-use-LTO. Packages can opt in or out of LTO compilation _via_ a UseLTO field in the DESCRIPTION file. (As usual this can be overridden by the command-line flags.) BUILDING R on Windows: * for GCC >= 8, FC_LEN_T is defined in config.h and hence character lengths are passed from C to Fortran in _inter alia_ BLAS and LAPACK calls. * There is a new text file src/gnuwin32/README.compilation, which outlines how C/Fortran code compilation is organized and documents new features: * R can be built with Link-Time Optimization with a suitable compiler - doing so with GCC 9.2 showed several inconsistencies which have been corrected. * There is support for cross-compiling the C and Fortran code in R and standard packages on suitable (Linux) platforms. This is mainly intended to allow developers to test later versions of compilers - for example using GCC 9.2 or 10.x has detected issues that GCC 8.3 in Rtools40 does not. * There is experimental support for cross-building R packages with C, C++ and/or Fortran code. * The R installer can now be optionally built to support a single architecture (only 64-bit or only 32-bit). PACKAGE INSTALLATION: * The default C++ standard has been changed to C++14 where available (which it is on all currently checked platforms): if not (as before) C++11 is used if available otherwise C++ is not supported. Packages which specify C++11 will still be installed using C++11. C++14 compilers may give deprecation warnings, most often for std::random_shuffle (deprecated in C++14 and removed in C++17). Either specify C++11 (see 'Writing R Extensions') or modernize the code and if needed specify C++14. The latter has been supported since R 3.4.0 so the package's DESCRIPTION would need to include something like Depends: R (>= 3.4) PACKAGE INSTALLATION on Windows: * R CMD INSTALL and R CMD SHLIB make use of their flag --use-LTO when the LTO_OPT make macro is set in file etc/${R_ARCH}/Makeconf or in a personal/site Makevars file. (For details see 'Writing R Extensions' SS4.5.) This provides a valuable check on code consistency. It does work with GCC 8.3 as in Rtools40, but that does not detect everything the CRAN checks with current GCC do. PACKAGE INSTALLATION on macOS: * The default personal library directory on builds with --enable-aqua (including CRAN builds) now differs by CPU type, one of ~/Library/R/x86_64/x.y/library ~/Library/R/arm64/x.y/library This uses the CPU type R (and hence the packages) were built for, so when a x86_64 build of R is run under Rosetta emulation on an arm64 Mac, the first is used. UTILITIES: * R CMD check can now scan package functions for bogus return statements, which were possibly intended as return() calls (wish of PR#17180, patch by Sebastian Meyer). This check can be activated via the new environment variable _R_CHECK_BOGUS_RETURN_, true for --as-cran. * R CMD build omits tarballs and binaries of previous builds from the top-level package directory. (PR#17828, patch by Sebastian Meyer.) * R CMD check now runs sanity checks on the use of LazyData, for example that a data directory is present and that LazyDataCompression is not specified without LazyData and has a documented value. For packages with large LazyData databases without specifying LazyDataCompression, there is a reference to the code given in 'Writing R Extensions' SS1.1.6 to test the choice of compression (as in all the CRAN packages tested a non-default method was preferred). * R CMD build removes LazyData and LazyDataCompression fields from the DESCRIPTION file of packages without a data directory. ENCODING-RELATED CHANGES: * The parser now treats \Unnnnnnnn escapes larger than the upper limit for Unicode points (\U10FFFF) as an error as they cannot be represented by valid UTF-8. Where such escapes are used for outputting non-printable (including unassigned) characters, 6 hex digits are used (rather than 8 with leading zeros). For clarity, braces are used, for example \U{0effff}. * The parser now looks for non-ASCII spaces on Solaris (as previously on most other OSes). * There are warnings (including from the parser) on the use of unpaired surrogate Unicode points such as \uD834. (These cannot be converted to valid UTF-8.) * Functions nchar(), tolower(), toupper() and chartr() and those using regular expressions have more support for inputs with a marked Latin-1 encoding. * The character-classification functions used (by default) to replace the system iswxxxxx functions on Windows, macOS and AIX have been updated to Unicode 13.0.0. The character-width tables have been updated to include new assignments in Unicode 13.0.0. * The code for evaluating default (extended) regular expressions now uses the same character-classification functions as the rest of R (previously they differed on Windows, macOS and AIX). * There is a build-time option to replace the system's wide-character wctrans C function by tables shipped with R: use configure option --with-internal-towlower or (on Windows) -DUSE_RI18N_CASE in CFLAGS when building R. This may be needed to allow tolower() and toupper() to work with Unicode characters beyond the Basic Multilingual Plane where not supported by system functions (e.g. on Solaris where it is the new default). * R is more careful when truncating UTF-8 and other multi-byte strings that are too long to be printed, passed to the system or libraries or placed into an internal buffer. Truncation will no longer produce incomplete multibyte characters. DEPRECATED AND DEFUNCT: * Function plclust() from the package stats and package.dependencies(), pkgDepends(), getDepList(), installFoundDepends(), and vignetteDepends() from package tools are defunct. * Defunct functions checkNEWS() and readNEWS() from package tools and CRAN.packages() from utils have been removed. * R CMD config CXXCPP is defunct (it was deprecated in R 3.6.2). * parallel::detectCores() drops support for Irix (retired in 2013). * The LINPACK argument to chol.default(), chol2inv(), solve.default() and svd() has been defunct since R 3.1.0. It was silently ignored up to R 4.0.3 but now gives an error. * Subsetting/indexing, such as ddd[*] or ddd$x on a DOTSXP (dot-dot-dot) object ddd has been disabled; it worked by accident only and was undocumented. BUG FIXES: * Many more C-level allocations (mainly by malloc and strdup) are checked for success with suitable alternative actions. * Bug fix for replayPlot(); this was turning off graphics engine display list recording if a recorded plot was replayed in the same session. The impact of the bug became visible if resize the device after replay OR if attempted another savePlot() after replay (empty display list means empty screen on resize or empty saved plot). * R CMD check etc now warn when a package exports non-existing S4 classes or methods, also in case of no "methods" presence. (Reported by Alex Bertram; reproducible example and patch by Sebastian Meyer in PR#16662.) * boxplot() now also accepts calls for labels such as ylab, the same as plot(). (Reported by Marius Hofert.) * The help page for xtabs() now correctly states that addNA is setting na.action = na.pass among others. (Reported as PR#17770 by Thomas Soeiro.) * The R CMD check <pkg> gives a longer and more comprehensible message when DESCRIPTION misses dependencies, e.g., in Imports:. (Thanks to the contributors of PR#17179.) * update.default() now calls the generic update() on the formula to work correctly for models with extended formulas. (As reported and suggested by Neal Fultz in PR#17865.) * The horizontal position of leaves in a dendrogram is now correct also with center = FALSE. (PR#14938, patch from Sebastian Meyer.) * all.equal.POSIXt() no longer warns about and subsequently ignores inconsistent "tzone" attributes, but describes the difference in its return value (PR#17277). This check can be disabled _via_ the new argument check.tzone = FALSE as suggested by Sebastian Meyer. * as.POSIXct() now populates the "tzone" attribute from its tz argument when x is a logical vector consisting entirely of NA values. * x[[2^31]] <- v now works. (Thanks to the report and patch by Suharto Anggono in PR#17330.) * In log-scale graphics, axis() ticks and label positions are now computed more carefully and symmetrically in their range, typically providing _more_ ticks, fulfilling wishes in PR#17936. The change really corresponds to an improved axisTicks() (package grDevices), potentially influencing grid and lattice, for example. * qnorm(<very large negative>, log.p=TRUE) is now correct to at least five digits where it was catastrophically wrong, previously. * sum(df) and similar "Summary"- and "Math"-group member functions now work for data frames df with logical columns, notably also of zero rows. (Reported to R-devel by Martin "b706".) * unsplit() had trouble with tibbles due to unsound use of rep(NA, len)-indexing, which should use NA_integer_ (Reported to R-devel by Mario Annau.) * pnorm(x, log.p = TRUE) underflows to -Inf slightly later. * show(<hidden S4 generic>) prints better and without quotes for non-hidden S4 generics. * read.table() and relatives treated an "NA" column name as missing when check.names = FALSE PR#18007. * Parsing strings containing UTF-16 surrogate pairs such as "\uD834\uDD1E" works better on some (uncommon) platforms. sprintf("%X", utf8ToInt("\uD834\uDD1E")) should now give "1D11E" on all platforms. * identical(x,y) is no longer true for differing DOTSXP objects, fixing PR#18032. * str() now works correctly for DOTSXP and related exotics, even when these are doomed. Additionally, it no longer fails for lists with a class and "irregular" method definitions such that e.g. lapply(*) will necessarily fail, as currently for different igraph objects. * Too long lines in environment files (e.g. Renviron) no longer crash R. This limit has been increased to 100,000 bytes. (PR#18001.) * There is a further workaround for FreeType giving incorrect italic font faces with cairo-based graphics devices on macOS. * add_datalist(*, force = TRUE) (from package tools) now actually updates an existing data/datalist file for new content. (Thanks to a report and patch by Sebastian Meyer in PR#18048.) * cut.Date() and cut.POSIXt() could produce an empty last interval for breaks = "months" or breaks = "years". (Reported as PR#18053 by Christopher Carbone.) * Detection of the encoding of 'regular' macOS locales such as en_US (which is UTF-8) had been broken by a macOS change: fortunately these are now rarely used with en_US.UTF-8 being preferred. * sub() and gsub(pattern, repl, x, *) now keep attributes of x such as names() also when pattern is NA (PR#18079). * Time differences ("difftime" objects) get a replacement and a rep() method to keep "units" consistent. (Thanks to a report and patch by Nicolas Bennett in PR#18066.) * The \RdOpts macro, setting defaults for \Sexpr options in an Rd file, had been ineffective since R 2.12.0: it now works again. (Thanks to a report and patch by Sebastian Meyer in PR#18073.) * mclapply and pvec no longer accidentally terminate parallel processes started before by mcparallel or related calls in package parallel (PR#18078). * grep and other functions for evaluating (extended) regular expressions handle in Unicode also strings not explicitly flagged UTF-8, but flagged native when running in UTF-8 locale. * Fixed a crash in fifo implementation on Windows (PR#18031). * Binary mode in fifo on Windows is now properly detected from argument open (PR#15600, PR#18031). ------------------------------------------------------------------- Tue May 18 13:10:15 UTC 2021 - Detlef Steuer <detlef.steuer@gmx.de> - improved spec file according to comments of dimstar in https://build.opensuse.org/request/show/892685 ------------------------------------------------------------------- Thu May 6 12:43:28 UTC 2021 - Detlef Steuer <detlef.steuer@gmx.de> - To get in sync with d:l:R:autoCRAN the Matrix package's split in -devel was reversed. ------------------------------------------------------------------- Wed Mar 31 18:41:20 UTC 2021 - Detlef Steuer <detlef.steuer@gmx.de> - CHANGES IN R 4.0.5: BUG FIXES: * The change to the internal table in R 4.0.4 for iswprint has been reverted: it contained some errors in printability of 'East Asian' characters. * For packages using LazyData, R CMD build ignored the --resave-data option and the BuildResaveData field of the DESCRIPTION file (in R versions 4.0.0 to 4.0.4). ------------------------------------------------------------------- Mon Feb 15 10:07:41 UTC 2021 - Detlef Steuer <detlef.steuer@gmx.de> - CHANGES IN R 4.0.4: NEW FEATURES: * File share/texmf/tex/latex/jss.cls has been updated to work with LaTeX versions since Oct 2020. * Unicode character width tables (as used by nchar(, type = "w")) have been updated to Unicode 12.1 by Brodie Gaslam (PR#17781), including many emoji. * The internal table for iswprint (used on Windows, macOS and AIX) has been updated to include many recent Unicode characters. INSTALLATION on a UNIX-ALIKE: * If an external BLAS is specified by --with-blas=foo or _via_ environment variable BLAS_LIBS is not found, this is now a configuration error. The previous behaviour was not clear from the documentation: it was to continue the search as if --with-blas=yes was specified. BUG FIXES: * all.equal(x,y) now "sees" the two different NAs in factors, thanks to Bill Dunlap and others in PR#17897. * (~ NULL)[1] and similar formula subsetting now works, thanks to a report and patch by Henrik Bengtsson in PR#17935. Additionally, subsetting leaving an empty formula now works too, thanks to suggestions by Suharto Anggono. * .traceback(n) keeps source references again, as before R 4.0.0, fixing a regression; introduced by the PR#17580, reported including two patch proposals by Brodie Gaslam. * unlist(plst, recursive=FALSE) no longer drops content for pairlists with list components, thanks to the report and patch by Suharto Anggono in PR#17950. * iconvlist() now also works on MUSL based (Linux) systems, from a report and patch suggestion by Wesley Chan in PR#17970. * round() and signif() no longer tolerate wrong argument names, notably in 1-argument calls; reported by Shane Mueller on R-devel (mailing list); later reported as PR#17976. * .Machine has longdouble.* elements only if capabilities("long.double") is true, as documented. (Previously they were included if the platform had long double identical to double, as ARM does.) * p.adjust(numeric(), n=0) now works, fixing PR#18002. * identical(x,y) no longer prints "Unknown Type .." for typeof(x) == "..." objects. * Fix (auto-)print()ing of named complex vectors, see PR#17868 and PR#18019. * all.equal(<language>, <...>) now works, fixing PR#18029. * as.data.frame.list(L, row.names=NULL) now behaves in line with data.frame(), disregarding names of components of L, fixing PR#18034, reported by Kevin Tappe. * checkRdaFiles(ff)$version is now correct also when ff contains files of different versions, thanks to a report and patch from Sebastian Meyer in PR#18041. * macOS: Quartz device live drawing could fail (no plot is shown) if the system changes the drawing context after view update (often the case since macOS Big Sur). System log may show "CGContextDelegateCreateForContext: invalid context" error. ------------------------------------------------------------------- Sat Oct 10 18:43:26 UTC 2020 - Detlef Steuer <detlef.steuer@gmx.de> - CHANGES IN R 4.0.3: NEW FEATURES: * On platforms using configure option --with-internal-tzcode, additional values "internal" and (on macOS only) "macOS" are accepted for the environment variable TZDIR. (See ?TZDIR.) On macOS, "macOS" is used by default if the system timezone database is a newer version than that in the R installation. * When install.packages(type = "source") fails to find a package in a repository it mentions package versions which are excluded by their R version requirement and links to hints on why a package might not be found. * The default value for options("timeout") can be set from enviromnent variable R_DEFAULT_INTERNET_TIMEOUT, still defaulting to 60 (seconds) if that is not set or invalid. This may be needed when child R processes are doing downloads, for example during the installation of source packages which download jars or other forms of data. LINK-TIME OPTIMIZATION on a UNIX-ALIKE: * There is now support for parallelized Link-Time Optimization (LTO) with GCC and for 'thin' LTO with clang _via_ setting the LTO macro. * There is support for setting a different LTO flag for the Fortran compiler, including to empty when mixing clang and gfortran (as on macOS). See file config.site. * There is a new LTO_LD macro to set linker options for LTO compilation, for example to select an alternative linker or to parallelize thin LTO. DEPRECATED AND DEFUNCT: * The LINPACK argument to chol.default(), chol2inv(), solve.default() and svd() has been defunct since R 3.1.0. Using it now gives a warning which will become an error in R 4.1.0. BUG FIXES: * The code mitigating stack overflow with PCRE regexps on very long strings is enabled for PCRE2 < 10.30 also when JIT is enabled, since stack overflows have been seen in that case. * Fix to correctly show the group labels in dotchart() (which where lost in the ylab improvement for R 4.0.0). * addmargins(*, ..) now also works when fn() is a local function, thanks to bug report and patch PR#17124 from Alex Bertram. * rank(x) and hence sort(x) now work when x is an object (as per is.object(x)) of type "raw" _and_ provides a valid `[` method, e.g., for gmp::as.bigz(.) numbers. * chisq.test(*, simulate.p.value=TRUE) and r2dtable() now work correctly for large table entries (in the millions). Reported by Sebastian Meyer and investigated by more helpers in PR#16184. * Low-level socket read/write operations have been fixed to correctly signal communication errors. Previously, such errors could lead to a segfault due to invalid memory access. Reported and debugged by Dmitriy Selivanov in PR#17850. * quantile(x, pr) works more consistently for pr values slightly outside [0,1], thanks to Suharto Anggono's PR#17891. Further, quantile(x, prN, names=FALSE) now works even when prN contains NAs, thanks to Anggono's PR#17892. Ditto for ordered factors or Date objects when type = 1 or 3, thanks to PR#17899. * Libcurl-based internet access, including curlGetHeaders(), was not respecting the "timeout" option. If this causes unanticipated timeouts, consider increasing the default by setting R_DEFAULT_INTERNET_TIMEOUT. * as.Date(<char>) now also works with an initial "", thanks to Michael Chirico's PR#17909. * isS3stdGeneric(f) now detects an S3 generic also when it it is trace()d, thanks to Gabe Becker's PR#17917. * R_allocLD() has been fixed to return memory aligned for long double type PR#16534. * fisher.test() no longer segfaults when called again after its internal stack has been exceeded PR#17904. * Accessing a long vector represented by a compact integer sequence no longer segfaults (reported and debugged by Hugh Parsonage). * duplicated() now works also for strings with multiple encodings inside a single vector PR#17809. * phyper(11, 15, 0, 12, log.p=TRUE) no longer gives NaN; reported as PR#17271 by Alexey Stukalov. * Fix incorrect calculation in logLik.nls() PR#16100, patch from Sebastian Meyer. * A very old bug could cause a segfault in model.matrix() when terms involved logical variables. Part of PR#17879. * model.frame.default() allowed data = 1, leading to involuntary variable capture (rest of PR#17879). * tar() no longer skips non-directory files, thanks to a patch by Sebastian Meyer, fixing the remaining part of PR#16716. ------------------------------------------------------------------- Mon Jun 22 09:18:01 UTC 2020 - Detlef Steuer <detlef.steuer@gmx.de> - CHANGES IN R 4.0.2: UTILITIES: * R CMD check skips vignette re-building (with a warning) if the VignetteBuilder package(s) are not available. BUG FIXES: * Paths with non-ASCII characters caused problems for package loading on Windows PR#17833. * Using tcltk widgets no longer crashes R on Windows. * source(*, echo=TRUE) no longer fails in some cases with empty lines; reported by Bill Dunlap in PR#17769. * on.exit() now correctly matches named arguments, thanks to PR#17815 (including patch) by Brodie Gaslam. * regexpr(*, perl=TRUE) no longer returns incorrect positions into text containing characters outside of the Unicode Basic Multilingual Plane on Windows. ------------------------------------------------------------------- Sat Jun 6 10:33:50 UTC 2020 - Detlef Steuer <detlef.steuer@gmx.de> - CHANGES IN R 4.0.1: NEW FEATURES: * paste() and paste0() gain a new optional argument recycle0. When set to true, zero-length arguments are recycled leading to character(0) after the sep-concatenation, i.e., to the empty string "" if collapse is a string and to the zero-length value character(0) when collapse = NULL. A package whose code uses this should depend on R (>= 4.0.1). * The summary(<warnings>) method now maps the counts correctly to the warning messages. BUG FIXES: * aov(frml, ...) now also works where the formula deparses to more than 500 characters, thanks to a report and patch proposal by Jan Hauffa. * Fix a dozen places (code, examples) as Sys.setlocale() returns the new rather than the previous setting. * Fix for adding two complex grid units via sum(). Thanks to Gu Zuguang for the report and Thomas Lin Pedersen for the patch. * Fix parallel::mclapply(..., mc.preschedule=FALSE) to handle raw vector results correctly. PR#17779 * Computing the base value, i.e., 2, "everywhere", now uses FLT_RADIX, as the original machar code looped indefinitely on the ppc64 architecture for the longdouble case. * In R 4.0.0, sort.list(x) when is.object(x) was true, e.g., for x <- I(letters), was accidentally using method = "radix". Consequently, e.g., merge(<data.frame>) was much slower than previously; reported in PR#17794. * plot(y ~ x, ylab = quote(y[i])) now works, as e.g., for xlab; related to PR#10525. * parallel::detect.cores(all.tests = TRUE) tries a matching OS name before the other tests (which were intended only for unknown OSes). * Parse data for raw strings is now recorded correctly. Reported by Gabor Csardi. ------------------------------------------------------------------- Fri Apr 24 08:08:31 UTC 2020 - Detlef Steuer <detlef.steuer@gmx.de> - CHANGES IN 4.0.0: SIGNIFICANT USER-VISIBLE CHANGES: * Packages need to be (re-)installed under this version (4.0.0) of R. * matrix objects now also inherit from class "array", so e.g., class(diag(1)) is c("matrix", "array"). This invalidates code incorrectly assuming that class(matrix_obj)) has length one. S3 methods for class "array" are now dispatched for matrix objects. * There is a new syntax for specifying _raw_ character constants similar to the one used in C++: r"(...)" with ... any character sequence not containing the sequence )". This makes it easier to write strings that contain backslashes or both single and double quotes. For more details see ?Quotes. * R now uses a stringsAsFactors = FALSE default, and hence by default no longer converts strings to factors in calls to data.frame() and read.table(). A large number of packages relied on the previous behaviour and so have needed/will need updating. * The plot() S3 generic function is now in package base rather than package graphics, as it is reasonable to have methods that do not use the graphics package. The generic is currently re-exported from the graphics namespace to allow packages importing it from there to continue working, but this may change in future. Packages which define S4 generics for plot() should be re-installed and package code using such generics from other packages needs to ensure that they are imported rather than rely on their being looked for on the search path (as in a namespace, the base namespace has precedence over the search path). REFERENCE COUNTING: * Reference counting is now used instead of the NAMED mechanism for determining when objects can be safely mutated in base C code. This reduces the need for copying in some cases and should allow further optimizations in the future. It should help make the internal code easier to maintain. This change is expected to have almost no impact on packages using supported coding practices in their C/C++ code. MIGRATION TO PCRE2: * This version of R is built against the PCRE2 library for Perl-like regular expressions, if available. (On non-Windows platforms PCRE1 can optionally be used if PCRE2 is not available at build time.) The version of PCRE in use can be obtained _via_ extSoftVersion(): PCRE1 (formerly known as 'PCRE') has versions <= 8, PCRE2 versions >= 10. * Making PCRE2 available when building R from source is strongly recommended (preferably version 10.30 or later) as PCRE1 is no longer developed: version 8.44 is 'likely to be the final release'. * PCRE2 reports errors for some regular expressions that were accepted by PCRE1. A hyphen now has to be escaped in a character class to be interpreted as a literal (unless first or last in the class definition). \R, \B and \X are no longer allowed in character classes (PCRE1 treated these as literals). * Option PCRE_study is no longer used with PCRE2, and is reported as FALSE when that is in use. NEW FEATURES: * assertError() and assertWarning() (in package tools) can now check for _specific_ error or warning classes _via_ the new optional second argument classes (which is not back compatible with previous use of an unnamed second argument). * DF2formula(), the utility for the data frame method of formula(), now works without