{
  "version": "https://jsonfeed.org/version/1.1",
  "title": "chem-bla-ics",
  "description": "Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.",
  "home_page_url": "https://chem-bla-ics.linkedchemistry.info/",
  "feed_url": "https://chem-bla-ics.linkedchemistry.info/2011/02/01/diy-running-r-from-within-bioclipse.json",
  "icon": "https://chem-bla-ics.linkedchemistry.info/assets/images/chem-bla-ics_logo.png",
  "language": "en",
  "authors": [
    {
      "name": "Egon Willighagen",
      "url": "https://orcid.org/0000-0001-7542-0286",
      "_orcid": "0000-0001-7542-0286"
    }
  ],
  "items": [

    {
      "id": "https://doi.org/10.59350/rqgjr-7b013",
      "url": "https://chem-bla-ics.linkedchemistry.info/2011/02/01/diy-running-r-from-within-bioclipse.html",
      "title": "DIY: Running R from within Bioclipse",
      "content_html": "<p><strong>Important: this blog post is about a development version of Bioclipse, not\nabout the stable 2.4 series. See also Gilleain’s comment for this post.</strong></p>\n\n<p>Arvid has done an excellent job in setting up <a href=\"http://pele.farmbio.uu.se/hudson/\">Hudson for Bioclipse</a>,\nwhich is not so trivial as for Maven projects. With the <a href=\"http://chem-bla-ics.blogspot.com/2011/02/running-r-from-within-bioclipse.html\">R functionality</a>\nI blogged about earlier today moved to the <a href=\"https://github.com/bioclipse/bioclipse.statistics\">bioclipse.statistics repository</a>,\nthings are automatically build when new patches hit the repository. And Hudson\ndoesn’t just compile the code, it also exports binaries. The main <a href=\"http://www.bioclipse.net/\">Bioclipse</a>\nproducts build can be downloaded <a href=\"http://pele.farmbio.uu.se/hudson/job/Bioclipse.product/\">here</a>\n(Windows, Linux, OS/X; if you need more, please let use know). And, all the\nadditional features got automatically uploaded to individual update sites, very\nmuch like Maven projects getting pushed to a Maven repository.</p>\n\n<p>So, here’s an Bioclipse-R install guide for the adventurous (i.e. Christian,\nRajarshi and Rebecca, perhaps Juuso :). I will describe it from a <a href=\"http://www.debian.org/\">Debian GNU/Linux</a>\nperspective.</p>\n\n<p>First, make sure you have <a href=\"http://www.r-project.org/\">R</a> and <a href=\"http://cran.r-project.org/web/packages/rJava/index.html\">rJava</a>\ninstalled. I strongly recommend the versions from <a href=\"http://www.debian.org/releases/unstable/\">sid/unstable</a>\n(2.12 and 0.8-8), which are more stable here than those from <a href=\"http://www.debian.org/releases/testing/\">testing</a>:</p>\n\n<div class=\"language-shell highlighter-rouge\"><div class=\"highlight\"><pre class=\"highlight\"><code>apt-get <span class=\"nb\">install </span>r-base-core/sid r-cran-rjava/sid\n</code></pre></div></div>\n\n<p>Then you download the nightly build of Bioclipse 2.5.x from Hudson, e.g. for\nmy 32bit Linux:</p>\n\n<div class=\"language-shell highlighter-rouge\"><div class=\"highlight\"><pre class=\"highlight\"><code><span class=\"nb\">cd</span> /tmp\nwget http://pele.farmbio.uu.se/hudson/job/Bioclipse.product/lastSuccessfulBuild/artifact/tmp/bioclipse/net.bioclipse.platform_feature_2.4.0-eclipse.feature/Bioclipse.2.5.0.linux.gtk.x86.zip\nunzip Bioclipse.2.5.0.linux.gtk.x86.zip\n<span class=\"nb\">cd </span>Bioclipse.2.5.0.linux.gtk.x86/&lt;/pre&gt;\n</code></pre></div></div>\n<p>But before we boot Bioclipse, we first need to tell it where to find the R instance,\nand we need to set two variables for that: <em>R_HOME</em> and <em>java.library.path</em>.\nThe latter is set via the <em>bioclipse.ini</em> file, by adding this line to the end:</p>\n\n<div class=\"language-shell highlighter-rouge\"><div class=\"highlight\"><pre class=\"highlight\"><code><span class=\"nt\">-Djava</span>.library.path<span class=\"o\">=</span>/usr/lib/R/site-library/rJava/jri\n</code></pre></div></div>\n\n<p>The other is an environment variable and can be set with:</p>\n\n<div class=\"language-shell highlighter-rouge\"><div class=\"highlight\"><pre class=\"highlight\"><code><span class=\"nb\">export </span><span class=\"nv\">R_HOME</span><span class=\"o\">=</span>//usr/lib/R\n</code></pre></div></div>\n\n<p>Then Bioclipse can be started:</p>\n\n<div class=\"language-shell highlighter-rouge\"><div class=\"highlight\"><pre class=\"highlight\"><code>./bioclipse\n</code></pre></div></div>\n\n<p>The first thing to do is install the <em>R Feature</em>. To do this open the <em>Install\nNew Software…</em> dialog from the <em>Help</em> menu, and add (with the <em>Add</em> button)\nthe Bioclipse Statistics update site on Hudson at <a href=\"http://pele.farmbio.uu.se/hudson/view/Release/job/Bioclipse.statistics/lastSuccessfulBuild/artifact/buckminster.output/net.bioclipse.statistics_site_1.0.0-eclipse.feature/site.p2/\">this Location</a>\n(copy/paste the Location URL into the below dialog):</p>\n\n<p><img src=\"/assets/images/bc26statsUpdateSite3.png\" alt=\"\" /></p>\n\n<p>When back in the Available Software dialog, select the new update site, and\nmark the <em>Bioclipse-R Integration</em> feature to be installed:</p>\n\n<p><img src=\"/assets/images/bc26statsUpdateSite2.png\" alt=\"\" /></p>\n\n<p>After the install is completed, which will require a reboot of Bioclipse (why?!?!),\nyou can open the R console by opening a dialog from the Window -&gt; Show View -&gt;\nOther… menu:</p>\n\n<p><img src=\"/assets/images/bc26statsUpdateSite4.png\" alt=\"\" /></p>\n\n<p>The <em>R Console</em> will then show up as view, as depicted in my <a href=\"http://chem-bla-ics.blogspot.com/2011/02/running-r-from-within-bioclipse.html\">earlier post</a>.</p>\n\n<p>Loading of libraries, like running <em>library(“<a href=\"http://cran.r-project.org/web/packages/rcdk/index.html\">rcdk</a>”)</em>\nor <em>library(“<a href=\"http://cran.r-project.org/web/packages/pls/index.html\">pls</a>”)</em>,\ncrashes the whole thing if you use R and rJava from Debian testing, and silently\nfails with those from unstable. It’s on my agenda.</p>",
      "summary": "Important: this blog post is about a development version of Bioclipse, not about the stable 2.4 series. See also Gilleain’s comment for this post.",
      "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/bc26statsUpdateSite3.png",
      "date_published": "2011-02-01T00:10:00+00:00",
      "date_modified": "2011-02-01T00:10:00+00:00",
      "tags": ["bioclipse","chemometrics"],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}