From pd.mes at cbs.dk Mon Feb 13 10:12:38 2012 From: pd.mes at cbs.dk (Peter Dalgaard) Date: Mon, 13 Feb 2012 10:12:38 +0100 Subject: Release plans for 2.14.2 and 2.15.0 Message-ID: <85FB2210-5B38-413C-9412-A30B007C19DE@cbs.dk> 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. -- Peter Dalgaard, Professor 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 Wed Feb 29 15:40:36 2012 From: pd.mes at cbs.dk (Peter Dalgaard) Date: Wed, 29 Feb 2012 15:40:36 +0100 Subject: R 2.14.2 is released + R anniversary Message-ID: 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 >= 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 at cbs.dk Priv: PDalgd at gmail.com From pd.mes at cbs.dk Fri Mar 30 11:07:41 2012 From: pd.mes at cbs.dk (Peter Dalgaard) Date: Fri, 30 Mar 2012 11:07:41 +0200 Subject: R 2.15.0 is released Message-ID: <6D8CC327-E4C9-4184-BF3F-3CB184FA7A3E@cbs.dk> 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, . 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() was incorrect in the multivariate case, for p >= 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
  • 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 at cbs.dk Priv: PDalgd at gmail.com From f.harrell at Vanderbilt.Edu Wed May 2 15:12:31 2012 From: f.harrell at Vanderbilt.Edu (Frank Harrell) Date: Wed, 2 May 2012 08:12:31 -0500 Subject: DEADLINE FAST APPROACHING for useR! 2012 Message-ID: <4FA132BF.5060604@vanderbilt.edu> 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 -- Frank E Harrell Jr Professor and Chairman School of Medicine Department of Biostatistics Vanderbilt University From pd.mes at cbs.dk Tue May 29 13:40:44 2012 From: pd.mes at cbs.dk (Peter Dalgaard) Date: Tue, 29 May 2012 13:40:44 +0200 Subject: Release plans: R-2.15.1 on June 22 Message-ID: Just a note, mainly to people who maintain larger R installations, that we intend to have a patch release version on June 22. The nickname will be "Roasted Marshmallows". This is somewhat later than previous .1 releases, but we are also now aiming for an annual rather than biannual release scheme. There have been very few issues with 2.15.0, but some people may be waiting superstitiously for a .1 release (or expecting one come along any day now) and need to be informed about the plans. -- Peter Dalgaard, Professor 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 Jun 22 11:33:55 2012 From: pd.mes at cbs.dk (Peter Dalgaard) Date: Fri, 22 Jun 2012 11:33:55 +0200 Subject: R 2.15.1 is released Message-ID: The build system has rolled up R-2.15.1.tar.gz (codename "Roasted Marshmallows") 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-2.15.1.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) = fa1101eba3c4c01ffa154053a5dcd2d6 MD5 (INSTALL) = 37adac6d0fbadf25b5a40e3f7535415e MD5 (NEWS) = 8d6a52daa2d18630a8aa7a8e7a58ddf6 MD5 (NEWS.html) = 4a8f2f5824ba44427719e2badc5128d1 MD5 (ONEWS) = 0c3e10eef74439786e5fceddd06dac71 MD5 (OONEWS) = b0d650eba25fc5664980528c147a20db MD5 (R-latest.tar.gz) = fcdf247e707fdade82b78bcf911a54f1 MD5 (README) = 296871fcf14f49787910c57b92655c76 MD5 (RESOURCES) = a7a02d98a407c3cb8674d067608f14fc MD5 (THANKS) = 159efc7bd4ae7b23dda07c1d431657bc MD5 (R-2/R-2.15.1.tar.gz) = fcdf247e707fdade82b78bcf911a54f1 This is the relevant part of the NEWS file: CHANGES IN R VERSION 2.15.1: NEW FEATURES: o source() now uses withVisible() rather than .Internal(eval.with.vis). This sometimes alters tracebacks slightly. o install.packages("pkg_version.tgz") on Mac OS X now has sanity checks that this is actually a binary package (as people have tried it with incorrectly named source packages). o splineDesign() and spline.des() in package splines have a new option sparse which can be used for efficient construction of a sparse B-spline design matrix (_via_ Matrix). o norm() now allows type = "2" (the 'spectral' or 2-norm) as well, mainly for didactical completeness. o pmin() and pmax()) now also work when one of the inputs is of length zero and others are not, returning a zero-length vector, analogously to, say, +. o colorRamp() (and hence colorRampPalette()) now also works for the boundary case of just one color when the ramp is flat. o qqline() has new optional arguments distribution, probs and qtype, following the example of lattice's panel.qqmathline(). o .C() gains some protection against the misuse