http://blog.gmane.org/gmane.comp.lang.r.announce hourly 1 1901-01-01T00:00+00:00 http://gmane.org/img/gmane-25t.png http://gmane.org http://comments.gmane.org/gmane.comp.lang.r.announce/127 <pre>DEADLINE FAST APPROACHING – 8th Annual International R User Conference useR! 2012, Nashville, Tennessee USA Registration Deadlines: Early Registration: Passed Regular Registration: Mar 1- May 12 Late Registration: May 13 – June 4 On-Site Registration: June 12 – June 15 Please note: Nashville is offering several large entertainment events the month of June, and hotels are quickly selling out. It's imperative that you make your hotel accommodations for the conference as soon as possible. Please join us at the 8th Annual International R User Conference useR! 2012 in Nashville, Tennessee. A draft program schedule, and other conference details are available. Please visit http://biostat.mc.vanderbilt.edu/UseR-2012 </pre> Frank Harrell 2012-05-02T13:12:31 http://comments.gmane.org/gmane.comp.lang.r.announce/126 <pre>The build system rolled up R-2.15.0.tar.gz (codename "Easter Beagle") at 9:00 this morning. This is the first release of the 2.15 series and contains several new features and changes; see the list below for details. You can get the source code from http://cran.r-project.org/src/base/R-2/R-2.15.0.tar.gz or wait for it to be mirrored at a CRAN site nearer to you. Binaries for various platforms will appear in due course. For the R Core Team Peter Dalgaard These are the md5sums for the freshly created files, in case you wish to check that they are uncorrupted: MD5 (AUTHORS) = cbf6da8f886ccd8d0dda0cc7ffd1b8ec MD5 (COPYING) = eb723b61539feef013de476e68b5c50a MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343 MD5 (FAQ) = c6cf7cff235e9bd3c823e6a1a3d76cd5 MD5 (INSTALL) = 37adac6d0fbadf25b5a40e3f7535415e MD5 (NEWS) = 31dee994d35636656c9e254bfb819d7c MD5 (NEWS.html) = 0551e23b675fa9dc709830d1a4ee738c MD5 (ONEWS) = 0c3e10eef74439786e5fceddd06dac71 MD5 (OONEWS) = b0d650eba25fc5664980528c147a20db MD5 (R-latest.tar.gz) = 905f638990492618559202cc1e48a867 MD5 (README) = 296871fcf14f49787910c57b92655c76 MD5 (RESOURCES) = a7a02d98a407c3cb8674d067608f14fc MD5 (THANKS) = 159efc7bd4ae7b23dda07c1d431657bc MD5 (R-2/R-2.15.0.tar.gz) = 905f638990492618559202cc1e48a867 This is the relevant part of the NEWS file CHANGES IN R VERSION 2.15.0: SIGNIFICANT USER-VISIBLE CHANGES: o The behaviour of unlink(recursive = TRUE) for a symbolic link to a directory has changed: it now removes the link rather than the directory contents (just as rm -r does). On Windows it no longer follows reparse points (including junctions and symbolic links). NEW FEATURES: o Environment variable RD2DVI_INPUTENC has been renamed to RD2PDF_INPUTENC. o .Deprecated() becomes a bit more flexible, getting an old argument. o Even data-only packages without R code need a namespace and so may need to be installed under R 2.14.0 or later. o assignInNamespace() has further restrictions on use apart from at top-level, as its help page has warned. Expect it to be disabled from programmatic use in the future. o system() and system2() when capturing output report a non-zero status in the new "status" attribute. o kronecker() now has an S4 generic in package methods on which packages can set methods. It will be invoked by X %x% Y if either X or Y is an S4 object. o pdf() accepts forms like file = "|lpr" in the same way as postscript(). o pdf() accepts file = NULL. This means that the device does NOT create a PDF file (but it can still be queried, e.g., for font metric info). o format() (and hence print()) on "bibentry" objects now uses options("width") to set the output width. o legend() gains a text.font argument. (Suggested by Tim Paine, PR#14719.) o nchar() and nzchar() no longer accept factors (as integer vectors). (Wish of PR#6899.) o summary() behaves slightly differently (or more precisely, its print() method does). For numeric inputs, the number of NAs is printed as an integer and not a real. For dates and datetimes, the number of NAs is included in the printed output (the latter being the wish of PR#14720). The "data.frame" method is more consistent with the default method: in particular it now applies zapsmall() to numeric/complex summaries. o The number of items retained with options(warn = 0) can be set by options(nwarnings=). o There is a new function assignInMyNamespace() which uses the namespace of the function it is called from. o attach() allows the default name for an attached file to be overridden. o bxp(), the work horse of boxplot(), now uses a more sensible default xlim in the case where at is specified differently from 1:n, see the discussion on R-devel, &lt;URL: https://stat.ethz.ch/pipermail/r-devel/2011-November/062586.html&gt;. o New function paste0(), an efficient version of paste(*, sep=""), to be used in many places for more concise (and slightly more efficient) code. o Function setClass() in package methods now returns, invisibly, a generator function for the new class, slightly preferred to calling new(), as explained on the setClass help page. o The "dendrogram" method of str() now takes its default for last.str from option str.dendrogram.last. o New simple fitted() method for "kmeans" objects. o The traceback() function can now be called with an integer argument, to display a current stack trace. (Wish of PR#14770.) o setGeneric() calls can be simplified when creating a new generic function by supplying the default method as the def argument. See ?setGeneric. o serialize() has a new option xdr = FALSE which will use the native byte-order for binary serializations. In scenarios where only little-endian machines are involved (these days, close to universal) and (un)serialization takes an appreciable amount of time this may speed up noticeably transferring data between systems. o The internal (un)serialization code is faster for long vectors, particularly with XDR on some platforms. (Based on a suggested patch by Michael Spiegel.) o For consistency, circles with zero radius are omitted by points() and grid.circle(). Previously this was device-dependent, but they were usually invisible. o NROW(x) and NCOL(x) now work whenever dim(x) looks appropriate, e.g., also for more generalized matrices. o PCRE has been updated to version 8.30. o The internal R_Srcref variable is now updated before the browser stops on entering a function. (Suggestion of PR#14818.) o There are 'bare-bones' functions .colSums(), .rowSums(), .colMeans() and .rowMeans() for use in programming where ultimate speed is required. o The formerly internal function .package_dependencies() from package tools for calculating (recursive) (reverse) dependencies on package databases has been renamed to package_dependencies() and is now exported. o There is a new function optimHess() to compute the (approximate) Hessian for an optim() solution if hessian = TRUE was forgotten. o .filled.contour() is a 'bare-bones' function to add a filled-contour rectangular plot to an already prepared plot region. o The stepping in debugging and single-step browsing modes has changed slightly: now left braces at the start of the body are stepped over for if statements as well as for for and while statements. (Wish of PR#14814.) o library() no longer warns about a conflict with a function from package:base if the function has the same code as the base one but with a different environment. (An example is Matrix::det().) o When deparsing very large language objects, as.character() now inserts newlines after each line of approximately 500 bytes, rather than truncating to the first line. o New function rWishart() generates Wishart-distributed random matrices. o Packages may now specify actions to be taken when the package is loaded (setLoadActions()). o options(max.print = Inf) and similar now give an error (instead of warnings later). o The "difftime" replacement method of units tries harder to preserve other attributes of the argument. (Wish of PR#14839.) o poly(raw = TRUE) no longer requires more unique points than the degree. (Requested by John Fox.) PACKAGE parallel: o There is a new function mcmapply(), a parallel version of mapply(), and a wrapper mcMap(), a parallel version of Map(). o A default cluster can be registered by the new function setDefaultCluster(): this will be used by default in functions such as parLapply(). o clusterMap() has a new argument .scheduling to allow the use of load-balancing. o There are new load-balancing functions parLapplyLB() and parSapplyLB(). o makePSOCKCluster() has a new option useXDR = FALSE which can be used to avoid byte-shuffling for serialization when all the nodes are known to be little-endian (or all big-endian). PACKAGE INSTALLATION: o Non-ASCII vignettes without a declared encoding are no longer accepted. o C/C++ code in packages is now compiled with -NDEBUG to mitigate against the C/C++ function assert being called in production use. Developers can turn this off during package development with PKG_CPPFLAGS = -UNDEBUG. o R CMD INSTALL has a new option --dsym which on Mac OS X (Darwin) dumps the symbols alongside the .so file: this is helpful when debugging with valgrind (and especially when installing packages into R.framework). [This can also be enabled by setting the undocumented environment variable PKG_MAKE_DSYM, since R 2.12.0.] o R CMD INSTALL will test loading under all installed sub-architectures even for packages without compiled code, unless the flag --no-multiarch is used. (Pure R packages can do things which are architecture-dependent: in the case which prompted this, looking for an icon in a Windows R executable.) o There is a new option install.packages(type = "both") which tries source packages if binary packages are not available, on those platforms where the latter is the default. o The meaning of install.packages(dependencies = TRUE) has changed: it now means to install the essential dependencies of the named packages plus the Suggests, but only the essential dependencies of dependencies. To get the previous behaviour, specify dependencies as a character vector. o R CMD INSTALL --merge-multiarch is now supported on OS X and other Unix-alikes using multiple sub-architectures. o R CMD INSTALL --libs-only now by default does a test load on Unix-alikes as well as on Windows: suppress with --no-test-load. UTILITIES: o R CMD check now gives a warning rather than a note if it finds inefficiently compressed datasets. With bzip2 and xz compression having been available since R 2.10.0, it only exceptionally makes sense to not use them. The environment variable _R_CHECK_COMPACT_DATA2_ is no longer consulted: the check is always done if _R_CHECK_COMPACT_DATA_ has a true value (its default). o Where multiple sub-architectures are to be tested, R CMD check now runs the examples and tests for all the sub-architectures even if one fails. o R CMD check can optionally report timings on various parts of the check: this is controlled by environment variable _R_CHECK_TIMINGS_ documented in 'Writing R Extensions'. Timings (in the style of R CMD BATCH) are given at the foot of the output files from running each test and the R code in each vignette. o There are new options for more rigorous testing by R CMD check selected by environment variables - see the 'Writing R Extensions' manual. o R CMD check now warns (rather than notes) on undeclared use of other packages in examples and tests: increasingly people are using the metadata in the DESCRIPTION file to compute information about packages, for example reverse dependencies. o The defaults for some of the options in R CMD check (described in the 'R Internals' manual) have changed: checks for unsafe and .Internal() calls and for partial matching of arguments in R function calls are now done by default. o R CMD check has more comprehensive facilities for checking compiled code and so gives fewer reports on entry points linked into .so/.dll files from libraries (including C++ and Fortran runtimes). Checking compiled code is now done on FreeBSD (as well as the existing supported platforms of Linux, Mac OS X, Solaris and Windows). o R CMD build has more options for --compact-vignettes: see R CMD build --help. o R CMD build has a new option --md5 to add an MD5 file (as done by CRAN): this is used by R CMD INSTALL to check the integrity of the distribution. If this option is not specified, any existing (and probably stale) MD5 file is removed. DEPRECATED AND DEFUNCT: o R CMD Rd2dvi is now defunct: use R CMD Rd2pdf. o Options such --max-nsize, --max-vsize and the function mem.limits() are now defunct. (Options --min-nsize and --min-vsize remain available.) o Use of library.dynam() without specifying all the first three arguments is now disallowed. Use of an argument chname in library.dynam() including the extension .so or .dll (which was never allowed according to the help page) is defunct. This also applies to library.dynam.unload() and to useDynLib directives in NAMESPACE files. o The internal functions .readRDS() and .saveRDS() are now defunct. o The off-line help() types "postscript" and "ps" are defunct. o Sys.putenv(), replaced and deprecated in R 2.5.0, is finally removed. o Some functions/objects which have been defunct for five or more years have been removed completely. These include .Alias(), La.chol(), La.chol2inv(), La.eigen(), Machine(), Platform(), Version, codes(), delay(), format.char(), getenv(), httpclient(), loadURL(), machine(), parse.dcf(), printNoClass(), provide(), read.table.url(), restart(), scan.url(), symbol.C(), symbol.For() and unix(). o The ENCODING argument to .C() is deprecated. It was intended to smooth the transition to multi-byte character strings, but can be replaced by the use of iconv() in the rare cases where it is still needed. INSTALLATION: o Building with a positive value of --with-valgrind-instrumentation now also instruments logical, complex and raw vectors. o There is experimental support for _link-time optimization_ with gcc 4.5.0 or later on platforms which support it. C-LEVEL FACILITIES: o Passing R objects other than atomic vectors, functions, lists and environments to .C() is now deprecated and will give a warning. Most cases (especially NULL) are actually coding errors. NULL will be disallowed in future. .C() now passes a pairlist as a SEXP to the compiled code. This is as was documented, but pairlists were in reality handled differently as a legacy from the early days of R. o call_R and call_S are deprecated. They still exist in the headers and as entry points, but are no longer documented and should not be used for new code. BUG FIXES: o str(x, width) now obeys its width argument also for function headers and other objects x where deparse() is applied. o The convention for x %/% 0L for integer-mode x has been changed from 0L to NA_integer_. (PR#14754) o The exportMethods directive in a NAMESPACE file now exports S4 generics as necessary, as the extensions manual said it does. The manual has also been updated to be a little more informative on this point. It is now required that there is an S4 generic (imported or created in the package) when methods are to be exported. o Reference methods cannot safely use non-exported entries in the namespace. We now do not do so, and warn in the documentation. o The namespace import code was warning when identical S4 generic functions were imported more than once, but should not (reported by Brian Ripley, then Martin Morgan). o merge() is no longer allowed (in some ways) to create a data frame with duplicate column names (which confused PR#14786). o Fixes for rendering raster images on X11 and Windows devices when the x-axis or y-axis scale is reversed. o getAnywhere() found S3 methods as seen from the utils namespace and not from the environment from which it was called. o selectMethod(f, sig) would not return inherited group methods when caching was off (as it is by default). o dev.copy2pdf(out.type = "cairo") gave an error. (PR#14827) o Virtual classes (e.g., class unions) had a NULL prototype even if that was not a legal subclass. See ?setClassUnion. o The C prototypes for zdotc and zdotu in R_ext/BLAS.h have been changed to the more modern style rather than that used by f2c. (Patch by Berwin Turlach.) o isGeneric() produced an error for primitives that can not have methods. o .C() or .Fortran() had a lack-of-protection error if the registration information resulted in an argument being coerced to another type. o boxplot(x=x, at=at) with non finite elements in x and non integer at could not generate a warning but failed. o heatmap(x, symm=TRUE, RowSideColors=*) no longer