Hi,
aroma.affymetrix v2.10.0 and friends 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 release is mainly about bug fixes, internal cleanups and some
minor speedups.
Cheers,
Henrik
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Updates to aroma.affymetrix
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Version: 2.10.0 [2013-08-04]
o CLEANUP: The formal package dependancy on Bioconductor packages
'aroma.light' and 'affxparser' has been relaxed so the package
can be installed without them.
o CLEANUP: Package now only imports matrixStats, R.oo, R.filesets
and aroma.apd.
o CLEANUP: Removed since-long defunct methods. Made deprecated
methods defunct.
o Bumped version for CRAN submission.
o Updated package dependences.
o Package passes all redundancy tests.
Version: 2.9.7 [2013-07-28]
o ROBUSTNESS: byPath() for DChipDcpSet was not decleared static.
o BUG FIX: In certain cases, calls to static method byPath() would
be affected by the NextMethod() '...' bug reported in R-devel thread
"Do *not* pass '...' to NextMethod() - it'll do it for you; missing
documentation, a bug or just me?" on 2012-10-16.
Version: 2.9.6 [2013-07-03]
o Added argument 'flavor' or doRMA() making it easier to replicate the
results of other packages, e.g. doRMA(..., flavor="oligo").
Version: 2.9.5 [2013-06-02]
o ROBUSTNESS: Now more methods are creating/writing signals atomically.
o BUG FIX: Since v2.9.0, doFIRMA() would give "Exception: Unknown
arguments: .onUnknownArgs" in the alternative splicing step.
o BUG FIX: calculateConfidenceScores() for CrlmmModel used defunct
method isHeterozygote() instead of isHeterozygous().
o BUG FIX: Certain methods could throw 'Error in UseMethod("getChecksum")
: no applicable method for 'getChecksum' applied to an object of class
"list"' if (and only if) R.cache package was not attached. The same
bug was fixed on aroma.core v2.9.2 recently.
Version: 2.9.4 [2013-05-30]
o Now it's possible to call aroma.affymetrix::doRMA() without first
loading package. Same for all other doNnn() methods, e.g. doCRMAv2(),
doFIRMA() and doGCRMA().
Version: 2.9.3 [2013-05-25]
o SPEEDUP: Replaced all rm() calls with NULL assignments.
Version: 2.9.2 [2013-05-22]
o CLEANUP: Now using getChecksum() instead of (internal)
R.filesets::digest2() with identical results.
o CLEANUP: Now getIdentifier() for CnagCfhFile utilizes
getChecksum() for the GenericDataFile class.
Version: 2.9.1 [2013-05-20]
o CRAN POLICY: Now all Rd \usage{} lines are at most 90 characters long.
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Updates to aroma.core
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Version: 2.10.0 [2013-08-03]
o Bumped version for CRAN submission.
o Updated package dependences.
o Package passes all redundancy tests.
Version: 2.9.7 [2013-07-20]
o CLEANUP: Replaced all internal x11() with dev.new() calls.
o CLEANUP: Moved more packages from Depends to Imports.
o Updated package dependences.
Version: 2.9.6 [2013-06-01]
o Added findFilesTodo() for AromaTransform.
Version: 2.9.5 [2013-05-30]
o DOCUMENTATION: Now help("doCBS") documents all doCBS() methods.
o Now it's possible to call aroma.core::doCBS() without loading package.
o Turned doCBS() into a default method, cf. aroma.affymetrix::doRMA().
Version: 2.9.4 [2013-05-25]
o SPEEDUP: Replaced all rm() calls with NULL assignments.
Version: 2.9.3 [2013-05-22]
o CLEANUP: Now using getChecksum() instead of (internal)
R.filesets::digest2() with identical results.
Version: 2.9.2 [2013-05-22]
o BUG FIX: extractRawCopyNumbers() for CopyNumberChromosomalModel
would throw 'Error in UseMethod("getChecksum") : no applicable
method for 'getChecksum' applied to an object of class "list"'
if (and only if) R.cache package was not attached.
Thanks Yadav Sapkota at University of Alberta for reporting on this.
Version: 2.9.1 [2013-05-20]
o CRAN POLICY: Now all Rd \usage{} lines are at most 90 characters long.
o CRAN POLICY: Now all Rd example lines are at most 100 characters long.
--
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