of character vector arguments. (An all too common error is to pass character(N), which initializes the elements to "", and then attempt to edit the strings in-place, sometimes forgetting to terminate them.) o Calls to the new function globalVariables() in package utils declare that functions and other objects in a package should be treated as globally defined, so that CMD check will not note them. o print(packageDescription(*)) trims the Collate field by default. o The included copy of zlib has been updated to version 1.2.7. o A new option "show.error.locations" has been added. When set to TRUE, error messages will contain the location of the most recent call containing source reference information. (Other values are supported as well; see ?options.) o The NA warning messages from e.g. pchisq() now report the call to the closure and not that of the .Internal. o Added Polish translations by <81>ukasz Daniel. PERFORMANCE IMPROVEMENTS: o In package parallel, makeForkCluster() and the multicore-based functions use native byte-order for serialization (deferred from 2.15.0). o lm.fit(), lm.wfit(), glm.fit() and lsfit() do less copying of objects, mainly by using .Call() rather than .Fortran(). o .C() and .Fortran() do less copying: arguments which are raw, logical, integer, real or complex vectors and are unnamed are not copied before the call, and (named or not) are not copied after the call. Lists are no longer copied (they are supposed to be used read-only in the C code). o tabulate() makes use of .C(DUP = FALSE) and hence does not copy bin. (Suggested by Tim Hesterberg.) It also avoids making a copy of a factor argument bin. o Other functions (often or always) doing less copying include cut(), dist(), the complex case of eigen(), hclust(), image(), kmeans(), loess(), stl() and svd(LINPACK = TRUE). o There is less copying when using primitive replacement functions such as names(), attr() and attributes(). DEPRECATED AND DEFUNCT: o The converters for use with .C() (see ?getCConverterDescriptions) are deprecated: use the .Call() interface instead. There are no known examples (they were never fully documented). UTILITIES: o For R CMD check, a few people have reported problems with junctions on Windows (although they were tested on Windows 7, XP and Server 2008 machines and it is unknown under what circumstances the problems occur). Setting the environment variable R_WIN_NO_JUNCTIONS to a non-empty value (e.g. in ~/.R/check.Renviron) will force copies to be used instead. INSTALLATION: o R CMD INSTALL with _R_CHECK_INSTALL_DEPENDS_ set to a true value (as done by R CMD check --as-cran) now restricts the packages available when lazy-loading as well as when test-loading (since packages such as ETLUtils and agsemisc had top-level calls to library() for undeclared packages). This check is now also available on Windows. C-LEVEL FACILITIES: o C entry points mkChar and mkCharCE now check that the length of the string they are passed does not exceed 2^31-1 bytes: they used to overflow with unpredictable consequences. o C entry points R_GetCurrentSrcref and R_GetSrcFilename have been added to the API to allow debuggers access to the source references on the stack. WINDOWS-SPECIFIC CHANGES: o Windows-specific changes will now be announced in this file (NEWS). Changes up and including R 2.15.0 remain in the CHANGES file. o There are two new environment variables which control the defaults for command-line options. If R_WIN_INTERNET2 is set to a non-empty value, it is as if --internet2 was used. If R_MAX_MEM_SIZE is set, it gives the default memory limit if --max-mem-size is not specified: invalid values being ignored. BUG FIXES: o lsfit() lost the names from the residuals. o More cases in which merge() could create a data frame with duplicate column names now give warnings. Cases where names specified in by match multiple columns are errors. o Nonsense uses such as seq(1:50, by = 5) (from package plotrix) and seq.int(1:50, by = 5) are now errors. o The residuals in the 5-number summary printed by summary() on an "lm" object are now explicitly labelled as weighted residuals when non-constant weights are present. (Wish of PR#14840.) o tracemem() reported that all objects were copied by .C() or .Fortran() whereas only some object types were ever copied. It also reported and marked as