-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathUpdateRstudioServer.html
505 lines (432 loc) · 14.1 KB
/
UpdateRstudioServer.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
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8" />
<meta name="generator" content="pandoc" />
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
<meta name="author" content="Paul Melloy" />
<meta name="date" content="2024-06-11" />
<title>Upgrade your personal Rstudio server</title>
<script src="site_libs/header-attrs-2.29/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/darkly.min.css" rel="stylesheet" />
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
<style>h1 {font-size: 34px;}
h1.title {font-size: 38px;}
h2 {font-size: 30px;}
h3 {font-size: 24px;}
h4 {font-size: 18px;}
h5 {font-size: 16px;}
h6 {font-size: 12px;}
code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
pre:not([class]) { background-color: white }</style>
<script src="site_libs/navigation-1.1/tabsets.js"></script>
<link href="site_libs/highlightjs-9.12.0/default.css" rel="stylesheet" />
<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
<link href="site_libs/font-awesome-6.5.2/css/all.min.css" rel="stylesheet" />
<link href="site_libs/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet" />
<style type="text/css">
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
span.underline{text-decoration: underline;}
div.column{display: inline-block; vertical-align: top; width: 50%;}
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
ul.task-list{list-style: none;}
</style>
<style type="text/css">code{white-space: pre;}</style>
<script type="text/javascript">
if (window.hljs) {
hljs.configure({languages: []});
hljs.initHighlightingOnLoad();
if (document.readyState && document.readyState === "complete") {
window.setTimeout(function() { hljs.initHighlighting(); }, 0);
}
}
</script>
<style type = "text/css">
.main-container {
max-width: 940px;
margin-left: auto;
margin-right: auto;
}
img {
max-width:100%;
}
.tabbed-pane {
padding-top: 12px;
}
.html-widget {
margin-bottom: 20px;
}
button.code-folding-btn:focus {
outline: none;
}
summary {
display: list-item;
}
details > summary > p:only-child {
display: inline;
}
pre code {
padding: 0;
}
</style>
<style type="text/css">
.dropdown-submenu {
position: relative;
}
.dropdown-submenu>.dropdown-menu {
top: 0;
left: 100%;
margin-top: -6px;
margin-left: -1px;
border-radius: 0 6px 6px 6px;
}
.dropdown-submenu:hover>.dropdown-menu {
display: block;
}
.dropdown-submenu>a:after {
display: block;
content: " ";
float: right;
width: 0;
height: 0;
border-color: transparent;
border-style: solid;
border-width: 5px 0 5px 5px;
border-left-color: #cccccc;
margin-top: 5px;
margin-right: -10px;
}
.dropdown-submenu:hover>a:after {
border-left-color: #adb5bd;
}
.dropdown-submenu.pull-left {
float: none;
}
.dropdown-submenu.pull-left>.dropdown-menu {
left: -100%;
margin-left: 10px;
border-radius: 6px 0 6px 6px;
}
</style>
<script type="text/javascript">
// manage active state of menu based on current page
$(document).ready(function () {
// active menu anchor
href = window.location.pathname
href = href.substr(href.lastIndexOf('/') + 1)
if (href === "")
href = "index.html";
var menuAnchor = $('a[href="' + href + '"]');
// mark the anchor link active (and if it's in a dropdown, also mark that active)
var dropdown = menuAnchor.closest('li.dropdown');
if (window.bootstrap) { // Bootstrap 4+
menuAnchor.addClass('active');
dropdown.find('> .dropdown-toggle').addClass('active');
} else { // Bootstrap 3
menuAnchor.parent().addClass('active');
dropdown.addClass('active');
}
// Navbar adjustments
var navHeight = $(".navbar").first().height() + 15;
var style = document.createElement('style');
var pt = "padding-top: " + navHeight + "px; ";
var mt = "margin-top: -" + navHeight + "px; ";
var css = "";
// offset scroll position for anchor links (for fixed navbar)
for (var i = 1; i <= 6; i++) {
css += ".section h" + i + "{ " + pt + mt + "}\n";
}
style.innerHTML = "body {" + pt + "padding-bottom: 40px; }\n" + css;
document.head.appendChild(style);
});
</script>
<!-- tabsets -->
<style type="text/css">
.tabset-dropdown > .nav-tabs {
display: inline-table;
max-height: 500px;
