1. ggtree
  2. Makefile
Browse code

update

Guangchuang Yu authored on 19/07/2023 07:16:02
Showing 1 changed files
Makefile
History View file @ 3c7c879
... ... 
@@ -81,6 +81,9 @@ release:
81 81 
 	git fetch --all
82 82
83 83
84 
+yulab:
85 
+	git push yulab devel
86 
+
84 87 
 update:
85 88 
 	git fetch --all;\
86 89 
 	git checkout devel;\
Browse code

yulab branch

Guangchuang Yu authored on 19/07/2023 07:09:06
Showing 1 changed files
Makefile
History View file @ 0b151d0
... ... 
@@ -80,19 +80,21 @@ release:
80 80 
 	git checkout $(BIOCVER);\
81 81 
 	git fetch --all
82 82
83 
+
83 84 
 update:
84 85 
 	git fetch --all;\
85 86 
 	git checkout devel;\
86 87 
 	git merge upstream/devel;\
87 
-	#git merge gitee/devel;\
88 
-	git merge origin/devel
88 
+	git merge origin/devel;\
89 
+	git merge yulab/devel
89 90
90 91 
 push:
91 92 
 	git push upstream devel;\
92 
-	#git push gitee devel;\
93 
+	git push yulab devel;\
93 94 
 	git push origin devel
94 95
95 96
97 
+
96 98 
 # svnignore:
97 99 
 # 	svn propset svn:ignore -F .svnignore .
98 100
Browse code

rm gitee

Guangchuang Yu authored on 01/07/2023 16:11:13
Showing 1 changed files
Makefile
History View file @ e9a7424
... ... 
@@ -84,7 +84,7 @@ update:
84 84 
 	git fetch --all;\
85 85 
 	git checkout devel;\
86 86 
 	git merge upstream/devel;\
87 
-	git merge gitee/devel;\
87 
+	#git merge gitee/devel;\
88 88 
 	git merge origin/devel
89 89
90 90 
 push:
Browse code

change to devel branch

Guangchuang Yu authored on 01/07/2023 16:09:50
Showing 1 changed files
Makefile
History View file @ 049d6bb
... ... 
@@ -82,15 +82,15 @@ release:
82 82
83 83 
 update:
84 84 
 	git fetch --all;\
85 
-	git checkout master;\
86 
-	git merge upstream/master;\
87 
-	git merge gitee/master;\
88 
-	git merge origin/master
85 
+	git checkout devel;\
86 
+	git merge upstream/devel;\
87 
+	git merge gitee/devel;\
88 
+	git merge origin/devel
89 89
90 90 
 push:
91 
-	git push upstream master;\
92 
-	#git push gitee master;\
93 
-	git push origin master
91 
+	git push upstream devel;\
92 
+	#git push gitee devel;\
93 
+	git push origin devel
94 94
95 95
96 96 
 # svnignore:
... ... 
@@ -99,8 +99,8 @@ push:
99 99 
 # svncommit:
100 100 
 # 	git checkout devel;\
101 101 
 # 	git svn rebase;\
102 
-# 	git merge master --log;\
102 
+# 	git merge devel --log;\
103 103 
 # 	git svn dcommit;\
104 104 
 # 	git push -u origin devel;\
105 
-# 	git checkout master;\
105 
+# 	git checkout devel;\
106 106 
 # 	git merge devel
Browse code

update bioc version

Guangchuang Yu authored on 03/05/2023 07:11:53
Showing 1 changed files
Makefile
History View file @ 9615606
... ... 
@@ -1,7 +1,7 @@
1 1 
 PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION)
2 2 
 PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION)
3 3 
 PKGSRC  := $(shell basename `pwd`)
4 
-BIOCVER := RELEASE_3_16
4 
+BIOCVER := RELEASE_3_17
5 5
6 6
7 7 
 all: rd check clean
Browse code

clean up code to remove R check notes

Guangchuang Yu authored on 04/04/2023 07:17:46
Showing 1 changed files
Makefile
History View file @ d1627ba
... ... 
@@ -22,8 +22,9 @@ sticker:
22 22 
 	rm Rplots.pdf
23 23
24 24 
 build:
25 
-	cd ..;\
26 
-	R CMD build $(PKGSRC)
25 
+	# cd ..;\
26 
+	# R CMD build $(PKGSRC)
27 
+	Rscript -e 'devtools::build()'
27 28
28 29 
 build2:
29 30 
 	cd ..;\
... ... 
@@ -33,10 +34,11 @@ install:
33 34 
 	cd ..;\
34 35 
 	R CMD INSTALL $(PKGNAME)_$(PKGVERS).tar.gz
35 36
36 
-check: rd build
37 
-	cd ..;\
38 
-	Rscript -e "rcmdcheck::rcmdcheck('$(PKGNAME)_$(PKGVERS).tar.gz')"
39 
-
37 
+check: rd
38 
+	#cd ..;\
39 
+	#Rscript -e "rcmdcheck::rcmdcheck('$(PKGNAME)_$(PKGVERS).tar.gz')"
40 
+	Rscript -e 'devtools::check()'
41 
+
40 42 
 check-dontrun: build
41 43 
 	cd ..;\
42 44 
 	Rscript -e 'rcmdcheck::rcmdcheck("$(PKGNAME)_$(PKGVERS).tar.gz", args=c("--run-dontrun"))'
Browse code

