R

R 3.0.0の大事な変更点

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大きめ目の変更点(個人目線)

  • Long Vectorのサポート(64bit版)。
    • 2^31-1以上の長さのベクトルが使用可能に。
    • 使えるのはraw/logical/integer/double/complex/characterのベクトルとlistも。
    • 文字ベクトルの要素の長さは今までどおり 2^31-1 bytes。
    • Long vectorに対するlength()doubleを返す。
    • インデクシングにはintegerではなくてdoubleを使うように。
    • 行列、配列の場合、各次元の長さが < 2^31-1なら次元数の総和が > 2^31-1 もOKに。でも挙動は微妙。
    • などなど。しばらくは使うときは要注意。
  • パフォーマンス改善(オブジェクトコピーを減らす、とか、関数呼び出し周りとか)。
  • baseパッケージでビット演算サポート。see > ?bitwise
  • S4クラスでrepresentationの代わりにslotsが推奨されるように。
  • R5のsetRefClass()がS4みたくジェネレータ関数を返すように。これまではジェネレータオブジェクトを返してて、obj$new(…)みたいな書式だった。これまでの書式もいまのところ利用可。
  • LocalReferenceClassesという何かが加わった。
  • (何のことやらという感じだと思うけど)parserパッケージの中身が本体に取り込まれた。コメントも扱えたりします。

という感じ。基本的に後方互換は保たれてるので、現在のコードが動かなくなるとか怪しくなる、というのは稀だと思います。deprecated/defunctは下の方にリストアップされてます。


以下、NEWSのテキトーな訳とかメモ。

SIGNIFICANT USER-VISIBLE CHANGES

  • Packages need to be (re-)installed under this version (3.0.0) of R.
    _
    パッケージの再インストールが必要。

  • 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.
    __
    2^31以上の数値インデクス(ベクトル要素とかの)の処理に変更。使ってる場合は注意。

  • 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.
    __
    64bit版ではOSによるメモリ割り当て制限のみ可能。

  • 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.
    __
    64bit windowsではメモリ制限はデフォルトではRAM容量。

  • 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.
    __
    数値による色指定時に負の値は常にエラー。以前は適当だった(そうなんか・・・)。

NEW FEATURES

  • identical() has a new argument, ignore.environment, used when comparing functions (with default FALSE as before).
    __
    identical()の新しい引数。ignore.environmentTRUEなら関数の環境は無視。

  • There is a new option, options(CBoundsCheck=), which controls how .C() and .Fortran() pass arguments to compiled code. If true (which can be enabled by setting the environment variable R_C_BOUNDS_CHECK to yes), raw, integer, double and complex arguments are always copied, and checked for writing off either end of the array on return from the compiled code (when a second copy is made). This also checks individual elements of character vectors passed to .C().
    __
    .C().Fortran()で引数を渡すときにコピー関連で諸々。

  • This is not intended for routine use, but can be very helpful in finding segfaults in package code.
    __
    ↑のやつは普段は使わないけどセグフォ対策の時に便利。

  • In layout(), the limits on the grid size have been raised (again).
    __
    layout()でグリッドサイズの上限がアップ。

  • New simple provideDimnames() utility function.
    __
    provideDimnames()っていう新しい関数。

  • Where methods for length() return a double value which is representable as an integer (as often happens for package Matrix), this is converted to an integer.
    __
    length()メソッドがdoubleを返すけどintegerで表せる場合はintegerに変換します。

  • Matrix indexing of dataframes by two-column numeric indices is now supported for replacement as well as extraction.
    __
    データフレームに対する2要素ベクトルでの行列風のインデクシングで代入できるように。df[c(2, 3)] <- hogeみたいな。

  • setNames() now has a default for its object argument, useful for a character result.


    setNames()に変更。

  • StructTS() has a revised additive constant in the loglik component of the result: the previous definition is returned as the loglik0 component. However, the help page has always warned of a lack of comparability of log-likelihoods for non-stationary models. (Suggested by Jouni Helske.)
    __

  • The logic in aggregate.formula() has been revised. It is now possible to use a formula stored in a variable; previously, it had to be given explicitly in the function call.
    __
    aggregate()でフォーミュラを変数で渡せるようになった。

  • install.packages() has a new argument quiet to reduce the amount of output shown.
    __
    install.packages()quiet引数。出力抑制。

  • Setting an element of the graphics argument lwd to a negative or infinite value is now an error. Lines corresponding to elements with values NA or NaN are silently omitted.
    __
    プロットでlwdに負や無限はエラー、NAとNaNは省略される。以前はデバイス依存でした。

  • Previously the behaviour was device-dependent.
    __

  • Setting graphical parameters cex, col, lty, lwd and pch in par() now requires a length-one argument. Previously some silently took the first element of a longer vector, but not always when documented to do so.
    __
    <<注>>par()cex,cel,lwd,pchは1要素の引数を渡す必要がある。以前は適当だった。