parsing and explicit evaluation, starting from Suharto Anggono's suggestion in PR#17555. * approxfun() and approx() gain a new argument na.rm defaulting to true. If set to false, missing y values now propagate into the interpolated values. * Long vectors are now supported as the seq argument of a for() loop. * str(x) gets a new deparse.lines option with a default to speed it up when x is a large call object. * The internal traceback object produced when an error is signalled (.Traceback), now contains the calls rather than the _deparse()d_ calls, deferring the deparsing to the user-level functions .traceback() and traceback(). This fulfils the wish of PR#17580, reported including two patch proposals by Brodie Gaslam. * data.matrix() now converts character columns to factors and from this to integers. * package.skeleton() now explicitly lists all exports in the NAMESPACE file. * New function .S3method() to register S3 methods in R scripts. * file.path() has some support for file paths not in the session encoding, e.g. with UTF-8 inputs in a non-UTF-8 locale the output is marked as UTF-8. * Most functions with file-path inputs will give an explicit error if a file-path input in a marked encoding cannot be translated (to the native encoding or in some cases on Windows to UTF-8), rather than translate to a different file path using escapes. Some (such as dir.exists(), file.exists(), file.access(), file.info(), list.files(), normalizePath() and path.expand()) treat this like any other non-existent file, often with a warning. * There is a new help document accessed by help("file path encoding") detailing how file paths with marked encodings are handled. * New function list2DF() for creating data frames from lists of variables. * iconv() has a new option sub = "Unicode" to translate UTF-8 input invalid in the to encoding using <U+xxxx> escapes. * There is a new function infoRDS() providing information about the serialization format of a serialized object. * S3 method lookup now by default skips the elements of the search path between the global and base environments. * Added an argument add_datalist(*, small.size = 0) to allow the creation of a data/datalist file even when the total size of the data sets is small. * The backquote function bquote() has a new argument splice to enable splicing a computed list of values into an expression, like ,@ in LISP's backquote. * The formula interface to t.test() and wilcox.test() has been extended to handle one-sample and paired tests. * The palette() function has a new default set of colours (which are less saturated and have better accessibility properties). There are also some new built-in palettes, which are listed by the new palette.pals() function. These include the old default palette under the name "R3". Finally, the new palette.colors() function allows a subset of colours to be selected from any of the built-in palettes. * n2mfrow() gains an option asp = 1 to specify the aspect ratio, fulfilling the wish and extending the proposal of Michael Chirico in PR#17648. * For head(x, n) and tail() the default and other S3 methods notably for _vector_ n, e.g. to get a "corner" of a matrix, has been extended to array's of higher dimension thanks to the patch proposal by Gabe Becker in PR#17652. Consequently, optional argument addrownums is deprecated and replaced by the (more general) argument keepnums. An invalid second argument n now leads to typically more easily readable error messages. * New function .class2() provides the full character vector of class names used for S3 method dispatch. * Printing methods(..) now uses a new format() method. * sort.list(x) now works for non-atomic objects x and method = "auto" (the default) or "radix" in cases order(x) works. * Where they are available, writeBin() allows long vectors. * New function deparse1() produces one string, wrapping deparse(), to be used typically in deparse1(substitute(*)), e.g., to fix PR#17671. * wilcox.test() enhancements: In the (non-paired) two-sample case, Inf values are treated as very large for robustness consistency. If exact computations are used, the result now has "exact" in the method element of its return value. New arguments tol.root and digits.rank where the latter may be used for stability to treat very close numbers as ties. * readBin() and writeBin() now report an error for an invalid endian value. The affected code needs to be fixed with care as the old undocumented behavior was to swap endian-ness in such cases. * sequence() is now an S3 generic with an internally implemented default method, and gains arguments to generate more complex sequences. Based on code from the S4Vectors Bioconductor package and the advice of Herv'e Pag`es. * print()'s default method and many other methods (by calling the default eventually and passing ...) now make use of a new optional width argument, avoiding the need for the user to set and reset options("width"). * memDecompress() supports the RFC 1952 format (e.g. in-memory copies of gzip-compressed files) as well as RFC 1950. * memCompress() and memDecompress() support long raw vectors for types "gzip" and "zx". * sweep() and slice.index() can now use names of dimnames for their MARGIN argument (apply has had this for almost a decade). * New function proportions() and marginSums(). These should replace the unfortunately named prop.table() and margin.table(). They are drop-in replacements, but also add named-margin functionality. The old function names are retained as aliases for back-compatibility. * Functions rbinom(), rgeom(), rhyper(), rpois(), rnbinom(), rsignrank() and rwilcox() which have returned integer since R 3.0.0 and hence NA when the numbers would have been outside the integer range, now return double vectors (without NAs, typically) in these cases. * matplot(x,y) (and hence matlines() and matpoints()) now call the corresponding methods of plot() and lines(), e.g, when x is a "Date" or "POSIXct" object; prompted by Spencer Graves' suggestion. * stopifnot() now allows customizing error messages via argument names, thanks to a patch proposal by Neal Fultz in PR#17688. * unlink() gains a new argument expand to disable wildcard and tilde expansion. Elements of x of value "~" are now ignored. * mle() in the stats4 package has had its interface extended so that arguments to the negative log-likelihood function can be one or more vectors, with similar conventions applying to bounds, start values, and parameter values to be kept fixed. This required a minor extension to class "mle", so saved objects from earlier versions may need to be recomputed. * The default for pdf() is now useDingbats = FALSE. * The default fill colour for hist() and boxplot() is now col = "lightgray". * The default order of the levels on the y-axis for spineplot() and cdplot() has been reversed. * If the R_ALWAYS_INSTALL_TESTS environment variable is set to a true value, R CMD INSTALL behaves as if the --install-tests option is always specified. Thanks to Reinhold Koch for the suggestion. * New function R_user_dir() in package tools suggests paths appropriate for storing R-related user-specific data, configuration and cache files. * capabilities() gains a new logical option Xchk to avoid warnings about X11-related capabilities. * The internal implementation of grid units has changed, but the only visible effects at user-level should be * a slightly different print format for some units (especially unit arithmetic), * faster performance (for unit operations) and * two new functions unitType() and unit.psum(). Based on code contributed by Thomas Lin Pedersen. * When internal dispatch for rep.int() and rep_len() fails, there is an attempt to dispatch on the equivalent call to rep(). * Object .Machine now contains new longdouble.* entries (when R uses long doubles internally). * news() has been enhanced to cover the news on R 3.x and 2.x. * For consistency, N <- NULL; N[[1]] <- val now turns N into a list also when val) has length one. This enables dimnames(r1)[[1]] <- "R1" for a 1-row matrix r1, fixing PR#17719 reported by Serguei Sokol. * deparse(..), dump(..), and dput(x, control = "all") now include control option "digits17" which typically ensures 1:1 invertibility. New option control = "exact" ensures numeric exact invertibility via "hexDigits". * When loading data sets via read.table(), data() now uses LC_COLLATE=C to ensure locale-independent results for possible string-to-factor conversions. * A server socket connection, a new connection type representing a listening server socket, is created via serverSocket() and can accept multiple socket connections via socketAccept(). * New function socketTimeout() changes the connection timeout of a socket connection. * The time needed to start a homogeneous PSOCK cluster on localhost with many nodes has been significantly reduced (package parallel). * New globalCallingHandlers() function to establish global condition handlers. This allows registering default handlers for specific condition classes. Developed in collaboration with Lionel Henry. * New function tryInvokeRestart() to invoke a specified restart if one is available and return without signaling an error if no such restart is found. Contributed by Lionel Henry in PR#17598. * str(x) now shows the length of attributes in some cases for a data frame x. * Rprof() gains a new argument filter.callframes to request that intervening call frames due to lazy evaluation or explicit eval() calls be omitted from the recorded profile data. Contributed by Lionel Henry in PR#17595. * The handling of ${FOO-bar} and ${FOO:-bar} in Renviron files now follows POSIX shells (at least on a Unix-alike), so the first treats empty environment variables as set and the second does not. Previously both ignored empty variables. There are several uses of the first form in etc/Renviron. * New classes argument for suppressWarnings() and suppressMessages() to selectively suppress only warnings or messages that inherit from particular classes. Based on patch from Lionel Henry submitted with PR#17619. * New function activeBindingFunction() retrieves the function of an active binding. * New "cairoFT" and "pango" components in the output of grSoftVersion(). * New argument symbolfamily in cairo-based graphics devices and new function cairoSymbolFont() that can be used to provide the value for that argument. Windows: * Rterm now works also when invoked from MSYS2 terminals. Line editing is possible when command winpty is installed. * normalizePath() now resolves symbolic links and normalizes case of long names of path elements in case-insensitive folders (PR#17165). * md5sum() supports UTF-8 file names with characters that cannot be translated to the native encoding (PR#17633). * Rterm gains a new option --workspace to specify the workspace to be restored. This allows equals to be part of the name when opening _via_ Windows file associations (reported by Christian Asseburg). * Rterm now accepts ALT+xxx sequences also with NumLock on. Tilde can be pasted with an Italian keyboard (PR#17679). * R falls back to copying when junction creation fails during package checking (patch from Duncan Murdoch). DEPRECATED AND DEFUNCT: * Make macro F77_VISIBILITY has been removed and replaced by F_VISIBILITY. * Make macros F77, FCPIFCPLAGS and SHLIB_OPENMP_FCFLAGS have been removed and replaced by FC, FPICFLAGS and SHLIB_OPENMP_FFLAGS respectively. (Most make programs will set F77 to the value of FC, which is set for package compilation. But portable code should not rely on this.) * The deprecated support for specifying C++98 for package installation has been removed. * R CMD config no longer knows about the unused settings F77 and FCPIFCPLAGS, nor CXX98 and similar. * Either PCRE2 or PCRE1 >= 8.32 (Nov 2012) is required: the deprecated provision for 8.20-8.31 has been removed. * Defunct functions mem.limits(), .readRDS(), .saveRDS(),..find.package(), and .path.package() from package base and allGenerics(), getAccess(), getAllMethods(), getClassName(), getClassPackage(), getExtends(), getProperties(), getPrototype(), getSubclasses(), getVirtual(), mlistMetaName(), removeMethodsObject(), seemsS4Object(), traceOff(), and traceOn() from methods have been removed. C-LEVEL FACILITIES: * installChar is now remapped in Rinternals.h to installTrChar, of which it has been a wrapper since R 3.6.0. Neither are part of the API, but packages using installChar can replace it if they depend on R >= 3.6.2. * Header R_ext/Print.h defines R_USE_C99_IN_CXX and hence exposes Rvprintf and REvprintf if used with a C++11 (or later) compiler. * There are new Fortran subroutines dblepr1, realpr1 and intpr1 to print a scalar variable (gfortran 10 enforces the distinction between scalars and length-one arrays). Also labelpr to print just a label. * R_withCallingErrorHandler is now available for establishing a calling handler in C code for conditions inheriting from class error. INSTALLATION on a UNIX-ALIKE: * User-set DEFS (e.g., in config.site) is now used for compiling packages (including base packages). * There is a new variant option --enable-lto=check for checking consistency of BLAS/LAPACK/LINPACK calls - see 'Writing R Extensions'. * A C++ compiler default is set only if the C++11 standard is supported: it no longer falls back to C++98. * PCRE2 is used if available. To make use of PCRE1 if PCRE2 is unavailable, configure with option --with-pcre1. * The minimum required version of libcurl is now 7.28.0 (Oct 2012). * New make target distcheck checks * R can be rebuilt from the tarball created by make dist, * the build from the tarball passes make check-all, * the build installs and uninstalls, * the source files are properly cleaned by make distclean. UTILITIES: * R --help now mentions the option --no-echo (renamed from --slave) and its previously undocumented short form -s. * R CMD check now optionally checks configure and cleanup scripts for non-Bourne-shell code ('bashisms'). * R CMD check --as-cran now runs \donttest examples (which are run by example()) instead of instructing the tester to do so. This can be temporarily circumvented during development by setting environment variable _R_CHECK_DONTTEST_EXAMPLES_ to a false value. PACKAGE INSTALLATION: * There is the beginnings of support for the recently approved C++20 standard, specified analogously to C++14 and C++17. There is currently only limited support for this in compilers, with flags such as -std=c++20 and -std=c++2a. For the time being the configure test is of accepting one of these flags and compiling C++17 code. BUG FIXES: * formula(x) with length(x) > 1 character vectors, is deprecated now. Such use has been rare, and has 'worked' as expected in some cases only. In other cases, wrong x have silently been truncated, not detecting previous errors. * Long-standing issue where the X11 device could lose events shortly after startup has been addressed (PR#16702). * The data.frame method for rbind() no longer drops <NA> levels from factor columns by default (PR#17562). * available.packages() and hence install.packages() now pass their ... argument to download.file(), fulfilling the wish of PR#17532; subsequently, available.packages() gets new argument quiet, solving PR#17573. * stopifnot() gets new argument exprObject to allow an R object of class expression (or other 'language') to work more consistently, thanks to suggestions by Suharto Anggono. * conformMethod() now works correctly in cases containing a "&& logic" bug, reported by Henrik Bengtsson. It now creates methods with "missing" entries in the signature. Consequently, rematchDefinition() is amended to use appropriate .local() calls with named arguments where needed. * format.default(*, scientific = FALSE) now corresponds to a practically most extreme options(scipen = n) setting rather than arbitrary n = 100. * format(as.symbol("foo")) now works (returning "foo"). * postscript(.., title = *) now signals an error when the title string contains a character which would produce corrupt PostScript, thanks to PR#17607 by Daisuko Ogawa. * Certain Ops (notably comparison such as ==) now also work for 0-length data frames, after reports by Hilmar Berger. * methods(class = class(glm(..))) now warns more usefully and only once. * write.dcf() no longer mangles field names (PR#17589). * Primitive replacement functions no longer mutate a referenced first argument when used outside of a complex assignment context. * A better error message for contour(*, levels = Inf). * The return value of contourLines() is no longer invisible(). * The Fortran code for calculating the coefficients component in lm.influence() was very inefficient. It has (for now) been replaced with much faster R code (PR#17624). * cm.colors(n) _etc_ no longer append the code for alpha = 1, "FF", to all colors. Hence all eight *.colors() functions and rainbow() behave consistently and have the same non-explicit default (PR#17659). * dnorm had a problematic corner case with sd == -Inf or negative sd which was not flagged as an error in all cases. Thanks to Stephen D. Weigand for reporting and Wang Jiefei for analyzing this; similar change has been made in dlnorm(). * The optional iter.smooth argument of plot.lm(), (the plot() method for lm and glm fits) now defaults to 0 for all glm fits. Especially for binary observations with high or low fitted probabilities, this effectively deleted all observations of 1 or 0. Also, the type of residuals used in the glm case has been switched to "pearson" since deviance residuals do not in general have approximately zero mean. * In plot.lm, Cook's distance was computed from unweighted residuals, leading to inconsistencies. Replaced with usual weighted version. (PR#16056) * Time-series ts(*, start, end, frequency) with fractional frequency are supported more consistently; thanks to a report from Johann Kleinbub and analysis and patch by Duncan Murdoch in PR#17669. * In case of errors mcmapply() now preserves attributes of returned "try-error" objects and avoids simplification, overriding SIMPLIFY to FALSE. (PR#17653) * as.difftime() gets new optional tz = "UTC" argument which should fix behaviour during daylight-savings-changeover days, fixing PR#16764, thanks to proposals and analysis by Johannes Ranke and Kirill M"uller. * round() does a better job of rounding _"to nearest"_ by _measuring_ and _"to even"_; thanks to a careful algorithm originally prompted by the report from Adam Wheeler and then others, in PR#17668. round(x, dig) for _negative_ digits is much more rational now, notably for large |dig|. * Inheritance information on S4 classes is maintained more consistently, particularly in the case of class unions (in part due to PR#17596 and a report from Ezra Tucker). * is() behaves more robustly when its argument class2 is a classRepresentation object. * The warning message when attempting to export an nonexistent class is now more readable; thanks to Thierry Onkelinx for recognizing the problem. * choose() misbehaved in corner cases where it switched n - k for k and n was only _nearly_ integer (report from Erik Scott Wright). * mle() in the stats4 package had problems combining use of box constraints and fixed starting values (in particular, confidence intervals were affected). * Operator ? now has lower precedence than = to work as documented, so = behaves like <- in help expressions (PR#16710). * smoothEnds(x) now returns integer type in _both_ cases when x is integer, thanks to a report and proposal by Bill Dunlap PR#17693. * The methods package does a better job of tracking inheritance relationships across packages. * norm(diag(c(1, NA)), "2") now works. * subset() had problems with 0-col dataframes (reported by Bill Dunlap, PR#17721). * Several cases of integer overflow detected by the 'undefined behaviour sanitizer' of clang 10 have been circumvented. One in rhyper() may change the generated value for large input values. * dotchart() now places the y-axis label (ylab) much better, not overplotting labels, thanks to a report and suggestion by Alexey Shipunov. * A rare C-level array overflow in chull() has been worked around. * Some invalid specifications of the day-of-the-year (_via_ %j, e.g. day 366 in 2017) or week plus day-of-the-week are now detected by strptime(). They now return NA but give a warning as they may have given random results or corrupted memory in earlier versions of R. * socketConnection(server = FALSE) now respects the connection timeout also on Linux. * socketConnection(server = FALSE) no longer leaks a connection that is available right away without waiting (e.g. on localhost). * Socket connections are now robust against spurious readability and spurious availability of an incoming connection. * blocking = FALSE is now respected also on the server side of a socket connection, allowing non-blocking read operations. * anova.glm() and anova.glmlist() computed incorrect score (Rao) tests in no-intercept cases. (Andr'e Gillibert, PR#17734) * summaryRprof() now should work correctly for the Rprof(*, memory.profiling=TRUE) case with small chunk size (and "tseries" or similar) thanks to a patch proposal by Benjamin Tyner, in PR#15886. * xgettext() ignores strings passed to ngettext(), since the latter is handled by xngettext(). Thanks to Daniele Medri for the report and all the recent work he has done on the Italian translations. * data(package = "P") for P in base and stats no longer reports the data sets from package datasets (which it did for back compatibility for 16 years), fixing PR#17730. * x[[Inf]] (returning NULL) no longer leads to undefined behavior, thanks to a report by Kirill M"uller in PR#17756. Further, x[[-Inf]] and x[[-n]] now give more helpful error messages. * Gamma() family sometimes had trouble storing link name PR#15891 BUG FIXES (Windows): * Sys.glob() now supports all characters from the Unicode Basic Multilingual Plane, no longer corrupting some (less commonly used) characters (PR#17638). * Rterm now correctly displays multi-byte-coded characters representable in the current native encoding (at least on Windows 10 they were sometimes omitted, PR#17632). * scan() issues with UTF-8 data when running in a DBCS locale have been resolved (PR#16520, PR#16584). * RTerm now accepts enhanced/arrow keys also with ConPTY. * R can can now be started _via_ the launcher icon in a user documents directory whose path is not representable in the system encoding. * socketConnection(server = FALSE) now returns instantly also on Windows when connection failure is signalled. * Problems with UTF-16 surrogate pairs have been fixed in several functions, including tolower() and toupper() (PR#17645). ------------------------------------------------------------------- Sat Feb 29 18:08:15 UTC 2020 - Detlef Steuer <detlef.steuer@gmx.de> - CHANGES IN R 3.6.3: NEW FEATURES: * The included LAPACK has been updated to version 3.9.0 (for the included routines, just bug fixes). BUG FIXES: * Fixed a C level integer overflow in rhyper(); reported by Benjamin Tyner in PR#17694. * Uses of url(gzcon(.)) needing to extend buffer size have failed (with HTTP/2 servers), reported by G'abor Cs'ardi. * predict(loess(..), se=TRUE) now errors out (instead of seg.faulting etc) for large sample sizes, thanks to a report and patch by Benjamin Tyner in PR#17121. * tools:assertCondition(., "error") and hence assertError() no longer return errors twice (invisibly). * update(form, new) in the case of a long new formula sometimes wrongly eliminated the intercept from form, or (more rarely) added a garbage term (or seg.faulted !); the fix happened by simplifying the C-level logic of terms.formula(). Reported by Mathias Amb"uhl in PR#16326. * The error message from stopifnot(.., <error producing call>) again contains the full "stopifnot(.......)" call: Its attempted suppression did not work consistently. * On Windows, download.file(., , "wininet", headers=character()) would fail; reported with patch proposal by Kevin Ushey in PR#17710. ------------------------------------------------------------------- Mon Jan 20 18:30:04 UTC 2020 - Dan Čermák <dcermak@suse.com> - Don't mark %{_libdir}/R/doc as %doc: This causes issues for rstudio, which requires the directory %{_libdir}/R/doc to exist, but the directory is not present if libzypp is configured to omit documentation. ------------------------------------------------------------------- Thu Dec 12 11:37:25 UTC 2019 - Detlef Steuer <detlef.steuer@gmx.de> - CHANGES IN R 3.6.2: NEW FEATURES: * runmed(x, *) gains a new option na.action determining _how_ to handle NaN or NA in x. * dotchart() gains new options ann, xaxt, frame.plot and log. INSTALLATION on a UNIX-ALIKE: * Detection of the C stack direction has been moved from run-time to configure: this is safer with LTO builds and allows the detection to be overridden - see file config.site. * Source-code changes enable installation on platforms using gcc -fno-common (the expected default for gcc 10.x). C-LEVEL FACILITIES: * installTrChar (which is nowadays is wrapped by installChar) is defined in Rinternals.h. (Neither are part of the API.) PACKAGE INSTALLATION: * Header Rconfig.h contains the value of FC_LEN_T deduced at installation which is used by the prototypes in headers R_ext/BLAS.h and R_ext/Lapack.h but to avoid extensive breakage this is only exposed when USE_FC_LEN_T is defined. If a package's C/C++ calls to BLAS/LAPACK allow for the 'hidden' arguments used by most Fortran compilers to pass the lengths of Fortran character arguments, define USE_FC_LEN_T and include Rconfig.h (possibly _via_ R.h) before including