From stvjc at channing.harvard.edu Fri Jan 8 11:01:14 2010 From: stvjc at channing.harvard.edu (Vincent Carey) Date: Fri, 8 Jan 2010 10:01:14 +0000 Subject: New issue (v1/n2) of R Journal now available; RSS feed as well Message-ID: <2c3c9e81001080201w2f2a1bc1j9228a11104c49fd@mail.gmail.com> On behalf of the editorial team, I am happy to inform you that the second issue of The R Journal is now available: http://journal.r-project.org/current.html Note that an RSS feed is now in place: http://journal.r-project.org/rss.xml I welcome Peter Dalgaard as the new Editor-In-Chief. -- Vincent Carey, PhD Biostatistics, Channing Lab Editor-In-Chief (Emeritus) The R Journal (ISSN 2073-4859) From kmullen at nist.gov Mon Feb 1 20:31:12 2010 From: kmullen at nist.gov (Katharine Mullen) Date: Mon, 1 Feb 2010 14:31:12 -0500 (EST) Subject: Abstract submission deadline, useR! 2010 Message-ID: The abstract submission deadline for the R Users Conference, useR! 2010, is just one month away. Submission deadline: 2010-03-01 Early registration will also close on 2010-03-01. Now is the perfect time to prepare an abstract presenting innovations or exciting applications of R. The call for abstracts along with the link for submission is available at: http://www.R-project.org/useR-2010/#Call This meeting of the R user community will take place at the Gaithersburg, Maryland, USA campus of the National Institute of Standards and Technology (NIST), July 21-23, 2010. The conference schedule is comprised of invited lectures and user-contributed sessions as well as half-day tutorials presented by R experts on July 20, 2010, prior to the conference. Invited speakers will include Mark Handcock, Frank Harrell Jr, Friedrich Leisch, Michael Meyer, Richard Stallman, Luke Tierney, and Diethelm Wuertz. The full spectrum of conference information is available from the webpage: http://www.R-project.org/useR-2010/ We hope to meet you in Gaithersburg! Kate Mullen, for the organizing committee From pd.mes at cbs.dk Mon Mar 22 11:38:23 2010 From: pd.mes at cbs.dk (Peter Dalgaard) Date: Mon, 22 Mar 2010 11:38:23 +0100 Subject: R 2.11.0 Scheduled for April 22, 2010 Message-ID: <785F3934-10B5-45F5-9829-010206E6FB00@cbs.dk> This is to announce that we plan to release R version 2.11.0 on Thursday, April 22, 2010. 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 -- O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907 -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com From dirk.eddelbuettel at r-project.org Tue Mar 23 16:08:27 2010 From: dirk.eddelbuettel at r-project.org (Dirk Eddelbuettel) Date: Tue, 23 Mar 2010 10:08:27 -0500 Subject: R Participation in the Google Summer of Code 2010 Message-ID: <19368.55659.435905.884614@ron.nulle.part> Dear R Users, We would like to highlight that R has once again been selected to participate in the Google Summer of Code. Suggested projects can be found in the R-Wiki: http://rwiki.sciviews.org/doku.php?id=developers:projects:gsoc2010. The GSoC is a program from Google that offers student developers stipends to write code for various open source software projects (more information can be found here: http://code.google.com/soc/). All discussion related to R and the Google Summer of Code should preferably tak place on the respective google group: http://groups.google.com/group/gsoc-r (gsoc-r at googlegroups.com). We are currently in a time period during which interested students can discuss an idea from the wiki with the respective project mentor, or contact the gsoc-r group to propose a new one and find a mentor. Please note that some projects on the R-Wiki also provide test questions, so please read these pages thoroughly before contacting a project mentor. The student application period opens on March 29th. Best regards, the R Project GSoC mentors From pd.mes at cbs.dk Thu Apr 22 11:01:10 2010 From: pd.mes at cbs.dk (Peter Dalgaard) Date: Thu, 22 Apr 2010 11:01:10 +0200 Subject: R 2.11.0 is released Message-ID: <48FC08AE-CFDC-41D0-A9A0-A462CF4E831A@cbs.dk> I've rolled up R-2.11.0.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. See the full list of changes below. NOTE: The build platform has been changed for this release. Please watch out extra carefully for anomalies. You can get it from http://cran.r-project.org/src/base/R-2/R-2.11.0.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) = 5b653442bedab476a4eff7468192fb5f MD5 (INSTALL) = 70447ae7f2c35233d3065b004aa4f331 MD5 (NEWS) = 59017734fb8474f98f994c7a5a27f9fb MD5 (ONEWS) = a8c985af5ad5e9c7e0a9f502d07baeb4 MD5 (OONEWS) = 4f004de59e24a52d0f500063b4603bcb MD5 (R-latest.tar.gz) = c6c1e866299f533617750889c729bfb3 MD5 (README) = 433182754c05c2cf7a04ad0da474a1d0 MD5 (RESOURCES) = 020479f381d5f9038dcb18708997f5da MD5 (THANKS) = f2ccf22f3e20ebaa86f8ee5cc6b0f655 MD5 (R-2/R-2.11.0.tar.gz) = c6c1e866299f533617750889c729bfb3 This is the relevant part of the NEWS file: CHANGES IN R VERSION 2.11.0 SIGNIFICANT USER-VISIBLE CHANGES o Packages must have been installed under R >= 2.10.0, as the current help system is the only one now supported. o A port to 64-bit Windows is now available as well as binary package repositiories: see the 'R Administration and Installation Manual'. o Argument matching for primitive functions is now done in the same way as for interpreted functions except for the deliberate exceptions call switch .C .Fortran .Call .External all of which use positional matching for their first argument, and also some internal-use-only primitives. o The default device for command-line R at the console on Mac OS X is now quartz() and not X11(). NEW FEATURES o The 'open' modes for connections are now interpreted more consistently. open = "r" is now equivalent to open = "rt" for all connections. The default open = "" now means "rt" for all connections except the compressed file connections gzfile(), bzfile() and xzfile() for which it means "rb". o R CMD INSTALL now uses the internal untar() in package utils: this ensures that all platforms can install bzip2- and xz-compressed tarballs. In case this causes problems (as it has on some Windows file systems when run from Cygwin tools) it can be overridden by the environment variable R_INSTALL_TAR: setting this to a modern external tar program will speed up unpacking of large (tens of Mb or more) tarballs. o help(try.all.packages = TRUE) is much faster (although the time taken by the OS to find all the packages the first time it is used can dominate the time). o R CMD check has a new option '--timings' to record per-example timings in file .Rcheck/-Ex.timings. o The TRE library has been updated to version 0.8.0 (minor bugfixes). o grep[l], [g]sub and [g]regexpr now work in bytes in an 8-bit locales if there is no marked UTF-8 input string: this will be somewhat faster, and for [g]sub() give the result in the native encoding rather than in UTF-8 (which returns to the behaviour prior to R 2.10.0). o A new argument 'skipCalls' has been added to browser() so that it can report the original context when called by other debugging functions. o More validity checking of UTF-8 and MBCS strings is done by agrep() and the regular-expression matching functions. o The undocumented restriction on gregexpr() to length(text) > 0 has been removed. o Package tcltk now sends strings to Tcl in UTF-8: this means that strings with a marked UTF-8 encoding are supported in non-UTF-8 locales. o The graphics engine now supports rendering of raster (bitmap) images, though not all graphics devices can provide (full) support. Packages providing graphics devices (e.g., Cairo, RSvgDevice, cairoDevice) will need to be reinstalled. There is also support in the graphics engine for capturing raster images from graphics devices (again not supported on all graphics devices). o R CMD check now also checks if the package and namespace can be unloaded: this provides a check of the .Last.lib() and .onUnload() hook functions (unless --install=fake). o prop.table(x) now accepts a one-dimensional table for x. o A new function vapply() has been added, based on a suggestion from Bill Dunlap. It requires that a template for the function value be specified, and uses it to determine the output type and to check for consistency in the function values. o The main HTML help page now links to a reformatted copy of this NEWS file. (Suggested