RELEASE HISTORY OF THE "MALDIquantForeign" PACKAGE
==================================================


CHANGES IN MALDIquantForeign VERSION 0.9 [2014-08-11]:
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IMPROVEMENTS

* `.readAnalyzeIntensity`: allow to specify a mass range of interest to reduce
  memory usage while importing Analyze files;
  affected functions: `import`, `importAnalyze`
* `importAnalyze`: use `as.double` after reading the image dimensions to avoid
  integer overflows in vector allocations (the Analyze 7.5 format specification
  limits the dimensions to integer).
  Thanks to Ken Frankel <kafrankel@gmail.com> for reporting this problem.
* `importImzMl`: add MD5 checksum support for imzML files.
  Thanks to Ken Frankel <kafrankel@gmail.com> for reporting this problem.


CHANGES IN MALDIquantForeign VERSION 0.8 [2014-06-16]:
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MODIFICATIONS

* `import`: set argument `centroided=FALSE` as default (was `NA` before). The
  automatically determination of profile/centroided data was too error prone.
  Now we read everything as profile data (use `centroided=TRUE` to read
  centroided data);
  affected functions: all `import` functions (e.g. `importBrukerFlex`,
  `importMzMl` ...).

IMPROVEMENTS

* `importAnalyze`: circumvent the limit of 32747 intensity values that is
  specified in the official Analyze 7.5 format.
  Thanks to Ken Frankel <kafrankel@gmail.com> for reporting this problem.

INTERNAL CHANGES

* Fix VignetteIndexEntry.
* Rename vignette output file from MALDIquantForeign.pdf to
  MALDIquantForeign-intro.pdf.
* Check availability of the "RNetCDF" package in the `importCdf` man page to
  avoid build failures on CRAN.
* Don't evaluate the remote import example in the vignette to avoid build
  failures on CRAN.


CHANGES IN MALDIquantForeign VERSION 0.7 [2014-04-11]:
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IMPROVEMENTS

* Add vignette.

INTERNAL CHANGES

* Move tests into tests/testthat to adapt to testthat 0.8 and new
  CRAN policy; close #10.

* Fix path of exampledata (needed because the test scripts moved to
  tests).


CHANGES IN MALDIquantForeign VERSION 0.6 [2014-01-28]:
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NEW FEATURES

* Add basic import support for CDF files [contributed by Pietro Franceschi];
  new function: `importCdf`.
* `import`: add arguments "massRange" and "minIntensity" to limit import range;
  affected functions: all `import*` functions.
* `import`: add argument "centroided" to allow import of centroided spectra as
  MassPeaks objects;
  affected functions: all `import*` functions.

IMPROVEMENTS

* Add "skip" argument to `.importCsv`, `.importTab`, `.autoSep` and
  `.autoHeader` to allow skipping first lines;
  affected functions: `import`, `importTxt`, `importTab`, `importCsv`

BUG FIXES

* `importAnalyze`: add support for ABSiex Analyze 7.5 files.
  Thanks to Pietro Franceschi for reporting this bug/odd behaviour.
* `.importTab`: use `.autoSep` and `.autoHeader`
  (before they were used only by `.importCsv`);
  affected functions: `import`, `importTxt`, `importTab`
* `.parseMzML`: fix assignment operation. Before all metaData of spectra were
  overwritten by the metaData of the last spectrum (affected only mzML files
  with more than one spectrum).
  affected functions: `importMzML`
* `export`: fix one file export;
  additional affected functions: `exportMzMl`.

INTERNAL CHANGES

* Regenerate man pages with new 'roxygen2' (3.0.0).


CHANGES IN MALDIquantForeign VERSION 0.5.1 [2013-09-18]:
--------------------------------------------------------

BUG FIXES

* Replace MALDIquant:::isMassSpectrum by MALDIquant::isMassSpectrum.
* Replace deprecated function isMassObjectList.


CHANGES IN MALDIquantForeign VERSION 0.5 [2013-09-08]:
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IMPROVEMENTS

* `import*`: add "excludePattern" argument to avoid import of specific files;
  closes #8.

BUGFIXES

* Fix "totalIonCurrent" test case.
* Add import("methods") to NAMESPACE (fixes #9).

INTERNAL CHANGES

* Update dependencies; now MALDIquantForeign depends on R 3.0.0.
* Replace all paste(..., sep="") by paste0.


CHANGES IN MALDIquantForeign VERSION 0.4 [2013-04-28]:
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NEW FEATURES

* Add basic import support for imzML files and Analyze 7.5 files.

IMPROVEMENTS

* `import`: add "removeEmptySpectra" argument; closes #7.

MODIFICATIONS

* `import`: change default argument "verbose" to TRUE.

BUGFIXES

* `.download`: respects "verbose" argument now (fixes #6).

INTERNAL CHANGES

* Remove LICENSE file.


CHANGES IN MALDIquantForeign VERSION 0.3 [2013-03-01]:
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NEW FEATURES

* Add basic support for mzML export.
* Add basic import support for Ciphergen XML files.
* `import`: add http(s):// and ftp:// support.
* `import`: add uncompression support to allow import of
  zip/tar.{gz,bz2,xz}-archives.

BUGFIXES

* Add missing "usage" section in `export` methods manual pages.
* `.files`: returns only unique file names;
  affected functions: all import functions.

INTERNAL CHANGES

* `.make.unique`: generates c("a1", "a2") instead of c("a", "a1") and
  c("a001", ...,  "a099", "a100") instead of c("a", ..., "a98", "a99");
  affected method: `export,list`.
* DESCRIPTION: move base64enc, digest, readBrukerFlexData, readMzXmlData and
  XML to "Imports".
* DESCRIPTION: remove MALDIquant from the "Imports" field.


CHANGES IN MALDIquantForeign VERSION 0.2 [2013-01-14]:
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IMPROVEMENTS

* `exportMsd`: complete rewrite, write xml files manually instead of using the
  XML package (increasing speed).

BUGFIXES

* `export`: fix empty filenames.
* `export,list`: stop if directory doesn't exist.
* `exportMsd`: fix peaks argument.
* `exportMsd` tests: respect endianness.
* `import`: respect verbose argument in `import(type="auto")`.


CHANGES IN MALDIquantForeign VERSION 0.1 [2012-12-10]:
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* First public release.
* Supported file formats:
  * Import: tab, txt, csv, Bruker Daltonics *flex files, mzXML, mzML
  * Export: tab, csv, msd

