VERSION 1.47.1
-------------

  o fix "R CMD check" error caused by some problem in org.EcK12.eg.db
  
  o remove org.EcK12.eg.db from Suggests for BioC build check
  
  o korg now include 10718 KEGG species or 951 new species beyond March 2024.


VERSION 1.43.1
-------------

  o add org.EcK12.eg.db to Suggests for BioC build check
  
  o korg now include 9767 KEGG species or 1485 new species beyond 2022.


VERSION 1.37.1/1.36.1
-------------

  o fix bug in download.kegg caused by recent change in kegg rest API
    urls (http to https).
  
  o korg now include 8282 KEGG species or 1449 new species beyond 2020.


VERSION 1.31.3/1.30.3
-------------

  o fix bug in mol.sum with single gene data reported by
    easygsea. Similarly add drop=F to a few other lines in mol.sum and
    node.map.
  
VERSION 1.31.2/1.30.2
-------------

  o solve the check error due to the change related to KEGGEdgeSubtype
    in KEGGgraph package (version 1.51.1).
  
VERSION 1.31.1/1.30.1
-------------
  
  o korg now include 6833 KEGG species or 1588 new species beyond 2017.

VERSION 1.29.1/1.28.1
-------------

  o developmental version now available on GitHub at:
    https://github.com/datapplab/pathview
  
  o fixed warning on "requireNamespace(pkg.name)" in geneannot.map.R
    and sim.mol.data.R. Now "import" from org.Hs.eg.db, instead of
    "suggest" it. Also import more functions and class from
    AnnotationDbi.

  o prevented potential error caused by class(exprs) == "data.frame"
    or "class()==" if conditions in multiple functions. class(exprs)
    now returns a vector of length 2, which caused the error.

VERSION 1.23.3/1.22.3
-------------
  
  o fix error and warning cause by geneannot.map() function. change
    if(in.type == out.type) to if(all(in.type == out.type)). change
    biocLite installation to BiocManager::install. make similar changes
    in sim.mol.data() function.

  o update NAMESPACE file on importFrom lines on AnnotationDbi and
    BiocManager.

VERSION 1.18.2
-------------
  
  o korg now include 5245 KEGG species. To speed up pathview package
    loading, an updated version of korg is now checked out from
    Pathview Web server only when it is acutally used and needed.

VERSION 1.17.7
-------------
  
  o updated combineKEGGnodes.R, i.e. changed the stop error to a
    warning message when a group node include different node types,
    i.e. both gene and compound. This problematic KEGG node definition
    does exist in pathway 04136 Autophagy - other, and caused error
    when calling pathview with kegg.native = F.

  o fixed bug in mol.sum introduced at 1.15.1, i.e. indexing using
    which(eff.idx). This problem only affect direct call of mol.sum
    with sum.method other than "sum" and "mean".


VERSION 1.17.1
-------------
  
  o major expansion in korg, which now include both KEGG and NCBI
    taxonomy IDs, two more gene ID types, i.e. NCBI protein and uniprot
    IDs. In addition, Entrez or NCBI Gene IDs are discontinued for most
    prokaryotes.

  o korg now include 4800 KEGG species, in the meantime, an updated
    version of korg is now checked out from Pathview Web server each
    time pathview package is loaded.


VERSION 1.15.1
-------------
  
  o fixed bug in node.map on single row/mapped data, and in mapped row
    numbers.

VERSION 1.10.2
-------------
  
  o fixed problem that no node mapped when one gene/protein ID maps to
    multiple Entrez Gene ID (like Enzyme IDs): id2eg call with unique.map=F.

VERSION 1.10.1
-------------

  o fix bug in reaction2edge function, which throw error for a few
    metabolic pathways with no multi-node reaction group (examples
    including 00072, 00100).