draws the colors in reversed order. o predict(&lt;ar&gt;) was incorrect in the multivariate case, for p &gt;= 2. o print(x, max=m) is now consistent when x is a "Date"; also the "reached ... max.print .." messages are now consistently using single brackets. o Closed the &lt;li&gt; tag in pages generated by Rd2HTML(). (PR#14841.) o Axis tick marks could go out of range when a log scale was used. (PR#14833.) o Signature objects in methods were not allocated as S4 objects (caused a problem with trace() reported by Martin Morgan). -- Peter Dalgaard, Professor Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd.mes&lt; at &gt;cbs.dk Priv: PDalgd&lt; at &gt;gmail.com </pre> Peter Dalgaard 2012-03-30T09:07:41 http://comments.gmane.org/gmane.comp.lang.r.announce/125 <pre>The build system rolled up R-2.14.2.tar.gz (codename "Gift-Getting Season") at 9:00 this morning. This is intended to be the final round-up release of the 2.14 series; see the list below for details. (The codename is still not part of the actual sources. That feature will have to wait for 2.15.0, "Easter Beagle"). This release also marks the 3rd anniversary of R-1.0.0. You can get the source code from http://cran.r-project.org/src/base/R-2/R-2.14.2.tar.gz or wait for it to be mirrored at a CRAN site nearer to you. Binaries for various platforms will appear in due course. For the R Core Team Peter Dalgaard These are the md5sums for the freshly created files, in case you wish to check that they are uncorrupted: MD5 (AUTHORS) = cbf6da8f886ccd8d0dda0cc7ffd1b8ec MD5 (COPYING) = eb723b61539feef013de476e68b5c50a MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343 MD5 (FAQ) = 748eae477f4c3c8d1f16cc82d9035d18 MD5 (INSTALL) = 70447ae7f2c35233d3065b004aa4f331 MD5 (NEWS) = 7fc0a51c884e59daae6ea82d7c36af85 MD5 (NEWS.html) = 2fa78a01a352723ab3cc8e9796fb5c19 MD5 (ONEWS) = 0c3e10eef74439786e5fceddd06dac71 MD5 (OONEWS) = b0d650eba25fc5664980528c147a20db MD5 (R-latest.tar.gz) = f5c8657543a293a80d025be58cf1ef71 MD5 (README) = 296871fcf14f49787910c57b92655c76 MD5 (RESOURCES) = 020479f381d5f9038dcb18708997f5da MD5 (THANKS) = 159efc7bd4ae7b23dda07c1d431657bc MD5 (R-2/R-2.14.2.tar.gz) = f5c8657543a293a80d025be58cf1ef71 This is the relevant part of the NEWS file CHANGES IN R VERSION 2.14.2: NEW FEATURES: o The internal untar() (as used by default by R CMD INSTALL) now knows about some pax headers which bsdtar (e.g., the default tar for Mac OS &gt;= 10.6) can incorrectly include in tar files, and will skip them with a warning. o PCRE has been upgraded to version 8.21: as well as bug fixes and greater Perl compatibility, this adds a JIT pattern compiler, about which PCRE's news says 'large performance benefits can be had in many situations'. This is supported on most but not all R platforms. o Function compactPDF() in package tools now takes the default for argument gs_quality from environment variable GS_QUALITY: there is a new value "none", the ultimate default, which prevents GhostScript being used in preference to qpdf just because environment variable R_GSCMD is set. If R_GSCMD is unset or set to "", the function will try to find a suitable GhostScript executable. o The included version of zlib has been updated to 1.2.6. o For consistency with the logLik() method, nobs() for "nls" files now excludes observations with zero weight. (Reported by Berwin Turlach.) UTILITIES: o R CMD check now reports by default on licenses not according to the description in 'Writing R Extensions'. o R CMD check has a new option --as-cran to turn on most of the customizations that CRAN uses for its incoming checks. PACKAGE INSTALLATION: o R CMD INSTALL will now no longer install certain file types from inst/doc: these are almost certainly mistakes and for some packages are wasting a lot of space. These are Makefile, files generated by running LaTeX, and unless the package uses a vignettes directory, PostScript and image bitmap files. Note that only PDF vignettes have ever been supported: some of these files come from DVI/PS output from the Sweave defaults prior to R 2.13.0. BUG FIXES: o R configured with --disable-openmp would mistakenly set HAVE_OPENMP (internal) and SUPPORT_OPENMP (in Rconfig.h) even though no OpenMP flags were populated. o The getS3method() implementation had an old computation to find an S4 default method. o readLines() could overflow a buffer if the last line of the file was not terminated. (PR#14766) o R CMD check could miss undocumented S4 objects in packages which used S4 classes but did not Depends: methods in their DESCRIPTION file. o The HTML Help Search page had malformed links. (PR#14769) o A couple of instances of lack of protection of SEXPs have been squashed. (PR#14772, PR#14773) o image(x, useRaster=TRUE) misbehaved on single-column x. (PR#14774) o Negative values for options("max.print") or the max argument to print.default() caused crashes. Now the former are ignored and the latter trigger an error. (PR#14779) o The text of a function body containing more than 4096 bytes was not properly saved by the parser when entered at the console. o Forgetting the #endif tag in an Rd file could cause the parser to go into a loop. (Reported by Hans-Jorg Bibiko.) o str(*, ....., strict.width="cut") now also obeys list.len = n. (Reported by S"oren Vogel.) o Printing of arrays did not have enough protection (C level), e.g., in the context of capture.output(). (Reported by Herv'e Pag`es and Martin Morgan.) o pdf(file = NULL) would produce a spurious file named NA. (PR#14808) o list2env() did not check the type of its envir argument. (PR#14807) o svg() could segfault if called with a non-existent file path. (PR#14790) o make install can install to a path containing + characters. (PR#14798) o The edit() function did not respect the options("keep.source") setting. (Reported by Cleridy Lennert.) o predict.lm(*, type="terms", terms=*, se.fit=TRUE) did not work. (PR#14817) o There is a partial workaround for errors in the TRE regular-expressions engine with named classes and repeat counts of at least 2 in a MBCS locale (PR#14408): these are avoided when TRE is in 8-bit mode (e.g. for useBytes = TRUE and when all the data are ASCII). o The C function R_ReplDLLdo1() did not call top-level handlers. o The Quartz device was unable to detect window sessions on Mac OS X 10.7 (Lion) and higher and thus it was not used as the default device on the console. Since Lion any application can use window sessions, so Quartz will now be the default device if the user's window session is active and R is not run via ssh which is at least close to the behavior in prior OS X versions. o mclapply() would fail in code assembling the translated error message if some (but not all) cores encountered an error. o format.POSIXlt(x) raised an arithmetic exception when x was an invalid object of class "POSIXlt" and parts were empty. o installed.packages() has some more protection against package installs going on in parallel. o .Primitive() could be mis-used to call .Internal() entry points. -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd.mes&lt; at &gt;cbs.dk Priv: PDalgd&lt; at &gt;gmail.com </pre> Peter Dalgaard 2012-02-29T14:40:36 http://comments.gmane.org/gmane.comp.lang.r.announce/124 <pre>It is the intention of the R Core Team to release the finalized version of the 2.14.x series at the end of February, and soon thereafter to start the run-in for 2.15.0. I.e., 2.14.2 "Gift-Getting Season" on Feb 29 (3rd anniversary of R-1.0.0!) 2.15.0 "Easter Beagle" on Mar 30 (We'll see about getting the nicknames into the actual sources this time.) Further details to follow. </pre> Peter Dalgaard 2012-02-13T09:12:38 http://comments.gmane.org/gmane.comp.lang.r.announce/123 <pre>The byte pixies have rolled up R-2.14.1.tar.gz (codename "December Snowflakes") at 9:00 this morning. This is a maintenance release; see the list below for details. You can get it from http://cran.r-project.org/src/base/R-2/R-2.14.1.tar.gz or wait for it to be mirrored at a CRAN site nearer to you. Binaries for various platforms will appear in due course. For the R Core Team Peter Dalgaard These are the md5sums for the freshly created files, in case you wish to check that they are uncorrupted: MD5 (AUTHORS) = cbf6da8f886ccd8d0dda0cc7ffd1b8ec MD5 (COPYING) = eb723b61539feef013de476e68b5c50a MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343 MD5 (FAQ) = 3a8fc6d4f7ae7c6f7e42b028240a46b0 MD5 (INSTALL) = 70447ae7f2c35233d3065b004aa4f331 MD5 (NEWS) = 99d2842cf6a964716e960fadead402c4 MD5 (NEWS.html) = 592a459fecefd8bb4573ba45ea9d3f36 MD5 (ONEWS) = 0c3e10eef74439786e5fceddd06dac71 MD5 (OONEWS) = b0d650eba25fc5664980528c147a20db MD5 (R-latest.tar.gz) = ba5b6fb15b660670ea29b885348f322a MD5 (README) = 296871fcf14f49787910c57b92655c76 MD5 (RESOURCES) = 020479f381d5f9038dcb18708997f5da MD5 (THANKS) = 159efc7bd4ae7b23dda07c1d431657bc MD5 (R-2/R-2.14.1.tar.gz) = ba5b6fb15b660670ea29b885348f322a This is the relevant part of the NEWS file (yes, I _have_ spotted the minor mishap....): CHANGES IN R VERSION 2.14.0 patched: NEW FEATURES: o parallel::detectCores() is now able to find the number of physical cores (rather than CPUs) on Sparc Solaris. It can also do so on most versions of Windows; however the default remains detectCores(logical = TRUE) on that platform. o Reference classes now keep a record of which fields are locked. $lock() with no arguments returns the names of the locked fields. o HoltWinters() reports a warning rather than an error for some optimization failures (where the answer might be a reasonable one). o tools::dependsOnPkg() now accepts the shorthand dependencies = "all". o parallel::clusterExport() now allows specification of an environment from which to export. o The quartz() device now does tilde expansion on its file argument. o tempfile() on a Unix-alike now takes the process ID into account. This is needed with multicore (and as part of parallel) because the parent and all the children share a session temporary directory, and they can share the C random number stream used to produce the uniaue part. Further, two children can call tempfile() simultaneously. o Option print in Sweave's RweaveLatex() driver now emulates auto-printing rather than printing (which can differ for an S4 object by calling show() rather than print()). o filled.contour() now accepts infinite values: previously it might have generated invalid graphics files (e.g. containing NaN values). INSTALLATION: o On 64-bit Linux systems, configure now only sets LIBnn to lib64 if /usr/lib64 exists. This may obviate setting LIBnn explicitly on Debian-derived systems. It is still necessary to set LIBnn = lib (or lib32) for 32-bit builds of R on a 64-bit OS on those Linux distributions capable for supporting that concept. o configure looks for inconsolata.sty, and if not found adjusts the default R_RD4PDF to not use it (with a warning, since it is needed for high-quality rendering of manuals). PACKAGE INSTALLATION: o R CMD INSTALL will now do a test load for all sub-architectures for which code was compiled (rather than just the primary sub-architecture). UTILITIES: o When checking examples under more than one sub-architecture, R CMD check now uses a separate directory examples_arch for each sub-architecture, and leaves the output in file pkgname-Ex_arch.Rout. Some packages expect their examples to be run in a clean directory .... BUG FIXES: o stack() now gives an error if no vector column is selected, rather than returning a 1-column data frame (contrary to its documentation). o summary.mlm() did not handle objects where the formula had been specified by an expression. (Reported by Helios de Rosario Martinez). o tools::deparseLatex(dropBraces=TRUE) could drop text as well as braces. o colormodel = "grey" (new in R 2.14.0)) did not always work in postscript() and pdf(). o file.append() could return TRUE for failures. (PR#14727) o gzcon() connections are no longer subject to garbage collection: it was possible for this to happen when unintended (e.g. when calling load()). o nobs() does not count zero-weight observations for glm() fits, for consistency with lm(). This affects the BIC() values reported for such glm() fits. (Spotted by Bill Dunlap.) o options(warn = 0) failed to end a (C-level) context with more than 50 accumulated warnings. (Spotted by Jeffery Horner.) o The internal plot.default() code did not do sanity checks on a cex argument, so invalid input could cause problems. (Reported by Ben Bolker.) o anyDuplicated(&lt;array&gt;, MARGIN=0) no longer fails. (Reported by Herv'e Pag`es.) o read.dcf() removes trailing blanks: unfortunately on some platforms this included \xa0 (non-breaking space) which is the trailing byte of a UTF-8 character. It now only considers ASCII space and tab to be 'blank'. o There was a sign error in part of the calculations for the variance returned by KalmanSmooth(). (PR#14738) o pbinom(10, 1e6, 0.01, log.p = TRUE) was NaN thanks to the buggy fix to PR#14320 in R 2.11.0. (PR#14739) o RweaveLatex() now emulates auto-printing rather than printing, by calling methods::show() when auto-printing would. o duplicated() ignored fromLast for a one-column data frame. (PR#14742) o source() and related functions did not put the correct timestamp on the source references; srcfilecopy() has gained a new argument timestamp to support this fix. (PR#14750) o LaTeX conversion of Rd files did not correctly handle preformatted backslashes. (PR#14751) o HTML conversion of Rd files did not handle markup within tabular cells properly. (PR#14708) o source() on an empty file with keep.source = TRUE tried to read from stdin(), in R 2.14.0 only. (PR#14753) o The code to check Rd files in packages would abort if duplicate description sections were present. -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd.mes&lt; at &gt;cbs.dk Priv: PDalgd&lt; at &gt;gmail.com </pre> Peter Dalgaard 2011-12-22T11:02:34 http://comments.gmane.org/gmane.comp.lang.r.announce/122 <pre>Dear All, The second issue of the third volume of The R Journal is now available: http://journal.r-project.org/current.html. Thanks to everyone involved. Heather -- Editor in chief Heather.Turner&lt; at &gt;r-project.org </pre> Heather Turner 2011-12-18T22:15:48 http://comments.gmane.org/gmane.comp.lang.r.announce/121 <pre>This is to announce that we plan to release R version 2.14.1 on Friday, December 22, 2011. Those directly involved should review the generic schedule at http://developer.r-project.org/release-checklist.html The source tarballs will be made available daily (barring build troubles) via http://cran.r-project.org/src/base-prerelease/ For the R Core Team Peter Dalgaard </pre> Peter Dalgaard 2011-12-08T14:30:26 http://comments.gmane.org/gmane.comp.lang.r.announce/120 <pre>To all Windows users: The binary build of 2.14.0 that was uploaded yesterday was missing Cairo support. I have rebuilt it, and uploaded a new copy. You can tell which one you have by running "svg()", which works on the new one, but not the old one. You can tell which one is on your CRAN mirror by looking at the last changed date: it is today (November 1) for the corrected build. Sorry for the inconvenience.... Duncan Murdoch </pre> Duncan Murdoch 2011-11-01T20:03:48 http://comments.gmane.org/gmane.comp.lang.r.announce/119 <pre>The byte pixies have rolled up R-2.14.0.tar.gz (codename "Great Pumpkin") at 9:00 this morning. This is a development release with several new features; see the list below for details. You can get it from http://cran.r-project.org/src/base/R-2/R-2.14.0.tar.gz or wait for it to be mirrored at a CRAN site nearer to you. Binaries for various platforms will appear in due course. For the R Core Team Peter Dalgaard These are the md5sums for the freshly created files, in case you wish to check that they are uncorrupted: MD5 (AUTHORS) = cbf6da8f886ccd8d0dda0cc7ffd1b8ec MD5 (COPYING) = eb723b61539feef013de476e68b5c50a MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343 MD5 (FAQ) = 7d14b4be550f30d8a73a830ab272e4f4 MD5 (INSTALL) = 70447ae7f2c35233d3065b004aa4f331 MD5 (NEWS) = 98ef8b3497d12fd43b56d3732c34f9cc MD5 (NEWS.html) = 3ec485820148d22864b9b7990347bf2c MD5 (ONEWS) = 0c3e10eef74439786e5fceddd06dac71 MD5 (OONEWS) = b0d650eba25fc5664980528c147a20db MD5 (R-latest.tar.gz) = 98cf8fe74e512e1061caf1ee0c2043a8 MD5 (README) = 296871fcf14f49787910c57b92655c76 MD5 (RESOURCES) = 020479f381d5f9038dcb18708997f5da MD5 (THANKS) = 159efc7bd4ae7b23dda07c1d431657bc MD5 (R-2/R-2.14.0.tar.gz) = 98cf8fe74e512e1061caf1ee0c2043a8 This is the relevant part of the NEWS file: CHANGES IN R VERSION 2.14.0: SIGNIFICANT USER-VISIBLE CHANGES: o All