Package: affxparser
===================

Version: 1.53.2 [2018-10-22]

DOCUMENTATION:

 * Link to Affx Fusion SDK archive on GitHub.
 
 * Spell corrections.


Version: 1.53.1 [2018-08-28]

 * Updated installation instructions in README.md.


Version: 1.53.0 [2018-04-30]

 * The version number was bumped for the Bioconductor devel version, which is
   now BioC 3.8 for R (>= 3.5.0).


Version: 1.52.0 [2018-04-30]

 * The version number was bumped for the Bioconductor release version, which is
   now BioC 3.7 for R (>= 3.5.0).
 

Version: 1.51.0 [2017-10-30]

 * The version number was bumped for the Bioconductor devel version, which is
   now BioC 3.7 for R (>= 3.5.0).


Version: 1.50.0 [2017-10-30]

 * The version number was bumped for the Bioconductor release version, which is
   now BioC 3.6 for R (>= 3.4.0).


Version: 1.49.0 [2017-04-23]

 * The version number was bumped for the Bioconductor devel version, which is
   now BioC 3.6 for R (>= 3.4.0).


Version: 1.48.0 [2017-04-23]

 * The version number was bumped for the Bioconductor release version, which is
   now BioC 3.5 for R (>= 3.4.0).


Version: 1.47.0 [2016-10-18]

NOTES:

 * The version number was bumped for the Bioconductor devel version, which
   is now BioC 3.5 for R (>= 3.4.0).


Version: 1.46.0 [2016-10-18]

NOTES:

 * The version number was bumped for the Bioconductor release version, which
   is now BioC 3.4 for R (>= 3.3.1).


Version: 1.45.1 [2016-09-16]

CODE REFACTORING:

 * Using c(x,y) instead of append(x,y) internally.

 * CLEANUP: Dropped obsolete src/R_affx_test.*cmdline.cpp files.


Version: 1.45.0 [2015-05-03]

NOTES:

 * The version number was bumped for the Bioconductor devel version, which
   is now BioC 3.4 for R (>= 3.3.0).


Version: 1.44.0 [2015-05-03]

NOTES:

 * The version number was bumped for the Bioconductor release version, which
   is now BioC 3.3 for R (>= 3.3.0).


Version: 1.43.2 [2016-04-05]

NEW FEATURES:

 * WINDOWS: Package now compiles with both the old gcc-4.6.3 toolchain as well
   as the new gcc-4.9.3 toolchain - introduced in R (>= 3.3.0).  Thanks to
   Jim Hester and Dan Tenenbaum for help with this.


Version: 1.43.1 [2016-02-28]

NEW FEATURES:

 * The DLL is now unloaded when the package is unloaded.

BUG FIXES:

 * Fixed a bug related to including <R.h> and extern C, reported by
   Brian Ripley.


Version: 1.43.0 [2015-10-23]

NOTES:

 * The version number was bumped for the Bioconductor devel version, which
   is now BioC 3.3 for R (>= 3.3.0).


Version: 1.42.0 [2015-10-13]

NOTES:

 * The version number was bumped for the Bioconductor release version, which
   is now BioC 3.2 for R (>= 3.2.2).


Version: 1.41.7 [2015-09-14]

CODE REFACTORING:

 * ROBUSTNESS: Explicitly importing core R functions. 


Version: 1.41.6 [2015-07-29]

NOTES:

 * Updated the BiocViews field of DESCRIPTION.


Version: 1.41.5 [2015-06-17]

NOTES:

 * New maintainer address (in all fields).


Version: 1.41.4 [2015-05-26]

NOTES:

 * New maintainer address.


Version: 1.41.3 [2015-05-13]

SIGNIFICANT CHANGES:

 * AVAILABILITY: Removed requirement for 'GNU make'.


Version: 1.41.2 [2015-05-05]

BUG FIXES:

 * readCelHeader() and readCel() would core dump R/affxparser if trying to
   read multi-channel CEL files (Issue #16). Now an error is generated instead.
   Multi-channel CEL files (e.g. Axiom) are not supported by affxparser.
   Thanks to Kevin McLoughlin (Lawrence Livermore National Laboratory, USA)
   for reporting on this.

 * readCelHeader() and readCel() on corrupt CEL files could core dump
   R/affparser (Issues #13 & #15).  Now an error is generated instead. Thanks
   to Benilton Carvalho (Universidade Estadual de Campinas, Sao Paulo, Brazil)
   and Malte Bismarck (Martin Luther University of Halle-Wittenberg) for
   reports.


Version: 1.41.1 [2015-04-25]

BUG FIXES:

 * Native functions R_affx_GetCHPEntries() and R_affx_ReadCHP() had unbalanced
   PROTECT()/UNPROTECT().  Also, native R_affx_GetCHPGenotypingResults() had
   two non-PROTECT():ed usages of mkString().  Thanks to Tomas Kalibera at
   Northeastern University for reporting on this.


Version: 1.41.0 [2015-04-16]

NOTES:

 * The version number was bumped for the Bioconductor devel version, which
   is now BioC 3.2 for R (>= 3.3.0).


Version: 1.40.0 [2015-04-16]

NOTES:

 * The version number was bumped for the Bioconductor release version, which
   is now BioC 3.1 for R (>= 3.2.0).
   

Version: 1.39.5 [2015-04-15]

SIGNIFICANT CHANGES:

 * Removed 'SystemRequirements: GNU make'.