  • Sys.which() when used with inputs which would be unsafe in a shell (e.g. absolute paths containing spaces) now uses appropriate quoting.
    __
    Sys.which()に渡された引数がやばそうな場合はクオートするようにしました。

  • as.tclObj() has been extended to handle raw vectors. Previously, it only worked in the other direction. (Contributed by Charlie Friedemann, PR#14939.)
    __

  • 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.
    __
    cite()citeNatbib()bibentryオブジェクトからテキスト内引用を作れるようになりました。

  • A sort() method has been added for "bibentry" objects.
    __
    bibentry用のsortメソッド追加。

  • The bibstyle() function now defaults to setting the default bibliography style. The getBibstyle() function has been added to report the name of the current default style.
    __
    bibstyle()ゴニョゴニョ。bibentryって結構みんな使ってるもんなのか?

  • scatter.smooth() now has an argument lpars to pass arguments to lines().
    __
    <<イイネ>> scatter.smooth()lines()のオプション指定が可能に。

  • pairs() has a new log argument, to allow some or all variables to be plotted on logarithmic scale. (In part, wish of PR#14919.)
    __
    <<イイネ>> pairs()がlog対応。

  • split() gains a sep argument.
    __
    split()sep引数。@@あとで挙動書く@@。

  • termplot() does a better job when given a model with interactions (and no longer attempts to plot interaction terms).
    __
    termplot()で交互作用項の扱いが上手に。

  • The parser now incorporates code from Romain Francois' parser package, to support more detailed computation on the code, such as syntax highlighting, comment-based documentation, etc. Functions getParseData() and getParseText() access the data.
    __
    parserパッケージのコードが組み込まれた。R式の動的処理がもっと細かく可能に。マニアックだけどいい。

  • There is a new function rep_len() analogous to rep.int() for when speed is required (and names are not).
    __
    rep_len()追加。rep.int()と同じだけど速い。

  • The undocumented use rep(NULL, length.out = n) for n > 0 (which returns NULL) now gives a warning.
    __
    未定義のrep(NULL, length.out = n)(n>0)は警告。NULLを返す。

  • demo() gains an encoding argument for those packages with non-ASCII demos: it defaults to the package encoding where there is one.
    __
    demo()encoding引数をサポート。

  • strwrap() converts inputs with a marked encoding to the current locale: previously it made some attempt to pass through as bytes inputs invalid in the current locale.
    __
    strwrap()がエンコーディングをうまくやるように。この関数知らなかった。

  • Specifying both rate and scale to [dpqr]gamma is a warning (if they are essentially the same value) or an error.
    __
    <<注>>ガンマ分布([dpqr]gammaratescaleの両方を与えると警告かエラーに。

  • merge() works in more cases where the data frames include matrices. (Wish of PR#14974.)
    __
    データフレームが行列を含んでる場合にもmerge可能に。

  • optimize() and uniroot() no longer use a shared parameter object across calls. (nlm(), nlminb() and optim() with numerical derivatives still do, as documented.)
    __
    _ optimzize()uniroot()が別の呼び出しで共通のパラメータを使わなくなった。nlm/nlminb/optimはまだ使うので注意。

  • The all.equal() method for date-times is now documented: times are regarded as equal (by default) if they differ by up to 1 msec.
    __
    日時クラスのall.equal()がドキュメント化。時間の場合、1ミリ秒未満の差なら同じとみなされる。

  • duplicated() and unique() gain a nmax argument which can be used to make them much more efficient when it is known that there are only a small number of unique entries. This is done automatically for factors.
    __
    duplicated()unique()nmax引数追加。ちょっとしか重複がないことがわかってる、というケースで高速化できる。

  • Functions rbinom(), rgeom(), rhyper(), rpois(), rnbinom(), rsignrank() and rwilcox() now return integer (not double) vectors. This halves the storage requirements for large simulations.
    __
    <<注>> 整数乱数生成系の関数がintegerを返すように(以前はdouble)。

  • sort(), sort.int() and sort.list() now use radix sorting for factors of less than 100,000 levels when method is not supplied. So does order() if called with a single factor, unless na.last = NA.
    __
    ソート系の関数で因子(<100000水準)で基数ソート。

  • diag() as used to generate a diagonal matrix has been re-written in C for speed and less memory usage. It now forces the result to be numeric in the case diag(x) since it is said to have ‘zero off-diagonal entries’.
    __
    <<注>> diag()の効率アップ。挙動がちょっと変わってる(あとで確認)。

  • backsolve() (and forwardsolve()) are now internal functions, for speed and support for large matrices.
    __
    backsolve()forwardsolve()は内部関数に。パッケージでは使えなくなる、ってことかな。

  • More matrix algebra functions (e.g. chol() and solve()) accept logical matrices (and coerce to numeric).
    __
    chol()とかsolve()とか他にも行列代数の関数で論理値行列でもOKに。

