Browse code

bioc3.15

Guangchuang Yu authored on 27/04/2022 06:54:55
Showing1 changed files
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@@ -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
Showing1 changed files
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@@ -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
Showing1 changed files
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@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
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@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
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@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
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@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
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@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing0 changed files
Browse code

new citation

guangchuang yu authored on 07/08/2017 05:38:14
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing0 changed files
Browse code

makefile

guangchuang yu authored on 25/07/2017 02:44:28
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing0 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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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)
guangchuang yu authored on 08/03/2017 08:42:56
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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:
guangchuang yu authored on 03/01/2017 10:03:26
Showing1 changed files
... ...
@@ -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 66
 
67 67
 svnignore:
68 68
 	svn propset svn:ignore -F .svnignore .
guangchuang yu authored on 03/01/2017 09:57:07
Showing1 changed files
... ...
@@ -55,12 +55,14 @@ mysoftware:
55 55
 
56 56
 mdfiles:
57 57
 	cd mkdocs;\
58
+	rm -rf docs/*md;\
58 59
 	Rscript -e 'library(ypages); gendoc("src/index.md", "blue", "docs/index.md")';\
59 60
 	Rscript -e 'library(ypages); gendoc("src/documentation.md", "blue", "docs/documentation.md")';\
60 61
 	Rscript -e 'library(ypages); gendoc("src/featuredArticles.md", "blue", "docs/featuredArticles.md")';\
61 62
 	Rscript -e 'library(ypages); gendoc("src/faq.md", "blue", "docs/faq.md")';\
62 63
 	cd docs;\
63
-	ln -f -s ../mysoftware/* ./
64
+	cp ../mysoftware/*.md ./
65
+
64 66
 
65 67
 svnignore:
66 68
 	svn propset svn:ignore -F .svnignore .
Browse code

treeio link

guangchuang yu authored on 03/01/2017 09:43:41
Showing1 changed files
... ...
@@ -50,6 +50,8 @@ mkdocs: mdfiles
50 50
 	rm -rf css/font-awesome*;\
51 51
 	Rscript -e 'library(ypages); add_biobabble("index.html")'
52 52
 
53
+mysoftware:
54
+	git submodule add -f git@github.com:GuangchuangYu/mysoftware.git mkdocs/mysoftware
53 55
 
54 56
 mdfiles:
55 57
 	cd mkdocs;\
Browse code

overlap parameter in groupOTU

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@124179 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 16/11/2016 05:50:08
Showing1 changed files
... ...
@@ -47,7 +47,9 @@ mkdocs: mdfiles
47 47
 	mkdocs build;\
48 48
 	cd ../docs;\
49 49
 	rm -rf fonts;\
50
-	rm -rf css/font-awesome*
50
+	rm -rf css/font-awesome*;\
51
+	Rscript -e 'library(ypages); add_biobabble("index.html")'
52
+
51 53
 
52 54
 mdfiles:
53 55
 	cd mkdocs;\
... ...
@@ -58,7 +60,6 @@ mdfiles:
58 60
 	cd docs;\
59 61
 	ln -f -s ../mysoftware/* ./
60 62
 
61
-
62 63
 svnignore:
63 64
 	svn propset svn:ignore -F .svnignore .
64 65
 
Browse code

biobabble

guangchuang yu authored on 10/11/2016 10:59:48
Showing1 changed files
... ...
@@ -48,7 +48,6 @@ mkdocs: mdfiles
48 48
 	cd ../docs;\
49 49
 	rm -rf fonts;\
50 50
 	rm -rf css/font-awesome*;\
51
-	cd ../../docs;\
52 51
 	Rscript -e 'library(ypages); add_biobabble("index.html")'
53 52
 
54 53
 
Browse code

biobabble

guangchuang yu authored on 10/11/2016 10:50:49
Showing1 changed files
... ...
@@ -47,7 +47,10 @@ mkdocs: mdfiles
47 47
 	mkdocs build;\
48 48
 	cd ../docs;\
49 49
 	rm -rf fonts;\
50
-	rm -rf css/font-awesome*
50
+	rm -rf css/font-awesome*;\
51
+	cd ../../docs;\
52
+	Rscript -e 'library(ypages); add_biobabble("index.html")'
53
+
51 54
 
52 55
 mdfiles:
53 56
 	cd mkdocs;\
... ...
@@ -58,7 +61,6 @@ mdfiles:
58 61
 	cd docs;\
59 62
 	ln -f -s ../mysoftware/* ./
60 63
 