NEW FEATURES:

 * ROBUSTNESS: Now readPgfEnv()/readPgf() validated 'indices', iff possible.

 * Now readPgfEnv()/readPgf() coerces some header fields to integers, iff they
   exists, specifically 'num-cols', 'num-rows', 'probesets', and 'datalines'.

 * CLEANUP: Package no longer gives readBin() warnings on "'signed = FALSE' is
   only valid for integers of sizes 1 and 2".

BUG FIXES:

 * convertCel() on a CCG/v1 CEL file could give "Error in sprintf(
   "GridCorner%s=%d %d\n" ... invalid format '%d' ...)".  Added package test
   for convertCel(), but in this particular case it would not have cought it
   because it only happened for chip types of particular dimensions.  Thanks
   to Malte Bismarck at UK Halle (Germany) for reporting on this.


Version: 1.39.4 [2015-01-18]

SIGNIFICANT CHANGES:

 * ROBUSTNESS: 'GNU make' is a SystemRequirements (for now).

CODE REFACTORING:

 * ROBUSTNESS: Did not seem to be needed, but package is now a good citizen
   and do library.dynlib.unload() when unloaded.

 * Now using requireNamespace() instead of require().

 * Internal cleanup of native code.


Version: 1.39.3 [2014-11-26]

BUG FIXES:

 * readPgf() and readPgfEnv() failed to read all units (probesets) on some
   systems.  Extensive package tests have been added to test this and other
   cases.  Thanks to Grischa Toedt at EMBL Germany for reporting on,
   troubleshooting, and helping out with patches for this bug.


Version: 1.39.2 [2014-10-28]

BUG FIXES:

 * The range test of argument 'units' to readCdf() and readCdfQc() was never
   performed due to a typo, meaning it was possible to request units out of
   range.  Depending on system this could result in either a core dump or
   random garbage read for the out of range units.

SOFTWARE QUALITY:

 * ROBUSTNESS: Added package system tests for out of range 'units' and
   'indices' arguments for most read functions.


Version: 1.39.1 [2014-10-26]

NEW FEATURES:

 * ROBUSTNESS: Now all methods gives an informative error message if zero
   elements are requested, i.e. via zero-length argument 'indices' or 'units'
   that is not NULL. Previously this case would access all values just like
   NULL does.

 * ROBUSTNESS: Now readCelRectangle() gives an informative error message if
   argument 'xrange' or 'yrange' is not of length two.

BUG FIXES:

 * readPgf() and readPgfEnv() would give an error if argument 'indices' was
   specifies as a double rather than as an integer vector.


Version: 1.39.0 [2014-10-13]

NOTES:

 * The version number was bumped for the Bioconductor devel version, which
   is now BioC 3.1 for R (>= 3.2.0).


Version: 1.38.0 [2014-10-13]

NOTES:

 * The version number was bumped for the Bioconductor release version, which
   is now BioC 3.0 for R (>= 3.1.1).


Version: 1.37.2 [2014-09-28]

NOTES:

 * Minor modifications due to the move to GitHub.


Version: 1.37.1 [2014-08-25]

SOFTWARE QUALITITY:

 * Removed R CMD check NOTEs that appeared in recent R versions.


Version: 1.37.0 [2014-04-11]

NOTES:

 * The version number was bumped for the Bioconductor devel version, which
   is now BioC 2.15 for R (>= 3.1.0).


Version: 1.36.0 [2014-04-11]

NOTES:

 * The version number was bumped for the Bioconductor release version, which
   is now BioC 2.14 for R (>= 3.1.0).


Version: 1.35.3 [2014-02-28]

NOTES:

 * Same updates as in release v1.34.2.


Version: 1.35.2 [2014-02-28]

SOFTWARE QUALITY:

 * Patches to Fusion SDK based on clang v3.4.


Version: 1.35.1 [2014-02-27]

NOTES:

 * Same updates as in release v1.34.1.


Version: 1.35.0 [2013-10-14]

NOTES:

 * The version number was bumped for the Bioconductor devel version.


Version: 1.34.2 [2014-02-28]

CODE REFACTORING:

 * CLEANUP: Removed unnecessary usage of ':::'.


Version: 1.34.1 [2014-02-27]

BUG FIXES:

 * readCelUnits() could throw 'Error in vector("double", nbrOfCells *
   nbrOfArrays) : vector size cannot be NA.  In addition: Warning message: In
   nbrOfCells * nbrOfArrays : NAs produced by integer overflow' when reading
   from a large number of arrays and/or a large number of units.  Previously
   the limit of nbrOfCells*nbrOfArrays was .Machine$integer.max (=2147483647),
   whereas now it is .Machine$double.xmax (=1.797693e+308).  Thanks to
   Damian Plichta at the Technical University of Denmark for reporting on this.


Version: 1.34.0 [2012-10-14]

NOTES:

 * The version number was bumped for the Bioconductor release version, which
   is now BioC 2.13 for R (>= 3.0.0).


Version: 1.33.4 [2013-09-23]

PERFORMANCE:

 * Package now uses which() instead of whichVector() of 'R.utils'.  Before
   R (< 2.11.0), which() used to be 10x slower than whichVector(), but now
   it's 3x faster.


Version: 1.33.3 [2013-06-29]

NOTES:

 * Same updates as in release v1.32.3.


Version: 1.33.2 [2013-05-25]

NOTES:

 * Same updates as in release v1.32.2.