copies _some_ transformations such as rexp(n, x): it no longer does so. o The plot() method for class "stepfun" only used the optional xval argument to compute xlim and not the points at which to plot (as documented). (PR#14864) o Names containing characters which need to be escaped were not deparsed properly. (PR#14846) o Trying to update (recommended) packages in R_HOME/library without write access is now dealt with more gracefully. Further, such package updates may be skipped (with a warning), when a newer installed version is already going to be used from .libPaths(). (PR#14866) o hclust() is now fast again (as up to end of 2003), with a different fix for the "median"/"centroid" problem. (PR#4195). o get_all_vars() failed when the data came entirely from vectors in the global environment. (PR#14847) o R CMD check with _R_CHECK_NO_RECOMMENDED_ set to a true value (as done by the --as-cran option) could issue false errors if there was an indirect dependency on a recommended package. o formatC() uses the C entry point str_signif which could write beyond the length allocated for the output string. o Missing default argument added to implicit S4 generic for backsolve(). (PR#14883) o Some bugs have been fixed in handling load actions that could fail to export assigned items or generate spurious warnings in CMD check on loading. o For tiff(type = "windows"), the numbering of per-page files except the last was off by one. o On Windows, loading package stats (which is done for a default session) would switch line endings on stdout and stderr from CRLF to LF. This affected Rterm and R CMD BATCH. o On Windows, the compatibility function x11() had not kept up with changes to windows(), and issued warnings about bad parameters. (PR#14880) o On Windows, the Sys.glob() function did not handle UNC paths as it was designed to try to do. (PR#14884) o In package parallel, clusterApply() and similar failed to handle a (pretty pointless) length-1 argument. (PR#14898) o Quartz Cocoa display reacted asynchronously to dev.flush() which means that the redraw could be performed after the plot has been already modified by subsequent code. The redraw is now done synchronously in dev.flush() to allow animations without sleep cycles. o Source locations reported in traceback() were incorrect when byte-compiled code was on the stack. o plogis(x, lower = FALSE, log.p = TRUE) no longer underflows early for large x (e.g. 800). o ?Arithmetic's "1 ^ y and y ^ 0 are 1, _always_" now also applies for integer vectors y. o X11-based pixmap devices like png(type = "Xlib") were trying to set the cursor style, which triggered some warnings and hangs. o Code executed by the built-in HTTP server no longer allows other HTTP clients to re-enter R until the current worker evaluation finishes, to prevent cascades. o The plot() and Axis() methods for class "table" now respect graphical parameters such as cex.axis. (Reported by Martin Becker.) o Under some circumstances package.skeleton() would give out progress reports that could not be translated and so were displayed by question marks. Now they are always in English. (This was seen for CJK locales on Windows, but may have occurred elsewhere.) o The evaluator now keeps track of source references outside of functions, e.g. when source() executes a script. o The replacement method for window() now works correctly for multiple time series of class "mts". (PR#14925) o is.unsorted() gave incorrect results on non-atomic objects such as data frames. (Reported by Matthew Dowle.) o The value returned by tools::psnice() for invalid pid values was not always NA as documented. o Closing an X11() window while locator() was active could abort the R process. o getMethod(f, sig) produced an incorrect error message in some cases when f was not a string). o Using a string as a "call" in an error condition with options(showErrorCalls=TRUE) could cause a segfault. (PR#14931) o The string "infinity" allowed by C99 was not accepted as a numerical string value by e.g. scan() and as.character(). (PR#14933) o In legend(), setting some entries of lwd to NA was inconsistent (depending on the graphics device) in whether it would suppress those lines; now it consistently does so. (PR#14926) o by() failed for a zero-row data frame. (Reported by Weiqiang Qian) o Yates correction in