R_ext/BLAS.h or R_ext/Lapack.h. * A package with Fortran source code and perhaps C (but not C++) sources can request for its shared object/DLL to be linked by the Fortran compiler by including a line USE_FC_TO_LINK= in src/Makevars[.win] and using $(SHLIB_OPENMP_FFLAGS) as part of PKG_LIBS. The known reason for doing so is a package which uses Fortran (only) OpenMP on a platform where the Fortran OpenMP runtime is incompatible with the C one (e.g. gfortran 9.x with clang). UTILITIES: * R CMD check has a new option to mitigate checks leaving files/directories in /tmp. See the 'R Internals' manual - this is part of --as-cran. Windows: * The default standard for C++ in package installation is C++11 (as it has been on other platforms where available since R 3.6.0: the default toolchain on Windows was defaulting to C++98). DEPRECATED AND DEFUNCT: * Support for specifying C++98 in package installation is deprecated. * Support in R CMD config for F77, FCPIFCPLAGS, CPP, CXXCPP and CXX98 and similar is deprecated. (CPP is found from the system make and may well not be set.) Use $CC -E and $CXX -E instead of CPP and CXXCPP. BUG FIXES: * runmed(x, *) when x contains missing values now works consistently for both algorithm="Stuetzle" and "Turlach", and no longer segfaults for "Turlach", as reported by Hilmar Berger. * apply(diag(3), 2:3, mean) now gives a helpful error message. * dgamma(x, shape, log=TRUE) now longer overflows to Inf for shape < 1 and very small x, fixing PR#17577, reported by Jonathan Rougier. * Buffer overflow in building error messages fixed. Reported by Benjamin Tremblay. * options(str = .) is correctly initialized at package utils load time, now. A consequence is that str() in scripts now is more consistent to interactive use, e.g., when displaying function(**) argument lists. * as.numeric(<call>) now gives correct error message. * Printing ls.str() no longer wrongly shows "<missing>" in rare cases. * Auto-printing S4 objects no longer duplicates the object, for faster speed and reduced memory consumption. Reported by Aaron Lun. * pchisq(<LRG>, <LRG>, ncp=100) no longer takes practically forever in some cases. Hence ditto for corresponding qchisq() calls. * x %% L for finite x no longer returns NaN when L is infinite, nor suffers from cancellation for large finite L, thanks to Long Qu's PR#17611. Analogously, x %/% L and L %/% x suffer less from cancellation and return values corresponding to limits for large L. * grepl(NA, *) now returns logical as documented. * options(warn=1e11) is an error now, instead of later leading to C stack overflow because of infinite recursion. * R_tryCatch no longer transfers control for all conditions. Reported and patch provided by Lionel Henry in PR#17617. * format(object.size(.), digits=NULL) now works, fixing PR#17628 reported by Jonathan Carroll. * get_all_vars(f, d) now also works for cases, e.g. where d contains a matrix. Reported by Simon Wood in 2009 and patch provided by Ben Bolker in PR#13624. Additionally, it now also works when some variables are data frames, fixing PR#14905, reported by Patrick Breheny. * barplot() could get spacings wrong if there were exactly two bars PR#15522. Patch by Michael Chirico. * power.t.test() works in more cases when returning values of n smaller than 2. * dotchart(*, pch=., groups=.) now works better. Reported by Robert and confirmed by Nic Rochette in PR#16953. * canCoerce(obj, cl) no longer assumes length(class(obj)) == 1. * plot.formula(*, subset = *) now also works in a boundary case reported by Robert Schlicht (TU Dresden). * readBin() and writeBin() of a rawConnection() now also work in large cases, thanks to a report and proposal by Taeke Harkema in PR#17665. ------------------------------------------------------------------- Thu Oct 17 12:34:46 UTC 2019 - Richard Brown <rbrown@suse.com> - Remove obsolete Groups tag (fate#326485) ------------------------------------------------------------------- Fri Aug 30 10:24:32 UTC 2019 - John Vandenberg <jayvdb@gmail.com> - Use %license ------------------------------------------------------------------- Sun Aug 11 06:08:45 UTC 2019 - John Vandenberg <jayvdb@gmail.com> - Fix Summary of R-core and R-core-devel ------------------------------------------------------------------- Fri Jul 5 07:41:49 UTC 2019 - Detlef Steuer <detlef.steuer@gmx.de> - CHANGES IN R 3.6.1: INSTALLATION on a UNIX-ALIKE: * The default detection of the shell variable libNN is overridden for derivatives of Debian Linux, some of which have started to have a /usr/lib64 directory. (E.g. Ubuntu 19.04.) As before, it can be specified in config.site. UTILITIES: * R CMD config knows the values of AR and RANLIB, often set for LTO builds. DEPRECATED AND DEFUNCT: * The use of a character vector with .Fortran() is formally deprecated and gives a non-portability warning. (It has long been strongly discouraged in 'Writing R Extensions'.) BUG FIXES: * On Windows, GUI package installation via menuInstallPkgs() works again, thanks to Len Weil's and Duncan Murdoch's PR#17556. * R CMD check on data() fixing PR#17558 thanks to Duncan Murdoch. * quasi(*, variance = list(..)) now works more efficiently, and should work in all cases fixing PR#17560. Further, quasi(var = mu(1-mu)) and quasi(var = "mu ^ 3") now work, and quasi(variance = "log(mu)") now gives a correct error message. * Creation of lazy loading database during package installation is again robust to Rprofile changing the current working directory (PR#17559). * boxplot(y ~ f, horizontal=TRUE) now produces correct x- and y-labels. * rbind.data.frame() allows to keep <NA> levels from factor columns (PR#17562) via new option factor.exclude. Additionally, it works in one more case with matrix-columns which had been reported on 2017-01-16 by Krzysztof Banas. * Correct messaging in C++ pragma checks in tools code for R CMD check, fixing PR#17566 thanks to Xavier Robin. * print()ing and auto-printing no longer differs for functions with a user defined print.function, thanks to Bill Dunlap's report. * On Windows, writeClipboard(.., format = <n>) now does correctly pass format to the underlying C code, thanks to a bug report (with patch) by Jenny Bryan. * as.data.frame() treats 1D arrays the same as vectors, PR#17570. * Improvements in smoothEnds(x, *) working with NAs (towards runmed() working in that case, in the next version of R). * vcov(glm(<quasi>), dispersion = *) works correctly again, fixing PR#17571 thanks to Pavel Krivitsky. * R CMD INSTALL of binary packages on Windows now works also with per-directory locking. * R CMD INSTALL and install.packages() on Windows are now more robust against a locked file in an earlier installation of the package to be installed. The default value of option install.lock on Windows has been changed to TRUE. * On Unix alikes (when readline is active), only expand tilde (~) file names starting with a tilde, instead of almost all tildes. * In R documentation (*.Rd) files, \item [..] is no longer treated specially when rendered in LaTeX and hence pdf, but rather shows the brackets in all cases. ------------------------------------------------------------------- Fri Apr 26 09:17:02 UTC 2019 - Detlef Steuer <detlef.steuer@gmx.de> - CHANGES IN R 3.6.0: SIGNIFICANT USER-VISIBLE CHANGES: * Serialization format version 3 becomes the default for serialization and saving of the workspace (save(), serialize(), saveRDS(), compiler::cmpfile()). Serialized data in format 3 cannot be read by versions of R prior to version 3.5.0. Serialization format version 2 is still supported and can be selected by version = 2 in the save/serialization functions. The default can be changed back for the whole R session by setting environment variables R_DEFAULT_SAVE_VERSION and R_DEFAULT_SERIALIZE_VERSION to 2. For maximal back-compatibility, files vignette.rds and partial.rdb generated by R CMD build are in serialization format version 2, and resave by default produces files in serialization format version 2 (unless the original is already in format version 3). * The default method for generating from a discrete uniform distribution (used in sample(), for instance) has been changed. This addresses the fact, pointed out by Ottoboni and Stark, that the previous method made sample() noticeably non-uniform on large populations. See PR#17494 for a discussion. The previous method can be requested using RNGkind() or RNGversion() if necessary for reproduction of old results. Thanks to Duncan Murdoch for contributing the patch and Gabe Becker for further assistance. The output of RNGkind() has been changed to also return the 'kind' used by sample(). NEW FEATURES: * Sys.setFileTime() has been vectorized so arguments path and time of length greater than one are now supported. * axis() gets new option gap.axis = NA for specifying a multiplication factor for the minimal "gap" (distance) between axis labels drawn. Its default is 1 for labels _parallel_ to the axis, and 0.25 for perpendicular ones. Perpendicular labels no longer overlap, fixing bug PR#17384. * The default method of plot() gains new arguments xgap.axis = NA and ygap.axis = NA to be passed to the x- and y- axis(.., gap.axis=*) calls. * removeSource() now works not only for functions but also for some language objects. * as.call(), rep.int(), rep_len() and nchar() dispatch internally. * is(object, class2) looks for class2 in the calling namespace after looking in the namespace of class(object). * extendrange(.., f) with a length-2 f now extends separately to the left and the right. * lengths() dispatches internally to S4 methods. * download.file() on Windows now uses URLdecode() to determine the file extension, and uses binary transfer (mode = "wb") also for file extension .rds. The help page for download.file() now contains the same information on all platforms. * Setting C locale for collation _via_ environment variables LC_ALL and LC_COLLATE and _via_ a call to Sys.setlocale() now takes precedence over environment variable R_ICU_LOCALE. * There is a new function, nullfile(), to give the file name of the null system device (e.g., /dev/null) on the current platform. * There are two new options, keep.parse.data and keep.parse.data.pkgs, which control whether parse data are included into sources when keep.source or keep.source.pkgs is TRUE. By default, keep.parse.data.pkgs is now FALSE, which changes previous behavior and significantly reduces space and time overhead when sources are kept when installing packages. * In rapply(x, ..), x can also be "list-like" and of length >= 2^{31}. * trimws() gets new optional whitespace argument, allowing more extensive definitions of "space", such as including Unicode spaces (as wished in PR#17431). * weighted.mean() no longer coerces the weights to a double/numeric vector, since sum() now handles integer overflow. This makes weighted.mean() more polymorphic and endomorphic, but be aware that the results are no longer guaranteed to be a vector of type double. * When loading namespaces, S3 method registrations which overwrite previous registrations are now noted by default (using packageStartupMessage()). * compiler::cmpfile() gains a version argument, for use when the output file should be saved in serialization format 2. * The axis labeling in the default method of pairs() may now be toggled by new options horOdd and verOdd. * (Not Windows nor macOS.) Package tcltk now supports an environment variable R_DONT_USE_TK which if set disables Tk initialization. This is intended for use to circumvent errors in loading the package, e.g. with recent Linux running under an address sanitizer. * The numeric method of all.equal() gets optional arguments countEQ and formatFUN. If countEQ is true, the mean error is more sensible when many entries are *eq*ual. * outer(x,y, FUN = "*") is more efficient using tcrossprod(u,v) instead of u %*% t(v). * vcov(<mlm>) is more efficient via new optional arguments in summary.mlm(). * The default method of summary() gets an option to choose the _kind_ of quantile()s to use; wish of PR#17438. * Fitting multiple linear models _via_ lm() does work with _matrix_ offsets, as suggested in PR#17407. * The new functions mem.maxVSize() and mem.maxMSize() allow the maximal size of the vector heap and the maximal number of nodes allowed in the current R process to be queried and set. * news() gains support for NEWS.md files. * An effort has been started to have our reference manuals, i.e., all help pages. show platform-independent information (rather than Windows or Unix-alike specifics visible only on that platform). Consequently, the Windows version of X11() / x11() got identical formal arguments to the Unix one. * sessionInfo()$running has been factored out in a new variable osVersion. * slice.index() now also works for multi-dimensional margins. * untar() used with an external tar command assumes this supports decompression including xz and automagically detecting the compression type. This has been true of all mainstream implementations since 2009 (for GNU tar, since version 1.22): older implementations are still supported _via_ the new argument support_old_tars whose default is controlled by environment variable R_SUPPORT_OLD_TARS. (It looks like NetBSD and OpenBSD have 'older' tar commands for this purpose.) * The new function asplit() allow splitting an array or matrix by its margins. * New functions errorCondition() and warningCondition() provide a convenient way to create structured error and warning objects. .Deprecated() now signals a warning of class "deprecatedWarning", and .Defunct() now signals an error of class "defunctError". * Many 'package not found' errors are now signaled as errors of class "packageNotFoundError". * As an experimental feature, when loadNamespace() fails because the requested package is not available the error is initially signaled with a retry_loadNamespace restart available. This allows a calling handler to try to install the package and continue. * S3method() directives in NAMESPACE can now also be used to perform _delayed_ S3 method registration. * Experimentally, setting environment variable _R_CHECK_LENGTH_1_LOGIC2_ will lead to warnings (or errors if the variable is set to a 'true' value) when && or || encounter and use arguments of length more than one. * Added "lines" and "chars" coordinate systems to grconvertX() and grconvertY(). * getOption() is more efficient notably for the rare case when called with two arguments, from several contributors in PR#17394. * In .col(dim) and .row(dim), dim now may also be an integer-valued "double". * sQuote() and dQuote() get an explicit q argument with obvious default instead of using getOption("fancyQuotes") implicitly and unconditionally. * unzip() can list archives with comments and with spaces in file names even using an external unzip command. * Command line completion has a new setting rc.settings(dots = FALSE) to remove ... from the list of possible function arguments. * library() no longer checks packages with compiled code match R.version$platform. loadNamespace() never has, and increasingly the 'canonical name' does not reflect the important characteristics of compiled code. * The primitive functions drop() and unclass() now avoid duplicating their data for atomic vectors that are large enough, by returning ALTREP wrapper objects with adjusted attributes. R-level assignments to change attributes will also use wrapper objects to avoid duplicating data for larger atomic vectors. R functions like structure() and unname() will therefore not duplicate data in these settings. Generic vectors as produced by list() are not yet covered by this optimization but may be in due course. * In formals(), envir becomes an optional argument instead of being hardwired. * Instead of signalling an error for an invalid S4 object x, str(x) now gives a warning and subsequently still shows most parts of x, e.g., when slots are missing. * gamma(x) and lgamma(x) no longer warn when correctly returning Inf or underflowing to zero. This helps maximum likelihood and similar computations. * convertColor() is now vectorized, so a lot faster for converting many colours at once. The new argument vectorized to colorConverter() ensures that non-vectorized colour converters still work. (Thanks to Brodie Gaslam.) * download.file() and url() get new argument headers for custom HTTP headers, e.g., allowing to perform basic http authentication, thanks to a patch contributed by G'abor Cs'ardi. * File-based connection functions file(), gzfile(), bzfile() and xzfile() now signal an error when used on a directory. * For approx(), splinefun() _etc_, a new setting ties = c("ordered", <fun>) allows skipping the sorting and still treat ties. * format(x) gives a more user friendly error message in the case where no method is defined. A minimal method is provided in format.default(x) when isS4(x) is true. * which(x) now also works when x is a long vector, thanks to Suharto Anggono's PR#17201. *NB*: this may return a double result, breaking the previous guarantee of an integer result. * seq.default() is more careful to return an integer (as opposed to double) result when its arguments are large and/or classed objects; see comment #9 of Suharto Anggono's PR#17497. * The plot() method for lm and glm fits, plot.lm(), gains a new option iter.smooth with a default of 0 for binomial fits, no longer down-weighting when smoothing the residuals. * zip() passes its list of files _via_ standard input to the external command when too long for the command line (on some platforms). * data() gains an overwrite argument. * t.test() now also returns the standard error (in list component stderr). * model.matrix(*, contrasts.arg = CC) now warns about invalid contrasts.args. * Performance of substr() and substring() has been improved. * stopifnot() has been simplified thanks to Suharto Anggono's proposals to become considerably faster for cheap expressions. * The default 'user agent' has been changed when accessing http:// and https:// sites using libcurl. (A site was found which caused libcurl to infinite-loop with the previous default.) * sessionInfo() now also contains RNGkind() and prints it when it differs from the default; based on a proposal and patch by Gabe Becker in PR#17535. Also, RNGversion(getRversion()) works directly. * library() and require() now allow more control over handling search path conflicts when packages are attached. The policy is controlled by the new conflicts.policy option. * barplot() gets a formula method, thanks to a patch proposal by Arni Magnusson in PR#17521. * pmax() and pmin(x) now also work for long vectors, thanks to Suharto Anggono's PR#17533. * bxp() now warns when omitting duplicated arguments. * New hcl.colors() function to provide wide range of HCL-based colour palettes with much better perceptual properties than the existing RGB/HSV-based palettes like rainbow(). Also a new hcl.pals() function to list available palette names for hcl.colors(). Contributed by Achim Zeileis. * The default colours for image() and filled.contour() are now based on hcl.colors(). * The palette-generating functions rainbow(), gray.colors(), etc. get a new rev argument to facilitate reversing the order of colors. * New str2lang() and str2expression() as streamlined versions of parse(text=., keep.source=FALSE) allow to abstract typical call constructions, e.g., in formula manipulations. (Somewhat experimental) * Add update_PACKAGES() for incrementally updating a package repository index, instead of rebuilding the index from scratch. Thanks to Gabe Becker in PR#17544 for the patch, based on part of his switchr package. INSTALLATION on a UNIX-ALIKE: * The options selected for the C++ compiler default to the C++11 standard if supported, otherwise to the C++98 standard. * Visibility macros such as C_VISIBILITY can now be user-set (including to empty), e.g. in config.site. * Macro FCLIBS, which has sometimes been needed on Solaris, has been renamed to FCLIBS_XTRA. * Macro F77 is always set to the value of FC, so the latter should be set to user-select the Fortran compiler for both fixed-form and free-form Fortran. In particular, gfortran is now the first choice for F77, not f95. Macros FFLAGS and FCFLAGS remain distinct to allow for a compiler which needs a flag to select free- or fixed-form Fortran (most use the source-file extension to choose: .f is fixed-form and .f90 and .f95 are free-form). If only one of them is set, its value is used for both. * The special-casing of CFLAGS, CXXFLAGS and FFLAGS for Intel compilers on Linux has been removed: we do not have recent experience but the generic defaults now chosen are the same as those previously special-cased for x86_64. If necessary, override the defaults on the configure command line or in file config.site. * Long-untested configure support for HP-UX and very old versions of Linux has been removed. * configure --with-blas (without specifying a value) includes OpenBLAS in its search (before ATLAS and a generic BLAS). This follows recent versions of the ax_blas autoconf macro. * The configure macro MAKEINFO has been updated to TEXI2ANY. * Support for make install-strip has been enhanced. PACKAGE INSTALLATION: * Source package installation is by default 'staged': the package is installed into a temporary location under the final library directory and moved into place once the installation is complete. The benefit is that partially-installed packages are hidden from other R sessions. The overall default is set by environment variable R_INSTALL_STAGED. R CMD INSTALL has new options --staged-install and --no-staged-install, and packages can use the StagedInstall field in their DESCRIPTION file to opt out. (That opt-out is a temporary measure which may be withdrawn in future.) Staged installation requires either --pkglock or --lock, one of which is used by default. * The interpretation of source code with extension .f is changing. Previously this denoted FORTRAN 77 code, but current compilers no longer have a FORTRAN 77 mode and interpret it as 'fixed-form' Fortran 90 (or later where supported) code. Extensions .f90 and .f95 continue to indicate 'free-form' Fortran code. Legal FORTRAN 77 code is also legal fixed-form Fortran 9x; however this change legitimizes the use of later features, in particular to replace features marked 'obsolescent' in Fortran 90 and 'deleted' in Fortran 2018 which gfortran 8.x and later warn about. * Packages containing files in the src directory with extensions .f90 or .f95 are now linked using the C or C++ compiler rather than the Fortran 9x compiler. This is consistent with fixed-form Fortran code and allows mixing of C++ and free-form Fortran on most platforms. Consequentially, a package which includes free-form Fortran 9x code which uses OpenMP should include SHLIB_OPENMP_CFLAGS (or the CXXFLAGS version if they also include C++ code) in PKG_LIBS rather than SHLIB_OPENMP_FCFLAGS - fortunately on almost all current platforms they are the same flag. * Macro PKG_FFLAGS will be used for the compilation of both fixed-form and free-form Fortran code unless PKG_FCFLAGS is also set (in src/Makevars or src/Makevars.win). * The make macro F_VISIBILITY is now preferred for both fixed-form and free-form Fortran, for use in src/Makevars and similar. * R CMD INSTALL gains a new option --strip which (where supported) strips installed shared object(s): this can also be achieved by setting the environment variable _R_SHLIB_STRIP_ to a true value. The new option --strip-lib attempts stripping of static and shared libraries installed under lib. These are most useful on platforms using GNU binutils (such as Linux) and compiling with -g flags. * There is more support for installing UTF-8-encoded packages in a strict Latin-1 locale (and probably for other Latin locales): non-ASCII comments in R code (and NAMESPACE files) are worked around better. UTILITIES: * R CMD check now optionally checks makefiles for correct and portable use of the SHLIB_OPENMP_*FLAGS macros. * R CMD check now evaluates \Sexpr{} expressions (including those in macros) before checking the contents of Rd files and so detects issues both in evaluating the expressions and in the expanded contents. * R CMD check now lists missing packages separated by commas and with regular quotes such as to be useful as argument in calling install.packages(c(..)); from a suggestion by Marcel Ramos. * tools::Rd2latex() now uses UTF-8 as its default output encoding. * R CMD check now checks line endings of files with extension .hpp and those under inst/include. The check now includes that a non-empty file is terminated with a newline. R CMD build will correct line endings in such files. * R CMD check now tries re-building all vignettes rather than stopping at the first error: whilst doing so it adds 'bookmarks' to the log. By default (see the 'R Internals' manual) it re-builds each vignette in a separate process. It now checks for duplicated vignette titles (also known as 'index entries'): they are used as hyperlinks on CRAN package pages and so do need to be unique. * R CMD check has more comprehensive checks on the data directory and the functioning of data() in a package. * R CMD check now checks autoconf-generated configure files have their corresponding source files, including optionally attempting to regenerate them on platforms with autoreconf. * R CMD build has a new option --compression to select the compression used for the tarball. * R CMD build now removes src/*.mod files on all platforms. C-LEVEL FACILITIES: * New pointer protection C functions R_PreserveInMSet and R_ReleaseFromMSet have been introduced to replace UNPROTECT_PTR, which is not safe to mix with UNPROTECT (and with PROTECT_WITH_INDEX). Intended for use in parsers only. * NAMEDMAX has been raised to 7 to allow further protection of intermediate results from (usually ill-advised) assignments in arguments to BUILTIN functions. Properly written package code should not be affected. * R_unif_index is now considered to be part of the C API. * R_GetCurrentEnv() allows C code to retrieve the current environment. DEPRECATED AND DEFUNCT: * Argument compressed of untar() is deprecated - it is only used for external tar commands which increasingly for extraction auto-detect compression and ignore their zjJ flags. * var(f) and hence sd(f) now give an error for factor arguments; they gave a deprecation warning since R 3.2.3, PR#16564. * Package tools' vignetteDepends() has been deprecated (it called a function deprecated since Feb 2016), being partly replaced by newly exported vignetteInfo(). * The f77_f2c script has been removed: it no longer sufficed to compile the .f files in R. * The deprecated legacy support of make macros such as CXX1X has been removed: use the CXX11 forms instead. * Make macro F77_VISIBILITY is deprecated in favour of F_VISIBILITY. * Make macros F77, FCPIFCPLAGS and SHLIB_OPENMP_FCFLAGS are deprecated in favour of FC, FPICFLAGS and SHLIB_OPENMP_FFLAGS respectively. * $.data.frame had become an expensive version of the default method, so has been removed. (Thanks to Radford Neal for picking this up and to Duncan Murdoch for providing a patch.) BUG FIXES: * replayPlot(r) now also works in the same R session when r has been "reproduced" from serialization, typically after saving to and reading from an RDS file. * substr() and substring() now signal an error when the input is invalid UTF-8. * file.copy() now works also when its argument to is of length greater than one. * mantelhaen.test() no longer suffers from integer overflow in largish cases, thanks to Ben Bolker's PR#17383. * Calling setGeneric("foo") in a package no longer fails when the enclosing environment of the implicit generic foo() is .GlobalEnv. * untar(file("<some>.tar.gz"), *) now gives a better error message, suggesting to use gzfile() instead. * Method dispatch uses more relevant environments when looking up class definitions. * The documentation for identify() incorrectly claimed that the indices of identified points were returned in the order that the points were selected. identify() now has a new argument order to allow the return value to include the order in which points were identified; the documentation has been updated. Reported by Richard Rowe and Samuel Granjeaud. * order(...., decreasing=c(TRUE, FALSE)) could fail in some cases. Reported from StackOverflow via Karl Nordstr"om. * User macros in Rd files now accept empty and multi-line arguments. * Changes in print.