Version: 1.33.1 [2013-05-20]

NOTES:

 * Same updates as in release v1.32.1.


Version: 1.33.0 [2013-04-03]

NOTES:

 * The version number was bumped for the Bioconductor devel version.


Version: 1.32.3 [2013-06-29]

BUG FIXES:

 * Since affxparser 1.30.2/1.31.2 (r72352; 2013-01-08), writeCdf() would
   incorrectly encode the unit types, iff the input 'cdf' argument specified
   them as integers, e.g. as done by writeCdf() for AffyGenePDInfo in
   aroma.affymetrix.  More specifically, the unit type index would be off by
   one, e.g. an 'expression' unit (1) would be encoded as an 'unknown' unit (0)
   and so on.  On the other  hand, if they were specified by their unit-type
   names (e.g. 'expression') the encoding should still be correct, e.g. if
   input is constructed from readCdf() of affxparser.  Thanks to Guido Hooiveld
   at Wageningen UR (The Netherlands) for reporting on this.

 * Similarily, writeCdf() has "always", at least affxparser 1.7.4 since
   (r21888; 2007-01-09), encoded unit directions and QC unit types incorrectly,
   iff they were specified as integers.


Version: 1.32.2 [2013-05-25]

PEFORMANCE:

 * Removed all remaining gc() calls.

 * Replaced all rm() calls with NULL assignments.


Version: 1.32.1 [2013-05-20]

CODE REFACTORING:

 * CRAN POLICY: Now all Rd \usage{} lines are at most 90 characters long.


Version: 1.32.0 [2013-04-03]

NOTES:

 * The version number was bumped for the Bioconductor release version.


Version: 1.31.4 [2013-03-19]

CODE REFACTORING:

 * Made example(invertMap) a bit faster so 'R CMD check' won't complain.


Version: 1.31.3 [2013-03-18]

CODE REFACTORING:

 * Internal isPackageLoaded() of findFiles() no longer uses defunct
   manglePackageName() function.


Version: 1.31.2 [2013-01-07]

NOTES:

 * Same updates as in release v1.30.2.


Version: 1.31.1 [2012-10-18]

NEW FEATURES:

 * Now compareCdfs() gives a more precise 'reason' attribute when there is a
   difference in (regular or QC) units.  It narrows down the first unit that
   differs and reports it unit number.


Version: 1.31.0 [2012-10-01]

NOTES:

 * The version number was bumped for the Bioconductor devel version.


Version: 1.30.2 [2013-01-07]

BUG FIXES:

 * writeCdf() did not encode unit types as decoded by readCdf().  Unit type
   'unknown' was incorrectly encoded such that readCdf() would decode it as
   'copynumber'.  Also, unit types 'genotypingcontrol' and 'expressioncontrol'
   where not encoded at all.


Version: 1.30.0 [2012-10-01]

NOTES:

 * The version number was bumped for the Bioconductor release version.


Version: 1.29.13 [2012-09-26]

NEW FEATURES:

 * Added argument 'cdf=FALSE' to createCel(). Note, the previous implementation
   corresponded to cdf=TRUE.

SOFTWARE QUALITY:

 * ROBUSTNESS: Now createCel() validates/sets CEL header field 'total' based on
   'cols' and 'rows'.

 * ROBUSTNESS: Added a system test for validating that the package can write
   and read a CEL.  The test is spawning of another R process so that the test
   is robust against core dumps.


Version: 1.29.12 [2012-09-12]

DOCUMENTATION:

 * Updated one Rd link.


Version: 1.29.11 [2012-09-01]

NEW FEATURES:

 * Added argument 'aliases' to arrangeCelFilesByChipType(), e.g.
   arrangeCelFilesByChipType(..., aliases=c("Focus"="HG-Focus")).

BUG FIXES:

 * arrangeCelFilesByChipType(pathnames) assumed 'pathnames' were files in
   the current directory.


Version: 1.29.10 [2012-08-29]

CODE REFACTORING:

 * Updated some internal files used solely for maintainance.


Version: 1.29.9 [2012-08-29]

BUG FIXES:

 * The move to Fusion SDK 1.1.2 caused the package to not compile on Windows.


Version: 1.29.8 [2012-08-14]

SIGNIFICANT CHANGES:

 * Upgraded to Fusion SDK 1.1.2.


Version: 1.29.7 [2012-08-14]

CODE REFACTORING:

 * Rearranged patchdir.


Version: 1.29.6 [2012-06-26]

 * Same updates as in v1.28.1.


Version: 1.29.5 [2012-06-19]

NEW FEATURES:

 * Added arrangeCelFilesByChipType() for moving CEL files to subdirectories
   named according to their chip types, which can be useful when for instance
   downloading GEO data sets.


Version: 1.29.4 [2012-06-14]

NEW FEATURES:

 * readPgfEnv(..., indices=NULL) no longer gives a warning.

 * Updated the error messages for the CLF and PGF parsers.


Version: 1.29.3 [2012-05-22]

SOFTWARE QUALITY:

 * Now system test tests/testWriteAndReadEmptyCdf.R generates an error that is
   detected and reported by R CMD check.


Version: 1.29.2 [2012-05-22]

SOFTWARE QUALITY:

 * GENERALIZATION: Now system tests that launch another R process no longer
   assumes R is on the OS's search path.

CODE REFACTORING:

 * ROBUSTNESS/CRAN POLICY: readCel() and readCelUnits() are no longer calling
   .Internal(qsort(...)).