by Henrik Bengtsson.) Package index files link to the package DESCRIPTION and NEWS files and a list of demos when using dynamic help. o The [ method for class "AsIs" allows the next method to change the underlying class. (Wish of Jens Oehlschl?gel.) o write.csv[2] no longer allow 'append' to be changed: as ever, direct calls to write.table() give more flexibility as well as more room for error. o The index page for HTML help for a package now collapses multiple signatures for S4 methods into a single entry. o The use of '.required' by require() and detach() has been replaced by '.Depends' which is set from the 'Depends' field of a package (even in packages with name spaces). By default detach() prevents such dependencies from being detached: this can be overridden by the argument 'force'. o bquote() has been extended to work on function definitions (wish of PR#14031). o detach() when applied to an object other than a package returns the environment that has been detached, to parallel attach(). o readline() in non-interactive use returns "" and does not attempt to read from the 'terminal'. o New function file_ext() in package 'tools'. o xtfrm() is now primitive and internally generic, as this allows S4 methods to be set on it without name-space scoping issues. There are now "AsIs" and "difftime" methods, and the default method uses unclass(x) if is.numeric(x) is true (which will be faster but relies on is.numeric() having been set correctly for the class). o is.numeric(x) is now false for a "difftime" object (multiplication and division make no sense for such objects). o The default method of weighted.mean(x, w) coerces 'w' to be numeric (aka double); previously only integer weights were coerced. Zero weights are handled specially so an infinite value with zero weight does not force an NaN result. There is now a "difftime" method. o bug.report() now has 'package' and 'lib.loc' arguments to generate bug reports about packages. When this is used, it looks for a BugReports field in the package DESCRIPTION file, which will be assumed to be a URL at which to submit the report, and otherwise generates an email to the package maintainer. (Suggested by Barry Rowlingson.) o quantile() now has a method for the date-time class "POSIXt", and types 1 and 3 (which never interpolate) work for Dates and ordered factors. o length() now returns the length of the corresponding abstract timedate-vector rather than always 9 (the length of the underlying list structure). (Wish of PR#14073 and PR#10507.) o The readline completion backend no longer sorts possible completions alphabetically (e.g., function argument names) if R was built with readline >= 6. o select.list() gains a 'graphics' argument to allow Windows/Mac users to choose the text interface. This changes the behaviour of new.packages(ask=TRUE) to be like update.packages(ask=TRUE) on those platforms in using a text menu: use ask="graphics" for a graphical menu. o New function chooseBioCmirror() to set the "BioC_mirror" option. o The R grammar prevents using the argument 'name' in signatures of S4 methods for '$' and '$<-', since they will always be called with a character string value for 'name'. The implicit S4 generic functions have been changed to reflect this: packages which included 'name' in the signature of their methods need to be updated and re-installed. o The handling of the 'method' argument of glm() has been refined following suggestions by Ioannis Kosmidis and Heather Turner. o str() gains a new argument 'list.len' with default 99, limiting the number of list() items (per level), thanks to suggestions from David Winsenius. o Having formal arguments of an S4 method in a different order from the generic is now an error (the warning having been ignored by some package maintainers for a long time). o New functions enc2native() and enc2utf8() convert character vectors with possibly marked encodings to the current locale and UTF-8 respectively. o Unrecognized escapes and embedded nuls in character strings are now an error, not just a warning. Thus option "warnEscapes" is no longer needed. rawToChar() now removes trailing nuls silently, but other embedded nuls become errors. o Informational messages about masked objects displayed when a package is attached are now more compact, using strwrap() instead of one object per line. o print.rle() gains argument 'prefix'. o download.file() gains a "curl" method, mainly for use on platforms which have 'curl' but not 'wget', but also for some hard-to-access URLs. o In Rd, \eqn and \deqn will render in HTML (and convert to text) upper- and lower-case Greek letters (entered as \alpha ...), \ldots, \dots, \ge and \le. o utf8ToInt() and intToUtf8() now map NA inputs to NA outputs. o file() has a new argument 'raw' which may help if it is used with something other than a regular file, e.g. a character device. o New function strtoi(), a wrapper for the C function strtol. o as.octmode() and as.hexmode() now allow inputs of length other than one. The format() and print() methods for "octmode" now preserve names and dimensions (as those for "hexmode" did). The format() methods for classes "octmode" and "hexmode" gain a 'width' argument. o seq.int() returns an integer result in some further cases where seq() does, e.g. seq.int(1L, 9L, by = 2L). o Added \subsection{}{} macro to Rd syntax, for subsections within sections. o n-dimensional arrays with dimension names can now be indexed by an n-column character matrix. The indices are matched against the dimension names. NA indices are propagated to the result. Unmatched values and "" are not allowed and result in an error. o interaction(drop=TRUE) uses less memory (related to PR#14121). o summary() methods have been added to the "srcref" and "srcfile" classes, and various encoding issues have been cleaned up. o If option "checkPackageLicense" is set to TRUE (not currently the default), users will be asked to agree to non-known-to-be-FOSS package licences at first use. o Checking setAs(a,b) methods only gives a message instead of a warning, when one of a or b is unknown. o New function norm() to compute a matrix norm. norm() and also backsolve() and sample() have implicit S4 generics. o Renviron.site and Rprofile.site can have architecture-specific versions on systems with sub-architectures. o R CMD check now (by default) also checks Rd files for auto-generated content in need of editing, and missing argument descriptions. o aggregate() gains a formula method thanks to a contribution by Arni Magnusson. The data frame method now allows summary functions to return arbitrarily many values. o path.expand() now propagates NA values rather than converting them to "NA". o file.show() now disallows NA values for file names, headers, and pager. o The 'fuzz' used by seq() and seq.int() has been reduced from 1e-7 to 1e-10, which should be ample for the double-precision calculations used in R. It ensures that the fuzz never comes into play with sequences of integers (wish of PR#14169). o The default value of RSiteSearch(restrict=) has been changed to include vignettes but to exclude R-help. The R-help archives available have been split, with a new option of "Rhelp10" for those from 2010. o New function rasterImage() in the 'graphics' package for drawing raster images. o stats:::extractAIC.coxph() now omits aliased terms when computing the degrees of freedom (suggestion of Terry Therneau). o cor() and cov() now test for misuse with non-numeric arguments, such as the non-bug report PR#14207. o pchisq(ncp =, log.p = TRUE) is more accurate for probabilities near one. E.g. pchisq(80, 4, ncp=1, log.p=TRUE). (Maybe what was meant in PR#14126.) o maintainer() has been added, to give convenient access to the name of the maintainer of a package (contributed by David Scott). o sample() and sample.int() allow zero items to be sampled from a zero-length input. sample.int() gains a default value 'size=n' to be more similar to sample(). o switch() returned NULL on error (not previously documented on the help page): it now does so invisibly, analogously to if-without-else. It is now primitive: this means that EXPR is always matched to the first argument and there is no danger of partial matching to later named arguments. o Primitive functions UseMethod(), attr(), attr<-(), on.exit(), retracemem() and