*(), thanks to Lionel Henry's patches in PR#17398: * Printing lists, pairlists or attributes containing calls with S3 class no longer evaluate those. * Printing S4 objects within lists and pairlists dispatches with show() rather than print(), as with auto-printing. * The indexing tags (names or [[<n>]]) of recursive data structures are now printed correctly in complex cases. * Arguments supplied to print() are now properly forwarded to methods when printing lists, pairlists or attributes containing S3 objects. * The print parameters are now preserved when printing S3 objects or deparsing symbols and calls. Previously, printing lists containing S3 objects or expressions would reset these parameters. * Printing lists, pairlists or attributes containing functions now uses srcref attributes if present. * Calling install.packages() with a length zero pkgs argument now is a no-op (PR#17422). * unlist(x) now returns a correct factor when x is a nested list with factor leaves, fixing PR#12572 and PR#17419. * The documentation help(family) gives more details about the aic component, thanks to Ben Bolker's prompting. * The documentation for attributes and `attributes<-` now gives x as name of the first and main argument which the implementation has been requiring, fixing PR#17434. For consistency, the first argument name is also changed from obj to x for `mostattributes<-`. * strwidth() now uses par("font") as default font face (PR#17352). * plot(<table>, log="x") no longer warns about log. * The print() method for "htest" objects now formats the test statistic and parameter directly and hence no longer rounds to units _before_ the decimal point. Consequently, printing of t.test() results with a small number of digits now shows non-large df's to the full precision (PR#17444). * kruskal.test() and fligner.test() no longer erroneously insist on numeric g group arguments (PR#16719). * Printing a news db via the browser now does a much better job (PR#17433). * print.aov() missed column names in the multivariate case due to misspelling (reported by Chris Andrews). * axis() now creates valid at locations also for small subnormal number ranges in log scale plots. * format.POSIXlt() now also recycles the zone and gmtoff list components to full length when needed, and its internal C code detects have_zone in more cases. In some cases, this changes its output to become compatible with format.POSIXct(). * On Windows, detectCores() in package parallel now detects processors in all processor groups, not just the group R is running in (impacts particularly systems with more than 64 logical processors). Reported by Arunkumar Srinivasan. * On Windows, socketSelect() would hang with more than 64 sockets, and hence parallel::clusterApplyLB() would hang with more than 64 workers. Reported by Arunkumar Srinivasan. * as(1L, "double") now does coerce (PR#17457). * lm.influence(), influence.measures(), rstudent() etc now work (more) correctly for multivariate models ("mlm"), thanks to (anonymous) stackoverflow remarks. * sample.int(2.9, *, replace=TRUE) again behaves as documented and as in R < 3.0.0, namely identically to sample.int(2, ..). * Fixes to convertColor() for chromatic adaptation; thanks to Brodie Gaslam PR#17473. * Using \Sexpr[stage=install]{..} to create an Rd section no longer gives a warning in R CMD check; problem originally posted by G'abor Cs'ardi, then reported as PR#17479 with a partial patch by Duncan Murdoch. * Parse data now include a special node for equal assignment. * split.default() no longer relies on [[<-(), so it behaves as expected when splitting an object by a factor with the empty string as one of its levels. Thanks to Brad Friedman for the report. * Line numbers in messages about .Rd files are now more reliable, thanks to a patch from Duncan Murdoch. * In the numeric method for all.equal(), a numeric scale argument is now checked to be positive and allowed to be of length > 1. (The latter worked originally and with a warning in recent years). * Deferred string conversions now record the OutDec option setting when not equal to the default. Reported by Michael Sannella. * When y is numeric and f a factor, plot(y ~ f) nicely uses "y" and "f" as y- and x-labels. The more direct boxplot(y ~ f) now does too. The new argument ann = FALSE may be used to suppress these. * Subassignment to no/empty rows of a data frame is more consistent and typically a no-op in all cases instead of sometimes an error; part of Emil Bode's PR#17483. * Calls like formatC(*, zero.print = "< 0.001") no longer give an error and are further improved via new optional argument replace.zero. Reported by David Hugh-Jones. * methods::formalArgs("<fn>") now finds the same function as formals("<fn>"), fixing Emil Bode's PR#17499. * The methods package better handles duplicated class names across packages. * The default method of seq() now avoids integer overflow, thanks to the report and "cumsum" patch of Suharto Anggono's PR#17497. * sub() no longer loses encodings for non-ASCII replacements (PR#17509). * Fix for rotated raster image on X11 device. (Partial fix for PR#17148; thanks to Mikko Korpela). * formula(model.frame(frml, ..)) now returns frml in all cases, thanks to Bill Dunlap. The previous behavior is available as DF2formula(<model.frame>). * ar.ols() also returns scalar var.pred in univariate case (PR#17517). * normalizePath() now treats NA path as non-existent and normalizes it to NA. file.access() treats NA file name as non-existent. file.edit() and connection functions such as file() now treat NA file names as errors. * The internal regularize.values() auxiliary of approx(), splinefun() etc now warns again when there are ties and the caller did not specify ties. Further, it no longer duplicates x and y unnecessarily when x is already sorted (PR#17515). * strtoi("", base) now gives NA on all platforms, following its documentation. Reported by Michael Chirico. * In the definition of an S4 class, prototype elements are checked against the slots of the class, with giving a prototype for an undefined slot now being an error. (Reported by Bill Dunlap.) * From setClassUnion(), if environment variable _R_METHODS_SHOW_CHECKSUBCLASSES is set to true, the internal .checkSubclasses() utility prints debugging info to see where it is used. * max.col(m) with an m of zero columns now returns integer NA (instead of 1). * axTicks() no longer returns small "almost zero" numbers (in exponential format) instead of zero, fixing Ilario Gelmetti's PR#17534. * isSymmetric(matrix(0, dimnames=list("A","b"))) is FALSE again, as always documented. * The cairo_pdf graphics device (and other Cairo-based devices) now clip correctly to the right and bottom border. There was an off-by-one-pixel bug, reported by Lee Kelvin. * as.roman(3) <= 2:4 and all other comparisons now work, as do group "Summary" function calls such as max(as.roman(sample(20))) and as.roman(NA). (Partly reported by Bill Dunlap in PR#17542.) * reformulate("x", response = "sin(y)") no longer produces extra back quotes, PR#17359, and gains new optional argument env. * When reading console input from stdin with re-encoding (R --encoding=enc < input) the code on a Unix-alike now ensures that each converted input line is terminated with a newline even if re-encoding fails. * as.matrix.data.frame() now produces better strings from logicals, thanks to PR#17548 from Gabe Becker. * The S4 generic signature of rowSums(), rowMeans(), colSums() and colMeans() is restricted to "x". * match(x, tab) now works for long _character_ vectors x, thanks to PR#17552 by Andreas Kersting. * Class unions are unloaded when their namespace is unloaded (PR#17531, adapted from a patch by Brodie Gaslam). * selectMethod() is robust to ANY-truncation of method signatures (thanks to Herve Pages for the report). ------------------------------------------------------------------- Mon Mar 11 09:00:15 UTC 2019 - Detlef Steuer <detlef.steuer@gmx.de> - CHANGES IN R 3.5.3: INSTALLATION on a UNIX-ALIKE: * Detection of flags for C++98/11/14/17 has been improved: in particular if CXX??STD is set, it is tried first with no additional flags. PACKAGE INSTALLATION: * New macro F_VISIBILITY as an alternative to F77_VISIBILITY. This will become the preferred form in R 3.6.0. BUG FIXES: * writeLines(readLines(fnam), fnam) now works as expected, thanks to Peter Meissner's PR#17528. * setClassUnion() no longer warns, but uses message() for now, when encountering "non local" subclasses of class members. * stopifnot(exprs = T) no longer fails. ------------------------------------------------------------------- Tue Jan 15 20:46:55 UTC 2019 - Todd R <toddrme2178@gmail.com> - Add architecture-independent package directory. Taken from the Fedora version of R. - Add RPM macros to ease installation of R packages. - Fix building on older versions of openSUSE. ------------------------------------------------------------------- Wed Dec 19 10:29:07 UTC 2018 - Detlef Steuer <detlef.steuer@gmx.de> - CHANGES IN R 3.5.2: PACKAGE INSTALLATION: * New macro CXX_VISIBILITY analogous to C_VISIBILITY (which several packages have been misusing for C++ code) for the default C++ compiler (but not necessarily one used for non-default C++ dialects like C++14). TESTING: * The random number generator tests in tests/p-r-random-tests.R no longer fail occasionally as they now randomly sample from "certified" random seeds. BUG FIXES: * The "glm" method of drop1() miscalculated the score test (test="Rao") when the model contained an offset. * Linear multiple empty models such as lm(y ~ 0) now have a correctly dimensioned empty coefficient matrix; reported by Brett Presnell. * vcov(<empty mlm>) and hence confint() now work (via a consistency change in summary.lm()). * confint(<multiple lm()>) now works correctly; reported on R-devel by Steven Pav. * quade.test() now also works correctly when its arguments are not yet sorted along groups, fixing PR#15842. * Installation on a Unix-alike tries harder to link to the pthread library where required (rather than relying on OpenMP to provide it: configuring with --disable-openmp was failing on some Linux systems). * The data.frame method for print(x) is fast now also for large data frames x and got an optional argument max, thanks to suggestions by Juan Telleria. * hist() no longer integer overflows in very rare cases, fixing PR#17450. * untar() ignored a character compressed argument: however many external tar programs ignore the flags which should have been set and automagically choose the compression type, and if appropriate gzip or bzip2 compression would have been chosen from the magic header of the tarball. * zapsmall(x) now works for more "number-like" objects. * The tools-internal function called from R CMD INSTALL now gets a warnOption = 1 argument and only sets options(warn = warnOption) when that increases the warning level (PR#17453). * Analogously, the tools-internal function called from R CMD check gets a warnOption = 1 argument and uses the larger of that and getOption("warn"), also allowing to be run with increased warning level. * Parse data now have deterministic parent nodes (PR#16041). * Calling match() with length one x and POSIXlt table gave a segfault (PR#17459). * Fork clusters could hang due to a race condition in cluster initialization (makeCluster()). * nextn(n) now also works for larger n and no longer loops infinitely for e.g, n <- 214e7. * cooks.distance() and rstandard() now work correctly for multiple linear models ("mlm"). * polym() and corresponding lm() prediction now also work for a boundary "vector" case fixing PR#17474, reported by Alexandre Courtiol. * With a very large number of variables terms() could segfault (PR#17480). * cut(rep(0, 7)) now works, thanks to Joey Reid and Benjamin Tyner (PR#16802). * download.file(*, method = "curl", cacheOK = FALSE) should work now on Windows, thanks to Kevin Ushey's patch in PR#17323. * duplicated(<dataframe with 'f'>) now works, too, thanks to Andreas Kersting's PR#17485; ditto for anyDuplicated(). * legend(*, cex = 1:2) now works less badly. * The print() method for POSIXct and POSIXlt now correctly obeys getOption("max.print"), fixing a long-standing typo, and it also gets a corresponding optional max argument. * Unserialization of raw vectors serialized in ASCII representation now works correctly. * <data frame>[TRUE, <new>] <- list(c1, c2) now works correctly, thanks to Suharto Anggono's PR#15362 and Emil Bode's patch in PR#17504. * seq.int(*, by=by, length=n) no longer wrongly "drops fractional parts" when by is integer, thanks to Suharto Anggono's report PR#17506. * Buffering is disabled for file() connections to non-regular files (like sockets), as well as fifo() and pipe() connections. Fixes PR#17470, reported by Chris Culnane. ------------------------------------------------------------------- Mon Jul 2 08:24:31 UTC 2018 - detlef.steuer@gmx.de - CHANGES IN R 3.5.1 : BUG FIXES: * file("stdin") is no longer considered seekable. * dput() and dump() are no longer truncating when options(deparse.max.lines = *) is set. * Calls with an S3 class are no longer evaluated when printed, fixing part of PR#17398, thanks to a patch from Lionel Henry. * Allow file argument of Rscript to include space even when it is first on the command line. * callNextMethod() uses the generic from the environment of the calling method. Reported by Herv'e Pag`es with well documented examples. * Compressed file connections are marked as blocking. * optim(*, lower = c(-Inf, -Inf)) no longer warns (and switches the method), thanks to a suggestion by John Nash. * predict(fm, newdata) is now correct also for models where the formula has terms such as splines::ns(..) or stats::poly(..), fixing PR#17414, based on a patch from Duncan Murdoch. * simulate.lm(glm(*, gaussian(link = <non-default>))) has been corrected, fixing PR#17415 thanks to Alex Courtiol. * unlist(x) no longer fails in some cases of nested empty lists. Reported by Steven Nydick. * qr.coef(qr(<all 0, w/ colnames>)) now works. Reported by Kun Ren. * The radix sort is robust to vectors with >1 billion elements (but long vectors are still unsupported). Thanks to Matt Dowle for the fix. * Terminal connections (e.g., stdin) are no longer buffered. Fixes PR#17432. * deparse(x), dput(x) and dump() now respect c()'s argument names recursive and use.names, e.g., for x <- setNames(0, "recursive"), thanks to Suharto Anggono's PR#17427. * Unbuffered connections now work with encoding conversion. Reported by Stephen Berman. * .Renviron on Windows with Rgui is again by default searched for in user documents directory when invoked _via_ the launcher icon. Reported by Jeroen Ooms. * printCoefmat() now also works with explicit right=TRUE. * print.noquote() now also works with explicit quote=FALSE. * The default method for pairs(.., horInd=*, verInd=*) now gets the correct order, thanks to reports by Chris Andrews and Gerrit Eichner. Additionally, when horInd or verInd contain only a subset of variables, all the axes are labeled correctly now. * agrep("..|..", .., fixed=FALSE) now matches when it should, thanks to a reminder by Andreas Kolter. * str(ch) now works for more invalid multibyte strings. ------------------------------------------------------------------- Mon Apr 23 08:32:02 UTC 2018 - detlef.steuer@gmx.de - CHANGES IN R 3.5.0: SIGNIFICANT USER-VISIBLE CHANGES: * All packages are by default byte-compiled on installation. This makes the installed packages larger (usually marginally so) and may affect the format of messages and tracebacks (which often exclude .Call and similar). NEW FEATURES: * factor() now uses order() to sort its levels, rather than sort.list(). This allows factor() to support custom vector-like objects if methods for the appropriate generics are defined. It 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. * diag() gets an optional names argument: this may require updates to packages defining S4 methods for it. * chooseCRANmirror() and chooseBioCmirror() no longer have a useHTTPS argument, not needed now all R builds support https:// downloads. * New summary() method for warnings() with a (somewhat experimental) print() method. * (methods package.) .self is now automatically registered as a global variable when registering a reference class method. * tempdir(check = TRUE) recreates the tempdir() directory if it is no longer valid (e.g. because some other process has cleaned up the /tmp directory). * New askYesNo() function and "askYesNo" option to ask the user binary response questions in a customizable but consistent way. (Suggestion of PR#17242.) * New low level utilities ...elt(n) and ...length() for working with ... parts inside a function. * isTRUE() is more tolerant and now true in x <- rlnorm(99) isTRUE(median(x) == quantile(x)["50%"]) New function isFALSE() defined analogously to isTRUE(). * The default symbol table size has been increased from 4119 to 49157; this may improve the performance of symbol resolution when many packages are loaded. (Suggested by Jim Hester.) * line() gets a new option iter = 1. * Reading from connections in text mode is buffered, significantly improving the performance of readLines(), as well as scan() and read.table(), at least when specifying colClasses. * order() is smarter about picking a default sort method when its arguments are objects. * available.packages() has two new arguments which control if the values from the per-session repository cache are used (default true, as before) and if so how old cached values can be to be used (default one hour). These arguments can be passed from install.packages(), update.packages() and functions calling that: to enable this available.packages(), packageStatus() and download.file() gain a ... argument. * packageStatus()'s upgrade() method no longer ignores its ... argument but passes it to install.packages(). * installed.packages() gains a ... argument to allow arguments (including noCache) to be passed from new.packages(), old.packages(), update.packages() and packageStatus(). * factor(x, levels, labels) now allows duplicated labels (not duplicated levels!). Hence you can map different values of x to the same level directly. * Attempting to use names<-() on an S4 derivative of a basic type no longer emits a warning. * The list method of within() gains an option keepAttrs = FALSE for some speed-up. * system() and system2() now allow the specification of a maximum elapsed time ('timeout'). * debug() supports debugging of methods on any object of S4 class "genericFunction", including group generics. * Attempting to increase the length of a variable containing NULL using length()<- still has no effect on the target variable, but now triggers a warning. * type.convert() becomes a generic function, with additional methods that operate recursively over list and data.frame objects. Courtesy of Arni Magnusson (PR#17269). * lower.tri(x) and upper.tri(x) only needing dim(x) now work via new functions .row() and .col(), so no longer call as.matrix() by default in order to work efficiently for all kind of matrix-like objects. * print() methods for "xgettext" and "xngettext" now use encodeString() which keeps, e.g. "\n", visible. (Wish of PR#17298.) * package.skeleton() gains an optional encoding argument. * approx(), spline(), splinefun() and approxfun() also work for long vectors. * deparse() and dump() are more useful for S4 objects, dput() now using the same internal C code instead of its previous imperfect workaround R code. S4 objects now typically deparse perfectly, i.e., can be recreated identically from deparsed code. dput(), deparse() and dump() now print the names() information only once, using the more readable (tag = value) syntax, notably for list()s, i.e., including data frames. These functions gain a new control option "niceNames" (see .deparseOpts()), which when set (as by default) also uses the (tag = value) syntax for atomic vectors. On the other hand, without deparse options "showAttributes" and "niceNames", names are no longer shown also for lists. as.character(list( c (one = 1))) now includes the name, as as.character(list(list(one = 1))) has always done. m:n now also deparses nicely when m > 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 = <your_own>), 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<N>) 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 <URL: https://svn.r-project.org/R/branches/ALTREP/ALTREP.html>. 