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

CHANGES in MALDIquantForeign VERSION 0.14.1 [2024-01-22]
--------------------------------------------------------

INTERNAL CHANGES

* Fix VignetteEngine NOTE.


CHANGES in MALDIquantForeign VERSION 0.14 [2023-08-11]
------------------------------------------------------

INTERNAL CHANGES

* Adapt unit tests for `writeMzMlDocument`/`writeMsdDocument`
  to `libdeflate` (new default compression for `memCompress`/`memDecompress`
  in R > 3.4.1).


CHANGES in MALDIquantForeign VERSION 0.13 [2021-12-23]
------------------------------------------------------

DOCUMENTATION

* `exportMzMl` and `exportImzMl` also support the export of
  `MALDIquant::MassPeaks` objects. (Before just `MassSpectrum` was mentioned.)

MODIFICATIONS

* Change URLs from http to https where possible.

INTERNAL CHANGES

* Test for `MassSpectrum` and `MassPeaks` list in `.write{Imz,Mz}MlDocument`.

* Remove `is.null(getGeneric(...))` tests before setting generics for
  S4 methods to avoid errors in package loading (especially with
  `pkgload::load_all()`).

* `.writeImzMlDocument` uses `MALDIquant::coordinates` explicitly to avoid
  method dispatch conflict in combination with the `sp` package.
  Reported by Denis Abu Sammour (#33).


CHANGES in MALDIquantForeign VERSION 0.12.2 [2020-09-18]:
---------------------------------------------------------

* Fix `.autoSep` and `.autoHeader` to look just in the first line of an ascii
  document for separator/header information. Before the whole file was search
  but just the first line reported anyway. This results in an unnecessary long
  reading time. Affected functions (if arguments "sep" and "header" where not
  given by the user: .csv, .tab, .txt import: `import`, `importCsv`,
  `importTab`, `importTxt`.


CHANGES in MALDIquantForeign VERSION 0.12.1 [2020-03-09]:
---------------------------------------------------------

* Fix reading of txt, csv, tab files if "skip" argument is used ("skip" was
  applied twice). Affected functions: .csv, .tab, .txt import: `import`,
  `importCsv`, `importTab`, `importTxt`.
  Bug reported by Samuel Granjeaud (#29).


CHANGES in MALDIquantForeign VERSION 0.12 [2019-01-30]:
-------------------------------------------------------

* Fix reading of mzML with "non-standard data" arrays.
  Bug reported by Paul Turner.


CHANGES in MALDIquantForeign VERSION 0.11.6 [2018-08-30]:
---------------------------------------------------------

* Ignore comments in `.autoSep` and `.autoHeader`. Affected functions: .tab and
  .csv import, `import`, `importCsv`, `importTab`, `importTxt`.
  Bug reported by Fernando Pineda.


CHANGES in MALDIquantForeign VERSION 0.11.5 [2018-08-14]:
---------------------------------------------------------

* Fix psidev URLs.


CHANGES in MALDIquantForeign VERSION 0.11.4 [2018-08-01]:
---------------------------------------------------------

BUGFIX

* Don't access `totalIonCurrent` for `MassPeaks` objects in `exportMzMl` and
  `exportImzMl`.


CHANGES in MALDIquantForeign VERSION 0.11.3 [2018-05-27]:
---------------------------------------------------------

BUGFIX

* Don't use scientific format for numeric values in (i)mzML export.
  Patch by F. Orlando Galashan (see #25).


CHANGES in MALDIquantForeign VERSION 0.11.2 [2018-03-18]:
---------------------------------------------------------

BUGFIX

* Fix missing unitName in intensity array in mzMl export.
  Reported by Jan Kobarg patch proposed by F. Orlando Galashan (see #22/#24).


CHANGES IN MALDIquantForeign VERSION 0.11.1 [2017-12-04]:
---------------------------------------------------------

BUGFIX

* Fix handling of "processed" argument in `.writeImzMlDocument`; see #21.
* Fix `export` method if there was no filename given.


CHANGES IN MALDIquantForeign VERSION 0.11 [2017-09-01]:
-------------------------------------------------------

BUGFIX

* Fix integer overflow in `.ibdOffsets`; see issue #20.
* Fix `exportImzMl` for missing coordinates, pixelSize and dimension; closes
* #20.

INTERNAL CHANGES

* Put MALDIquant into single quotes in the DESCRIPTION file.
* Rezip inst/compressed/csv.tar.gz using `gzip -n` to avoid lintian's
  package-contains-timestamped-gzip warning; see
  https://wiki.debian.org/ReproducibleBuilds for details.


CHANGES IN MALDIquantForeign VERSION 0.10 [2015-10-31]:
-------------------------------------------------------

IMPROVEMENTS

* Add parallel support on unix-based platforms using the parallel package.
  All `import*` functions support the "mc.cores" argument (default is 1, means
  no parallel import). Please read also `?"MALDIquantForeign-parallel"`.
* Add importer for .msd (mMass) files: `importMsd`.
* Add basic export support for imzML files: `exportImzMl`.
* `.importImzMl`: add "coordinates" argument to access specific spectra by
  their x, y coordinates within an imzML file; closes #14;
  affected functions: `import`, `importImzMl`.
  Thanks to Heath Patterson <heath.patterson@umontreal.ca> for this idea.

MODIFICATIONS

* Remove dependency "downloader". Since R 3.2.2 https is supported on all
  platforms by `base::download.file`.
* Use "verbose = interactive()" in `import`.
* Replace old imzML example files in inst/exampledata.
* `exportMzMl`: improve documentation of the "path" argument.
* `.importImzMl`: if the imzML file doesn't contain any UUID a warning is thrown
  instead of an error;
  affected functions: `import`, `importImzMl`.
* `.importImzMl`: if the imzML file doesn't contain any checksum for its
  corresponding idb file a warning is thrown (before it was an error);
  affected functions: `import`, `importImzMl`.

INTERNAL CHANGES

* Import non-base functions/methods via NAMESPACE.
* Use MALDIquant's new `coordinates` method.
* Replace `require` by `requireNamespace` as suggested by "Writing R
  Extensions".
* Rezip gzip'ed files using `gzip -n` to avoid lintian's
  package-contains-timestamped-gzip warning; see
  https://wiki.debian.org/ReproducibleBuilds for details.


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

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]:
------------------------------------------------------

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]:
------------------------------------------------------

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]:
------------------------------------------------------

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]:
------------------------------------------------------

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]:
------------------------------------------------------

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]:
------------------------------------------------------

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]:
------------------------------------------------------

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]:
------------------------------------------------------

* First public release.
* Supported file formats:
  * Import: tab, txt, csv, Bruker Daltonics *flex files, mzXML, mzML
  * Export: tab, csv, msd
