Interview Rapid-I -Ingo Mierswa and Simon Fischer

Here is an interview with Dr Ingo Mierswa , CEO of Rapid -I and Dr Simon Fischer, Head R&D. Rapid-I makes the very popular software Rapid Miner – perhaps one of the earliest leading open source software in business analytics and business intelligence. It is quite easy to use, deploy and with it’s extensions and innovations (including compatibility with R )has continued to grow tremendously through the years.

In an extensive interview Ingo and Simon talk about algorithms marketplace, extensions , big data analytics, hadoop, mobile computing and use of the graphical user interface in analytics.

Special Thanks to Nadja from Rapid I communication team for helping coordinate this interview.( Statuary Blogging Disclosure- Rapid I is a marketing partner with Decisionstats as per the terms in https://decisionstats.com/privacy-3/)

Ajay- Describe your background in science. What are the key lessons that you have learnt while as scientific researcher and what advice would you give to new students today.

Ingo: My time as researcher really was a great experience which has influenced me a lot. I have worked at the AI lab of Prof. Dr. Katharina Morik, one of the persons who brought machine learning and data mining to Europe. Katharina always believed in what we are doing, encouraged us and gave us the space for trying out new things. Funnily enough, I never managed to use my own scientific results in any real-life project so far but I consider this as a quite common gap between science and the “real world”. At Rapid-I, however, we are still heavily connected to the scientific world and try to combine the best of both worlds: solving existing problems with leading-edge technologies.

Simon: In fact, during my academic career I have not worked in the field of data mining at all. I worked on a field some of my colleagues would probably even consider boring, and that is theoretical computer science. To be precise, my research was in the intersection of game theory and network theory. During that time, I have learnt a lot of exciting things, none of which had any business use. Still, I consider that a very valuable experience. When we at Rapid-I hire people coming to us right after graduating, I don’t care whether they know the latest technology with a fancy three-letter acronym – that will be forgotten more quickly than it came. What matters is the way you approach new problems and challenges. And that is also my recommendation to new students: work on whatever you like, as long as you are passionate about it and it brings you forward.

Ajay-  How is the Rapid Miner Extensions marketplace moving along. Do you think there is a scope for people to say create algorithms in a platform like R , and then offer that algorithm as an app for sale just like iTunes or Android apps.

 Simon: Well, of course it is not going to be exactly like iTunes or Android apps are, because of the more business-orientated character. But in fact there is a scope for that, yes. We have talked to several developers, e.g., at our user conference RCOMM, and several people would be interested in such an opportunity. Companies using data mining software need supported software packages, not just something they downloaded from some anonymous server, and that is only possible through a platform like the new Marketplace. Besides that, the marketplace will not only host commercial extensions. It is also meant to be a platform for all the developers that want to publish their extensions to a broader community and make them accessible in a comfortable way. Of course they could just place them on their personal Web pages, but who would find them there? From the Marketplace, they are installable with a single click.

Ingo: What I like most about the new Rapid-I Marketplace is the fact that people can now get something back for their efforts. Developing a new algorithm is a lot of work, in some cases even more that developing a nice app for your mobile phone. It is completely accepted that people buy apps from a store for a couple of Dollars and I foresee the same for sharing and selling algorithms instead of apps. Right now, people can already share algorithms and extensions for free, one of the next versions will also support selling of those contributions. Let’s see what’s happening next, maybe we will add the option to sell complete RapidMiner workflows or even some data pools…

Ajay- What are the recent features in Rapid Miner that support cloud computing, mobile computing and tablets. How do you think the landscape for Big Data (over 1 Tb ) is changing and how is Rapid Miner adapting to it.

Simon: These are areas we are very active in. For instance, we have an In-Database-Mining Extension that allows the user to run their modelling algorithms directly inside the database, without ever loading the data into memory. Using analytic databases like Vectorwise or Infobright, this technology can really boost performance. Our data mining server, RapidAnalytics, already offers functionality to send analysis processes into the cloud. In addition to that, we are currently preparing a research project dealing with data mining in the cloud. A second project is targeted towards the other aspect you mention: the use of mobile devices. This is certainly a growing market, of course not for designing and running analyses, but for inspecting reports and results. But even that is tricky: When you have a large screen you can display fancy and comprehensive interactive dashboards with drill downs and the like. On a mobile device, that does not work, so you must bring your reports and visualizations very much to the point. And this is precisely what data mining can do – and what is hard to do for classical BI.

Ingo: Then there is Radoop, which you may have heard of. It uses the Apache Hadoop framework for large-scale distributed computing to execute RapidMiner processes in the cloud. Radoop has been presented at this year’s RCOMM and people are really excited about the combination of RapidMiner with Hadoop and the scalability this brings.

 Ajay- Describe the Rapid Miner analytics certification program and what steps are you taking to partner with academic universities.

Ingo: The Rapid-I Certification Program was created to recognize professional users of RapidMiner or RapidAnalytics. The idea is that certified users have demonstrated a deep understanding of the data analysis software solutions provided by Rapid-I and how they are used in data analysis projects. Taking part in the Rapid-I Certification Program offers a lot of benefits for IT professionals as well as for employers: professionals can demonstrate their skills and employers can make sure that they hire qualified professionals. We started our certification program only about 6 months ago and until now about 100 professionals have been certified so far.

Simon: During our annual user conference, the RCOMM, we have plenty of opportunities to talk to people from academia. We’re also present at other conferences, e.g. at ECML/PKDD, and we are sponsoring data mining challenges and grants. We maintain strong ties with several universities all over Europe and the world, which is something that I would not want to miss. We are also cooperating with institutes like the ITB in Dublin during their training programmes, e.g. by giving lectures, etc. Also, we are leading or participating in several national or EU-funded research projects, so we are still close to academia. And we offer an academic discount on all our products 🙂

Ajay- Describe the global efforts in making Rapid Miner a truly international software including spread of developers, clients and employees.

