CHANGES IN VERSION 1.48.0
-------------------------

BUG FIXES AND MINOR IMPROVEMENTS

    o  Updated `viableIDs.rda` file in `extdata` directory (@lshep)
    o  Added `rmarkdown` to `Suggests` in `DESCRIPTION` file


CHANGES IN VERSION 1.41.0
-------------------------

MODIFICATIONS

    o  1.41.5 Add RUnit to Suggest
    o  1.41.3 Update viableID.rda for upcoming release
    o  1.41.2 Use dbExecute() instead of dbGetQuery() or dbSendQuery() to avoid warnings

ENHANCEMENT

    o  1.41.4 Knoknok Optimizations and allow specification of the desired Ensembl release
    o  1.41.1 James MacDonald Fixed makeOrgPackageFromNCBI to use existing downloaded files

CHANGES IN VERSION 1.39.0
-------------------------

MODIFICATIONS

    o 1.39.1 Update to REST query for uniprot
    o 1.39.2 Update viableID.rda for upcoming release

CHANGES IN VERSION 1.34.0
-------------------------

NEW FEATURES

    o Removed UniGene from OrgDb and ChipDb packages
    o Added Gene Type table to OrgDb and ChipDb packages
    o Added functionality to build Orthology.eg.db package which maps NCBI Gene IDs between species
    o RSQLite deprecated usage of dbGetQuery for database altering statements; updated to use dbExecute instead

CHANGES IN VERSION 1.28.0
------------------------

NEW FEATURES

    o (version 1.27.1) `makeOrgPackage()` supports GO ontologies.


CHANGES IN VERSION 1.18.0
------------------------

MODIFICATIONS

    o RSQLite deprecated dbGetPreparedQuery/dbSendPreparedQuery; Updated with
    dbGetQuery/dbSendQuery/dbBind/dbFetch

    o update for building BioC 3.5

BUG FIXES

    o Resolve tmp issue, change outputDir to NCBIFilesDir

    o Fixed a bug in makeOrgPackageFromNCBI when there are no GO terms

CHANGES IN VERSION 1.16.0
------------------------

NEW FEATURES

    o add check that required db0 package is installed in makeDBPackage()

    o add script to create viableIDs data file

MODIFICATIONS

    o remove outdated unit test and deprecate MAPCOUNTS in ChipDb
      package templates

    o update ChipDb package templates to load DBI in unit tests

    o allow build without --keep-empty-dirs flag

    o misc code cleanup
      - No duplicate dependencies in DESCRIPTION
      - resolve symbols in name space
      - re-usable unit tests (new rather than reuse of temporary files)
      - avoid unnecesary paste(), e.g, message(paste())
      - use of loadNamespace() rather than require()
      - avoid 1:n iterations
      - formatting, e.g., of SQL and if () {} else {}

    o remove unused tests/runalltests.Rout.save file in
      AnnDbPkg-templates

    o use https: rather than http: for NCBI access

    o rename R code and man page files consistent with high level functions

    o bump OrgDb version for 3.4 release

    o add explicit AnnotationDbi:::NCBIORG_DB_SeedGenerator()


BUG FIXES

    o getFastaSpeciesDirs() trims '\r' on Windows


CHANGES IN VERSION 1.14.0
------------------------

NEW FEATURES

    o build 'alias' table in OrgDbs sqlite db for frog, chimp, rhesus and
      mosquito

MODIFICATIONS

    o update AnnDbPkg template man to reference select() interface

    o work on makeOrgPackageFromNCBI:
      - error early when tax id is not found in gene_info.gz
      - add 'rebuildCache' arg to control repeated downloads
      - remove old code and comments
      - update man page

    o add PFAM and PROSITE man pages to NCBICHIP  and NCBIORG package
      templates

    o allow passing of directory location in wrapBaseDBPackages()

    o change format of licence; report current version of AnnotationDbi

    o modify appendArabidopsisGenes() to check for null 'gene_id'

    o add DBI to 'Suggests'; load DBI in _dbconn man page

    o load SQLite in vignettes; no longer free from
      AnnotationDbi::dbFileConnect()


CHANGES IN VERSION 1.8.0
------------------------

NEW FEATURES

    o Adds support for making orgDb objects/databases for all NCBI
      taxIDs where there is sufficient data (for adding to
      AnnotationHub).  This makes objects for 1100 organisms.


CHANGES IN VERSION 1.6.0
------------------------

NEW FEATURES

    o Adds support for a generalized makeChipPackage() function so
      that users with a probe that maps to an ID can make a chip package
      providing only that they have access to an org package (no .db0
      package required).

    o Adds support for making new inparanoid8 databases (for loading
      into AnnotationHub)


CHANGES IN VERSION 1.4.0
------------------------

NEW FEATURES

    o adds more general mechanism for creating organism packages.
      makeOrgPackage() will now allow users to pass in a series of
      data.frames, and (provided that they are formatted correctly) will
      compile those into a gene-centric organism package.  The aim is to
      provide a more general mechanism for people who are working on
      organisms that are off the beaten path.

    o updates to the documentation (new vignettes) to better clarify
      how users who need to make new organism packages should do so.


CHANGES IN VERSION 1.0.0
------------------------

    o All of the code that used to live in AnnotationDbi but was
      primarily involved in the creation of new annotation packages
      now lives here.

NEW FEATURES

    o New biocViews tags have been added to the code that generates all
      the new Annotation packages.  These allow users to search
      annotation packages by the type of annotation package that they
      are.  So for example you can now quickly list only the
      TranscriptDb packages by using the web site.