min-height: 44px;
overflow-y: auto;
border: 1px solid #ddd;
border-radius: 4px;
}
.tabset-dropdown > .nav-tabs > li.active:before, .tabset-dropdown > .nav-tabs.nav-tabs-open:before {
content: "\e259";
font-family: 'Glyphicons Halflings';
display: inline-block;
padding: 10px;
border-right: 1px solid #ddd;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {
content: "\e258";
font-family: 'Glyphicons Halflings';
border: none;
}
.tabset-dropdown > .nav-tabs > li.active {
display: block;
}
.tabset-dropdown > .nav-tabs > li > a,
.tabset-dropdown > .nav-tabs > li > a:focus,
.tabset-dropdown > .nav-tabs > li > a:hover {
border: none;
display: inline-block;
border-radius: 4px;
background-color: transparent;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open > li {
display: block;
float: none;
}
.tabset-dropdown > .nav-tabs > li {
display: none;
}
</style>
<!-- code folding -->
</head>
<body>
<div class="container-fluid main-container">
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-bs-toggle="collapse" data-target="#navbar" data-bs-target="#navbar">
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="index.html">Paul Melloy</a>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="index.html">Home</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
Blogs
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="https://paulmelloy.github.io/UpdateRstudioServer.html">Updating Rstudio server</a>
</li>
<li>
<a href="https://paulmelloy.github.io/SharedRlibrary.html">Shared R library</a>
</li>
<li>
<a href="https://paulmelloy.github.io/RDM_webdav.html">Zotero Webdavs</a>
</li>
<li>
<a href="https://openplantpathology.netlify.app/posts/2022-04-01-powerful-tea-using-nasapower-and-tealeaves-to-obtain-leaf-temperatures/">Leaf Tm from NASA POWER</a>
</li>
<li>
<a href="https://thefungaljungle.blogspot.com/">Old FungalJungle Blog</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
Shiny Apps
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="https://viticolr.paulmelloy.com.au/shiny/viticolR_dst/">ViticolaR DST</a>
</li>
<li>
<a href="https://agroecology.canola-allies.cloud.edu.au/shiny/epiphytrainR_app/">epiphytrainR</a>
</li>
<li>
<a href="https://paulmelloy.shinyapps.io/22_electoralboundaries/">2022 electoral data</a>
</li>
<li>
<a href="https://paulmelloy.shinyapps.io/UniSuperDBD/">UniSuperDBD</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
R Packages
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="https://paulmelloy.github.io/cercospoRa/">cercospoRa</a>
</li>
<li>
<a href="https://ihsankhaliq.github.io/ascotraceR/">ascotraceR</a>
</li>
<li>
<a href="https://paulmelloy.github.io/epiphytoolR/">epiphytoolR</a>
</li>
</ul>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="mailto:<[email protected]>">
<span class="fa fa-envelope fa-lg"></span>
</a>
</li>
<li>
<a href="http://github.com/PaulMelloy/">
<span class="fa fa-github fa-lg"></span>
</a>
</li>
<li>
<a href="https://twitter.com/PaulMelloy">
<span class="fa fa-brands fa-twitter"></span>
</a>
</li>
<li>
<a href="https://orcid.org/0000-0003-4253-7167">
<span class="fa fa-brands fa-orcid"></span>
</a>
</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
<div id="header">
<h1 class="title toc-ignore">Upgrade your personal Rstudio server</h1>
<h4 class="author">Paul Melloy</h4>
<h4 class="date">2024-06-11</h4>
</div>
<div id="update-your-rstudio-server" class="section level2">
<h2>Update your Rstudio server</h2>
<p>I was surprised how little documentation was available on how to
update Rstudio Servers. I use a Rstudio server deployed on the
Australian Research and Data Commons (ARDC), NECTAR service. It took me
too long to figure this out as all the current documentation was old and
obsolete.</p>
<p><a
href="https://www.r-bloggers.com/2023/05/r-install-and-configure-rstudio-server-in-ubuntu/">This
post</a> by <a
href="https://www.r-bloggers.com/author/zhenguo-zhang/">Zhenguo
Zhang</a> was helpful, However not specific to my use case of just
wanting to <em>upgrade</em> my server.</p>
<p><strong>NOTE:</strong> Upgrading the software will need
<code>sudo</code> privileges on the machine.</p>
<p><br></p>
<div id="stop-the-service" class="section level3">
<h3>1. Stop the service</h3>
