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Package 544/658HostnameOS / ArchBUILDCHECKBUILD BIN
RMassBank 1.1.1
Michael Stravs, Emma Schymanski
Snapshot Date: 2013-03-23 17:02:20 -0700 (Sat, 23 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RMassBank
Last Changed Rev: 74064 / Revision: 74756
Last Changed Date: 2013-03-08 02:48:57 -0800 (Fri, 08 Mar 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  ERROR 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  ERROR  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK [ ERROR ] OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK  ERROR  OK 

Summary

Package: RMassBank
Version: 1.1.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R --arch x86_64 CMD check --no-vignettes --timings --no-multiarch RMassBank_1.1.1.tar.gz
StartedAt: 2013-03-24 04:27:28 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-24 04:29:29 -0700 (Sun, 24 Mar 2013)
EllapsedTime: 121.7 seconds
RetCode: 1
Status:  ERROR 
CheckDir: RMassBank.Rcheck
Warnings: NA

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/RMassBank.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: x86_64-apple-darwin9.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'RMassBank/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RMassBank' version '1.1.1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'RMassBank' can be installed ... [13s/13s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... ERROR
Running examples in 'RMassBank-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getCtsRecord
> ### Title: Retrieve information from CTS
> ### Aliases: getCtsRecord
> 
> ### ** Examples
> 
> getCtsRecord("benzene", "name")
<html>
<head>
  <title>CTS: Chemical Translation Service</title>

  <link rel="stylesheet" href="/cts/css/main.css"/>

  <style type="text/css">@import url("/cts/css/pagination.css");</style>
  <style type="text/css">@import url("/cts/css/font.css");</style>


  <!--
  <link rel="shortcut icon" href="/cts/images/favicon.ico" type="image/x-icon"/>
  -->

  
  <meta name="layout" content="main"/>


  <script type="text/javascript" src="/cts/js/application.js"></script>

  <script type="text/javascript" src="/cts/js/prototype/prototype.js"></script>


  <meta name="layout" content="main"/>

</head>
<body class="BodyBackground">
<div id="spinner" class="spinner" style="display:none;">
  <img src="/cts/images/spinner.gif" alt="Spinner"/>
</div>

<!-- testing for the browser and print an error message in case they use the internet explorer -->
<script type="text/javascript">

  if (navigator.appName == 'Microsoft Internet Explorer') {
    document.write('<div class=\"box\"><div class=\"errors-center\" >we recommend that you use Firefox, Safari or Google Chrome for the best expirience! Right now you are using the Microsoft Internet Eplorer and we do not actively support or recommend it!</div></div>');
  }

</script>




<div id="main">

  <div class="page_header">
    Chemical Translation Service
  </div>


  <div class="box">
    <h3><a href="/cts/homePage/index" class="home">Home</a></h3>
    <div class="line"></div>

  </div>

  <div class="box">

    <h3>Ooops, what did just happen?</h3>

    <div class="line"></div>

    <div class="message">
      oh dear this is rather embarissing, but it looks like you discovered a bug. To help us avoiding this in the future, would you mind to send a bug report to <a href="mailto:wohlgemuth@ucdavis.edu">Gert Wohlgemuth</a> with as many informations as possible, so we can reproduce this and fix it!

    </div>

    <h3>Error Details</h3>

    <div class="line"></div>

    <div class="errors">
      <strong>Error 500:</strong> Cannot load default configuration from jar<br/>
      <strong>Servlet:</strong> default<br/>
      <strong>URI:</strong> /cts/massLookup/masstransform<br/>

      
        <strong>Exception Message:</strong> Cannot load default configuration from jar <br/>
        <strong>Caused by:</strong> Cannot load default configuration from jar <br/>
        <strong>Class:</strong> Unknown <br/>
        <strong>At Line:</strong> [-1] <br/>
        <strong>Code Snippet:</strong><br/>
        <div class="snippet">
          