chisq.test() could be bigger than the terms it corrected, previously leading to an infinite test statistic in some corner cases which are now reported as NaN. o xgettext() and related functions sometimes returned items that were not strings for translation. (PR#14935) o plot(, which=5) now correctly labels the factor level combinations for the special case where all h[i,i] are the same. (PR#14837) -- Peter Dalgaard, Professor 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 plummerM at iarc.fr Wed Jul 11 09:57:26 2012 From: plummerM at iarc.fr (Martyn Plummer) Date: Wed, 11 Jul 2012 09:57:26 +0200 Subject: The R Journal, Vol. 4 Issue 1 Message-ID: <1341993446.1963.42.camel@braque.iarc.fr> Dear All, The first issue of the fourth volume of The R Journal is now available at http://journal.r-project.org/current.html Thanks to everyone involved. Martyn Plummer Editor-in-Chief ----------------------------------------------------------------------- This message and its attachments are strictly confidenti...{{dropped:8}} From pd.mes at cbs.dk Tue Oct 2 12:08:19 2012 From: pd.mes at cbs.dk (Peter Dalgaard) Date: Tue, 2 Oct 2012 12:08:19 +0200 Subject: [R] Release plans: R-2.15.2 on October 26 Message-ID: Just a note that we intend to have a second patch release version on October 26. The nickname will be "Trick or Treat". Details of current changes can be found at http://stat.ethz.ch/R-manual/R-devel/doc/html/NEWS.html (scroll past the R-devel stuff and look at 2.15.1 patched.) -- Peter Dalgaard, Professor 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 26 13:57:07 2012 From: pd.mes at cbs.dk (Peter Dalgaard) Date: Fri, 26 Oct 2012 13:57:07 +0200 Subject: R 2.15.2 is released Message-ID: The build system has rolled up R-2.15.2.tar.gz (codename "Trick or Treat") 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-2.15.2.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) = 358176af07d3200c9cd70b5c313d1779 MD5 (INSTALL) = 37adac6d0fbadf25b5a40e3f7535415e MD5 (NEWS) = 2fa905e20f935ca03369d1738e41d079 MD5 (NEWS.html) = 5f9f281cb579b51a6dbfc31831ac6c99 MD5 (ONEWS) = 0c3e10eef74439786e5fceddd06dac71 MD5 (OONEWS) = b0d650eba25fc5664980528c147a20db MD5 (R-latest.tar.gz) = 346d16bab26fcae15e53755be8a69b00 MD5 (README) = 296871fcf14f49787910c57b92655c76 MD5 (RESOURCES) = c7cb32499ebbf85deb064aab282f93a4 MD5 (THANKS) = 7a87321ccf0ecd2bece697e39dce5e67 MD5 (R-2/R-2.15.2.tar.gz) = 346d16bab26fcae15e53755be8a69b00 This is the relevant part of the NEWS file: CHANGES IN R VERSION 2.15.2: NEW FEATURES: o The X11() window gains an icon: the latter may be especially useful on Ubuntu's 'Unity' interface. The WM_CLASS should be set in circumstances where the Window Manager failed to make use of X11 resource settings. (Contributed by Philip Johnson.) o The "Date" and "POSIXt" methods for cut() will accept an unsorted breaks argument (as the default method does, although this was undocumented). (Wish of PR#14961.) o Reference class methods (in the methods package) that use other methods in an indirect way (e.g., by sapply()) must tell the code analysis to include that method. They can now do so by invoking $usingMethods(). o More Polish translations are available: for the RGui menus and for several recommended packages. o Multistratum MANOVA works. In fact, it seems to have done so for years in spite of the help page claiming it did not. o qqline() has new optional arguments distribution, probs and qtype, following the example of lattice's panel.qqmathline(). o The handling of single quotes in the en at quot pseudo-language has been slightly improved. Double quotes are no longer converted. o New functions checkPoFiles() and checkPoFile() have been added to the tools package to check for consistency of format strings in translation files. o model.matrix(~1, ...) now also contains the same rownames that less trivial formulae produce. (Wish of PR#14992, changes the output of several packages.) o Misuse of rep() on undocumented types of objects (e.g. calls) is now reported as an error. o The included LAPACK has been updated to 3.4.1, with some patches from the current SVN sources. (_Inter alia_, this resolves PR#14692.) o file.copy(recursive = TRUE) has some additional checks on user error leading to attempted infinite recursion (and on some platforms to crashing R). o PCRE has been