packages must have a namespace, and one is created on installation if not supplied in the sources. This means that any package without a namespace must be re-installed under this version of R (but previously-installed data-only packages without R code can still be used). o The yLineBias of the X11() and windows() families of devices has been changed from 0.1 to 0.2: this changes slightly the vertical positioning of text in the margins (including axis annotations). This is mainly for consistency with other devices such as quartz() and pdf(). (Wish of PR#14538.) There is a new graphics parameter "ylbias" which allows the y-line bias of the graphics device to be tweaked, including to reproduce output from earlier versions of R. o Labeling of the p-values in various anova tables has been rationalized to be either "Pr(&gt;F)" or "Pr(&gt;Chi)" (i.e. the "Pr(F)", "Pr(Chi)" and "P(&gt;|Chi|)" variants have been eliminated). Code which extracts the p value _via_ indexing by name may need adjustment. o :: can now be used for datasets made available for lazy-loading in packages with namespaces (which makes it consistent with its use for data-only packages without namespaces in earlier versions of R). o There is a new package parallel. It incorporates (slightly revised) copies of packages multicore and snow (excluding MPI, PVM and NWS clusters). Code written to use the higher-level API functions in those packages should work unchanged (apart from changing any references to their namespaces to a reference to parallel, and links explicitly to multicore or snow on help pages). It also contains support for multiple RNG streams following L'Ecuyer _et al_ (2002), with support for both mclapply and snow clusters. This replaces functions like clusterSetupRNG() from snow (which are not in parallel). The version released for R 2.14.0 contains base functionality: higher-level convenience functions are planned (and some are already available in the 'R-devel' version of R). o Building PDF manuals (for R itself or packages, e.g. _via_ R CMD check) by default requires the LaTeX package inconsolata: see the section on 'Making the manuals' in the 'R Installation and Administration Manual'. o axTicks(*, log=TRUE) has changed in some cases to satisfy the documented behavior and be consistent. NEW FEATURES: o txtProgressBar() can write to an open connection instead of the console. o Non-portable package names ending in . are no longer allowed. Nor are single-character package names (R was already disallowed). o regexpr() and gregexpr() with perl = TRUE allows Python-style named captures. (Wish and contribution of PR#14518.) o The placement of 'plotmath' text in the margins of plots done by base graphics now makes the same vertical adjustment as ordinary text, so using ordinary and plotmath text on the same margin line will seem better aligned (but not exactly aligned, since ordinary text has descenders below the baseline and plotmath places them on the baseline). (Related to PR#14537.) o sunflowerplot() now has a formula interface. (Wish of PR#14541.) o iconv() has a new argument toRaw to handle encodings such as UTF-16 with embedded nuls (as was possible before the CHARSXP cache was introduced). It will also accept as input the type of list generated with toRaw = TRUE. o Garbage-collecting an unused input text connection no longer gives a warning (since it 'connects' to nothing outside R). o read.table() and scan() have gained a text argument, to allow reading data from a (possibly literal) character string. o optim(*, method = .) now allows method = "Brent" as an interface to optimize(), for use in cases such as mle() where optim() is used internally. o mosaicplot() gains a border argument. (Wish of PR#14550.) o smooth.spline() gains a tol argument which controls how different x values need to be to be treated as distinct. The default has been changed to be more reliable for inputs whose range is small compared to their maximum absolute value. (Wish of PR#14452.) o gl() runs faster by avoiding calling factor(). o The print() method for object.size() accepts B as well as b as an abbreviation for 'bytes'. o unlink() gains a force argument to work like rm -f and if possible override restrictive permissions. o pbirthday() and qbirthday() now use exact calculations for coincident = 2. o unzip() and unz() connections have been updated with support for more recent Zip64 features (including large file sizes and bzip2 compression, but not UTF-8 file names). unzip() has a new option to restore file times from those recorded (in an unknown timezone) in the zip file. o update.packages() now accepts a character vector of package names for the oldPkgs argument. (Suggestion of Tal Galili.) o The special reference class fields .self and .refClassDef are now read-only to prevent corrupting the object. o decompose() now returns the original series as part of its value, so it can be used (rather than reconstructed) when plotting. (Suggestion of Rob Hyndman.) o Rao's efficient score test has been implemented for glm objects. Specifically, the add1, drop1, and anova methods now allow test = "Rao". o If a saved workspace (e.g. .RData) contains objects that cannot be loaded, R will now start with an warning message and an empty workspace, rather than failing to start. o strptime() now accepts times such as 24:00 for midnight at the end of the day, for although these are disallowed by POSIX 1003.1-2008, ISO 8601:2004 allows them. o Assignment of names() to S4 objects now checks for a corresponding "names" slot, and generates a warning or an error if that slot is not defined. See the section on slots in ?Classes. o The default methods for is.finite(), is.infinite() and is.nan() now signal an error if their argument is not an atomic vector. o The formula method for plot() no longer places package stats on the search path (it loads the namespace instead). o There now is a genuine "function" method for plot() rather than the generic dispatching internally to graphics::plot.function(). It is now exported, so can be called directly as plot.function(). o The one-sided ks.test() allows exact = TRUE to be specified in the presence of ties (but the approximate calculation remains the default: the 'exact' computation makes assumptions known to be invalid in the presence of ties). o The behaviour of curve(add = FALSE) has changed: it now no longer takes the default x limits from the previous plot (if any): rather they default to c(0, 1) just as the "function" method for plot(). To get the previous behaviour use curve(add = NA), which also takes the default for log-scaling of the x-axis from the previous plot. o Both curve() and the plot() method for functions have a new argument xname to facilitate plots such as sin(t) _vs_ t. o The local argument to source() can specify an environment as well as TRUE (parent.env()) and FALSE (.GlobalEnv). It gives better error messages for other values, such as NA. o vcov() gains methods for classes "summary.lm" and "summary.glm". o The plot() method for class "profile.nls" gains ylab and lty arguments, and passes ... on to plot.default. o Character-string arguments such as the mode argument of vector(), as.vector() and is.vector() and the description argument of file() are required to be of length exactly one, rather than any further elements being silently discarded. This helps catch incorrect usage in programming. o The length argument of vector() and its wrappers such as numeric() is required to be of length exactly one (other values are now an error rather than giving a warning as previously). o vector(len) and length(x) &lt;- len no longer acccept TRUE/FALSE for len (not that they were ever documented to, but there was special-casing in the C code). o There is a new function Sys.setFileTime() to set the time of a file (including a directory). See its help for exactly which times it sets on various OSes. o The file times reported by file.info() are reported to sub-second resolution on systems which support it. (Currently the POSIX 2008 and FreeBSD/Darwin/NetBSD methods are detected.) o New function getCall(m) as an abstraction for m$call, enabling update()'s default method to apply more universally. (NB: this can be masked by existing functions in packages.) o Sys.info() gains a euser component to report the 'effective' user on OSes which have that concept. o The result returned by try() now contains the original error condition object as the "condition" attribute. o All packages with R code are lazy-loaded irrespective of the LazyLoad field in the DESCRIPTION file. A warning is given if the LazyLoad field is overridden. o Rd markup has a new \figure tag so that figures can be included in help pages when converted to HTML or LaTeX. There are examples on the help pages for par() and points(). o The built-in httpd server now allows access to files in the session temporary directory tempdir(), addressed as the /session directory on the httpd server. o Development versions of R are no longer referred to by the number under which they might be released, e.g. in the startup banner, R --version and sessionUtils(). The correct way to refer to a development version of R is 'R-devel', preferably with the date and SVN version number. E.g. R-devel (2011-07-04 r56266) o There is a new function texi2pdf() in package tools, currently a convenience wrapper for texi2dvi(pdf = TRUE). o There are two new options for typesetting PDF manuals from Rd files. These are beramono and inconsolata, and used the named font for monospaced output. They are intended to be used in combination with times, and times,inconsolata,hyper is now the default for the reference manual and package manuals. If you do not have that font installed, you can set R_RD4PF to one of the other options: see the 'R Installation and Administration Manual'. o Automatic printing for reference classes is now done by the $show() method. A method is defined for class envRefClass and may be overriden for user classes (see the ?ReferenceClasses example). S4 show() methods should no longer be needed for reference classes. o tools::Rdiff (by default) and R CMD Rdiff now ignore differences in pointer values when comparing printed environments, compiled byte code, etc. o The "source" attribute on functions created with keep.source=TRUE has been replaced with a "srcref" attribute. The "srcref" attribute references an in-memory copy of the source file using the "srcfilecopy" class or the new "srcfilealias" class. o New items User Manuals and Technical Papers have been added to the HTML help main page. These link to vignettes in the base and recommended packages and to a collection of papers about R issues, respectively. o Documentation and messages have been standardized to use "namespace" rather than "name space". o setGeneric() now looks in the default packages for a non-generic version of a function if called from a package with a namespace. (It always did for packages without a namespace.) o Setting the environment variable _R_WARN_ON_LOCKED_BINDINGS_ will give a warning if an attempt is made to change a locked binding. o \SweaveInput is now supported when generating concordances in Sweave(). o findLineNum() and setBreakpoint() now allow the environment to be specified indirectly; the latter gains a clear argument to allow it to call untrace(). o The body of a closure can be one of further types of R objects, including enviroments and external pointers. o The Rd2HTML() function in package tools now has a stylesheet argument, allowing pages to be displayed in alternate formats. o New function requireNamespace() analogous to require(), returning a logical value after attempting to load a namespace. o There is a new type of RNG, "L'Ecuyer-CMRG", implementing L'Ecuyer (1999)'s 'combined multiple-recursive generator' MRG32k3a. See the comments on ?RNG. o help.search() and ?? can now display vignettes and demos as well as help pages. The new option "help.search.types" controls the types of documentation and the order of their display. This also applies to HTML searches, which now give results in all of help pages, vignettes and demos. o socketConnection() now has a timeout argument. It is now documented that large values (package snow used a year) do not work on some OSes. o The initialization of the random-number generator now uses the process ID as well as the current time, just in case two R processes are launched very rapidly on a machine with low-resolution wall clock (some have a resolution of a second; modern systems have microsecond-level resolution). o New function pskill() in the tools package to send a terminate signal to one or more processes, plus constants such as SIGTERM to provide a portable way to refer to signals (since the numeric values are OS-dependent). o New function psnice() in the tools package to return or change the 'niceness' of a process. (Refers to the 'priority class' on Windows.) o list.dirs() gains a recursive argument. o An Authors&lt; at &gt;R field in a package DESCRIPTION file can now be used to generate Author and Maintainer fields if needed, and to auto-generate package citations. o New utility getElement() for accessing either a list component or a slot in an S4 object. o stars() gains a col.lines argument, thanks to Dustin Sallings. (Wish of PR#14657.) o New function regmatches() for extracting or replacing matched or non-matched substrings from match data obtained by regexpr(), gregexpr() and regexec(). o help(package = "pkg_name", help_type = "HTML") now gives HTML help on the package rather than text help. (This gives direct access to the HTML version of the package manual shown _via_ help.start()'s 'Packages' menu.) o agrep() gains a fixed argument to optionally allow approximate regular expression matching, and a costs argument to specify possibly different integer match costs for insertions, deletions and substitutions. o read.dcf() and write.dcf() gain a keep.white argument to indicate fields where whitespace should be kept as is. o available.packages() now works around servers that fail to return an error code when PACKAGES.gz does not exist. (Patch submitted by Seth Schommer.) o readBin() can now read more than 2^31 - 1 bytes in a single call (the previously documented limitation). o New function regexec() for finding the positions of matches as well as all substrings corresponding to parenthesized subexpressions of the given regular expression. o New function adist() in package utils for computing 'edit' (generalized Levenshtein) distances between strings. o Class "raster" gains an is.na method to avoid confusion from the misuse of the matrix method (such as PR#14618). o The identical() function gains an ignore.bytecode argument to control comparison of compiled functions. o pmin and pmax now warn if an argument is partially recycled (wish of PR#14638). o The default for image(useRaster=) is now taken from option "preferRaster": for the small print see ?image. o str() now displays reference class objects and their fields, rather than treating them as classical S4 classes. o New function aregexec() in package utils for finding the positions of approximate string matches as well as all substrings corresponding to parenthesized subexpressions of the given regular expression. o download.file() has an extra argument to pass additional command-line options to the non-default methods using command-line utilities. cacheOK = FALSE is now supported for method = "curl". o interaction.plot(*, type = .) now also allows type "o" or "c". o axTicks(*, log=TRUE) did sometimes give more values than the ticks in the corresponding graphics::axis(). By default, it now makes use of the new (graphics-package independent) axisTicks() which can make use of a new utility .axisPars(). Further, it now returns a decreasing sequence (as for log=FALSE) when usr is decreasing. o Using fix() or edit() on a R object (except perhaps a matrix or data frame) writes its temporary file with extension .R so editors which select their mode based on the extension will select a suitable mode. GRAPHICS DEVICES: o The pdf() device makes use of Flate compression: this is controlled by the new logical argument compress, and is enabled by default. o Devices svg(), cairo_pdf() and cairo_ps() gain a family argument. On a Unix-alike X11() gains a family argument. This is one of the x11.options() and so can be passed as an argument to the bmp(), jpeg(), png() and tiff() devices. Analogous changes have been made on Windows, so all built-in R graphics devices now have a family argument except pictex() (which has no means to change fonts). o The