61
-
62 64
 svnignore:
63 65
 	svn propset svn:ignore -F .svnignore .
64 66
 
Browse code

update docs

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@122813 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 19/10/2016 12:23:24
Showing1 changed files
1 1
new file mode 100644
... ...
@@ -0,0 +1,72 @@
1
+PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION)
2
+PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION)
3
+PKGSRC  := $(shell basename `pwd`)
4
+
5
+all: rd readme check clean
6
+
7
+alldocs: rd readme mkdocs
8
+
9
+rd:
10
+	Rscript -e 'roxygen2::roxygenise(".")'
11
+
12
+readme:
13
+	Rscript -e 'rmarkdown::render("README.Rmd")'
14
+
15
+build:
16
+	cd ..;\
17
+	R CMD build $(PKGSRC)
18
+
19
+build2:
20
+	cd ..;\
21
+	R CMD build --no-build-vignettes $(PKGSRC)
22
+
23
+install:
24
+	cd ..;\
25
+	R CMD INSTALL $(PKGNAME)_$(PKGVERS).tar.gz
26
+
27
+check: build
28
+	cd ..;\
29
+	Rscript -e 'rcmdcheck::rcmdcheck("$(PKGNAME)_$(PKGVERS).tar.gz")'
30
+
31
+check2: build
32
+	cd ..;\
33
+	R CMD check $(PKGNAME)_$(PKGVERS).tar.gz
34
+
35
+bioccheck:
36
+	cd ..;\
37
+	Rscript -e 'BiocCheck::BiocCheck("$(PKGNAME)_$(PKGVERS).tar.gz")'
38
+
39
+clean:
40
+	cd ..;\
41
+	$(RM) -r $(PKGNAME).Rcheck/
42
+
43
+site: mkdocs
44
+
45
+mkdocs: mdfiles
46
+	cd mkdocs;\
47
+	mkdocs build;\
48
+	cd ../docs;\
49
+	rm -rf fonts;\
50
+	rm -rf css/font-awesome*
51
+
52
+mdfiles:
53
+	cd mkdocs;\
54
+	Rscript -e 'library(ypages); gendoc("src/index.md", "blue", "docs/index.md")';\
55
+	Rscript -e 'library(ypages); gendoc("src/documentation.md", "blue", "docs/documentation.md")';\
56
+	Rscript -e 'library(ypages); gendoc("src/featuredArticles.md", "blue", "docs/featuredArticles.md")';\
57
+	Rscript -e 'library(ypages); gendoc("src/faq.md", "blue", "docs/faq.md")';\
58
+	cd docs;\
59
+	ln -f -s ../mysoftware/* ./
60
+
61
+
62
+svnignore:
63
+	svn propset svn:ignore -F .svnignore .
64
+
65
+svncommit:
66
+	git checkout devel;\
67
+	git svn rebase;\
68
+	git merge master --log;\
69
+	git svn dcommit;\
70
+	git push -u origin devel;\
71
+	git checkout master;\
72
+	git merge devel
Browse code

meshes

guangchuang yu authored on 17/10/2016 05:28:39
Showing1 changed files
... ...
@@ -51,10 +51,10 @@ mkdocs: mdfiles
51 51
 
52 52
 mdfiles:
53 53
 	cd mkdocs;\
54
-	Rscript -e 'library(ypages); gendoc("private/index.md", "blue", "docs/index.md")';\
55
-	Rscript -e 'library(ypages); gendoc("private/documentation.md", "blue", "docs/documentation.md")';\
56
-	Rscript -e 'library(ypages); gendoc("private/featuredArticles.md", "blue", "docs/featuredArticles.md")';\
57
-	Rscript -e 'library(ypages); gendoc("private/faq.md", "blue", "docs/faq.md")';\
54
+	Rscript -e 'library(ypages); gendoc("src/index.md", "blue", "docs/index.md")';\
55
+	Rscript -e 'library(ypages); gendoc("src/documentation.md", "blue", "docs/documentation.md")';\
56
+	Rscript -e 'library(ypages); gendoc("src/featuredArticles.md", "blue", "docs/featuredArticles.md")';\
57
+	Rscript -e 'library(ypages); gendoc("src/faq.md", "blue", "docs/faq.md")';\
58 58
 	cd docs;\
59 59
 	ln -f -s ../mysoftware/* ./
60 60
 