substitute() now use standard argument matching (rather than positional matching). This means that all multi-argument primitives which are not internal now use standard argument matching except where positional matching is desirable (as for switch(), call(), .C() ...). o All the one-argument primitives now check that any name supplied for their first argument is a partial match to the argument name as documented on the help page: this also applies to replacement functions of two arguments. o base::which() uses a new .Internal function when arr.ind is FALSE resulting in a 10x speedup. Thanks to Patrick Aboyoun for implementation suggestions. o Help conversion to text now uses the first part of \enc{}{} markup if it is representable in the current output encoding. On the other hand, conversion to LaTeX with the default outputEncoding = "ASCII" uses the second part. o A new class "listOfMethods" has been introduced to represent the methods in a methods table, to replace the deprecated class "MethodsList". o any() and all() return early if possible. This may speed up operations on long vectors. o strptime() now accepts "%z" (for the offset from UTC in the RFC822 format of +/-hhmm). o The PCRE library has been updated to version 8.02, a bug-fix release which also updates tables to Unicode 5.02. o Functions which may use a graphical select.list() (including menu() and install.packages()) now check on a Unix-alike that Tk can be started (and not just capabilities("tcltk") && capabilities("X11")). o The parser no longer marks strings containing octal or hex escapes as being in UTF-8 when entered in a UTF-8 locale. o On platforms with cairo but not Pango (notably Mac OS X) the initial default X11() type is set to "Xlib": this avoids several problems with font selection when done by cairo rather than Pango (at least on Mac OS X). o New arrayInd() such that which(x, arr.ind = TRUE) for an array 'x' is now equivalent to arrayInd(which(x), dim(x), dimnames(x)). DEPRECATED & DEFUNCT o Bundles of packages are defunct. o stats::clearNames() is defunct: use unname(). o Basic regular expressions are defunct, and strsplit(), grep(), grepl(), sub(), gsub(), regexpr() and gregexpr() no longer have an 'extended' argument. o methods::trySilent() is defunct. o index.search() (which was deprecated in 2.10.0) is no longer exported and has a different argument list. o Use of multiple arguments to return() is now defunct. o The use of UseMethod() with more than two arguments is now defunct. o In the 'methods' package, the MethodsList metadata objects which had been superseded by hash tables (environments) since R 2.8.0 are being phased out. Objects of this class are no longer assigned or used as metadata by the package. getMethods() is now deprecated, with its internal use replaced by findMethods() and other changes. Creating objects from the MethodsList class is also deprecated. o Parsing strings containing both octal/hex and Unicode escapes now gives a warning and will become an error in R 2.12.0. INSTALLATION o UTF-8 is now used for the reference manual and package manuals. This requires LaTeX '2005/12/01' or later. o configure looks for a POSIX compliant tr, Solaris's /usr/ucb/tr having been found to cause Rdiff to malfunction. o configure is now generated with autoconf-2.65, which works better on recent systems and on Mac OS X. PACKAGE INSTALLATION o Characters in R source which are not translatable to the current locale are now handled more tolerantly: these will be converted to hex codes with a warning. Such characters are only really portable if they appear in comments. o R CMD INSTALL now tests that the installed package can be loaded (and backs out the installation if it cannot): this can be suppressed by --no-test-load. This avoids installing/updating a package that cannot be used: common causes of failures to load are missing/incompatible external software and missing/broken dependent packages. o Package installation on Windows for a package with a src directory now checks if a DLL is created unless there is a src/Makefile.win file: this helps catch broken installations where the toolchain has not reported problems in building the DLL. (Note: this can be any DLL, not just one named .dll.) BUG FIXES o Using with(), eval() etc with a list with some unnamed elements now works. (PR#14035) o The "quick" dispatch of S4 methods for primitive functions was not happening, forcing a search each time. (Dispatch for closures was not affected.) A side effect is that default values for arguments in a method that do not have defaults in the generic will now be ignored. o Trying to dispatch S4 methods for primitives during the search for inherited methods slows that search down and potentially could cause an infinite recursion. An internal switch was added to turn off all such methods from findInheritedMethods(). o R framework installation (on Mac OS X) would not work properly if a rogue Resources directory was present at the top level. Such a non-symlink will now be renamed to Resources.old (and anything previously named Resources.old removed) as part of the framework installation process. o The checks for conforming S4 method arguments could fail when the signature of the generic function omitted some of the formal arguments (in addition to ...). Arguments omitted from the method definition but conforming (per the documentation) should now be ignored (treated as "ANY") in dispatching. o The computations for S4 method evaluation when '...' was in the signature could fail, treating '...' as an ordinary symbol. This has been fixed, for the known cases. o Various ar() fitting methods have more protection for singular fits. o callNextMethod now works again with the drop= argument in `[` o parse() and parse_Rd() miscounted columns when multibyte UTF-8 characters were present. o Formatting of help pages has had minor improvements: extra blank lines have been removed from the text format, and empty package labels removed from HTML. o cor(A, B) where A has n x 1 and B a 1-dimensional array segfaulted or gave an internal error. (The case cor(B, A) was PR#7116.) o cut.POSIXt() applied to a start value after the DST transition on a DST-change day could give the wrong time for 'breaks' in units of days or longer. (PR#14208) o do_par() UNPROTECTed too early (PR#14214) o subassignment x[[....]] <- y didn't check for a zero-length right hand side, and inserted rubbish value. (PR#14217) o fisher.test() no longer gives a P-value *very* slightly > 1, in some borderline cases. o Internal function matchArgs no longer modifies the general purpose bits of the SEXPs that make up the formals list of R functions. This fixes an invalid error message that would occur when a garbage collection triggered a second call to matchArgs for the same function via a finalizer. o gsub() in 2.10.x could fail from stack overflow for extremely long strings due to temporary data being allocated on the stack. Also, gsub() with fixed=TRUE is in some circumstances considerably faster. o Several primitives, including attributes(), attr<-() interactive(), nargs() and proc.time(), did not check that they were called with the correct number of arguments. o A potential race condition in list.files() when other processes are operating on the directory has been fixed; the code now dynamically allocates memory for file listings in a single pass instead of making an initial count pass. o mean(x, trim=, na.rm = FALSE) failed to return NA if 'x' contained missing values. (Reported by Bill Dunlap.) o Extreme tail behavior of, pbeta() {and hence pf()}, e.g., pbeta(x, 3, 2200, lower.tail=FALSE, log.p=TRUE) now returns finite values instead of jumping to -Inf too early (PR#14230). o parse(text=x) misbehaved for objects 'x' that were not coerced internally to character, notably symbols. (Reported to R-devel by Bill Dunlap.) o The internal C function 'coerceSymbol' now handles coercion to character, and warns if coercion fails (rather than silently returning NULL). This allows a name to be given where a character vector is required in functions which coerce internally. o The interpretation by strptime() of %c was non-standard (not that it is ever advisable to use locale- and system-specific input formats). o capabilities("X11") now works the same way