CHANGES IN iRefR VERSION 0.97:

  SIGNIFICANT USER-VISIBLE CHANGES:

    • None.

  NEW FEATURES:

    • None.

  DEPRECATED & DEFUNCT:

    • None.

  INSTALLATION:

    • None.

  BUG FIXES:

    • Minor changes to follow the size and execution time policies of CRAN.

CHANGES IN iRefR VERSION 0.96:

  SIGNIFICANT USER-VISIBLE CHANGES:

    • iRefR depends again from "igraph", which has changed and now considers all vectors starting from position one and not from position zero. From now on, "iRefR" will depend on "igraph" 0.6 or higher. The "iRefR and igraph" tutorial was also changed accordingly (see: ftp://ftp.no.embnet.org/irefindex/iRefR/current/).

  NEW FEATURES:

    • None.

  DEPRECATED & DEFUNCT:

    • None.

  INSTALLATION:

    • None.

  BUG FIXES:

    • Minor change to create_id_conversion_table: Now the default option is getwd().

CHANGES IN iRefR VERSION 0.95:

  SIGNIFICANT USER-VISIBLE CHANGES:

    • Temporarily, iRefR will not depend on "igraph" but on "igraph0" instead. This is due to the fact that the announced next version of "igraph" will be incompatible with the previous one, and the igraph maintainers have kept the old version as a package called "igraph0", i.e., "igraph0" is identical to "igraph" v.0.5.5. When the new igraph is released and tested, we may use "igraph" again.

  NEW FEATURES:

    • None.

  DEPRECATED & DEFUNCT:

    • None.

  INSTALLATION:

    • None.

  BUG FIXES:

    • None.

CHANGES IN iRefR VERSION 0.94:

  SIGNIFICANT USER-VISIBLE CHANGES:

    • None.

  NEW FEATURES:

    • Minor change to select_database.Rd, specifying the four new databases (InnateDB, MatrixDB, mpilit, mpiimex) that can be now selected.

  DEPRECATED & DEFUNCT:

    • Test data-set file removed.

  INSTALLATION:

    • None.

  BUG FIXES:

    • Date of current version of iRefIndex has been updated.

CHANGES IN iRefR VERSION 0.93:

  SIGNIFICANT USER-VISIBLE CHANGES:

    • Rnw files removed from distribution. Only pdf files included.
    • Minor updates to iRefR_tutorial, get_irefindex.Rd and summary_table.Rd.

  NEW FEATURES:

    • None.

  DEPRECATED & DEFUNCT:

    • None

  INSTALLATION:

    • None.

  BUG FIXES:

    • None.

CHANGES IN iRefR VERSION 0.92:

  SIGNIFICANT USER-VISIBLE CHANGES:

    • Directory tempdir() used to store iRefIndex files in examples (Rd documentation files).
    • if(interactive()) {} condition used in "summary_graph.Rd" examples.

  NEW FEATURES:

    • None.

  DEPRECATED & DEFUNCT:

    • None

  INSTALLATION:

    • BuildVignettes set to FALSE at the DESCRIPTION file.

  BUG FIXES:

    • None.

CHANGES IN iRefR VERSION 0.91:

  SIGNIFICANT USER-VISIBLE CHANGES:

    • Parameter "home" for the get_irefindex.R function used in documentation files.

  NEW FEATURES:

    • Optional parameter "home" added to get_irefindex.R to save files in the "R.home()" directory.

  DEPRECATED & DEFUNCT:

    • None

  INSTALLATION:

    • None

  BUG FIXES:

    • None.

CHANGES IN iRefR VERSION 0.9:

  SIGNIFICANT USER-VISIBLE CHANGES:

    • Function "convert_MITAB_to_complexList" includes now an option to generate complexes from binaries having no bait-prey information.
    • "iRefR and igraph" vignette created and released (as an additional file at the FTP site, not as a part of the package).

  NEW FEATURES:

    • None

  DEPRECATED & DEFUNCT:

    • None

  INSTALLATION:

    • None

  BUG FIXES:

    • Minor corrections to the text in the iRefR tutorial.
    • Minor correction to function "summary_protein": Now column name tables contain the word "irigid" or "icrigid" depending on the case.

CHANGES IN iRefR VERSION 0.8:

  SIGNIFICANT USER-VISIBLE CHANGES:

    • iRefR Tutorial improved and written using Sweave.
    • NAMESPACE file added.
    • Function "convert_complexList_to_MITAB" re-written; now more efficient.
    • print statements replaced by cat statements

  NEW FEATURES:

    • None

  DEPRECATED & DEFUNCT:

    • None

  INSTALLATION:

    • None

  BUG FIXES:

    • iRefR tutorial now specifies how to select only human-human interactions before doing all analyses.

CHANGES IN iRefR VERSION 0.7:

  SIGNIFICANT USER-VISIBLE CHANGES:

    • Most examples in Rd files were changed by faster ones.
    • NEWS file added.

  NEW FEATURES:

    • None

  DEPRECATED & DEFUNCT:

    • None

  INSTALLATION:

    • None

  BUG FIXES:

    • Examples in Rd files and tutorial involving specific iROGs and icROGs, work now with iRefIndex v.8.0 instead of "current". This is because the iROGs are specific for each release and the examples wouldn't give the same results when working with a future release.