rm gitee

Guangchuang Yu authored on 04/04/2023 03:16:37
Showing 1 changed files
Makefile
History View file @ bf926cd
... ... 
@@ -87,7 +87,7 @@ update:
87 87
88 88 
 push:
89 89 
 	git push upstream master;\
90 
-	git push gitee master;\
90 
+	#git push gitee master;\
91 91 
 	git push origin master
92 92
93 93
Browse code

update bioc version

Guangchuang Yu authored on 01/11/2022 06:25:03
Showing 1 changed files
Makefile
History View file @ 10df052
... ... 
@@ -1,7 +1,7 @@
1 1 
 PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION)
2 2 
 PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION)
3 3 
 PKGSRC  := $(shell basename `pwd`)
4 
-BIOCVER := RELEASE_3_15
4 
+BIOCVER := RELEASE_3_16
5 5
6 6
7 7 
 all: rd check clean
Browse code

bioc3.15

Guangchuang Yu authored on 27/04/2022 06:54:55
Showing 1 changed files
Makefile
History View file @ 5734dc1
... ... 
@@ -1,7 +1,7 @@
1 1 
 PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION)
2 2 
 PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION)
3 3 
 PKGSRC  := $(shell basename `pwd`)
4 
-BIOCVER := release_3_15
4 
+BIOCVER := RELEASE_3_15
5 5
6 6
7 7 
 all: rd check clean
Browse code

bioc3.15

Guangchuang Yu authored on 27/04/2022 06:52:50
Showing 1 changed files
Makefile
History View file @ 2bcc3e3
... ... 
@@ -1,7 +1,7 @@
1 1 
 PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION)
2 2 
 PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION)
3 3 
 PKGSRC  := $(shell basename `pwd`)
4 
-BIOCVER := RELEASE_3_14
4 
+BIOCVER := release_3_15
5 5
6 6
7 7 
 all: rd check clean
Browse code

bioc version

Guangchuang Yu authored on 28/10/2021 05:05:36
Showing 1 changed files
Makefile
History View file @ 0eaef85
... ... 
@@ -1,8 +1,7 @@
1 1 
 PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION)
2 2 
 PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION)
3 3 
 PKGSRC  := $(shell basename `pwd`)
4 
-BIOCOLD := RELEASE_3_13
5 
-BIOCCUR := RELEASE_3_14
4 
+BIOCVER := RELEASE_3_14
6 5
7 6
8 7 
 all: rd check clean
... ... 
@@ -72,11 +71,11 @@ giteeinit:
72 71 
 	git remote add gitee git@gitee.com:GuangchuangYu/$(PKGNAME).git;\
73 72 
 	git fetch --all
74 73
75 
-rmoldrelease:
76 
-	git branch -D $(BIOCOLD)
74 
+rmrelease:
75 
+	git branch -D $(BIOCVER)
77 76
78 77 
 release:
79 
-	git checkout $(BIOCCUR);\
78 
+	git checkout $(BIOCVER);\
80 79 
 	git fetch --all
81 80
82 81 
 update:
Browse code

update

Guangchuang Yu authored on 28/10/2021 01:52:55
Showing 1 changed files
Makefile
History View file @ 83017e8
... ... 
@@ -1,6 +1,9 @@
1 1 
 PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION)
2 2 
 PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION)
3 3 
 PKGSRC  := $(shell basename `pwd`)
4 
+BIOCOLD := RELEASE_3_13
5 
+BIOCCUR := RELEASE_3_14
6 
+
4 7
5 8 
 all: rd check clean
6 9
... ... 
@@ -70,10 +73,10 @@ giteeinit:
70 73 
 	git fetch --all
71 74
72 75 
 rmoldrelease:
73 
-	git branch -D RELEASE_3_13
76 
+	git branch -D $(BIOCOLD)
74 77
75 78 
 release:
76 
-	git checkout RELEASE_3_14;\
79 
+	git checkout $(BIOCCUR);\
77 80 
 	git fetch --all
78 81
79 82 
 update:
Browse code

update bioc version

Guangchuang Yu authored on 28/10/2021 01:45:37
Showing 1 changed files
Makefile
History View file @ 1523340
... ... 
@@ -70,10 +70,10 @@ giteeinit:
70 70 
 	git fetch --all
71 71
72 72 
 rmoldrelease:
73 
-	git branch -D RELEASE_3_12
73 
+	git branch -D RELEASE_3_13
74 74
75 75 
 release:
76 
-	git checkout RELEASE_3_13;\
76 
+	git checkout RELEASE_3_14;\
77 77 
 	git fetch --all
78 78
79 79 
 update:
Browse code

new release

Guangchuang Yu authored on 20/05/2021 05:55:18
Showing 1 changed files
Makefile
History View file @ 2e42b85
... ... 
@@ -70,10 +70,10 @@ giteeinit:
70 70 
 	git fetch --all
71 71
72 72 
 rmoldrelease:
73 
-	git branch -D RELEASE_3_11
73 
+	git branch -D RELEASE_3_12
74 74
75 75 
 release:
76 
-	git checkout RELEASE_3_12;\
76 
+	git checkout RELEASE_3_13;\
77 77 
 	git fetch --all
78 78
79 79 
 update:
Browse code

v2.5.1

Guangchuang Yu authored on 08/01/2021 07:39:52
Showing 1 changed files
Makefile
History View file @ 0acf2bd
... ... 
@@ -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
Browse code