<pre class="bash"><code>sudo rstudio-server stop</code></pre>
<p><br></p>
</div>
<div id="remove-the-old-service" class="section level3">
<h3>2. Remove the old service</h3>
<pre class="bash"><code>sudo apt-get remove rstudio-server</code></pre>
<p><br></p>
</div>
<div id="install-new-version" class="section level3">
<h3>3. Install new version</h3>
<p>This step can mostly be followed from the POSIT website: <a
href="https://posit.co/download/rstudio-server/"
class="uri">https://posit.co/download/rstudio-server/</a></p>
<p><br></p>
<div id="disto-dependant" class="section level4">
<h4>Disto dependant</h4>
<p>Be aware the following is linux distribution dependant. My version is
“Ubuntu 22.04.4 LTS” however yours might be slightly different.</p>
<p>If gdebi-core is not already installed from the old Rstudio server
install it again</p>
<ol style="list-style-type: lower-alpha">
<li>install gdebi-core to allow debian package manager to install the
new version</li>
</ol>
<pre class="bash"><code>sudo apt-get install gdebi-core</code></pre>
<ol start="2" style="list-style-type: lower-alpha">
<li>Install the new Rstudio version</li>
</ol>
<p>You may need to get the most recent line of code from the <a
href="https://posit.co/download/rstudio-server/">posit website</a>.</p>
<pre class="bash"><code># Download
wget https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2024.04.2-764-amd64.deb
# Install
sudo gdebi rstudio-server-2024.04.2-764-amd64.deb</code></pre>
<p><br></p>
</div>
</div>
<div id="start-the-new-service" class="section level3">
<h3>4. Start the new service</h3>
<p>Verify installation</p>
<pre class="bash"><code>sudo rstudio-server verify-installation</code></pre>
<p>Start the a new session</p>
<pre class="bash"><code>sudo rstudio-server start</code></pre>
<p>Verify the a new session has started and is active</p>
<pre class="bash"><code>sudo rstudio-server active-sessions</code></pre>
<p>Once the service is active make put the service back online</p>
<pre class="bash"><code>sudo rstudio-server online</code></pre>
<ul>
<li>and that should be it!!</li>
</ul>
<p><br><br />
<br></p>
</div>
<div id="troubleshooting" class="section level3">
<h3>Troubleshooting</h3>
<p>Restarting your service</p>
<pre class="bash"><code>sudo rstudio-server restart</code></pre>
<ul>
<li>Check the ports are open rstudio server is usually
<code>8787</code></li>
</ul>
<pre class="bash"><code># list ports in use
sudo netstat -tulpn</code></pre>
<ul>
<li>Check the rstudio configuration files</li>
</ul>
<pre class="bash"><code>nano /etc/rstudio/rserver.conf</code></pre>
<div id="links-to-other-instructions" class="section level4">
<h4>Links to other instructions</h4>
<p><a
href="https://www.r-bloggers.com/2023/05/r-install-and-configure-rstudio-server-in-ubuntu/"
class="uri">https://www.r-bloggers.com/2023/05/r-install-and-configure-rstudio-server-in-ubuntu/</a><br />
<a href="https://posit.co/download/rstudio-server/"
class="uri">https://posit.co/download/rstudio-server/</a><br />
<a
href="https://forum.posit.co/t/cant-start-rstudio-server-ubuntu-18-0-4-bionic/11835/3"
class="uri">https://forum.posit.co/t/cant-start-rstudio-server-ubuntu-18-0-4-bionic/11835/3</a><br />
<a
href="https://forum.posit.co/t/how-to-update-r-in-rstudio-server/102011"
class="uri">https://forum.posit.co/t/how-to-update-r-in-rstudio-server/102011</a></p>
</div>
</div>
</div>
</div>
<script>
// add bootstrap table styles to pandoc tables
function bootstrapStylePandocTables() {
$('tr.odd').parent('tbody').parent('table').addClass('table table-condensed');
}
$(document).ready(function () {
bootstrapStylePandocTables();
});
</script>
<!-- tabsets -->
<script>
$(document).ready(function () {
window.buildTabsets("TOC");
});
$(document).ready(function () {
$('.tabset-dropdown > .nav-tabs > li').click(function () {
$(this).parent().toggleClass('nav-tabs-open');
});
});
</script>
<!-- code folding -->
<!-- dynamically load mathjax for compatibility with self-contained -->
<script>
(function () {
var script = document.createElement("script");
script.type = "text/javascript";
script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";
document.getElementsByTagName("head")[0].appendChild(script);
})();
</script>
</body>
</html>