on Mac OS X as on other platforms (and as documented: it was always true for R built with --with-aqua, as the CRAN builds are). o The X11() device with cairo but not Pango (notably Mac OS X) now checks validity of text strings in UTF-8 locales (since Pango does but cairo it seems does not). o read.fwf() misread multi-line records when n was specified. (PR#14241) o all.equal(*, tolerance = e) passes the numeric tolerance also to the comparison of the attributes. o pgamma(0,0), a boundary case, now returns 0, its limit from the left, rather than the limit from the right. o Issuing POST requests to the internal web server could stall the request under certain circumstances. o gzcon( ), an error, no longer damages the connection (in a way to have it seg.fault). (PR#14237) o All the results from hist() now use the nominal 'breaks' not those adjusted by the numeric 'fuzz": in recent versions the nominal 'breaks' were reported but the 'density' referred to the intervals used in the calculation -- which mattered very slightly for one of the extreme bins. (Based on a report by Martin Becker.) o If xy[z].coords (used internally by many graphics functions) are given a list as 'x', they now check that the list has suitable names and give a more informative error message. (PR#13936) -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com From pd.mes at cbs.dk Thu May 20 12:03:09 2010 From: pd.mes at cbs.dk (Peter Dalgaard) Date: Thu, 20 May 2010 12:03:09 +0200 Subject: R 2.11.1 Scheduled for May 31 Message-ID: This is to announce that we plan to release R version 2.11.1 on Monday, May 31, 2010. 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 -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com From pd.mes at cbs.dk Mon May 31 11:16:36 2010 From: pd.mes at cbs.dk (Peter Dalgaard) Date: Mon, 31 May 2010 11:16:36 +0200 Subject: [R] R 2.11.1 is released Message-ID: <43D125EC-EEB8-4282-8036-6914335B4159@cbs.dk> I've rolled up R-2.11.1.tar.gz a short while ago. This is an update release, which fixes a number of mostly minor issues. The most annoying one was probably the problem with format.POSIXlt causing C stack overflow on long date vectors. See the full list of changes below. You can get it from http://cran.r-project.org/src/base/R-2/R-2.11.1.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) = 15600c9a568cbfcb72ea074f2bc5bfb3 MD5 (INSTALL) = 70447ae7f2c35233d3065b004aa4f331 MD5 (NEWS) = 32e5abe211dc0a7d13758d576ba20c01 MD5 (ONEWS) = a8c985af5ad5e9c7e0a9f502d07baeb4 MD5 (OONEWS) = 4f004de59e24a52d0f500063b4603bcb MD5 (R-latest.tar.gz) = 7421108ade3e9223263394b9bbe277ce MD5 (README) = 433182754c05c2cf7a04ad0da474a1d0 MD5 (RESOURCES) = 020479f381d5f9038dcb18708997f5da MD5 (THANKS) = f2ccf22f3e20ebaa86f8ee5cc6b0f655 MD5 (R-2/R-2.11.1.tar.gz) = 7421108ade3e9223263394b9bbe277ce This is the relevant part of the NEWS file: CHANGES IN R VERSION 2.11.1 NEW FEATURES o R CMD INSTALL checks if dependent packages are available early on in the installation of source packages, thereby giving clearer error messages. o R CMD INSTALL --build now names the file in the format used for Mac OS X binary files on that platform. o BIC() in package stats4 now also works with multiple fitted models, analogously to AIC(). DEPRECATED & DEFUNCT o Use of file extension .C for C++ code in packages is now deprecated: it has caused problems for some 'make's on case-insensitive file systems (although it currently works with the recommended toolkits). INSTALLATION o Command 'gnutar' is preferred to 'tar' when configure sets TAR. This is needed on Mac OS 10.6, where the default tar, bsdtar 2.6.2, has been reported to produce archives with illegal extensions to tar (according to the POSIX standard). BUG FIXES o The C function mkCharLenCE now no longer reads past 'len' bytes (unlikely to be a problem except in user code). (PR#14246) o On systems without any default LD_LIBRARY_PATH (not even /usr/local/lib), [DY]LIB_LIBRARY_PATH is now set without a trailing colon. (PR#13637) o More efficient utf8ToInt() on long multi-byte strings with many multi-byte characters. (PR#14262) o aggregate.ts() gave platform-depedent results due to rounding error for ndeltat != 1. o package.skeleton() sometimes failed to fix filenames for .R or .Rd files to start with an alphanumeric. (PR#14253) It also failed when only an S4 class without any methods was defined. (PR#14280) o splinefun(*, method = "monoH.FC") was not quite monotone in rare cases. (PR#14215) o Rhttpd no longer crashes due to SIGPIPE when the client closes the connection prematurely. (PR#14266) o format.POSIXlt() could cause a stack overflow and crash when used on very long vectors. (PR#14267) o Rd2latex() incorrectly escaped special characters in \usage sections. o mcnemar.test() could alter the levels (dropping unused levels) if passed 'x' and 'y' as factors (reported by Greg Snow). o Rd2pdf sometimes needed a further pdflatex pass to get hyperlinked pages correct. o interaction() produced malformed results when levels were duplicated, causing segfaults in split(). o cut(d, breaks = ) now also works for "Date" or "POSIXt" argument d. (PR#14288) o memDecompress() could decompress incompletely rare xz-compressed input due to incorrect documentation of xz utils. (Report and patch from Olaf Mersmann.) o The S4 initialize() methods for "matrix", "array", and "ts" have been fixed to call validObject(). (PR#14284) o R CMD INSTALL now behaves the same way with or without --no-multiarch on platforms with only one installed architecture. (It used to clean the src directory without --no-multiarch.) o [<-.data.frame was not quite careful enough in assigning (and potentially deleting) columns right-to-left. (PR#14263) o rbeta(n, a,b) no longer occasionally returns NaN for a >> 1 > b. (PR#14291) o pnorm(x, log.p = TRUE) could return NaN not -Inf for x near (minus for lower.tail=TRUE) the largest representable number. o Compressed data files *.(txt|tab|csv).(gz|bz2|xz) were not recognized for the list of data topics and hence for packages using LazyData. (PR#14273) o textConnection() did an unnecessary translation on strings in a foreign encoding (e.g. UTF-8 strings on Windows) and so was slower than it could have been on very long input strings. (PR#14286) o tools::Rd2txt() did not render poorly written Rd files consistently with other renderers. o na.action() did not extract the 'na.action' component as duplicated, causing segfaults in split(). o cut(d, breaks = ) now also works for "Date" or "POSIXt" argument d. (PR#14288) o memDecompress() could decompress incompletely rare xz-compressed o On systems without any default LD_LIBRARY_PATH (not even /usr/local/lib), [DY]LIB_LIBRARY_PATH is now set without a trailing colon. (PR#13637) o More efficient utf8ToInt() on long multi-byte strings with many multi-byte characters. (PR#14262) o aggregate.ts() gave platform-depedent results due to rounding error for ndeltat != 1. o package.skeleton() sometimes failed to fix filenames for .R or .Rd files to start with an alphanumeric. (PR#14253) It also failed when only an S4 class without any methods was defined. (PR#14280) o splinefun(*, method = "monoH.FC") was not quite monotone in rare cases. (PR#14215) o Rhttpd no longer crashes due to SIGPIPE when the client closes the connection prematurely. (PR#14266) o format.POSIXlt() could cause a stack overflow and crash when used on very long vectors. (PR#14267) o Rd2latex() incorrectly escaped special characters in \usage sections. o mcnemar.test() could alter the levels (dropping unused levels) if passed 'x' and 'y' as factors (reported by Greg Snow). o Rd2pdf sometimes needed a further pdflatex pass to get hyperlinked pages correct. o interaction() produced malformed results when levels were duplicated, causing segfaults in split(). o cut(d, breaks = ) now also works for "Date" or "POSIXt" argument d. (PR#14288) o memDecompress() could decompress incompletely rare xz-compressed input due to incorrect documentation of xz utils. (Report and patch from Olaf Mersmann.) o The S4 initialize() methods for "matrix", "array", and "ts" have been fixed to call validObject(). (PR#14284) o R CMD INSTALL now behaves the same way with or without --no-multiarch on platforms with only one installed architecture. (It used to clean the src directory without --no-multiarch.) o [<-.data.frame was not quite careful enough in assigning (and potentially deleting) columns right-to-left. (PR#14263) o rbeta(n, a,b) no longer occasionally returns NaN for a >> 1 > b. (PR#14291) o pnorm(x, log.p = TRUE) could return NaN not -Inf for x near (minus for lower.tail=TRUE) the largest representable number. o Compressed data files *.