@@ -4,3 +4,5 @@ appveyor.yml

 .gitignore

 .svnignore

 Makefile

+^appveyor\.yml$

+README.Rmd

@@ -5,3 +5,5 @@ Makefile

 TODO.md

 README.md

 appveyor.yml

+.travis.yml

+README.Rmd

@@ -1,34 +1,38 @@

 ## reference: http://docs.travis-ci.com/user/languages/r/

 language: r

+r:

+  - devel

+  - bioc-devel

+  

+cache: packages

 bioc_required: true

+os:

+  - linux

+  - osx

+

+

 apt_packages:

   - libfftw3-dev

-r_packages:

-  - ape

-  - phylobase

-  - colorspace

-  - grid

-  - ggplot2

-  - gridExtra

-  - jsonlite

-  - magrittr

-  - reshape2

-  - rmarkdown

-  - testthat

-  - knitr

-bioc_packages:

-  - Biostrings

-  - EBImage

-  - BiocStyle

+env:

+  global:

+    - _R_CHECK_FORCE_SUGGESTS_=False

+    - R_LIBS="http://cran.rstudio.com"

+

 after_failure:

   - ./travis-tool.sh dump_logs

-notifications:

-  email:

-    on_success: change

-    on_failure: change

+r_github_packages:

+  - jimhester/covr

+

+after_success:

+- Rscript -e 'library(covr); codecov()'

+

+## notifications:

+##   email:

+##     on_success: change

+##     on_failure: change

@@ -1,18 +1,27 @@

-#  ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data

+ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data

+===========================================================================================================================

-<!--[![Build Status](https://travis-ci.org/GuangchuangYu/ggtree.svg?branch=master)](https://travis-ci.org/GuangchuangYu/ggtree)

-[![Build Status](https://ci.appveyor.com/api/projects/status/github/GuangchuangYu/ggtree?svg=true)](https://ci.appveyor.com/project/GuangchuangYu/ggtree/branch/master)-->

-[![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives)

-[![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/)

-[![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)

-[![post](http://www.bioconductor.org/shields/posts/ggtree.svg)](https://support.bioconductor.org/t/ggtree/)

-[![commit](http://www.bioconductor.org/shields/commits/bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#svn_source)

-[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree/)

+[![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/) [![Linux/Mac Travis Build Status](https://img.shields.io/travis/GuangchuangYu/ggtree/master.svg?label=Mac%20OSX%20%26%20Linux)](https://travis-ci.org/GuangchuangYu/ggtree) [![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/ggtree/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/ggtree)

+[![packageversion](https://img.shields.io/badge/Package%20version-1.5.7-green.svg?style=flat)](https://github.com/GuangchuangYu/ggtree/blob/master/DESCRIPTION) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![post](http://www.bioconductor.org/shields/posts/ggtree.svg)](https://support.bioconductor.org/t/ggtree/) [![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree/) [![Twitter](https://img.shields.io/twitter/url/https/github.com/GuangchuangYu/ggtree.svg?style=social)](https://twitter.com/intent/tweet?hashtags=ggtree&url=https://guangchuangyu.github.io/ggtree)

-The `ggtree` package extending the `ggplot2` package. It based on grammar of graphics and takes all the good parts of `ggplot2`. 

+[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg) [![Last-changedate](https://img.shields.io/badge/last%20change-2016--08--09-yellowgreen.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![commit](http://www.bioconductor.org/shields/commits/bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#svn_source) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers)

-`ggtree` is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree. 

+The `ggtree` package extending the `ggplot2` package. It based on grammar of graphics and takes all the good parts of `ggplot2`.

+`ggtree` is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree.

+

+Please cite the following article when using `ggtree`:

+

+**G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ***Methods in Ecology and Evolution***. *accepted*

+

+------------------------------------------------------------------------

 For details, please visit our project website, <https://guangchuangyu.github.io/ggtree>.

+

+-   [Documentation](https://guangchuangyu.github.io/ggtree/documentation/)

+-   [FAQ](https://guangchuangyu.github.io/ggtree/faq/)

+-   [Feedback](https://guangchuangyu.github.io/ggtree/#feedback)

+-   [Example](https://guangchuangyu.github.io/ggtree/featuredArticles/)

+

+[![](https://guangchuangyu.github.io/ggtree/featured_img/2015_peiyu_1-s2.0-S1567134815300721-gr1.jpg)](https://guangchuangyu.github.io/ggtree/featuredArticles/)

@@ -1,29 +1,43 @@

-environment:

-  R_CHECK_ARGS: --no-manual

+# DO NOT CHANGE the "init" and "install" sections below

+# Download script file from GitHub

 init:

   ps: |

         $ErrorActionPreference = "Stop"

         Invoke-WebRequest http://raw.github.com/krlmlr/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1"

         Import-Module '..\appveyor-tool.ps1'

-  

 install:

   ps: Bootstrap

+# Adapt as necessary starting from here

+

 build_script:

+  - travis-tool.sh install_bioc BiocStyle Biostrings  

   - travis-tool.sh install_deps

-  - travis-tool.sh install_bioc BiocStyle Biostrings EBImage

-##  - travis-tool.sh install_bioc_deps

-  

+

 test_script:

   - travis-tool.sh run_tests

 on_failure:

-  - travis-tool.sh dump_logs

+  - 7z a failure.zip *.Rcheck\*

+  - appveyor PushArtifact failure.zip

+

+artifacts:

+  - path: '*.Rcheck\**\*.log'

+    name: Logs

+

+  - path: '*.Rcheck\**\*.out'

+    name: Logs

+

+  - path: '*.Rcheck\**\*.fail'

+    name: Logs

+

+  - path: '*.Rcheck\**\*.Rout'

+    name: Logs

-notifications:

-  email:

-    on_success: change

-    on_failure: change

+  - path: '\*_*.tar.gz'

+    name: Linux Package

+  - path: '\*_*.zip'

+    name: Windows Package