Browse code

removing site

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@122180 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 11/10/2016 02:34:23
Showing1 changed files
1 1
deleted file mode 100644
... ...
@@ -1,72 +0,0 @@
1
-PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION)
2
-PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION)
3
-PKGSRC  := $(shell basename `pwd`)
4
-
5
-all: rd readme check clean
6
-
7
-alldocs: rd readme mkdocs
8
-
9
-rd:
10
-	Rscript -e 'roxygen2::roxygenise(".")'
11
-
12
-readme:
13
-	Rscript -e 'rmarkdown::render("README.Rmd")'
14
-
15
-build:
16
-	cd ..;\
17
-	R CMD build $(PKGSRC)
18
-
19
-build2:
20
-	cd ..;\
21
-	R CMD build --no-build-vignettes $(PKGSRC)
22
-
23
-install:
24
-	cd ..;\
25
-	R CMD INSTALL $(PKGNAME)_$(PKGVERS).tar.gz
26
-
27
-check: build
28
-	cd ..;\
29
-	Rscript -e 'rcmdcheck::rcmdcheck("$(PKGNAME)_$(PKGVERS).tar.gz")'
30
-
31
-check2: build
32
-	cd ..;\
33
-	R CMD check $(PKGNAME)_$(PKGVERS).tar.gz
34
-
35
-bioccheck:
36
-	cd ..;\
37
-	Rscript -e 'BiocCheck::BiocCheck("$(PKGNAME)_$(PKGVERS).tar.gz")'
38
-
39
-clean:
40
-	cd ..;\
41
-	$(RM) -r $(PKGNAME).Rcheck/
42
-
43
-site: mkdocs
44
-
45
-mkdocs: mdfiles
46
-	cd mkdocs;\
47
-	mkdocs build;\
48
-	cd ../docs;\
49
-	rm -rf fonts;\
50
-	rm -rf css/font-awesome*
51
-
52
-mdfiles:
53
-	cd mkdocs;\
54
-	Rscript -e 'library(ypages); gendoc("private/index.md", "blue", "docs/index.md")';\
55
-	Rscript -e 'library(ypages); gendoc("private/documentation.md", "blue", "docs/documentation.md")';\
56
-	Rscript -e 'library(ypages); gendoc("private/featuredArticles.md", "blue", "docs/featuredArticles.md")';\
57
-	Rscript -e 'library(ypages); gendoc("private/faq.md", "blue", "docs/faq.md")';\
58
-	cd docs;\
59
-	ln -f -s ../mysoftware/* ./
60
-
61
-
62
-svnignore:
63
-	svn propset svn:ignore -F .svnignore .
64
-
65
-svncommit:
66
-	git checkout devel;\
67
-	git svn rebase;\
68
-	git merge master --log;\
69
-	git svn dcommit;\
70
-	git push -u origin devel;\
71
-	git checkout master;\
72
-	git merge devel
Browse code

devel branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@122178 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 11/10/2016 02:20:22
Showing1 changed files
... ...
@@ -67,5 +67,6 @@ svncommit:
67 67
 	git svn rebase;\
68 68
 	git merge master --log;\
69 69
 	git svn dcommit;\
70
+	git push -u origin devel;\
70 71
 	git checkout master;\
71 72
 	git merge devel
Browse code

devel branch

guangchuang yu authored on 11/10/2016 02:15:58
Showing1 changed files
... ...
@@ -67,5 +67,6 @@ svncommit:
67 67
 	git svn rebase;\
68 68
 	git merge master --log;\
69 69
 	git svn dcommit;\
70
+	git push -u origin devel;\
70 71
 	git checkout master;\
71 72
 	git merge devel