Version: 1.29.1 [2012-05-18]

BUG FIXES:

 * Replaced several throw() with stop(), because the former assumes that
   R.methodsS3 is loaded, which it may not be.

SOFTWARE QUALITY:

 * ROBUSTNESS: Added a system test for validating that the package can write
   and read a CDF.  The test is spawning of another R process so that the test
   is robust against core dumps.


Version: 1.29.0 [2012-03-30]

NOTES:

 * The version number was bumped for the Bioconductor devel version.


Version: 1.28.1 [2012-06-26]

 * COMPATIBILITY: Now package compile also with gcc/g++ 4.7. Thanks Dan
   Tenenbaum (Bioconductor Core Team), Fred Hutchinson Cancer Research Center,
   USA for this.


Version: 1.28.0 [2012-03-30]

NOTES:

 * The version number was bumped for the Bioconductor 2.10 release version.


Version: 1.27.5 [2012-03-19]

SOFTWARE QUALITY:

 * ROBUSTNESS: Now the native code throws R errors, instead of printing an
   error message to stdout/stderr and then returning null, that is translated
   to errors at the R level.


Version: 1.27.4 [2012-03-05]

BUG FIXES:

 * affxparser would not build on Windows with the new Rtools toolchain
   (Rtools 2.15.0.1915-1919).


Version: 1.27.3 [2011-11-18]

SOFTWARE QUALITY:

 * ROBUSTNESS: Added sanity checks asserting that the internal readers did
   indeed read something and not just returned NULL.  It should be very
   unlikely that this occurs, but there is still a small risk that after
   asserting that a file exists, but before the internal Fusion SDK parsers
   access the file, the file has been removed.


Version: 1.27.1 [2011-11-01]

NOTES:

 * Same updates as in v1.26.1.


Version: 1.27.0 [2011-10-31]

NOTES:

 * The version number was bumped for the Bioconductor devel version.


Version: 1.26.4 [2012-03-06]

BUG FIXES:

 * affxparser would not build on Windows with the new Rtools toolchain
   (Rtools 2.15.0.1915-1919), which is for R (> 2.14.1), i.e. also for
   R 2.14.2 (but not 2.14.1). This is the same bug fix that was first
   done in v1.27.4.


Version: 1.26.2 [2011-11-16]

NOTES:

 * The version number was bumped by Bioconductor to trigger a build.


Version: 1.26.1 [2011-11-01]

BUG FIXES:

 * FIX: Fixed warning on "In readBin(con, what = "integer", size = 4, n = 1, 
   signed = FALSE, 'signed = FALSE' is only valid for integers of sizes 1 
   and 2" that some read methods would generated.


Version: 1.26.0 [2011-10-31]

NOTES:

 * The version number was bumped for the Bioconductor 2.9 release version.


Version: 1.25.1 [2011-09-27]

NOTES:

 * Maintainer email was updated.


Version: 1.25.0 [2011-04-13]

NOTES:

 * The version number was bumped for the Bioconductor devel version.


Version: 1.24.0 [2011-04-13]

NOTES:

 * The version number was bumped for the Bioconductor 2.8 release version.


Version: 1.23.3 [2011-02-22]

DOCUMENTATION:

 * DOCUMENTATION: Added a section on what it means by setting a new (different)
   chip type for the output in convertCel().

BUG FIXES:

 * The internal .unwrapDatHeaderString(), used by convertCel() among others,
   would throw "Internal error: Failed to extract 'pixelRange' and 'sampleName'
   from DAT header. They became identical: ..." in case the DAT header of the
   CEL file did not contain all fields.  The function has now been updated to
   be more forgiving and robust so that missing values are returned for such
   fields instead.


Version: 1.23.2 [2011-02-15]

DOCUMENTATION:

 * Added a clarification to the help page on 'Cell coordinates and cell
   indices' that the convention in affxparser is to use one-based cell indices,
   because they are more convenient to use in R.  In order to clearly
   distinguish these from the redudant zero-based index values that also exist
   in CDF file, an additional section was added on that topic.  Moreover, help
   pages for methods querying CDF files are now referring to the above page,
   where applicable.  Thanks to William Mounts (Pfizer) and Todd Allen for
   pointing out these ambiguities in the documentation.


Version: 1.23.1 [2010-12-16]

CODE REFACTORING:

 * ROBUSTNESS: Now matrix(...) is used instead of .Interal(matrix(...)).


Version: 1.23.0 [2010-10-17]

NOTES:

 * The version number was bumped for the Bioconductor devel version.


Version: 1.22.0 [2010-10-17]

NOTES:

 * The version number was bumped for the Bioconductor 2.7 release version.


Version: 1.21.1 [2010-10-05]

NEW FEATURES:

 * Now readCdfDataFrame() also returns the cell field 'expos'.


Version: 1.21.0 [2010-04-22]

NOTES:

 * The version number was bumped for the Bioconductor devel version.


Version: 1.20.0 [2010-04-22]

NOTES:

 * The version number was bumped for the Bioconductor 2.6 release version.


Version: 1.19.6 [2010-02-11]

BUG FIXES:

 * More fixes.


Version: 1.19.5 [2010-02-09]

BUG FIXES:

 * More fixes.


Version: 1.19.4 [2010-02-06]

BUG FIXES:

 * More fixes.


Version: 1.19.3 [2010-02-06]

BUG FIXES:

 * A couple of patches to Fusion SDK courtesy of Brian Ripley; they are needed
   for Windows (64).


