NEWS.md
In HenrikBengtsson/affxparser: Affymetrix File Parsing SDK

Version 1.75.2 [2024-02-06]

Fixed one sprintf-related coercion issue, reported by the GCC compiler, that would produce an incorrect warning message.
Fixed two sprintf-related flag issues, reported by the GCC compiler, in internal assertions, which would never be reached.

Version 1.75.1 [2024-02-05]

Fix incorrectly documented arguments in a few functions.

Version 1.75.0 [2023-10-24]

The version number was bumped for the Bioconductor develop version, which is now Bioconductor 3.19 for R (>= 4.4.0).

Version 1.74.0 [2023-10-24]

The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.18 for R (>= 4.3.1).

Version 1.73.0 [2023-04-25]

The version number was bumped for the Bioconductor develop version, which is now Bioconductor 3.18 for R (>= 4.4.0).

Version 1.72.0 [2023-04-25]

The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.17 for R (>= 4.3.0).

Version 1.71.2 [2023-04-23]

fix to src/_mingw.h provided by Tomas Kalibera.

Version 1.71.1 [2023-04-04]

Fix two instances of "watching polymorphic type 'class Except' by value [-Wcatch-value=]" compiler warnings.

Version 1.71.0 [2022-11-01]

The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.17 for R devel.

Version 1.70.0 [2022-11-01]

Remove extra backslash escaping in a few help pages.

The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.16 for R (>= 4.2.2).

Version 1.69.1 [2022-04-28]

Ported bug fix from affxparser 1.68.1.

Version 1.69.0 [2022-04-26]

Version 1.68.1 [2022-04-28]

affxparser (>= 1.67.1) failed to install with R built with -fpic flag. The symptom was a linking error ld: 000.init.o: relocation R_X86_64_32 against '.rodata' can not be used when making a shared object; recompile with -fPIC collect2: error: ld returned 1 exit status.

Version 1.68.0 [2022-04-26]

Version 1.67.1 [2022-03-23]

This packages requires R (>= 4.0.0) when build on MS Windows. This is due to the added support for UCRT on MS Windows, which is required for the upcoming R 4.2.0.

Updates to build package from source on MS Windows with UCRT. Thanks to Tomas Kalibera for the contribution.
Now registering native routines - apparently never happened before.

Version 1.67.0 [2021-10-27]

Version 1.66.0 [2021-10-27]

Version 1.65.3 [2021-09-22]

Making sure all pathnames are of length 100 or shorter.

Version 1.65.2 [2021-09-22]

Now properly registering native routines.

Version 1.65.1 [2021-09-09]

The package did not install on macOS with the M1 chip with error: use of undeclared identifier 'finite'; did you mean 'isfinite'?. This issue goes back to 2014, when macOS produced warning: 'finite' is deprecated: first deprecated in OS X 10.9 [-Wdeprecated-declarations]. isOk = finite(x);. Patched by using isfinite() instead of finite().

Version 1.64.0 [2021-05-19]

Version 1.62.0 [2020-10-27]

Version 1.60.0 [2020-04-27]

Version 1.58.0 [2019-10-29]

Version 1.56.0 [2019-05-02]

Version 1.55.0 [2018-10-30]

Version 1.54.0 [2018-10-30]

Version 1.53.2 [2018-10-22]

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

Version 1.53.1 [2018-08-28]

Version 1.53.0 [2018-04-30]

Version 1.52.0 [2018-04-30]

Version 1.51.0 [2017-10-30]

Version 1.50.0 [2017-10-30]

Version 1.49.0 [2017-04-23]

Version 1.48.0 [2017-04-23]

Version 1.47.0 [2016-10-18]

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

Version 1.46.0 [2016-10-18]

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

Version 1.45.1 [2016-09-16]

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]

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

Version 1.44.0 [2015-05-03]

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

Version 1.43.2 [2016-04-05]

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]

The DLL is now unloaded when the package is unloaded.

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

Version 1.43.0 [2015-10-23]

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

Version 1.42.0 [2015-10-13]

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

Version 1.41.7 [2015-09-14]

ROBUSTNESS: Explicitly importing core R functions.

Version 1.41.6 [2015-07-29]

Updated the BiocViews field of DESCRIPTION.

Version 1.41.5 [2015-06-17]

New maintainer address (in all fields).

Version 1.41.4 [2015-05-26]

New maintainer address.

Version 1.41.3 [2015-05-13]

AVAILABILITY: Removed requirement for 'GNU make'.

Version 1.41.2 [2015-05-05]

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]

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]

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

Version 1.40.0 [2015-04-16]

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

Version 1.39.5 [2015-04-15]

Removed SystemRequirements: GNU make.

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.

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]

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

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]

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]

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.

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

Version 1.39.1 [2014-10-26]

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.

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]

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

Version 1.38.0 [2014-10-13]

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

Version 1.37.2 [2014-09-28]

Minor modifications due to the move to GitHub.

Version 1.37.1 [2014-08-25]

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

Version 1.37.0 [2014-04-11]

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

Version 1.36.0 [2014-04-11]

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

Version 1.35.3 [2014-02-28]

Same updates as in release v1.34.2.

