Hi all,
aroma.affymetrix v2.8.0 has been released. Update by:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
Bug fixes, improved fault tolerance, more unique caching, improved
creation of CDF files from Bioconductor PDInfo packages and more. As
usual, details below.
Merry Xmas,
Henrik
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Updates to aroma.affymetrix
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Version: 2.8.0 [2012-12-21]
o No updates.
o Bumped version for CRAN submission.
o Package passes all redundancy tests.
Version: 2.7.9 [2012-12-21]
o Bumped up package dependencies.
o Utilizing new startupMessage() of R.oo.
o Now using argument 'colClasses' (was 'colClassPatterns')
for all readDataFrame():s and elsewhere.
o ROBUSTNESS: Now all internal pathnames are shorter than 100
characters, which is the upper limit that 'tar' supports.
Version: 2.7.8 [2012-12-18]
o ROBUSTNESS: Added argument 'unitsBy' (and 'namesBy') to writeCdf()
for AffyGenePDInfo, where 'unitsBy' defaults to "transcript". It
now also drops any duplicated probe entries. Furthermore, calling
writeCdf() for other classes of DBPDInfo objects will now give a
more informative error message that those classes are yet not
supported. Thanks Guido Hooiveld (Wageningen University, Netherlands)
for suggestions and tests.
o Now validate() for AffymetrixCdfFile accepts empty unit names as
long as the unit is not empty.
o BUG FIX: writeCdf(..., useTranscriptCluster=FALSE) for AffyGenePDInfo
could generate empty unit names files for units with 'fsetid' <= 9999.
Version: 2.7.7 [2012-12-10]
o BUG FIX: getTimestamp() for AffymetrixCelFile would throw an error
if the CEL file header did not have a timestamp. Thanks Guido
Hooiveld (Wageningen University, Netherlands) for reporting this.
Version: 2.7.6 [2012-12-06]
o ROBUSTNESS: Utilizing new getOneFile() internally.
Version: 2.7.5 [2012-12-01]
o BUG FIX/ROBUSTNESS: convertToUnique() for AffymetrixCelSet would
return all CEL files found in the output directory, not just the ones
corresponding to the input set, and possibly in a different order.
Version: 2.7.4 [2012-11-29]
o DOCUMENTATION: Added help pages to more methods.
o ROBUSTNESS: updateUnits() for ResidualSet did not update the
files in lexicographic order as previously claimed.
Version: 2.7.3 [2012-11-28]
o ROBUSTNESS: Added system test scripts for building UGP and UFL
file from Affymetrix CSF and NetAffx CSV files for GenomeWideSNP_6.
o BUG FIX: Static allocateFromCdf() for AromaUfcFile and AromaUflFile
would throw errors on "Cannot retrieve writable file/directory
because it is NA.". This turns out to be related to the trap
reported in R-devel thread 'Do *not* pass '...' to NextMethod() -
it'll do it for you; missing documentation, a bug or just me?'
on Oct 16, 2012. Thanks Ioana Cutcutache (Duke-NUS in Singapore)
for reporting on this.
Version: 2.7.2 [2012-11-28]
o ROBUSTNESS: Added the FileCacheKeyInterface to all classes directly
extending GenericDataFile and TabularTextFile.
o MEMORY: readUnits() for ChipEffectFile, FirmaFile, ParameterCelFile,
ResidualFile, and WeightsFile no longer cache results in memory
by default.
Version: 2.7.1 [2012-11-26]
o Lowered the package dependencies to aroma.light (>= 1.22.0)
and affxparser (>= 1.26.4) so that this package can be easily
installed on R (>= 2.14.0).
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Updates to aroma.core
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Version: 2.8.0 [2012-12-21]
o No updates.
o Bumped version for CRAN submission.
o Package passes all redundancy tests.
Version: 2.7.6 [2012-12-20]
o Bumped up package dependencies.
o Now using argument 'colClasses' (was 'colClassPatterns')
for all readDataFrame():s.
o Utilizing new startupMessage() of R.oo.