new release

Guangchuang Yu authored on 28/10/2020 00:32:17
Showing 1 changed files
Makefile
History View file @ 4e15ce1
... ... 
@@ -64,10 +64,10 @@ giteeinit:
64 64 
 	git fetch --all
65 65
66 66 
 rmoldrelease:
67 
-	git branch -D RELEASE_3_10
67 
+	git branch -D RELEASE_3_11
68 68
69 69 
 release:
70 
-	git checkout RELEASE_3_11;\
70 
+	git checkout RELEASE_3_12;\
71 71 
 	git fetch --all
72 72
73 73 
 update:
Browse code

new release 3.11

Guangchuang Yu authored on 13/05/2020 10:21:06
Showing 1 changed files
Makefile
History View file @ 207991e
... ... 
@@ -64,10 +64,10 @@ giteeinit:
64 64 
 	git fetch --all
65 65
66 66 
 rmoldrelease:
67 
-	git branch -D RELEASE_3_9
67 
+	git branch -D RELEASE_3_10
68 68
69 69 
 release:
70 
-	git checkout RELEASE_3_10;\
70 
+	git checkout RELEASE_3_11;\
71 71 
 	git fetch --all
72 72
73 73 
 update:
Browse code

update makefile

Guangchuang Yu authored on 19/02/2020 08:27:25
Showing 1 changed files
Makefile
History View file @ c9910e6
... ... 
@@ -60,7 +60,7 @@ biocinit:
60 60 
 	git fetch --all
61 61
62 62 
 giteeinit:
63 
-	git remote add gitee git@gitee.com:GuangchuangYu/ggtree.git;\
63 
+	git remote add gitee git@gitee.com:GuangchuangYu/$(PKGNAME).git;\
64 64 
 	git fetch --all
65 65
66 66 
 rmoldrelease:
Browse code

gitee backup

Guangchuang Yu authored on 30/10/2019 07:41:23
Showing 1 changed files
Makefile
History View file @ b57ec7d
... ... 
@@ -59,6 +59,10 @@ biocinit:
59 59 
 	git remote add upstream git@git.bioconductor.org:packages/$(PKGNAME).git;\
60 60 
 	git fetch --all
61 61
62 
+giteeinit:
63 
+	git remote add gitee git@gitee.com:GuangchuangYu/ggtree.git;\
64 
+	git fetch --all
65 
+
62 66 
 rmoldrelease:
63 67 
 	git branch -D RELEASE_3_9
64 68
... ... 
@@ -70,10 +74,12 @@ update:
70 74 
 	git fetch --all;\
71 75 
 	git checkout master;\
72 76 
 	git merge upstream/master;\
77 
+	git merge gitee/master;\
73 78 
 	git merge origin/master
74 79
75 80 
 push:
76 81 
 	git push upstream master;\
82 
+	git push gitee master;\
77 83 
 	git push origin master
78 84
79 85
Browse code

update makefile

Guangchuang Yu authored on 30/10/2019 02:08:50
Showing 1 changed files
Makefile
History View file @ c2cfbee
... ... 
@@ -59,6 +59,9 @@ biocinit:
59 59 
 	git remote add upstream git@git.bioconductor.org:packages/$(PKGNAME).git;\
60 60 
 	git fetch --all
61 61
62 
+rmoldrelease:
63 
+	git branch -D RELEASE_3_9
64 
+
62 65 
 release:
63 66 
 	git checkout RELEASE_3_10;\
64 67 
 	git fetch --all
Browse code

fixed warning

Guangchuang Yu authored on 30/10/2019 02:03:01
Showing 1 changed files
Makefile
History View file @ db6d5e2
... ... 
@@ -60,7 +60,7 @@ biocinit:
60 60 
 	git fetch --all
61 61
62 62 
 release:
63 
-	git checkout RELEASE_3_9;\
63 
+	git checkout RELEASE_3_10;\
64 64 
 	git fetch --all
65 65
66 66 
 update:
Browse code

bioc 3.9

Guangchuang Yu authored on 29/05/2019 05:52:01
Showing 1 changed files
Makefile
History View file @ 6f1a9cf
... ... 
@@ -60,7 +60,7 @@ biocinit:
60 60 
 	git fetch --all
61 61
62 62 
 release:
63 
-	git checkout RELEASE_3_8;\
63 
+	git checkout RELEASE_3_9;\
64 64 
 	git fetch --all
65 65
66 66 
 update:
Browse code

update readme

Guangchuang Yu authored on 13/12/2018 05:40:30
Showing 1 changed files
Makefile
History View file @ 18618ec
... ... 
@@ -11,7 +11,7 @@ rd:
11 11 
 # Rscript -e 'roxygen2::roxygenise(".")'
12 12
13 13 
 readme:
14 
-	Rscript -e 'rmarkdown::render("README.Rmd")'
14 
+	Rscript -e 'rmarkdown::render("README.Rmd", encoding="UTF-8")'
15 15
16 16 
 sticker:
17 17 
 	Rscript -e 'source("ggtree_sticker.R")';
Browse code

update docs

Guangchuang Yu authored on 19/11/2018 08:17:45
Showing 1 changed files
Makefile
History View file @ e97f14c
... ... 
@@ -31,7 +31,7 @@ install:
31 31
32 32 
 check: rd build
33 33 
 	cd ..;\
34 
-	Rscript -e 'rcmdcheck::rcmdcheck("$(PKGNAME)_$(PKGVERS).tar.gz")'
34 
+	Rscript -e "rcmdcheck::rcmdcheck('$(PKGNAME)_$(PKGVERS).tar.gz')"
35 35
36 36 
 check2: rd build
37 37 
 	cd ..;\
... ... 
@@ -43,7 +43,7 @@ check3: rd build2
43 43
44 44 
 bioccheck:
45 45 
 	cd ..;\
46 
-	Rscript -e 'BiocCheck::BiocCheck("$(PKGNAME)_$(PKGVERS).tar.gz")'
46 
+	Rscript -e "BiocCheck::BiocCheck('$(PKGNAME)_$(PKGVERS).tar.gz')"
47 47
48 48 
 clean:
49 49 
 	cd ..;\
Browse code