        </div>
      

    </div>

    
      <h3>Stack Trace</h3>

      <div class="line"></div>

      <div class="errors">
        <pre>java.lang.IllegalStateException: Cannot load default configuration from jar
<br/>	at org.codehaus.groovy.grails.web.sitemesh.Grails5535Factory.loadSitemeshXML(Grails5535Factory.java:146)
<br/>	at org.codehaus.groovy.grails.web.sitemesh.Grails5535Factory.loadConfig(Grails5535Factory.java:73)
<br/>	at org.codehaus.groovy.grails.web.sitemesh.Grails5535Factory.refresh(Grails5535Factory.java:272)
<br/>	at com.opensymphony.module.sitemesh.Factory.getInstance(Factory.java:56)
<br/>	at com.opensymphony.sitemesh.webapp.SiteMeshFilter.initContentProcessor(SiteMeshFilter.java:107)
<br/>	at org.codehaus.groovy.grails.web.sitemesh.GrailsPageFilter.doFilter(GrailsPageFilter.java:114)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.codehaus.groovy.grails.web.servlet.mvc.GrailsWebRequestFilter.doFilterInternal(GrailsWebRequestFilter.java:69)
<br/>	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.codehaus.groovy.grails.web.filters.HiddenHttpMethodFilter.doFilterInternal(HiddenHttpMethodFilter.java:69)
<br/>	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:88)
<br/>	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76)
<br/>	at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:237)
<br/>	at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:167)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:474)
<br/>	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:119)
<br/>	at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:480)
<br/>	at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:226)
<br/>	at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:935)
<br/>	at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:404)
<br/>	at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:184)
<br/>	at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:870)
<br/>	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:117)
<br/>	at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:247)
<br/>	at org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:151)
<br/>	at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116)
<br/>	at org.eclipse.jetty.server.Server.handle(Server.java:346)
<br/>	at org.eclipse.jetty.server.HttpConnection.handleRequest(HttpConnection.java:596)
<br/>	at org.eclipse.jetty.server.HttpConnection$RequestHandler.headerComplete(HttpConnection.java:1051)
<br/>	at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:592)
<br/>	at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:214)
<br/>	at org.eclipse.jetty.server.HttpConnection.handle(HttpConnection.java:426)
<br/>	at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(SelectChannelEndPoint.java:520)
<br/>	at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectChannelEndPoint.java:40)
<br/>	at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:528)
<br/>	at java.lang.Thread.run(Thread.java:619)
<br/></pre>
      </div>
    

  </div>

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<!-- google anlytics, do not change -->

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</html>:36: parser error : AttValue: " or ' expected
    document.write('<div class=\"box\"><div class=\"errors-center\" >we recommen
                               ^
<html>
<head>
  <title>CTS: Chemical Translation Service</title>

  <link rel="stylesheet" href="/cts/css/main.css"/>

  <style type="text/css">@import url("/cts/css/pagination.css");</style>
  <style type="text/css">@import url("/cts/css/font.css");</style>


  <!--
  <link rel="shortcut icon" href="/cts/images/favicon.ico" type="image/x-icon"/>
  -->

  
  <meta name="layout" content="main"/>


  <script type="text/javascript" src="/cts/js/application.js"></script>

  <script type="text/javascript" src="/cts/js/prototype/prototype.js"></script>


  <meta name="layout" content="main"/>

</head>
<body class="BodyBackground">
<div id="spinner" class="spinner" style="display:none;">
  <img src="/cts/images/spinner.gif" alt="Spinner"/>
</div>

<!-- testing for the browser and print an error message in case they use the internet explorer -->
<script type="text/javascript">

  if (navigator.appName == 'Microsoft Internet Explorer') {
    document.write('<div class=\"box\"><div class=\"errors-center\" >we recommend that you use Firefox, Safari or Google Chrome for the best expirience! Right now you are using the Microsoft Internet Eplorer and we do not actively support or recommend it!</div></div>');
  }

</script>




<div id="main">

  <div class="page_header">
    Chemical Translation Service
  </div>


  <div class="box">
    <h3><a href="/cts/homePage/index" class="home">Home</a></h3>
    <div class="line"></div>

  </div>

  <div class="box">

    <h3>Ooops, what did just happen?</h3>

    <div class="line"></div>

    <div class="message">
      oh dear this is rather embarissing, but it looks like you discovered a bug. To help us avoiding this in the future, would you mind to send a bug report to <a href="mailto:wohlgemuth@ucdavis.edu">Gert Wohlgemuth</a> with as many informations as possible, so we can reproduce this and fix it!