Version 1.35.2 [2014-02-28]

Patches to Fusion SDK based on clang v3.4.

Version 1.35.1 [2014-02-27]

Same updates as in release v1.34.1.

Version 1.35.0 [2013-10-14]

The version number was bumped for the Bioconductor devel version.

Version 1.34.2 [2014-02-28]

CLEANUP: Removed unnecessary usage of :::.

Version 1.34.1 [2014-02-27]

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]

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

Version 1.33.4 [2013-09-23]

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]

Same updates as in release v1.32.3.

Version 1.33.2 [2013-05-25]

Same updates as in release v1.32.2.

Version 1.33.1 [2013-05-20]

Same updates as in release v1.32.1.

Version 1.33.0 [2013-04-03]

The version number was bumped for the Bioconductor devel version.

Version 1.32.3 [2013-06-29]

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]

Removed all remaining gc() calls.
Replaced all rm() calls with NULL assignments.

Version 1.32.1 [2013-05-20]

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

Version 1.32.0 [2013-04-03]

The version number was bumped for the Bioconductor release version.

Version 1.31.4 [2013-03-19]

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

Version 1.31.3 [2013-03-18]

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

Version 1.31.2 [2013-01-07]

Same updates as in release v1.30.2.

Version 1.31.1 [2012-10-18]

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]

The version number was bumped for the Bioconductor devel version.

Version 1.30.2 [2013-01-07]

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]

The version number was bumped for the Bioconductor release version.

Version 1.29.13 [2012-09-26]

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

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]

Updated one Rd link.

Version 1.29.11 [2012-09-01]

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

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

Version 1.29.10 [2012-08-29]

Updated some internal files used solely for maintainance.

Version 1.29.9 [2012-08-29]

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

Version 1.29.8 [2012-08-14]

Upgraded to Fusion SDK 1.1.2.

Version 1.29.7 [2012-08-14]

Rearranged patchdir.

Version 1.29.6 [2012-06-26]

Version 1.29.5 [2012-06-19]

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]

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]

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]

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

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

Version 1.29.1 [2012-05-18]

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

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]

The version number was bumped for the Bioconductor devel version.

Version 1.28.1 [2012-06-26]

Version 1.28.0 [2012-03-30]

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

Version 1.27.5 [2012-03-19]

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]

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

Version 1.27.3 [2011-11-18]

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]

Same updates as in v1.26.1.

Version 1.27.0 [2011-10-31]

The version number was bumped for the Bioconductor devel version.

Version 1.26.4 [2012-03-06]

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]

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

Version 1.26.1 [2011-11-01]

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]

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

Version 1.25.1 [2011-09-27]

Maintainer email was updated.

Version 1.25.0 [2011-04-13]

The version number was bumped for the Bioconductor devel version.

Version 1.24.0 [2011-04-13]

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

Version 1.23.3 [2011-02-22]

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

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]

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]

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

Version 1.23.0 [2010-10-17]

The version number was bumped for the Bioconductor devel version.

Version 1.22.0 [2010-10-17]

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

Version 1.21.1 [2010-10-05]

Now readCdfDataFrame() also returns the cell field expos.

Version 1.21.0 [2010-04-22]

The version number was bumped for the Bioconductor devel version.

Version 1.20.0 [2010-04-22]

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

Version 1.19.6 [2010-02-11]

More fixes.

Version 1.19.5 [2010-02-09]

More fixes.

Version 1.19.4 [2010-02-06]

More fixes.

Version 1.19.3 [2010-02-06]

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

Version 1.19.2 [2010-02-02]

A fix to the Windows build.

Version 1.19.1 [2010-01-29]

Updated Fusion SDK to 1.1.0.

Version 1.19.0 [2009-10-27]

Devel version bumped because of the new Bioconductor release.

Version 1.18.0 [2009-10-27]

Release version bumped because of the new Bioconductor 2.5 release.

Version 1.17.5 [2009-09-22]

Fixed broken link in an Rd file.

Version 1.17.4 [2009-09-21]

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]

Added applyCdfGroupFields() and cdfSetDimension().

Version 1.17.2 [2009-02-20]

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]

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

Version 1.17.0 [2009-04-20]

Devel version bumped because of the new Bioconductor release.

Version 1.16.0 [2009-04-20]

Release version bumped because of the new Bioconductor 2.4 release.

Version 1.15.6 [2009-02-20]

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

Removed all gc() calls in convertCel().

Version 1.15.5 [2009-02-14]

Version 1.15.4 [2009-02-10]

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]

Fixed a minor Rd problem.

Version 1.15.2 [2008-12-30]

Same bug fix as in release version v1.14.2.

Version 1.15.1 [2008-12-04]

Same bug fix as in release version v1.14.1.

Version 1.15.0 [2008-10-21]

Devel version bumped because of the new Bioconductor release.

Version 1.14.2 [2008-12-30]

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

Version 1.14.1 [2008-12-04]

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]

Release version bumped because of the new Bioconductor 2.3 release.