bmp(), jpeg(), png() and tiff() devices now make use of the antialias argument for type = "quartz". o There are several new built-in font mappings for X11(type = "Xlib"): see the help on X11Fonts(). o There is a new type X11(type = "dbcairo") which updates the screeen less frequently: see its help page. o The X11() device now makes use of cursors to distinguish its states. The normal cursor is an arrow (rather than a crosshair); the crosshair is used when the locator is in use, and a watch cursor is shown when plotting computations are being done. (These are the standard names for X11 cursors: how they are actually displayed depends on the window manager.) o New functions dev.hold() and dev.flush() for use with graphics devices with buffering. These are used for most of the high-level graphics functions such as boxplot(), so that the plot is only displayed when the page is complete. Currently implemented for windows(buffered = TRUE), quartz() and the cairographics-based X11() types with buffering (which are the default on-screen devices). o New function dev.capture() for capture of bitmap snapshots of image-based devices (a superset of the functionality provided by grid.cap() in grid). o The default colormodel for pdf() and postscript() is now called "srgb" to more accurately describe it. (Instead of "rgb", and in the case of postscript() it no longer switches to and from the gray colorspace, by default.) The colormodel for postscript() which does use both gray and sRGB colorspaces is now called "srgb+gray". Plots which are known to use only black/white/transparent can advantageously use colormodel = "gray" (just as before, but there is now slightly more advantage in doing so). o postscript() with values colormodel = "rgb" and colormodel = "rgb-nogray" give the behaviour prior to R 2.13.0 of uncalibrated RGB, which under some circumstances can be rendered much faster by a viewer. pdf(colormodel = "rgb") gives the behaviour prior to R 2.13.0 of uncalibrated RGB, which under some circumstances can be rendered faster by a viewer, and the files will be smaller (by about 9KB if compression is not used). o The postscript() device only includes the definition of the sRGB colorspace in the output file for the colormodels which use it. o The postscript() and pdf() devices now output greyscale raster images (and not RGB) when colormodel = "gray". o postscript(colormodel = "gray") now accepts non-grey colours and uses their luminance (as pdf() long has). o colormodel = "grey" is allowed as an alternative name for postscript() and pdf(). o pdf() in the default sRGB colorspace outputs many fewer changes of colorspace, which may speed up rendering in some viewing applications. o There is a new function dev.capabilities() to query the capabilities of the current device. The initial set of capabilities are support for semi-transparent colours, rendering and capturing raster images, the locator and for interactive events. o For pdf(), maxRasters is increased as needed so the argument is no longer used. SWEAVE &amp; VIGNETTES: o Options keep.source = TRUE, figs.only = FALSE are now the default. o The way the type of user-defined options is determined has changed. Previously they were all regarded as logical: now the type is determined by the value given at first use. o The allowed values of logical options are now precisely those allowed for character inputs to as.logical(): this means that t and f are no longer allowed (although T and F still are). o The preferred location for vignette sources is now the directory vignettes and not inst/doc: R CMD build will now re-build vignettes in directory vignettes and copy the .Rnw (etc) files and the corresponding PDFs to inst/doc. Further files to be copied to inst/doc can be specified _via_ the file vignettes/.install_extras. o R CMD Sweave now supports a --driver option to select the Sweave driver: the default is equivalent to --driver=RweaveLatex. o R CMD Sweave and R CMD Stangle support options --encoding and --options. o The Rtangle() driver allows output = "stdout" or output = "stderr" to select the output or message connection. This is convenient for scripting using something like R CMD Stangle --options='output="stdout"' foo.Rnw &gt; foo2.R o There is a new option pdf.compress controlling whether PDF figures are generated using Flate compression (they are by default). o R CMD Sweave now has a --pdf option to produce a PDF version of the processed Sweave document. o It is no longer allowed to have two vignettes with the same vignette basename (e.g. vig.Rnw and vig.Snw). (Previously one vignette hid the other in the vignette() function.) C-LEVEL FACILITIES: o Function R_tmpnam2 has been added to the API to allow a temporary filename to include a specified extension. PACKAGE INSTALLATION: o Package DESCRIPTION file field KeepSource forces the package to be installed with keep.source = TRUE (or FALSE). (Suggestion of Greg Snow. Note that as all packages are lazy-loaded, this is now only relevant at installation.) There are corresponding options --with-keep.source and --without-keep.source for R CMD INSTALL. o R CMD INSTALL has a new option --byte-compile to byte-compile the packages during installation (since all packages are now lazy-loaded). This can be controlled on a per-package basis by the optional field ByteCompile in the DESCRIPTION file. o A package R code but without a NAMESPACE file will have a default one created at R CMD build or R CMD INSTALL time, so all packages will be installed with namespaces. A consequence of this is that .First.lib() functions need to be copied to .onLoad() (usually) or .onAttach(). For the time being, if there is an auto-generated NAMESPACE file and no .onLoad() nor .onAttach() function is found but .First.lib() is, it will be run as the attach hook (unless the package is one of a list of known exceptions, when it will be run as the load hook). o A warning is given if test-loading a package changes a locked binding in a package other than itself. It is likely that this will be disallowed in future releases. (There are _pro tem_ some exceptions to the warning.) o A dependency on SVN revision is allowed for R, e.g. R (&gt;= r56550). This should be used in conjunction with a version number, e.g. R (&gt;= 2.14.0), R (&gt;= r56550) to distinguish beteen R-patched and R-devel versions with the same SVN revision. o installed.packages() now hashes the names of its cache files to avoid very rare problems with excessively long path names. (PR#14669) o A top-level COPYING file in a package is no longer installed (file names LICENSE or LICENCE having long been preferred). UTILITIES: o R CMD check now gives an error if the R code in a vignette fails to run, unless this is caused by a missing package. o R CMD check now unpacks tarballs in the same way as R CMD INSTALL, including making use of the environment variable R_INSTALL_TAR to override the default behaviour. o R CMD check performs additional code analysis of package startup functions, and notifies about incorrect argument lists and (incorrect) calls to functions which modify the search path or inappropriately generate messages. o R CMD check now also checks compiled code for symbols corresponding to functions which might terminate R or write to stdout/stderr instead of the console. o R CMD check now uses a pdf() device when checking examples (rather than postscript()). o R CMD check now checks line-endings of makefiles and C/C++/Fortran sources in subdirectories of src as well as in src itself. o R CMD check now reports as a NOTE what look like methods documented with their full names even if there is a namespace and they are exported. In almost all cases they are intended to be used only as methods and should use the \method markup. In the other rare cases the recommended form is to use a function such as coefHclust which would not get confused with a method, document that and register it in the NAMESPACE file by s3method(coef, hclust, coefHclust). o The default for the environment variable _R_CHECK_COMPACT_DATA2_ is now true: thus if using the newer forms of compression introduced in R 2.10.0 would be beneficial is now checked (by default). o Reference output for a vignette can be supplied when checking a package by R CMD check: see 'Writing R Extensions'. o R CMD Rd2dvi allows the use of LaTeX package inputenx rather than inputenc: the value of the environment variable RD2DVI_INPUTENC is used. (LaTeX package inputenx is an optional install which provides greater coverage of the UTF-8 encoding.) o Rscript on a Unix-alike now accepts file names containing spaces (provided these are escaped or quoted in the shell). o R CMD build on a Unix-alike (only) now tries to preserve dates on files it copies from its input directory. (This was the undocumented behaviour prior to R 2.13.0.) DEPRECATED AND DEFUNCT: o require() no longer has a save argument. o The gamma argument to hsv(), rainbow(), and rgb2hsv() has been removed. o The --no-docs option for R CMD build --binary is defunct: use --install-args instead. o The option --unsafe to R CMD INSTALL is defunct: use the identical option --no-lock instead. o The entry point pythag formerly in Rmath.h is defunct: use instead the C99 function hypot. o R CMD build --binary is formally defunct: R CMD INSTALL --build has long been the preferred alternative. o zip.file.extract() is now defunct: use unzip() or unz() instead. o R CMD Rd2dvi without the --pdf option is now deprecated: only PDF output will be supported in future releases (since this allows the use of fonts only supported for PDF), and only R CMD Rd2pdf will be available. o Options such as --max-nsize and the function mem.limits() are now deprecated: these limits are nowadays almost never used, and are reported by gc() when they are in use. o Forms like binomial(link = "link") for GLM families deprecated since R 2.4.0 are now defunct. o The declarativeOnly argument to loadNamespace() (not relevant since R 2.13.0) has been removed. o Use of library.dynam() without specifying all the first three arguments is deprecated. (It is often called from a namespace, and the defaults are only appropriate to a package.) Use of chname in library.dynam() with the extension .so or .dll (which is clearly not allowed according to the help page) is deprecated. This also applies to library.dynam.unload() and useDynLib directives in NAMESPACE files. o It is deprecated to use mean(x) and sd(x) directly on data frames (or also matrices, for sd) x, instead of simply using sapply. In the same spirit, median(x) now gives an error for a data frame x (it often gave nonsensical results). o The keep.source argument to library() and require() is deprecated: it was only used for packages installed without lazy-loading, and now all packages are lazy-loaded. o Using a false value for the DESCRIPTION field LazyLoad is deprecated. INSTALLATION: o The base and recommended packages are now byte-compiled (equivalent to make bytecode in R 2.13.x). o Configure option --with-system-zlib now only makes use of the basic interface of zlib and not the C function gzseek which has shown erroneous behaviour in zlib 1.2.4 and 1.2.5. o The zlib in the R sources is now version 1.2.5. (This is safe even on 32-bit Linux systems because only the basic interface is now used.) o The .afm files in package grDevices are now installed as compressed files (as long done on Windows), saving ca 2MB on the installed size. o The non-screen cairo-based devices are no longer in the X11 module and so can be installed without X11. (We have never seen a Unix-alike system with cairographics installed but not X11, but a user might select --without-x.) o Configure will try to use -fobjc-exceptions for the Objective-C compiler (if present) to ensure that even compilers that do not enable exceptions by default (such as vanilla gcc) can be used. (Objective-C is currently only used on Mac OS X.) o The system call times is required. o The C99 functions acosh, asinh, atanh, snprintf and vsnprintf are now required. o There is no longer support for making DVI manuals _via_ make dvi, make install-dvi and similar. Only PDF manuals are supported (to allow the use of fonts which are only available for PDF.) o The configure arguments used during configuration of R are included as a comment in Makeconf for informative purposes on Unix-alikes in a form suitable for shell execution. Note that those are merely command-line arguments, they do not include environment variables (one more reason to use configure variables instead) or site configuration settings. o Framework installation now supports DESTDIR (Mac OS X only). o Java detection (R CMD javareconf) works around bogus java.library.path property in recent Oracle Java binaries. BUG FIXES: o The locale category LC_MONETARY was only being set on startup on Windows: that is now done on Unix-alikes where supported. o Reference class utilities will detect an attempt to modify methods or fields in a locked class definition (e.g., in a namespace) and generate an error. o The formula methods for lines(), points() and text() now work even if package stats is not on the search path. o In principle, S4 classes from different packages could have the same name. This has not previously worked. Changes have now been installed that should allow such classes and permit methods to use them. New functions className() and multipleClasses() are related tools for programming. o Work around an issue in Linux (a system select call resetting tv) which prevented internet operations from timing out properly. o Several stack trampling and overflow issues have been fixed in TRE, triggered by agrep and friends with long patterns. (PR#14627.) o ("design infelicity") Field assignments in reference classes are now consistent with slots in S4 classes: the assigned value must come from the declared class (if any) for the field or from a subclass. o The methods objects constructed for "coerce" and "coerce&lt;-" were lacking some essential information in the generic, defined and target slots; as() did not handle duplicate class definitions correctly. o The parser no longer accepts the digit 8 in an octal character code in a string, nor does it accept unterminated strings in a file. (Reported by Bill Dunlap.) o The print() method for class "summary.aov" did not pass on argument digits when summary() was called on a single object, and hence used more digits than documented. o The X11() device's cairo back-end produced incorrect capture snapshot images on big-endian machines. o loglin() gave a spurious error when argument margin consisted of a single element of length one. (PR#14690) o loess() is better protected against misuse, e.g. zero-length span. (PR#14691) o HoltWinters() checks that the optimization succeeded. (PR#14694) o The (undocumented) inclusion of superclass objects in default initializing of reference classes overwrote explicit field arguments. The bug is fixed, the feature documented and a test added. o round(x, -Inf) now does something sensible (return zero rather than NA). o signif(x, -Inf) now behaves as documented (signif(x, 1)) rather than giving zero. o The "table" method for Axis() hardcoded side = 1, hence calls to plot(&lt;vector&gt;, &lt;table&gt;) labelled the wrong axis. (PR#14699) o Creating a connection might fail under gctorture(TRUE). o stack() and unstack() converted character columns to factors. unstack() sometimes produced incorrect results (a list or a vector) if the factor on which to un-split had only one level. o On some systems help(".C", help_type = "pdf") and similar generated file names that TeX was unable to handle. o Non-blocking listening socket connections continued to report isIncomplete() as true even when the peer had closed down and all available input had been read. o The revised HTML search system now generates better hyperlinks to help topics found: previously it gave problems with help pages with names containing e.g. spaces and slashes. o A late change in R 2.13.2 broke \Sexpr expressions in Rd files. o The creation of ticks on log axes (including axTicks() sometimes incorrectly omitted a tick at one end o The creation of ticks on log axes (including by axTicks()) sometimes incorrectly omitted a tick at one end of the range by rounding error in a platform-dependent way. This could be seen in the examples for axTicks(), where with axis limits c(0.2, 88) the tick for 0.2 was sometimes omitted. o qgamma() for small shape underflows to 0 rather than sometimes giving NaN. (PR#8528, PR#14710) o mapply() now gives an explicit error message (rather than an obscure one) is