(txt|tab|csv).(gz|bz2|xz) were not recognized for the list of data topics and hence for packages using LazyData. (PR#14273) o textConnection() did an unnecessary translation on strings in a foreign encoding (e.g. UTF-8 strings on Windows) and so was slower than it could have been on very long input strings. (PR#14286) o tools::Rd2txt() did not render poorly written Rd files consistently with other renderers. o na.action() did not extract the 'na.action' component as documented. From pd.mes at cbs.dk Wed Jun 30 13:05:23 2010 From: pd.mes at cbs.dk (Peter Dalgaard) Date: Wed, 30 Jun 2010 13:05:23 +0200 Subject: The R Journal, Vol.2 Issue 1 Message-ID: <4C2B24F3.9040009@cbs.dk> The first issue of the second volume of The R Journal will shortly be available at journal at r-project.org/current.html. Thanks to everyone involved. Peter Dalgaard Editor-in-chief -- Peter Dalgaard Center for Statistics, Copenhagen Business School Phone: (+45)38153501 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com From pd.mes at cbs.dk Wed Jun 30 22:32:44 2010 From: pd.mes at cbs.dk (Peter Dalgaard) Date: Wed, 30 Jun 2010 22:32:44 +0200 Subject: [R] The R Journal, Vol.2 Issue 1 In-Reply-To: <4C2B24F3.9040009@cbs.dk> References: <4C2B24F3.9040009@cbs.dk> Message-ID: <4C2BA9EC.1010503@cbs.dk> Peter Dalgaard wrote: > The first issue of the second volume of The R Journal will shortly be > available at journal at r-project.org/current.html. Thanks to everyone As no less than 16 people has informed me, that of course wants to be http://journal.r-project.org/current.html (That's what you get for doing editorial duties while on holiday in Barcelona....., -ed.) > involved. > > Peter Dalgaard > Editor-in-chief > > -- Peter Dalgaard Center for Statistics, Copenhagen Business School Phone: (+45)38153501 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com From pdalgd at gmail.com Wed Jun 30 18:05:38 2010 From: pdalgd at gmail.com (Peter Dalgaard) Date: Wed, 30 Jun 2010 18:05:38 +0200 Subject: [R] The R Journal, Vol.2 Issue 1 In-Reply-To: <4C2B24F3.9040009@cbs.dk> References: <4C2B24F3.9040009@cbs.dk> Message-ID: <4C2B6B52.9000804@gmail.com> Peter Dalgaard wrote: > The first issue of the second volume of The R Journal will shortly be > available at journal at r-project.org/current.html. Thanks to everyone As no less than 16 people has informed me, that of course wants to be http://journal.r-project.org/current.html (That's what you get for doing editorial duties while on holiday in Barcelona....., -ed.) > involved. > > Peter Dalgaard > Editor-in-chief > > -- Peter Dalgaard Center for Statistics, Copenhagen Business School Phone: (+45)38153501 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com From pd.mes at cbs.dk Fri Jul 30 17:10:37 2010 From: pd.mes at cbs.dk (Peter Dalgaard) Date: Fri, 30 Jul 2010 17:10:37 +0200 Subject: Next release of R planned to be 2.12.0 Message-ID: <56B157DD-AB7C-4AC6-A53B-EB40146CA22E@cbs.dk> This mainly as a thumbs-up to sysadmins planning installation for the Fall semester: Only a small number of low-impact bugs have been found since the 2.11.1 release so we have decided NOT to do a 2.11.2, but head straight for 2.12.0 some time in October. For the R Core Team Peter Dalgaard -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com From Heather.Turner at warwick.ac.uk Tue Aug 10 13:12:27 2010 From: Heather.Turner at warwick.ac.uk (Heather Turner) Date: Tue, 10 Aug 2010 12:12:27 +0100 Subject: useR! 2011: announcement and call for tutorials Message-ID: <4C61341B.2000501@warwick.ac.uk> We are pleased to announce that the R user conference useR! 2011 is scheduled for August 16-18, 2011, and will take place at the University of Warwick, Coventry, UK. As for the predecessor conferences, the program will consist of two parts: invited lectures and user-contributed sessions (abstract submission will be available online later this year). Prior to the conference, there will be tutorials on R (proposals for tutorials should be sent before October 29, 2010, see below). INVITED SPEAKERS Adrian Bowman, Lee Edlefsen, Ulrike Gr?mping, Wolfgang Huber, Brian Ripley, Jonathan Rougier, Simon Urbanek, and Brandon Whitcher. USER-CONTRIBUTED SESSIONS The conference will feature both talks and posters illustrating the use of R in practice. Contributions are welcome that introduce recent developments in the R Project (including CRAN packages), demonstrate applications of R in areas of current interest, or otherwise engage and inspire participants in their use of R. PRE-CONFERENCE TUTORIALS Before the official program, half-day tutorials will be offered on Monday, August 15. We invite R users to submit proposals for three hour tutorials on special topics regarding R. The proposals should give a brief description of the tutorial, including goals, detailed outline, justification of why the tutorial is important, background knowledge required and potential attendees. The proposals should be sent before October 29, 2010 to useR-2011_at_R-project.org. A web page offering more information on the `useR!' conference is available at http://www.R-project.org/useR-2011 We hope to see you in Coventry! The organizing committee: John Aston, Julia Brettschneider, David Firth, Ashley Ford, Ioannis Kosmidis, Tom Nichols, Elke Th?nnes and Heather Turner From pdalgd at gmail.com Mon Sep 13 19:12:15 2010 From: pdalgd at gmail.com (peter dalgaard) Date: Mon, 13 Sep 2010 19:12:15 +0200 Subject: R 2.12.0 scheduled for October 15 Message-ID: This is to announce that we plan to release R version 2.12.0 on Friday, October, 2010. 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 -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com From pd.mes at cbs.dk Mon Sep 13 19:15:47 2010 From: pd.mes at cbs.dk (Peter Dalgaard) Date: Mon, 13 Sep 2010 19:15:47 +0200 Subject: R 2.12.0 scheduled for October 15 Message-ID: <67CD7196-645E-484B-A476-199D3A2F0839@cbs.dk> This is to announce that we plan to release R version 2.12.0 on Friday, October 15, 2010. 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 -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com From pd.mes at cbs.dk Fri Oct 15 11:15:50 2010 From: pd.mes at cbs.dk (Peter Dalgaard) Date: Fri, 15 Oct 2010 11:15:50 +0200 Subject: R 2.12.0 is released Message-ID: <33418B16-385D-47C1-B0CD-6D16B4B353B3@cbs.dk> I've rolled up R-2.12.0.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. See the full list of changes below. You can get it from http://cran.r-project.org/src/base/R-2/R-2.12.0.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) = dbdfe3f2451a4394b4f982e45ba4395c MD5 (INSTALL) = 70447ae7f2c35233d3065b004aa4f331 MD5 (NEWS) = 8431585f21ee3e9a1cb83e1eb552d0e5 MD5 (ONEWS) = 0c3e10eef74439786e5fceddd06dac71 MD5 (OONEWS) = 58d5b3b614888a6e366ff0c60073584f MD5 (R-latest.tar.gz) = aa003654d238d70bf5bc7433b8257aac MD5 (README) = 296871fcf14f49787910c57b92655c76 MD5 (RESOURCES) = 020479f381d5f9038dcb18708997f5da MD5 (THANKS) = f2ccf22f3e20ebaa86f8ee5cc6b0f655 MD5 (R-2/R-2.12.0.tar.gz) = aa003654d238d70bf5bc7433b8257aac This is the relevant part of the NEWS file (hoping that the new format survives email...) R News CHANGES IN R VERSION 2.12.0: NEW FEATURES: ? Reading a packages's CITATION file now defaults to ASCII rather than Latin-1: a package with a non-ASCII CITATION file should declare an encoding in its DESCRIPTION file and use that encoding for the CITATION file. ? difftime() now defaults to the "tzone" attribute of "POSIXlt" objects rather than to the current timezone as set by the default for the tz argument. (Wish of PR#14182.) ? pretty() is now generic, with new methods for "Date" and "POSIXt" classes (based on code contributed by Felix Andrews). ? unique() and match() are now faster on character vectors where all elements are in the global CHARSXP cache and have unmarked encoding (ASCII). Thanks to Matthew Dowle for suggesting improvements to the way the hash code is generated in unique.c. ? The enquote() utility, in use internally, is exported now. ? .C() and .Fortran() now map non-zero return values (other than NA_LOGICAL) for logical vectors to TRUE: it has been an implicit assumption that they are treated as true. ? The print() methods for "glm" and "lm" objects now insert linebreaks in long calls in the same way that the print() methods for "summary.