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(<data.frame>) 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(<matrix>, 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 = <n>) 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 = "<n> 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 <pkg> 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(<data.frame>, drop=FALSE) no longer calls the function on <empty> 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(<name>, package="<pkg>") } 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.) ------------------------------------------------------------------- Wed Mar 28 16:13:57 UTC 2018 - darin@darins.net - added gcc-c++ build dependency ------------------------------------------------------------------- Tue Mar 20 16:21:31 UTC 2018 - detlef.steuer@gmx.de - Setting correctly R_UNZIPCMD Corrects this bug: http://bugzilla.suse.com/show_bug.cgi?id=1083075 ------------------------------------------------------------------- Thu Mar 15 09:21:05 UTC 2018 - detlef.steuer@gmx.de - 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(<large ints>, <stuff>) 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. ------------------------------------------------------------------- Mon Mar 12 20:29:28 UTC 2018 - crrodriguez@opensuse.org - Do not buildrequire xorg-x11-devel but individual x libs. ------------------------------------------------------------------- Thu Nov 30 10:17:27 UTC 2017 - detlef.steuer@gmx.de - 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. ------------------------------------------------------------------- Fri Sep 29 07:47:28 UTC 2017 - detlef.steuer@gmx.de - 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. (<URL: https://stat.ethz.ch/pipermail/r-devel/2017-July/074680.html>) * 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(<very large string>) 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. ------------------------------------------------------------------- Thu Jul 27 08:01:11 UTC 2017 - detlef.steuer@gmx.de - 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. ------------------------------------------------------------------- Fri Jun 30 10:40:03 UTC 2017 - detlef.steuer@gmx.de - 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(<data.frame>, 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) ------------------------------------------------------------------- Fri Apr 21 17:11:31 UTC 2017 - detlef.steuer@gmx.de - 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 <NA>, 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 = <factor> 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(<looooooooong_string>) 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(<formula>, *) 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(<lm>, 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(<citation>, 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 <URL: http://www.tcl.tk/man/> 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). ------------------------------------------------------------------- Tue Apr 18 08:27:14 UTC 2017 - detlef.steuer@gmx.de - And again that ldconfig call. Newline was obviously wrong. Hopefully correct now. ------------------------------------------------------------------- Tue Apr 4 09:12:24 UTC 2017 - detlef.steuer@gmx.de - Jan Engelhardt <jengelh@inai.de> asked for reverting the change to the ldconfig call. So be it. ------------------------------------------------------------------- Tue Mar 21 12:19:32 UTC 2017 - detlef.steuer@gmx.de - improvements for a) calling /sbin/ldconfig, which no longer gives a warning b) unregistering info-pages in %preun instead of %postun ------------------------------------------------------------------- Tue Mar 7 08:25:48 UTC 2017 - detlef.steuer@gmx.de - a change in OBS now requires a BuildRequire: shadow for some openSUSE releases. ------------------------------------------------------------------- Mon Mar 6 11:36:54 UTC 2017 - detlef.steuer@gmx.de - 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(<long>, <short>, 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). ------------------------------------------------------------------- Mon Oct 31 11:50:08 UTC 2016 - detlef.steuer@gmx.de - 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(<AsIs>) 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<dist>(), 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(<very_long>, *) 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(<lm>, 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.) ------------------------------------------------------------------- Fri Jul 1 16:17:11 UTC 2016 - toddrme2178@gmail.com - Fix typo in Group tag. ------------------------------------------------------------------- Tue Jun 21 09:26:17 UTC 2016 - detlef.steuer@gmx.de - 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(<difftime>) now keeps the "units" attribute, as subtraction already did, PR#16940. ------------------------------------------------------------------- Wed May 18 07:58:59 UTC 2016 - detlef.steuer@gmx.de - further cleanup of spec file. Removed unneeded explicit Requires for libcairo2/libfreetype6/liblzma5/libreadline6 Removed removal of backup file that was meanwhile removed upstream. ------------------------------------------------------------------- Wed May 11 14:36:53 UTC 2016 - detlef.steuer@gmx.de - clean up of spec file after comments from Jan Engelhardt in https://build.opensuse.org/request/show/393426 Some unneeded explicit BuildRequires removed. ------------------------------------------------------------------- Tue May 3 13:31:13 UTC 2016 - detlef.steuer@gmx.de - tre.patch was removed. ------------------------------------------------------------------- Tue May 3 11:30:09 UTC 2016 - detlef.steuer@gmx.de - and libbz2-devel needed, too. ------------------------------------------------------------------- Tue May 3 11:00:15 UTC 2016 - detlef.steuer@gmx.de - added BuildRequires: bzip2 for i586. ------------------------------------------------------------------- Tue May 3 10:24:09 UTC 2016 - detlef.steuer@gmx.de - 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 <URL: https://github.com/pmur002/R-display-list>. * 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 <Anonymous>. 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. ------------------------------------------------------------------- Fri Apr 15 08:40:10 UTC 2016 - detlef.steuer@gmx.de - CHANGES IN R 3.2.5: BUG FIXES: • format.POSIXlt() behaved incorrectly in R 3.2.4. E.g. the output of format(as.POSIXlt(paste0(1940:2000,"-01-01"), tz = "CET"), usetz = TRUE) ended in two "CEST" time formats. • A typo in the Makefile for src/extra/xz prevented builds of liblzma.a. (Notice that this will become unbundled in 3.3.0.) ------------------------------------------------------------------- Thu Mar 17 09:32:01 UTC 2016 - detlef.steuer@gmx.de - upstrem releases minorst bug fix release NEWS: The 3.2.4 release had two annoyances which we would rather not have in an "ultra-stable" release, designed to hang around for the duration of the 3.3 series. One was a relatively minor Makefile issue affecting system using R's bundled lzma library. The other, rather more serious, affected printing and formatting of POSIXlt objects, which would unpredictably get the Daylight Savings Time wrong. ------------------------------------------------------------------- Fri Mar 11 15:53:46 UTC 2016 - detlef.steuer@gmx.de - Some version numbers of recommended packages corrected ------------------------------------------------------------------- Fri Mar 11 15:38:35 UTC 2016 - detlef.steuer@gmx.de - Release numbers for sub-packages improved ------------------------------------------------------------------- Fri Mar 11 09:58:13 UTC 2016 - detlef.steuer@gmx.de - added MakefileTypo.patch to enable building for 12.2 was a one charcter show stopper ------------------------------------------------------------------- Thu Mar 10 12:52:04 UTC 2016 - detlef.steuer@gmx.de - upstream release 3.2.4, only minor improvements CHANGES IN R 3.2.4: NEW FEATURES: • install.packages() and related functions now give a more informative warning when an attempt is made to install a base package. • summary(x) now prints with less rounding when x contains infinite values. (Request of PR#16620.) • provideDimnames() gets an optional unique argument. • shQuote() gains type = "cmd2" for quoting in cmd.exe in Windows. (Response to PR#16636.) • The data.frame method of rbind() gains an optional argument stringsAsFactors (instead of only depending on getOption("stringsAsFactors")). • smooth(x, *) now also works for long vectors. • tools::texi2dvi() has a workaround for problems with the texi2dvi script supplied by texinfo 6.1. It extracts more error messages from the LaTeX logs when in emulation mode. UTILITIES: • R CMD check will leave a log file build_vignettes.log from the re-building of vignettes in the .Rcheck directory if there is a problem, and always if environment variable _R_CHECK_ALWAYS_LOG_VIGNETTE_OUTPUT_ is set to a true value. DEPRECATED AND DEFUNCT: • Use of SUPPORT_OPENMP from header Rconfig.h is deprecated in favour of the standard OpenMP define _OPENMP. (This has been the recommendation in the manual for a while now.) • The make macro AWK which is long unused by R itself but recorded in file etc/Makeconf is deprecated and will be removed in R 3.3.0. • The C header file S.h is no longer documented: its use should be replaced by R.h. ------------------------------------------------------------------- Mon Mar 7 12:54:57 UTC 2016 - detlef.steuer@gmx.de - The big split up. What was a monolithic R-base*rpm now is divided over 30 something packages, with the following layout. R-base-3.2.3: dummy packages, contains all of R Use R-base, if you don´t have a good understandig what it means to install only parts of it! R-base-devel-3.2.3: dummy, contains R-core-devel R-core-3.2.3: R core, no packages at all R-core-devel-3.2.3: devel files R-core-libs-3.2.3: contains Rlib R-core-doc-3.2.3: all the documentation of R-core R-core-packages-3.2.3: dummy package to load all core packages, that are R-compiler-3.2.3, R-datasets-3.2.3, R-grDevices-3.2.3, R-graphics-3.2.3, R-grid-3.2.3, R-methods-3.2.3, R-parallel-3.2.3, R-splines-3.2.3, R-stats-3.2.3, R-stats4-3.2.3, R-tcltk-3.2.3, R-tools-3.2.3, R-utils-3.2.3. Each of these packages may be installed alone. R-recommended-packages-3.2.3: dummy package to load all recommeded packages, that are R-boot-1.3.17, R-class-7.3.14, R-cluster-2.0.3, R-codetools-0.2.14, R-foreign-0.8.66, R-KernSmooth-2.23.15, R-lattice-0.20.33, R-MASS-7.3.45, R-Matrix-1.2.3, R-Matrix-devel-1.2.3, R-mgcv-1.8.9, R-nlme-3.1.122, R-nnet-7.3.11, R-rpart-4.1.10, R-spatial-7.3.11, R-survival-2.38.3. Each of these packages may be installed alone. ------------------------------------------------------------------- Fri Dec 11 08:46:52 UTC 2015 - detlef.steuer@gmx.de - Upstream release R-3.2.3 CHANGES IN R 3.2.3: NEW FEATURES: * Some recently-added Windows time zone names have been added to the conversion table used to convert these to Olson names. (Including those relating to changes for Russia in Oct 2014, as in PR#16503.) * (Windows) Compatibility information has been added to the manifests for Rgui.exe, Rterm.exe and Rscript.exe. This should allow win.version() and Sys.info() to report the actual Windows version up to Windows 10. * Windows "wininet" FTP first tries EPSV / PASV mode rather than only using active mode (reported by Dan Tenenbaum). * which.min(x) and which.max(x) may be much faster for logical and integer x and now also work for long vectors. * The 'emulation' part of tools::texi2dvi() has been somewhat enhanced, including supporting quiet = TRUE. It can be selected by texi2dvi = "emulation". (Windows) MiKTeX removed its texi2dvi.exe command in Sept 2015: tools::texi2dvi() tries texify.exe if it is not found. * (Windows only) Shortcuts for printing and saving have been added to menus in Rgui.exe. (Request of PR#16572.) * loess(..., iterTrace=TRUE) now provides diagnostics for robustness iterations, and the print() method for summary(<loess>) shows slightly more. * The included version of PCRE has been updated to 8.38, a bug-fix release. * View() now displays nested data frames in a more friendly way. (Request with patch in PR#15915.) INSTALLATION and INCLUDED SOFTWARE: * The included configuration code for libintl has been updated to that from gettext version 0.19.5.1 - this should only affect how an external library is detected (and the only known instance is under OpenBSD). (Wish of PR#16464.) * configure has a new argument --disable-java to disable the checks for Java. * The configure default for MAIN_LDFLAGS has been changed for the FreeBSD, NetBSD and Hurd OSes to one more likely to work with compilers other than gcc (FreeBSD 10 defaults to clang). * configure now supports the OpenMP flags -fopenmp=libomp (clang) and -qopenmp (Intel C). * Various macros can be set to override the default behaviour of configure when detecting OpenMP: see file config.site. * Source installation on Windows has been modified to allow for MiKTeX installations without texi2dvi.exe. See file MkRules.dist. BUG FIXES: * regexpr(pat, x, perl = TRUE) with Python-style named capture did not work correctly when x contained NA strings. (PR#16484) * The description of dataset ToothGrowth has been improved/corrected. (PR#15953) * model.tables(type = "means") and hence TukeyHSD() now support "aov" fits without an intercept term. (PR#16437) * close() now reports the status of a pipe() connection opened with an explicit open argument. (PR#16481) * Coercing a list without names to a data frame is faster if the elements are very long. (PR#16467) * (Unix-only) Under some rare circumstances piping the output from Rscript or R -f could result in attempting to close the input file twice, possibly crashing the process. (PR#16500) * (Windows) Sys.info() was out of step with win.version() and did not report Windows 8. * topenv(baseenv()) returns baseenv() again as in R 3.1.0 and earlier. This also fixes compilerJIT(3) when used in .Rprofile. * detach()ing the methods package keeps .isMethodsDispatchOn() true, as long as the methods namespace is not unloaded. * Removed some spurious warnings from configure about the preprocessor not finding header files. (PR#15989) * rchisq(*, df=0, ncp=0) now returns 0 instead of NaN, and dchisq(*, df=0, ncp=*) also no longer returns NaN in limit cases (where the limit is unique). (PR#16521) * pchisq(*, df=0, ncp > 0, log.p=TRUE) no longer underflows (for ncp > ~60). * nchar(x, "w") returned -1 for characters it did not know about (e.g. zero-width spaces): it now assumes 1. It now knows about most zero-width characters and a few more double-width characters. * Help for which.min() is now more precise about behavior with logical arguments. (PR#16532) * The print width of character strings marked as "latin1" or "bytes" was in some cases computed incorrectly. * abbreviate() did not give names to the return value if minlength was zero, unlike when it was positive. * (Windows only) dir.create() did not always warn when it failed to create a directory. (PR#16537) * When operating in a non-UTF-8 multibyte locale (e.g. an East Asian locale on Windows), grep() and related functions did not handle UTF-8 strings properly. (PR#16264) * read.dcf() sometimes misread lines longer than 8191 characters. (Reported by Herv'e Pag`es with a patch.) * within(df, ..) no longer drops columns whose name start with a ".". * The built-in HTTP server converted entire Content-Type to lowercase including parameters which can cause issues for multi-part form boundaries (PR#16541). * Modifying slots of S4 objects could fail when the methods package was not attached. (PR#16545) * splineDesign(*, outer.ok=TRUE) (splines) is better now (PR#16549), and interpSpline() now allows sparse=TRUE for speedup with non-small sizes. * If the expression in the traceback was too long, traceback() did not report the source line number. (Patch by Kirill M"uller.) * The browser did not truncate the display of the function when exiting with options("deparse.max.lines") set. (PR#16581) * When bs(*, Boundary.knots=) had boundary knots inside the data range, extrapolation was somewhat off. (Patch by Trevor Hastie.) * var() and hence sd() warn about factor arguments which are deprecated now. (PR#16564) * loess(*, weights = *) stored wrong weights and hence gave slightly wrong predictions for newdata. (PR#16587) * aperm(a, *) now preserves names(dim(a)). * poly(x, ..) now works when either raw=TRUE or coef is specified. (PR#16597) * data(package=*) is more careful in determining the path. * prettyNum(*, decimal.mark, big.mark): fixed bug introduced when fixing PR#16411. ------------------------------------------------------------------- Thu Dec 10 15:48:39 UTC 2015 - detlef.steuer@gmx.de - Reverse the whole split. Back to the big package. Had user reports of broken installations. R-base, R-base-devel and R-base-libs are provided for now. The big split will come for 3.3.0 ------------------------------------------------------------------- Wed Dec 9 10:11:26 UTC 2015 - detlef.steuer@gmx.de - R-base was changed from a giant monolith to thirty-some packages. There were requests to use the libs without the interpreter. Furthermore it is now possible to use a frugal installation of R. The following binaries are built now: R-base-3.2.2-5.1.x86_64.rpm : A Meta-package. Use this, and it looks just like it looked the last 10 years. Requires base and recommended packages. R-base-devel-3.2.2-5.1.x86_64.rpm: Just for backward compatibility. R-core-3.2.2-5.1.x86_64.rpm R-core-libs-3.2.2-5.1.x86_64.rpm R-core-devel-3.2.2-5.1.x86_64.rpm : The R-core packages install a bare-bones R. No packages inculded. R-grid-3.2.2-5.1.x86_64.rpm R-graphics-3.2.2-5.1.x86_64.rpm R-grDevices-3.2.2-5.1.x86_64.rpm R-datasets-3.2.2-5.1.x86_64.rpm R-stats4-3.2.2-5.1.x86_64.rpm R-methods-3.2.2-5.1.x86_64.rpm R-tcltk-3.2.2-5.1.x86_64.rpm R-compiler-3.2.2-5.1.x86_64.rpm R-parallel-3.2.2-5.1.x86_64.rpm R-splines-3.2.2-5.1.x86_64.rpm R-stats-3.2.2-5.1.x86_64.rpm R-utils-3.2.2-5.1.x86_64.rpm R-tools-3.2.2-5.1.x86_64.rpm : All the base packages. R-recommended-3.2.2-5.1.x86_64.rpm : A meta-package including all recommended packages. R-cluster-2.0.3-5.1.x86_64.rpm R-nlme-3.1.121-5.1.x86_64.rpm R-lattice-0.20.33-5.1.x86_64.rpm R-class-7.3.13-5.1.x86_64.rpm R-Matrix-devel-1.2.2-5.1.x86_64.rpm R-codetools-0.2.14-5.1.x86_64.rpm R-survival-2.38.3-5.1.x86_64.rpm R-rpart-4.1.10-5.1.x86_64.rpm R-MASS-7.3.43-5.1.x86_64.rpm R-mgcv-1.8.7-5.1.x86_64.rpm R-foreign-0.8.65-5.1.x86_64.rpm R-nnet-7.3.10-5.1.x86_64.rpm R-Matrix-1.2.2-5.1.x86_64.rpm R-boot-1.3.17-5.1.x86_64.rpm R-KernSmooth-2.23.15-5.1.x86_64.rpm R-spatial-7.3.10-5.1.x86_64.rpm : All recommended packaged. Note: They now have their own version numbers, so it should be much easier to use newer Versions of the recommended packages. And the source RPM for all the above. R-base-3.2.2-5.1.src.rpm ------------------------------------------------------------------- Wed Aug 19 08:47:27 UTC 2015 - badshah400@gmail.com - Disable building man files for openSUSE:42. ------------------------------------------------------------------- Mon Aug 17 14:41:24 UTC 2015 - detlef.steuer@gmx.de - Upstream release 3.2.2 - Most important CHANGES IN R 3.2.2: SIGNIFICANT USER-VISIBLE CHANGES: * It is now easier to use secure downloads from https:// URLs on builds which support them: no longer do non-default options need to be selected to do so. In particular, packages can be installed from repositories which offer https:// URLs, and those listed by setRepositories() now do so (for some of their mirrors). Support for https:// URLs is available on Windows, and on other platforms if support for libcurl was compiled in and if that supports the https protocol (system installations can be expected to do). So https:// support can be expected except on rather old OSes (an example being OS X 'Snow Leopard', where a non-system version of libcurl can be used). (Windows only) The default method for accessing URLs _via_ download.file() and url() has been changed to be "wininet" using Windows API calls. This changes the way proxies need to be set and security settings made: there have been some reports of sites being inaccessible under the new default method (but the previous methods remain available). NEW FEATURES: * cmdscale() gets new option list. for increased flexibility when a list should be returned. * configure now supports texinfo version 6.0, which (unlike the change from 4.x to 5.0) is a minor update. (Wish of PR#16456.) * (Non-Windows only) download.file() with default method = "auto" now chooses "libcurl" if that is available and a https:// or ftps:// URL is used. * (Windows only) setInternet2(TRUE) is now the default. The command-line option --internet2 and environment variable R_WIN_INTERNET2 are now ignored. Thus by default the "internal" method for download.file() and url() uses the "wininet" method: to revert to the previous default use setInternet2(FALSE). This means that https:// can be read by default by download.file() (they have been readable by file() and url() since R 3.2.0). There are implications for how proxies need to be set (see ?download.file): also, cacheOK = FALSE is not supported. * chooseCRANmirror() and chooseBioCmirror() now offer HTTPS mirrors in preference to HTTP mirrors. This changes the interpretation of their ind arguments: see their help pages. * capture.output() gets optional arguments type and split to pass to sink(), and hence can be used to capture messages. C-LEVEL FACILITIES: * Header Rconfig.h now defines HAVE_ALLOCA_H if the platform has the alloca.h header (it is needed to define alloca on Solaris and AIX, at least: see 'Writing R Extensions' for how to use it). INSTALLATION and INCLUDED SOFTWARE: * The libtool script generated by configure has been modified to support FreeBSD >= 10 (PR#16410). BUG FIXES: * The HTML help page links to demo code failed due to a change in R 3.2.0. (PR#16432) * If the na.action argument was used in model.frame(), the original data could be modified. (PR#16436) * getGraphicsEvent() could cause a crash if a graphics window was closed while it was in use. (PR#16438) * matrix(x, nr, nc, byrow = TRUE) failed if x was an object of type "expression". * strptime() could overflow the allocated storage on the C stack when the timezone had a non-standard format much longer than the standard formats. (Part of PR#16328.) * options(OutDec = s) now signals a warning (which will become an error in the future) when s is not a string with exactly one character, as that has been a documented requirement. * prettyNum() gains a new option input.d.mark which together with other changes, e.g., the default for decimal.mark, fixes some format()ting variants with non-default getOption("OutDec") such as in PR#16411. * download.packages() failed for type equal to either "both" or "binary". (Reported by Dan Tenenbaum.) * The dendrogram method of labels() is much more efficient for large dendrograms, now using rapply(). (Comment #15 of PR#15215) * The "port" algorithm of nls() could give spurious errors. (Reported by Radford Neal.) * Reference classes that inherited from reference classes in another package could invalidate methods of the inherited class. Fixing this requires adding the ability for methods to be "external", with the object supplied explicitly as the first argument, named .self. See "Inter-Package Superclasses" in the documentation. * readBin() could fail on the SPARC architecture due to alignment issues. (Reported by Radford Neal.) * qt(*, df=Inf, ncp=.) now uses the natural qnorm() limit instead of returning NaN. (PR#16475) * Auto-printing of S3 and S4 values now searches for print() in the base namespace and show() in the methods namespace instead of searching the global environment. * polym() gains a coefs = NULL argument and returns class "poly" just like poly() which gets a new simple=FALSE option. They now lead to correct predict()ions, e.g., on subsets of the original data. * rhyper(nn, <large>) now works correctly. (PR#16489) * ttkimage() did not (and could not) work so was removed. Ditto for tkimage.cget() and tkimage.configure(). Added two Ttk widgets and missing subcommands for Tk's image command: ttkscale(), ttkspinbox(), tkimage.delete(), tkimage.height(), tkimage.inuse(), tkimage.type(), tkimage.types(), tkimage.width(). (PR#15372, PR#16450) * getClass("foo") now also returns a class definition when it is found in the cache more than once. ------------------------------------------------------------------- Thu Jun 18 11:59:24 UTC 2015 - detlef.steuer@gmx.de - Upstream release 3.2.1 - Improvement of build: include libcurl and texlive-dvips/ texlive-hevetic - Most important CHANGES IN R 3.2.1: NEW FEATURES: * utf8ToInt() now checks that its input is valid UTF-8 and returns NA if it is not. * install.packages() now allows type = "both" with repos = NULL if it can infer the type of file. * nchar(x, *) and nzchar(x) gain a new argument keepNA which governs how the result for NAs in x is determined. For the R 3.2.x series, the default remains FALSE which is fully back compatible. From R 3.3.0, the default will change to keepNA = NA and you are advised to consider this for code portability. * news() more flexibly extracts dates from package NEWS.Rd files. * lengths(x) now also works (trivially) for atomic x and hence can be used more generally as an efficient replacement of sapply(x, length) and similar. * The included version of PCRE has been updated to 8.37, a bug-fix release. * diag() no longer duplicates a matrix when extracting its diagonal. * as.character.srcref() gains an argument to allow characters corresponding to a range of source references to be extracted. BUG FIXES: * acf() and ccf() now guarantee values strictly in [-1,1] (instead of sometimes very slightly outside). PR#15832. * as.integer("111111111111") now gives NA (with a warning) as it does for the corresponding numeric or negative number coercions. Further, as.integer(M + 0.1) now gives M (instead of NA) when M is the maximal representable integer. * On some platforms nchar(x, "c") and nchar(x, "w") would return values (possibly NA) for inputs which were declared to be UTF-8 but were not, or for invalid strings without a marked encoding in a multi-byte locale, rather than give an error. Additional checks have been added to mitigate this. * apply(a, M, function(u) c(X = ., Y = .)) again has dimnames containing "X" and "Y" (as in R < 3.2.0). * (Windows only) In some cases, the --clean option to R CMD INSTALL could fail. (PR#16178) * (Windows only) choose.files() would occasionally include characters from the result of an earlier call in the result of a later one. (PR#16270) * A change in RSiteSearch() in R 3.2.0 caused it to submit invalid URLs. (PR#16329) * Rscript and command line R silently ignored incomplete statements at the end of a script; now they are reported as parse errors. (PR#16350) * Parse data for very long strings was not stored. (PR#16354) * plotNode(), the workhorse of the plot method for "dendrogram"s is no longer recursive, thanks to Suharto Anggono, and hence also works for deeply nested dendrograms. (PR#15215) * The parser could overflow internally when given numbers in scientific format with extremely large exponents. (PR#16358) * If the CRAN mirror was not set, install.packages(type = "both") and related functions could repeatedly query the user for it. (Part of PR#16362) * The low-level functions .rowSums() etc. did not check the length of their argument, so could segfault. (PR#16367) * The quietly argument of library() is now correctly propagated from .getRequiredPackages2(). * Under some circumstances using the internal PCRE when building R fron source would cause external libs such as -llzma to be omitted from the main link. * The .Primitive default methods of the logic operators, i.e., !, & and |, now give correct error messages when appropriate, e.g., for `&`(TRUE) or `!