Hi,

aroma.affymetrix v2.12.0 has been released and is available on CRAN
(where the package is hosted).  Update by:

  source("http://aroma-project.org/hbLite.R";)
  hbInstall("aroma.affymetrix")

This update contains a few bug fixes (thanks for the reports), a few
speedups plus some small bells and whistles.  I recommend that
everyone updates.

Finally a heads up: R 3.1.0 is going to be released on April 10, 2014
- a full year after R 3.0.0 was released.  If you are still running R
2.15.3 or older, I strongly recommend to update, particularly since
there were so many important and useful updates in R 3.0.0.
Currently, aroma.affymetrix supports R (>= 2.15.1), but to simplify
maintenance I'll eventually upgrade the requirements to R (>= 3.0.2).
R 3.0.2 was released Sept 2013.  Note that the latest stable release
is R 3.0.3 (March 6, 2014).

Cheers,

Henrik


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Updates to aroma.affymetrix
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Version: 2.12.0 [2014-03-07]
o Bumped version for CRAN submission.
o Updated package dependencies.
o Package passes all redundancy tests.

Version: 2.11.3 [2014-02-28]
o Now methods that supports searching sibling root directories do so by
  default.  Previously this had to be explicitly enabled via an option.
o CLEANUP: Removed defunct methods.  Made previously deprecated defunct.

Version: 2.11.2 [2014-01-04]
o CLEANUP: Dropped defunct methods '[' and '[[' for AffymetrixCelSet
  and CnagCfhSet (which have been defunct since 2013-04-29).

Version: 2.11.1 [2013-10-17]
o DOCUMENTATION: Minor tweaks to the help for the doNNN() methods.


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Updates to aroma.core
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Version: 2.12.1 [2014-03-04]
o CRAN POLICY: Now limiting the number of registered S3 methods in
  NAMESPACE for R (< 3.1.0).  Used to be R (< 3.0.2).

Version: 2.12.0 [2014-03-01]
o Bumped version for CRAN submission.
o Updated package dependencies.
o Package passes all redundancy tests.

Version: 2.11.7 [2014-02-28]
o Now methods that supports searching sibling root directories do so by
  default.  Previously this had to be explicitly enabled via an option.
o Updated package dependencies.
o CLEANUP: Defuncted previously deprecated downloadPackagePatch()
  and patchPackage() as well as patch() for AromaPackage.
o CLEANUP: Removed defunct methods.

Version: 2.11.6 [2014-02-17]
o BUG FIX: The GladModel would not pass user-specified arguments.  Thanks
  to Hans-Ulrich Klein at University of M√ľnster for reporting on this.

Version: 2.11.5 [2014-02-03]
o BUG FIX: readDataFrame() for AromaGenomeTextFile and AromaUcscGenomeTextFile
  explicitly passed arguments '...' to NextMethod(), which would cause them
  to be duplicated in certain cases.

Version: 2.11.4 [2014-01-17]
o CLEANUP: Now all Explorer classes utilize R.rsp::rfile() for compiling
  RSP files instead of the to-be-deprecated rspToHtml().

Version: 2.11.3 [2014-01-16]
o BUG FIX: getGenericSummary() for RichDataFrame would throw "Error in
  data[i, , drop = FALSE] : subscript out of bounds" if it had zero rows.

Version: 2.11.2 [2013-12-11]
o Added findChangePointsByState() for SegmentedGenomicSignalsInterface.
o DOCUMENTATION: Added documentation for exportAromaUnitPscnBinarySet().

Version: 2.11.1 [2013-11-15]
o Added argument 'onMissing' to getOutputDataSet() for AromaTransform.
  This replaces argument 'incomplete', which will be dropped in a
  future version, but is for now supported as well.


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Updates to R.filesets
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Version: 2.4.1 [2014-02-28]
o FIX / DOCUMENTATION: The system test for GenericDataFile would fail
  with linkTo() on Windows systems without necessary privileges.  Made
  the test less conservative.  Also, added an Rd section on privileges
  required on Windows for linkTo() to work.  Thanks to Brian Ripley
  for reporting on this.

