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<channel>
	<title>OLIO - A Miscellany</title>
	<atom:link href="http://olioinfo.net/blog/?feed=rss2" rel="self" type="application/rss+xml" />
	<link>http://olioinfo.net/blog</link>
	<description>A little of anything and everything</description>
	<lastBuildDate>Thu, 02 Sep 2010 14:57:27 +0000</lastBuildDate>
	<language>en</language>
	<sy:updatePeriod>hourly</sy:updatePeriod>
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		<item>
		<title>Maven and missing dependencies</title>
		<link>http://olioinfo.net/blog/?p=1654</link>
		<comments>http://olioinfo.net/blog/?p=1654#comments</comments>
		<pubDate>Thu, 02 Sep 2010 14:51:06 +0000</pubDate>
		<dc:creator>tracy</dc:creator>
				<category><![CDATA[Uncategorized]]></category>
		<category><![CDATA[dependencies]]></category>
		<category><![CDATA[maven]]></category>

		<guid isPermaLink="false">http://olioinfo.net/blog/?p=1654</guid>
		<description><![CDATA[If you can&#8217;t immediately resolve a Maven dependency, use the following sites to help you find it &#8211; try these in order. http://oss.sonatype.org/ http://repository.apache.org http://www.jarvana.com http://mvnrepository.com http://www.artifact-repository.org http://www.mvnbrowser.com http://mavensearch.net I normally jump to http://oss.sonatype.org/ and do a basic search. When I find the artifact I&#8217;m looking for, I select the entry and then look to [...]]]></description>
			<content:encoded><![CDATA[<p>If you can&#8217;t immediately resolve a Maven dependency, use the following sites to help you find it &#8211; try these in order.</p>
<ul>
<li><a href="http://oss.sonatype.org/">http://oss.sonatype.org/</a></li>
<li><a href="http://repository.apache.org">http://repository.apache.org</a></li>
<li><a href="http://www.jarvana.com">http://www.jarvana.com</a></li>
<li><a href="http://mvnrepository.com">http://mvnrepository.com</a></li>
<li><a href="http://www.artifact-repository.org">http://www.artifact-repository.org</a></li>
<li><a href="http://www.mvnbrowser.com">http://www.mvnbrowser.com</a></li>
<li><a href="http://mavensearch.net">http://mavensearch.net</a></li>
</ul>
<p>I normally jump to <a href="http://oss.sonatype.org/">http://oss.sonatype.org/</a> and do a basic search. When I find the artifact I&#8217;m looking for, I select the entry and then look to the lower detail area. The detail area provides:</p>
<ul>
<li>The repository that contains the artifact</li>
<li>The artifiact, the artifact pom and the maven dependency fragment</li>
</ul>
<p>This then should lead directly to the correct POM dependency entry, (and POM repository entry if needed).</p>
<p>A few screen shots to help you along.</p>
<p><a href="http://olioinfo.net/blog/wp-content/uploads/2010/09/OSS-Sonatype-1-small.png"><img class="alignnone size-full wp-image-1657" title="OSS-Sonatype-1-small" src="http://olioinfo.net/blog/wp-content/uploads/2010/09/OSS-Sonatype-1-small.png" alt="" width="640" height="130" /></a><a href="http://olioinfo.net/blog/wp-content/uploads/2010/09/OSS-Sonatype-3.png"></a></p>
<p><a href="http://olioinfo.net/blog/wp-content/uploads/2010/09/OSS-Sonatype-3.png"><img class="alignnone size-full wp-image-1658" title="OSS-Sonatype-3" src="http://olioinfo.net/blog/wp-content/uploads/2010/09/OSS-Sonatype-3.png" alt="" width="359" height="279" /></a></p>