  • sample.int() has some support for n >= 2^31: see its help for the limitations.
    __
    `sample.int()でn >- 2^31が可能に。

  • 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.
    __
    sample.int()(sample()も?で、nとsizeによって異なるアルゴリズムが使われるように。

  • approxfun() and splinefun() now return a wrapper to an internal function in the stats namespace rather than a .C() or .Call() call. This is more likely to work if the function is saved and used in a different session.
    __
    approxfun()splinefun()の挙動が微妙に変更。関数オブジェクトをセーブして別セッションでロードしても使える可能性が高くなった。

  • The functions .C(), .Call(), .External() and .Fortran() now give an error (rather than a warning) if called with a named first argument.
    __
    <<注>> .C/.Call/.Externa/.Fortranで最初の引数が名前付きだとエラーに(以前は警告)。

  • Sweave() by default now reports the locations in the source file(s) of each chunk.
    __
    Sweave()でチャンクのソースファイルの場所を報告するように。

  • clearPushBack() is now a documented interface to a long-existing internal call.
    __
    clearPushBack()というのがドキュメント化。

  • aspell() gains filters for R code, Debian Control Format and message catalog files, and support for R level dictionaries. In addition, package utils now provides functions aspell_package_R_files() and aspell_package_C_files() for spell checking R and C level message strings in packages.
    __
    aspell()(スペルチェッカ)の機能拡張。

  • bibentry() gains some support for “incomplete” entries with a crossref field.
    __

  • gray() and gray.colors() finally allow alpha to be specified.
    <<イイネ>> gray()gray.colors()でアルファ値の設定が可能に。今までできなかったのか。

  • monthplot() gains parameters to control the look of the reference lines. (Suggestion of Ian McLeod.)
    __
    monthplot()で基準線(?)の見た目指定が可能に。前は多分、基準線を描く関数を渡してた。

  • Added support for new %~% relation (“is distributed as”) in plotmath.
    __
    plotmath(数式)で「Xはほげほげ分布に従う」の記号%~%をサポート。

  • domain = NA is accepted by gettext() and ngettext(), analogously to stop() etc.
    __
    gettext/ngettextstop()と同様にdomain=NAが可能に。

  • termplot() gains a new argument plot = FALSE which returns information to allow the plots to be modified for use as part of other plots, but does not plot them. (Contributed by Terry Therneau, PR#15076.)
    __
    termplot()plot = FALSE引数追加。プロットはしないで情報だけ返す。

  • quartz.save(), formerly an undocumented part of R.app, is now available to copy a device to a quartz() device. dev.copy2pdf() optionally does this for PDF output: quartz.save() defaults to PNG.
    __
    quartz.save()公式に追加。dev.copy2pdf()でもこのオプションを選べるように。(要動作確認)。

  • The default method of pairs() now allows text.panel = NULL and the use of .panel = NULL is now documented.
    __
    pairs()のデフォルトメソッドの振る舞い変更(要確認)。

  • setRefClass() and getRefClass() now return class generator functions, similar to setClass(), but still with the reference fields and methods as before (suggestion of Romain Francois).
    __
    <<注>> setRefClass()/getRefClass()setClass()と同じようにクラス生成関数を返すように。後方互換で参照フィールドとかも残ってる。
    なんかヤバイ香りが漂う・・・。

  • New functions bitwNot(), bitwAnd(), bitwOr() and bitwXor(), using the internal interfaces previously used for classes "octmode" and "hexmode".
    __
    bitwNot/bitwAnd/bitwOr/bitxwXor関数追加。bitwShiftL/Rも。ビット演算サポートってことかな。要確認。

  • Also bitwShiftL() and bitwShiftR() for shifting bits in elements of integer vectors.
    __

  • New option "deparse.cutoff" to control the deparsing of language objects such as calls and formulae when printing. (Suggested by a comment of Sarah Goslee.)
    __
    deparse()deparse.cutoff引数追加。呼び出しとかフォーミュラとか表示するときに長すぎる場合にいいようにする(多分)。

  • colors() gains an argument distinct.
    __
    colors()関数にdistinct引数追加。完全に異なる色名だけがリストアップされる(多分)。

  • New demo(colors) and demo(hclColors), with utility functions.
    __
    colorsとかのデモ追加。

  • list.files() (aka dir()) gains a new optional argument no.. which allows to exclude "." and ".." from listings.
    __
    <<イイネ>> list.files/dir...を除くためのno..引数。名前はダサい。

  • Multiple time series are also of class "matrix"; consequently, head(), e.g., is more useful.
    __
    <<イイネ>> 多次元時系列は行列クラスに。headが便利になってる。(前は確か先頭N系列が全部表示されてた)。

  • encodeString() preserves UTF-8 marked encodings. Thus if factor levels are marked as UTF-8 an attempt is made to print them in UTF-8 in RGui on Windows.
    __
    encodeString()でUTF-8の扱いが良くなった(よく知らん)。

