Browse code

v2.5.1

Guangchuang Yu authored on 08/01/2021 07:39:52
Showing4 changed files

... ...
@@ -1,7 +1,7 @@
1 1
 Package: ggtree
2 2
 Type: Package
3 3
 Title: an R package for visualization of tree and annotation data
4
-Version: 2.5.0.993
4
+Version: 2.5.1
5 5
 Authors@R: c(
6 6
        person("Guangchuang", "Yu",     email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0002-6485-8781")),
7 7
        person("Tommy Tsan-Yuk", "Lam", email = "tylam.tommy@gmail.com",   role = c("aut", "ths")),
... ...
@@ -4,6 +4,8 @@ PKGSRC  := $(shell basename `pwd`)
4 4
 
5 5
 all: rd check clean
6 6
 
7
+for-release: rd check-dontrun clean readme
8
+
7 9
 alldocs: rd readme
8 10
 
9 11
 rd:
... ...
@@ -33,6 +35,10 @@ check: rd build
33 35
 	cd ..;\
34 36
 	Rscript -e "rcmdcheck::rcmdcheck('$(PKGNAME)_$(PKGVERS).tar.gz')"
35 37
 
38
+check-dontrun: build
39
+	cd ..;\
40
+	Rscript -e 'rcmdcheck::rcmdcheck("$(PKGNAME)_$(PKGVERS).tar.gz", args=c("--run-dontrun"))'
41
+
36 42
 check2: rd build
37 43
 	cd ..;\
38 44
 	R CMD check $(PKGNAME)_$(PKGVERS).tar.gz
... ...
@@ -1,4 +1,4 @@
1
-# ggtree 2.5.0.993
1
+# ggtree 2.5.1
2 2
 
3 3
 + update man file of `geom_rootpoint` (2021-01-08, Fri)
4 4
 + `label` and `offset.label` introduced in `geom_treescale` layer (2020-12-23, Wed)
... ...
@@ -1,18 +1,19 @@
1 1
 <!-- README.md is generated from README.Rmd. Please edit that file -->
2 2
 
3
-# ggtree: an R package for visualization of phylogenetic trees with their annotation data
3
+ggtree: an R package for visualization of phylogenetic trees with their annotation data
4
+=======================================================================================
4 5
 
5 6
 <a href="https://yulab-smu.github.io/treedata-book/"><img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /></a>
6 7
 
7 8
 [![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives)
8
-[![](https://img.shields.io/badge/release%20version-2.2.4-green.svg)](https://www.bioconductor.org/packages/ggtree)
9
+[![](https://img.shields.io/badge/release%20version-2.4.1-green.svg)](https://www.bioconductor.org/packages/ggtree)
9 10
 [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree)
10 11
 [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
11 12
 
12 13
 <!--
13 14
 [![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)
14 15
 [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)
15
-[![Last-changedate](https://img.shields.io/badge/last%20change-2020--08--27-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
16
+[![Last-changedate](https://img.shields.io/badge/last%20change-2021--01--08-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
16 17
 
17 18
 ` r badge_devel("guangchuangyu/ggtree", "green")`
18 19
 ` r badge_bioc_download("ggtree", "total", "blue")`
... ...
@@ -25,15 +26,17 @@ grammar of graphics. ‘ggtree’ is designed for visualization and
25 26
 annotation of phylogenetic trees and other tree-like structures with
26 27
 their annotation data.
27 28
 
28
-For details, please visit <https://yulab-smu.top/treedata-book/>.
29
+For details, please visit
30
+<a href="https://yulab-smu.top/treedata-book/" class="uri">https://yulab-smu.top/treedata-book/</a>.
29 31
 
30
-## :writing\_hand: Authors
32
+:writing\_hand: Authors
33
+-----------------------
31 34
 
32 35
 Guangchuang YU
33 36
 
34 37
 School of Basic Medical Sciences, Southern Medical University
35 38
 
36
-<https://guangchuangyu.github.io>
39
+<a href="https://guangchuangyu.github.io" class="uri">https://guangchuangyu.github.io</a>
37 40
 
38 41
 [![Twitter](https://img.shields.io/twitter/url/http/shields.io.svg?style=social&logo=twitter)](https://twitter.com/intent/tweet?hashtags=ggtree&url=http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract&screen_name=guangchuangyu)
39 42
 [![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://saythanks.io/to/GuangchuangYu)
... ...
@@ -46,14 +49,14 @@ list:
46 49
 1.  **G Yu**. Using ggtree to visualize data on tree-like structures.
47 50
     ***Current Protocols in Bioinformatics***, 2020, 69:e96. doi:
48 51
     [10.1002/cpbi.96](https://doi.org/10.1002/cpbi.96).
49
-      - [Source code and data to reproduce figures in the
52
+    -   [Source code and data to reproduce figures in the
50 53
         article](https://github.com/GuangchuangYu/ggtree-current-protocols)
51 54
 2.  **G Yu**<sup>\*</sup>, TTY Lam, H Zhu, Y Guan<sup>\*</sup>. Two
52 55
     methods for mapping and visualizing associated data on phylogeny
53 56
     using ggtree. ***Molecular Biology and Evolution***, 2018,
54 57
     35(2):3041-3043. doi:
55 58
     [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).
56
-      - [Source code to produce Supplementary
59
+    -   [Source code to produce Supplementary
57 60
         Material](https://github.com/GuangchuangYu/plotting_tree_with_data)
58 61
 3.  **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an
59 62
     R package for visualization and annotation of phylogenetic trees
... ...
@@ -61,8 +64,9 @@ list:
61 64
     Ecology and Evolution***. 2017, 8(1):28-36. doi:
62 65
     [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).
63 66
 
64
-## :sparkling\_heart: Contributing
67
+:sparkling\_heart: Contributing
68
+-------------------------------
65 69
 
66
-We welcome any contributions\! By participating in this project you
67
-agree to abide by the terms outlined in the [Contributor Code of
70
+We welcome any contributions! By participating in this project you agree
71
+to abide by the terms outlined in the [Contributor Code of
68 72
 Conduct](CONDUCT.md).