VERSION 1.9.3
-------------

  o pathview can accept a vector of multiple pathway ids, and
    map/render the user data onto all these pathways in one call.

  o one extra column "all.mapped" was added to pathview output
    data.frames as to show all the gene/compound IDs mapped to each
    node.

  o add geneannot.map as a generic function for gene ID or annotation
    mapping.

  o sim.mol.data now generate data with all major gene ID types for
    all 19 species in bods, not just human.

  o download.kegg now let the user to choose from xml, png or both
    file types to download for each input pathway. In the meantime, it
    uses the KEGG REST API instead of the classical KEGG download
    links. All potential pathways including the general pathways can be
    downloaded this way.

  o solve the redundant import from graph package.

  o import specific instead of all functions from XML package.

VERSION 1.9.1
-------------

  o solve the install error due to the recent change in KEGGgraph
    package.

VERSION 1.5.4
-------------

  o adjust run-time messages into 3 consistent classes: Info (on
    progress), Note and Warning.

  o include paths.hsa data, the full list of human pathway ID/names
    from KEGG, as to help user specify target pathways when calling
    pathview.

  o updated korg to included over 80 newly added species, such as
    sheep, apple, mandarin orange etc. Pathview can work with 3050
    species now.

  o adjust the definitions of 7 arguments for pathview function:
    discrete, limit,bins, both.dirs, trans.fun, low, mid, high. These
    used to be a list of two logical elements with "gene" and "cpd" as
    the names. They can be vectors of two or one element(s) now. This
    makes pathview easier to use now.

  o Vigette has been reformatted: add a Citation section, and some
    example on reading user data into R, fix a few typos.


VERSION 1.4.2
-------------

  o fixed bug in render.kegg.node function, which generates black
    lines in some nodes of multiple sample view.

VERSION 1.3.6
-------------

  o ajusted node x coordinate by +0.5 to better fit the color blocks
    in 2 layer native kegg views.

VERSION 1.3.4
-------------

  o updated bods to included an extra column of id.type, the default
    gene ID type.


VERSION 1.2.4
-------------

  o updated korg to included over 600 newly added species. Pathview
    can work with 2970 species now.

  o Make returned values from pathview, keggview.native and
    keggview.graph functions invisible.

VERSION 1.2.3
-------------

  o Fixed bug in node.map function, which produces 0 values when all
    multiple genes in a node are NA's.

VERSION 1.2.2
-------------

  o Fixed bug in mol.sum function, which generates "incorrect number of
    dimension" or NA's when sum.method="median" etc.

VERSION 1.2.1
-------------

  o Fixed bug in "missing red disease gene node labels" in diease
    pathways. To avoid interfering with node coloring, set all disease
    gene labels to black instead.

VERSION 1.1.7
-------------

  o Graphviz view can automatic choose different types of legends,
    either on nodes, edges or both depending on the specific pathways.

  o Vigette has been reformatted: the "Quick start" section added

VERSION 1.1.6
-------------
  o Pathview can plot/integrate/compare multiple states/samples in the
    same graph. Several functions and data objects are revised:
    including pathview, keggview.native, keggview.graph,
    render.kegg.node etc. New section on multiple state data with
    working exampleshas been added.

  o Vigette has been reformatted: Data integration section splitted
    into multiple sub-sections.

VERSION 1.1.5
-------------
  o Pathview works with species where default KEGG gene ID is not
    Entrez Gene. Several functions and data objects are revised:
    including pathview, node.map, sim.mol.data, kegg.species.code,
    korg. New section on KEGG species and Gene ID usage with working
    exampleshas been added.

VERSION 1.1.3
-------------
  o Pathview paper published in Bioinformatics

VERSION 1.0.0
-------------
  o Initial release with Bioconductor

  o Main function: pathview

  o Four functional modules: 
    -Downloader: download.kegg;
    -Parser: node.info, combineKEGGnodes, reaction2edge;
    -Mapper: node.map, eg2id, id2eg, cpdkegg2name, cpdname2kegg,
    	     cpd2kegg, cpdidmap, kegg.species.code, mol.sum, 
	     sim.mol.data;
    -Viewer: keggview.native, keggview.graph, node.color, 
    	     col.key, wordwrap, strfit