updated to version 8.31, a bug-fix release. o The included version of liblzma has been updated to version 5.0.4, a minor bug-fix release. o New function .bincode(), a 'bare-bones' version of cut.default(labels = FALSE) for use in packages with image() methods. o The HTML manuals now use directional single quotes. o maintainer() now converts embedded new lines to spaces. It no longer gives a non-obvious error for non-installed packages. o The X11() device has some protection against being used with forked processes _via_ package parallel. o Setting the environment variable R_OSX_VALGRIND (to any value) allows R to be run under valgrind on Mac OS 10.6 and 10.7 (valgrind currently has very limited support for 10.8), provided system() is not used (directly or indirectly). This should not be needed for valgrind >= 3.8.1. o The model.frame() method for "lm" uses xlevels: this is safer if data was supplied or model = FALSE was used and the levels of factors used in the fit had been re-ordered since fitting. Similarly, model.frame(fm, data=) copies across the variables used for safe prediction from the fit. o Functions such as parLapply() in package parallel can make use of a default cluster if one is set. (Reported by Martin Morgan.) o chol(pivot = TRUE, LINPACK = FALSE) is now available using LAPACK 3.2 subroutine DPSTRF. o The functions .C(), .Call(), .External() and .Fortran() now check that they are called with an unnamed first argument: the formal arguments were changed from name= to .NAME= in R 2.13.0, but some packages were still using the old name. This is currently a warning, but will be an error in future. o step() no longer tries to improve a model with AIC of -Inf (a perfect fit). o spline() and splinefun() gain a new method "hyman", an implementation of Hyman's method of constructing monotonic interpolation splines. (Based on contributions of Simon Wood and Rob Hyndman.) o On Windows, the C stack size has been increased to 64MB (it has been 10MB since the days of 32MB RAM systems). PERFORMANCE IMPROVEMENTS: o array() is now implemented in C code (for speed) when data is atomic or an unclassed list (so it is known that as.vector(data) will have no class to be used by rep()). o rep() is faster and uses less memory, substantially so in some common cases (e.g. if times is of length one or length.out is given, and each = 1). o findInterval(), tabulate(), cut(), hist() and image.default() all use .Call() and are more efficient. o duplicated(), unique() and similar now support vectors of lengths above 2^29 on 64-bit platforms. o Omitting PACKAGE in .C() etc calls was supposed to make use of the DLL from the namespace within which the enclosing function was defined. It was less successful in doing so than it might be, and gave no indication it had failed. A new search strategy is very successful and gives a warning when it fails. In most cases this is because the entry point is not actually provided by that package (and so PACKAGE should be used to indicate which package is intended) but in some the namespace does not have a DLL specified by a useDynLib() directive so PACKAGE is required. UTILITIES: o R CMD check now checks if a package can be loaded by library(pkgname, lib.loc = "somewhere") without being on the library search path (unless it is already installed in .Library, when it always will be). o R CMD check --as-cran notes 'hidden' files and directories (with names starting with a dot) that are not needed for the operation of R CMD INSTALL or R CMD build: such files should be excluded from the published tarball. o R CMD check (if checking subdirectories) checks that the R code in any demos is ASCII and can be parsed, and warns if not. o When R CMD Rd2pdf is used with inputenx.sty, it allows further characters (mainly for Eastern European languages) by including ix-utf8enc.dfu (if available). (Wish of PR#14989.) o R CMD build now omits several types of hidden files/directories, including inst/doc/.Rinstignore, vignettes/.Rinstignore, (.Rinstignore should be at top level), .deps under src, .Renviron, .Rprofile, .Rproj.user, .backups, .cvsignore, .cproject, .directory, .dropbox, .exrc, .gdb.history, .gitattributes, .gitignore, .gitmodules, .hgignore, .hgtags, .htaccess, .latex2html-init, .project, .seed, .settings, .tm_properties and various leftovers. o R CMD