<p><a href="http://olioinfo.net/blog/wp-content/uploads/2010/09/OSS-Sonatype-4.png"><img class="alignnone size-full wp-image-1660" title="OSS-Sonatype-4" src="http://olioinfo.net/blog/wp-content/uploads/2010/09/OSS-Sonatype-4.png" alt="" width="449" height="281" /></a></p>
<p><a href="http://olioinfo.net/blog/wp-content/uploads/2010/09/OSS-Sonatype-5.png"><img class="alignnone size-full wp-image-1661" title="OSS-Sonatype-5" src="http://olioinfo.net/blog/wp-content/uploads/2010/09/OSS-Sonatype-5.png" alt="" width="449" height="281" /></a></p>
]]></content:encoded>
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		</item>
		<item>
		<title>OS X and Apache Web server</title>
		<link>http://olioinfo.net/blog/?p=1649</link>
		<comments>http://olioinfo.net/blog/?p=1649#comments</comments>
		<pubDate>Mon, 23 Aug 2010 14:37:16 +0000</pubDate>
		<dc:creator>tracy</dc:creator>
				<category><![CDATA[Uncategorized]]></category>
		<category><![CDATA[apache2]]></category>
		<category><![CDATA[os x]]></category>
		<category><![CDATA[web server]]></category>

		<guid isPermaLink="false">http://olioinfo.net/blog/?p=1649</guid>
		<description><![CDATA[OS X Snow Leopard and the Apache Web server This is the server run from System Preferences &#62; Sharing &#62; Web Sharing The inspired location for configuration files is &#8230; wait for it &#8230;. /etc/apache2]]></description>
			<content:encoded><![CDATA[<p>OS X Snow Leopard and the Apache Web server</p>
<p>This is the server run from System Preferences &gt; Sharing &gt; Web Sharing</p>
<p>The inspired location for configuration files is &#8230; wait for it &#8230;. /etc/apache2</p>
]]></content:encoded>
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		</item>
		<item>
		<title>Netbeans 6.9.1 and Ruby debugging</title>
		<link>http://olioinfo.net/blog/?p=1640</link>
		<comments>http://olioinfo.net/blog/?p=1640#comments</comments>
		<pubDate>Sun, 22 Aug 2010 21:19:51 +0000</pubDate>
		<dc:creator>tracy</dc:creator>
				<category><![CDATA[Uncategorized]]></category>
		<category><![CDATA[debug]]></category>
		<category><![CDATA[debugging]]></category>
		<category><![CDATA[netbeans]]></category>
		<category><![CDATA[ruby]]></category>

		<guid isPermaLink="false">http://olioinfo.net/blog/?p=1640</guid>
		<description><![CDATA[Some notes made while trying to get Netbeans 6.9.1 to debug Rails applications running on various Ruby stacks. First and foremost, no success at all trying to use the Ruby debugging support internal to Netbeans with any combination of stacks based on Ruby MRI 1.8.6. Mind you, in every case, the code ran flawlessly under [...]]]></description>
			<content:encoded><![CDATA[<p>Some notes made while trying to get Netbeans 6.9.1 to debug Rails applications running on various Ruby stacks.</p>
<p>First and foremost, no success at all trying to use the Ruby debugging support internal to Netbeans with any combination of stacks based on Ruby MRI 1.8.6. Mind you, in every case, the code <span style="color: #ff0000;"><strong>ran</strong></span> flawlessly under Netbeans, just not in debug mode.</p>
<p>When trying to run attaching the debugger to an external Ruby interpreter running in debug mode, success every time.</p>
<p>Combinations that were tried and succeeded. Others too numerous to mention failed somewhere along &#8211; compile, install, etc.</p>
<table>
<thead>
<tr>
<th>OS</th>
<th>Ruby</th>
<th>RubyGems</th>
<th>ruby-debug-ide</th>
<th>ruby-debug-base</th>
<th>linecache</th>
</tr>
</thead>
<tbody>
<tr>
<td>OS X 10.6.4</td>
<td>1.8.6 p111</td>
<td>1.0.1</td>
<td>0.4.4</td>
<td>0.10.3</td>
<td>0.3</td>