[g]lm" objects have long done. This does change the layout of the examples for a number of packages, e.g. MASS. (PR#14250) ? constrOptim() can now be used with method "SANN". (PR#14245) It gains an argument hessian to be passed to optim(), which allows all the ... arguments to be intended for f() and grad(). (PR#14071) ? curve() now allows expr to be an object of mode "expression" as well as "call" and "function". ? The "POSIX[cl]t" methods for Axis() have been replaced by a single method for "POSIXt". There are no longer separate plot() methods for "POSIX[cl]t" and "Date": the default method has been able to handle those classes for a long time. This _inter alia_ allows a single date-time object to be supplied, the wish of PR#14016. The methods had a different default ("") for xlab. ? Classes "POSIXct", "POSIXlt" and "difftime" have generators .POSIXct(), .POSIXlt() and .difftime(). Package authors are advised to make use of them (they are available from R 2.11.0) to proof against planned future changes to the classes. The ordering of the classes has been changed, so "POSIXt" is now the second class. See the document ?Updating packages for changes in R 2.12.x? on for the consequences for a handful of CRAN packages. ? The "POSIXct" method of as.Date() allows a timezone to be specified (but still defaults to UTC). ? New list2env() utility function as an inverse of as.list() and for fast multi-assign() to existing environment. as.environment() is now generic and uses list2env() as list method. ? There are several small changes to output which ?zap? small numbers, e.g. in printing quantiles of residuals in summaries from "lm" and "glm" fits, and in test statisics in print.anova(). ? Special names such as "dim", "names", etc, are now allowed as slot names of S4 classes, with "class" the only remaining exception. ? File .Renviron can have architecture-specific versions such as .Renviron.i386 on systems with sub-architectures. ? installed.packages() has a new argument subarch to filter on sub-architecture. ? The summary() method for packageStatus() now has a separate print() method. ? The default summary() method returns an object inheriting from class "summaryDefault" which has a separate print() method that calls zapsmall() for numeric/complex values. ? The startup message now includes the platform and if used, sub-architecture: this is useful where different (sub-)architectures run on the same OS. ? The getGraphicsEvent() mechanism now allows multiple windows to return graphics events, through the new functions setGraphicsEventHandlers(), setGraphicsEventEnv(), and getGraphicsEventEnv(). (Currently implemented in the windows() and X11() devices.) ? tools::texi2dvi() gains an index argument, mainly for use by R CMD Rd2pdf. It avoids the use of texindy by texinfo's texi2dvi >= 1.157, since that does not emulate 'makeindex' well enough to avoid problems with special characters (such as (, {, !) in indices. ? The ability of readLines() and scan() to re-encode inputs to marked UTF-8 strings on Windows since R 2.7.0 is extended to non-UTF-8 locales on other OSes. ? scan() gains a fileEncoding argument to match read.table(). ? points() and lines() gain "table" methods to match plot(). (Wish of PR#10472.) ? Sys.chmod() allows argument mode to be a vector, recycled along paths. ? There are |, & and xor() methods for classes "octmode" and "hexmode", which work bitwise. ? Environment variables R_DVIPSCMD, R_LATEXCMD, R_MAKEINDEXCMD, R_PDFLATEXCMD are no longer used nor set in an R session. (With the move to tools::texi2dvi(), the conventional environment variables LATEX, MAKEINDEX and PDFLATEX will be used. options("dvipscmd") defaults to the value of DVIPS, then to "dvips".) ? New function isatty() to see if terminal connections are redirected. ? summaryRprof() returns the sampling interval in component sample.interval and only returns in by.self data for functions with non-zero self times. ? print(x) and str(x) now indicate if an empty list x is named. ? install.packages() and remove.packages() with lib unspecified and multiple libraries in .libPaths() inform the user of the library location used with a message rather than a warning. ? There is limited support for multiple compressed streams on a file: all of [bgx]zfile() allow streams to be appended to an existing file, but bzfile() reads only the first stream. ? Function person() in package utils now uses a given/family scheme in preference to first/middle/last, is vectorized to handle an arbitrary number of persons, and gains a role argument to specify person roles using a controlled vocabulary (the MARC relator terms). ? Package utils adds a new "bibentry" class for representing and manipulating bibliographic information in enhanced BibTeX style, unifying and enhancing the previously existing mechanisms. ? A bibstyle() function has been added to the tools package with default JSS style for rendering "bibentry" objects, and a mechanism for registering other rendering styles. ? Several aspects of the display of text help are now customizable using the new Rd2txt_options() function. options("help_text_width") is no longer used. ? Added \href tag to the Rd format, to allow hyperlinks to URLs without displaying the full URL. ? Added \newcommand and \renewcommand tags to the Rd format, to allow user-defined macros. ? New toRd() generic in the tools package to convert objects to fragments of Rd code, and added "fragment" argument to Rd2txt(), Rd2HTML(), and Rd2latex() to support it. ? Directory R_HOME/share/texmf now follows the TDS conventions, so can be set as a texmf tree (?root directory? in MiKTeX parlance). ? S3 generic functions now use correct S4 inheritance when dispatching on an S4 object. See ?Methods, section on ?Methods for S3 Generic Functions? for recommendations and details. ? format.pval() gains a ... argument to pass arguments such as nsmall to format(). (Wish of PR#9574) ? legend() supports title.adj. (Wish of PR#13415) ? Added support for subsetting "raster" objects, plus assigning to a subset, conversion to a matrix (of colour strings), and comparisons (== and !=). ? Added a new parseLatex() function (and related functions deparseLatex() and latexToUtf8()) to support conversion of bibliographic entries for display in R. ? Text rendering of \itemize in help uses a Unicode bullet in UTF-8 and most single-byte Windows locales. ? Added support for polygons with holes to the graphics engine. This is implemented for the pdf(), postscript(), x11(type="cairo"), windows(), and quartz() devices (and associated raster formats), but not for x11(type="Xlib") or xfig() or pictex(). The user-level interface is the polypath() function in graphics and grid.path() in grid. ? File NEWS is now generated at installation with a slightly different format: it will be in UTF-8 on platforms using UTF-8, and otherwise in ASCII. There is also a PDF version, NEWS.pdf, installed at the top-level of the R distribution. ? kmeans(x, 1) now works. Further, kmeans now returns between and total sum of squares. ? arrayInd() and which() gain an argument useNames. For arrayInd, the default is now false, for speed reasons. ? As is done for closures, the default print method for the formula class now displays the associated environment if it is not the global environment. ? A new facility has been added for inserting code into a package without re-installing it, to facilitate testing changes which can be selectively added and backed out. See ?insertSource. ? New function readRenviron to (re-)read files in the format of ~/.Renviron and Renviron.site. ? require() will now return FALSE (and not fail) if loading the package or one of its dependencies fails. ? aperm() now allows argument perm to be a character vector when the array has named dimnames (as the results of table() calls do). Similarly, array() allows MARGIN to be a character vector. (Based on suggestions of Michael Lachmann.) ? Package utils now exports