check now checks for .C(), .Call(), .External() and .Fortran() calls in other packages, and gives a warning on those found from R itself (which are not part of the API and change without notice: many will changed for R 2.16.0). C-LEVEL FACILITIES: o The limit for R_alloc on 64-bit platforms has been raised to just under 32GB (from just under 16GB). o The misuse of .C("name", ..., PACKAGE = foo) where foo is an arbitrary R object is now an error. The misuse .C("name",..., PACKAGE = "") is now warned about in R CMD check, and will be an error in future. DEPRECATED AND DEFUNCT: o Use of array() with a 0-length dim argument is deprecated with a warning (and was contrary to the documentation). o Use of tapply() with a 0-length INDEX list is deprecated with a warning. o Translation packages are deprecated. o Calling rep() or rep.int() on a pairlist is deprecated and will give a warning. In any case, rep() converted a pairlist to a list so you may as well do that explicitly. o Entry point rcont2 is no longer part of the API, and will move to package stats in R 2.16.0. o The 'internal' graphics device invoked by .Call("R_GD_nullDevice", package = "grDevices") is about to be removed: use pdf(file = NULL) instead. o eigen(EISPACK = TRUE), chol(pivot = FALSE, LINPACK = TRUE), chol2inv(LINPACK = TRUE), solve(LINPACK = TRUE) and svd(LINPACK = TRUE) are deprecated and give a warning. They were provided for compatibility with R 1.7.0 (Mar 2003)! o The 'internal function' kappa.tri() has been renamed to .kappa_tri() so it is not inadvertently called as a method for class "tri". o Functions sessionData() and browseAll() in package methods are on a help page describing them as 'deprecated' and are now formally deprecated. PACKAGE INSTALLATION: o For a Windows or Mac OS X binary package install, install.packages() will check if a source package is available on the same repositories, and report if it is a later version or there is a source package but no binary package available. This check can be suppressed: see the help page. o install.packages(type = "both") has been enhanced. In interactive use it will ask whether to choose the source version of a package if the binary version is older and contains compiled code, and also asks if source packages with no binary version should be installed). INSTALLATION: o There is a new configure option --with-libtiff (mainly in case the system installation needs to be avoided). o LAPACK 3.4.1 does use some Fortran 90 features, so g77 no longer suffices. o If an external LAPACK is used, it must be version 3.2 or later. BUG FIXES: o On Windows, starting Rterm via R.exe caused Ctrl-C to misbehave. (PR#14948) o The tools::latexToUtf8() function missed conversions that were contained within braces. o Long timezone specifications (such as a file name preceded by :) could crash as.POSIXlt. (PR#14945) o R CMD build --resave-data could fail if there was no data directory but there was an R/sysdata.rda file. (PR#14947) o is.na() misbehaved on a 0-column data frame. (PR#14959) o anova.lmlist() failed if test was supplied. (PR#14960) It was unable to compute Cp tests for object of class "lm" (it assumed class "glm"). o The formula method for sunflowerplot() now allows xlab and ylab to be set. (Reported by Gerrit Eichner.) o The "POSIXt" and "Date" methods for hist() could fail on Windows where adjustments to the right-hand boundary crossed a DST transition time. o On Windows, the code in as.POSIXct() to handle incorrectly specified isdst fields might have resulted in NA being returned. o aov() and manova() gave spurious warning about singular error model in the multiresponse case. o In ns() and bs(), specifying knots = NULL is now equivalent to omitting it, also when df is specified. (PR#14970) o sprintf() did not accept numbered arguments ending in zero. (PR#14975) o rWishart() could overflow the C stack and maybe crash the R process for dimensions of several hundreds or more. (Reported by Michael Braun on R-sig-mac.) o Base package vignettes (e.g. vignette("Sweave")) were not fully installed in builds of R from the tarball. o lchoose() and choose() could overflow the C stack and crash R. o When given a 0-byte file and asked to keep source references, parse() read input from stdin() instead. o pdf(compress = TRUE) did not delete temporary files it created