update make file

Guangchuang Yu authored on 07/11/2018 08:01:36
Showing 1 changed files
Makefile
History View file @ 68b2591
... ... 
@@ -60,7 +60,7 @@ biocinit:
60 60 
 	git fetch --all
61 61
62 62 
 release:
63 
-	git checkout RELEASE_3_7;\
63 
+	git checkout RELEASE_3_8;\
64 64 
 	git fetch --all
65 65
66 66 
 update:
Browse code

update makefile

Guangchuang Yu authored on 21/07/2018 13:45:28
Showing 1 changed files
Makefile
History View file @ e0740bd
... ... 
@@ -55,6 +55,10 @@ gitmaintain:
55 55 
 	git prune -v;\
56 56 
 	git fsck --full
57 57
58 
+biocinit:
59 
+	git remote add upstream git@git.bioconductor.org:packages/$(PKGNAME).git;\
60 
+	git fetch --all
61 
+
58 62 
 release:
59 63 
 	git checkout RELEASE_3_7;\
60 64 
 	git fetch --all
Browse code

geom_tiplab(parse="emoji") compatible with upcoming ggplot2 v=2.3.0

guangchuang yu authored on 23/05/2018 03:06:13
Showing 1 changed files
Makefile
History View file @ 8dab519
... ... 
@@ -56,7 +56,7 @@ gitmaintain:
56 56 
 	git fsck --full
57 57
58 58 
 release:
59 
-	git checkout RELEASE_3_6;\
59 
+	git checkout RELEASE_3_7;\
60 60 
 	git fetch --all
61 61
62 62 
 update:
Browse code

remove website

guangchuang yu authored on 05/03/2018 04:17:02
Showing 1 changed files
Makefile
History View file @ deb8e67
... ... 
@@ -4,7 +4,7 @@ PKGSRC  := $(shell basename `pwd`)
4 4
5 5 
 all: rd check clean
6 6
7 
-alldocs: site rd readme
7 
+alldocs: rd readme
8 8
9 9 
 rd:
10 10 
 	Rscript -e 'library(methods); devtools::document()'
... ... 
@@ -49,25 +49,6 @@ clean:
49 49 
 	cd ..;\
50 50 
 	$(RM) -r $(PKGNAME).Rcheck/
51 51
52 
-site:
53 
-	cd site_src;\
54 
-	ln -s ../../software/themes themes;\
55 
-	Rscript -e 'blogdown::build_site()';\
56 
-	rm themes;\
57 
-	cd ..
58 
-
59 
-vignette:
60 
-	cd site_src/vignettes;\
61 
-	Rscript -e 'ff = list.files(pattern=".R|rmd"); sapply(ff, function(f) rmarkdown::render(f))';\
62 
-	mv *html ../../docs/vignettes/
63 
-
64 
-preview:
65 
-	cd site_src;\
66 
-	ln -s ../../software/themes themes;\
67 
-	Rscript -e 'blogdown::serve_site()';\
68 
-	rm themes;\
69 
-	cd ..
70 
-
71 52
72 53 
 gitmaintain:
73 54 
 	git gc --auto;\
... ... 
@@ -89,19 +70,6 @@ push:
89 70 
 	git push origin master
90 71
91 72
92 
-# mkdocs: mdfiles
93 
-# 	cd mkdocs;\
94 
-# 	mkdocs build;\
95 
-# 	cd ../docs;\
96 
-# 	rm -rf fonts;\
97 
-# 	rm -rf css/font-awesome*
98 
-
99 
-# mdfiles:
100 
-# 	cd mkdocs;\
101 
-# 	Rscript -e 'source("render.R")';\
102 
-# 	cd docs;\
103 
-# 	ln -f -s ../mysoftware/* ./
104 
-
105 73 
 # svnignore:
106 74 
 # 	svn propset svn:ignore -F .svnignore .
107 75
Browse code

update geom_tippoint

guangchuang yu authored on 02/02/2018 07:58:26
Showing 1 changed files
Makefile
History View file @ a67ffa2
... ... 
@@ -86,7 +86,6 @@ update:
86 86
87 87 
 push:
88 88 
 	git push upstream master;\
89 
-	git push;\
90 89 
 	git push origin master
91 90
92 91
Browse code

update makefile

guangchuang yu authored on 26/01/2018 05:07:17
Showing 1 changed files
Makefile
History View file @ d64c3b9
... ... 
@@ -86,6 +86,7 @@ update:
86 86
87 87 
 push:
88 88 
 	git push upstream master;\
89 
+	git push;\
89 90 
 	git push origin master
90 91
91 92
Browse code

update vignettes

guangchuang yu authored on 03/01/2018 09:55:53
Showing 1 changed files
Makefile
History View file @ 0266c28
... ... 
@@ -2,7 +2,7 @@ PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION)
2 2 
 PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION)
3 3 
 PKGSRC  := $(shell basename `pwd`)
4 4
5 
-all: rd readme check clean
5 
+all: rd check clean
6 6
7 7 
 alldocs: site rd readme
8 8
Browse code