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@122176 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 11/10/2016 02:10:31
Showing1 changed files
1 1
new file mode 100644
... ...
@@ -0,0 +1,71 @@
1
+PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION)
2
+PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION)
3
+PKGSRC  := $(shell basename `pwd`)
4
+
5
+all: rd readme check clean
6
+
7
+alldocs: rd readme mkdocs
8
+
9
+rd:
10
+	Rscript -e 'roxygen2::roxygenise(".")'
11
+
12
+readme:
13
+	Rscript -e 'rmarkdown::render("README.Rmd")'
14
+
15
+build:
16
+	cd ..;\
17
+	R CMD build $(PKGSRC)
18
+
19
+build2:
20
+	cd ..;\
21
+	R CMD build --no-build-vignettes $(PKGSRC)
22
+
23
+install:
24
+	cd ..;\
25
+	R CMD INSTALL $(PKGNAME)_$(PKGVERS).tar.gz
26
+
27
+check: build
28
+	cd ..;\
29
+	Rscript -e 'rcmdcheck::rcmdcheck("$(PKGNAME)_$(PKGVERS).tar.gz")'
30
+
31
+check2: build
32
+	cd ..;\
33
+	R CMD check $(PKGNAME)_$(PKGVERS).tar.gz
34
+
35
+bioccheck:
36
+	cd ..;\
37
+	Rscript -e 'BiocCheck::BiocCheck("$(PKGNAME)_$(PKGVERS).tar.gz")'
38
+
39
+clean:
40
+	cd ..;\
41
+	$(RM) -r $(PKGNAME).Rcheck/
42
+
43
+site: mkdocs
44
+
45
+mkdocs: mdfiles
46
+	cd mkdocs;\
47
+	mkdocs build;\
48
+	cd ../docs;\
49
+	rm -rf fonts;\
50
+	rm -rf css/font-awesome*
51
+
52
+mdfiles:
53
+	cd mkdocs;\
54
+	Rscript -e 'library(ypages); gendoc("private/index.md", "blue", "docs/index.md")';\
55
+	Rscript -e 'library(ypages); gendoc("private/documentation.md", "blue", "docs/documentation.md")';\
56
+	Rscript -e 'library(ypages); gendoc("private/featuredArticles.md", "blue", "docs/featuredArticles.md")';\
57
+	Rscript -e 'library(ypages); gendoc("private/faq.md", "blue", "docs/faq.md")';\
58
+	cd docs;\
59
+	ln -f -s ../mysoftware/* ./
60
+
61
+
62
+svnignore:
63
+	svn propset svn:ignore -F .svnignore .
64
+
65
+svncommit:
66
+	git checkout devel;\
67
+	git svn rebase;\
68
+	git merge master --log;\
69
+	git svn dcommit;\
70
+	git checkout master;\
71
+	git merge devel
guangchuang yu authored on 11/10/2016 02:07:36
Showing1 changed files
1 1
new file mode 100644
... ...
@@ -0,0 +1,71 @@
1
+PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION)
2
+PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION)
3
+PKGSRC  := $(shell basename `pwd`)
4
+
5
+all: rd readme check clean
6
+
7
+alldocs: rd readme mkdocs
8
+
9
+rd:
10
+	Rscript -e 'roxygen2::roxygenise(".")'
11
+
12
+readme:
13
+	Rscript -e 'rmarkdown::render("README.Rmd")'
14
+
15
+build:
16
+	cd ..;\
17
+	R CMD build $(PKGSRC)
18
+
19
+build2:
20
+	cd ..;\
21
+	R CMD build --no-build-vignettes $(PKGSRC)
22
+
23
+install:
24
+	cd ..;\
25
+	R CMD INSTALL $(PKGNAME)_$(PKGVERS).tar.gz
26
+
27
+check: build
28
+	cd ..;\
29
+	Rscript -e 'rcmdcheck::rcmdcheck("$(PKGNAME)_$(PKGVERS).tar.gz")'
30
+
31
+check2: build
32
+	cd ..;\
33
+	R CMD check $(PKGNAME)_$(PKGVERS).tar.gz
34
+
35
+bioccheck:
36
+	cd ..;\
37
+	Rscript -e 'BiocCheck::BiocCheck("$(PKGNAME)_$(PKGVERS).tar.gz")'
38
+
39
+clean:
40
+	cd ..;\
41
+	$(RM) -r $(PKGNAME).Rcheck/
42
+
43
+site: mkdocs
44
+
45
+mkdocs: mdfiles
46
+	cd mkdocs;\
47
+	mkdocs build;\
48
+	cd ../docs;\
49
+	rm -rf fonts;\
50
+	rm -rf css/font-awesome*
51
+
52
+mdfiles:
53
+	cd mkdocs;\
54
+	Rscript -e 'library(ypages); gendoc("private/index.md", "blue", "docs/index.md")';\
55
+	Rscript -e 'library(ypages); gendoc("private/documentation.md", "blue", "docs/documentation.md")';\
56
+	Rscript -e 'library(ypages); gendoc("private/featuredArticles.md", "blue", "docs/featuredArticles.md")';\
57
+	Rscript -e 'library(ypages); gendoc("private/faq.md", "blue", "docs/faq.md")';\
58
+	cd docs;\
59
+	ln -f -s ../mysoftware/* ./
60
+
61
+
62
+svnignore:
63
+	svn propset svn:ignore -F .svnignore .
64
+
65
+svncommit:
66
+	git checkout devel;\
67
+	git svn rebase;\
68
+	git merge master --log;\
69
+	git svn dcommit;\
70
+	git checkout master;\
71
+	git merge devel
Browse code

