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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).
‘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’.
‘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)