and documents functions aspell_package_Rd_files() and aspell_package_vignettes() for spell checking package Rd files and vignettes using Aspell, Ispell or Hunspell. ? Package news can now be given in Rd format, and news() prefers these inst/NEWS.Rd files to old-style plain text NEWS or inst/NEWS files. ? New simple function packageVersion(). ? The PCRE library has been updated to version 8.10. ? The standard Unix-alike terminal interface declares its name to readline as 'R', so that can be used for conditional sections in ~/.inputrc files. ? ?Writing R Extensions? now stresses that the standard sections in .Rd files (other than \alias, \keyword and \note) are intended to be unique, and the conversion tools now drop duplicates with a warning. The .Rd conversion tools also warn about an unrecognized type in a \docType section. ? ecdf() objects now have a quantile() method. ? format() methods for date-time objects now attempt to make use of a "tzone" attribute with "%Z" and "%z" formats, but it is not always possible. (Wish of PR#14358.) ? tools::texi2dvi(file, clean = TRUE) now works in more cases (e.g. where emulation is used and when file is not in the current directory). ? New function droplevels() to remove unused factor levels. ? system(command, intern = TRUE) now gives an error on a Unix-alike (as well as on Windows) if command cannot be run. It reports a non-success exit status from running command as a warning. On a Unix-alike an attempt is made to return the actual exit status of the command in system(intern = FALSE): previously this had been system-dependent but on POSIX-compliant systems the value return was 256 times the status. ? system() has a new argument ignore.stdout which can be used to (portably) ignore standard output. ? system(intern = TRUE) and pipe() connections are guaranteed to be avaliable on all builds of R. ? Sys.which() has been altered to return "" if the command is not found (even on Solaris). ? A facility for defining reference-based S4 classes (in the OOP style of Java, C++, etc.) has been added experimentally to package methods; see ?ReferenceClasses. ? The predict method for "loess" fits gains an na.action argument which defaults to na.pass rather than the previous default of na.omit. Predictions from "loess" fits are now named from the row names of newdata. ? Parsing errors detected during Sweave() processing will now be reported referencing their original location in the source file. ? New adjustcolor() utility, e.g., for simple translucent color schemes. ? qr() now has a trivial lm method with a simple (fast) validity check. ? An experimental new programming model has been added to package methods for reference (OOP-style) classes and methods. See ?ReferenceClasses. ? bzip2 has been updated to version 1.0.6 (bug-fix release). --with-system-bzlib now requires at least version 1.0.6. ? R now provides jss.cls and jss.bst (the class and bib style file for the Journal of Statistical Software) as well as RJournal.bib and Rnews.bib, and R CMD ensures that the .bst and .bib files are found by BibTeX. ? Functions using the TAR environment variable no longer quote the value when making system calls. This allows values such as tar --force-local, but does require additional quotes in, e.g., TAR = "'/path with spaces/mytar'". DEPRECATED & DEFUNCT: ? Supplying the parser with a character string containing both octal/hex and Unicode escapes is now an error. ? File extension .C for C++ code files in packages is now defunct. ? R CMD check no longer supports configuration files containing Perl configuration variables: use the environment variables documented in ?R Internals? instead. ? The save argument of require() now defaults to FALSE and save = TRUE is now deprecated. (This facility is very rarely actually used, and was superseded by the Depends field of the DESCRIPTION file long ago.) ? R CMD check --no-latex is deprecated in favour of --no-manual. ? R CMD Sd2Rd is formally deprecated and will be removed in R 2.13.0. PACKAGE INSTALLATION: ? install.packages() has a new argument libs_only to optionally pass --libs-only to R CMD INSTALL and works analogously for Windows binary installs (to add support for 64- or 32-bit Windows). ? When sub-architectures are in use, the installed architectures are recorded in the Archs field of the DESCRIPTION file. There is a new default filter, "subarch", in available.packages() to make use of this. Code is compiled in a copy of the src directory when a package is installed for more than one sub-architecture: this avoid problems with cleaning the sources between building sub-architectures. ? R CMD INSTALL --libs-only no longer overrides the setting of locking, so a previous version of the package will be restored unless --no-lock is specified. UTILITIES: ? R CMD Rprof|build|check are now based on R rather than Perl scripts. The only remaining Perl scripts are the deprecated R CMD Sd2Rd and install-info.pl (used only if install-info is not found) as well as some maintainer-mode-only scripts. *NB:* because these have been completely rewritten, users should not expect undocumented details of previous implementations to have been duplicated. R CMD no longer manipulates the environment variables PERL5LIB and PERLLIB. ? R CMD check has a new argument --extra-arch to confine tests to those needed to check an additional sub-architecture. Its check for ?Subdirectory 'inst' contains no files? is more thorough: it looks for files, and warns if there are only empty directories. Environment variables such as R_LIBS and those used for customization can be set for the duration of checking _via_ a file ~/.R/check.Renviron (in the format used by .Renviron, and with sub-architecture specific versions such as ~/.R/check.Renviron.i386 taking precedence). There are new options --multiarch to check the package under all of the installed sub-architectures and --no-multiarch to confine checking to the sub-architecture under which check is invoked. If neither option is supplied, a test is done of installed sub-architectures and all those which can be run on the current OS are used. Unless multiple sub-architectures are selected, the install done by check for testing purposes is only of the current sub-architecture (_via_ R CMD INSTALL --no-multiarch). It will skip the check for non-ascii characters in code or data if the environment variables _R_CHECK_ASCII_CODE_ or _R_CHECK_ASCII_DATA_ are respectively set to FALSE. (Suggestion of Vince Carey.) ? R CMD build no longer creates an INDEX file (R CMD INSTALL does so), and --force removes (rather than overwrites) an existing INDEX file. It supports a file ~/.R/build.Renviron analogously to check. It now runs build-time \Sexpr expressions in help files. ? R CMD Rd2dvi makes use of tools::texi2dvi() to process the package manual. It is now implemented entirely in R (rather than partially as a shell script). ? R CMD Rprof now uses utils::summaryRprof() rather than Perl. It has new arguments to select one of the tables and to limit the number of entries printed. ? R CMD Sweave now runs R with --vanilla so the environment setting of R_LIBS will always be used. C-LEVEL FACILITIES: ? lang5() and lang6() (in addition to pre-existing lang[1-4]()) convenience functions for easier construction of eval() calls. If you have your own definition, do wrap it inside #ifndef lang5 .... #endif to keep it working with old and new R. ? Header R.h now includes only the C headers it itself needs, hence no longer includes errno.h. (This helps avoid problems when it is included from C++ source files.) ? Headers Rinternals.h and R_ext/Print.h include the C++ versions of stdio.h and stdarg.h respectively if included from a C++ source file. INSTALLATION: ? A C99 compiler is now required, and more C99 language features will be used in the R sources. ? Tcl/Tk >= 8.4 is now required (increased from 8.3). ? System functions access, chdir and getcwd are now essential to configure R. (In practice they have been required for some time.) ? make check compares the output of the examples from several of the base packages to reference output rather than the previous output (if any). Expect some differences due to differences in floating-point computations between platforms. ? File NEWS is no longer in the sources, but generated as part of