update makefile

guangchuang yu authored on 02/01/2018 08:09:19
Showing 1 changed files
Makefile
History View file @ 38cc474
... ... 
@@ -76,8 +76,7 @@ gitmaintain:
76 76
77 77 
 release:
78 78 
 	git checkout RELEASE_3_6;\
79 
-	make update
80 
-
79 
+	git fetch --all
81 80
82 81 
 update:
83 82 
 	git fetch --all;\
Browse code

update makefile

guangchuang yu authored on 28/12/2017 08:29:53
Showing 1 changed files
Makefile
History View file @ ead856b
... ... 
@@ -74,13 +74,18 @@ gitmaintain:
74 74 
 	git prune -v;\
75 75 
 	git fsck --full
76 76
77 
+release:
78 
+	git checkout RELEASE_3_6;\
79 
+	make update
80 
+
81 
+
77 82 
 update:
78 83 
 	git fetch --all;\
79 84 
 	git checkout master;\
80 85 
 	git merge upstream/master;\
81 86 
 	git merge origin/master
82 87
83 
-push: update
88 
+push:
84 89 
 	git push upstream master;\
85 90 
 	git push origin master
86 91
Browse code

extra vignette in homepage

guangchuang yu authored on 27/12/2017 06:01:35
Showing 1 changed files
Makefile
History View file @ 6cda60e
... ... 
@@ -56,6 +56,11 @@ site:
56 56 
 	rm themes;\
57 57 
 	cd ..
58 58
59 
+vignette:
60 
+	cd site_src/vignettes;\
61 
+	Rscript -e 'ff = list.files(pattern=".R|rmd"); sapply(ff, function(f) rmarkdown::render(f))';\
62 
+	mv *html ../../docs/vignettes/
63 
+
59 64 
 preview:
60 65 
 	cd site_src;\
61 66 
 	ln -s ../../software/themes themes;\
Browse code

tidytree

guangchuang yu authored on 07/12/2017 11:44:15
Showing 1 changed files
Makefile
History View file @ 9904896
... ... 
@@ -7,7 +7,8 @@ all: rd readme check clean
7 7 
 alldocs: site rd readme
8 8
9 9 
 rd:
10 
-	Rscript -e 'roxygen2::roxygenise(".")'
10 
+	Rscript -e 'library(methods); devtools::document()'
11 
+# Rscript -e 'roxygen2::roxygenise(".")'
11 12
12 13 
 readme:
13 14 
 	Rscript -e 'rmarkdown::render("README.Rmd")'
... ... 
@@ -28,11 +29,11 @@ install:
28 29 
 	cd ..;\
29 30 
 	R CMD INSTALL $(PKGNAME)_$(PKGVERS).tar.gz
30 31
31 
-check: build
32 
+check: rd build
32 33 
 	cd ..;\
33 34 
 	Rscript -e 'rcmdcheck::rcmdcheck("$(PKGNAME)_$(PKGVERS).tar.gz")'
34 35
35 
-check2: build
36 
+check2: rd build
36 37 
 	cd ..;\
37 38 
 	R CMD check $(PKGNAME)_$(PKGVERS).tar.gz
38 39
Browse code

remove paml_rst, codeml_mlc, codeml and jplace fortify methods according to the change of treeio (v = 1.3.3)

guangchuang yu authored on 07/12/2017 07:21:58
Showing 1 changed files
Makefile
History View file @ 6be958c
... ... 
@@ -36,6 +36,10 @@ check2: build
36 36 
 	cd ..;\
37 37 
 	R CMD check $(PKGNAME)_$(PKGVERS).tar.gz
38 38
39 
+check3: rd build2
40 
+	cd ..;\
41 
+	R CMD check --ignore-vignettes $(PKGNAME)_$(PKGVERS).tar.gz
42 
+
39 43 
 bioccheck:
40 44 
 	cd ..;\
41 45 
 	Rscript -e 'BiocCheck::BiocCheck("$(PKGNAME)_$(PKGVERS).tar.gz")'
Browse code

update docs

guangchuang yu authored on 01/10/2017 03:28:40
Showing 1 changed files
Makefile
History View file @ 0b103e3
... ... 
@@ -58,46 +58,12 @@ preview:
58 58 
 	rm themes;\
59 59 
 	cd ..
60 60
61 
-mkdocs: mdfiles
62 
-	cd mkdocs;\
63 
-	mkdocs build;\
64 
-	cd ../docs;\
65 
-	rm -rf fonts;\
66 
-	rm -rf css/font-awesome*
67 
-
68 
-mdfiles:
69 
-	cd mkdocs;\
70 
-	Rscript -e 'source("render.R")';\
71 
-	cd docs;\
72 
-	ln -f -s ../mysoftware/* ./
73 
-
74 
-svnignore:
75 
-	svn propset svn:ignore -F .svnignore .
76 
-
77 
-svncommit:
78 
-	git checkout devel;\
79 
-	git svn rebase;\
80 
-	git merge master --log;\
81 
-	git svn dcommit;\
82 
-	git push -u origin devel;\
83 
-	git checkout master;\
84 
-	git merge devel
85 
-
86 61
87 62 
 gitmaintain:
88 63 
 	git gc --auto;\
89 64 
 	git prune -v;\
90 65 
 	git fsck --full
91 66
92 
-
93 
-pushX:
94 
-	git push -u origin master;\
95 
-	git checkout bioc;\
96 
-	git pull;\
97 
-	git merge master;\
98 
-	git push upstream master;\
99 
-	git checkout master
100 
-
101 67 
 update:
102 68 
 	git fetch --all;\
103 69 
 	git checkout master;\
... ... 
@@ -107,3 +73,29 @@ update:
107 73 
 push: update
108 74 
 	git push upstream master;\
109 75 
 	git push origin master
76 
+
77 
+
78 
+# mkdocs: mdfiles
79 
+# 	cd mkdocs;\
80 
+# 	mkdocs build;\
81 
+# 	cd ../docs;\
82 
+# 	rm -rf fonts;\
83 
+# 	rm -rf css/font-awesome*
84 
+
85 
+# mdfiles:
86 
+# 	cd mkdocs;\
87 
+# 	Rscript -e 'source("render.R")';\
88 
+# 	cd docs;\
89 
+# 	ln -f -s ../mysoftware/* ./
90 
+
91 
+# svnignore:
92 
+# 	svn propset svn:ignore -F .svnignore .
93 
+
94 
+# svncommit:
95 
+# 	git checkout devel;\
96 
+# 	git svn rebase;\
97 
+# 	git merge master --log;\
98 
+# 	git svn dcommit;\
99 
+# 	git push -u origin devel;\
100 
+# 	git checkout master;\
101 
+# 	git merge devel
Browse code