Version 1.13.8 [2008-08-28]

Version 1.13.7 [2008-08-23]

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

Version 1.13.6 [2008-08-21]

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

Version 1.13 [2008-08-14]

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

Version 1.13.5 [2008-08-09]

Made readCdf() recognize more unit types.

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]

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

Renamed the HISTORY file to NEWS.

Version 1.13.3 [2008-05-20]

Now writeTpmap() works.

Version 1.13.2 [2008-05-08]

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

Version 1.13.1 [2008-05-02]

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

Version 1.13.0 [2008-04-29]

Devel version bumped because of the new Bioconductor release.

Version 1.12.2 [2008-05-09]

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

Version 1.12.1 [2008-05-02]

Added readChp(). Contribution by Robert Gentleman.

Version 1.12.0 [2008-04-29]

Release version bumped because of the new Bioconductor 2.2 release.

Version 1.11.13 [2008-04-13]

Updated to Fusion SDK v1.0.10b.

Version 1.11 [2008-03-06]

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]

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

Version 1.11.5 [2008-02-29]

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

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]

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.

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]

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]

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.

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

Version 1.11.1 [2007-10-12]

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

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]

Version bumped because of the new Bioconductor release.

Version 1.9.5 [2007-09-16]

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.

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/.

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]

Updated to Fusion SDK v1.0.9.

Version 1.9.3 [2007-08-16]

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]

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

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

Version 1.8.3 [NA]

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.

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]

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

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

Version 1.8.1 [2007-07-26]

Now affxparser install on OSX with PPC.

Version 1.8.0 [2007-04-24]

The version number was bumped up with the Bioconductor release.

Version 1.7.5 [2007-03-08]

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]

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]

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".

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]

Added argument isPm to readCdf().

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]

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.

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]

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.

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.

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

Version 1.6.0 [2006-10-03]

The version number was bumped up with the Bioconductor release.

Version 1.5 [2006-09-21]

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().

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.

Now the package passes R CMD check without warnings.

Version 1.5.4 [2006-08-18]

Updated Fusion SDK to version 1.0.7.

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]

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.

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]

Updated Fusion SDK to version 1.0.6.

Version 1.5.1 [2006-05-15]

Updated Fusion SDK to version 1.0.5.

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.

Made changes to the Makevars, _Makefile and cmd_line scripts.

Version 1.5.0 [2006-05-12]

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

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.

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]

The stable version for Bioconductor 1.8.

Version 1.3.3 [2006-04-15]

The package now works on Solaris.
Updated the Fusion SDK to version 1.0.5 (an unofficial release).

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.

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 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]

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

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

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.

Further optimization in speed and memory for most methods.

Version 1.3.1 [NA]

HenrikBengtsson/affxparser documentation built on Feb. 9, 2024, 3:13 a.m.

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HenrikBengtsson/affxparser Affymetrix File Parsing SDK

NEWS.md In HenrikBengtsson/affxparser: Affymetrix File Parsing SDK

Version 1.75.2 [2024-02-06]

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Version 1.75.1 [2024-02-05]

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Version 1.75.0 [2023-10-24]

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Bug Fixes

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Version 1.69.1 [2022-04-28]

Bug Fixes

Version 1.69.0 [2022-04-26]

Version 1.68.1 [2022-04-28]

Bug Fixes

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Significant Changes

Software Quality

Version 1.67.0 [2021-10-27]

Version 1.66.0 [2021-10-27]

Version 1.65.3 [2021-09-22]

Software Quality

Version 1.65.2 [2021-09-22]

Software Quality

Version 1.65.1 [2021-09-09]

Bug Fixes

Version 1.64.0 [2021-05-19]

Version 1.62.0 [2020-10-27]

Version 1.60.0 [2020-04-27]

Version 1.58.0 [2019-10-29]

Version 1.56.0 [2019-05-02]

Version 1.55.0 [2018-10-30]

Version 1.54.0 [2018-10-30]

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Documentation

Version 1.53.1 [2018-08-28]

Version 1.53.0 [2018-04-30]

Version 1.52.0 [2018-04-30]

Version 1.51.0 [2017-10-30]

Version 1.50.0 [2017-10-30]

Version 1.49.0 [2017-04-23]

Version 1.48.0 [2017-04-23]

Version 1.47.0 [2016-10-18]

Notes

Version 1.46.0 [2016-10-18]

Notes

Version 1.45.1 [2016-09-16]

Code Refactoring

Version 1.45.0 [2015-05-03]

Notes

Version 1.44.0 [2015-05-03]

Notes

Version 1.43.2 [2016-04-05]

New Features

Version 1.43.1 [2016-02-28]

New Features

Bug Fixes

Version 1.43.0 [2015-10-23]

Notes

Version 1.42.0 [2015-10-13]

Notes

Version 1.41.7 [2015-09-14]

Code Refactoring

Version 1.41.6 [2015-07-29]

Notes

Version 1.41.5 [2015-06-17]

HenrikBengtsson/affxparser
Affymetrix File Parsing SDK

NEWS.md
In HenrikBengtsson/affxparser: Affymetrix File Parsing SDK