  • readLines() and scan() (and hence read.table()) in a UTF-8 locale now discard a UTF-8 byte-order-mark (BOM). Such BOMs are allowed but not recommended by the Unicode Standard: however Microsoft applications can produce them and so they are sometimes found on websites.
    __
    readLines/scae/read.tableとかでUTF-8のBOMを削除するようになった。Unicodeでは推奨されてませんが、マイクロソフトのアプリケーションでBOMをつける奴がいるんですよ。

  • The encoding name "UTF-8-BOM" for a connection will ensure that a UTF-8 BOM is discarded.
    __
    で、絶対にBOMを付きでBOMを切りたい、という場合にはエンコード名"UTF-8-BOM"を使うとよい。

  • mapply(FUN, a1, ..) now also works when a1 (or a further such argument) needs a length() method (which the documented arguments never do). (Requested by Hervé Pagès; with a patch.)
    __
    mapply(FUN, a1, ..)a1とか以降の引数がlengthメソッドを必要な場合にも動くようになった。状況がよくわからん(@@要確認)。

  • .onDetach() is supported as an alternative to .Last.lib. Unlike .Last.lib, this does not need to be exported from the package's namespace.
    __
    .onDetach().Last.libの代わりにつかえる。.Last.libとは違ってパッケージ名前空間からエクスポートされない。

  • The srcfile argument to parse() may now be a character string, to be used in error messages.
    __
    parse()へのsrcfile引数は文字列でもOKに。エラーメッセージで使われる(@@要確認)。

  • The format() method for ftable objects gains a method argument, propagated to write.ftable() and print(), allowing more compact output, notably for LaTeX formatting, thanks to Marius Hofert.
    __
    ftableオブジェクトのformat()メソッドに変更。

  • The utils::process.events() function has been added to trigger immediate event handling.
    __
    イベントハンドリングを行う関数追加(@要調査)。

  • Sys.which() now returns NA (not "") for NA inputs (related to PR#15147).
    __
    <<注>> Sys.which()がNAに対してNA返す。今まではエラー。こういうのって絶対バグ出てくるよな・・・。

  • The print() method for class "htest" gives fewer trailing spaces (wish of PR#15124).
    __
    htestクラス、HoltWinters()/nls()の結果のprintがちょっと変更。

  • Also print output from HoltWinters(), nls() and others.
    __

  • loadNamespace() allows a version specification to be given, and this is used to check version specifications given in the Imports field when a namespace is loaded.
    __
    loadNamespace()でパッケージのバージョン指定が可能に。

  • setClass() has a new argument, slots, clearer and less ambiguous than representation. It is recommended for future code, but should be back-compatible. At the same time, the allowed slot specification is slightly more general. See the documentation for details.
    __
    <<注>> setClass()slots引数追加。representationsよりベターだからこれからはこっちを使うように。

  • mget() now has a default for envir (the frame from which it is called), for consistency with get() and assign().
    __
    mget()envir引数がデフォルトでは呼び出し環境に。get/assignと同じ。

  • close() now returns an integer status where available, invisibly. (Wish of PR#15088.)
    __
    close()が整数値で結果を返す(可能なら、こっそりと)。

  • The internal method of tar() can now store paths too long for the ustar format, using the (widely supported) GNU extension. It can also store long link names, but these are much less widely supported. There is support for larger files, up to the ustar limit of 8GB.
    __
    tar()が良くなった。

  • Local reference classes have been added to package methods. These are a technique for avoiding unneeded copying of large components of objects while retaining standard R functional behavior. See ?LocalReferenceClasses.
    __
    <<注>> 局所的参照クラスLocalReferenceClassesという何かが加わった。でかいもののコピーを抑制する。@@要確認。

  • untar() has a new argument restore_times which if false (not the default) discards the times in the tarball. This is useful if they are
    incorrect (some tarballs submitted to CRAN have times in a local timezone or many years in the past even though the standard required them to be in UTC).
    __
    untar()がタイムスタンプを無視出来るようになった。

  • replayplot() cannot (and will not attempt to) replay plots recorded under R < 3.0.0. It may crash the R session if an attempt is made to replay plots created in a different build of R >= 3.0.0.
    __
    replayplot()は3.0より前のバージョンで記録したプロットを再生しない。3.0以上でも異なるビルドの場合クラッシュするかも。

  • Palette changes get recorded on the display list, so replaying plots (including when resizing screen devices and using dev.copy()) will work better when the palette is changed during a plot.
    __
    パレットの変更がディスプレイリストに記録されるようになった。

  • chol(pivot = TRUE) now defaults to LAPACK, not LINPACK.
    __
    chol(pivot = TRUE)のバックエンドがデフォルトでLAPACKに(以前はLINPACK)。

  • The parse() function has a new parameter keep.source, which defaults to options("keep.source").
    parsekeep.source引数。まんま。多分parserでコメントとか扱えるようになったからかな。