Version: 2.4.0 [2014-02-26]
o No updates. Bumped the version for CRAN release.

Version: 2.3.15 [2014-02-26]
o Bumped up package dependencies.

Version: 2.3.14 [2014-01-24]
o Now readColumns() for TabularTextFile handles also header-less files.

Version: 2.3.13 [2014-01-18]
o CLEANUP: Removed namespace patch for R.utils (< 1.27.5)

Version: 2.3.12 [2014-01-13]
o copyTo() for GenericDataFileSet no longer passes '...' to byPath()
  when constructing the return data set.

Version: 2.3.11 [2014-01-09]
o Now renameTo() passes '...' to R.utils::renameFile() making it
  possible to also overwrite existing files.

Version: 2.3.10 [2014-01-07]
o Added is.na() for GenericDataFile and GenericDataFileSet and
  na.omit() for the latter, which already supports anyNA().
o Added linkTo() for GenericDataFile, which create a symbolic link at
  a given destination pathname analogously to how copyTo() creates a
  file copy at a given destination pathname.

Version: 2.3.9 [2014-01-06]
o copyTo() for GenericDataFile passes '...' to R.utils::copyFile().
o CLEANUP: copyTo() and renameTo() for GenericDataFile had verbose
  output enabled by default.
o CLEANUP: digest2() is now defunct.

Version: 2.3.8 [2014-01-04]
o Added duplicated(), anyDuplicated() and unique() for GenericDataSet,
  which all compare GenericDataFile:s using the equals() method.
o Now c() for GenericDataFileSet also works to append GenericDataFile:s.
  Added package system test for common use cases of c().

Version: 2.3.7 [2013-12-18]
o Now readDataFrame(..., header=FALSE) works as expected for tabular
  text files without headers.
o Added nbrOfColumns() for GenericTabularFile, which, if the number
  of columns cannot be inferred from the column names, will fall back
  to read the first row of data and use that as the number of columns.
o Now nbrOfColumns() for ColumnNamesInterface returns NA if column names
  cannot be inferred and hence not be counted.
o BUG FIX: Now getReadArguments() for TabularTextFile returns a
  'colClasses' vector of the correct length also in the case when
  there are no column names.

Version: 2.3.6 [2013-11-27]
o Added a generic loadRDS() available for plain files and RdsFile:s.

Version: 2.3.5 [2013-11-21]
o Added RdsFile and RdsFileSet objects for handling *.rds file sets.
o CLEANUP: There's no longer a need to reset class for GenericSummary.

Version: 2.3.4 [2013-11-19]
o Added ChecksumFile and ChecksumFileSet.

Version: 2.3.3 [2013-11-15]
o Now extract() for GenericDataFileSet also handles when the data set to
  be extracted is empty, e.g. extract(GenericDataFileSet(), NA_integer_).
  Also, added support for argument onMissing="dropall", which drops all
  files if one or more missing files where requested.
  Added package system tests for these case.

Version: 2.3.2 [2013-11-11]
o SPEEDUP: GenericDataFileSet$byPath(..., recursive=TRUE) would be very
  slow setting up the individual files, especially for large data sets.
  Now it's only slow for the first file.

Version: 2.3.1 [2013-11-01]
o Added "[["(x, i) for GenericDataFileSet, which gets a
  GenericDataFile by index 'i' in [1,length(x)].  When
  'i' is non-numeric, the next "[["(x, i) method in the
  class hiearchy is used, e.g. the one for Object:s.
o Added gzip()/gunzip() for GenericDataFileSet.
o Added anyNA() to GenericDataFileSet to test whether any of
  the pathnames are NA, or not.

-- 
-- 
When reporting problems on aroma.affymetrix, make sure 1) to run the latest 
version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.


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