inputs of zero and positive length are mixed. o Setting a Hershey font family followed by string height query would crash R. o R CMD javareconf -e would fail for some shells due to a shift error. Also the resulting paths will no longer contain $(JAVA_HOME) as that can result in an unintended substitution based on Makeconf instead of the shell setting. -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd.mes&lt; at &gt;cbs.dk Priv: PDalgd&lt; at &gt;gmail.com </pre> Peter Dalgaard 2011-10-31T09:56:33 http://comments.gmane.org/gmane.comp.lang.r.announce/118 <pre>The byte pixies have rolled up R-2.13.2.tar.gz at 9:00 this morning. This is intended to be the final release of the 2.13 series, for the benefit of those apprehensive of putting 2.14.x into production use. The run-in for 2.14.0 starts on Monday, with a planned release on Oct 31 (The Great Pumpkin Man Release). You can get it from http://cran.r-project.org/src/base/R-2/R-2.13.2.tar.gz or wait for it to be mirrored at a CRAN site nearer to you. Binaries for various platforms will appear in due course. For the R Core Team Peter Dalgaard These are the md5sums for the freshly created files, in case you wish to check that they are uncorrupted: MD5 (AUTHORS) = cbf6da8f886ccd8d0dda0cc7ffd1b8ec MD5 (COPYING) = eb723b61539feef013de476e68b5c50a MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343 MD5 (FAQ) = 9313f40d1614e33bb2872dcdf09bdf1b MD5 (INSTALL) = 70447ae7f2c35233d3065b004aa4f331 MD5 (NEWS) = af38550b8f19f81357158effdbc44fc3 MD5 (NEWS.html) = 2c0741963f34888f5095225217e51666 MD5 (ONEWS) = 0c3e10eef74439786e5fceddd06dac71 MD5 (OONEWS) = b0d650eba25fc5664980528c147a20db MD5 (R-latest.tar.gz) = fbad74f6415385f86425d0f3968dd684 MD5 (README) = 296871fcf14f49787910c57b92655c76 MD5 (RESOURCES) = 020479f381d5f9038dcb18708997f5da MD5 (THANKS) = 159efc7bd4ae7b23dda07c1d431657bc MD5 (R-2/R-2.13.2.tar.gz) = fbad74f6415385f86425d0f3968dd684 This is the relevant part of the NEWS file: CHANGES IN R VERSION 2.13.2: NEW FEATURES: o mem.limits() now reports values larger than the maximum integer (previously documented to be reported as NA), and allows larger values to be set, including Inf to remove the limit. o The print() methods for classes "Date", "POSIXct" and "POSIXlt" respect the option "max.print" and so are much faster for very long datetime vectors. (Suggestion of Yohan Chalabi.) o untar2() now works around errors generated with tar files that use more than the standard 6 digits for the checksum. (https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14654PR#14654) o install.packages() with Ncpus &gt; 1 guards against simultaneous installation of indirect dependencies as well as direct ones. o Sweave now knows about a few more Windows' encodings (including cp1250 and cp1257) and some inputenx encodings such as koi8-r. o postscript(colormodel = "rgb-nogray") no longer sets the sRGB colorspace for each colour and so some viewers may render its files much faster than the default colormodel ="rgb". o The default for pdf(maxRasters=) has been increased from 64 to 1000. o readBin() now warns if signed = FALSE is used inappropriately (rather than being silently ignored). It enforces the documented limit of 2^31-1 bytes in a single call. o PCRE has been updated to version 8.13, a bug-fix release with updated Unicode tables (version 6.0.0). An additional patch (r611 from PCRE 8.20-to-be) has been added to fix a collation symbol recognition issue. INSTALLATION: o It is possible to build in src/extra/xdr on more platforms. (Needed since glibc 2.14 hides its RPC implementation.) o configure will find the Sun TI-RPC implementation of xdr (in libtirpc) provided its header files are in the search path: see the 'R Installation and Administration Manual'. PACKAGE INSTALLATION: o Using a broad exportPattern directive in a NAMESPACE file is no longer allowed to export internal objects such as .onLoad and .__S3MethodsTable__. . These are also excluded from imports, along with .First.lib. BUG FIXES: o fisher.test() had a buglet: If arguments were factors with unused levels, levels were dropped and you would get an error saying that there should be at least two levels, inconsistently with pre-tabulated data. (Reported by Michael Fay). o package.skeleton() will no longer dump S4 objects supplied directly rather than in a code file. These cannot be restored correctly from the dumped version. o Build-time expressions in help files did not have access to functions in the package being built (with R CMD build). o Because quote() did not mark its result as being in use, modification of the result could in some circumstances modify the original call. o Plotting pch = '.' now guarantees at least a one-pixel dot if cex &gt; 0. o The very-rarely-used command-line option --max-vsize was incorrectly interpreted as a number of Vcells and not in bytes as documented. (Spotted by Christophe Rhodes.) o The HTML generated by Rd2HTML() comes closer to being standards compliant. o filter(x, recursive = TRUE) gave incorrect results on a series containing NAs. (Spotted by Bill Dunlap.) o Profiling stats::mle() fits with a fixed parameter was not supported. (https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14646PR#14646) o retracemem() was still using positional matching. (https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14650PR#14650) o The quantile method for "ecdf" objects now works and is documented. o xtabs(~ .., ..., sparse=TRUE) now also works together with an exclude = .. specification. o decompose() computed an incorrect seasonal component for time series with odd frequencies. o The pdf() device only includes the definition of the sRGB colorspace in the output file for the "rgb" colormodel (and not for "gray" nor "cmyk"): this saves ca 9KB in the output file. o .hasSlot() wrongly gave FALSE in some cases. o Sweave() with keep.source=TRUE could generate spurious NA lines when a chunk reference appeared last in a code chunk. o \Sexpr[results=rd] in an .Rd file now first tries parse_Rd(fragment=FALSE) to allow Rd section-level macros to be inserted. o The print() method for class "summary.aov" did not pass on arguments such as signif.stars when summary() was called on a single object. (https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14684PR#14684) o In rare cases ks.test() could return a p-value very slightly less than 0 by rounding error. (https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14671PR#14671) o If trunc() was called on a "POSIXlt" vector and the result was subsetted, all but the first element was converted to NA. (https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14679PR#14679) o cbind() and rbind() could cause memory corruption when used on a combination of raw and logical/integer vectors. -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd.mes&lt; at &gt;cbs.dk Priv: PDalgd&lt; at &gt;gmail.com </pre> Peter Dalgaard 2011-09-30T08:50:49 http://comments.gmane.org/gmane.comp.lang.r.announce/117 <pre>This is to announce that we plan to release R version 2.14.0 on Monday, October 31, 2011. As a new feature, we will precede the run-in sequence for 2.14.0 with a final release of the 2.13 series, 2.13.2. No further patching of this series is intended. Those directly involved should review the generic schedule at http://developer.r-project.org/release-checklist.html The source tarballs will be made available daily (barring build troubles) via http://cran.r-project.org/src/base-prerelease/ For the R Core Team Peter Dalgaard </pre> Peter Dalgaard 2011-09-19T12:37:44 http://comments.gmane.org/gmane.comp.lang.r.announce/116 <pre>I've rolled up R-2.13.1.tar.gz a short while ago. This is a maintenance release to consolidate various minor fixes to 2.13.0. The Licencing change to GPL-2 | GPL-3 may be of interest to some. You can get it from http://cran.r-project.org/src/base/R-2/R-2.13.1.tar.gz or wait for it to be mirrored at a CRAN site nearer to you. Binaries for various platforms will appear in due course. For the R Core Team Peter Dalgaard These are the md5sums for the freshly created files, in case you wish to check that they are uncorrupted: MD5 (AUTHORS) = ac9746b4845ae866661f51cfc99262f5 MD5 (COPYING) = eb723b61539feef013de476e68b5c50a MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343 MD5 (FAQ) = a6f58169fec241d4fa4ab283d8cb12de MD5 (INSTALL) = 70447ae7f2c35233d3065b004aa4f331 MD5 (NEWS) = 8347135398220ba817bbf1c97586ec53 MD5 (ONEWS) = 0c3e10eef74439786e5fceddd06dac71 MD5 (OONEWS) = b0d650eba25fc5664980528c147a20db MD5 (R-latest.tar.gz) = 28dd0d68ac3a0eab93fe7035565a1c30 MD5 (README) = 296871fcf14f49787910c57b92655c76 MD5 (RESOURCES) = 020479f381d5f9038dcb18708997f5da MD5 (THANKS) = 03d783ff71270c77d497fd573d711fd8 MD5 (R-2/R-2.13.1.tar.gz) = 28dd0d68ac3a0eab93fe7035565a1c30 This is the relevant part of the NEWS file: R News CHANGES IN R VERSION 2.13.1: NEW FEATURES: • iconv() no longer translates NA strings as "NA". • persp(box = TRUE) now warns if the surface extends outside the box (since occlusion for the box and axes is computed assuming the box is a bounding box). (PR#202.) • RShowDoc() can now display the licences shipped with R, e.g. RShowDoc("GPL-3"). • New wrapper function showNonASCIIfile() in package tools. • nobs() now has a "mle" method in package stats4. • trace() now deals correctly with S4 reference classes and corresponding reference methods (e.g., $trace()) have been added. • xz has been updated to 5.0.3 (very minor bugfix release). • tools::compactPDF() gets more compression (usually a little, sometimes a lot) by using the compressed object streams of PDF 1.5. • cairo_ps(onefile = TRUE) generates encapsulated EPS on platforms with cairo &gt;= 1.6. • Binary reads (e.g. by readChar() and readBin()) are now supported on clipboard connections. (Wish of PR#14593.) • as.POSIXlt.factor() now passes ... to the character method (suggestion of Joshua Ulrich). [Intended for R 2.13.0 but accidentally removed before release.] • vector() and its wrappers such as integer() and double() now warn if called with a length argument of more than one element. This helps track down user errors such as calling double(x) instead of as.double(x). INSTALLATION: • Building the vignette PDFs in packages grid and utils is now part of running make from an SVN checkout on a Unix-alike: a separate make vignettes step is no longer required. These vignettes are now made with keep.source = TRUE and hence will be laid out differently. • make install-strip failed under some configuration options. • Packages can customize non-standard installation of compiled code via a src/install.libs.R script. This allows packages that have architecture-specific binaries (beyond the package's shared objects/DLLs) to be installed in a multi-architecture setting. SWEAVE &amp; VIGNETTES: • Sweave() and Stangle() gain an encoding argument to specify the encoding of the vignette sources if the latter do not contain a \usepackage[]{inputenc} statement specifying a single input encoding. • There is a new Sweave option figs.only = TRUE to run each figure chunk only for each selected graphics device, and not first using the default graphics device. This will become the default in R 2.14.0. • Sweave custom graphics devices can have a custom function foo.off() to shut them down. • Warnings are issued when non-portable filenames are found for graphics files (and chunks if split = TRUE). Portable names are regarded as alphanumeric plus hyphen, underscore, plus and hash (periods cause problems with recognizing file extensions). • The Rtangle() driver has a new option show.line.nos which is by default false; if true it annotates code chunks with a comment giving the line number of the first line in the sources (the behaviour of R &gt;= 2.12.0). • Package installation tangles the vignette sources: this step now converts the vignette sources from the vignette/package encoding to the current encoding, and records the encoding (if not ASCII) in a comment line at the top of the installed .R file. LICENCE: • No parts of R are now licensed solely under GPL-2. The licences for packages rpart and survival have been changed, which means that the licence terms for R as distributed are GPL-2 | GPL-3. DEPRECATED AND DEFUNCT: • The internal functions .readRDS() and .saveRDS() are now deprecated in favour of the public functions readRDS() and saveRDS() introduced in R 2.13.0. • Switching off lazy-loading of code _via_ the LazyLoad field of the DESCRIPTION file is now deprecated. In future all packages will be lazy-loaded. • The off-line help() types "postscript" and "ps" are deprecated. UTILITIES: • R CMD check on a multi-architecture installation now skips the user's .Renviron file for the architecture-specific tests (which do read the architecture-specific Renviron.site files). This is consistent with single-architecture checks, which use --no-environ. • R CMD build now looks for DESCRIPTION fields BuildResaveData and BuildKeepEmpty for per-package overrides. See ‘Writing R Extensions’. BUG FIXES: • plot.lm(which = 5) was intended to order factor levels in increasing order of mean standardized residual. It ordered the factor labels correctly, but could plot the wrong group of residuals against the label. (PR#14545) • mosaicplot() could clip the factor labels, and could overlap them with the cells if a non-default value of cex.axis was used. (Related to PR#14550.) • dataframe[[row,col]] now dispatches on [[ methods for the selected column (spotted by Bill Dunlap). • sort.int() would strip the class of an object, but leave its object bit set. (Reported by Bill Dunlap.) • pbirthday() and qbirthday() did not implement the algorithm exactly as given in their reference and so were unnecessarily inaccurate. pbirthday() now solves the approximate formula analytically rather than using uniroot() on a discontinuous function. The description of the problem was inaccurate: the probability is a tail probablity (‘2 _or more_ people share a birthday’) • Complex arithmetic sometimes warned incorrectly about producing NAs when there were NaNs in the input. • seek(origin = "current") incorrectly reported it was not implemented for a gzfile() connection. • c(), unlist(), cbind() and rbind() could silently overflow the maximum vector length and cause a segfault. (PR#14571) • The fonts argument to X11(type = "Xlib") was being ignored. • Reading (e.g. with readBin()) from a raw connection was not advancing the pointer, so successive reads would read the same value. (Spotted by Bill Dunlap.) • Parsed text containing embedded newlines was printed incorrectly by as.character.srcref(). (Reported by Hadley Wickham.) • decompose() used with a series of a non-integer number of periods returned a seasonal component shorter than the original series. (Reported by Rob Hyndman.) • fields = list() failed for setRefClass(). (Reported by Michael Lawrence.) • Reference classes could not redefine an inherited field which had class "ANY". (Reported by Janko Thyson.) • Methods that override previously loaded versions will now be installed and called. (Reported by Iago Mosqueira.) • addmargins() called numeric(apos) rather than numeric(length(apos)). • The HTML help search sometimes produced bad links. (PR#14608) • Command completion will no longer be broken if tail.default() is redefined by the user. (Problem reported by Henrik Bengtsson.) • LaTeX rendering of markup in titles of help pages has been improved; in particular, \eqn{} may be used there. • isClass() used its own namespace as the default of the where argument inadvertently. • Rd conversion to latex mis-handled multi-line titles (including cases where there was a blank line in the \title section). -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd.mes&lt; at &gt;cbs.dk Priv: PDalgd&lt; at &gt;gmail.com </pre> Peter Dalgaard 2011-07-08T10:16:40 http://comments.gmane.org/gmane.comp.lang.r.announce/115 <pre>This is to announce that we plan to release R version 2.13.1 on Friday, July 8, 2011. The 2.13.0 release has been quite solid, but some people expect an x.y.1 to roll out on larger installations for the next academic year. Of course, there have also been a sampling of minor bug fixes. Those directly involved should review the generic schedule at http://developer.r-project.org/release-checklist.html (We are breaking the schedule a little this time because of traveling.) The source tarballs will be made available daily (barring build troubles) via http://cran.r-project.org/src/base-prerelease/ For the R Core Team Peter Dalgaard </pre> Peter Dalgaard 2011-06-30T12:13:18 http://comments.gmane.org/gmane.comp.lang.r.announce/114 <pre>Dear All, The first issue of the third volume of The R Journal is now available at http://journal.r-project.org/current.html. Thanks to everyone involved. Heather -- Editor in chief Heather.Turner&lt; at &gt;r-project.org </pre> Heather Turner 2011-06-23T10:13:41 http://comments.gmane.org/gmane.comp.lang.r.announce/113 <pre>I've rolled up R-2.13.0.tar.gz a short while ago. This is a development release which contains a number of new features. Also, a number of mostly minor bugs have been fixed (but notice that serious build issues were fixed in 2.12.2). See the full list of changes below. You can get it from http://cran.r-project.org/src/base/R-2/R-2.13.0.tar.gz or wait for it to be mirrored at a CRAN site nearer to you. Binaries for various platforms will appear in due course. For the R Core Team Peter Dalgaard These are the md5sums for the freshly created files, in case you wish to check that they are uncorrupted: MD5 (AUTHORS) = ac9746b4845ae866661f51cfc99262f5 MD5 (COPYING) = eb723b61539feef013de476e68b5c50a MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343 MD5 (FAQ) = 3cbcd5d33708d03431cd13f695d1bcb0 MD5 (INSTALL) = 70447ae7f2c35233d3065b004aa4f331 MD5 (NEWS) = de39d09adf2c02e573722507c610d0f6 MD5 (ONEWS) = 0c3e10eef74439786e5fceddd06dac71 MD5 (OONEWS) = b0d650eba25fc5664980528c147a20db MD5 (R-latest.tar.gz) = ecfb928067cfd932e75135f8b8bba3e7 MD5 (README) = 296871fcf14f49787910c57b92655c76 MD5 (RESOURCES) = 020479f381d5f9038dcb18708997f5da MD5 (THANKS) = 03d783ff71270c77d497fd573d711fd8 MD5 (R-2/R-2.13.0.tar.gz) = ecfb928067cfd932e75135f8b8bba3e7 This is the relevant part of the NEWS file: R News CHANGES IN R VERSION 2.13.0: SIGNIFICANT USER-VISIBLE CHANGES: • replicate() (by default) and vapply() (always) now return a higher-dimensional array instead of a matrix in the case where the inner function value is an array of dimension &gt;= 2. • Printing and formatting of floating point numbers is now using the correct number of digits, where it previously rarely differed by a few digits. (See “scientific” entry below.) This affects _many_ *.Rout.save checks in packages. NEW FEATURES: • normalizePath() has been moved to the base package (from utils): this is so it can be used by library() and friends. It now does tilde expansion. It gains new arguments winslash (to select the separator on Windows) and mustWork to control the action if a canonical path cannot be found. • The previously barely documented limit of 256 bytes on a symbol name has been raised to 10,000 bytes (a sanity check). Long symbol names can sometimes occur when deparsing expressions (for example, in model.frame). • reformulate() gains a intercept argument. • cmdscale(add = FALSE) now uses the more common definition that there is a representation in n-1 or less dimensions, and only dimensions corresponding to positive eigenvalues are used. (Avoids confusion such as PR#14397.) • Names used by c(), unlist(), cbind() and rbind() are marked with an encoding when this can be ascertained. • R colours are now defined to refer to the sRGB color space. The PDF, PostScript, and Quartz graphics devices record this fact. X11 (and Cairo) and Windows just assume that your screen conforms. • system.file() gains a mustWork argument (suggestion of Bill Dunlap). • new.env(hash = TRUE) is now the default. • list2env(envir = NULL) defaults to hashing (with a suitably sized environment) for lists of more than 100 elements. • text() gains a formula method. • IQR() now has a type argument which is passed to quantile(). • as.vector(), as.double() etc duplicate less when they leave the mode unchanged but remove attributes. as.vector(mode = "any") no longer duplicates when it does not remove attributes. This helps memory usage in matrix() and array(). matrix() duplicates less if data is an atomic vector with attributes such as names (but no class). dim(x) &lt;- NULL duplicates less if x has neither dimensions nor names (since this operation removes names and dimnames). • setRepositories() gains an addURLs argument. • chisq.test() now also returns a stdres component, for standardized residuals (which have unit variance, unlike the Pearson residuals). • write.table() and friends gain a fileEncoding argument, to simplify writing files for use on other OSes (e.g. a spreadsheet intended for Windows or Mac OS X Excel). • Assignment expressions of the form foo::bar(x) &lt;- y and foo:::bar(x) &lt;- y now work; the replacement functions used are foo::`bar&lt;-` and foo:::`bar&lt;-`. • Sys.getenv() gains a names argument so Sys.getenv(x, names = FALSE) can replace the common idiom of as.vector(Sys.getenv()). The default has been changed to not name a length-one result. • Lazy loading of environments now preserves attributes and locked status. (The locked status of bindings and active bindings are still not preserved; this may be addressed in the future). • options("install.lock") may be set to FALSE so that install.packages() defaults to --no-lock installs, or (on Windows) to TRUE so that binary installs implement locking. • sort(partial = p) for large p now tries Shellsort if quicksort is not appropriate and so works for non-numeric atomic vectors. • sapply() gets a new option simplify = "array" which returns a “higher rank” array instead of just a matrix when FUN() returns a dim() length of two or more. replicate() has this option set by default, and vapply() now behaves that way internally. • aperm() becomes S3 generic and gets a table method which preserves the class. • merge() and as.hclust() methods for objects of class "dendrogram" are now provided. • as.POSIXlt.factor() now passes ... to the character method (suggestion of Joshua Ulrich). • The character method of as.POSIXlt() now tries to find a format that works for all non-NA inputs, not just the first one. • str() now has a method for class "Date" analogous to that for class "POSIXt". • New function file.link() to create hard links on those file systems (POSIX, NTFS but not FAT) that support them. • New Summary() group method for class "ordered" implements min(), max() and range() for ordered factors. • mostattributes&lt;-() now consults the "dim" attribute and not the dim() function, making it more useful for objects (such as data frames) from classes with methods for dim(). It also uses attr&lt;-() in preference to the generics name&lt;-(), dim&lt;-() and dimnames&lt;-(). (Related to PR#14469.) • There is a new option "browserNLdisabled" to disable the use of an empty (e.g. via the ‘Return’ key) as a synonym for c in browser() or n under debug(). (Wish of PR#14472.) • example() gains optional new arguments character.only and give.lines enabling programmatic exploration. • serialize() and unserialize() are no longer described as ‘experimental’. The interface is now regarded as stable, although the serialization format may well change in future releases. (serialize() has a new argument version which would allow the current format to be written if that happens.) New functions saveRDS() and readRDS() are public versions of the ‘internal’ functions .saveRDS() and .readRDS() made available for general use. The dot-name versions remain available as several package authors have made use of them, despite the documentation. saveRDS() supports compress = "xz". • Many functions when called with a not-open connection will now ensure that the connection is left not-open in the event of error. These include read.dcf(), dput(), dump(), load(), parse(), readBin(), readChar(), readLines(), save(), writeBin(), writeChar(), writeLines(), .readRDS(), .saveRDS() and tools::parse_Rd(), as well as functions calling these. • Public functions find.package() and path.package() replace the internal dot-name versions. • The default method for terms() now looks for a "terms" attribute if it does not find a "terms" component, and so works for model frames. • httpd() handlers receive an additional argument containing the full request headers as a raw vector (this can be used to parse cookies, multi-part forms etc.). The recommended full signature for handlers is therefore function(url, query, body, headers, ...). • file.edit() gains a fileEncoding argument to specify the encoding of the file(s). • The format of the HTML package listings has changed. If there is more than one library tree , a table of links to libraries is provided at the top and bottom of the page. Where a library contains more than 100 packages, an alphabetic index is given at the top of the section for that library. (As a consequence, package names are now sorted case-insensitively whatever the locale.) • isSeekable() now returns FALSE on connections which have non-default encoding. Although documented to record if ‘in principle’ the connection supports seeking, it seems safer to report FALSE when it may not work. • R CMD REMOVE and remove.packages() now remove file R.css when removing all remaining packages in a library tree. (Related to the wish of PR#14475: note that this file is no longer installed.) • unzip() now has a unzip argument like zip.file.extract(). This allows an external unzip program to be used, which can be useful to access features supported by Info-ZIP's unzip version 6 which is now becoming more widely available. • There is a simple zip() function, as wrapper for an external zip command. • bzfile() connections can now read from concatenated bzip2 files (including files written with bzfile(open = "a")) and files created by some other compressors (such as the example of PR#14479). • The primitive function c() is now of type BUILTIN. • plot(&lt;dendrogram&gt;, .., nodePar=*) now obeys an optional xpd specification (allowing clipping to be turned off completely). • nls(algorithm="port") now shares more code with nlminb(), and is more consistent with the other nls() algorithms in its return value. • xz has been updated to 5.0.1 (very minor bugfix release). • image() has gained a logical useRaster argument allowing it to use a bitmap raster for plotting a regular grid instead of polygons. This can be more efficient, but may not be supported by all devices. The default is FALSE. • list.files()/dir() gains a new argument include.dirs() to include directories in the listing when recursive = TRUE. • New function list.dirs() lists all directories, (even empty ones). • file.copy() now (by default) copies read/write/execute permissions on files, moderated by the current setting of Sys.umask(). • Sys.umask() now accepts mode = NA and returns the current umask value (visibly) without changing it. • There is a ! method for classes "octmode" and "hexmode": this allows xor(a, b) to work if both a and b are from one of those classes. • as.raster() no longer fails for vectors or matrices containing NAs. • New hook "before.new.plot" allows functions to be run just before advancing the frame in plot.new, which is potentially useful for custom figure layout implementations. • Package tools has a new function compactPDF() to try to reduce the size of PDF files _via_ qpdf or gs. • tar() has a new argument extra_flags. • dotchart() accepts more general objects x such as 1D tables which can be coerced by as.numeric() to a numeric vector, with a warning since that might not be appropriate. • The previously internal function create.post() is now exported from utils, and the documentation for bug.report() and help.request() now refer to that for create.post(). It has a new method = "mailto" on Unix-alikes similar to that on Windows: it invokes a default mailer via open (Mac OS X) or xdg-open or the default browser (elsewhere). The default for ccaddress is now getOption("ccaddress") which is by default unset: using the username as a mailing address nowadays rarely works as expected. • The default for options("mailer") is now "mailto" on all platforms. • unlink() now does tilde-expansion (like most other file functions). • file.rename() now allows vector arguments (of the same length). • The "glm" method for logLik() now returns an "nobs" attribute (which stats4::BIC() assumed it did). The "nls" method for logLik() gave incorrect results for zero weights. • There is a new generic function nobs() in package stats, to extract from model objects a suitable value for use in BIC calculations. An S4 generic derived from it is defined in package stats4. • Code for S4 reference-class methods is now examined for possible errors in non-local assignments. • findClasses, getGeneric, findMethods and hasMethods are revised to deal consistently with the package= argument and be consistent with soft namespace policy for finding objects. • tools::Rdiff() now has the option to return not only the status but a character vector of observed differences (which are still by default sent to stdout). • The startup environment variables R_ENVIRON_USER, R_ENVIRON, R_PROFILE_USER and R_PROFILE are now treated more consistently. In all cases an empty value is considered to be set and will stop the default being used, and for the last two tilde expansion is performed on the file name. (Note that setting an empty value is probably impossible on Windows.) • Using R --no-environ CMD, R --no-site-file CMD or R --no-init-file CMD sets environment variables so these settings are passed on to child R processes, notably those run by INSTALL, check and build. R --vanilla CMD sets these three options (but not --no-restore). • smooth.spline() is somewhat faster. With cv=NA it allows some leverage computations to be skipped, • The internal (C) function scientific(), at the heart of R's format.info(x), format(x), print(x), etc, for numeric x, has been re-written in order to provide slightly more correct results, fixing PR#14491, notably in border cases including when digits &gt;= 16, thanks to substantial contributions (code and experiments) from Petr Savicky. This affects a noticable amount of numeric output from R. • A new function grepRaw() has been introduced for finding subsets of raw vectors. It supports both literal searches and regular expressions. • Package compiler is now provided as a standard package. See ?compiler::compile for information on how to use the compiler. This package implements a byte code compiler for R: by default the compiler is not used in this release. See the ‘R Installation and Administration Manual’ for how to compile the base and recommended packages. • Providing an exportPattern directive in a NAMESPACE file now causes classes to be exported according to the same pattern, for example the default from package.skeleton() to specify all names starting with a letter. An explicit directive to exportClassPattern will still over-ride. • There is an additional marked encoding "bytes" for character strings. This is intended to be used for non-ASCII strings which should be treated as a set of bytes, and never re-encoded as if they were in the encoding of the currrent locale: useBytes = TRUE is autmatically selected in functions such as writeBin(), writeLines(), grep() and strsplit(). Only a few character operations are supported (such as substr()). Printing, format() and cat() will represent non-ASCII bytes in such strings by a \xab escape. • The new function removeSource() removes the internally stored source from a function. • "srcref" attributes now include two additional line number values, recording the line numbers in the order they were parsed. • New functions have been added for source reference access: getSrcFilename(), getSrcDirectory(), getSrcLocation() and getSrcref(). • Sys.chmod() has an extra argument use_umask which defaults to true and restricts the file mode by the current setting of umask. This means that all the R functions which manipulate file/directory permissions by default respect umask, notably R CMD INSTALL. • tempfile() has an extra argument fileext to create a temporary filename with a specified extension. (Suggestion and initial implementation by Dirk Eddelbuettel.) There are improvements in the way Sweave() and Stangle() handle non-ASCII vignette sources, especially in a UTF-8 locale: see ‘Writing R Extensions’ which now has a subsection on this topic. • factanal() now returns the rotation matrix if a rotation such as "promax" is used, and hence factor correlations are displayed. (Wish of PR#12754.) • The gctorture2() function provides a more refined interface to the GC torture process. Environment variables R_GCTORTURE, R_GCTORTURE_WAIT, and R_GCTORTURE_INHIBIT_RELEASE can also be used to control the GC torture process. • file.copy(from, to) no longer regards it as an error to supply a zero-length from: it now simply does nothing. • rstandard.glm gains a type argument which