</tr>
<tr>
<td>OS X 10.6.4</td>
<td>1.8.6 p111</td>
<td>1.3.3</td>
<td>0.4.9</td>
<td>0.10.3</td>
<td>0.43</td>
</tr>
<tr>
<td>OS X 10.6.4</td>
<td>1.8.6 p111</td>
<td>1.3.5</td>
<td>0.4.9</td>
<td>0.10.3</td>
<td>0.43</td>
</tr>
</tbody>
</table>
<p>No testing with Ruby debugging under jRuby in any combination. That&#8217;s yet to come.</p>
<p>A few conclusions (may be obvious to some!):</p>
<ul>
<li>The combination of Ruby and RubyGems version is critical</li>
<li>It seems, after RubyGems 1.1 (more likely 1.2), the debug support stabilized</li>
<li>With RubyGems 1.3.x, the latest debug support is likely the best.</li>
</ul>
<p>A final note, not particularly related to debugging, but rather to multiple Ruby platform support in Netbeans.</p>
<p>Using the same base version of Ruby for all the tests led to unmitigated user confusion when configuring the different stacks &#8211; Tools &gt; Ruby Platforms.</p>
<p>An egregious hack that hasn&#8217;t appeared to hurt anything  is to manually edit the file <em>~/.netbeans/6.9/build.properties</em> and add some text to the <em>ruby_version</em> tag for each different Ruby installation to differentiate one from another.</p>
<p><strong>An example</strong></p>
<p>In a console, run a command similar to:</p>
<p><code>rdebug-ide _0.4.9_ -p 7000 -d -- mongrel_rails start</code></p>
<p>Open the project in Netbeans, Debug &gt; Attach Debugger and accept the defaults.  Then use Netbeans debugging tools normally.</p>
]]></content:encoded>
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		</item>
		<item>
		<title>Ruby and Debugging</title>
		<link>http://olioinfo.net/blog/?p=1637</link>
		<comments>http://olioinfo.net/blog/?p=1637#comments</comments>
		<pubDate>Sun, 22 Aug 2010 21:05:17 +0000</pubDate>
		<dc:creator>tracy</dc:creator>
				<category><![CDATA[Uncategorized]]></category>
		<category><![CDATA[debug]]></category>
		<category><![CDATA[debugging]]></category>
		<category><![CDATA[ruby]]></category>

		<guid isPermaLink="false">http://olioinfo.net/blog/?p=1637</guid>
		<description><![CDATA[A small gathering of information about Ruby and debugging tools. All debugging tools for Ruby ultimately exploit the same feature of Ruby &#8211; the ability of the Ruby interpreter to single-step through code and set breakpoints.  Usually, two pieces are involved &#8211; the copy of the Ruby interpreter running the Ruby code in debug mode [...]]]></description>
			<content:encoded><![CDATA[<p>A small gathering of information about Ruby and debugging tools.</p>
<p>All debugging tools for Ruby ultimately exploit the same feature of Ruby &#8211; the ability of the Ruby interpreter to single-step through code and set breakpoints.  Usually, two pieces are involved &#8211; the copy of the Ruby interpreter running the Ruby code in debug mode and the program issuing debug commands (via an established interface).</p>
<p>Ruby comes with its own command-line debugger &#8211; rdebug. In this case, rdebug acts a shell that sends debug commands to the Ruby program executing in the same instance of Ruby. It involves a little trickery, but is no different in concept to any other debugging technique.</p>
<p>IDEs and other tools use essentially the same hooks, accessed through interfaces such as ruby-debug or ruby-debug-ide. In these cases, the IDE presents the source code and execution context of the program in a user-friendly fashion. When a user clicks on a breakpoint, or runs the program, the IDE sends an appropriate debug command to the Ruby interpreter running the application in debug mode.</p>