Version: 1.19.2 [2010-02-02]

BUG FIXES:

 * A fix to the Windows build.


Version: 1.19.1 [2010-01-29]

SIGNIFICANT CHANGES:

 * Updated Fusion SDK to 1.1.0.


Version: 1.19.0 [2009-10-27]

NOTES:

 * Devel version bumped because of the new Bioconductor release.


Version: 1.18.0 [2009-10-27]

NOTES:

 * Release version bumped because of the new Bioconductor 2.5 release.


Version: 1.17.5 [2009-09-22]

DOCUMENTATION:

 * Fixed broken link in an Rd file.


Version: 1.17.4 [2009-09-21]

NEW FEATURES:

 * Added parseDatHeaderString(), which in combination with readCelHeader() can
   be used to infer the timestamp in the header of a CEL file.


Version: 1.17.3 [2009-05-29]

NEW FEATURES:

 * Added applyCdfGroupFields() and cdfSetDimension().


Version: 1.17.2 [2009-02-20]

BUG FIXES:

 * readChp() would crash (segmentation fault) for (at least) some CHP files
   for GenomeWideSNP_5 generated by Affymetrix Power Tools.

 * Updated compareCels() to work with new readCelHeader().


Version: 1.17.1 [2009-05-09]

NEW FEATURES:

 * Now readCelHeader() also reads DAT headers from Calvin CEL files.


Version: 1.17.0 [2009-04-20]

NOTES:

 * Devel version bumped because of the new Bioconductor release.


Version: 1.16.0 [2009-04-20]

NOTES:

 * Release version bumped because of the new Bioconductor 2.4 release.


Version: 1.15.6 [2009-02-20]

NEW FEATURES:

 * Added optional argument 'newChipType' to convertCel() for overriding the
   default chip type.  Useful for updating the formal chip type of old CEL
   files.

CODE REFACTORING:

 * Removed all gc() calls in convertCel().


Version: 1.15.5 [2009-02-14]

 * Updated Fusion from 1.11 to 1.12.

BUG FIXES:

 * Fixed a bug related to SET_VECTOR_ELT/SET_ELEMENR used on strings, which
   adffected readChp().

 * Fixed a bug related to naming of the list structures (we assigned a list
   instead of a character as the name. Affected readCdfUnits() and
   readCdfCellIndices().

 * Fixed a bug in the example for readCdfUnitsWriteMap(): the package
   AffymetrixDataTestFiles was misspelled, so the tests were never run.


Version: 1.15.4 [2009-02-10]

BUG FIXES:

 * readCcg() and readCcgHeader() no longer give warnings on 'truncating string
   with embedded nul' in rawToChar().  These warnings made no difference, but
   were annoying.


Version: 1.15.3 [2009-01-22]

DOCUMENTATION:

 * Fixed a minor Rd problem.


Version: 1.15.2 [2008-12-30]

NOTES:

 * Same bug fix as in release version v1.14.2.


Version: 1.15.1 [2008-12-04]

NOTES:

 * Same bug fix as in release version v1.14.1.


Version: 1.15.0 [2008-10-21]

NOTES:

 * Devel version bumped because of the new Bioconductor release.


Version: 1.14.2 [2008-12-30]

BUG FIXES:

 * readChp() would not read all data.  Thanks Gabor Csardi for reporting this
   and providing a patch.


Version: 1.14.1 [2008-12-04]

BUG FIXES:

 * When the CDF file is on a Windows network, that is, has a pathname starting
   with '//' or '\\', then the 'chiptype' reported by readCdfHeader() contains
   a path component as well.  This seems to be due to a bug in Fusion SDK.


Version: 1.14.0 [2008-10-21]

NOTES:

 * Release version bumped because of the new Bioconductor 2.3 release.


Version: 1.13.8 [2008-08-28]

 * Fix of include statements in Fusion, details are described in
   inst/info/changes2fusion.txt. This fixes an issue with GCC 4.3.


Version: 1.13.7 [2008-08-23]

PERFORMANCE:

 * readCcg() is substantially faster after removing all gc() calls.


Version: 1.13.6 [2008-08-21]

SIGNIFICANT CHANGES:

 * Updated Fusion SDK from 1.0.10b (Jan 2008) to 1.0.11 (July 2008).


Version: 1.13.x [2008-08-14]

DOCUMENTATION:

 * Fixed typos and incorrect equation in help page '2. Cell coordinates and
   cell indices'.


Version: 1.13.5 [2008-08-09]

NEW FEATURES:

 * Made readCdf() recognize more unit types.

BUG FIXES:

 * writeCdf() would write 'CustomSeq' units as 'Tag' units, and vice versa.
   This means that *ASCII* CDFs containing such units and converted with
   convertCdf() would be have an incorrect unit type for these units.
   Also, unit type 'Copy Number' is reported as "copynumber" and no longer
   as "unknown".

 * The increase of the internal buffer for reading the 'refseq' header field
   of ASCII CDFs that was done in 1.11.2 was mistakenly undone in 1.13.3.


Version: 1.13.4 [2008-08-05]

DOCUMENTATION:

 * Now help(createCel) (and its example) clarifies that the template CEL header
   can be of v3 (ASCII), v4 (binary;XDA), or v1 (binary;Calvin).

CODE REFACTORING:

 * Renamed the HISTORY file to NEWS.


