{"id":59,"date":"2013-09-26T16:54:53","date_gmt":"2013-09-26T16:54:53","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/icsf\/?page_id=59"},"modified":"2024-10-07T14:38:54","modified_gmt":"2024-10-07T14:38:54","slug":"rstudio","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/software\/applications\/rstudio\/","title":{"rendered":"RStudio"},"content":{"rendered":"<h2>Overview<\/h2>\n<p><a href=\"http:\/\/www.rstudio.com\">RStudio<\/a> is a user interface and development environment for <a href=\"http:\/\/www.r-project.org\/\">R<\/a>, the statistical computing environment.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>There are no access restrictions as it is free and open source software (AGPLv3 license)<\/p>\n<h2>Set up procedure<\/h2>\n<p>Load the modulefile according to how you are accessing the system and the version of Rstudio and R required (the R modulefile for the version indicated in the table will be loaded automatically):<\/p>\n<p><strong>PLEASE NOTE<\/strong>: See the <a href=\"\/icsf\/software\/applications\/r\/\">iCSF R page<\/a> for versions of R which could possibly be used with the <code>-any-r<\/code> Rstudio modulefiles listed below.<\/p>\n<ul>\n<li><strong>Rstudio 2024.09.0-any-r<\/strong> OR <strong>Rstudio 2024.04.2-any-r<\/strong> <strong>[RECOMMENDED]<\/strong> (for suitable versions of R modulefiles, which must be loaded <em>before<\/em> the R studio modulefile, please see the <a href=\"\/icsf\/software\/applications\/r\/#Versions_available\">R page<\/a>.)\n<pre>\r\n# <strong>Firstly, load an R modulefile<\/strong>\r\nmodule load apps\/gcc\/R\/<em>x.y.z<\/em>                      # See the R page for available versions of R\r\n                                                  # Latest is: apps\/gcc\/R\/4.4.1\r\n\r\n<strong># Secondly, load <em>one<\/em> of the following rstudio modulefiles<\/strong>\r\nmodule load apps\/binapps\/rstudio\/2024.09.0-any-r  # <strong>New October 2024<\/strong>\r\n\r\nmodule load apps\/binapps\/rstudio\/2024.04.2-any-r  # <strong>Mac users: this has been tested and works<\/strong>\r\n                                                  # <strong>on at least MacOS 13.6.4 with X2GO or<\/strong>\r\n                                                  # <strong>direct \"ssh -X incline2000\"<\/strong>\r\n<\/pre>\n<p>To test whether Rstudio is working and can display fonts in a plot, please try a simple example inside RStudio by running the command:<\/p>\n<pre>\r\n# This will only work if you've loaded a newer R modulefile recommended for the iCSF.\r\n# At the R &gt; prompt in rstudio, run this command:\r\nsource(file.path(Sys.getenv(\"REXAMPLE\"), \"vehicles.R\"))\r\n<\/pre>\n<p>Note that to make fonts work when using a Macbook, we have added the following line to the R code &#8211; you may need to use this in your own code:<\/p>\n<pre>options(bitmapType='cairo')\r\n<\/pre>\n<p>See the <a href=\"\/icsf\/software\/applications\/r\/#hints\">R Hints and Tips section<\/a> for an example R script that will display and graph with labels. We have tested that this works on Macbooks!<\/li>\n<\/ul>\n<div class=\"note\">\nIn newer versions of RStudio, there are some architectural changes implemented which prevents users from browsing\/selecting paths outside users home directory, if the default settings are not modified.<br \/>\nTo enable this functionality, go to:<\/p>\n<p><strong>Tools  >  Global Options<\/strong><\/p>\n<p>In the <strong>General<\/strong> section of the window that appears, click on <strong>Advanced tab<\/strong>.<\/p>\n<p>Under that menu, put a check mark in front of the line that says:<br \/>\n<strong>Use native file and message dialog boxes<\/strong><\/p>\n<p>Finally, click <strong>OK<\/strong>\n<\/div>\n<h3>Older versions<\/h3>\n<div class=\"note\">Versions below may not run correctly on the iCSF now that it has had an O\/S upgrade. If you are having problems with any of the versions below, please try a newer version (see above) <em>before<\/em> contacting the Research Infrastructure team. <strong>In any request for help, please indicate which versions you have tried<\/strong>.<\/div>\n<ul>\n<li><strong>Rstudio 2023.06.2-any-r<\/strong> (<strong>This version, and older versions below, may not run correctly on the incline2000 nodes!<\/strong>)\n<pre>module load apps\/gcc\/R\/<em>x.y.z<\/em>                      # See the R page for available versions of R\r\nmodule load apps\/binapps\/rstudio\/2023.06.2-any-r  # <strong>Mac users: you may need to use an older<\/strong>\r\n                                                  # <strong>version if this doesn't work when using x2go.<\/strong>\r\n                                                  # <strong>See below.<\/strong>\r\n<\/pre>\n<\/li>\n<li><strong>Rstudio 2022.07.2-any-r<\/strong>\n<pre>module load apps\/gcc\/R\/<em>x.y.z<\/em>\r\nmodule load apps\/binapps\/rstudio\/2022.07.2-any-r  # <strong>Mac users: you may need to use an older<\/strong>\r\n                                                  # <strong>version if this doesn't work when using x2go.