aroma.affymetrix 3.1.0 release

[Henrik Bengtsson]

aroma.affymetrix 3.1.0 and friends have been updated and are being
rolled out on CRAN. These days I mostly do maintenance, fix bugs,
refactor code, and optimize the performance of these packages. As
usual, all released undergo rigorous validation based on system tests
running for ~50 CPU hours (so a lot of tests).

For full update details, see the end of this message. To update, just
do update.packages() or:

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


Also, don't forget that it's extremely simple to process samples in
parallel (when the algorithm allows). For instance, call:

library("future")
plan(multiprocess)

before starting your analysis and the samples will run in parallel on
your local machine. If you call,

library("future.BatchJobs")
plan(batchjobs_torque)

then the samples will be processed in parallel via the TORQUE / PBS
scheduler on your HPC cluster (if you have one). See
http://aroma-project.org/howtos/parallel_processing/ for other
alternatives.

Cheers,

Henrik
(http://www.aroma-project.org/)

Details on updated since aroma.affymetrix 3.0.0 (2016-01-09).

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Updates to aroma.affymetrix
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Version: 3.1.0 [2017-03-23]

NEW FEATURES:

o Now file and object sizes are reported using IEC binary prefixes,
i.e. bytes, KiB, MiB, GiB, TiB, ..., YiB.

o Now doNnn() methods can be called directly from the command line, e.g.
Rscript -e aroma.affymetrix::doCRMAv2 --dataSet=HapMap270
--chipType=GenomeWideSNP_6

o Objects no longer report on memory (RAM) usage.

REFACTORIZATION:

o Used partial element name 'coef' instead of 'coefficients' for lm() fit.

BUG FIXES:

o Package used %<=% internally with was deprecated in future (>= 1.4.0).

o ROBUSTNESS: Some regular expression patterns used for locating files
would match any symbol when it intended to match only a period.

o The International HapMap Project (http://www.hapmap.org/) is being retired
and HTTP server http://hapmap.ncbi.nlm.nih.gov/downloads/raw_data/ is
decomissioned. System test scripts updated to download HapMap CEL files
from the FTP server ftp://ftp.ncbi.nlm.nih.gov/hapmap/raw_data/ instead.

DEPRECATED AND DEFUNCT:

o Methods bgAdjustRma(), bgAdjustOptical() and bgAdjustGcrma() for
AffymetrixCelFile as well as bgAdjustGcrma() for AffymetrixCelSet
are now defunct.


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Updates to aroma.core
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Version: 3.1.0 [2017-03-22]

NEW FEATURES:

o Now file sizes are reported using IEC binary prefixes, i.e. bytes, KiB,
MiB, GiB, TiB, ..., YiB.

o Now genomic positions / distances are reported in 'Mbp' (was 'MB' and 'Mb').

o Objects no longer report on memory (RAM) usage.

BUG FIXES:

o Package used %<=% internally with was deprecated in future (>= 1.4.0).

o exportTotalCnRatioSet() for AromaUnitTotalCnBinarySet and
exportFracBDiffSet() for AromaUnitFracBCnBinarySet would return files with
file names matching `.asb`, which would incorrectly also include `.asb.md5`
files. Thanks to Thomas Grombacher at the Merck Group for the report.

DEPRECATED AND DEFUNCT:

o Default method whatDataType() is now defunct.

o Argument '.old' of getChipType() for AromaMicroarrayTabularBinaryFile is
now defunct (was deprecated in 2008!).

o Previously deprecated argument 'maxNAFraction' to getRawCnData() of
CopyNumberChromosomalModel and for fit() of CopyNumberSegmentationModel
is now defunct.

o Removed previously defunct apply() for SampleAnnotationFile.


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Updates to R.filesets
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Version: 2.11.0 [2017-02-27]

SIGNIFICANT CHANGES:

o Package requires R (>= 3.1.2) and BioC (>= 3.0) both released in
October 2014.

NEW FEATURES:

o Now getChecksum() for ChecksumFile defaults to not creating a checksum file
(which is the default for other types of file), but instead always return
the checksum of the file by only calculating and in memory. This prevents
for instance the equals() test on two different checksum files to generate
another set of checksum files on themselves.

o Now findByName() for GenericDataFileSet reports on the non-existing
root paths in error messages.

o GenericDataFile and GenericDataFileSet no longer report on memory (RAM)
usage of objects.

CLEANUP:

o dsApply(..., .parallel="future") now used future_lapply() of the future
package internally. dsApply() will soon be deprecated (see below).

INSTALLATION:

o Package no longer needs to depend on listenv.

DEPRECATED AND DEFUNCT:

o Argument 'colClassPatterns' of readDataFrame() for TabularTextFile is
now defunct. Use 'colClasses' instead.

o Argument 'files' of extractMatrix() for GenericTabularFileSet is defunct.

o dsApply() with either .parallel = "BiocParallel::BatchJobs"
or "BatchJobs" is deprecated. Instead, use future::future_lapply()
with whatever choice of future::plan() preferred.

o Defunct argument 'aliased' of getDefaultFullName() for GenericDataFile
and defunct argument 'alias' of GenericDataFileSet() have been removed.