Version: 1.13.3 [2008-05-20]

BUG FIXES:

 * Now writeTpmap() works.


Version: 1.13.2 [2008-05-08]

NOTES:

 * Copied all updates in v1.12.2 (release) to v1.13.2 (devel).


Version: 1.13.1 [2008-05-02]

NOTES:

 * Copied all updates in v1.12.1 (release) to v1.13.1 (devel).


Version: 1.13.0 [2008-04-29]

NOTES:

 * Devel version bumped because of the new Bioconductor release.


Version: 1.12.2 [2008-05-09]

BUG FIXES:

 * affxparser 1.12.1 would not build on Windows.  Fix by Martin Morgan.


Version: 1.12.1 [2008-05-02]

NEW FEATURES:

 * Added readChp(). Contribution by Robert Gentleman.


Version: 1.12.0 [2008-04-29]

NOTES:

 * Release version bumped because of the new Bioconductor 2.2 release.


Version: 1.11.13 [2008-04-13]

SIGNIFICANT CHANGES:

 * Updated to Fusion SDK v1.0.10b.


Version: 1.11.? [2008-03-06]

BUG FIXES:

 * Regular expression pattern 'a-Z' is illegal on (at least) some locale, e.g.
   'C' (where 'A-z' works). The only way to specify the ASCII alphabet is to
   list all characters explicitly, which we now do in all methods of the
   package.  See the r-devel thread "invalid regular expression '[a-Z]'" on
   2008-03-05 for details.


Version: 1.11.6 [2008-03-04]

NEW FEATURES:

 * Added trial versions of readClf() and readPgf().


Version: 1.11.5 [2008-02-29]

NEW FEATURES:

 * Updated cdfMergeStrands() to merge any even number of groups, not only units
   with two or four group pairs.

BUG FIXES:

 * The code in findFiles() for testing if R.utils is loaded or not was not
   correct making it fail to detect R.utils.


Version: 1.11.4 [2008-02-20]

NEW FEATURES:

 * Added argument 'allFiles=TRUE' to findFiles().

 * Updated readCcg() according to the newer file format specifications. Now it
   is possible to do low-level reading of copy-number CNCHP files generated by
   the Affymetrix Genotype Console v2.

CODE REFACTORING:

 * Now findFiles() and hence findCdf() is only utilizing the R.utils package
   if it is already loaded.  It will no longer try to load R.utils.


Version: 1.11.3 [2007-12-01]

NEW FEATURES:

 * Removed argument 'reorder' from readCel() and readCelUnits() since its name
   was misleading (the returned value was identical regardless of 'reorder',
   but the reading speed was faster when 'reorder' was TRUE, which is how it
   is now hardwired).


Version: 1.11.2 [2007-11-06]

BUG FIXES:

 * Reading a CDF that has a 'refseq' header field longer than 65,000 symbols
   would crash R, e.g. when reading certain CDFs for resequencing chip types.
   A buffer size internal of Fusion SDK was increased from 65,000 to 400,000
   bytes.  Thanks Wenyi Wang for reporting this.

 * Argument 'verbose' of tpmap2bpmap() was not coerced to integer before
   passed to the native code.

 * The internal .initializeCdf(), used when creating new CDFs, had an error
   message refering to an invalid 'qcUnitLengths' when it was supposed to be
   'unitLengths'.  Thanks Elizabeth Purdom for reporting this.

CODE REFACTORING:

 * created a Makefile in /inst/info for comparing Fusion SDK with affxparser.


Version: 1.11.1 [2007-10-12]

NEW FEATURES:

 * convertCel() will no longer generate a warning if the corresponding CDF
   file was not found.
   
BUG FIXES:

 * For some Calvin CEL files the CEL header does not contain "parent parameter"
   'affymetrix-dat-header' but only parameter 'affymetrix-partial-dat-header'.
   In that case convertCel() would throw an error about 'sprintf("DatHeader=
   %s\n", datHeader)'.  Now a "fake" DAT header is created from the partial
   one.  If neither is found, a slightly more informative exception is thrown.


Version: 1.11.0 [2007-10-02]

NOTES:

 * Version bumped because of the new Bioconductor release.


Version: 1.9.5 [2007-09-16]

NEW FEATURES:

 * Added argument 'recursive=TRUE' to findCdf().  Note, the current working
   directory is always scanned first, but never recursively (unless explicitly
   added to the search path). This is to avoid "endless" scans in case the
   search path has not been set.

 * findFiles() now do a breath-first search in lexicographic order.

 * Removed default search paths cdf/ and data/cdf/.  We do not want to enforce
   a standard path.

CODE REFACTORING:

 * Now the examples (as well as test scripts) utilize data available in the
   new Bioconductor AffymetrixDataTestFiles package.  This means that
   'R CMD check' now runs much more tests, which is good.

 * CLEAN UP: Removed many of the old testscripts/ scripts.  They are now under
   tests/.

BUG FIXES:

 * findFiles() was not robust against broken Unix links.

 * If the destination file already existed, convertCel() would correctly
   detect that, but would report the name of the source file.


Version: 1.9.4 [2007-08-25]

SIGNIFICANT CHANGES:

 * Updated to Fusion SDK v1.0.9.


Version: 1.9.3 [2007-08-16]

NOTES:

 * See updated made to release v1.8.3 below.

 * The only difference between v1.9.3 and v1.8.3 is the modification of
   findCdf() in v1.9.2.


