R 3.0 launched #rstats

The 3.0 Era for R starts today! Changes include better Big Data support.

Read the NEWS here

install.packages() has a new argument quiet to reduce the amount of output shown.
New functions cite() and citeNatbib() have been added, to allow generation of in-text citations from "bibentry" objects. A cite() function may be added to bibstyle() environments.
merge() works in more cases where the data frames include matrices. (Wish of PR#14974.)
sample.int() has some support for n >= 2^31: see its help for the limitations.A different algorithm is used for (n, size, replace = FALSE, prob = NULL) for n > 1e7 and size <= n/2. This is much faster and uses less memory, but does give different results.
list.files() (aka dir()) gains a new optional argument no.. which allows to exclude "." and ".." from listings.
Profiling via Rprof() now optionally records information at the statement level, not just the function level.
available.packages() gains a "license/restricts_use" filter which retains only packages for which installation can proceed solely based on packages which are guaranteed not to restrict use.
File ‘share/licenses/licenses.db’ has some clarifications, especially as to which variants of ‘BSD’ and ‘MIT’ is intended and how to apply them to packages. The problematic licence ‘Artistic-1.0’ has been removed.
The breaks argument in hist.default() can now be a function that returns the breakpoints to be used (previously it could only return the suggested number of breakpoints).

LONG VECTORS

This section applies only to 64-bit platforms.

There is support for vectors longer than 2^31 – 1 elements. This applies to raw, logical, integer, double, complex and character vectors, as well as lists. (Elements of character vectors remain limited to 2^31 – 1 bytes.)
Most operations which can sensibly be done with long vectors work: others may return the error ‘long vectors not supported yet’. Most of these are because they explicitly work with integer indices (e.g. anyDuplicated() and match()) or because other limits (e.g. of character strings or matrix dimensions) would be exceeded or the operations would be extremely slow.
length() returns a double for long vectors, and lengths can be set to 2^31 or more by the replacement function with a double value.
Most aspects of indexing are available. Generally double-valued indices can be used to access elements beyond 2^31 – 1.
There is some support for matrices and arrays with each dimension less than 2^31 but total number of elements more than that. Only some aspects of matrix algebra work for such matrices, often taking a very long time. In other cases the underlying Fortran code has an unstated restriction (as was found for complex svd()).
dist() can produce dissimilarity objects for more than 65536 rows (but for example hclust() cannot process such objects).
serialize() to a raw vector is unlimited in size (except by resources).
The C-level function R_alloc can now allocate 2^35 or more bytes.
agrep() and grep() will return double vectors of indices for long vector inputs.
Many calls to .C() have been replaced by .Call() to allow long vectors to be supported (now or in the future). Regrettably several packages had copied the non-API .C() calls and so failed.
.C() and .Fortran() do not accept long vector inputs. This is a precaution as it is very unlikely that existing code will have been written to handle long vectors (and the R wrappers often assume that length(x) is an integer).
Most of the methods for sort() work for long vectors.

rank(), sort.list() and order() support long vectors (slowly except for radix sorting).
sample() can do uniform sampling from a long vector.

PERFORMANCE IMPROVEMENTS

More use has been made of R objects representing registered entry points, which is more efficient as the address is provided by the loader once only when the package is loaded.
This has been done for packages base, methods, splines and tcltk: it was already in place for the other standard packages.

Since these entry points are always accessed by the R entry points they do not need to be in the load table which can be substantially smaller and hence searched faster. This does mean that .C / .Fortran / .Call calls copied from earlier versions of R may no longer work – but they were never part of the API.
Many .Call() calls in package base have been migrated to .Internal() calls.
solve() makes fewer copies, especially when b is a vector rather than a matrix.
eigen() makes fewer copies if the input has dimnames.
Most of the linear algebra functions make fewer copies when the input(s) are not double (e.g. integer or logical).
A foreign function call (.C() etc) in a package without a PACKAGE argument will only look in the first DLL specified in the ‘NAMESPACE’ file of the package rather than searching all loaded DLLs. A few packages needed PACKAGE arguments added.
The @<- operator is now implemented as a primitive, which should reduce some copying of objects when used. Note that the operator object must now be in package base: do not try to import it explicitly from package methods.

SIGNIFICANT USER-VISIBLE CHANGES

Packages need to be (re-)installed under this version (3.0.0) of R.
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.
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.