CHANGES IN VERSION 1.16.02 (04 April 2019)
--------------------------------------------
+ update NEWS format

CHANGES IN VERSION 1.16.01 (01 March 2019)
--------------------------------------------
+ Change the address of cgdsr: http://www.cbioportal.org/ instead http://www.cbioportal.org/public-portal/

CHANGES IN VERSION 1.11.01 (16 October 2018)
--------------------------------------------
+ update NEWS format file

CHANGES IN VERSION 1.11.01 (15 April 2018)
--------------------------------------------
+ rm gamma = 1.5 argument for grDevices::rainbow function

CHANGES IN VERSION 1.7.04 (17 April 2017)
--------------------------------------------
+ get Manual from Bioconductor.org
+ browseURL('http://www.bioconductor.org/packages/3.4/bioc/vignettes/canceR/inst/doc/canceR.pdf')

CHANGES IN VERSION 1.7.3 (17 February 2017)
--------------------------------------------
+ dontrun examples

CHANGES IN VERSION 1.7.2 (17 January 2017)
--------------------------------------------
+ resolve issue when computing mutation frequency

CHANGES IN VERSION 1.5.2 (01 Septembre 2016)
--------------------------------------------
+ resolve issue 1 about "tl not found"
+ delete file R/getGeneticProfiles.R
+ resolve 'no visible binding for global variable'
+ add R/aaa.R

CHANGES IN VERSION 1.3.91 (01 May 2016)
---------------------------------------
+ rm canceR.pdf and lines from canceR.Rnw
+ %\VignetteEngine{R.rsp::tex}
+ %\VignetteKeyword{R}
+ %\VignetteKeyword{package}
+ %\VignetteKeyword{vignette}
+ %\VignetteKeyword{LaTeX}
+ %\VignetteAuthor{Karim Mezhoud}
+ %\VignetteDepends{}
+ %\VignetteKeywords{A Graphical User Interface for accessing and modeling the MSKCC Cancer Genomics +Data.}
+ %\VignettePackage{canceR}

CHANGES IN VERSION 1.3.7 (07 April 2016)
------------------------
+ add /extdata/canceR.pdf

CHANGES IN VERSION 1.3.6 (05 April 2016)
------------------------
+ fix paths in running examples

CHANGES IN VERSION 1.3.5 (04 April 2016)
------------------------
+ git reset --hard HEAD~
+ bash ../update_remotes.sh
+ add vignette/image, pump version, delete canceR.tex
+ git commit -m "fix vignette rm canceR.tex"
+ git svn rebase
+ git svn dcommit --add-author-from

CHANGES IN VERSION 1.3.2 (28 Mars 2016)
------------------------
+ Bioc devel canceR is not updated to version 1.3.1
+ Just add image in README

CHANGES IN VERSION 1.3.1 (24 Mars 2016)
------------------------
rewrite documents using roxygen
rewrite test package
include .travis check system

CHANGES IN VERSION 1.1.2 (12 May 2015)
------------------------
+ add Circos function to plot Menu
+ Function 1:    getGeneListmSigDB(): get Gene list and their gene Sets from MSigDB
+ Function 1.1: dialoggetGeneListMSigDB(): Select Gene Sets from list and extract hem genes

+ Function 2: getListProfData(): This function save Profiles Data of cancer in lists;
            Outputs:myGlobalEnv$ListProfData$Expression 
                    myGlobalEnv$ListProfData$CNA    
                    myGlobalEnv$ListMetData$HM450$StudiesRef
                    myGlobalEnv$ListMetData$HM27$StudiesRef
                    myGlobalEnv$ListProfData$RPPA$StudiesRef
                    myGlobalEnv$ListProfData$miRNA$StudiesRef
                    myGlobalEnv$ListMutData$StudiesRef
                    myGlobalEnv$Freq_DfMutData

+ Function 3 : getCircos(dimension="All"): Main fucntion of Circos plot: plot Tracks        
            (dimensions) and Sectors (diseases)
+ Function 3.1: getCor_ExpCNAMet(ListMatrix, dimension)
+ Function 3.2: dialogOptionCircos(): specifing which dimension and Threshold gene 
                dimensions levels will be plot.

+  dialogMetOption(): add "Circos" argument to make the difference between getMetDataMultipleGene() and getListMetData()
+  getGeneList(): add rm("GeneListMSigDB"", envir="myGlobalEnv")

CHANGES IN VERSION 1.1.1 (27 April 2015)
------------------------
+  Survival plot
+ add getSurvival(Coxph) and getSurvival.Rd file
+ getOptionGSEAlm(s, ClinicalData): add line 105
    ### only for Survival plot
    myGlobalEnv$variable <- as.formula(sprintf("Surv(OS_MONTHS,OS_STATUS)~%s", coVariables))
+ cancer.latex file: add Survival plot paragraph
+ add image in /image folder: KM.png, Coxph.png
+ getCasesGenProfs(): add getSurvival in Plot menu


RELEASE 1.0.0 (17 April 2015)
-------------------------

CHANGES IN VERSION 0.99.3
-------------------------

    + getProfilesDataMultipleGenes: line 78: Test only Genetic Profiles having mRNA expression to get Profile Data.
    +  getMutData(): line 96  change .GlobalEnv to myGlobalEnv)
    +  getProfDataMultipleGenes(): line 7 add testCheckedCaseGenProf()

CHANGES IN VERSION 0.99.2
-------------------------

    + Add documentation for RUN.GSEA() function
    + Remove dependency of RSvgDevice. This package is not available for Windows OS.

CHANGES IN VERSION 0.99.1
-------------------------

    + Add examples in documents

    + Add documentation for RUN.GSEA() function

    + Remove dependency of RSvgDevice. This package is not available for Windows OS.

CHANGES IN VERSION 0.99.1
--------------------------

+ SIGNIFICANT USER-VISIBLE CHANGES

    - Add examples in documents

+ NEW FEATURES

    - Package released