Simon: Our clients already are very international. We have a partner network in America, Asia, and Australia, and, while I am responding to these questions, we have a training course in the US. Developers working on the core of RapidMiner and RapidAnalytics, however, are likely to stay in Germany for the foreseeable future. We need specialists for that, and it would be pointless to spread the development team over the globe. That is also owed to the agile philosophy that we are following.

Ingo: Simon is right, Rapid-I already is acting on an international level. Rapid-I now has more than 300 customers from 39 countries in the world which is a great result for a young company like ours. We are of course very strong in Germany and also the rest of Europe, but also concentrate on more countries by means of our very successful partner network. Rapid-I continues to build this partner network and to recruit dynamic and knowledgeable partners and in the future. However, extending and acting globally is definitely part of our strategic roadmap.

Biography

Dr. Ingo Mierswa is working as Chief Executive Officer (CEO) of Rapid-I. He has several years of experience in project management, human resources management, consulting, and leadership including eight years of coordinating and leading the multi-national RapidMiner developer team with about 30 developers and contributors world-wide. He wrote his Phd titled “Non-Convex and Multi-Objective Optimization for Numerical Feature Engineering and Data Mining” at the University of Dortmund under the supervision of Prof. Morik.

Dr. Simon Fischer is heading the research & development at Rapid-I. His interests include game theory and networks, the theory of evolutionary algorithms (e.g. on the Ising model), and theoretical and practical aspects of data mining. He wrote his PhD in Aachen where he worked in the project “Design and Analysis of Self-Regulating Protocols for Spectrum Assignment” within the excellence cluster UMIC. Before, he was working on the vtraffic project within the DFG Programme 1126 “Algorithms for large and complex networks”.

http://rapid-i.com/content/view/181/190/ tells you more on the various types of Rapid Miner licensing for enterprise, individual and developer versions.

(Note from Ajay- to receive an early edition invite to Radoop, click here http://radoop.eu/z1sxe)

 

Amazon goes HPC and GPU: Dirk E to revise his R HPC book

Looking south above Interstate 80, the Eastsho...
Image via Wikipedia

Amazon just did a cluster Christmas present for us tech geek lizards- before Google could out doogle them with end of the Betas (cough- its on NDA)

Clusters used by Academic Departments now have a great chance to reduce cost without downsizing- but only if the CIO gets the email.

While Professor Goodnight of SAS / North Carolina University is still playing time sharing versus mind sharing games with analytical birdies – his 70 mill server farm set in Feb last is about to get ready

( I heard they got public subsidies for environment- but thats historic for SAS– taking public things private -right Prof as SAS itself began as a publicly funded project. and that was in the 1960s and they didnt even have no lobbyists as well. )

In realted R news, Dirk E has been thinking of a R HPC book without paying attention to Amazon but would now have to include Amazon

(he has been thinking of writing that book for 5 years, but hey he’s got a day job, consulting gigs with revo, photo ops at Google, a blog, packages to maintain without binaries, Dirk E we await thy book with bated holes.

Whos Dirk E – well http://dirk.eddelbuettel.com/ is like the Terminator of R project (in terms of unpronounceable surnames)

Back to the cause du jeure-

 

From http://aws.amazon.com/ec2/hpc-applications/ but minus corporate buzz words.

 

Unique to Cluster Compute and Cluster GPU instances is the ability to group them into clusters of instances for use with HPC

applications. This is particularly valuable for those applications that rely on protocols like Message Passing Interface (MPI) for tightly coupled inter-node communication.

Cluster Compute and Cluster GPU instances function just like other Amazon EC2 instances but also offer the following features for optimal performance with HPC applications:

  • When run as a cluster of instances, they provide low latency, full bisection 10 Gbps bandwidth between instances. Cluster sizes up through and above 128 instances are supported.
  • Cluster Compute and Cluster GPU instances include the specific processor architecture in their definition to allow developers to tune their applications by compiling applications for that specific processor architecture in order to achieve optimal performance.

The Cluster Compute instance family currently contains a single instance type, the Cluster Compute Quadruple Extra Large with the following specifications:

23 GB of memory
33.5 EC2 Compute Units (2 x Intel Xeon X5570, quad-core “Nehalem” architecture)
1690 GB of instance storage
64-bit platform
I/O Performance: Very High (10 Gigabit Ethernet)
API name: cc1.4xlarge

The Cluster GPU instance family currently contains a single instance type, the Cluster GPU Quadruple Extra Large with the following specifications:

22 GB of memory
33.5 EC2 Compute Units (2 x Intel Xeon X5570, quad-core “Nehalem” architecture)
2 x NVIDIA Tesla “Fermi” M2050 GPUs
1690 GB of instance storage
64-bit platform
I/O Performance: Very High (10 Gigabit Ethernet)
API name: cg1.4xlarge

.

Sign Up for Amazon EC2

So what’s new in R 2.12.0

PoissonCDF
Image via Wikipedia

and as per http://cran.r-project.org/src/base/NEWS

the answer is plenty is new in the newR.

While you and me, were busy writing and reading blogs, or generally writing code for earning more money, or our own research- Uncle Peter D and his band of merry men have been really busy in a much more upgraded R.

————————————–

CHANGES————————-

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@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.

 

 

So what's new in R 2.12.0

PoissonCDF
Image via Wikipedia

and as per http://cran.r-project.org/src/base/NEWS

the answer is plenty is new in the newR.

While you and me, were busy writing and reading blogs, or generally writing code for earning more money, or our own research- Uncle Peter D and his band of merry men have been really busy in a much more upgraded R.

————————————–

CHANGES————————-

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@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.