new gallery image

guangchuang yu authored on 13/09/2017 09:29:19
Showing 1 changed files
Makefile
History View file @ d30f654
... ... 
@@ -52,7 +52,11 @@ site:
52 52 
 	cd ..
53 53
54 54 
 preview:
55 
-	Rscript -e 'setwd("site_src"); blogdown::serve_site()'
55 
+	cd site_src;\
56 
+	ln -s ../../software/themes themes;\
57 
+	Rscript -e 'blogdown::serve_site()';\
58 
+	rm themes;\
59 
+	cd ..
56 60
57 61 
 mkdocs: mdfiles
58 62 
 	cd mkdocs;\
Browse code

update docs

guangchuang yu authored on 22/08/2017 06:08:09
Showing 1 changed files
Makefile
History View file @ 30a6bb4
... ... 
@@ -46,7 +46,9 @@ clean:
46 46
47 47 
 site:
48 48 
 	cd site_src;\
49 
+	ln -s ../../software/themes themes;\
49 50 
 	Rscript -e 'blogdown::build_site()';\
51 
+	rm themes;\
50 52 
 	cd ..
51 53
52 54 
 preview:
Browse code

update makefile

guangchuang yu authored on 17/08/2017 09:18:45
Showing 1 changed files
Makefile
History View file @ c84682c
... ... 
@@ -84,7 +84,7 @@ gitmaintain:
84 84 
 	git fsck --full
85 85
86 86
87 
-push:
87 
+pushX:
88 88 
 	git push -u origin master;\
89 89 
 	git checkout bioc;\
90 90 
 	git pull;\
... ... 
@@ -92,3 +92,12 @@ push:
92 92 
 	git push upstream master;\
93 93 
 	git checkout master
94 94
95 
+update:
96 
+	git fetch --all;\
97 
+	git checkout master;\
98 
+	git merge upstream/master;\
99 
+	git merge origin/master
100 
+
101 
+push: update
102 
+	git push upstream master;\
103 
+	git push origin master
Browse code

git conflict

guangchuang yu authored on 17/08/2017 08:10:06
Showing 0 changed files
Browse code

new citation

guangchuang yu authored on 07/08/2017 05:38:14
Showing 1 changed files
Makefile
History View file @ 8a00546
... ... 
@@ -4,7 +4,7 @@ PKGSRC  := $(shell basename `pwd`)
4 4
5 5 
 all: rd readme check clean
6 6
7 
-alldocs: rd readme mkdocs
7 
+alldocs: site rd readme
8 8
9 9 
 rd:
10 10 
 	Rscript -e 'roxygen2::roxygenise(".")'
Browse code

update site

guangchuang yu authored on 25/07/2017 05:29:36
Showing 1 changed files
Makefile
History View file @ 09d9e07
... ... 
@@ -44,11 +44,14 @@ clean:
44 44 
 	cd ..;\
45 45 
 	$(RM) -r $(PKGNAME).Rcheck/
46 46
47 
-site:
47 
+site:
48 48 
 	cd site_src;\
49 49 
 	Rscript -e 'blogdown::build_site()';\
50 50 
 	cd ..
51 51
52 
+preview:
53 
+	Rscript -e 'setwd("site_src"); blogdown::serve_site()'
54 
+
52 55 
 mkdocs: mdfiles
53 56 
 	cd mkdocs;\
54 57 
 	mkdocs build;\
Browse code

Merge branch 'master' of github.com:GuangchuangYu/ggtree

guangchuang yu authored on 25/07/2017 02:44:32
Showing 0 changed files
Browse code

makefile

guangchuang yu authored on 25/07/2017 02:44:28
Showing 1 changed files
Makefile
History View file @ e9f4129
... ... 
@@ -80,6 +80,7 @@ gitmaintain:
80 80 
 push:
81 81 
 	git push -u origin master;\
82 82 
 	git checkout bioc;\
83 
+	git pull;\
83 84 
 	git merge master;\
84 85 
 	git push upstream master;\
85 86 
 	git checkout master
Browse code