Version: 1.9.2 [2007-07-27]

SIGNIFICANT CHANGES:

 * This BioC devel version requires R v2.6.0 due to a change of how strings
   are handled in C by Bioconductor.

NEW FEATURES:

 * Modified findCdf() such that it is possible to set an alternative function
   for how CDFs are located.


Version: 1.8.3 [2007-08-16] (also added to devel v1.9.3)

NEW FEATURES:

 * Made several updated so that affxparser better supports CEL files in the
   new Command Console (Calvin) file format:
   - isCelFile() recognized Calvin CEL files.
   - convertCel() can convert a Calvin CEL files into v4 CEL files.
   - writeCelHeader() can write v4 CEL headers given Calvin CEL header.

CODE REFACTORING:

 * Added internal/private function to read Command Console Generic (CCG) files,
   also known as Calvin files.  Note, these functions are currently *not*
   utilizing the Fusion SDK library, but are instead written from scratch
   based on the Affymetrix' file format definitions.


Version: 1.8.2 [2007-08-01]

PERFORMANCE:

 * Optimized writeCdfHeader() for memory.  For a CDF with 1,200,000+ units
   just writing the unit names would consume 1-1.5GB RAM.  Now it writes unit
   names in chunks keeping the memory overhead around 100-200MB.

 * Made convertCdf() more memory efficient.

BUG FIXES:

 * error message in isCelFile() when the file was not found was broken.


Version: 1.8.1 [2007-07-26]

SIGNIFICANT CHANGES:

 * Now affxparser install on OSX with PPC.


Version: 1.8.0 [2007-04-24]

NOTES:

 * The version number was bumped up with the Bioconductor release.


Version: 1.7.5 [2007-03-08]

NEW FEATURES:

 * Added argument 'truncateGroupNames' to readCdfGroupNames() which defaults
   to TRUE for backward compatibility.  When TRUE, any prefix of group names
   identical to the unit name will be stripped of the group names.


Version: 1.7.4 [2007-02-21]

NEW FEATURES:

 * Now readCelUnits() can handle unit groups for which there are no probes,
   e.g. when stratifying on PM in a unit containing only MMs.

 * Added writeCdfHeader(), writeCdfQcUnits() and writeCdfUnits().  These are
   all used by writeCdf(). They also make it possible to write a CDF in chunks
   in order to for instance convertCdf() in constant memory.


Version: 1.7.3 [2007-01-05]

NEW FEATURES:

 * Added cdfAddPlasqTypes().

 * Now readCdfUnits(..., readDirections=TRUE) also returns group directions.

 * Now readCdf() reads all unit and group fields by default.

 * In addition to optimizing IO time, read maps can be used to unrotate CEL
   data rotated by the dChip software. For more information, see help on
   "Cell-index maps for reading and writing".

BUG FIXES:

 * Using read maps for readCel() would give an error saying the read map is
   invalid even when it is not.


Version: 1.7.2 [2006-12-10]

NEW FEATURES:

 * Added argument 'isPm' to readCdf().
 
BUG FIXES:

 * readCdfUnits() and readCdfCellIndices() with stratifyBy="mm" would return
   the same as stratifyBy="pm".  Options "pm" and "pmmm" are unaffected by
   this fix.


Version: 1.7.1 [2006-11-03]

SIGNIFICANT CHANGES:

 * Updated to Fusion SDK v1.0.8.

 * Windows build change: The Windows version is building against the Windows
   code of Fusion SDK not the POSIX code. In order to do this we have had to
   patch the preprocessor code in several of the Fusion SDK source-code files,
   which has to be redone manually whenever Fusion is updated.  Starting with
   this version, we instead set the _MSC_VER flag used in the Fusion code to
   indicate Windows (set by the Microsoft Visual C++ compiler). Since we are
   using MINGW this flag is obviously not set. Faking _MSC_VER this way leaves
   us only having to patch one single file in the Fusion release instead of
   10-20. Hopefully there are no other side effects.

BUG FIXES:

 * In Fusion SDK (v1.0.5) that previous version of affxparser used, a CDF file
   was never closed on Unix platforms (this bug was not in the Windows
   version).  Since Fusion allocated memory for the complete CDF (even if a
   subset is only read), this caused the memory usage to blow up, when reading
   the same or different CDF files multiple times, because the memory was
   never deallocated.  Thanks Seth Falcon and Ken Simpson for reporting this
   problem.


Version: 1.7.0 [2006-10-25]

NEW FEATURES:

 * Made readCelUnits() a bit more clever if a 'cdf' structure with only cell
   indices is passed. Then all fields are just indices and one can call unlist
   immediately.  This speeds things up a bit.

BUG FIXES:

 * writeCdf() would create an invalid CDF file if there were no QC units.
   This would in turn make readCdfUnits() etc core dump.

 * Similar to get bug fix in the C code for readCelHeader(), much of the
   C-level code for CDF (and BPMAP) files assumes that the strings from Fusion
   SDK have a null terminator. At least for CDF unit names, this is not
   necessarily the case.  To be on the safe side, for all retrieved Fusion SDK
   strings we now make sure there is a null terminator before converting it
   into an R string.  Thanks to Ken Simpson at WEHI for all the troubleshooting.

 * Because of the above bug fix, the ASCII mouse exon CDF can now be converted
   into a valid binary CDF.

NOTES:

 * The devel version number was bumped up with the Bioconductor release.