  • Profiling via Rprof() now optionally records information at the statement level, not just the function level.
    __
    Rprof()のプロファイルで関数じゃなくて式レベルでの情報を記録できるように。

  • The Rprof() function now quotes function names in in its output file on Windows, to be consistent with the quoting in Unix.
    __
    Rprof()がwindows環境で出力ファイル中の関数名をクォート。

  • Profiling via Rprof() now optionally records information about time spent in GC.
    __
    Rprof()でガベコレの経過時間も記録できるように。

  • The HTML help page for a package now displays non-vignette documentation files in a more accessible format.
    __
    パッケージのHTMLヘルプで、vignettじゃないドキュメントをもっと上手に表示。

  • To support options(stringsAsFactors = FALSE), model.frame(), model.matrix() and replications() now automatically convert character vectors to factors without a warning.
    __
    <<ヤバイ>> model.frame(), model.matrix(), replications()文字列は勝手に因子にします。警告はしない。

  • The print method for objects of class "table" now detects tables with 0-extents and prints the results as, e.g., < table of extent 0 x 1 x 2 >. (Wish of PR#15198.)
    __
    tableの表示が良くなっった。

  • Deparsing involving calls to anonymous functions and has been made closer to reversible by the addition of extra parentheses.
    __
    無名関数呼び出しのdeparseの仕様がちょい変更。

  • The function utils::packageName() has been added as a lightweight version of methods::getPackageName().
    __
    utils::packageName()で手軽にパッケージ名を得られるように。

  • find.package(lib.loc = NULL) now treats loaded namespaces preferentially in the same way as attached packages have been for a long time.
    __
    find.package(lib.loc = NULL)で、ずっとアタッチされてるパッケージと同じようにロードされたパッケージも優先して扱うように。

  • In Windows, the Change Directory dialog now defaults to the current working directory, rather than to the last directory chosen in that dialog.
    __
    Windowsでディレクトリ変更ダイアログの初期表示がカレントディレクトリに。最後に使ったのじゃなくて。

  • 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.
    __
    available.packages()でlicense/restricts_useフィルタ的なものをサポート。

  • New check_packages_in_dir() function in package tools for conveniently checking source packages along with their reverse dependencies.
    __
    check_packages_in_dir()関数追加。

  • R's completion mechanism has been improved to handle help requests (starting with a question mark). In particular, help prefixes are now supported, as well as quoted help topics. To support this, completion inside quotes are now handled by R by default on all platforms.
    __
    補完機能改善。

  • The memory manager now allows the strategy used to balance garbage collection and memory growth to be controlled by setting the environment variable R_GC_MEM_GROW. See ?Memory for more details.
    __
    ガベコレ改善。

  • (‘For experts only’, as the introductory manual says.) The use of environment variables R_NSIZE and R_VSIZE to control the initial (= minimum) garbage collection trigger for number of cons cels and size of heap has been restored: they can be overridden by the command-line options --min-nsize and --min-vsize; see ?Memory.
    __

  • On Windows, the device name for bitmap devices as reported by .Device and .Devices no longer includes the file name. This is for consistency with other platforms and was requested by the lattice maintainer.
    __
    windowsで.Deviceがbmpデバイスにファイル名含まないように。

  • win.metafile() still uses the file name: the exact form is used by package tkrplot.
    __
    win.metafileの方はまだファイル名含みます。

  • set.seed(NULL) re-initializes .Random.seed as done at the beginning of the session if not already set. (Suggestion of Bill Dunlap.)
    __
    set.seed(NULL)でセッション開始時と同じようにランダムシードが再初期化されます。@@要確認。

  • 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).
    __
    <<イイネ>> hist.default()breaks引数が関数でOKになった。

  • 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.
    __
    'share/licenses/licenses.db'ちょい変更。

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.

PACKAGE INSTALLATION

  • The transitional support for installing packages without namespaces (required since R 2.14.0) has been removed. R CMD build will still add a namespace, but a .First.lib() function will need to be converted.

  • R CMD INSTALL no longer adds a namespace (so installation will fail), and a .First.lib() function in a package will be ignored (with an installation warning for now).

  • As an exception, packages without a ‘R’ directory and no ‘NAMESPACE’ file can still be installed.

  • Packages can specify in their ‘DESCRIPTION file’ a line like

  •  Biarch: yes
    
  • to be installed on Windows with --force-biarch.

  • Package vignettes can now be processed by other engines besides Sweave; see ‘Writing R Extensions’ and the tools::vignetteEngine help topic for details.

  • The ‘.R’ tangled source code for vignettes is now included in tarballs when R CMD build is used to produce them. In R 3.0.0, ‘.R’ files not in the sources will be produced at install time, but eventually this will be dropped.

  • The package type "mac.binary" now looks in a path in the repository without any Mac subtype (which used to be universal or leopard): it looks in ‘bin/macosx/contrib/3.0’ rather than ‘bin/macosx/leopard/contrib/2.15’). This is the type used for the CRAN binary distribution for OS X as from R 3.0.0.

