-
Notifications
You must be signed in to change notification settings - Fork 16
/
Copy pathrelease_notes_3_9_1.html
217 lines (181 loc) · 8.2 KB
/
release_notes_3_9_1.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>Cytoscape 3.9.1 Release Notes</title>
<meta name="description" content="Release Notes for Cytoscape">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<script src="https://code.jquery.com/jquery-2.1.4.min.js"></script>
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css" integrity="sha512-dTfge/zgoMYpP7QbHy4gWMEGsbsdZeCXz7irItjcC3sPUFtf0kuFbDz/ixG7ArTxmDjLXDmezHubeNikyKGVyQ==" crossorigin="anonymous">
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/js/bootstrap.min.js" integrity="sha512-K1qjQ+NcF2TYO/eI3M6v8EiNYZfA95pQumfvcVrTHtwQVDG+aHRqLi/ETn2uB+1JqwYqVG3LIvdm9lj6imS/pQ==" crossorigin="anonymous"></script>
<link href="css/main.bootstrap.css" rel="stylesheet">
<!-- For Scroll -->
<script src="js/smooth-scroll.min.js"></script>
</head>
<body>
<div class="white belt">
<div class="container">
<h1 class="centering">Release Notes for Cytoscape 3.9.1</h1>
</div>
<div class="container">
<div class="row">
<img src="images/screenshots/cy_3_8_0_desktop.png" class="image-fit">
</div>
</div>
</div>
<div class="narrow white">
<div class="container">
<div class="row">
<div class="col-xs-12 col-md-3">
<p>
<a class="btn btn-primary btn-lg btn-block" href="#new_features" data-scroll>
New Features
</a>
</p>
</div>
<div class="col-xs-12 col-md-3">
<p>
<a class="btn btn-primary btn-lg btn-block" href="#system_requirements" data-scroll>
System Requirements
</a>
</p>
</div>
<div class="col-xs-12 col-md-3">
<p>
<a class="btn btn-primary btn-lg btn-block" href="#manual" data-scroll>
Manual
</a>
</p>
</div>
<div class="col-xs-12 col-md-3">
<p>
<a class="btn btn-warning btn-lg btn-block" href="#known_issues" data-scroll>
Known Issues
</a>
</p>
</div>
</div>
</div>
</div>
<div id="new_features" class="white">
<div class="container centering">
<h1 class="centering">About Version 3.9.1</h1>
<p class="lead light-text">
Cytoscape 3.9.1 is a Cytoscape Desktop BugFix release, addressing the following issues:
<ul>
<li>Updated log4j dependencies in core to 2.17.1 via pax-logging (1.11.13)</li>
<li>Updated log4j dependencies to 2.17.1 in SBMLReader core app</li>
<li>Automation: updates to annotation and app-related commands</li>
<li>Minor fixes to table equations</li>
</ul>
</p>
</div>
</div>
<div id="system_requirements" class="narrow white">
<div class="container">
<h1 class="centering">System Requirements</h1>
<p class="lead">
No changes.
</p>
</div>
</div>
<h3 class="warn centering">Java 11 is Required -- Automatically Installed</h3>
<div class="row">
<div class="col-xs-12 col-md-offset-2 col-md-8">
<p class="lead">
For Windows and Mac users, the Cytoscape installer automatically downloads and installs Java 11 if it's not available on your workstation. For Linux, please use Java 11 as described below.
</p>
</div>
</div>
<div class="row">
<div class="col-xs-12 col-md-4">
<h3>Windows</h3>
<ul>
<li>Windows XP and newer (including Windows 7, 8 and 10). <strong>64 bit version is recommended</strong>.
</li>
<li>Cytoscape installer automatically downloads a suitable Java 11 if none is available on your workstation. You can manually download and install latest version of <a href="https://adoptopenjdk.net/">
OpenJDK 11</a>. Oracle Java and other implementations are not tested.
</li>
</ul>
</div>
<div class="col-xs-12 col-md-4">
<h3>Mac</h3>
<ul>
<li>Mac OS X 10.11 (El Capitan) and later</li>
<li>Cytoscape installer automatically downloads a suitable Java 11 if none is available on your workstation. You can manually download and install latest version of <a href="https://adoptopenjdk.net/">OpenJDK 11</a>.</li>
</ul>
</div>
<div class="col-xs-12 col-md-4">
<h3>Linux</h3>
<p>
</p>
<ul>
<li>Tested on
<a href="https://docs.google.com/spreadsheets/d/1aEGtWvxksnCgXbtfadjB1e59qrGUxq-Ei_w3AHX4lBo/">these
distributions.</a>
</li>
<li>
Latest version of Java is required (minimum Java 11.0.6).
</li>
<li>
For Ubuntu, a simple way of installing the OpenJDK JVM is described
<a href="https://adoptopenjdk.net/installation.html?variant=openjdk11&jvmVariant=hotspot#x64_linux-jre">here</a>.
</li>
<li>Java 11 must be on the PATH (ahead of any other JVM) or referenced by JAVA_HOME environment variable.</li>
</ul>
</div>
</div>
</div>
</div>
<div id="manual" class="narrow snow-white">
<h1 class="centering">User Manual</h1>
<div class="container">
<div class="row">
<div class="col-md-6 centering">
<a href="http://manual.cytoscape.org/">
<h3>HTML Version</h3>
</a>
</div>
<div class="col-md-6 centering">
<a href="manual/Cytoscape3_8_0Manual.pdf">
<h3>PDF version</h3>
</a>
</div>
</div>
</div>
</div>
<div class="belt light-blue">
<div class="container">
<div class="row">
<div class="col-md-6">
<h2>How to Report Bugs</h2>
<p class="lead">
Your bug reports are very important to improve quality of future versions of Cytoscape 3. If you notice any problems, please report them from:
</p>
<blockquote>Help → Report a bug...</blockquote>
<p class="lead">
Or, you can directly report it from
<a href="bug-report.html">Report a bug</a> link on the navigation bar.
</p>
</div>
<div class="col-md-6">
<h2>Need Help?</h2>
<p class="lead">
We need your feedback to improve Cytoscape 3! Please send your questions and comments to our <a href="https://groups.google.com/forum/?fromgroups#!forum/cytoscape-helpdesk">
mailing list</a>.
</p>
</div>
</div>
</div>
</div>
<footer></footer>
<script src="js/load_cyjs.js"></script>
<script src="js/setup_page.js"></script>
<script>
smoothScroll.init({
speed: 1000,
easing: 'easeInOutCubic'
});
</script>
</body>
</html>