changes in version 2.11.1 (2014-09-04)
	*removed ENA functions requiring updates to new data warehouse

changes in version 2.5.1 (2013-03-18)
	* fixed bug in read.gff to parse locus_tag instead of old_locus_tag 
	  if present (see NC_000908.gff from Mycoplasma genitalium G37)
	* added new columns (taxid and center) to proks and euks datasets. Also 
	  replaced non ASCII characters in center names (which cause Warnings).
	* updated plot.genomes and plotby to extend x-axis to current date.
	* replaced 6 ena* functions with a single ena() function to retrieve data 
	  from the REST browser and a separate enaParse() function to parse XML output

changes in version 2.3.3 (2012-09-14)
        * update ncbiTaxonomy function due to changes in eSummary output 
	* added functions to read files in NCBI genomes ftp including GRange 
          objects (gff, ptt, rnt, GeneMarkHMM, Glimmer, Prodigal files) and 
          Biostrings (faa, fna, ffn, frn sequence files).  read.ncbi.ftp is a wrapper. 
        * added ftpList to list directories and files in NCBI and other ftps.  
        * deleted sra table due to recent problems with many SRA taxonomy links

changes in version 2.3.2 (2012-07-01)
        * deleted lproks tables that no longer exists (and removed related pub and 
          complete tables)
	* added abstract to ncbiPubmed

changes in version 2.3.1 (2012-04-03)
        * updated plot genomes to use other date columns like created or submitted
        * removed subset genome functions since these are not really needed
        * fixed second elink in ncbiGenome (other Genome sequences).  This was returning an
          error instead of first elink (assemblies) if no results were found. 
	* added new proks, euks, and virus genome tables from genomes/GENOME_REPORTS ftp.
	* removed old leuks and lenvs genome project tables that are no 
          longer supported (since Aug 2011). The lproks table receives only "complete" 
          genome updates and was kept for now.

changes in version 2.1.5 (2012-03-23)
	* added stop() to esearch and elink if no results found - needed if 
          nesting functions like esummary(esearch())

changes in version 2.1.4 (2012-03-13)
	* added 5 new E-utility scripts (einfo, esearch, esummary, efetch and elink)
        * updated ncbi* functions to use new e-utility functions
	* dropped required lattice package
	* updated package datasets - note that leuks, lenvs and lproks (assemblies) 
	  are no longer supported (no updates since Aug 2011). The new genome tables 
	  at www.ncbi.nlm.nih.gov/genome/browse will be included in future releases.

changes in version 2.1.3 (2012-02-13)
	* enaProject was updated to parse new XML format
        * The Entrez Genome Database was updated by NCBI on Nov 9,2011.  The
	  new ncbiGenome only returns summaries and a new function ncbiGenomeNuc 
	  returns linked neighbors.
	* E-fetch no longer supports retrievals to the Genome database (the first 
          example in ncbiSubmit was changed to use the nucleotide database).

changes in version 1.99.1 (2011-10-24)
        * added functions to query European Nucleotide Archive (ENA) using a 
          taxonomy name or id (enaTaxonomy, enaSRA, and enaProject)
        * added functions to query ENA using a SRA accession
          (enaStudy, enaSubmission, enaExperiment, and enaFiles)
	* added sra dataset listing all microbial SRA samples from ENA
	* added ncbiInfo to list NCBI databases and fields. 
        * updated and renamed functions to query specific Entrez databases 
          (ncbiTaxonomy, ncbiProject, ncbiGenome, ncbiNucleotide)
        * updated and renamed functions to return release dates in Revsion 
          History (ncbiRelease) or publication dates (ncbiPubmed)
        * added ncbiSubmit to return GenBank submission dates
	* removed duplicate project ids from lproks table (35 on Oct 2011)

changes in version 1.9.3 (2011-9-1)
	* added option to include current date in plotby
	* added dates to 725 assemblies with missing release dates (these
	  assembles only have a Genbank accession). The dates will be lost 
	  after updating the table.
	* added dataset for complete microbial genomes with release date,
	  revision history date, published date, assembly release date (if
	  available previously as WGS).

changes in version 1.9.2 (2011-7-14)
	* updated acc2date to query revision history display in Entrez
	  (girevhist.cgi is no longer available)
	* added acc2dateCommon to find earliest relased date from replaced
	  sequences (the "Common revision history link" in defunct
	  girevhist.cgi)
	* fixed term2summary to query bioproject instead of old genomeprj

changes in version 1.9.1 (2011-6-7)
	* removed query using sequencing status in term2summary example
	  (genome project is being replaced by bioproject and some queries
	  are returning errors) 
	* fixed abbrev to skip unkwown species

changes in version 1.7.1 (2011-3-15)
	* added pub2date to retrieve publications details from PubMed.  
	* added acc2date to retrieve release dates from Revision History. 
	* added functions to parse month or year from release dates
	* removed the gold dataset since GOLD is no longer freely
	  available (see email 3/2011 - "we cannot support redistribution in any
	  form"). HMP uses GOLD data so I removed that dataset too.
	
changes in version 1.5.6 (2010-10-14)

	* updated biocViews in DESCRIPTION
	* fixed updatelproks to replace latin characters before removing
	  extra spaces (which caused an error) 
	* set released dates with 2000-1-1 to NA in lproks

changes in version 1.5.4 (2010-8-2)

	* deleted Sweave file about Entrez queries (remote queries were
	  causing frequent errors in package builds)

changes in version 1.5.3 (2010-7-30)

	* moved sort01 routine before option to limit matrix to 50 rows in
	  image2
	* fixed term2summary.  Searches in genome projects may return
	  matches but not "genome sequencing" types, so this caused an 
	  unhelpful error message.

changes in version 1.5.2 (2010-5-18)

	* added image2 to plot a matrix
	* fixed error in plotby.  Previously limited to 10 groups.
	* fixed update(lproks) after refseq ids were added to all three
	  lproks tabs and genbank accessions were added to in progress tab
	* fixed update(virus) after modified date added to table

changes in version 1.5.1 (2010-4-23)

	* removed the wgs dataset.  The lproks table again reports release
	  dates for assembly genomes (no release dates were added between
	  9/15/09 and 4/15/10)

changes in version 1.4.0 (2010-4-13)

	* fixed the main url (eutils.ncbi.. not www.ncbi) and added tool
	  and email options to E-utility scripts (now required by NCBI).
	* added details to genomes-update about reporting counts of new
	  IDs added and old IDs removed.

changes in version 1.3.1 (2010-4-11)

	* added print.genomes method to print the first few rows and
	  columns of a genome table (also reordered the datasets so
	  id, name, status, and released is in first 4 columns)
	* improved messages for updating genomes.  Now the number of new
	  project ids added AND old projects ids removed is reported
	* modified package to import XML package (no longer depends on
	  XML)
	* added subset.genomes and [.genomes to extract parts of a genome
	  table (and preserve some genome class attributes and not others)
	* added latin2char function to replace a few latin characters in
	  NCBI tables with ASCII. Now R CMD check runs without the "Portable
	  packages use only ASCII characters in their datasets" warning
	* added new summary methods for tables without status column

version 1.3.0 uploaded to BioConductor for review (2010-2-19)