  • File ‘etc/Makeconf’ makes more use of the macros $(CC), $(CXX), $(F77) and $(FC), so the compiler in use can be changed by setting just these (and if necessary the corresponding flags and FLIBS) in file ‘~/.R/Makevars’.

  • This is convenient for those working with binary distributions of R, e.g. on OS X.

UTILITIES

  • R CMD check now gives a warning rather than a note if it finds calls to abort, assert or exit in compiled code, and has been able to find the ‘.o’ file in which the calls occur.

  • Such calls can terminate the R process which loads the package.

  • The location of the build and check environment files can now be specified by the environment variables R_BUILD_ENVIRON and R_CHECK_ENVIRON, respectively.

  • R CMD Sweave gains a --compact option to control possibly reducing the size of the PDF file it creates when --pdf is given.

  • R CMD build now omits Eclipse's ‘.metadata’ directories, and R CMD check warns if it finds them.

  • R CMD check now does some checks on functions defined within reference classes, including of .Call() etc calls.

  • R CMD check --as-cran notes assignments to the global environment, calls to data() which load into the global environment, and calls to attach().

  • R CMD build by default uses the internal method of tar() to prepare the tarball. This is more likely to produce a tarball compatible with R CMD INSTALL and R CMD check: an external tar program, including options, can be specified via the environment variable R_BUILD_TAR.

  • tools::massageExamples() is better protected against packages which re-define base functions such as cat() and get() and so can cause R CMD check to fail when checking examples.

  • R CMD javareconf has been enhanced to be more similar to the code used by configure.

  • There is now a test that a JNI program can be compiled (like configure did) and only working settings are used.

  • It makes use of custom settings from configuration recorded in ‘etc/javaconf’.

  • The --no-vignettes argument of R CMD build has been renamed to the more accurate --no-build-vignettes: its action has always been to (re)build vignettes and never omitted them.

  • R CMD check accepts --no-build-vignettes as a preferred synonym for --no-rebuild-vignettes.

DEPRECATED AND DEFUNCT

  • The ENCODING argument to .C() is defunct. Use iconv() instead.
    __
    .C()ENCODINGがdefunct

  • The .Internal(eval.with.vis) non-API function has been removed.
    __
    .Internal(eval.with.vis)がなくなった。

  • Support for the converters for use with .C() has been removed, including the oft misused non-API header ‘R_ext/RConverters.h’.
    .C()での変換サポートがなくなった。

  • The previously deprecated uses of array() with a 0-length dim argument and tapply() with a 0-length INDEX list are now errors.
    __
    array()で長さ0の次元指定(array(1:3, dim=c()))はエラー。以前は警告。
    tapply()で長さ0のインデクスリストはエラー(tapply(1:5, list()))。以前は警告。

  • Translation packages are defunct.
    __
    まんま。

  • Calling rep() or rep.int() on a pairlist or other non-vector object is now an error.
    __
    rep/rep.intでpairlistかvector以外のオブジェクト渡すとエラー。何があるんだろう。

  • Several non-API entry points have been transferred to packages (e.g. R_zeroin2) or replaced by different non-API entry points (e.g. R_tabulate).
    __
    気にしなくていい。

  • The ‘internal’ graphics device invoked by .Call("R_GD_nullDevice", package = "grDevices") has been removed: use pdf(file = NULL) instead.
    __
    .Call("R_GD_nullDevice", package = "grDevices")だめ。代わりにpdf(file = NULL)使う。

  • The .Fortran() entry point "dqrls" which has not been used by R since version 2.15.1 is no longer available.
    __
    .fortran()dqrlsは使えなくなった。

  • Functions traceOn() and traceOff() in package methods are now defunct.
    __
    traceOn/traceOffはdefunct。trace/untraceを使う。

  • Function CRAN.packages() is finally defunct.
    __
    まんま。

  • Use of col2rgb(0) is defunct: use par("bg") or NA instead.
    __
    col2rgb(0)もうだめ。

  • The long-defunct functions Rd_parse(), anovalist.lm(), categpry(), clearNames(), gammaCody(), glm.fit.null(), lm.fit.null(), lm.wfit.null(), manglePackageNames(), mauchley.test(), package.contents(), print.coefmat(), reshapeLong(), reshapeWide(), tkclose(), tkcmd(), tkfile.dir(), tkfile.tail(), tkopen(), tkputs(), tkread(), trySilent() and zip.file.extract() have been removed entirely (but are still documented in the help system).
    __
    defunctだった↑の関数は削除。

  • The unused dataPath argument to attachNamespace() has been removed.
    __
    まんま。

  • grid.prompt() has been removed: use devAskNewPage() instead.
    __
    まんま。

  • The long-deprecated intensities component is no longer returned by hist().
    __
    hist()intensitiesは返らなくなった。

  • mean() for data frames and sd() for data frames and matrices are defunct.
    __
    データフレームと行列に対するmean/sdがdeprecatedからdefunctに。