website transit to hugo

GuangchuangYu authored on 24/07/2017 15:41:08
Showing 1 changed files
Makefile
History View file @ 69ce680
... ... 
@@ -44,7 +44,10 @@ clean:
44 44 
 	cd ..;\
45 45 
 	$(RM) -r $(PKGNAME).Rcheck/
46 46
47 
-site: mkdocs
47 
+site:
48 
+	cd site_src;\
49 
+	Rscript -e 'blogdown::build_site()';\
50 
+	cd ..
48 51
49 52 
 mkdocs: mdfiles
50 53 
 	cd mkdocs;\
Browse code

bioc git transition

guangchuang yu authored on 18/07/2017 08:10:02
Showing 0 changed files
Browse code

update

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@131307 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 18/07/2017 07:59:43
Showing 1 changed files
Makefile
History View file @ f8d29c4
... ... 
@@ -70,3 +70,8 @@ svncommit:
70 70 
 	git push -u origin devel;\
71 71 
 	git checkout master;\
72 72 
 	git merge devel
73 
+
74 
+gitmaintain:
75 
+	git gc --auto;\
76 
+	git prune -v;\
77 
+	git fsck --full
Browse code

update makefile

guangchuang yu authored on 17/07/2017 10:17:29
Showing 1 changed files
Makefile
History View file @ 3c4c8dc
... ... 
@@ -70,3 +70,8 @@ svncommit:
70 70 
 	git push -u origin devel;\
71 71 
 	git checkout master;\
72 72 
 	git merge devel
73 
+
74 
+gitmaintain:
75 
+	git gc --auto;\
76 
+	git prune -v;\
77 
+	git fsck --full
Browse code

ggimage

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@127721 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 27/03/2017 01:58:54
Showing 1 changed files
Makefile
History View file @ c42351b
... ... 
@@ -12,6 +12,10 @@ rd:
12 12 
 readme:
13 13 
 	Rscript -e 'rmarkdown::render("README.Rmd")'
14 14
15 
+sticker:
16 
+	Rscript -e 'source("ggtree_sticker.R")';
17 
+	rm Rplots.pdf
18 
+
15 19 
 build:
16 20 
 	cd ..;\
17 21 
 	R CMD build $(PKGSRC)
... ... 
@@ -47,17 +51,11 @@ mkdocs: mdfiles
47 51 
 	mkdocs build;\
48 52 
 	cd ../docs;\
49 53 
 	rm -rf fonts;\
50 
-	rm -rf css/font-awesome*;\
51 
-	Rscript -e 'library(ypages); add_biobabble("index.html")'
52 
-
54 
+	rm -rf css/font-awesome*
53 55
54 56 
 mdfiles:
55 57 
 	cd mkdocs;\
56 
-	Rscript -e 'library(ypages); gendoc("src/index.md", "blue", "docs/index.md")';\
57 
-	Rscript -e 'library(ypages); gendoc("src/documentation.md", "blue", "docs/documentation.md")';\
58 
-	Rscript -e 'library(ypages); gendoc("src/featuredArticles.md", "blue", "docs/featuredArticles.md")';\
59 
-	Rscript -e 'library(ypages); gendoc("src/gallery.md", "blue", "docs/gallery.md")';\
60 
-	Rscript -e 'library(ypages); gendoc("src/faq.md", "blue", "docs/faq.md")';\
58 
+	Rscript -e 'source("render.R")';\
61 59 
 	cd docs;\
62 60 
 	ln -f -s ../mysoftware/* ./
63 61
Browse code

new sticker

guangchuang yu authored on 13/03/2017 11:26:48
Showing 1 changed files
Makefile
History View file @ 2d18b91
... ... 
@@ -12,6 +12,10 @@ rd:
12 12 
 readme:
13 13 
 	Rscript -e 'rmarkdown::render("README.Rmd")'
14 14
15 
+sticker:
16 
+	Rscript -e 'source("ggtree_sticker.R")';
17 
+	rm Rplots.pdf
18 
+
15 19 
 build:
16 20 
 	cd ..;\
17 21 
 	R CMD build $(PKGSRC)
Browse code

badge

guangchuang yu authored on 08/03/2017 08:42:56
Showing 1 changed files
Makefile
History View file @ 0bef889
... ... 
@@ -47,9 +47,7 @@ mkdocs: mdfiles
47 47 
 	mkdocs build;\
48 48 
 	cd ../docs;\
49 49 
 	rm -rf fonts;\
50 
-	rm -rf css/font-awesome*;\
51 
-	Rscript -e 'library(ypages); add_biobabble("index.html")'
52 
-
50 
+	rm -rf css/font-awesome*
53 51
54 52 
 mdfiles:
55 53 
 	cd mkdocs;\
Browse code

update docs

guangchuang yu authored on 08/03/2017 07:27:32
Showing 1 changed files
Makefile
History View file @ 975b531
... ... 
@@ -53,11 +53,7 @@ mkdocs: mdfiles
53 53
54 54 
 mdfiles:
55 55 
 	cd mkdocs;\
56 
-	Rscript -e 'library(ypages); gendoc("src/index.md", "blue", "docs/index.md")';\
57 
-	Rscript -e 'library(ypages); gendoc("src/documentation.md", "blue", "docs/documentation.md")';\
58 
-	Rscript -e 'library(ypages); gendoc("src/featuredArticles.md", "blue", "docs/featuredArticles.md")';\
59 
-	Rscript -e 'library(ypages); gendoc("src/gallery.md", "blue", "docs/gallery.md")';\
60 
-	Rscript -e 'library(ypages); gendoc("src/faq.md", "blue", "docs/faq.md")';\
56 
+	Rscript -e 'source("render.R")';\
61 57 
 	cd docs;\
62 58 
 	ln -f -s ../mysoftware/* ./
63 59
Browse code

