Revisions of R-base
Dominique Leuenberger (dimstar_suse)
accepted
request 780561
from
Detlef Steuer (dsteuer)
(revision 72)
- 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.
Dominique Leuenberger (dimstar_suse)
accepted
request 765989
from
Marco Varlese (mvarlese)
(revision 71)
Dominique Leuenberger (dimstar_suse)
accepted
request 756062
from
Detlef Steuer (dsteuer)
(revision 70)
- 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
Dominique Leuenberger (dimstar_suse)
accepted
request 727204
from
Detlef Steuer (dsteuer)
(revision 69)
Use %license (forwarded request 727202 from jayvdb)
Dominique Leuenberger (dimstar_suse)
accepted
request 726998
from
Detlef Steuer (dsteuer)
(revision 68)
Fix summary of R-core and R-core-devel (forwarded request 726862 from jayvdb)
Dominique Leuenberger (dimstar_suse)
accepted
request 713566
from
Detlef Steuer (dsteuer)
(revision 67)
- 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.
Yuchen Lin (maxlin_factory)
accepted
request 698133
from
Detlef Steuer (dsteuer)
(revision 66)
- 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
Stephan Kulow (coolo)
accepted
request 683741
from
Detlef Steuer (dsteuer)
(revision 65)
- 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.
Dominique Leuenberger (dimstar_suse)
accepted
request 670208
from
Detlef Steuer (dsteuer)
(revision 64)
- 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. (forwarded request 667336 from TheBlackCat)
Dominique Leuenberger (dimstar_suse)
accepted
request 660243
from
Detlef Steuer (dsteuer)
(revision 63)
- 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
Dominique Leuenberger (dimstar_suse)
accepted
request 620182
from
Detlef Steuer (dsteuer)
(revision 62)
- 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
Dominique Leuenberger (dimstar_suse)
accepted
request 600354
from
Detlef Steuer (dsteuer)
(revision 61)
- 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.
Dominique Leuenberger (dimstar_suse)
accepted
request 589689
from
Detlef Steuer (dsteuer)
(revision 60)
- Setting correctly R_UNZIPCMD Corrects this bug: http://bugzilla.suse.com/show_bug.cgi?id=1083075
Dominique Leuenberger (dimstar_suse)
accepted
request 587453
from
Detlef Steuer (dsteuer)
(revision 59)
- 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)
Dominique Leuenberger (dimstar_suse)
accepted
request 586283
from
Detlef Steuer (dsteuer)
(revision 58)
- Do not buildrequire xorg-x11-devel but individual x libs. (forwarded request 586069 from elvigia)
Dominique Leuenberger (dimstar_suse)
accepted
request 546684
from
Detlef Steuer (dsteuer)
(revision 57)
- 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.
Dominique Leuenberger (dimstar_suse)
accepted
request 529866
from
Detlef Steuer (dsteuer)
(revision 56)
- 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)
Dominique Leuenberger (dimstar_suse)
accepted
request 512757
from
Detlef Steuer (dsteuer)
(revision 55)
- 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.
Dominique Leuenberger (dimstar_suse)
accepted
request 507288
from
Detlef Steuer (dsteuer)
(revision 54)
- 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
Dominique Leuenberger (dimstar_suse)
accepted
request 489881
from
Detlef Steuer (dsteuer)
(revision 53)
- 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).
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