  • chol(pivot = FALSE, LINPACK = TRUE), ch2inv(LINPACK = TRUE), eigen(EISPACK = TRUE), solve(LINPACK = TRUE) and svd(LINPACK = TRUE) are defunct: LAPACK will be used, with a warning.
    __
    LINPACK系のやつがdefunctに。代わりにLAPACK使います。警告は出します。

  • The keep.source argument to library() and require() is defunct. This option needs to be set at install time.
    __
    libraryrequirekeep.sourceがdefunct。

  • Documentation for real(), as.real() and is.real() has been moved to ‘defunct’ and the functions removed.
    __
    real/as.real/is.realがなくなった。

  • The maxRasters argument of pdf() (unused since R 2.14.0) has been removed.
    __
    まんま。

  • The unused fontsmooth argument has been removed from the quartz() device.
    __
    まんま。

  • All the (non-API) EISPACK entry points in R have been removed.
    __
    まんま

  • chol(pivot = TRUE, LINPACK = TRUE) is deprecated.
    __
    まんま。

  • The long-deprecated use of \synopsis in the Usage section of ‘.Rd’ files will be removed in R 3.1.0.
    __
    .Rdでの\synopsisセクションがR 3.1.0でなくなります。

  • .find.package() and .path.package() are deprecated: only the public versions without the dot have ever been in the API.
    __
    .find.package()/.path.package()はdeprecated。ドット無しバージョンでがありますから。

  • In a package's ‘DESCRIPTION’ file,

  • License: X11
    
  • is deprecated, since it includes ‘Copyright (C) 1996 X Consortium’ which cannot be appropriate for a current R package. Use ‘MIT’ or ‘BSD_2_clause’ instead.
    __
    パッケージのDESCRIPTIONのLICENSEでX11はダメ。代わりにMITかBSD_2_clauseを使うように。

CODE MIGRATION

  • The C code underlying base graphics has been migrated to the graphics package (and hence no longer uses .Internal() calls).

  • Most of the .Internal() calls used in the stats package have been migrated to C code in that package.

  • This means that a number of .Internal() calls which have been used by packages no longer exist, including .Internal(cor) .Internal(cov), .Internal(optimhess) and .Internal(update.formula).

  • Some .External() calls to the base package (really to the R executable or shared library) have been moved to more appropriate packages. Packages should not have been using such calls, but some did (mainly those used by integrate()).

PACKAGE parallel

  • There is a new function mcaffinity() which allows getting or setting the CPU affinity mask for the current R process on systems that supports this (currently only Linux has been tested successfully). It has no effect on systems which do not support process affinity. Users are not expected to use this function directly (with the exception of fixing libraries that break affinity settings like OpenBLAS) – the function is rather intended to support affinity control in high-level parallel functions. In the future, R may supplement lack of affinity control in the OS by its own bookkeeping via mcaffinity() related to processes and threads it spawns.

  • mcparallel() has a new argument mc.affinity which attempts to set the affinity of the child process according to the specification contained therein.

  • The port used by socket clusters is chosen randomly: this should help to avoid clashes observed when two users of a multi-user machine try to create a cluster at the same time. To reproduce the previous behaviour set environment variable R_PARALLEL_PORT to 10187.

C-LEVEL FACILITIES

  • There has been some minor re-organization of the non-API header files. In particular, ‘Rinternals.h’ no longer includes the non-API header ‘R_exts/PrtUtil.h’, and that no longer includes ‘R_exts/Print.h’.

  • Passing NULL to .C() is now an error.

  • .C() and .Fortran() now warn if "single" arguments are used with DUP = FALSE, as changes to such arguments are not returned to the caller.

  • C entry points R_qsort and R_qsort_I now have start and end as size_t to allow them to work with longer vectors on 64-bit platforms. Code using them should be recompiled.

  • A few recently added C entry points were missing the remapping to Rf_, notably [dpq]nbinom_mu.

  • Some of the interface pointers formerly available only to R.app are now available to front-ends on all Unix-alikes: one has been added for the interface to View().

  • PACKAGE = "" is now an error in .C() etc calls: it was always contrary to the documentation.

  • Entry point rcont2 has been migrated to package stats and so is no longer available.

  • R_SVN_REVISION in ‘Rversion.h’ is now an integer (rather than a string) and hence usable as e.g. #if R_SVN_REVISION < 70000.

  • The entry points rgb2hsv and hsv2rgb have been migrated to package grDevices and so are no longer available.

  • R_GE_version has been increased to 10 and name2col removed (use R_GE_str2col instead). R internal colour codes are now defined using the typedef rcolor.

  • The REPROTECT macro now checks that the protect index is valid.

  • Several non-API entry points no longer used by R have been removed, including the Fortran entry points chol, chol2inv, cg, ch and rg, and the C entry points Brent_fmin, fft_factor and fft_work.