<p>When trying to understand why Ruby debugging sometimes doesn&#8217;t work, it helps to know that the following elements must all be in agreement:</p>
<ul>
<li>The version of the OS</li>
<li>The Ruby interpreter and the debugging interface it makes available</li>
<li>The version of RubyGems</li>
<li>The library that provides &#8216;packaged&#8217; access to the debugging interface (usually ruby-debug-ide or ruby-debug)</li>
<li>The implementation of the Ruby debug support in the IDE</li>
</ul>
<p>There is no magic solution here &#8211; a lot of googling and trial and error.</p>
<p><strong>An example</strong></p>
<p>It is instructive to set up an IDE to debug Ruby externally, connect to a command-line instance of the program being debugged, and watch the debug console.</p>
<p>In a console window, in the directory containing the program, issue a command similar to:</p>
<p><code>rdebug-ide _0.4.9_ -p 7000 -d -- mongrel_rails start<br />
</code></p>
<p>In the IDE of choice,  open up the application and attach to the remote debugging session &#8211; in this case running on localhost on port 7000.</p>
<p>Issue breakpoints, run commands, variable inspections in the IDE and watch the activity in the console window.</p>
]]></content:encoded>
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		</item>
		<item>
		<title>Ruby on Rails startup errors</title>
		<link>http://olioinfo.net/blog/?p=1635</link>
		<comments>http://olioinfo.net/blog/?p=1635#comments</comments>
		<pubDate>Sun, 22 Aug 2010 14:25:03 +0000</pubDate>
		<dc:creator>tracy</dc:creator>
				<category><![CDATA[Uncategorized]]></category>
		<category><![CDATA[rails]]></category>
		<category><![CDATA[ruby]]></category>

		<guid isPermaLink="false">http://olioinfo.net/blog/?p=1635</guid>
		<description><![CDATA[Ruby on Rails startup errors If you see something similar to the following when starting Rails: !!! Path to log file not valid: log/m All you need to do is to create the ./log directory.]]></description>
			<content:encoded><![CDATA[<p>Ruby on Rails startup errors</p>
<p>If you see something similar to the following when starting Rails:</p>
<p>!!! Path to log file not valid: log/m</p>
<p>All you need to do is to create the ./log directory.</p>
]]></content:encoded>
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		</item>
		<item>
		<title>Ruby &#8211; internal configuration information</title>
		<link>http://olioinfo.net/blog/?p=1632</link>
		<comments>http://olioinfo.net/blog/?p=1632#comments</comments>
		<pubDate>Fri, 20 Aug 2010 17:50:35 +0000</pubDate>
		<dc:creator>tracy</dc:creator>
				<category><![CDATA[Uncategorized]]></category>
		<category><![CDATA[configuration]]></category>
		<category><![CDATA[ruby]]></category>

		<guid isPermaLink="false">http://olioinfo.net/blog/?p=1632</guid>
		<description><![CDATA[Ruby &#8211; to see Ruby internal configuration information require 'rbconfig' Config::CONFIG.inspect More usefully, something like: Config::CONFIG["prefix"] List of properties: DESTDIR INSTALL prefix EXEEXT ruby_install_name RUBY_INSTALL_NAME RUBY_SO_NAME SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACKAGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix bindir sbindir libexecdir datarootdir datadir sysconfdir sharedstatedir localstatedir includedir oldincludedir docdir infodir htmldir dvidir pdfdir psdir libdir localedir mandir ECHO_C ECHO_N [...]]]></description>