remove site

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@122175 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 11/10/2016 02:01:09
Showing1 changed files
1 1
deleted file mode 100644
... ...
@@ -1,64 +0,0 @@
1
-PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION)
2
-PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION)
3
-PKGSRC  := $(shell basename `pwd`)
4
-
5
-all: rd readme check clean
6
-
7
-alldocs: rd readme mkdocs
8
-
9
-rd:
10
-	Rscript -e 'roxygen2::roxygenise(".")'
11
-
12
-readme:
13
-	Rscript -e 'rmarkdown::render("README.Rmd")'
14
-
15
-build:
16
-	cd ..;\
17
-	R CMD build $(PKGSRC)
18
-
19
-build2:
20
-	cd ..;\
21
-	R CMD build --no-build-vignettes $(PKGSRC)
22
-
23
-install:
24
-	cd ..;\
25
-	R CMD INSTALL $(PKGNAME)_$(PKGVERS).tar.gz
26
-
27
-check: build
28
-	cd ..;\
29
-	Rscript -e 'rcmdcheck::rcmdcheck("$(PKGNAME)_$(PKGVERS).tar.gz")'
30
-
31
-check2: build
32
-	cd ..;\
33
-	R CMD check $(PKGNAME)_$(PKGVERS).tar.gz
34
-
35
-bioccheck:
36
-	cd ..;\
37
-	Rscript -e 'BiocCheck::BiocCheck("$(PKGNAME)_$(PKGVERS).tar.gz")'
38
-
39
-clean:
40
-	cd ..;\
41
-	$(RM) -r $(PKGNAME).Rcheck/
42
-
43
-site: mkdocs
44
-
45
-mkdocs: mdfiles
46
-	cd mkdocs;\
47
-	mkdocs build;\
48
-	cd ../docs;\
49
-	rm -rf fonts;\
50
-	rm -rf css/font-awesome*
51
-
52
-mdfiles:
53
-	cd mkdocs;\
54
-	Rscript -e 'library(ypages); gendoc("private/index.md", "blue", "docs/index.md")';\
55
-	Rscript -e 'library(ypages); gendoc("private/documentation.md", "blue", "docs/documentation.md")';\
56
-	Rscript -e 'library(ypages); gendoc("private/featuredArticles.md", "blue", "docs/featuredArticles.md")';\
57
-	Rscript -e 'library(ypages); gendoc("private/faq.md", "blue", "docs/faq.md")';\
58
-	cd docs;\
59
-	ln -f -s ../mysoftware/* ./
60
-
61
-
62
-svnignore:
63
-	svn propset svn:ignore -F .svnignore .
64
-
Browse code

remove site

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@122175 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 11/10/2016 02:01:09
Showing1 changed files
1 1
deleted file mode 100644
... ...
@@ -1,64 +0,0 @@
1
-PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION)
2
-PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION)
3
-PKGSRC  := $(shell basename `pwd`)
4
-
5
-all: rd readme check clean
6
-
7
-alldocs: rd readme mkdocs
8
-
9
-rd:
10
-	Rscript -e 'roxygen2::roxygenise(".")'
11
-
12
-readme:
13
-	Rscript -e 'rmarkdown::render("README.Rmd")'
14
-
15
-build:
16
-	cd ..;\
17
-	R CMD build $(PKGSRC)
18
-
19
-build2:
20
-	cd ..;\
21
-	R CMD build --no-build-vignettes $(PKGSRC)
22
-
23
-install:
24
-	cd ..;\
25
-	R CMD INSTALL $(PKGNAME)_$(PKGVERS).tar.gz
26
-
27
-check: build
28
-	cd ..;\
29
-	Rscript -e 'rcmdcheck::rcmdcheck("$(PKGNAME)_$(PKGVERS).tar.gz")'
30
-
31
-check2: build
32
-	cd ..;\
33
-	R CMD check $(PKGNAME)_$(PKGVERS).tar.gz
34
-
35
-bioccheck:
36
-	cd ..;\
37
-	Rscript -e 'BiocCheck::BiocCheck("$(PKGNAME)_$(PKGVERS).tar.gz")'
38
-
39
-clean:
40
-	cd ..;\
41
-	$(RM) -r $(PKGNAME).Rcheck/
42
-
43
-site: mkdocs
44
-
45
-mkdocs: mdfiles
46
-	cd mkdocs;\
47
-	mkdocs build;\
48
-	cd ../docs;\
49
-	rm -rf fonts;\
50
-	rm -rf css/font-awesome*
51
-
52
-mdfiles:
53
-	cd mkdocs;\
54
-	Rscript -e 'library(ypages); gendoc("private/index.md", "blue", "docs/index.md")';\
55
-	Rscript -e 'library(ypages); gendoc("private/documentation.md", "blue", "docs/documentation.md")';\
56
-	Rscript -e 'library(ypages); gendoc("private/featuredArticles.md", "blue", "docs/featuredArticles.md")';\
57
-	Rscript -e 'library(ypages); gendoc("private/faq.md", "blue", "docs/faq.md")';\
58
-	cd docs;\
59
-	ln -f -s ../mysoftware/* ./
60
-
61
-
62
-svnignore:
63
-	svn propset svn:ignore -F .svnignore .
64
-