emoji supported

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@126768 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 16/02/2017 07:35:52
Showing 1 changed files
Makefile
History View file @ 275491b
... ... 
@@ -56,6 +56,7 @@ mdfiles:
56 56 
 	Rscript -e 'library(ypages); gendoc("src/index.md", "blue", "docs/index.md")';\
57 57 
 	Rscript -e 'library(ypages); gendoc("src/documentation.md", "blue", "docs/documentation.md")';\
58 58 
 	Rscript -e 'library(ypages); gendoc("src/featuredArticles.md", "blue", "docs/featuredArticles.md")';\
59 
+	Rscript -e 'library(ypages); gendoc("src/gallery.md", "blue", "docs/gallery.md")';\
59 60 
 	Rscript -e 'library(ypages); gendoc("src/faq.md", "blue", "docs/faq.md")';\
60 61 
 	cd docs;\
61 62 
 	ln -f -s ../mysoftware/* ./
Browse code

gallery page

GuangchuangYu authored on 21/01/2017 04:04:10
Showing 1 changed files
Makefile
History View file @ 6949e7b
... ... 
@@ -56,6 +56,7 @@ mdfiles:
56 56 
 	Rscript -e 'library(ypages); gendoc("src/index.md", "blue", "docs/index.md")';\
57 57 
 	Rscript -e 'library(ypages); gendoc("src/documentation.md", "blue", "docs/documentation.md")';\
58 58 
 	Rscript -e 'library(ypages); gendoc("src/featuredArticles.md", "blue", "docs/featuredArticles.md")';\
59 
+	Rscript -e 'library(ypages); gendoc("src/gallery.md", "blue", "docs/gallery.md")';\
59 60 
 	Rscript -e 'library(ypages); gendoc("src/faq.md", "blue", "docs/faq.md")';\
60 61 
 	cd docs;\
61 62 
 	ln -f -s ../mysoftware/* ./
Browse code

makefile

guangchuang yu authored on 03/01/2017 11:03:14
Showing 1 changed files
Makefile
History View file @ e855a3e
... ... 
@@ -51,14 +51,6 @@ mkdocs: mdfiles
51 51 
 	Rscript -e 'library(ypages); add_biobabble("index.html")'
52 52
53 53
54 
-mysoftware:
55 
-	git submodule add -f git@github.com:GuangchuangYu/mysoftware.git mkdocs/mysoftware;\
56 
-	mv mkdocs/mysoftware mkdocs/mysoftware2;\
57 
-	git submodule deinit mkdocs/mysoftware;\
58 
-	git rm mkdocs/mysoftware;\
59 
-	mv mkdocs/mysoftware2 mkdocs/mysoftware;\
60 
-	rm -rf mkdocs/mysoftware/.git
61 
-
62 54 
 mdfiles:
63 55 
 	cd mkdocs;\
64 56 
 	Rscript -e 'library(ypages); gendoc("src/index.md", "blue", "docs/index.md")';\
Browse code

update makefile

guangchuang yu authored on 03/01/2017 10:13:51
Showing 1 changed files
Makefile
History View file @ d91c5b7
... ... 
@@ -50,9 +50,13 @@ mkdocs: mdfiles
50 50 
 	rm -rf css/font-awesome*;\
51 51 
 	Rscript -e 'library(ypages); add_biobabble("index.html")'
52 52
53 
+
53 54 
 mysoftware:
54 55 
 	git submodule add -f git@github.com:GuangchuangYu/mysoftware.git mkdocs/mysoftware;\
55 
-	rm -rf .gitmodules;\
56 
+	mv mkdocs/mysoftware mkdocs/mysoftware2;\
57 
+	git submodule deinit mkdocs/mysoftware;\
58 
+	git rm mkdocs/mysoftware;\
59 
+	mv mkdocs/mysoftware2 mkdocs/mysoftware;\
56 60 
 	rm -rf mkdocs/mysoftware/.git
57 61
58 62 
 mdfiles:
Browse code

test

guangchuang yu authored on 03/01/2017 10:03:26
Showing 1 changed files
Makefile
History View file @ 6fe12e6
... ... 
@@ -51,18 +51,18 @@ mkdocs: mdfiles
51 51 
 	Rscript -e 'library(ypages); add_biobabble("index.html")'
52 52
53 53 
 mysoftware:
54 
-	git submodule add -f git@github.com:GuangchuangYu/mysoftware.git mkdocs/mysoftware
54 
+	git submodule add -f git@github.com:GuangchuangYu/mysoftware.git mkdocs/mysoftware;\
55 
+	rm -rf .gitmodules;\
56 
+	rm -rf mkdocs/mysoftware/.git
55 57
56 58 
 mdfiles:
57 59 
 	cd mkdocs;\
58 
-	rm -rf docs/*md;\
59 60 
 	Rscript -e 'library(ypages); gendoc("src/index.md", "blue", "docs/index.md")';\
60 61 
 	Rscript -e 'library(ypages); gendoc("src/documentation.md", "blue", "docs/documentation.md")';\
61 62 
 	Rscript -e 'library(ypages); gendoc("src/featuredArticles.md", "blue", "docs/featuredArticles.md")';\
62 63 
 	Rscript -e 'library(ypages); gendoc("src/faq.md", "blue", "docs/faq.md")';\
63 64 
 	cd docs;\
64 
-	cp ../mysoftware/*.md ./
65 
-
65 
+	ln -f -s ../mysoftware/* ./
66