  • If a .External call is registered with a number of arguments (other than -1), the number of arguments passed is checked for each call (as for other foreign function calls).

  • It is now possible to write custom connection implementations outside core R using ‘R_ext/Connections.h’. Please note that the implementation of connections is still considered internal and may change in the future (see the above file for details).

INTERNATIONALIZATION

  • The management of translations has been converted to R code: see ?tools::update_pkg_po.

  • The translations for the R interpreter and RGui.exe are now part of the base package (rather than having sources in directory ‘po’ and being installed to ‘share/locale’). Thus the base package supports three translation domains, R-base, R and RGui.

  • The compiled translations which ship with R are all installed to the new package translations for easier updating. The first package of that name found on .libPaths() at the start of the R session will be used. (It is possible messages will be used before .libPaths() is set up in which case the default translations will be used: set environment variable R_TRANSLATIONS to point to the location of the intended translations package to use this right from the start.)

  • The translations form a separate group in the Windows installer, so can be omitted if desired.

  • The markup for many messages has been changed to make them easier to translate, incorporating suggestions from Łukasz Daniel.

INSTALLATION

  • There is again support for building without using the C ‘long double’ type. This is required by C99, but system implementations can be slow or flawed. Use configure option --disable-long-double.

  • make pdf and make install-pdf now make and install the full reference index (including all base and recommended packages).

  • The 'reference manual' on the Windows GUI menu and included in the installer is now the full reference index, including all base and recommended packages.

  • R help pages and manuals have no ISBNs because ISBN rules no longer allow constantly changing content to be assigned an ISBN.

  • The Windows installer no longer installs a Start Menu link to the static help pages; as most pages are generated dynamically, this led to a lot of broken links.

  • Any custom settings for Java configuration are recorded in file ‘etc/javaconf’ for subsequent use by R CMD javareconf.

  • There is now support for makeinfo version 5.0 (which requires a slightly different ‘.texi’ syntax).

  • The minimum versions for --use-system-zlib and --use-system-pcre are now tested as 1.2.5 and 8.10 respectively.

  • On Windows, the stack size is reduced to 16MB on 32-bit systems: misguided users were launching many threads without controlling the stack size.

  • configure no longer looks for file ‘~/.Rconfig’: ‘~/.R/config’ has long been preferred.

BUG FIXES

  • When R CMD build is run in an encoding other than the one specified in the package's ‘DESCRIPTION’ file it tries harder to expand the authors@R field in the specified encoding. (PR#14958)

  • If R CMD INSTALL is required to expand the authors@R field of the ‘DESCRIPTION’ file, it tries harder to do so in the encoding specified for the package (rather than using ASCII escapes).

  • Fix in package grid for pushing a viewport into a layout cell, where the layout is within a viewport that has zero physical width OR where the layout has zero total relative width (likewise for height). The layout column widths (or row heights) in this case were being calculated with non-finite values. (Reported by Winston Chang.)

  • solve(A, b) for a vector b gave the answer names from colnames(A) for LINPACK = TRUE but not in the default case.

  • La.svd() accepts logical matrices (as documented, and as svd() did).

  • legend() now accepts negative pch values, in the same way points() long has.

  • Parse errors when installing files now correctly display the name of the file containing the bad code.

  • In Windows, tcltk windows were not always properly constructed. (PR#15150)

  • The internal functions implementing parse(), tools::parseLatex() and tools::parse_Rd() were not reentrant, leading to errors in rare circumstances such as a garbage collection triggering a recursive call.

  • Field assignments in reference class objects via $<- were not being checked because the magic incantation to turn methods on for that primitive operator had been inadvertently omitted.

  • setHook(hookname, value, action="replace") set the hook to be the value, rather than a list containing the value as documented. (PR#15167)

  • If a package used a ‘NEWS.Rd’ file, the main HTML package index page did not link to it. (Reported by Dirk Eddelbuettel.)

  • The primitive implementation of @<- was not checking the class of the replacement. It now does a check, quicker but less general than slot<-. See the help.

  • split(x, f) now recycles classed objects x in the same way as vectors. (Reported by Martin Morgan.)

  • pbeta(.28, 1/2, 2200, lower.tail=FALSE, log.p=TRUE) is no longer -Inf; ditto for corresponding pt() and pf() calls, such as pt(45, df=5000, lower.tail=FALSE, log.p=TRUE). (PR#15162)

  • The Windows graphics device would crash R if a user attempted to load the graphics history from a variable that was not a saved history. (PR#15230)

  • The workspace size for the predict() method for loess() could exceed the maximum integer size. (Reported by Hiroyuki Kawakatsu.)

  • ftable(x, row.vars, col.vars) now also works when the *.vars arguments are (integer or character vectors) of length zero.

  • Calling cat() on a malformed UTF-8 string could cause the Windows GUI to lock up. (PR#15227)

  • removeClass(cc) gave "node stack overflow" for some class definitions containing "array" or "matrix".