`(). (PR#16385) * cummax(x) now correctly propagates NAs also when x is of type integer and begins with an NA. * summaryRprof() could fail when the profile contained only two records. (PR#16395) * HTML vignettes opened using vignette() did not support links into the rest of the HTML help system. (Links worked properly when the vignette was opened using browseVignettes() or from within the help system.) * arima(*, xreg = .) (for d >= 1) computes estimated variances based on a the number of effective observations as in R version 3.0.1 and earlier. (PR#16278) * slotNames(.) is now correct for "signature" objects (mostly used internally in methods). * On some systems, the first string comparison after a locale change would result in NA. ------------------------------------------------------------------- Thu Apr 16 14:52:43 UTC 2015 - detlef.steuer@gmx.de - Upstream release 3.2.0 - Most important CHANGES IN 3.2.0: NEW FEATURES: * anyNA() gains a recursive argument. * When x is missing and names is not false (including the default value), Sys.getenv(x, names) returns an object of class "Dlist" and hence prints tidily. * (Windows.) shell() no longer consults the environment variable SHELL: too many systems have been encountered where it was set incorrectly (usually to a path where software was compiled, not where it was installed). R_SHELL, the preferred way to select a non-default shell, can be used instead. * Some unusual arguments to embedFonts() can now be specified as character vectors, and the defaults have been changed accordingly. * Functions in the Summary group duplicate less. (PR#15798) * (Unix-alikes.) system(cmd, input = ) now uses 'shell-execution-environment' redirection, which will be more natural if cmd is not a single command (but requires a POSIX-compliant shell). (Wish of PR#15508) * read.fwf() and read.DIF() gain a fileEncoding argument, for convenience. * Graphics devices can add attributes to their description in .Device and .Devices. Several of those included with R use a "filepath" attribute. * pmatch() uses hashing in more cases and so is faster at the expense of using more memory. (PR#15697) * pairs() gains new arguments to select sets of variables to be plotted against each other. * file.info(, extra_cols = FALSE) allows a minimal set of columns to be computed on Unix-alikes: on some systems without properly-configured caching this can be significantly faster with large file lists. * New function dir.exists() in package base to test efficiently whether one or more paths exist and are directories. * dput() and friends gain new controls hexNumeric and digits17 which output double and complex quantities as, respectively, binary fractions (exactly, see sprintf("%a")) and as decimals with up to 17 significant digits. * save(), saveRDS() and serialize() now support ascii = NA which writes ASCII files using sprintf("%a") for double/complex quantities. This is read-compatible with ascii = TRUE but avoids binary->decimal->binary conversions with potential loss of precision. Unfortunately the Windows C runtime's lack of C99 compliance means that the format cannot be read correctly there in R before 3.1.2. * The default for formatC(decimal.mark =) has been changed to be getOption("OutDec"); this makes it more consistent with format() and suitable for use in print methods, e.g. those for classes "density", "ecdf", "stepfun" and "summary.lm". getOption("OutDec") is now consulted by the print method for class "kmeans", by cut(), dendrogram(), plot.ts() and quantile() when constructing labels and for the report from legend(trace = TRUE). (In part, wish of PR#15819.) * printNum() and hence format() and formatC() give a warning if big.mark and decimal.mark are set to the same value (period and comma are not uncommonly used for each, and this is a check that conventions have not got mixed). * merge() can create a result which uses long vectors on 64-bit platforms. * dget() gains a new argument keep.source which defaults to FALSE for speed (dput() and dget() are most often used for data objects where this can make dget() many times faster). * Packages may now use a file of common macro definitions in their help files, and may import definitions from other packages. * A number of macros have been added in the new share/Rd directory for use in package overview help pages, and promptPackage() now makes use of them. * tools::parse_Rd() gains a new permissive argument which converts unrecognized macros into text. This is used by utils:::format.bibentry to allow LaTeX markup to be ignored. * options(OutDec =) can now specify a multi-byte character, e.g., options(OutDec = "\u00b7") in a UTF-8 locale. * is.recursive(x) is no longer true when x is an external pointer, a weak reference or byte code; the first enables all.equal(x, x) when x <- getClass(.). * ls() (aka objects()) and as.list.environment() gain a new argument sorted. * The "source" attribute (which has not been added to functions by R since before R version 2.14.0) is no longer treated as special. * Function returnValue() has been added to give on.exit() code access to a function's return value for debugging purposes. * crossprod(x, y) allows more matrix coercions when x or y are vectors, now equalling t(x) %*% y in these cases (also reported by Radford Neal). Similarly, tcrossprod(x,y) and %*% work in more cases with vector arguments. * Utility function dynGet() useful for detecting cycles, aka infinite recursions. * The byte-code compiler and interpreter include new instructions that allow many scalar subsetting and assignment and scalar arithmetic operations to be handled more efficiently. This can result in significant performance improvements in scalar numerical code. * apply(m, 2, identity) is now the same as the matrix m when it has _named_ row names. * A new function debuggingState() has been added, allowing to temporarily turn off debugging. * example() gets a new optional argument run.donttest and tools::Rd2ex() a corresponding commentDonttest, with a default such that example(..) in help examples will run \donttest code only if used interactively (a change in behaviour). * rbind.data.frame() gains an optional argument make.row.names, for potential speedup. * New function extSoftVersion() to report on the versions of third-party software in use in this session. Currently reports versions of zlib, bzlib, the liblzma from xz, PCRE, ICU, TRE and the iconv implementation. A similar function grSoftVersion() in package grDevices reports on third-party graphics software. Function tcltk::tclVersion() reports the Tcl/Tk version. * Calling callGeneric() without arguments now works with primitive generics to some extent. * vapply(x, FUN, FUN.VALUE) is more efficient notably for large length(FUN.VALUE); as extension of PR#16061. * as.table() now allows tables with one or more dimensions of length 0 (such as as.table(integer())). * names(x) <- NULL now clears the names of call and ... objects. * library() will report a warning when an insufficient dependency version is masking a sufficient one later on the library search path. * A new plot() method for class "raster" has been added. * New check_packages_in_dir_changes() function in package tools for conveniently analyzing how changing sources impacts the check results of their reverse dependencies. * Speed-up from Peter Haverty for ls() and methods:::.requirePackage() speeding up package loading. (PR#16133) * New get0() function, combining exists() and get() in one call, for efficiency. * match.call() gains an envir argument for specifying the environment from which to retrieve the ... in the call, if any; this environment was wrong (or at least undesirable) when the definition argument was a function. * topenv() has been made .Internal() for speedup, based on Peter Haverty's proposal in PR#16140. * getOption() no longer calls options() in the main case. * Optional use of libcurl (version 7.28.0 from Oct 2012 or later) for Internet access: * capabilities("libcurl") reports if this is available. * libcurlVersion() reports the version in use, and other details of the "libcurl" build including which URL schemes it supports. * curlGetHeaders() retrieves the headers for http://, https://, ftp:// and ftps:// URLs: analysis of these headers can provide insights into the `existence' of a URL (it might for example be permanently redirected) and is so used in R CMD check --as-cran. * download.file() has a new optional method "libcurl" which will handle more URL schemes, follow redirections, and allows simultaneous downloads of multiple URLs. * url() has a new method "libcurl" which handles more URL schemes and follows redirections. The default method is controlled by a new option url.method, which applies also to the opening of URLs _via_ file() (which happens implicitly in functions such as read.table.) * When file() or url() is invoked with a https:// or ftps:// URL which the current method cannot handle, it switches to a suitable method if one is available. * (Windows.) The DLLs internet.dll and internet2.dll have been merged. In this version it is safe to switch (repeatedly) between the internal and Windows internet functions within an R session. The Windows internet functions are still selected by flag --internet2 or setInternet2(). This can be overridden for an url() connection _via_ its new method argument. download.file() has new method "wininet", selected as the default by --internet2 or setInternet2(). * parent.env<- can no longer modify the parent of a locked namespace or namespace imports environment. Contributed by Karl Millar. * New function isLoadedNamespace() for readability and speed. * names(env) now returns all the object names of an environment env, equivalently to ls(env, all.names = TRUE, sorted = FALSE) and also to the names of the corresponding list, names(as.list(env, all.names = TRUE)). Note that although names() returns a character vector, the names have no particular ordering. * The memory manager now grows the heap more aggressively. This reduces the number of garbage collections, in particular while data or code are loaded, at the expense of slightly increasing the memory footprint. * New function trimws() for removing leading/trailing whitespace. * cbind() and rbind() now consider S4 inheritance during S3 dispatch and also obey deparse.level. * cbind() and rbind() will delegate recursively to methods::cbind2 (methods::rbind2) when at least one argument is an S4 object and S3 dispatch fails (due to ambiguity). * (Windows.) download.file(quiet = FALSE) now uses text rather than Windows progress bars in non-interactive use. * New function hsearch_db() in package utils for building and retrieving the help search database used by help.search(), along with functions for inspecting the concepts and keywords in the help search database. * New function .getNamespaceInfo(), a no-check version of getNamespaceInfo() mostly for internal speedups. * The help search system now takes \keyword entries in Rd files which are not standard keywords (as given in KEYWORDS in the R documentation directory) as concepts. For standard keyword entries the corresponding descriptions are additionally taken as concepts. * New lengths() function for getting the lengths of all elements in a list. * New function toTitleCase() in package tools, tailored to package titles. * The matrix methods of cbind() and rbind() allow matrices as inputs which have 2^31 or more elements. (For cbind(), wish of PR#16198.) * The default method of image() has an explicit check for a numeric or logical matrix (which was always required). * URLencode() will not by default encode further URLs which appear to be already encoded. * BIC(mod) and BIC(mod, mod2) now give non-NA numbers for arima() fitted models, as nobs(mod) now gives the number of "used" observations for such models. This fixes PR#16198, quite differently than proposed there. * The print() methods for "htest", "pairwise.htest" and "power.htest" objects now have a digits argument defaulting to (a function of) getOption("digits"), and influencing all printed numbers coherently. Unavoidably, this changes the display of such test results in some cases. * Code completion for namespaces now recognizes all loaded namespaces, rather than only the ones that are also attached. * The code completion mechanism can now be replaced by a user-specified completer function, for (temporary) situations where the usual code completion is inappropriate. * unzip() will now warn if it is able to detect truncation when unpacking a file of 4GB or more (related to PR#16243). * methods() reports S4 in addition to S3 methods; output is simplified when the class argument is used. .S3methods() and methods::.S4methods() report S3 and S4 methods separately. * Higher order functions such as the apply functions and Reduce() now force arguments to the functions they apply in order to eliminate undesirable interactions between lazy evaluation and variable capture in closures. This resolves PR#16093. INSTALLATION and INCLUDED SOFTWARE: * The \donttest sections of R's help files can be tested by make check TEST_DONTTEST=TRUE . * It is possible to request the use of system valgrind headers _via_ configure option --with-system-valgrind-headers: note the possible future incompatibility of such headers discussed in the 'R Installation and Administration' manual. (Wish of PR#16068.) * The included version of liblzma has been updated to xz-utils 5.0.7 (minor bug fixes from 5.0.5). * configure options --with-system-zlib, --with-system-bzlib and --with-system-pcre are now the default. For the time being there is fallback to the versions included in the R sources if no system versions are found or (unlikely) if they are too old. Linux users should check that the -devel or -dev versions of packages zlib, bzip2/libbz2 and pcre as well as xz-devel/liblzma-dev (or similar names) are installed. * configure by default looks for the texi2any script from texinfo 5.1 or later, rather than the makeinfo program. (makeinfo is a link to the Perl script texi2any in texinfo 5.x.) * R CMD INSTALL gains an option --built-timestamp=STAMP allowing 100% reproducible package building, thanks to Dirk Eddelbuettel. UTILITIES: * There is support for testing the \dontrun and \donttest parts of examples in packages. tools::testInstalledPackage() accepts new arguments commentDontrun = FALSE and commentDonttest = FALSE. R CMD check gains options --run-dontrun and --run-donttest. * The HTML generated by tools::Rd2HTML() and tools::toHTML() methods is now 'XHTML 1.0 Strict'. * The compiler package's utility function setCompilerOptions() now returns the old values invisibly. The initial optimization level can also be set with the environment variable R_COMPILER_OPTIMIZE. * R CMD build adds a NeedsCompilation field if one is not already present in the DESCRIPTION file. * R CMD check gains option --test-dir to specify an alternative set of tests to run. * R CMD check will now by default continue with testing after many types of errors, and will output a summary count of errors at the end if any have occurred. * R CMD check now checks that the Title and Description fields are correctly terminated. * R CMD check --as-cran now: * checks a README.md file can be processed: this needs pandoc installed. * checks the existence and accessibility of URLs in the DESCRIPTION, CITATION, NEWS.Rd and README.md files and in the help files (provided the build has libcurl support). * reports non-ASCII characters in R source files when there is no package encoding declared in the DESCRIPTION file. * reports (apparent) S3 methods exported but not registered. * reports overwriting registered S3 methods from base/recommended packages. (Such methods are replaced in the affected package for the rest of the session, even if the replacing namespace is unloaded.) * reports if the Title field does not appear to be in title case (see 'Writing R Extensions': there may be false positives, but note that technical words should be single-quoted and will then be accepted). Most of these checks can also be selected by environment variables: see the 'R Internals' manual. C-LEVEL FACILITIES: * New C API utility logspace_sum(logx[], n). * Entry points rbinom_mu, rnbinom_mu and rmultinom are remapped (by default) to Rf_rbinom_mu etc. This requires packages using them to be re-installed. * .C(DUP = FALSE) and .Fortran(DUP = FALSE) are now ignored, so arguments are duplicated if DUP = TRUE would do so. As their help has long said, .Call() is much preferred. * New entry point R_allocLD, like R_alloc but guaranteed to have sufficient alignment for long double pointers. * isPairList() now returns TRUE for DOTSXP. WINDOWS BUILD CHANGES: A number of changes to the Windows build system are in development. The following are currently in place. * Installation using external binary distributions of zlib, bzip2, liblzma, pcre, libpng, jpeglib and libtiff is now required, and the build instructions have been revised. * A new make target rsync-extsoft has been added to obtain copies of the external libraries from CRAN. * Building the manuals now requires texi2any from texinfo 5.1 or later. CRAN binary builds include the manuals, but by default builds from source will not, and they will be accessed from CRAN. See the comments in src/gnuwin32/MkRules.dist for how to specify the location of texi2any. * (Windows) Changes have been made to support an experimental Windows toolchain based on GCC 4.9.2. The default toolchain continues to be based on GCC 4.6.3, as the new toolchain is not yet stable enough. A change to a new toolchain is expected during the R 3.2.x lifetime. PACKAGE INSTALLATION: * (Windows) The use of macro ZLIB_LIBS in file src/Makevars.win (which has not been documented for a long time) now requires an external libz.a to be available (it is part of the 'goodies' used to compile Windows binary packages). It would be simpler to use -lz instead. * The default for option pkgType on platforms using binary packages is now "both", so source packages will be tried if binary versions are not available or not up to date. There are options for what install.packages(type = "both") (possibly called _via_ update.packages()) will do if compilation of a source package is desirable: see ?options (under utils). If you intend not to accept updates as source packages, you should use update.packages(type = "binary"). DEPRECATED AND DEFUNCT: * download.file(method = "lynx") is defunct. * Building R using the included versions of zlib, bzip2, xz and PCRE is deprecated: these are frozen (bar essential bug-fixes) and will be removed for R 3.3.0. * The configure option --with-valgrind-instrumentation=3 has been withdrawn, as it did not work with recent valgrind headers: it is now treated as level 2. * The MethodsList class in package methods had been deprecated in R 2.11.0 and is defunct now. Functions using it are defunct if they had been deprecated in R 2.11.0, and are deprecated now, otherwise. BUG FIXES: * Fixed two obscure bugs in pairlist subassignment, reported by Radford Neal as part of pqR issue 16. * Fixes for bugs in handling empty arguments and argument matching by name in log(). * all.equal() gains methods for environments and refClasses. * [<- and [[<- gain S4 data.frame methods to avoid corruption of S4 class information by the S3 methods. * callNextMethod() should now work within a .local call when ... is absent from formals(.local). * dput(pairlist(x)) generates a call to the pairlist constructor instead of the list constructor. * Fix missing() when arguments are propagated through ... . (PR#15707) * eigen(m) now defaults to symmetric = TRUE even when the dimnames are asymmetric if the matrix is otherwise symmetric. (PR#16151) * Fix issues with forwarding ... through callGeneric() and callNextMethod(). (PR#16141) * callGeneric() now works after a callNextMethod(). * Subclass information is kept consistent when replacing an ordinary S4 class with an "old class" _via_ the S4Class argument to setOldClass(). Thus, for example, a data.frame is valid for a list argument in the signature, and a factor is valid for vector arguments. * In qbeta() the inversion of pbeta() is much more sophisticated. This works better in corner cases some of which failed completely previously (PR#15755), or were using too many iterations. * Auto-printing no longer duplicates objects when printing is dispatched to a method. * kmeans(x, k) would fail when nrow(x) >= 42949673. (Comment 6 of PR#15364) * 'Abbreviated' locale-specific day and month names could have been truncated in those rare locales where there are the same as the full names. * An irrelevant warning message from updating subclass information was silenced (the namespace would not be writable in this case). ------------------------------------------------------------------- Mon Mar 9 10:26:51 UTC 2015 - detlef.steuer@gmx.de - Upstream release 3.1.3 - Most important CHANGES IN R 3.1.3: NEW FEATURES: * The internal method of download.file() can now handle files larger than 2GB on 32-bit builds which support such files (tested on 32-bit R running on 64-bit Windows). * kruskal.test() warns on more types of suspicious input. * The as.dendrogram() method for "hclust" objects gains a check argument protecting against memory explosion for invalid inputs. * capabilities() has a new item long.double which indicates if the build uses a long double type which is longer than double. * nlm() no longer modifies the callback argument in place (a new vector is allocated for each invocation, which mimics the implicit duplication that occurred in R < 3.1.0); note that this is a change from the previously documented behavior. (PR#15958) * icuSetCollate() now accepts locale = "ASCII" which uses the basic C function strcmp and so collates strings byte-by-byte in numerical order. * sessionInfo() tries to report the OS version in use (not just that compiled under, and including details of Linux distributions). * model.frame() (used by lm() and many other modelling functions) now warns when it drops contrasts from factors. (Wish of PR#16119) * install.packages() and friends now accept the value type = "binary" as a synonym for the native binary type on the platform (if it has one). * Single source or binary files can be supplied for install.packages(type = "both") and the appropriate type and repos = NULL will be inferred. * New function pcre_config() to report on some of the configuration options of the version of PCRE in use. In particular, this reports if regular expressions using \p{xx} are supported. * (Windows.) download.file(cacheOK = FALSE) is now supported when internet2.dll is used. * browseURL() has been updated to work with Firefox 36.0 which has dropped support for the -remote interface. INSTALLATION and INCLUDED SOFTWARE: * The included version of PCRE has been updated to 8.36. * configure accepts MAKEINFO=texi2any as another way to ensure texinfo 5.x is used when both 5.x and 4.x are installed. UTILITIES: * R CMD check now checks the packages used in \donttest sections of the examples are specified in the DESCRIPTION file. (These are needed to run the examples interactively.) * R CMD check checks for the undeclared use of GNU extensions in Makefiles, and for Makefiles with a missing final linefeed. R CMD build will correct line endings in all Makefiles, not just those in the src directory. * R CMD check notes uses of library() and require() in package code: see the section 'Suggested packages' of 'Writing R Extensions' for good practice. DEPRECATED AND DEFUNCT: * The configure option --with-valgrind-instrumentation=3 is deprecated and will be removed in R 3.2.0. BUG FIXES: * (Windows.) Rscript.exe was missing a manifest specifying the modern style for common controls (e.g., the download progress bar). * If a package had extra documentation files but no vignette, the HTML help system produced an empty index page. * The parser now gives an error if a null character is included in a string using Unicode escapes. (PR#16046) * qr.Q() failed on complex arguments due to pre-3.0(!) typo. (PR#16054) * abs() failed with named arguments when the argument was complex. (PR#16047) * "noquote" objects may now be used as columns in dataframes. (PR#15997) * Some values with extremely long names were printed incorrectly. (PR#15999) * Extremely large exponents on zero expressed in scientific notation (e.g. 0.0e50000) could give NaN. (PR#15976) * download.file() reported downloaded sizes as 0KB if less than 1MB, only for R 3.1.2 and only on big-endian platforms. * prompt() did not escape percent signs in the automatically generated usage section of help files. * drop.terms() dropped some of the attributes of the object it was working with. (PR#16029) * (Windows.) The command completion in Rgui.exe messed up the console. (PR#15791) * (Windows.) The choose.files() command returned a blank string when the user asked for a single file but cancelled the request. (PR#16074) * Math2 S4 group generics failed to correctly dispatch "structure"- and "nonStructure"-derived classes. * loadNamespace() imposed undocumented restrictions on the versionCheck parameter. (Reported by Geoff Lee.) * Rare over-runs detected by AddressSanitizer in substr() and its replacement version have been avoided. _Inter