			<content:encoded><![CDATA[<p>Ruby &#8211; to see Ruby internal configuration information</p>
<p><code>require 'rbconfig'<br />
Config::CONFIG.inspect</code></p>
<p>More usefully, something like:</p>
<p><code>Config::CONFIG["prefix"]</code></p>
<p>List of properties:</p>
<ul>
<li>DESTDIR</li>
<li>INSTALL</li>
<li>prefix</li>
<li>EXEEXT</li>
<li>ruby_install_name</li>
<li>RUBY_INSTALL_NAME</li>
<li>RUBY_SO_NAME</li>
<li>SHELL</li>
<li>PATH_SEPARATOR</li>
<li>PACKAGE_NAME</li>
<li>PACKAGE_TARNAME</li>
<li>PACKAGE_VERSION</li>
<li>PACKAGE_STRING</li>
<li>PACKAGE_BUGREPORT</li>
<li>exec_prefix</li>
<li>bindir</li>
<li>sbindir</li>
<li>libexecdir</li>
<li>datarootdir</li>
<li>datadir</li>
<li>sysconfdir</li>
<li>sharedstatedir</li>
<li>localstatedir</li>
<li>includedir</li>
<li>oldincludedir</li>
<li>docdir</li>
<li>infodir</li>
<li>htmldir</li>
<li>dvidir</li>
<li>pdfdir</li>
<li>psdir</li>
<li>libdir</li>
<li>localedir</li>
<li>mandir</li>
<li>ECHO_C</li>
<li>ECHO_N</li>
<li>ECHO_T</li>
<li>LIBS</li>
<li>build_alias</li>
<li>host_alias</li>
<li>target_alias</li>
<li>MAJOR</li>
<li>MINOR</li>
<li>TEENY</li>
<li>build</li>
<li>build_cpu</li>
<li>build_vendor</li>
<li>build_os</li>
<li>host</li>
<li>host_cpu</li>
<li>host_vendor</li>
<li>host_os</li>
<li>target</li>
<li>target_cpu</li>
<li>target_vendor</li>
<li>target_os</li>
<li>CC</li>
<li>CFLAGS</li>
<li>LDFLAGS</li>
<li>CPPFLAGS</li>
<li>OBJEXT</li>
<li>CPP</li>
<li>GREP</li>
<li>EGREP</li>
<li>GNU_LD</li>
<li>CPPOUTFILE</li>
<li>OUTFLAG</li>
<li>YACC</li>
<li>YFLAGS</li>
<li>RANLIB</li>
<li>AR</li>
<li>AS</li>
<li>ASFLAGS</li>
<li>NM</li>
<li>WINDRES</li>
<li>DLLWRAP</li>
<li>OBJDUMP</li>
<li>LN_S</li>
<li>SET_MAKE</li>
<li>INSTALL_PROGRAM</li>
<li>INSTALL_SCRIPT</li>
<li>INSTALL_DATA</li>
<li>RM</li>
<li>CP</li>
<li>MAKEDIRS</li>
<li>ALLOCA</li>
<li>DLDFLAGS</li>
<li>ARCH_FLAG</li>
<li>STATIC</li>
<li>CCDLFLAGS</li>
<li>LDSHARED</li>
<li>DLEXT</li>
<li>DLEXT2</li>
<li>LIBEXT</li>
<li>LINK_SO</li>
<li>LIBPATHFLAG</li>
<li>RPATHFLAG</li>
<li>LIBPATHENV</li>
<li>TRY_LINK</li>
<li>STRIP</li>
<li>EXTSTATIC</li>
<li>setup</li>
<li>MINIRUBY</li>
<li>PREP</li>
<li>RUNRUBY</li>
<li>EXTOUT</li>
<li>ARCHFILE</li>
<li>RDOCTARGET</li>
<li>XCFLAGS</li>
<li>XLDFLAGS</li>
<li>LIBRUBY_LDSHARED</li>
<li>LIBRUBY_DLDFLAGS</li>
<li>rubyw_install_name</li>
<li>RUBYW_INSTALL_NAME</li>
<li>LIBRUBY_A</li>
<li>LIBRUBY_SO</li>
<li>LIBRUBY_ALIASES</li>
<li>LIBRUBY</li>
<li>LIBRUBYARG</li>
<li>LIBRUBYARG_STATIC</li>
<li>LIBRUBYARG_SHARED</li>
<li>SOLIBS</li>
<li>DLDLIBS</li>
<li>ENABLE_SHARED</li>
<li>MAINLIBS</li>
<li>COMMON_LIBS</li>
<li>COMMON_MACROS</li>
<li>COMMON_HEADERS</li>
<li>EXPORT_PREFIX</li>
<li>MAKEFILES</li>
<li>arch</li>
<li>sitearch</li>
<li>sitedir</li>
<li>configure_args</li>
<li>NROFF</li>
<li>MANTYPE</li>
<li>ruby_version</li>
<li>rubylibdir</li>
<li>archdir</li>
<li>sitelibdir</li>
<li>sitearchdir</li>
<li>topdir</li>
<li>CONFIG.each{|k,v| MAKEFILE_CONFIG[k] = v.dup}</li>
</ul>
]]></content:encoded>
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		</item>
		<item>
		<title>OS X and Apache Web server</title>
		<link>http://olioinfo.net/blog/?p=1629</link>
		<comments>http://olioinfo.net/blog/?p=1629#comments</comments>
		<pubDate>Tue, 17 Aug 2010 17:08:28 +0000</pubDate>
		<dc:creator>tracy</dc:creator>
				<category><![CDATA[Uncategorized]]></category>
		<category><![CDATA[apache]]></category>
		<category><![CDATA[os x]]></category>

		<guid isPermaLink="false">http://olioinfo.net/blog/?p=1629</guid>