Version: 2.7.5 [2012-12-06]
o ROBUSTNESS: Utilizing new getOneFile() internally.
Version: 2.7.4 [2012-12-04]
o CLEANUP: Dropped inst/reports/templates/html/archive/,
inst/reports/templates/rsp/archive/ and inst/archive/,
which all contained old/legacy Explorer versions.
Version: 2.7.3 [2012-11-29]
o Renamed lapply() for AromaTabularBinaryFile to colApply().
Version: 2.7.2 [2012-11-28]
o Made several file classes implement FileCacheKeyInterface.
o Added CacheKeyInterface and FileCacheKeyInterface.
Version: 2.7.1 [2012-11-26]
o Lowered the package dependencies to aroma.light (>= 1.22.0)
such that this package can be installed easily on R (>= 2.14.0).
o BUG FIX: getRam() and setRam() for AromaSettings did not use
'memory/ram'.
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Updates to R.filesets
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Version: 1.9.0 [2012-12-20]
o Argument 'colClassPatterns' of readDataFrame() for TabularTextFile
has been renamed to 'colClasses'.
Version: 1.8.2 [2012-12-19]
o Bumped up package dependencies.
o Utilizing new startupMessage() of R.oo.
o ROBUSTNESS: Now indexOf() for GenericDataFileSet throws an
exception if use tries to pass an argument 'names'.
Version: 1.8.1 [2012-12-09]
o Added head() and tail() for GenericTabularFile.
o Added subsetting via [() to GenericTabularFile.
o BUG FIX: nbrOfRows() for TabularTextFile forgot to exclude comment
rows in the file header.
o BUG FIX: readColumns() for GenericTabularFile would not preserve
the order of the requested 'columns'.
Version: 1.8.0 [2012-12-06]
o Added getOneFile() for GenericDataFileSet, which returns the first
GenericDataFile with a non-missing pathname.
o Added argument 'absolute=FALSE' to getPathname() for GenericDataFile.
o ROBUSTNESS: Now GenericDataFile stores the absolute pathname of
the file, even if a relative pathname is given. This makes sure
that the file is found also when the working directory is changed.
o BUG FIX: equals() for GenericDataFileSet would only compare the first
GenericDataFile in each set.
Version: 1.7.3 [2012-12-03]
o Added isGzipped() to GenericDataFile.
Version: 1.7.2 [2012-12-03]
o Generalized writeColumnsToFiles() to GenericTabularFile. Used
to be available only for TabularTextFile.
o CLEANUP: Now package only imports 'digest' and 'R.methodsS3'.
Added 'stats' to list of imported packages.
o ROBUSTNESS: Now package declares S3 methods in the namespace.
Version: 1.7.1 [2012-12-02]
o BUG FIX: getDefaultColumnNames() for TabularTextFile did not use
'columnNames' if it was set when creating the TabularTextFile object.
o BUG FIX: Now getReadArguments() for TabularTextFile drops arguments
that are NULL, because they could cause errors downstreams, e.g.
readDataFrame() calling read.table(..., colClasses=NULL) =>
rep_len(NULL, x) => "Error in rep_len(colClasses, cols) :
cannot replicate NULL to a non-zero length".
Version: 1.7.0 [2012-11-30]
o Updated as.list() for GenericDataSet to return a *named* list of
GenericDataFile:s (previously it had no names). The names are
the (translated) full names of the GenericDataFile:s.
o CLEANUP: Removed lapply() and sapply() for GenericDataSet because
the corresponding functions in the 'base' package utilizes
as.list().
Version: 1.6.1 [2012-11-28]
o Now GenericDataFile() retrieves the file time stamps such that
hasBeenModified() returns a correct value also when first called,
and not only TRUE just in case. This has the effect that
getChecksum() will detected cached results already at the
second call as long as the file has to been modified. Previously
it took two calls to getChecksum() for it to be properly cached.
o Now declaring more internal and temporary Object fields as "cached",
which means they will be cleared if clearCache() or gc() is called on
the corresponding object.
o Added further verbose output to TabularTextFileSet.
o DOCUMENTATION: Minor corrections to help pages.
--
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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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