can be used to request standardized Pearson residuals. • A start on a Turkish translation, thanks to Murat Alkan. • .libPaths() calls normalizePath(winslash = "/") on the paths: this helps (usually) present them in a user-friendly form and should detect duplicate paths accessed via different symbolic links. SWEAVE CHANGES: • Sweave() has options to produce PNG and JPEG figures, and to use a custom function to open a graphics device (see ?RweaveLatex). (Based in part on the contribution of PR#14418.) • The default for Sweave() is to produce only PDF figures (rather than both EPS and PDF). • Environment variable SWEAVE_OPTIONS can be used to supply defaults for existing or new options to be applied after the Sweave driver setup has been run. • The Sweave manual is now included as a vignette in the utils package. • Sweave() handles keep.source=TRUE much better: it could duplicate some lines and omit comments. (Reported by John Maindonald and others.) C-LEVEL FACILITIES: • Because they use a C99 interface which a C++ compiler is not required to support, Rvprintf and REvprintf are only defined by R_ext/Print.h in C++ code if the macro R_USE_C99_IN_CXX is defined when it is included. • pythag duplicated the C99 function hypot. It is no longer provided, but is used as a substitute for hypot in the very unlikely event that the latter is not available. • R_inspect(obj) and R_inspect3(obj, deep, pvec) are (hidden) C-level entry points to the internal inspect function and can be used for C-level debugging (e.g., in conjunction with the p command in gdb). • Compiling R with --enable-strict-barrier now also enables additional checking for use of unprotected objects. In combination with gctorture() or gctorture2() and a C-level debugger this can be useful for tracking down memory protection issues. UTILITIES: • R CMD Rdiff is now implemented in R on Unix-alikes (as it has been on Windows since R 2.12.0). • R CMD build no longer does any cleaning in the supplied package directory: all the cleaning is done in the copy. It has a new option --install-args to pass arguments to R CMD INSTALL for --build (but not when installing to rebuild vignettes). There is new option, --resave-data, to call tools::resaveRdaFiles() on the data directory, to compress tabular files (.tab, .csv etc) and to convert .R files to .rda files. The default, --resave-data=gzip, is to do so in a way compatible even with years-old versions of R, but better compression is given by --resave-data=best, requiring R &gt;= 2.10.0. It now adds a datalist file for data directories of more than 1Mb. Patterns in .Rbuildignore are now also matched against all directory names (including those of empty directories). There is a new option, --compact-vignettes, to try reducing the size of PDF files in the inst/doc directory. Currently this tries qpdf: other options may be used in future. When re-building vignettes and a inst/doc/Makefile file is found, make clean is run if the makefile has a clean: target. After re-building vignettes the default clean-up operation will remove any directories (and not just files) created during the process: e.g. one package created a .R_cache directory. Empty directories are now removed unless the option --keep-empty-dirs is given (and a few packages do deliberately include empty directories). If there is a field BuildVignettes in the package DESCRIPTION file with a false value, re-building the vignettes is skipped. • R CMD check now also checks for filenames that are case-insensitive matches to Windows' reserved file names with extensions, such as nul.Rd, as these have caused problems on some Windows systems. It checks for inefficiently saved data/*.rda and data/*.RData files, and reports on those large than 100Kb. A more complete check (including of the type of compression, but potentially much slower) can be switched on by setting environment variable _R_CHECK_COMPACT_DATA2_ to TRUE. The types of files in the data directory are now checked, as packages are _still_ misusing it for non-R data files. It now extracts and runs the R code for each vignette in a separate directory and R process: this is done in the package's declared encoding. Rather than call tools::checkVignettes(), it calls tool::buildVignettes() to see if the vignettes can be re-built as they would be by R CMD build. Option --use-valgrind now applies only to these runs, and not when running code to rebuild the vignettes. This version does a much better job of suppressing output from successful vignette tests. The 00check.log file is a more complete record of what is output to stdout: in particular contains more details of the tests. It now check all syntactically valid Rd usage entries, and warns about assignments (unless these give the usage of replacement functions). .tar.xz compressed tarballs are now allowed, if tar supports them (and setting environment variable TAR to internal ensures so on all platforms). • R CMD check now warns if it finds inst/doc/makefile, and R CMD build renames such a file to inst/doc/Makefile. INSTALLATION: • Installing R no longer tries to find perl, and R CMD no longer tries to substitute a full path for awk nor perl - this was a legacy from the days when they were used by R itself. Because a couple of packages do use awk, it is set as the make (rather than environment) variable AWK. • make check will now fail if there are differences from the reference output when testing package examples and if environment variable R_STRICT_PACKAGE_CHECK is set to a true value. • The C99 double complex type is now required. The C99 complex trigonometric functions (such as csin) are not currently required (FreeBSD lacks most of them): substitutes are used if they are missing. • The C99 system call va_copy is now required. • If environment variable R_LD_LIBRARY_PATH is set during configuration (for example in config.site) it is used unchanged in file etc/ldpaths rather than being appended to. • configure looks for support for OpenMP and if found compiles R with appropriate flags and also makes them available for use in packages: see ‘Writing R Extensions’. This is currently experimental, and is only used in R with a single thread for colSums() and colMeans(). Expect it to be more widely used in later versions of R. This can be disabled by the --disable-openmp flag. PACKAGE INSTALLATION: • R CMD INSTALL --clean now removes copies of a src directory which are created when multiple sub-architectures are in use. (Following a comment from Berwin Turlach.) • File R.css is now installed on a per-package basis (in the package's html directory) rather than in each library tree, and this is used for all the HTML pages in the package. This helps when installing packages with static HTML pages for use on a webserver. It will also allow future versions of R to use different stylesheets for the packages they install. • A top-level file .Rinstignore in the package sources can list (in the same way as .Rbuildignore) files under inst that should not be installed. (Why should there be any such files? Because all the files needed to re-build vignettes need to be under inst/doc, but they may not need to be installed.) • R CMD INSTALL has a new option --compact-docs to compact any PDFs under the inst/doc directory. Currently this uses qpdf, which must be installed (see ‘Writing R Extensions’). • There is a new option --lock which can be used to cancel the effect of --no-lock or --pkglock earlier on the command line. • Option --pkglock can now be used with more than one package, and is now the default if only one package is specified. • Argument lock of install.packages() can now be use for Mac binary installs as well as for Windows ones. The value "pkglock" is now accepted, as well as TRUE and FALSE (the default). • There is a new option --no-clean-on-error for R CMD INSTALL to retain a partially installed package for forensic analysis. • Packages with names ending in . are not portable since Windows does not work correctly with such directory names. This is now warned about in R CMD check, and will not be allowed in R 2.14.x. • The vignette indices are more comprehensive (in the style of browseVignetttes()). DEPRECATED &amp; DEFUNCT: • require(save = TRUE) is defunct, and use of the save argument is deprecated. • R CMD check --no-latex is defunct: use --no-manual instead. • R CMD Sd2Rd is defunct. • The gamma argument to hsv(), rainbow(), and rgb2hsv() is deprecated and no longer has any effect. • The previous options for R CMD build --binary (--auto-zip, --use-zip-data and --no-docs) are deprecated (or defunct): use the new option --install-args instead. • When a character value is used for the EXPR argument in switch(), only a single unnamed alternative value is now allowed. • The wrapper utils::link.html.help() is no longer available. • Zip-ing data sets in packages (and hence R CMD INSTALL options --use-zip-data and --auto-zip, as well as the ZipData: yes field in a DESCRIPTION file) is defunct. Installed packages with zip-ed data sets can still be used, but a warning that they should be re-installed will be given. • The ‘experimental’ alternative specification of a name space via .Export() etc is now defunct. • The option --unsafe to R CMD INSTALL is deprecated: use the identical option --no-lock instead. • The entry point pythag in Rmath.h is deprecated in favour of the C99 function hypot. A wrapper for hypot is provided for R 2.13.x only. • Direct access to the "source" attribute of functions is deprecated; use deparse(fn, control="useSource") to access it, and removeSource(fn) to remove it. • R CMD build --binary is now formally deprecated: R CMD INSTALL --build has long been the preferred alternative. • Single-character package names are deprecated (and R is already disallowed to avoid confusion in Depends: fields). BUG FIXES: • drop.terms and the [ method for class "terms" no longer add back an intercept. (Reported by Niels Hansen.) • aggregate preserves the class of a column (e.g. a date) under some circumstances where it discarded the class previously. • p.adjust() now always returns a vector result, as documented. In previous versions it copied attributes (such as dimensions) from the p argument: now it only copies names. • On PDF and PostScript devices, a line width of zero was recorded verbatim and this caused problems for some viewers (a very thin line combined with a non-solid line dash pattern could also cause a problem). On these devices, the line width is now limited at 0.01 and for very thin lines with complex dash patterns the device may force the line dash pattern to be solid. (Reported by Jari Oksanen.) • The str() method for class "POSIXt" now gives sensible output for 0-length input. • The one- and two-argument complex maths functions failed to warn if NAs were generated (as their numeric analogues do). • Added .requireCachedGenerics to the dont.mind list for library() to avoid warnings about duplicates. • $&lt;-.data.frame messed with the class attribute, breaking any S4 subclass. The S4 data.frame class now has its own $&lt;- method, and turns dispatch on for this primitive. • Map() did not look up a character argument f in the correct frame, thanks to lazy evaluation. (PR#14495) • file.copy() did not tilde-expand from and to when to was a directory. (PR#14507) • It was possible (but very rare) for the loading test in R CMD INSTALL to crash a child R process and so leave around a lock directory and a partially installed package. That test is now done in a separate process. • plot(&lt;formula&gt;, data=&lt;matrix&gt;,..) now works in more cases; similarly for points(), lines() and text(). • edit.default() contained a manual dispatch for matrices (the "matrix" class didn't really exist when it was written). This caused an infinite recursion in the no-GUI case and has now been removed. • data.frame(check.rows = TRUE) sometimes worked when it should have detected an error. (PR#14530) • scan(sep= , strip.white=TRUE) sometimes stripped trailing spaces from within quoted strings. (The real bug in PR#14522.) • The rank-correlation methods for cor() and cov() with use = "complete.obs" computed the ranks before removing missing values, whereas the documentation implied incomplete cases were removed first. (PR#14488) They also failed for 1-row matrices. • The perpendicular adjustment used in placing text and expressions in the margins of plots was not scaled by par("mex"). (Part of PR#14532.) • Quartz Cocoa device now catches any Cocoa exceptions that occur during the creation of the device window to prevent crashes. It also imposes a limit of 144 ft^2 on the area used by a window to catch user errors (unit misinterpretation) early. • The browser (invoked by debug(), browser() or otherwise) would display attributes such as "wholeSrcref" that were intended for internal use only. • R's internal filename completion now properly handles filenames with spaces in them even when the readline library is used. This resolves PR#14452 provided the internal filename completion is used (e.g., by setting rc.settings(files = TRUE)). • Inside uniroot(f, ...), -Inf function values are now replaced by a maximally *negative* value. • rowsum() could silently over/underflow on integer inputs (reported by Bill Dunlap). • as.matrix() did not handle "dist" objects with zero rows. CHANGES IN R VERSION 2.12.2 patched: NEW FEATURES: • max() and min() work harder to ensure that NA has precedence over NaN, so e.g. min(NaN, NA) is NA. (This was not previously documented except for within a single numeric vector, where compiler optimizations often defeated the code.) BUG FIXES: • A change to the C function R_tryEval had broken error messages in S4 method selection; the error message is now printed. • PDF output with a non-RGB color model used RGB for the line stroke color. (PR#14511) • stats4::BIC() assumed without checking that an object of class "logLik" has an "nobs" attribute: glm() fits did not and so BIC() failed for them. • In some circumstances a one-sided mantelhaen.test() reported the p-value for the wrong tail. (PR#14514) • Passing the invalid value lty = NULL to axis() sent an invalid value to the graphics device, and might cause the device to segfault. • Sweave() with concordance=TRUE could lead to invalid PDF files; Sweave.sty has been updated to avoid this. • Non-ASCII characters in the titles of help pages were not rendered properly in some locales, and could cause errors or warnings. • checkRd() gave a spurious error if the \href macro was used. -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd.mes&lt; at &gt;cbs.dk Priv: PDalgd&lt; at &gt;gmail.com </pre> Peter Dalgaard 2011-04-13T09:03:39 http://comments.gmane.org/gmane.comp.lang.r.announce/111 <pre>This is to announce that we plan to release R version 2.13.0 on Wednesday, April 13, 2011. Those directly involved should review the generic schedule at http://developer.r-project.org/release-checklist.html The source tarballs will be made available daily (barring build troubles) via http://cran.r-project.org/src/base-prerelease/ For the R Core Team Peter Dalgaard </pre> Peter Dalgaard 2011-03-13T09:55:37 http://comments.gmane.org/gmane.comp.lang.r.announce/110 <pre>I've rolled up R-2.12.2.tar.gz a short while ago. This is an update release, which fixes a number of mostly minor issues, and one major issue in which complex arithmetic was being messed up on some compiler platform. You can get it from http://cran.r-project.org/src/base/R-2/R-2.12.2.tar.gz or wait for it to be mirrored at a CRAN site nearer to you. Binaries for various platforms will appear in due course. For the R Core Team Peter Dalgaard These are the md5sums for the freshly created files, in case you wish to check that they are uncorrupted: MD5 (AUTHORS) = ac9746b4845ae866661f51cfc99262f5 MD5 (COPYING) = eb723b61539feef013de476e68b5c50a MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343 MD5 (FAQ) = 72deeabefdf6fd14e83bf5703dce9176 MD5 (INSTALL) = 70447ae7f2c35233d3065b004aa4f331 MD5 (NEWS) = 30b55e4f34c155fcb2fafa7ebb55528e MD5 (ONEWS) = 0c3e10eef74439786e5fceddd06dac71 MD5 (OONEWS) = b0d650eba25fc5664980528c147a20db MD5 (R-latest.tar.gz) = bc70b51dddab8aa39066710624e55d5e MD5 (README) = 296871fcf14f49787910c57b92655c76 MD5 (RESOURCES) = 020479f381d5f9038dcb18708997f5da MD5 (THANKS) = f2ccf22f3e20ebaa86f8ee5cc6b0f655 MD5 (R-2/R-2.12.2.tar.gz) = bc70b51dddab8aa39066710624e55d5e This is the relevant part of the NEWS file: R News CHANGES IN R VERSION 2.12.2: SIGNIFICANT USER-VISIBLE CHANGES: • Complex arithmetic (notably z^n for complex z and integer n) gave incorrect results since R 