[aroma.affymetrix] aroma.affymetrix v2.14.0 released

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[aroma.affymetrix] aroma.affymetrix v2.14.0 released

Henrik Bengtsson
Hi,

aroma.affymetrix v2.14.0 (and friends) has been released and is now
available on CRAN for all the major operating systems. Install/update
by:

  source("http://callr.org/install#aroma.affymetrix")

This will take care of all dependencies and recommended packages as
well (also those hosted on Bioconductor and elsewhere).


What's new?
* This round of updates contains mostly bug fixes and robustness
improvements (== you spend less time troubleshooting and more time
doing science).  For full details on what's updated, see below.
* If you're using PSCBS for segmentation or aroma.light for TumorBoost
normalization, please not that argument 'preserveScale' for
segmentByPairedPSCBS() / normalizeTumorBoost() now defaults to FALSE.
The transition from using TRUE (to FALSE) as the default started in
March 2014 and is now complete.

Cheers,

Henrik


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Updates to aroma.affymetrix
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Version: 2.14.0 [2015-10-24]
o AvgPlm, used by for instance doCRMAv2(), would give harmless warning
  "Argument 'centers' for matrixStats::rowMads() has been renamed to
  'center'. Please update code accordingly."
o ROBUSTNESS: Explicitly importing core R functions.
o CLEANUP: Removed methods marked as defunct in v2.11.3 (Feb 2014).
o ROBUSTNESS: fitCnProbes() for UnitModel could in rare cases give an
  error on one of the internal sanity checks.
o BUG FIX: extractAlleleSet() for SnpChipEffectSet now needs to
  load namspace 'oligoClasses' explicitly.
o BUG FIX: writeCdf() for AffyGenePDInfo gave "Error in
  affxparser::writeCdf(...) : unused argument (pathname = ..." due to
  a bug/typo introduced in 2.13.2.  Thanks to Guillaume Devailly for
  reporting on this.

Version: 2.13.2 [2015-05-26]
o ROBUSTNESS: Many functions now assert that they don't return file
  data sets with duplicated entries.
o ROBUSTNESS: Package now declares all S3 methods.
o Package now requires R (>= 3.1.1) released July 2014. This allows
  us to use BioC (>= 3.0) (October 2014).

Version: 2.13.1 [2015-01-23]
o Now a pre-existing monocell CDF can be recreated and overwritten
  using getMonocellCdf(cdf, force=TRUE).
o BUG FIX: getMonocellCdf() for AffymetrixCdfFile would throw
  "Error in (...) : 3 arguments passed to '(' which requires 1".
  This was due to a typo (erroneous newline) introduced in 2.13.0.
  Add package tests for this.  Thanks to Qingzhou Zhang for reporting
  on this.


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Updates to aroma.core
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Version: 2.14.0 [2015-10-20]
o ROBUSTNESS: Explicitly importing core R functions.
o CLEANUP: Renamed apply() for SampleAnnotationFile to applyTo().
o CLEANUP: One rowMads(..., centers) to rowMads(..., center).
o CLEANUP: Drop prototype code never used.
o CLEANUP: Deprecated internal whatDataType() method.
o CLEANUP: Defuncted previously deprecated methods: nbrOfArrays() for
  readData() for AromaMicroarrayDataSetTuple, AromaMicroarrayDataSet and
  AromaUnitTotalCnBinarySet, as well as readData() for SampleAnnotationFile.
o CLEANUP: Removed previously (Feb 2014) defunct method patchPackage()
  and patch().
o BUG FIX: writeRegions(..., format="wig") gave an error.

Version: 2.13.1 [2015-05-25]
o Package now requires R (>= 3.1.1) released July 2014. This allows us
  to use BioC (>= 3.0) (October 2014).
o Relaxed sanity checks; now it's possible to allocate Aroma tabular
  binary files with 200e6 rows (was 100e6 rows).
o getOutputDataSet() for AromaTransform gives more informative error
  messages.
o ROBUSTNESS: exportAromaUnitPscnBinarySet() asserts that no
  duplicated files are returned.
o ROBUSTNESS: Package now declares all S3 methods.
o BUG FIX: getOutputDataSet() for AromaTransform would sometimes given
  an error due to the same output file being identified more than
  once, for instance, when the full name of an output file is also
  the prefix of another file.  Thanks to Benilton Carvalho (Universidade
  Estadual de Campinas, Sao Paulo, Brazil) for reporting on this.
o BUG FIX: extractRawMirroredAlleleBFractions() for RawAlleleBFractions
  gave "Error in setSignals(res, dh) : object 'res' not found".


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Updates to R.filesets
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Version: 2.9.0 [2015-10-20]
o Add support for dsApply(..., .parallel="future"), which utilizes
  the future package.
o CLEANUP: Defunct methods dropped.
o Package now requires R (>= 3.1.1) released July 2014. This allows
  us to use BioC (>= 3.0) (October 2014).

Version: 2.8.0 [2015-08-06]
o Added support for sortBy(..., by="mixedroman") for GenericDataFileSet.
o Now commentChar="" and commentChar=FALSE also disables searching for
  comment characters (just as commentChar=NULL) for TabularTextFile.
o Explicit import of 'utils' functions.
o Package requires R (>= 3.1.0) released March 2014.
o BUG FIX: readDataFrame() for TabularTextFile with column-names
  translators set, could give an error "Number of read data columns
  does not match the number of column headers: ...". This was due to
  an update in utils::read.table() as of R v3.2.1 svn rev 68831.