alia_ that fix gives the documented behaviour for substr(x, 1, 2) <- "" (subsequently reported as PR#16214). * Loading packages incorrectly defining an S4 generic followed by a function of the same name caused an erroneous cyclic namespace dependency error. * Declared vignette encodings are now always passed to the vignette engine. * Port Tomas Kalibera's fix from R-devel that restores the loadMethod() fast path, effectively doubling the speed of S4 dispatch. * power.t.test() and power.prop.test() now make use of the extendInt option of uniroot() and hence work in more extreme cases. (PR#15792) * If a package was updated and attached when its namespace was already loaded, it could end up with parts from one version and parts from the other. (PR#16120) * tools:::.Rdconv() didn't accept --encoding= due to a typo. (PR#16121) * Unix-alike builds without a suitable makeinfo were documented to link the missing HTML manuals to CRAN, but did not. * save(*, ascii=TRUE) and load() now correctly deal with NaN's. (PR#16137) * split.Date() retains fractional representations while avoiding incomplete class propagation. * R_ext/Lapack.h had not been updated for changes made by LAPACK to the argument lists of its (largely internal) functions dlaed2 and dlaed3. (PR#16157) * RShowDoc("NEWS", "txt") had not been updated for the layout changes of R 3.1.0. * The xtfrm() method for class "Surv" has been corrected and its description expanded. * mode(x) <- y would incorrectly evaluate x before changing its mode. (PR#16215) * besselJ(1, 2^64) and besselY(..) now signal a warning, returning NaN instead of typically segfaulting. (Issue 3 of PR#15554) * HTML conversion of \href markup in .Rd files did not remove the backslash from \% and so gave an invalid URL. In a related change, the \ escape is now required in such URLs. ------------------------------------------------------------------- Fri Dec 12 13:16:25 UTC 2014 - sbahling@suse.com - Remove tex(inconsolata.sty) BuildRequires for SLE_12 builds (like older SLE releases). ------------------------------------------------------------------- Fri Oct 31 11:59:25 UTC 2014 - detlef.steuer@gmx.de - Upstream release 3.1.2 - Most important CHANGES IN R 3.1.2: NEW FEATURES: * embedFonts() now defaults to format = "ps2write" for .ps and .eps files. This is available in Ghostscript 9.x (since 2010) whereas the previous default, format = "pswrite", was removed in Ghostscript 9.10. * For consistency with [dpqr]norm(), [dp]lnorm(sdlog = 0) model a point mass at exp(mulog) rather than return NaN (for an error). * capabilities() now reports if ICU is compiled in for use for collation (it is only actually used if a suitable locale is set for collation, and never for a C locale). * (OS X only.) Package tcltk checks when loaded if it is linked against the CRAN X11-based Tcl/Tk and if so that the Tcl/Tk component and the X11 libraries are installed. This allows more informative error messages to be given advising the installation of the missing component or of XQuartz. The X11() device and X11-based versions of the data editor and viewer (invoked by edit() and View() for data frames and matrices from command-line R) check that the X11 libraries are installed and if not advises installing XQuartz. * icuSetCollate() allows locale = "default", and locale = "none" to use OS services rather than ICU for collation. Environment variable R_ICU_LOCALE can be used to set the default ICU locale, in case the one derived from the OS locale is inappropriate (this is currently necessary on Windows). * New function icuGetCollate() to report on the ICU collation locale in use (if any). * utils::URLencode() was updated to use unreserved and reserved characters from RFC 3986, <URL: http://tools.ietf.org/html/rfc3986>, instead of RFC 1738. * unique(warnings()) and c(warnings()) are now supported. * The Bioconductor 'version' used by setRepositories() now defaults to 3.0. (It can be set at runtime _via_ environment variable R_BIOC_VERSION.) INSTALLATION and INCLUDED SOFTWARE: * The configure script reports on the more important capabilities/options which will not be compiled in. More types of external BLAS are recognized by name in that report. * When building R as a shared library, the -L${R_HOME}/lib${R_ARCH} flag is placed earlier in the link commands used during installation and when packages are installed: this helps ensure that the current build has priority if an R shared library has already been installed by e.g. install-libR in a library mentioned in LDFLAGS (and not in 'your system's library directory' as documented). (Wish of PR#15790.) * LaTeX package upquote is no longer required for R's use of inconsolata. * (Windows only) If both 32 and 64 bit versions of R are installed, the bin/R.exe and bin/Rscript.exe executables now run 64 bit R. (To run 32 bit R, overwrite these files with copies of bin/i386/Rfe.exe.) UTILITIES: * Running R CMD check with _R_CHECK_DEPENDS_ONLY_ true now makes the VignetteBuilder packages available even if they are listed in Suggests, since they are needed to recognise and process non-Sweave vignettes. * R CMD check now reports empty importFrom declarations in a NAMESPACE file, as these are common errors (writing importFrom(Pkg) where import(Pkg) was intended). * R CMD check now by default checks code usage directly on the package namespace without loading and attaching the package and its suggests and enhances. For good practice with packages in the Suggests field, see SS1.1.3.1 of 'Writing R Extensions'. For use of lazy-data objects in the package's own code, see ?data. BUG FIXES: * dmultinom() did not handle non-finite probabilities correctly. * prettyNum(x, zero.print=*) now also works when x contains NAs. * A longstanding bug exhibited by nlminb() on Windows was traced to a compiler bug in gcc 4.6.3; a workaround has been put in place. (PR#15244 and PR#15914). * Rendering of \command in HTML versions of help pages has been improved: this is particularly evident on the help page for INSTALL. * as.hexmode(x) and as.octmode(x) now behave correctly for some numeric x, e.g., c(NA, 1) or c(1, pi). * drop1() failed if the scope argument had no variables to drop. (PR#15935) * edit() (and hence fix()) failed if an object had a non-character attribute named "source" (an attribute that had been used in R prior to version 2.14.0). * callGeneric() could fail if the generic had ... as a formal argument. (PR#15937). * Forking in package parallel called C entry point exit in the child. This was unsafe (_exit should have been called), and could flush stdin of the main R process (seen most often on Solaris). As good practice, stdout is now flushed before forking a child. * R objects such as list(`a\b` = 1) now print correctly. * getAnywhere("C_pbinom") now returns correctly a single object (rather than unlisting it). * The confint() method for nls() fits failed it these has specified parameter limits despite using an algorithm other than "port". (PR#15960) * Subclassing an S4 class failed if the class required arguments to the generator, through its initialize() method. * removeSource() did not properly handle expressions containing arguments that were supplied as missing, e.g. x[i,]. (PR#15957) * as.environment(list()) now works, and as.list() of such an environment is now the same as list(). * Several tcltk functions failed when run in unusual environments. (PR#15970) * options(list()) now works (trivially). (PR#15979) * merge(<dendrogram>, ..) now works correctly for two `independent' dendrograms (PR#15648), and still compatibly via adjust = "auto" e.g. for two branches of an existing dendrogram. * The plot method for "hclust" objects gets an optional argument check; When that is true (the default) it checks more carefully for valid input. * (Windows only) If a user chose to install 64 bit R but not 32 bit R, the bin/R and bin/Rscript executables failed to run. (PR#15981) * Various possible buffer overruns have been prevented, and missed memory protection added. (PR#15990) * Rscript no longer passes --args to R when there are no extra ("user") arguments. * objects like getClass("refClass")@prototype now print() and str() without error. * identical() now also looks at the S4 bit. * hist(x, breaks) is more robust in adding a small fuzz to few breaks when some are very large. (PR#15988) * sub() and gsub() did not handle regular expressions like "\s{2,}" properly if the text contained NA or non-ascii elements in a UTF-8 locale. Part of this was due to a bug in the TRE library. (PR#16009) * RShowDoc("NEWS") now displays the PDF version. * Matrices and arrays with last dimension zero did not print at all or incompletely. (PR#16012) * plot.histogram() and hence hist() now respect the xaxs, yaxs and lab graphics parameters. (PR#16021) * bw.SJ(x) and other bw.*() no longer segfault when x contains non-finite values. (PR#16024) * R CMD Rd2pdf unintentionally ignored its --os option. * The internal method of download.file() was not reporting file sizes and progress correctly on files larger than 2GB (inherited from libxml2). This is corrected for 64-bit builds (32-bit platforms may not support such files, but where possible will be supported in future versions of R). * Work around a bug in OS X Yosemite where key environment variables may be duplicated causing issues in subprocesses. The duplicates are now removed on R startup (via Rprofile). (PR#16042) * Adjust X11 auto-launch detection in DISPLAY on OS X to recognize latest XQuartz. ------------------------------------------------------------------- Thu Jul 10 12:35:42 UTC 2014 - detlef.steuer@gmx.de - Added Provides: R-parallel - Upstream release 3.1.1 - Most impotant CHANGES IN R 3.1.1: CHANGES IN R 3.1.1: NEW FEATURES: * When attach() reports conflicts, it does so compatibly with library() by using message(). * R CMD Sweave no longer cleans any files by default, compatibly with versions of R prior to 3.1.0. There are new options --clean, --clean=default and --clean=keepOuts. * tools::buildVignette() and tools::buildVignettes() with clean = FALSE no longer remove any created files. buildvignette() gains a keep argument for more cleaning customization. * The Bioconductor 'version' used by setRepositories() can now be set by environment variable R_BIOC_VERSION at runtime, not just when R is installed. (It has been stated that Bioconductor will switch from 'version' 2.14 to 'version' 3.0 during the lifetime of the R 3.1 series.) * Error messages from bugs in embedded Sexpr code in Sweave documents now report the source location. * type.convert(), read.table() and similar read.*() functions get a new numerals argument, specifying how numeric input is converted when its conversion to double precision loses accuracy. The default value, "allow.loss" allows accuracy loss, as in R versions before 3.1.0. * For some compilers, integer addition could overflow without a warning. R's internal code for both integer addition and subtraction is more robust now. (PR#15774) * The function determining the default number of knots for smooth.spline() is now exported, as .nknots.smspl(). * dbeta(, a,b), pbeta(), qbeta() and rbeta() are now defined also for a = 0, b = 0, or infinite a and b (where they typically returned NaN before). * Many package authors report that the RStudio graphics device does not work correctly with their package's use of dev.new(). The new option dev.new(noRStudioGD = TRUE) replaces the RStudio override by the default device as selected by R itself, still respecting environment variables R_INTERACTIVE_DEVICE and R_DEFAULT_DEVICE. * readRDS() now returns visibly. * Modifying internal logical scalar constants now results in an error instead of a warning. * install.packages(repos = NULL) now accepts http:// or ftp:// URLs of package archives as well as file paths, and will download as required. In most cases repos = NULL can be deduced from the extension of the URL. * The warning when using partial matching with the $ operator on data frames is now only given when options("warnPartialMatchDollar") is TRUE. * Package help requests like package?foo now try the package foo whether loaded or not. * General help requests now default to trying all loaded packages, not just those on the search path. * Added a new function promptImport(), to generate a help page for a function that was imported from another package (and presumably re-exported, or help would not be needed). INSTALLATION and INCLUDED SOFTWARE: * configure option --with-internal-tzcode can now be used with variable rsharedir. * The included version of PCRE has been updated to 8.35. * There is a new target make uninstall-libR to remove an installed shared/static libR. make install-libR now works if a sub-architecture is used, although the user will need to specify libdir differently for different sub-architectures. * There is more extensive advice on which LaTeX packages are required to install R or to make package manuals (as done by R CMD check) in the 'Writing R Extensions' manual. * Compilers/linkers were handling the visibility controls in src/extra/xz inconsistently (and apparently in some cases incorrectly), so it has been simplified. (PR#15327) * (Windows) There is updated support for the use of ICU for collation: see the 'R Installation and Administration Manual'. BUG FIXES: * dbinom(x, n), pbinom(), dpois(), etc, are slightly less restrictive in checking if n is integer-valued. (Wish of PR#15734.) * pchisq(x, df, ncp, log.p = TRUE) is more accurate and no longer underflows for small x and ncp < 80, e.g, for pchisq(1e-5, df = 100, ncp = 1, log = TRUE). (Based on PR#15635 and a suggestion by Roby Joehanes.) * The s ("step into") command in the debugger would cause R to step into expressions evaluated there, not just into functions being debugged. (PR#15770) * The C code used by strptime() rejected time-zone offsets of more than +1200 (+1245, +1300 and +1400 can occur). (PR#15768) * (Windows only.) png(type = "cairo", antialias = "gray") was not accepted. (PR#15760) * Use of save(..., envir=) with named objects could fail. (PR#15758) * Sweave() mis-parsed Sexpr expressions that contained backslashes. (PR#15779) * The return value from options(foo = NULL) was not the previous value of the option. (PR#15781) * enc2utf8() and enc2native() did not always mark the encoding of the return values when it was known. * dnbinom(x, size = <large>, mu, log = TRUE) no longer underflows to -Inf for large mu, thanks to a suggestion from Alessandro Mammana (MPI MolGen, Berlin). * pbeta(x, a, b, log = TRUE) no longer behaves discontinuously (in a small x-region) because of denormalized numbers. Also, pbeta(1-1e-12, 1e30, 1.001, log=TRUE) now terminates "in real time". * The "CRAN" filter (see available.packages()) no longer removes duplicates other than of packages on CRAN, and does not fail if there is no CRAN repository in getOption("repos"). * The device listing from dev2bitmap() and bitmap() was truncated to 1000 characters: modern versions of GhostScript on most platforms have many more devices. * (Windows.) Commands such as Sys.which() and pipe() which needed to find the full path to a command could segfault if the 'long' path name was much longer than the 'short' path name (which Sys.which() returns), as the behaviour of the Windows API call had changed. * R CMD build will fail with an error if one of the packages specified in the VignetteBuilder field is not installed. (Without loading those packages it cannot be ascertained which files are intended to be vignettes. This means that the VignetteBuilder packages have to be installed for package checking too.) (Wish of PR#15775.) * Misguided attempts to use chull() with non-finite points now give an error (related to PR#15777). * For a formula with exactly 32 variables the 32nd variable was aliased to the intercept in some C-level computations of terms, so that for example attempting to remove it would remove the intercept instead (and leave a corrupt internal structure). (PR#15735) * anyDuplicated() silently returned wrong values when the first duplicate was at an index which was too large to be stored in an integer vector (although a lot of RAM and patience would have been needed to encounter this). * tools::Rd2ex(commentDontrun = FALSE) failed if the block had only one line. * Hexadecimal constants such as 0x110p-5L which were incorrectly qualified by L were parsed incorrectly since R 3.0.0, with a slightly garbled warning. (PR#15753) * system() returned success on some platforms even if the system was unable to launch a process. (PR#15796) * (Windows Rgui console.) Unbuffered output was sometimes not output immediately if the prompt was not on the last line of the console. * The built-in help server did not declare the encoding for the DESCRIPTION or other text files to be the package encoding, so non-ASCII characters could be displayed incorrectly. * R is now trying harder to not cleanup child processes that were not spawned by mcparallel() on platforms that provide information about the source process of the SIGCHLD signal. This allows 3rd party libraries to manage the exit status of children that they spawn without R interfering. * mcmapply() was only parallelizing if the number of jobs was bigger than the number of cores. It now parallelizes if the number of jobs is more than one. * Auto-printing would re-evaluate its argument when trying to dispatch to a print method. This is now avoided when possible. * Unserializing (including load() and readRDS()) could silently return incorrect numeric values from ASCII saves if there was a read error. * getParseData() could return incorrect values for the parents of some elements. (Reported by Andrew Redd.) * Attempting to use data frames of 2^31 or more rows with merge() or to create a merged data frame of that size now gives a clearer error message. * parse() did not check its file argument was a connection if it was not a character string, so e.g. parse(FALSE) attempted to read from stdin. Nor did dump() and dput(). * The "help.try.all.packages" option was ignored when the shortcut syntax for help was used, e.g. ?foo. * A potential segfault in string allocation has been fixed. (Found by Radford Neal.) * Potential memory protection errors in sort() and D() have been fixed. (Found by Radford Neal.) * Fixed a lack of error checking in graphics event functions. (Found by Radford Neal; a different patch used here than the one in pqR.) * numericDeriv() sometimes miscalculated the gradient. (PR#15849, reported originally by Radford Neal) ------------------------------------------------------------------- Fri Jun 20 18:26:23 UTC 2014 - darin@darins.net - added parallel provides ------------------------------------------------------------------- Fri May 9 18:18:25 UTC 2014 - detlef.steuer@gmx.de - Removed / commented out symlink to %{_bindir}/r new package 'littler' should be used instead for packages that need /usr/bin/r ------------------------------------------------------------------- Thu May 1 15:29:30 UTC 2014 - darin@darins.net - Add make dependency for Rcmd ------------------------------------------------------------------- Tue Apr 29 15:31:15 UTC 2014 - darin@darins.net - Created symlink to %{_bindir}/r Many CRAN packages ship with scripts which call %{_bindir}/r, which creates a dependency on it, this fixes that. ------------------------------------------------------------------- Thu Apr 10 10:58:30 UTC 2014 - detlef.steuer@gmx.de - Upstream release 3.1.0 - Most impotant CHANGES IN R 3.1.0: NEW FEATURES: * type.convert() (and hence by default read.table()) returns a character vector or factor when representing a numeric input as a double would lose accuracy. Similarly for complex inputs. If a file contains numeric data with unrepresentable numbers of decimal places that are intended to be read as numeric, specify colClasses in read.table() to be "numeric". * tools::Rdiff(useDiff = FALSE) is closer to the POSIX definition of diff -b (as distinct from the description in the man pages of most systems). * New function anyNA(), a version of any(is.na(.)) which is fast for atomic vectors, based on a proposal by Tim Hesterberg. (Wish of PR#15239.) * arrayInd(*, useNames = TRUE) and, analogously, which(*, arr.ind = TRUE) now make use of names(.dimnames) when available. * is.unsorted() now also works for raw vectors. * The "table" method for as.data.frame() (also useful as as.data.frame.table()) now passes sep and base arguments to provideDimnames(). * uniroot() gets new optional arguments, notably extendInt, allowing to auto-extend the search interval when needed. The return value has an extra component, init.it. * switch(f, ...) now warns when f is a factor, as this typically happens accidentally where the useR meant to pass a character string, but f is treated as integer (as always documented). * The parser has been modified to use less memory. * The way the unary operators (+ - !) handle attributes is now more consistent. If there is no coercion, all attributes (including class) are copied from the input to the result: otherwise only names, dims and dimnames are. * colorRamp() and colorRampPalette() now allow non-opaque colours and a ramp in opacity via the new argument alpha = TRUE. (Suggested by Alberto Krone-Martins, but optionally as there are existing uses which expect only RGB values.) * grid.show.layout() and grid.show.viewport() get an optional vp.ex argument. * There is a new function find_gs_cmd() in the tools package to locate a GhostScript executable. (This is an enhanced version of a previously internal function there.) * object.size() gains a format() method. * There is a new family, "ArialMT", for the pdf() and postscript() devices. This will only be rendered correctly on viewers which have access to Monotype TrueType fonts (which are sometimes requested by journals). * The text and PDF news files, including NEWS and NEWS.2, have been moved to the doc directory. * combn(x, simplify = TRUE) now gives a factor result for factor input x (previously user error). (Related to PR#15442.) * Added utils::fileSnapshot() and utils::changedFiles() functions to allow snapshots and comparison of directories of files. * make.names(names, unique=TRUE) now tries to preserve existing names. (Suggestion of PR#15452.) * New functions cospi(x), sinpi(x), and tanpi(x), for more accurate computation of cos(pi*x), etc, both in R and the C API. Using these gains accuracy in some cases, e.g., inside lgamma() or besselI(). (Suggested by Morten Welinder in PR#15529.) * print.table(x, zero.print = ".") now also has an effect when x is not integer-valued. * There is more support to explore the system's idea of time-zone names. Sys.timezone() tries to give the current system setting by name (and succeeds at least on Linux, OS X, Solaris and Windows), and OlsonNames() lists the names in the system's Olson database. Sys.timezone(location = FALSE) gives the previous behaviour. * Platforms with a 64-bit time_t type are allowed to handle conversions between the "POSIXct" and "POSIXlt" classes for date-times outside the 32-bit range (before 1902 or after 2037): the existing workarounds are used on other platforms. (Note that time-zone information for post-2037 is speculative at best, and the OS services are tested for known errors and so not used on OS X.) Currently time_t is usually long and hence 64-bit on Unix-alike 64-bit platforms: however it several cases the time-zone database is 32-bit. On R for Windows it is 64-bit (for both architectures as from this version). * The "save.defaults" option can include a value for compression_level. (Wish of PR#15579.) * colSums() and friends now have support for arrays and data-frame columns with 2^31 or more elements. * as.factor() is faster when f is an unclassed integer vector (for example, when called from tapply()). * fft() now works with longer inputs, from the 12 million previously supported up to 2 billion. (PR#15593) * Complex svd() now uses LAPACK subroutine ZGESDD, the complex analogue of the routine used for the real case. * Sweave now outputs .tex files in UTF-8 if the input encoding is declared to be UTF-8, regardless of the local encoding. The UTF-8 encoding may now be declared using a LaTeX comment containing the string %\SweaveUTF8 on a line by itself. * file.copy() gains a copy.date argument. * Printing of date-times will make use of the time-zone abbreviation in use at the time, if known. For example, for Paris pre-1940 this could be LMT, PMT, WET or WEST. To enable this, the "POSIXlt" class has an optional component "zone" recording the abbreviation for each element. For platforms which support it, there is also a component "gmtoff" recording the offset from GMT where known. * (On Windows, by default on OS X and optionally elsewhere.) The system C function strftime has been replaced by a more comprehensive version with closer conformance to the POSIX 2008 standard. * dnorm(x, log = FALSE) is more accurate (but somewhat slower) for |x| > 5; as suggested in PR#15620. * Some versions of the tiff() device have further compression options. * read.table(), readLines() and scan() have a new argument to influence the treatment of embedded nuls. * Avoid duplicating the right hand side values in complex assignments when possible. This reduces copying of replacement values in expressions such as Z$a <- a0 and ans[[i]] <- tmp: some package code has relied on there being copies. Also, a number of other changes to reduce copying of objects; all contributed by or based on suggestions by Michael Lawrence. * The fast argument of