    </div>

    <h3>Error Details</h3>

    <div class="line"></div>

    <div class="errors">
      <strong>Error 500:</strong> Cannot load default configuration from jar<br/>
      <strong>Servlet:</strong> default<br/>
      <strong>URI:</strong> /cts/massLookup/masstransform<br/>

      
        <strong>Exception Message:</strong> Cannot load default configuration from jar <br/>
        <strong>Caused by:</strong> Cannot load default configuration from jar <br/>
        <strong>Class:</strong> Unknown <br/>
        <strong>At Line:</strong> [-1] <br/>
        <strong>Code Snippet:</strong><br/>
        <div class="snippet">
          
        </div>
      

    </div>

    
      <h3>Stack Trace</h3>

      <div class="line"></div>

      <div class="errors">
        <pre>java.lang.IllegalStateException: Cannot load default configuration from jar
<br/>	at org.codehaus.groovy.grails.web.sitemesh.Grails5535Factory.loadSitemeshXML(Grails5535Factory.java:146)
<br/>	at org.codehaus.groovy.grails.web.sitemesh.Grails5535Factory.loadConfig(Grails5535Factory.java:73)
<br/>	at org.codehaus.groovy.grails.web.sitemesh.Grails5535Factory.refresh(Grails5535Factory.java:272)
<br/>	at com.opensymphony.module.sitemesh.Factory.getInstance(Factory.java:56)
<br/>	at com.opensymphony.sitemesh.webapp.SiteMeshFilter.initContentProcessor(SiteMeshFilter.java:107)
<br/>	at org.codehaus.groovy.grails.web.sitemesh.GrailsPageFilter.doFilter(GrailsPageFilter.java:114)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.codehaus.groovy.grails.web.servlet.mvc.GrailsWebRequestFilter.doFilterInternal(GrailsWebRequestFilter.java:69)
<br/>	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.codehaus.groovy.grails.web.filters.HiddenHttpMethodFilter.doFilterInternal(HiddenHttpMethodFilter.java:69)
<br/>	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:88)
<br/>	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76)
<br/>	at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:237)
<br/>	at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:167)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:474)
<br/>	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:119)
<br/>	at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:480)
<br/>	at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:226)
<br/>	at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:935)
<br/>	at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:404)
<br/>	at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:184)
<br/>	at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:870)
<br/>	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:117)
<br/>	at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:247)
<br/>	at org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:151)
<br/>	at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116)
<br/>	at org.eclipse.jetty.server.Server.handle(Server.java:346)
<br/>	at org.eclipse.jetty.server.HttpConnection.handleRequest(HttpConnection.java:596)
<br/>	at org.eclipse.jetty.server.HttpConnection$RequestHandler.headerComplete(HttpConnection.java:1051)
<br/>	at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:592)
<br/>	at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:214)
<br/>	at org.eclipse.jetty.server.HttpConnection.handle(HttpConnection.java:426)
<br/>	at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(SelectChannelEndPoint.java:520)
<br/>	at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectChannelEndPoint.java:40)
<br/>	at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:528)
<br/>	at java.lang.Thread.run(Thread.java:619)
<br/></pre>
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</html>:36: parser error : attributes construct error
    document.write('<div class=\"box\"><div class=\"errors-center\" >we recommen
                               ^
<html>
<head>
  <title>CTS: Chemical Translation Service</title>

  <link rel="stylesheet" href="/cts/css/main.css"/>

  <style type="text/css">@import url("/cts/css/pagination.css");</style>
  <style type="text/css">@import url("/cts/css/font.css");</style>