until the end of the R session. (PR#14991) o logLik() did not detect the error of applying it to a multiple-response linear model. (PR#15000) o file.copy(recursive = TRUE) did not always report FALSE for a failure two or more directories deep. o qgeom() could return -1 for extremely small q. (PR#14967.) o smooth.spline() used DUP = FALSE which allowed its compiled C code to change the function: this was masked by the default byte-compilation. (PR#14965.) o In Windows, the GUI preferences for foreground color were not always respected. (Reported by Benjamin Wells.) o On OS X, the Quartz versions of the bitmap devices did not respect antialias = "none". (PR#15006.) o unique() and similar would infinite-loop if called on a vector of length > 2^29 (but reported that the vector was too long for 2^30 or more). o parallel::stopCluster() now works with MPI clusters without snow being on the search path. o terms.formula() could exhaust the stack, and the stack check did not always catch this before the segfault. (PR#15013) o sort.list(method = "radix") could give incorrect results on certain compilers (seen with clang on Mac OS 10.7 and Xcode 4.4.1). o backsolve(T, b) gave incorrect results when nrows(b) > ncols(T) and b had more than one column. It could segfault or give nonsense if k was specified as more than ncols(T). o smooth.spline() did not check that a specified numeric spar was of length 1, and gave corrupt results if it was of length 0. o Protection added to do_system. (PR#15025) o Printing of vectors with names > 1000 characters now works correctly rather than truncating. (PR#15028) o qr() for a complex matrix did not pivot the column names. o --with-blas='-framework vecLib' now also works on OS X 10.8. o R CMD check no longer fails with an error if a DESCRIPTION file incorrectly contains a blank line. (Reported by Bill Dunlap.) o install.packages(type = "both") could call chooseCRANmirror() twice. o lm.wfit() could segfault in R 2.15.1 if all the weights were zero. (PR#15044) o A malformed package name could cause R CMD INSTALL to write outside the target library. o Some of the quality control functions (e.g. tools::checkFF()) were wrongly identifying the source of S4 methods in a package and so not checking them. o The default type of display by browseEnv() when using R.app on Mac OS X has been incorrect for a long time. o The implementation of importMethodsFrom in a NAMESPACE file could be confused and fail to find generics when importing from multiple packages (reported and fixed by Michael Lawrence). o The detection of the C stack direction is better protected against compiler optimization. (PR#15011.) o Long custom line types would sometimes segfault on the cairographics-based devices. (PR#15055.) o tools::checkPoFile() unprotected too early in its C code and so segfaulted from time to time. o The Fortran code underlying nlminb() could infinite-loop if any of the input functions returned NA or NaN. This is now an error for the gradient or Hessian, and a warning for the function (with the value replaced by Inf). (In part, PR#15052.) o The code for creating coerce() methods could generate false notes about ambiguous selection; the notes have been suppressed for this function. o arima.sim() could give too long an output in some corner cases (in part, PR#15068). o anova.glm() with test = "Rao" didn't work when models included an offset. (Reported by Soren Feodor Nielsen.) o as.data.frame.matrix() could return invalid data frame with no row.names attribute for 0-row matrix. (Reported by Herv'e Pag`es.) o Compilation with the vecLib or Accelerate frameworks on OS X without using that also for LAPACK is more likely to be successful. -- Peter Dalgaard, Professor 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 martyn.plummer at r-project.org Fri Dec 14 16:23:08 2012 From: martyn.plummer at r-project.org (Martyn Plummer) Date: Fri, 14 Dec 2012 16:23:08 +0100 Subject: The R Journal, Volume 4, Issue 2 Message-ID: <1355498588.2084.43.camel@braque.iarc.fr> Dear All, The latest issue of The R Journal is now available at http://journal.r-project.org/current.html Thanks to everyone involved. Martyn Plummer Editor-in-Chief ----------------------------------------------------------------------- This message and its attachments are strictly confidenti...{{dropped:8}}