the installation. The primary source for changes is now doc/NEWS.Rd. ? The popen system call is now required to build R. This ensures the availability of system(intern = TRUE), pipe() connections and printing from postscript(). ? The pkg-config file libR.pc now also works when R is installed using a sub-architecture. ? R has always required a BLAS that conforms to IE60559 arithmetic, but after discovery of more real-world problems caused by a BLAS that did not, this is tested more thoroughly in this version. BUG FIXES: ? Calls to selectMethod() by default no longer cache inherited methods. This could previously corrupt methods used by as(). ? The densities of non-central chi-squared are now more accurate in some cases in the extreme tails, e.g. dchisq(2000, 2, 1000), as a series expansion was truncated too early. (PR#14105) ? pt() is more accurate in the left tail for ncp large, e.g. pt(-1000, 3, 200). (PR#14069) ? The default C function (R_binary) for binary ops now sets the S4 bit in the result if either argument is an S4 object. (PR#13209) ? source(echo=TRUE) failed to echo comments that followed the last statement in a file. ? S4 classes that contained one of "matrix", "array" or "ts" and also another class now accept superclass objects in new(). Also fixes failure to call validObject() for these classes. ? Conditional inheritance defined by argument test in methods::setIs() will no longer be used in S4 method selection (caching these methods could give incorrect results). See ?setIs. ? The signature of an implicit generic is now used by setGeneric() when that does not use a definition nor explicitly set a signature. ? A bug in callNextMethod() for some examples with "..." in the arguments has been fixed. See file src/library/methods/tests/nextWithDots.R in the sources. ? match(x, table) (and hence %in%) now treat "POSIXlt" consistently with, e.g., "POSIXct". ? Built-in code dealing with environments (get(), assign(), parent.env(), is.environment() and others) now behave consistently to recognize S4 subclasses; is.name() also recognizes subclasses. ? The abs.tol control parameter to nlminb() now defaults to 0.0 to avoid false declarations of convergence in objective functions that may go negative. ? The standard Unix-alike termination dialog to ask whether to save the workspace takes a EOF response as n to avoid problems with a damaged terminal connection. (PR#14332) ? Added warn.unused argument to hist.default() to allow suppression of spurious warnings about graphical parameters used with plot=FALSE. (PR#14341) ? predict.lm(), summary.lm(), and indeed lm() itself had issues with residual DF in zero-weighted cases (the latter two only in connection with empty models). (Thanks to Bill Dunlap for spotting the predict() case.) ? aperm() treated resize = NA as resize = TRUE. ? constrOptim() now has an improved convergence criterion, notably for cases where the minimum was (very close to) zero; further, other tweaks inspired from code proposals by Ravi Varadhan. ? Rendering of S3 and S4 methods in man pages has been corrected and made consistent across output formats. ? Simple markup is now allowed in \title sections in .Rd files. ? The behaviour of as.logical() on factors (to use the levels) was lost in R 2.6.0 and has been restored. ? prompt() did not backquote some default arguments in the \usage section. (Reported by Claudia Beleites.) ? writeBin() disallows attempts to write 2GB or more in a single call. (PR#14362) ? new() and getClass() will now work if Class is a subclass of "classRepresentation" and should also be faster in typical calls. ? The summary() method for data frames makes a better job of names containing characters invalid in the current locale. ? [[ sub-assignment for factors could create an invalid factor (reported by Bill Dunlap). ? Negate(f) would not evaluate argument f until first use of returned function (reported by Olaf Mersmann). ? quietly=FALSE is now also an optional argument of library(), and consequently, quietly is now propagated also for loading dependent packages, e.g., in require(*, quietly=TRUE). ? If the loop variable in a for loop was deleted, it would be recreated as a global variable. (Reported by Radford Neal; the fix includes his optimizations as well.) ? Task callbacks could report the wrong expression when the task involved parsing new code. (PR#14368) ? getNamespaceVersion() failed; this was an accidental change in 2.11.0. (PR#14374) ? identical() returned FALSE for external pointer objects even when the pointer addresses were the same. ? L$a at x[] <- val did not duplicate in a case it should have. ? tempfile() now always gives a random file name (even if the directory is specified) when called directly after startup and before the R RNG had been used. (PR#14381) ? quantile(type=6) behaved inconsistently. (PR#14383) ? backSpline(.) behaved incorrectly when the knot sequence was decreasing. (PR#14386) ? The reference BLAS included in R was assuming that 0*x and x*0 were always zero (whereas they could be NA or NaN in IEC 60559 arithmetic). This was seen in results from tcrossprod, and for example that log(0) %*% 0 gave 0. ? The calculation of whether text was completely outside the device region (in which case, you draw nothing) was wrong for screen devices (which have [0, 0] at top-left). The symptom was (long) text disappearing when resizing a screen window (to make it smaller). (PR#14391) ? model.frame(drop.unused.levels = TRUE) did not take into account NA values of factors when deciding to drop levels. (PR#14393) ? library.dynam.unload required an absolute path for libpath. (PR#14385) Both library() and loadNamespace() now record absolute paths for use by searchpaths() and getNamespaceInfo(ns, "path"). ? The self-starting model NLSstClosestX failed if some deviation was exactly zero. (PR#14384) ? X11(type = "cairo") (and other devices such as png using cairographics) and which use Pango font selection now work around a bug in Pango when very small fonts (those with sizes between 0 and 1 in Pango's internal units) are requested. (PR#14369) ? Added workaround for the font problem with X11(type = "cairo") and similar on Mac OS X whereby italic and bold styles were interchanged. (PR#13463 amongst many other reports.) ? source(chdir = TRUE) failed to reset the working directory if it could not be determined - that is now an error. ? Fix for crash of example(rasterImage) on x11(type="Xlib"). ? Force Quartz to bring the on-screen display up-to-date immediately before the snapshot is taken by grid.cap() in the Cocoa implementation. (PR#14260) ? model.frame had an unstated 500 byte limit on variable names. (Example reported by Terry Therneau.) ? The 256-byte limit on names is now documented. ? Subassignment by [, [[ or $ on an expression object with value NULL coerced the object to a list. -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com From pd.mes at cbs.dk Mon Dec 6 11:19:37 2010 From: pd.mes at cbs.dk (Peter Dalgaard) Date: Mon, 6 Dec 2010 11:19:37 +0100 Subject: R 2.12.1 scheduled for December 16 Message-ID: This is to announce that we plan to release R version 2.12.1 on Thursday, December 16, 2010. 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 -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com From pd.mes at cbs.dk Thu Dec 16 10:35:01 2010 From: pd.mes at cbs.dk (Peter Dalgaard) Date: Thu, 16 Dec 2010 10:35:01 +0100 Subject: [R] R 2.12.1 is released Message-ID: <36B535C9-D476-450F-96FA-A85158C416B7@cbs.dk> 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). ? 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(, 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 [[<- 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. ? [[<- 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 < 1.6, will be better than before, though still a little clunky. With Cairo >= 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. -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com From pd.mes at cbs.dk Thu Dec 30 23:37:20 2010 From: pd.mes at cbs.dk (Peter Dalgaard) Date: Thu, 30 Dec 2010 23:37:20 +0100 Subject: [R] The R Journal, Vol.2 Issue 2 Message-ID: <9DFEF59F-1FEE-4CF3-B360-F987CAC98F1D@cbs.dk> 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 -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com