I'm pleased to announce that aroma.affymetrix v1.3.0 has been released
and is now available for installation/update:
source("http://www.braju.com/R/hbLite.R";);
hbInstall("aroma.affymetrix");
We have now moved to R v2.10.0 and the packages has been thoroughly
validated to work with it. Although it should be backward compatible
with earlier version, we recommend that everyone start using this
latest stable release of R.
There has been a few bug fixes, more work on making the code more
robust against various types of errors and provide more informative
error messages. The package is also more robust against external
failures such as power failures. All data files written are now
written to a temporary file first which is then renamed to the final
data files. This minimizes the risk for ending up with
incomplete/corrupt data files. All this is done so that we all can
spend more time on the research and less on troubleshooting.
Further details on the updates can be found below.
Work is also done on setting up a new website with documentation that
is better structured. This will be easier to maintain that the
current Google Group site (which we cannot edit since May 2009 because
of the risk of getting erroneously flagged as a spam group by Google).
We'll keep the Google Group mailing list though. ll let you know when
the new site is available.
Cheers,
Henrik
PS. It took some struggle and a lot of waiting (10 days) before this
new version was rolled out on CRAN, but now it's there for all
platforms.
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Updates to aroma.affymetrix
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Version: 1.3.0 [2009-11-01]
o New public release.
o More recent dependencies on Bioconductor packages.
o Package passes R CMD check on R v2.10.0 and all redundancy tests.
Version: 1.2.3 [2009-10-26]
o BUG FIX: Fitting RlmPlm() would give an error reporting on a
call to an internal preprocessCore function is incompatible.
This occured with preprocessCore v1.7.1 or newer.
o Added getExtensionPattern() to those GenericDataFile classes that
have "single" filename extension, e.g. *.cfh but not *.cdf.bin.
The other will be incorporated when we have thoroughly gone through
the impact of including those as well.
Version: 1.2.2 [2009-10-16]
o CLEAN UP: Cleaned up dependencies in DESCRIPTION.
Version: 1.2.1 [2009-10-02]
o Added argument 'onDuplicates' to importFromAffymetrixProbeTabFile() for
AromaCellSequenceFile. If "error" ("warning"), an exception (warning)
is generated whenever duplicated cell indices are detected in the probe
tab file. If "ignore", they are ignored, which means that the last
duplicated probe sequence will be what is finally imported.
o Added argument 'keepSequenceLengths' to importFromAffymetrixProbeTabFile()
for AromaCellSequenceFile so that one can drop sequences of incorrect
lengths, cf. HuGene-1_0-st-v1.probe.tab.
o Added getDefaultFullName() to AffymetrixFileSet and CnagCfhSet.
o CLEAN UP: Updated to use byPath() instead fromFiles().
o CLEAN UP: Removed all getFullName() for all GenericDatFileSet classes.
o BUG FIX: Now getCdf() for AffymetrixProbeTabFile first searches
for a CDF with filename <chipType>.cdf, then <chipType>,.*.cdf.
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Updates to aroma.core
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Version: 1.3.1 [2009-11-03]
o Replaced Rd cross references to sfit and HaarSeg packages with
plain text in order to meet the CRAN requirements that all
Rd links must exist on the CRAN servers.
Version: 1.3.0 [2009-11-01]
o New public release.
o More recent dependencies on Bioconductor packages.
o Package passes R CMD check on R v2.10.0 and all redundancy tests.
Version: 1.2.3 [2009-10-25]
o Added getExtensionPattern() to most GenericDataFile classes.
Version: 1.2.2 [2009-10-16]
o Added setName() for RawGenomicSignals.
o Stricter dependencies.
Version: 1.2.1 [2009-10-02]
o CLEAN UP: Updated to use byPath() instead fromFiles().
o CLEAN UP: Move the Interface class to the R.oo package.
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Updates to R.filesets
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Version: 0.6.5 [2009-10-30]
o ROBUSTIFICATION: Now translateFullName() of FullNameInterface
and translateColumnNames() of GenericTabularFile throw an
exception if some fullnames were translated into NA. They
also assert that no names were dropped or added in the process.
o BUG FIX: After doing append() to a GenericDataFileSet, the
total file size reported would remain the same.
o BUG FIX: Appending empty data sets using append() of GenericDataFileSet
would give error Error in this$files[[1]] : subscript out of bounds.
Version: 0.6.4 [2009-10-25]
o Added get- and setExtensionPattern() to FullNameInterface.
o Added getExtension() to GenericDataFile.
Version: 0.6.3 [2009-10-23]
o Added appendFullNameTranslatorBylist() which makes it possible to do
setup a sequence of fullnames translators fnt1, fnt2, fnt3 by calling
setFullNameTranslator(..., list(fnt1, fnt2, fnt3)).
Version: 0.6.2 [2009-10-22]
o Added support for having a sequence of fullname translator
functions. These can be added using appendFullNameTranslator().
o Added an example() to FullNameInterface.
Version: 0.6.1 [2009-10-06]
o Added subsetting via [() to TabularTextFile.
Version: 0.6.0 [2009-10-02]
o Added the FullNameInterface, which is the interface class that
defines what fullnames, names, tags etc are.
o Now setFullName*s*Translator() for GenericDataFileSet dispatches
on the 'by' argument. If that is not possible, it call
setFullNameTranslator() for each file in the set (as before).
o CLEAN UP: Renamed fromFiles() to byPath(). For backward
compatibility the former calls the latter.
o CLEAN UP: GenericDataFile and GenericDataFileSet implements
the FullNameInterface, which mean less redundant code.
--
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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