		<description><![CDATA[How to configure and run the Apache Web server included on OS X]]></description>
			<content:encoded><![CDATA[<p>How to configure and run the Apache Web server included on OS X</p>
]]></content:encoded>
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		</item>
		<item>
		<title>Netbeans 6.9.1 and Ruby debugging</title>
		<link>http://olioinfo.net/blog/?p=1624</link>
		<comments>http://olioinfo.net/blog/?p=1624#comments</comments>
		<pubDate>Tue, 17 Aug 2010 01:25:57 +0000</pubDate>
		<dc:creator>tracy</dc:creator>
				<category><![CDATA[Uncategorized]]></category>

		<guid isPermaLink="false">http://olioinfo.net/blog/?p=1624</guid>
		<description><![CDATA[A quick trial with Netbeans 6.9.1 and Ruby 1.8.6 demonstrated a need for ruby-debug-ide 0.4.x Download from ruby-debug-ide-0.4.4 (0.4.4 builds under Snow Leopard, ruby 1.8.6, rubygems 1.0.1). Needs ruby-debug-base-0.10.3.zip]]></description>
			<content:encoded><![CDATA[<p>A quick trial with Netbeans 6.9.1 and Ruby 1.8.6 demonstrated a need for</p>
<pre>ruby-debug-ide 0.4.x
</pre>
<p>Download from <a href="http://olioinfo.net/blog/wp-content/uploads/2010/08/ruby-debug-ide-0.4.4.zip">ruby-debug-ide-0.4.4</a> (0.4.4 builds under Snow Leopard, ruby 1.8.6, rubygems 1.0.1).</p>
<p>Needs <a href="http://olioinfo.net/blog/wp-content/uploads/2010/08/ruby-debug-base-0.10.3.zip">ruby-debug-base-0.10.3.zip</a></p>
]]></content:encoded>
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		</item>
		<item>
		<title>Post using Curl</title>
		<link>http://olioinfo.net/blog/?p=1611</link>
		<comments>http://olioinfo.net/blog/?p=1611#comments</comments>
		<pubDate>Sat, 31 Jul 2010 07:03:08 +0000</pubDate>
		<dc:creator>tracy</dc:creator>
				<category><![CDATA[Uncategorized]]></category>
		<category><![CDATA[curl]]></category>

		<guid isPermaLink="false">http://olioinfo.net/blog/?p=1611</guid>
		<description><![CDATA[To send an HTTP POST using curl echo '&#60;doc&#62;&#60;item&#62;Some content.&#60;/item&#62;&#60;/doc&#62;' &#124; curl -X POST -H 'Content-type: text/xml' -d @- http://example.com/restapi]]></description>
			<content:encoded><![CDATA[<p>To send an HTTP POST using curl</p>
<pre>echo '&lt;doc&gt;&lt;item&gt;Some content.&lt;/item&gt;&lt;/doc&gt;' |
  curl -X POST -H 'Content-type: text/xml' -d @- http://example.com/restapi</pre>
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		<item>
		<title>OpenSSL and message digests</title>
		<link>http://olioinfo.net/blog/?p=1608</link>
		<comments>http://olioinfo.net/blog/?p=1608#comments</comments>
		<pubDate>Sun, 25 Jul 2010 10:21:15 +0000</pubDate>
		<dc:creator>tracy</dc:creator>
				<category><![CDATA[Uncategorized]]></category>
		<category><![CDATA[digest]]></category>
		<category><![CDATA[openssl]]></category>

		<guid isPermaLink="false">http://olioinfo.net/blog/?p=1608</guid>
		<description><![CDATA[To use OpenSSL to generate message digests from the command line specify: openssl dgst -&#60;digest type&#62; &#60;file name&#62; For example, to get the MD5 checksum for file &#8216;some.jar&#8217;: openssl dgst -md5 some.jar]]></description>
			<content:encoded><![CDATA[<p>To use OpenSSL to generate message digests from the command line specify:</p>
<pre>openssl dgst -&lt;digest type&gt; &lt;file name&gt;</pre>
<p>For example, to get the MD5 checksum for file &#8216;some.jar&#8217;:</p>
<pre>openssl dgst -md5 some.jar</pre>
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