<\/strong>\r\n                                                  # <strong>See below.<\/strong><\/pre>\n<\/li>\n<li><strong>Rstudio 1.3.1073-any-r<\/strong>\n<pre>module load apps\/gcc\/R\/<em>x.y.z<\/em>\r\nmodule load apps\/binapps\/rstudio\/1.3.1073-any-r  # <strong>Mac users: you may need to use an older<\/strong>\r\n                                                 # <strong>version if this doesn't work when using x2go.<\/strong>\r\n                                                 # <strong>See below.<\/strong>\r\n<\/pre>\n<\/li>\n<li><strong>Rstudio 1.2.5019<\/strong>\n<pre>module load apps\/gcc\/R\/<em>x.y.z<\/em>\r\nmodule load apps\/binapps\/rstudio\/1.2.5019-any-r<\/pre>\n<\/li>\n<li><strong>Rstudio 1.2.1335<\/strong>\n<pre>module load apps\/gcc\/R\/<em>x.y.z<\/em>\r\nmodule load apps\/binapps\/rstudio\/1.2.1335-any-r\r\n<\/pre>\n<\/li>\n<li><strong>Rstudio 1.1.423<\/strong>\n<pre>module load apps\/gcc\/R\/<em>x.y.z<\/em>\r\nmodule load apps\/binapps\/rstudio\/1.1.423-any-r\r\n<\/pre>\n<\/li>\n<li><strong>Rstudio 1.0.153<\/strong>\n<pre>module load apps\/gcc\/R\/<em>x.y.z<\/em>\r\nmodule load apps\/binapps\/rstudio\/1.0.153-any-r<\/pre>\n<\/li>\n<li><strong>Rstudio 0.98.1103<\/strong>\n<pre>module load apps\/gcc\/R\/<em>x.y.z<\/em>\r\nmodule load apps\/binapps\/rstudio\/0.98.1103-any-r<\/pre>\n<\/li>\n<li><strong>Rstudio 0.98.1103<\/strong> using R 3.4.2 specifically:\n<pre>module load apps\/gcc\/R\/3.4.2\r\nmodule load apps\/binapps\/rstudio\/0.98.1103-any-r\r\n<\/pre>\n<\/li>\n<li><strong>Rstudio 0.98.983<\/strong>\n<pre>module load apps\/gcc\/R\/<em>x.y.z<\/em>\r\nmodule load apps\/binapps\/rstudio\/0.98.983-any-r\r\n<\/pre>\n<\/li>\n<li><strong>Rstudio 0.98.983<\/strong> using R 3.1.0 specifically:\n<pre>module load apps\/binapps\/rstudio\/0.98.983\r\n<\/pre>\n<\/li>\n<li><strong>Rstudio 0.97.551<\/strong> (not recommended) using R 3.0.2 specifically:\n<pre>### If logging in from nyx3\/nyx4 virtual desktop:\r\nmodule load apps\/gcc\/rstudio\/0.97.551\r\n\r\n### If logging in via ssh (PuTTY\/MobaXterm\/ssh)\r\nmodule load apps\/binapps\/rstudio\/0.97.551\r\n<\/pre>\n<\/li>\n<\/ul>\n<h2>Running the application<\/h2>\n<p>Once you have loaded the modulefile use the following command to start RStudio:<\/p>\n<pre>rstudio\r\n<\/pre>\n<p>Once the RStudio user interface starts try running the following command in the console section if new to RSudio:<\/p>\n<pre>demo(graphics)\r\n\r\n<\/pre>\n<h2>Known issues<\/h2>\n<ul>\n<li>If you are having font display problems in a plot please try adding <code>options(bitmapType='cairo')<\/code> to the start of your plotting code (see the <a href=\"\/icsf\/software\/applications\/r\/#hints\">R &#8211; Hints and Tips section<\/a> for a sample R script.)<\/li>\n<li>If you see an error <code>segmentation fault<\/code> when you run rstudio then you have the wrong modulefile loaded for how you are accessing the iCSF.<\/li>\n<li>If you see an error &#8220;The SUID sandbox helper binary was found, but is not configured correctly. Rather than run without sandboxing I&#8217;m aborting now.&#8221;\u00a0 when you run rstudio 2023.06.2 then you need to run rstudio &#8211;no-sandbox.<\/li>\n<\/ul>\n<h2>Further info<\/h2>\n<p>RStudio <a href=\"http:\/\/www.rstudio.com\/ide\/docs\/\">online documentation<\/a>.<\/p>\n<p>If you need to add packages, please see the <a href=\"\/icsf\/software\/applications\/r\/\">iCSF R documenation<\/a> for further details.<\/p>\n<h2>Updates<\/h2>\n<p>None.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview RStudio is a user interface and development environment for R, the statistical computing environment. Restrictions on use There are no access restrictions as it is free and open source software (AGPLv3 license) Set up procedure Load the modulefile according to how you are accessing the system and the version of Rstudio and R required (the R modulefile for the version indicated in the table will be loaded automatically): PLEASE NOTE: See the iCSF R.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/software\/applications\/rstudio\/\">Read more &raquo;<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":43,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-59","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/59","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/comments?post=59"}],"version-history":[{"count":25,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/59\/revisions"}],"predecessor-version":[{"id":1457,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/59\/revisions\/1457"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/43"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/media?parent=59"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}