git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@119974 bc3139a8-67e5-0310-9ffc-ced21a209358
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@@ -1,34 +1,38 @@ |
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## reference: http://docs.travis-ci.com/user/languages/r/ |
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language: r |
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+r: |
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+ - devel |
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+ - bioc-devel |
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+ |
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+cache: packages |
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bioc_required: true |
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+os: |
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+ - linux |
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+ - osx |
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+ |
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+ |
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apt_packages: |
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- libfftw3-dev |
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-r_packages: |
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- - ape |
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- - phylobase |
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- - colorspace |
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- - grid |
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- - ggplot2 |
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- - gridExtra |
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- - jsonlite |
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- - magrittr |
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- - reshape2 |
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- - rmarkdown |
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- - testthat |
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- - knitr |
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-bioc_packages: |
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- - Biostrings |
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- - EBImage |
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- - BiocStyle |
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+env: |
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+ global: |
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+ - _R_CHECK_FORCE_SUGGESTS_=False |
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+ - R_LIBS="http://cran.rstudio.com" |
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+ |
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after_failure: |
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- ./travis-tool.sh dump_logs |
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-notifications: |
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- email: |
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- on_success: change |
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- on_failure: change |
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+r_github_packages: |
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+ - jimhester/covr |
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+ |
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+after_success: |
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+- Rscript -e 'library(covr); codecov()' |
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+ |
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+## notifications: |
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+## email: |
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+## on_success: change |
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+## on_failure: change |
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|
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@@ -1,18 +1,27 @@ |
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-# ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data |
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+ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data |
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+=========================================================================================================================== |
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-<!--[](https://travis-ci.org/GuangchuangYu/ggtree) |
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-[](https://ci.appveyor.com/project/GuangchuangYu/ggtree/branch/master)--> |
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-[](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) |
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-[](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/) |
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-[](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) |
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-[](https://support.bioconductor.org/t/ggtree/) |
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-[](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#svn_source) |
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-[](https://bioconductor.org/packages/stats/bioc/ggtree/) |
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+[](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/) [](https://travis-ci.org/GuangchuangYu/ggtree) [](https://ci.appveyor.com/project/GuangchuangYu/ggtree) |
|
11 | 5 |
|
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+[](https://github.com/GuangchuangYu/ggtree/blob/master/DESCRIPTION) [](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [](https://support.bioconductor.org/t/ggtree/) [](https://bioconductor.org/packages/stats/bioc/ggtree/) [](https://twitter.com/intent/tweet?hashtags=ggtree&url=https://guangchuangyu.github.io/ggtree) |
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-The `ggtree` package extending the `ggplot2` package. It based on grammar of graphics and takes all the good parts of `ggplot2`. |
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+[](http://www.repostatus.org/#active) [](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg) [](https://github.com/GuangchuangYu/ggtree/commits/master) [](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#svn_source) [](https://github.com/GuangchuangYu/ggtree/network) [](https://github.com/GuangchuangYu/ggtree/stargazers) |
|
14 | 9 |
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-`ggtree` is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree. |
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+The `ggtree` package extending the `ggplot2` package. It based on grammar of graphics and takes all the good parts of `ggplot2`. |
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16 | 11 |
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+`ggtree` is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree. |
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+ |
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+Please cite the following article when using `ggtree`: |
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+ |
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+**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* |
|
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+ |
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+------------------------------------------------------------------------ |
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For details, please visit our project website, <https://guangchuangyu.github.io/ggtree>. |
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+ |
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+- [Documentation](https://guangchuangyu.github.io/ggtree/documentation/) |
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+- [FAQ](https://guangchuangyu.github.io/ggtree/faq/) |
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+- [Feedback](https://guangchuangyu.github.io/ggtree/#feedback) |
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+- [Example](https://guangchuangyu.github.io/ggtree/featuredArticles/) |
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+ |
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+[](https://guangchuangyu.github.io/ggtree/featuredArticles/) |
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@@ -1,29 +1,43 @@ |
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-environment: |
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- R_CHECK_ARGS: --no-manual |
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+# DO NOT CHANGE the "init" and "install" sections below |
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+# Download script file from GitHub |
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init: |
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ps: | |
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$ErrorActionPreference = "Stop" |
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Invoke-WebRequest http://raw.github.com/krlmlr/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1" |
8 | 8 |
Import-Module '..\appveyor-tool.ps1' |
9 | 9 |
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- |
|
11 | 10 |
install: |
12 | 11 |
ps: Bootstrap |
13 | 12 |
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+# Adapt as necessary starting from here |
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+ |
|
14 | 15 |
build_script: |
16 |
+ - travis-tool.sh install_bioc BiocStyle Biostrings |
|
15 | 17 |
- travis-tool.sh install_deps |
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- - travis-tool.sh install_bioc BiocStyle Biostrings EBImage |
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-## - travis-tool.sh install_bioc_deps |
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- |
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+ |
|
19 | 19 |
test_script: |
20 | 20 |
- travis-tool.sh run_tests |
21 | 21 |
|
22 | 22 |
on_failure: |
23 |
- - travis-tool.sh dump_logs |
|
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+ - 7z a failure.zip *.Rcheck\* |
|
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+ - appveyor PushArtifact failure.zip |
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+ |
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+artifacts: |
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+ - path: '*.Rcheck\**\*.log' |
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+ name: Logs |
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+ |
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+ - path: '*.Rcheck\**\*.out' |
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+ name: Logs |
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+ |
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+ - path: '*.Rcheck\**\*.fail' |
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+ name: Logs |
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+ |
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+ - path: '*.Rcheck\**\*.Rout' |
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+ name: Logs |
|
24 | 38 |
|
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-notifications: |
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- email: |
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- on_success: change |
|
28 |
- on_failure: change |
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+ - path: '\*_*.tar.gz' |
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+ name: Linux Package |
|
29 | 41 |
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+ - path: '\*_*.zip' |
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+ name: Windows Package |