2.10.0 on platforms without C99 complex support. This and some lesser issues in trignometric functions have been corrected. Such platforms were rare (we know of Cygwin and FreeBSD). However, because of new compiler optimizations in the way complex arguments are handled, the same code was selected on x86_64 Linux with gcc 4.5.x at the default -O2 optimization (but not at -O). • There is a workaround for crashes seen with several packages on systems using zlib 1.2.5: see the INSTALLATION section. NEW FEATURES: • PCRE has been updated to 8.12 (two bug-fix releases since 8.10). • rep(), seq(), seq.int() and seq_len() report more often when the first element is taken of an argument of incorrect length. • The Cocoa back-end for the quartz() graphics device on Mac OS X provides a way to disable event loop processing temporarily (useful, e.g., for forked instances of R). • kernel()'s default for m was not appropriate if coef was a set of coefficients. (Reported by Pierre Chausse.) • bug.report() has been updated for the current R bug tracker, which does not accept emailed submissions. • R CMD check now checks for the correct use of $(LAPACK_LIBS) (as well as $(BLAS_LIBS)), since several CRAN recent submissions have ignored ‘Writing R Extensions’. INSTALLATION: • The zlib sources in the distribution are now built with all symbols remapped: this is intended to avoid problems seen with packages such as XML and rggobi which link to zlib.so.1 on systems using zlib 1.2.5. • The default for FFLAGS and FCFLAGS with gfortran on x86_64 Linux has been changed back to -g -O2: however, setting -g -O may still be needed for gfortran 4.3.x. PACKAGE INSTALLATION: • A LazyDataCompression field in the DESCRIPTION file will be used to set the value for the --data-compress option of R CMD INSTALL. • Files R/sysdata.rda of more than 1Mb are now stored in the lazyload daabase using xz compression: this for example halves the installed size of package Imap. • R CMD INSTALL now ensures that directories installed from inst have search permission for everyone. It no longer installs files inst/doc/Rplots.ps and inst/doc/Rplots.pdf. These are almost certainly left-overs from Sweave runs, and are often large. DEPRECATED &amp; DEFUNCT: • The ‘experimental’ alternative specification of a name space via .Export() etc is now deprecated. • zip.file.extract() is now deprecated. • Zip-ing data sets in packages (and hence R CMD INSTALL --use-zip-data and the ZipData: yes field in a DESCRIPTION file) is deprecated: using efficiently compressed .rda images and lazy-loading of data has superseded it. BUG FIXES: • identical() could in rare cases generate a warning about non-pairlist attributes on CHARSXPs. As these are used for internal purposes, the attribute check should be skipped. (Reported by Niels Richard Hansen). • If the filename extension (usually .Rnw) was not included in a call to Sweave(), source references would not work properly and the keep.source option failed. (PR#14459) • format.data.frame() now keeps zero character column names. • pretty(x) no longer raises an error when x contains solely non-finite values. (PR#14468) • The plot.TukeyHSD() function now uses a line width of 0.5 for its reference lines rather than lwd = 0 (which caused problems for some PDF and PostScript viewers). • The big.mark argument to prettyNum(), format(), etc. was inserted reversed if it was more than one character long. • R CMD check failed to check the filenames under man for Windows' reserved names. • The "Date" and "POSIXt" methods for seq() could overshoot when to was supplied and by was specified in months or years. • The internal method of untar() now restores hard links as file copies rather than symbolic links (which did not work for cross-directory links). • unzip() did not handle zip files which contained filepaths with two or more leading directories which were not in the zipfile and did not already exist. (It is unclear if such zipfiles are valid and the third-party C code used did not support them, but PR#14462 created one.) • combn(n, m) now behaves more regularly for the border case m = 0. (PR#14473) • The rendering of numbers in plotmath expressions (e.g. expression(10^2)) used the current settings for conversion to strings rather than setting the defaults, and so could be affected by what has been done before. (PR#14477) • The methods of napredict() and naresid() for na.action = na.exclude fits did not work correctly in the very rare event that every case had been omitted in the fit. (Reported by Simon Wood.) • weighted.residuals(drop0=TRUE) returned a vector when the residuals were a matrix (e.g. those of class "mlm"). (Reported by Bill Dunlap.) • Package HTML index files &lt;pkg&gt;/html/00Index.html were generated with a stylesheet reference that was not correct for static browsing in libraries. • ccf(na.action = na.pass) was not implemented. • The parser accepted some incorrect numeric constants, e.g. 20x2. (Reported by Olaf Mersmann.) • format(*, zero.print) did not always replace the full zero parts. • Fixes for subsetting or subassignment of "raster" objects when not both i and j are specified. • R CMD INSTALL was not always respecting the ZipData: yes field of a DESCRIPTION file (although this is frequently incorrectly specified for packages with no data or which specify lazy-loading of data). R CMD INSTALL --use-zip-data was incorrectly implemented as --use-zipdata since R 2.9.0. • source(file, echo=TRUE) could fail if the file contained #line directives. It now recovers more gracefully, but may still display the wrong line if the directive gives incorrect information. • atan(1i) returned NaN+Infi (rather than 0+Infi) on platforms without C99 complex support. • library() failed to cache S4 metadata (unlike loadNamespace()) causing failures in S4-using packages without a namespace (e.g. those using reference classes). • The function qlogis(lp, log.p=TRUE) no longer prematurely overflows to Inf when exp(lp) is close to 1. • Updating S4 methods for a group generic function requires resetting the methods tables for the members of the group (patch contributed by Martin Morgan). • In some circumstances (including for package XML), R CMD INSTALL installed version-control directories from source packages. • Added PROTECT calls to some constructed expressions used in C level eval calls. • utils:::create.post() (used by bug.report() and help.request()) failed to quote arguments to the mailer, and so often failed. • bug.report() was naive about how to extract maintainer email addresses from package descriptions, so would often try mailing to incorrect addresses. • debugger() could fail to read the environment of a call to a function with a ... argument. (Reported by Charlie Roosen.) • prettyNum(c(1i, NA), drop0=TRUE) or str(NA_complex_) now work correctly. </pre> Peter Dalgaard 2011-02-25T12:49:42 http://comments.gmane.org/gmane.comp.lang.r.announce/109 <pre>This is to announce that we plan to release R version 2.12.2 on Friday, February 25, 2011. (Mainly to sort out complex arithmetic issues with some compiler platforms.) Those directly involved should review the generic schedule at http://developer.r-project.org/release-checklist.html The source tarballs will be made available daily (barring build troubles) via http://cran.r-project.org/src/base-prerelease/ For the R Core Team Peter Dalgaard </pre> Peter Dalgaard 2011-02-14T14:59:39 http://comments.gmane.org/gmane.comp.lang.r.announce/108 <pre>We are happy to inform you that abstract submission and registration for useR! 2011 is now available online, see http://www.R-project.org/useR-2011 This meeting of the R user community will take place at the University of Warwick, Coventry, UK, August 16-18, 2011. The conference schedule comprises invited lectures and user-contributed sessions. In addition half-day tutorials presented by R experts will run on August 15, 2011, prior to the conference. We invite you to submit abstracts for oral or poster presentations on innovative and exciting applications of R. The call for papers along with the link for abstract submission is available at http://www.R-project.org/useR-2011/#Call In addition to the regular contributed talks, all participants are invited to present a Lightning Talk, for which no abstract is required. These talks provide a 5-minute platform to speak on any R-related topic and should particularly appeal to R newbies. Participants wishing to give such a talk must provide an informative title on their registration form. We hope to see you in Coventry! The organizing committee: John Aston, Julia Brettschneider, David Firth, Ashley Ford, Ioannis Kosmidis, Tom Nichols, Elke Thönnes and Heather Turner </pre> useR-2011< at >r-project.org 2011-01-15T12:18:14 http://comments.gmane.org/gmane.comp.lang.r.announce/107 <pre>The second issue of the second volume of The R Journal is now available at http://journal.r-project.org/current.html. Thanks to everyone involved. Next year, Heather Turner will be Editor-in-chief, and Hadley Wickham joins the Editorial Board, and Vince Carey leaves us. Peter Dalgaard Editor-in-chief </pre> Peter Dalgaard 2010-12-30T22:37:20 http://comments.gmane.org/gmane.comp.lang.r.announce/106 <pre>I've rolled up R-2.12.1.tar.gz a short while ago. This is an update release, which fixes a number of mostly minor issues, and some consolidation within the area of reference classes. The most serious issues were probably that we were not catching misspelled NAMESPACE directives and not catching accidentally unnamed switch() arguments (notice that fixing either will likely uncover errors in preexisting code) You can get it from http://cran.r-project.org/src/base/R-2/R-2.12.1.tar.gz or wait for it to be mirrored at a CRAN site nearer to you. Binaries for various platforms will appear in due course. For the R Core Team Peter Dalgaard These are the md5sums for the freshly created files, in case you wish to check that they are uncorrupted: MD5 (AUTHORS) = ac9746b4845ae866661f51cfc99262f5 MD5 (COPYING) = eb723b61539feef013de476e68b5c50a MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343 MD5 (FAQ) = 49b596b26b3e5c082dfde8bacfdffcb0 MD5 (INSTALL) = 70447ae7f2c35233d3065b004aa4f331 MD5 (NEWS) = 453317871e758763aa9bf385b545bdc6 MD5 (ONEWS) = 0c3e10eef74439786e5fceddd06dac71 MD5 (OONEWS) = 58d5b3b614888a6e366ff0c60073584f MD5 (R-latest.tar.gz) = 078e8d1179fc9a762e326e6da2725468 MD5 (README) = 296871fcf14f49787910c57b92655c76 MD5 (RESOURCES) = 020479f381d5f9038dcb18708997f5da MD5 (THANKS) = f2ccf22f3e20ebaa86f8ee5cc6b0f655 MD5 (R-2/R-2.12.1.tar.gz) = 078e8d1179fc9a762e326e6da2725468 This is the relevant part of the NEWS file: R News CHANGES IN R VERSION 2.12.1: NEW FEATURES: • The DVI/PDF reference manual now includes the help pages for all the standard packages: splines, stats4 and tcltk were previously omitted (intentionally). • &lt;URL: http://www.rforge.net&gt; has been added to the default set of repositories known to setRepositories(). • xz-utils has been updated to version 5.0.0. • reshape() now makes use of sep when forming names during reshaping to wide format. (PR#14435) • legend() allows the length of lines to be set by the end user _via_ the new argument seg.len. • New reference class utility methods copy(), field(), getRefClass() and getClass() have been added. • When a character value is used for the EXPR argument in switch(), a warning is given if more than one unnamed alternative value is given. This will become an error in R 2.13.0. • StructTS(type = "BSM") now allows series with just two seasons. (Reported by Birgit Erni.) INSTALLATION: • The PDF reference manual is now built as PDF version 1.5 with object compression, which on platforms for which this is not the default (notably MiKTeX) halves its size. • Variable FCLIBS can be set during configuration, for any additional library flags needed when linking a shared object with the Fortran 9x compiler. (Needed with Solaris Studio 12.2.) BUG FIXES: • seq.int() no longer sometimes evaluates arguments twice. (PR#14388) • The data.frame method of format() failed if a column name was longer than 256 bytes (the maximum length allowed for an R name). • predict(&lt;lm object&gt;, type ="terms", ...) failed if both terms and interval were specified. (Reported by Bill Dunlap.) Also, if se.fit = TRUE the standard errors were reported for all terms, not just those selected by a non-null terms. • The TRE regular expressions engine could terminate R rather than give an error when given certain invalid regular expressions. (PR#14398) • cmdscale(eig = TRUE) was documented to return n-1 eigenvalues but in fact only returned k. It now returns all n eigenvalues. cmdscale(add = TRUE) failed to centre the return configuration and sometimes lost the labels on the points. Its return value was described wrongly (it is always a list and contains component ac). • promptClass() in package methods now works for reference classes and gives a suitably specialized skeleton of documentation. Also, callSuper() now works via the methods() invocation as well as for initially specified methods. • download.file() could leave the destination file open if the URL was not able to be opened. (PR#14414) • Assignment of an environment to functions or as an attribute to other objects now works for S4 subclasses of "environment". • Use of [[&lt;- for S4 subclasses of "environment" generated an infinite recursion from the method. The method has been replaced by internal code. • In a reference class S4 method, callSuper() now works in initialize() methods when there is no explicit superclass method. • ! dropped attributes such as names and dimensions from a length-zero argument. (PR#14424) • When list2env() created an environment it was missing a PROTECT call and so was vulnerable to garbage collection. • Sweave() with keep.source=TRUE dropped comments at the start and end of code chunks. It could also fail when \SweaveInput was combined with named chunks. • The Fortran code used by nls(algorithm = "port") could infinite-loop when compiled with high optimization on a modern version of gcc, and SAFE_FFLAGS is now used to make this less likely. (PR#14427, seen with 32-bit Windows using gcc 4.5.0 used from R 2.12.0.) • sapply() with default simplify = TRUE and mapply() with default SIMPLIFY = TRUE wrongly simplified language-like results, as, e.g., in mapply(1:2, c(3,7), FUN = function(i,j) call(':',i,j)). • Backreferences to undefined patterns in [g]sub(pcre = TRUE) could cause a segfault. (PR#14431) • The format() (and hence the print()) method for class "Date" rounded fractional dates towards zero: it now always rounds them down. • Reference S4 class creation could generate ambiguous inheritance patterns under very special circumstances. • [[&lt;- turned S4 subclasses of "environment" into plain environments. • Long titles for help pages were truncated in package indices and a few other places. • Additional utilities now work correctly with S4 subclasses of "environment" (rm, locking tools and active bindings). • spec.ar() now also work for the "ols" method. (Reported by Hans-Ruedi Kuensch.) • The initialization of objects from S4 subclasses of "environment" now allocates a new environment object. • R CMD check has more protection against (probably erroneous) example or test output which is invalid in the current locale. • qr.X() with column names and pivoting now also pivots the column names. (PR#14438) • unit.pmax() and unit.pmin() in package grid gave incorrect results when all inputs were of length 1. (PR#14443) • The parser for NAMESPACE files ignored misspelled directives, rather than signalling an error. For 2.12.x a warning will be issued, but this will be correctly reported as an error in later releases. (Reported by Charles Berry.) • Fix for subsetting of "raster" objects when only one of i or j is specified. • grid.raster() in package grid did not accept "nativeRaster" objects (like rasterImage() does). • Rendering raster images in PDF output was resetting the clipping region. • Rendering of raster images on Cairo X11 device was wrong, particularly when a small image was being scaled up using interpolation. With Cairo &lt; 1.6, will be better than before, though still a little clunky. With Cairo &gt;= 1.6, should be sweet as. • Several bugs fixed in read.DIF(): single column inputs caused errors, cells marked as "character" could be converted to other types, and (in Windows) copying from the clipboard failed. </pre> Peter Dalgaard 2010-12-16T09:35:01 Search the mailing list at Gmane query http://search.gmane.org/?group=$group=gmane.comp.lang.r.announce