Version: 2.7.2 [2015-05-24]
o ROBUSTNESS: Added getFullNames(..., onRemapping) to GenericDataFileSet
  to warn/err on full-name translations that generates inconsistent
  fullname-to-index maps before and after.
o CONSISTENCY: Analogously to lapply(), dsApply() returns a list
  with names corresponds to the full names of the data set.
o BUG FIX: linkTo(..., skip=TRUE) would give error "No permission to
  modify existing file: ..." also in the case when the proper link
  already exists and there is no need to create a new one.
o BUG FIX: Now getReadArguments() for TabularTextFile let duplicated
  named 'colClasses' entries override earlier ones, e.g.
  colClasses=c("*"=NA, "*"="NULL", a="integer") is effectively the
  same as colClasses=c("*"="NULL", a="integer").  Added package test.

Version: 2.7.1 [2015-04-27]
o ROBUSTNESS: Now nchar(..., type="chars") is used internally for
  all file and directory names (including tags).
o BUG FIX: as.character() for GenericDataFile with a missing (NA)
  pathname on recent R-devel (>= 2015-04-23) related to an update
  on how nchar() handles missing values
o Bumped package dependencies.

Version: 2.7.0 [2015-02-23]
o Now `[[` for GenericDataFileSet returns a GenericDataFile not only
  if a numeric index is given but also if a character string is given.
o Now argument 'idx' for getFile() for GenericDataFileSet can also
  be a character string, in which case the file returned is identified
  using indexOf(..., pattern=idx, by="exact", onMissing="error").
o Added RDataFile and RDataFileSet classes for *.RData files.
o Package requires R (>= 3.1.0) released March 2014. This allows us
  to use BioC (>= 2.14) (April 2014).  These are in fact old; it's
  recommended to use a more recent version of R.
o ROBUSTNESS: Package test coverage is 51%.

Version: 2.6.2 [2015-01-05]
o CLEANUP: Using requireNamespace() instead of require() internally.

Version: 2.6.1 [2014-12-27]
o ROBUSTNESS: Added test for reading subset of a large tabular file.
o BUG FIX: as.character() for ChecksumFile gave an error when
  the checksum files was missing.


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PSCBS
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Version: 0.50.0 [2015-10-14]
o Now argument 'preserveScale' for segmentByPairedPSCBS() defaults
  to FALSE.  In the past the default has effectively been TRUE, but
  has given a warning since v0.43.0 (June 2014) that it eventually
  will be changed to FALSE.  Now it will give a warning that it
  has changed, unless the option is explicitly specified.  This
  new warning will eventually be removed in a future version.

Version: 0.45.1 [2015-09-16]
o More informative error messages when append() for CBS or PSCBS fail.
o BUG FIX: segmentByCBS(, ..., w, knownSegments) would give internal
  assertion errors if one of the priorly known segments would have
  zero data points.  Thanks to Kirill Tsukanov (Moscow) and
  Eric Talevich (UCSF) for reporting on this.

Version: 0.45.0 [2015-09-11]
o segmentByCBS() gained argument 'avg'.
o Add writeWIG() for CBS objects.
o pruneByHClust() no longer gives a message about method "ward"
  is now named "ward.D".
o Added skip=TRUE to report().
o ROBUSTNESS: Package test coverage is 62%.
o ROBUSTNESS: Explicitly importing core R functions.
o FIX: plotTracks() for CBS ignored arguments 'cex', 'col' and
  'meanCol' if two or more chromosomes were plotted.
o BUG FIX: joinSegments(), resetSegments() and pruneBySdUndo() gave
  errors for multi-chromosome (>= 2) segmentation results.
o BUG FIX: segmentByCBS() would ignore argument 'w' (weights) if
  more than one chromosome was fitted.
o BUG FIX: tileChromosomes() for CBS returned incorrect locus data.
o BUG FIX: gapsToSegments(gaps) gave an error if nrow(gaps) == 0
  or contained no 'chromosome' column.
o BUG FIX: findLargeGaps() could return NULL. Now it always returns
  a data.frame.
o BUG FIX: The report() RSP-embedded TeX templates for CBS and
  PairedPSCBS data did not escape sample and data set names
  to LaTeX in all places needed.
o Package now requires R (>= 3.1.1) released July 2014. This allows
  us to use BioC (>= 3.0) (October 2014).


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aroma.light
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Version: 2.9.0 [2015-09-17]
o Argument 'preserveScale' for normalizeTumorBoost() now defaults
  to FALSE.  Since 1.33.3 (2014-04-30) it had no default and
  prior to that it was TRUE.

Version: 2.5.3 [2015-09-13]
o ROBUSTNESS: Explicitly importing core R functions.
o BUG FIX: rowAverages() and normalizeAverages() would give an error
  if some of the argument default functions are overridden by
  non-functions of the same name in the calling environment.

Version: 2.5.2 [2015-06-16]
o Relaxed package test for backtransformPrincipalCurve().

Version: 2.5.1 [2015-05-24]
o CLEANUP: Removed obsolete wpca(..., method="dsvdc"); was only
  needed for backward compatibility with R (< 1.7.0).
o Bumped package dependencies.

--
--
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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