KalmanLike(), KalmanRun() and KalmanForecast() has been replaced by update, which instead of updating mod in place, optionally returns the updated model in an attribute "mod" of the return value. * arima() and makeARIMA() get a new optional argument SSinit, allowing the choice of a different *s*tate *s*pace initialization which has been observed to be more reliable close to non-stationarity: see PR#14682. * warning() has a new argument noBreaks., to simplify post-processing of output with options(warn = 1). * pushBack() gains an argument encoding, to support reading of UTF-8 characters using scan(), read.table() and related functions in a non-UTF-8 locale. * all.equal.list() gets a new argument use.names which by default labels differing components by names (if they match) rather than by integer index. Saved R output in packages may need to be updated. * The methods for all.equal() and attr.all.equal() now have argument check.attributes after ... so it cannot be partially nor positionally matched (as it has been, unintentionally). A side effect is that some previously undetected errors of passing empty arguments (no object between commas) to all.equal() are detected and reported. There are explicit checks that check.attributes is logical, tolerance is numeric and scale is NULL or numeric. This catches some unintended positional matching. The message for all.equal.numeric() reports a "scaled difference" only for scale != 1. * all.equal() now has a "POSIXt" method replacing the "POSIXct" method. * The "Date" and "POSIXt" methods of seq() allows by = "quarter" for completeness (by = "3 months" always worked). * file.path() removes any trailing separator on Windows, where they are invalid (although sometimes accepted). This is intended to enhance the portability of code written by those using POSIX file systems (where a trailing / can be used to confine path matching to directories). * New function agrepl() which like grepl() returns a logical vector. * fifo() is now supported on Windows. (PR#15600) * sort.list(method = "radix") now allows negative integers (wish of PR#15644). * Some functionality of print.ts() is now available in .preformat.ts() for more modularity. * mcparallel() gains an option detach = TRUE which allows execution of code independently of the current session. It is based on a new estranged = TRUE argument to mcfork() which forks child processes such that they become independent of the parent process. * The pdf() device omits circles and text at extremely small sizes, since some viewers were failing on such files. * The rightmost break for the "months", "quarters" and "years" cases of hist.POSIXlt() has been increased by a day. (Inter alia, fixes PR#15717.) * The handling of DF[i,] <- a where i is of length 0 is improved. (Inter alia, fixes PR#15718.) * hclust() gains a new method "ward.D2" which implements Ward's method correctly. The previous "ward" method is "ward.D" now, with the old name still working. Thanks to research and proposals by Pierre Legendre. * The sunspot.month dataset has been amended and updated from the official source, whereas the sunspots and sunspot.year datasets will remain immutable. The documentation and source links have been updated correspondingly. * The summary() method for "lm" fits warns if the fit is essentially perfect, as most of the summary may be computed inaccurately (and with platform-dependent values). Programmers who use summary() in order to extract just a component which will be reliable (e.g. $cov.unscaled) should wrap their calls in suppressWarnings(). INSTALLATION and INCLUDED SOFTWARE: * The included version of LAPACK has been updated to 3.5.0. * There is some support for parallel testing of an installation, by setting TEST_MC_CORES to an integer greater than one to indicate the maximum number of cores to be used in parallel. (It is worth specifying at least 8 cores if available.) Most of these require a make program (such as GNU make and dmake) which supports the $MAKE -j nproc syntax. Except on Windows: the tests of standard package examples in make check are done in parallel. This also applies to running tools::testInstalledPackages(). The more time-consuming regression tests are done in parallel. The package checks in make check-devel and make check-recommended are done in parallel. * More of make check will work if recommended packages are not installed: but recommended packages remain needed for thorough checking of an R build. * The version of tzcode included in src/extra/tzone has been updated. (Formerly used only on Windows.) * The included (64-bit) time-zone conversion code and Olson time-zone database can be used instead of the system version: use configure option --with-internal-tzcode. This is the default on Windows and OS X. (Note that this does not currently work if a non-default rsharedir configure variable is used.) (It might be necessary to set environment variable TZ on OSes where this is not already set, although the system timezone is deduced correctly on at least Linux, OS X and Windows.) This option also switches to the version of strftime included in directory src/extra/tzone. * configure now tests for a C++11-compliant compiler by testing some basic features. This by default tries flags for the compiler specified by CXX, but an alternative compiler, options and standard can be specified by variables CXX1X, CXX1XFLAGS and CXX1XSTD (e.g. -std=gnu++11). * R can now optionally be compiled to use reference counting instead of the NAMED mechanism by defining SWITCH_TO_REFCNT in Rinternals.h. This may become the default in the future. * There is a new option --use-system-tre to use a suitable system tre library: at present this means a version from their git repository, after corrections. (Wish of PR#15660.) ------------------------------------------------------------------- Thu Mar 6 10:08:59 UTC 2014 - detlef.steuer@gmx.de - Upstream release 3.0.3 - Most important CHANGES IN R 3.0.3: NEW FEATURES: * On Windows there is support for making .texi manuals using texinfo 5.0 or later: the setting is in file src/gnuwin32/MkRules.dist. A packaging of the Perl script and modules for texinfo 5.2 has been made available at <URL: http://www.stats.ox.ac.uk/pub/Rtools/>. * write.table() now handles matrices of 2^31 or more elements, for those with large amounts of patience and disc space. * There is a new function, La_version(), to report the version of LAPACK in use. * The HTML version of 'An Introduction to R' now has links to PNG versions of the figures. * There is some support to produce manuals in ebook formats. (See doc/manual/Makefile. Suggested by Mauro Cavalcanti.) * On a Unix-alike Sys.timezone() returns NA if the environment variable TZ is unset, to distinguish it from an empty string which on some OSes means the UTC time zone. * The backtick may now be escaped in strings, to allow names containing them to be constructed, e.g. `\``. (PR#15621) * read.table(), readLines() and scan() now warn when an embedded nul is found in the input. (Related to PR#15625 which was puzzled by the behaviour in this unsupported case.) * (Windows only.) file.symlink() works around the undocumented restriction of the Windows system call to backslashes. (Wish of PR#15631.) * KalmanForecast(fast = FALSE) is now the default, and the help contains an example of how fast = TRUE can be used in this version. (The usage will change in 3.1.0.) * strptime() now checks the locale only when locale-specific formats are used and caches the locale in use: this can halve the time taken on OSes with slow system functions (e.g. OS X). * strptime() and the format() methods for classes "POSIXct", "POSIXlt" and "Date" recognize strings with marked encodings: this allows, for example, UTF-8 French month names to be read on (French) Windows. * iconv(to = "utf8") is now accepted on all platforms (some implementations did already, but GNU libiconv did not: however converted strings were not marked as being in UTF-8). The official name, "UTF-8" is still preferred. * available.packages() is better protected against corrupt metadata files. (A recurring problem with Debian package shogun-r: PR#14713.) * Finalizers are marked to be run at garbage collection, but run only at a somewhat safer later time (when interrupts are checked). This circumvents some problems with finalizers running arbitrary code during garbage collection (the known instances being running options() and (C-level) path.expand() re-entrantly). ------------------------------------------------------------------- Fri Sep 27 13:20:39 UTC 2013 - detlef.steuer@gmx.de - Removed outdated source file ------------------------------------------------------------------- Wed Sep 25 14:01:26 UTC 2013 - detlef.steuer@gmx.de - Upstream release 3.0.2 - Most important CHANGES IN R 3.0.2: NEW FEATURES: * The NEWS files have been re-organized. This file contains news for R >= 3.0.0: news for the 0.x.y, 1.x.y and 2.x.y releases is in files NEWS.0, NEWS.1 and NEWS.2. The latter files are now installed when R is installed. An HTML version of news from 2.10.0 to 2.15.3 is available as doc/html/NEWS.2.html. * sum() for integer arguments now uses an integer accumulator of at least 64 bits and so will be more accurate in the very rare case that a cumulative sum exceeds 2^53 (necessarily summing more than 4 million elements). * The example() and tools::Rd2ex() functions now have parameters to allow them to ignore \dontrun markup in examples. (Suggested by Peter Solymos.) * str(x) is considerably faster for very large lists, or factors with 100,000 levels, the latter as in PR#15337. * col2rgb() now converts factors to character strings not integer codes (suggested by Bryan Hanson). * tail(warnings()) now works, via the new `[` method. * There is now support for the LaTeX style file zi4.sty which has in some distributions replaced inconsolata.sty. * unlist(x) now typically returns all non-list xs unchanged, not just the "vector" ones. Consequently, format(lst) now also works when the list lst has non-vector elements. * The tools::getVignetteInfo() function has been added to give information about installed vignettes. * New assertCondition(), etc. utilities in tools, useful for testing. * Profiling now records non-inlined calls from byte-compiled code to BUILTIN functions. * Various functions in stats and elsewhere that use non-standard evaluation are now more careful to follow the namespace scoping rules. E.g. stats::lm() can now find stats::model.frame() even if stats is not on the search path or if some package defines a function of that name. * If an invalid/corrupt .Random.seed object is encountered in the workspace it is ignored with a warning rather than giving an error. (This allows R itself to rely on a working RNG, e.g. to choose a random port.) * seq() and seq.int() give more explicit error messages if called with invalid (e.g. NaN) inputs. * When parse() finds a syntax error, it now makes partial parse information available up to the location of the error. (Request of Reijo Sund.) * Methods invoked by NextMethod() had a different dynamic parent to the generic. This was causing trouble where S3 methods invoked via lazy evaluation could lose track of their generic. (PR#15267) * Code for the negative binomial distribution now treats the case size == 0 as a one-point distribution at zero. * abbreviate() handles without warning non-ASCII input strings which require no abbreviation. * read.dcf() no longer has a limit of 8191 bytes per line. (Wish of PR#15250.) * formatC(x) no longer copies the class of x to the result, to avoid misuse creating invalid objects as in PR#15303. A warning is given if a class is discarded. * Dataset npk has been copied from MASS to allow more tests to be run without recommended packages being installed. * The initialization of the regression coefficients for non-degenerate differenced models in arima() has been changed and in some examples avoids a local maximum. (PR#15396) * termplot() now has an argument transform.x to control the display of individual terms in the plot. (PR#15329) * format() now supports digits = 0, to display nsmall decimal places. * There is a new read-only par() parameter called "page", which returns a logical value indicating whether the next plot.new() call will start a new page. * Processing Sweave and Rd documents to PDF now renders backticks and single quotes better in several instances, including in \code and \samp expressions. * utils::modifyList() gets a new argument keep.null allowing NULL components in the replacement to be retained, instead of causing corresponding components to be deleted. * tools::pkgVignettes() gains argument check; if set to TRUE, it will warn when it appears a vignette requests a non-existent vignette engine. ------------------------------------------------------------------- Mon Aug 26 14:19:31 UTC 2013 - schwab@suse.de - tre.patch: Fix tre library for aarch64 where wchar_t is unsigned int ------------------------------------------------------------------- Thu May 16 13:17:09 UTC 2013 - detlef.steuer@gmx.de - Improved spec file: R-base-devel requires R-base ------------------------------------------------------------------- Thu May 16 11:21:09 UTC 2013 - detlef.steuer@gmx.de - Upstream release 3.0.1 - Most important CHANGES IN R 3.0.1: NEW FEATURES: o chooseCRANmirror() and chooseBioCmirror() gain an ind argument (like setRepositories()). o mcparallel has a new argument mc.interactive which can modify the interactive flag in the child process. The new default is FALSE which makes child processes non-interactive by default (this prevents lock-ups due to children waiting for interactive input). o scan() now warns when end-of-file occurs within a quoted string. o count.fields() is now consistent with scan() in its handling of newlines in quoted strings. Instead of triggering an error, this results in the current line receiving NA as the field count, with the next line getting the total count of the two lines. o The default method of image() will plot axes of the class of xlim and ylim (and hence of x and y if there is a suitable range() method). Based on a suggestion of Michael Sumner. o load() now has a verbose argument for debugging support, to print the names of objects just before loading them. o When loading a serialized object encounters a reference to a namespace which cannot be loaded, this is replaced by a reference to the global environment, with a warning. o pairs() gains a line.main option for title placement. o The remaining instances in which serialization to a raw vector was limited to 2GB have been unlimited on a 64-bit platform, and in most cases serialization to a vector of more than 1GB will be substantially faster. - Improved spec file. Lots of commented out lines finally removed ------------------------------------------------------------------- Wed Apr 10 07:26:36 UTC 2013 - detlef.steuer@gmx.de - R-base.spec improved: now uses R-%{version}.tar.bz2 explicitly. Mistake when version bumping to 3.0.0 corrected ------------------------------------------------------------------- Wed Apr 3 18:39:35 UTC 2013 - detlef.steuer@gmx.de - Upstream release 3.0.0 - News for package: some new translation files - News upstream: /usr/lib/R/doc/NEWS.html - Most important CHANGES IN R 3.0.0: SIGNIFICANT USER-VISIBLE CHANGES: o Packages need to be (re-)installed under this version (3.0.0) of R. o There is a subtle change in behaviour for numeric index values 2^31 and larger. These never used to be legitimate and so were treated as NA, sometimes with a warning. They are now legal for long vectors so there is no longer a warning, and x[2^31] <- y will now extend the vector on a 64-bit platform and give an error on a 32-bit one. o It is now possible for 64-bit builds to allocate amounts of memory limited only by the OS. It may be wise to use OS facilities (e.g. ulimit in a bash shell, limit in csh), to set limits on overall memory consumption of an R process, particularly in a multi-user environment. A number of packages need a limit of at least 4GB of virtual memory to load. 64-bit Windows builds of R are by default limited in memory usage to the amount of RAM installed: this limit can be changed by command-line option --max-mem-size or setting environment variable R_MAX_MEM_SIZE. o Negative numbers for colours are consistently an error: previously they were sometimes taken as transparent, sometimes mapped into the current palette and sometimes an error. ------------------------------------------------------------------- Mon Mar 18 14:38:57 UTC 2013 - schwab@suse.de - Override LIBnn from %{_lib} ------------------------------------------------------------------- Fri Mar 1 12:15:30 UTC 2013 - detlef.steuer@gmx.de - There were a few new files in foreign and rpart. Fixed now. Builds fine. ------------------------------------------------------------------- Fri Mar 1 10:25:32 UTC 2013 - detlef.steuer@gmx.de - Upstream release 2.15.3 - see, as usual, /usr/lib/R/doc/NEWS.html - This is mostly a bugfix release and the final release for the R-2.x.y series. - Most important additions: NEW FEATURES: o lgamma(x) for very small x (in the denormalized range) is no longer Inf with a warning. o image() now sorts an unsorted breaks vector, with a warning. o The internal methods for tar() and untar() do a slightly more general job for 'ustar'-style handling of paths of more than 100 bytes. o Packages compiler and parallel have been added to the reference index (refman.pdf). o untar(tar = "internal") has some support for pax headers as produced by e.g. gnutar --posix (which seems prevalent on OpenSUSE 12.2) or bsdtar --format pax, including long path and link names. o sQuote() and dQuote() now handle 0-length inputs. (Suggestion of Ben Bolker.) o summaryRprof() returns zero-row data frames rather than throw an error if no events are recorded, for consistency. o The included version of PCRE has been updated to 8.32. o The tcltk namespace can now be re-loaded after unloading. The Tcl/Tk event loop is inhibited in a forked child from package parallel (as in e.g. mclapply()). o parallel::makeCluster() recognizes the value random for the environment variable R_PARALLEL_PORT: this chooses a random value for the port and reduces the chance of conflicts when multiple users start a cluster at the same time. ------------------------------------------------------------------- Fri Oct 26 12:35:44 UTC 2012 - detlef.steuer@gmx.de - Upstream release 2.15.2 - see, as usual, /usr/lib/R/doc/NEWS.html - most relevant change for rpm are some added translation files ------------------------------------------------------------------- Tue Jul 10 08:37:58 UTC 2012 - werner@suse.de - Make it build with latest TeXLive 2012 with new package layout ------------------------------------------------------------------- Fri Jun 22 14:22:25 UTC 2012 - detlef.steuer@gmx.de - Fixed: R-base-2.15.1-48.1.x86_64.rpm: directories not owned by a package: - /usr/lib64/R/share/locale/pl - /usr/lib64/R/share/locale/pl/LC_MESSAGES ------------------------------------------------------------------- Fri Jun 22 13:43:05 UTC 2012 - detlef.steuer@gmx.de - one more forgotten file in polish translation ... ------------------------------------------------------------------- Fri Jun 22 12:38:18 UTC 2012 - detlef.steuer@gmx.de - spec file update to incorporate new polish translation ------------------------------------------------------------------- Fri Jun 22 11:53:39 UTC 2012 - detlef.steuer@gmx.de - Upstream bugfix only release 2.15.1 - see, as usual, /usr/lib/R/doc/NEWS.html ------------------------------------------------------------------- Tue Apr 10 21:51:18 UTC 2012 - gregkh@opensuse.org - make R-base-devel require R-base as some packages think this dependancy is already there (i.e. some KDE packages). ------------------------------------------------------------------- Fri Mar 30 09:26:11 UTC 2012 - detlef.steuer@gmx.de - Upstream updated to 2.15.0 - see, as usual, /usr/lib/R/doc/NEWS.html ------------------------------------------------------------------- Wed Feb 29 18:00:59 UTC 2012 - detlef.steuer@gmx.de - upstream minor version increase to 2.14.2 - see, as usual, /usr/lib/R/doc/NEWS.html for details. ------------------------------------------------------------------- Fri Feb 17 20:53:49 UTC 2012 - detlef.steuer@gmx.de - Minor cleanup for easier automativ building of R-patched.spec ------------------------------------------------------------------- Wed Feb 15 19:41:43 UTC 2012 - detlef.steuer@gmx.de - changed licence string to "GPL-2.0 or GPL-3.0" ------------------------------------------------------------------- Mon Feb 13 22:39:51 UTC 2012 - detlef.steuer@gmx.de - uninstall rule for R.conf more than useless ... reverted. ------------------------------------------------------------------- Mon Feb 13 21:59:13 UTC 2012 - detlef.steuer@gmx.de - Applications like KDE's Cantor search for the R standard library - using the library search path. However, in openSUSE's package, - libraries are installed to %{_libdir}/R/lib, hence attempts to - load them from these applications will fail. - This revision adds a R.conf file to ld.so.conf.d to enable - searching for libraries where R is installed. Once this change - is in, applications are able to use libR.so. - Thx to einar@heavensinferno.net for spotting this. - Thought had done this for release of 2.14.0. ------------------------------------------------------------------- Thu Dec 22 12:19:10 UTC 2011 - steuer@unibw-hamburg.de - Upstream updated to 2.14.1 - see, as usual, /usr/lib/R/doc/NEWS.html for details. - Only minor bug fixes + workaround for missing inconsolata.sty - on older systems. ------------------------------------------------------------------- Mon Oct 31 12:40:03 UTC 2011 - detlef.steuer@gmx.de - merged change infor Oct 5th into working copy ------------------------------------------------------------------- Mon Oct 31 12:34:30 UTC 2011 - detlef.steuer@gmx.de - corrected subpackge version number in R-base-devel ------------------------------------------------------------------- Mon Oct 31 11:12:24 UTC 2011 - detlef.steuer@gmx.de - Upstream updated to 2.14.0 - see, as usual, /usr/lib/R/doc/NEWS.html for details. - On system side most important, that /etc/ld.so.conf.d/R-base.conf - was added to help third party programs, i.e. rpy2, tp link against - R-base ------------------------------------------------------------------- Wed Oct 5 07:13:03 UTC 2011 - detlef.steuer@gmx.de - corrected version string for Matrix subpackage ------------------------------------------------------------------- Tue Oct 4 14:00:04 UTC 2011 - detlef.steuer@gmx.de - removed 4 warnings about unescaped macros in comments ------------------------------------------------------------------- Tue Oct 4 12:13:18 UTC 2011 - detlef.steuer@gmx.de - explicitly added some locale directories. Worked before implicitly. ------------------------------------------------------------------- Tue Oct 4 11:10:56 UTC 2011 - detlef.steuer@gmx.de - update to upstream version 2.13.2 - see, as usual, /usr/lib/R/doc/NEWS.html for details. ------------------------------------------------------------------- Sat Sep 17 10:18:38 UTC 2011 - jengelh@medozas.de - Remove redundant tags/sections from specfile - Use %_smp_mflags for parallel build ------------------------------------------------------------------- Fri Jul 8 19:32:45 UTC 2011 - detlef.steuer@gmx.de - resolved some conflicts for R-base.spec after osc up -e && osc pull ------------------------------------------------------------------- Fri Jul 8 12:51:05 UTC 2011 - detlef.steuer@gmx.de - corrected version string in R-base.spec ------------------------------------------------------------------- Fri Jul 8 11:51:35 UTC 2011 - detlef.steuer@gmx.de - Upstream updated to 2.13.1. Licence change from GPLv2 to GPLv2 || GPLv3. Packages rpart and survival now GPLed, too. Various minor bugfixes. See /usr/lib/R/doc/NEWS.html for details. ------------------------------------------------------------------- Thu May 12 13:45:43 UTC 2011 - detlef.steuer@gmx.de - Removed possible dangerous links of libraries. R`s internal libraries now are only available in $lib/R/lib . ------------------------------------------------------------------- Fri May 6 07:33:40 UTC 2011 - detlef.steuer@gmx.de - Changed Licence string to GPLv2, taken from opensuse`s list aof allowed licences, as requested from coolo ------------------------------------------------------------------- Wed Apr 13 11:13:38 UTC 2011 - detlef.steuer@gmx.de - Upstream update to 2.13.0; new package 'compiler'; some new language files ------------------------------------------------------------------- Fri Mar 4 12:36:54 UTC 2011 - detlef.steuer@gmx.de - update to 2.12.2 minor bugfixes see /usr/lib/R/doc/html/NEWS.html for details ------------------------------------------------------------------- Mon Jan 10 16:56:55 CET 2011 - detlef.steuer@gmx.de - removed -n parameter from %build/%install - removed %doc from man/info pages in files section ------------------------------------------------------------------- Fri Dec 17 14:05:39 UTC 2010 - detlef.steuer@gmx.de reverting mandir/infodir directiven, didn't build in some releases- ------------------------------------------------------------------- Fri Dec 17 12:40:12 UTC 2010 - detlef.steuer@gmx.de sorted out list of problems shown bei mrueckert- ------------------------------------------------------------------- Mon Nov 29 20:08:31 UTC 2010 - detlef.steuer@gmx.de Version, to be submitted to factory-
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