Version: 1.6.0 [2006-10-03]

NOTES:

 * The version number was bumped up with the Bioconductor release.


Version: 1.5.x [2006-09-21]

NEW FEATURES:

 * Added compareCdfs() to verify that a converted CDF is correct.

 * Added convertCdf() utilizing the new writeCdf().

 * Added trial version of createCel().

 * Added trial version of updateCelUnits().

BUG FIXES:

 * The C code for readCelHeader() did not allocate space for the string null
   terminator for the header elements that originates from wide C++ string.
   This caused readCelHeader() to contain string elements with random
   characters at the end.

 * nrows and ncols were swapped in the CDF header when written by writeCdf().
   This was missed because all tested CDFs were square.
   
SOFTWARE QUALITY:

 * Now the package passes R CMD check without warnings.


Version: 1.5.4 [2006-08-18]

SIGNIFICANT CHANGES:

 * Updated Fusion SDK to version 1.0.7.

BUG FIXES:

 * The new implementation of updateCel() utilizing raw vectors was not correct;
   extra zeros was written too.  The example code of updateCel() reveals such
   errors much easier now.

 * updateCel() would in some cases give "Error: subscript out of bounds" when
   writing the last chunk.


Version: 1.5.3 [2006-07-24]
 
NEW FEATURES:

 * Added functional prototype of updateCel() to *update* binary (v4) CEL files.
   Currently, the code does make use the Fusion SDK.  There is currently no
   writeCel() to create a CEL file from scratch.  However, with the auxillary
   function copyCel() one can copy an existing CEL file and then update that
   one.  Thus, it is now possible to write, say, normalized probe intensities
   to a CEL file.  Note that this is only a first prototype and functions may
   change in a future release.

PERFORMANCE:

 * Improved the speed of updateCel() substantially by first working with raw
   vector in memory and then write binary data to file.  Data is also written
   in chunks (instead of all at once), to minimize the memory overhead of
   using raw vectors, which is especially important for the larger chips,
   e.g. 500K.


Version: 1.5.2 [2006-05-31]

SIGNIFICANT CHANGES:

 * Updated Fusion SDK to version 1.0.6.


Version: 1.5.1 [2006-05-15]

SIGNIFICANT CHANGES:

 * Updated Fusion SDK to version 1.0.5.

BUG FIXES:

 * Made small changes to the SDK to allow it to compile under Mac OS X with
   GCC-4.0.3 shipping with R-2.3.0.

CODE REFACTORING:

 * Made changes to the Makevars, _Makefile and cmd_line scripts.


Version: 1.5.0 [2006-05-12]

NEW FEATURES:

 * Added cdfOrderBy() and cdfOrderColumnsBy() for restructuring group fields
   in a CDF list structure.  Added cdfGetGroups() too.

DOCUMENTATION:

 * Cleaned up and restructured the help pages; several Rd pages are now made
   "internal" so they do not show up on the help index page.  Instead they are
   accessable from within other help pages (if you browsing via HTML that is).
   Added a help page on common terms.

 * Added a bit more documentation on how to set the default CDF path.

BUG FIXES:

 * On Linux 64-bit read CEL intensities would all be zero.  This was due to
   compiler settings in the Fusion SDK package, which is circumvented by
   gcc compile it with a lower optimization level.

 * When argument 'cdf' was a CDF list structure with elements 'type' or
   'direction', readCelUnits() would not read the correct cells because the
   values of 'type' and 'direction' would be included in the extracted list
   of cell indices.


Version: 1.4.0 [2006-04-27]

NOTES:

 * The stable version for Bioconductor 1.8.


Version: 1.3.3 [2006-04-15]

SIGNIFICANT CHANGES:

 * The package now works on Solaris.

 * Updated the Fusion SDK to version 1.0.5 (an unofficial release).

NEW FEATURES:

 * New method readCdfCellIndices(), which is a 5-10 times faster special-case
   implementation of readCdfUnits() to read cell indices only.

 * Renamed readCdfUnitsMap() to readCdfUnitsWriteMap().

 * New method invertMap() for fast inversion of maps.

PERFORMANCE:

 * Now readCelUnits() sorts the cell indices before reading the data from each
   file.  This minimizes the amount of jumping around in the CEL files
   resulting in a speed-up of about 5-10 times.

KNOWN ISSUES:

 * KNOWN BUGS: The weird bug as in v1.3.2 remains with the new Fusion SDK,
   R v2.3.0 beta (2006-04-10 r37715) on WinXP. Internally readCdfCellIndices()
   replaces readCdfUnits(), but the error is still the same.


Version: 1.3.2 [2006-03-28]

SIGNIFICANT CHANGES:

 * All cell and unit indices are now starting from one and not from zero.
   This change requires that all code that have been using a previous version
   of this package have to be updated!

NEW FEATURES:

 * New methods readCelRectangle() to read probe signals from a specify area
   of the chip.

DOCUMENTATION:

 * Added extensive help on cell coordinates and cell indices as well read and
   write maps.

KNOWN ISSUES:

 * KNOWN BUGS: At least on WinXP, heavy use of readCelUnits() will sooner or
   later core dump R; it seems to be a memory related from that occur when
   reading the CDF and extracting the name of the unit.  However, when
   "torturing" readCdfUnits() the crash won't happen so it might be that
   readCel() does something.  Have not tried on other platforms.

PERFORMANCE:

 * Further optimization in speed and memory for most methods.


Version: 1.3.1

 * ...