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@122174 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 11/10/2016 01:56:09
Showing1 changed files
1 1
new file mode 100644
... ...
@@ -0,0 +1,64 @@
1
+PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION)
2
+PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION)
3
+PKGSRC  := $(shell basename `pwd`)
4
+
5
+all: rd readme check clean
6
+
7
+alldocs: rd readme mkdocs
8
+
9
+rd:
10
+	Rscript -e 'roxygen2::roxygenise(".")'
11
+
12
+readme:
13
+	Rscript -e 'rmarkdown::render("README.Rmd")'
14
+
15
+build:
16
+	cd ..;\
17
+	R CMD build $(PKGSRC)
18
+
19
+build2:
20
+	cd ..;\
21
+	R CMD build --no-build-vignettes $(PKGSRC)
22
+
23
+install:
24
+	cd ..;\
25
+	R CMD INSTALL $(PKGNAME)_$(PKGVERS).tar.gz
26
+
27
+check: build
28
+	cd ..;\
29
+	Rscript -e 'rcmdcheck::rcmdcheck("$(PKGNAME)_$(PKGVERS).tar.gz")'
30
+
31
+check2: build
32
+	cd ..;\
33
+	R CMD check $(PKGNAME)_$(PKGVERS).tar.gz
34
+
35
+bioccheck:
36
+	cd ..;\
37
+	Rscript -e 'BiocCheck::BiocCheck("$(PKGNAME)_$(PKGVERS).tar.gz")'
38
+
39
+clean:
40
+	cd ..;\
41
+	$(RM) -r $(PKGNAME).Rcheck/
42
+
43
+site: mkdocs
44
+
45
+mkdocs: mdfiles
46
+	cd mkdocs;\
47
+	mkdocs build;\
48
+	cd ../docs;\
49
+	rm -rf fonts;\
50
+	rm -rf css/font-awesome*
51
+
52
+mdfiles:
53
+	cd mkdocs;\
54
+	Rscript -e 'library(ypages); gendoc("private/index.md", "blue", "docs/index.md")';\
55
+	Rscript -e 'library(ypages); gendoc("private/documentation.md", "blue", "docs/documentation.md")';\
56
+	Rscript -e 'library(ypages); gendoc("private/featuredArticles.md", "blue", "docs/featuredArticles.md")';\
57
+	Rscript -e 'library(ypages); gendoc("private/faq.md", "blue", "docs/faq.md")';\
58
+	cd docs;\
59
+	ln -f -s ../mysoftware/* ./
60
+
61
+
62
+svnignore:
63
+	svn propset svn:ignore -F .svnignore .
64
+
Browse code

fixed theme_tree2

guangchuang yu authored on 05/10/2016 06:28:33
Showing1 changed files
... ...
@@ -25,6 +25,10 @@ install:
25 25
 	R CMD INSTALL $(PKGNAME)_$(PKGVERS).tar.gz
26 26
 
27 27
 check: build
28
+	cd ..;\
29
+	Rscript -e 'rcmdcheck::rcmdcheck("$(PKGNAME)_$(PKGVERS).tar.gz")'
30
+
31
+check2: build
28