  <!--
  <link rel="shortcut icon" href="/cts/images/favicon.ico" type="image/x-icon"/>
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  <meta name="layout" content="main"/>


  <script type="text/javascript" src="/cts/js/application.js"></script>

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  }

</script>




<div id="main">

  <div class="page_header">
    Chemical Translation Service
  </div>


  <div class="box">
    <h3><a href="/cts/homePage/index" class="home">Home</a></h3>
    <div class="line"></div>

  </div>

  <div class="box">

    <h3>Ooops, what did just happen?</h3>

    <div class="line"></div>

    <div class="message">
      oh dear this is rather embarissing, but it looks like you discovered a bug. To help us avoiding this in the future, would you mind to send a bug report to <a href="mailto:wohlgemuth@ucdavis.edu">Gert Wohlgemuth</a> with as many informations as possible, so we can reproduce this and fix it!

    </div>

    <h3>Error Details</h3>

    <div class="line"></div>

    <div class="errors">
      <strong>Error 500:</strong> Cannot load default configuration from jar<br/>
      <strong>Servlet:</strong> default<br/>
      <strong>URI:</strong> /cts/massLookup/masstransform<br/>

      
        <strong>Exception Message:</strong> Cannot load default configuration from jar <br/>
        <strong>Caused by:</strong> Cannot load default configuration from jar <br/>
        <strong>Class:</strong> Unknown <br/>
        <strong>At Line:</strong> [-1] <br/>
        <strong>Code Snippet:</strong><br/>
        <div class="snippet">
          
        </div>
      

    </div>

    
      <h3>Stack Trace</h3>

      <div class="line"></div>

      <div class="errors">
        <pre>java.lang.IllegalStateException: Cannot load default configuration from jar
<br/>	at org.codehaus.groovy.grails.web.sitemesh.Grails5535Factory.loadSitemeshXML(Grails5535Factory.java:146)
<br/>	at org.codehaus.groovy.grails.web.sitemesh.Grails5535Factory.loadConfig(Grails5535Factory.java:73)
<br/>	at org.codehaus.groovy.grails.web.sitemesh.Grails5535Factory.refresh(Grails5535Factory.java:272)
<br/>	at com.opensymphony.module.sitemesh.Factory.getInstance(Factory.java:56)
<br/>	at com.opensymphony.sitemesh.webapp.SiteMeshFilter.initContentProcessor(SiteMeshFilter.java:107)
<br/>	at org.codehaus.groovy.grails.web.sitemesh.GrailsPageFilter.doFilter(GrailsPageFilter.java:114)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.codehaus.groovy.grails.web.servlet.mvc.GrailsWebRequestFilter.doFilterInternal(GrailsWebRequestFilter.java:69)
<br/>	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.codehaus.groovy.grails.web.filters.HiddenHttpMethodFilter.doFilterInternal(HiddenHttpMethodFilter.java:69)
<br/>	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:88)
<br/>	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76)
<br/>	at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:237)
<br/>	at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:167)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:474)
<br/>	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:119)
<br/>	at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:480)
<br/>	at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:226)
<br/>	at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:935)
<br/>	at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:404)
<br/>	at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:184)
<br/>	at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:870)
<br/>	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:117)
<br/>	at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:247)
<br/>	at org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:151)
<br/>	at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116)
<br/>	at org.eclipse.jetty.server.Server.handle(Server.java:346)
<br/>	at org.eclipse.jetty.server.HttpConnection.handleRequest(HttpConnection.java:596)
<br/>	at org.eclipse.jetty.server.HttpConnection$RequestHandler.headerComplete(HttpConnection.java:1051)
<br/>	at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:592)
<br/>	at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:214)
<br/>	at org.eclipse.jetty.server.HttpConnection.handle(HttpConnection.java:426)
<br/>	at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(SelectChannelEndPoint.java:520)
<br/>	at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectChannelEndPoint.java:40)
<br/>	at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:528)
<br/>	at java.lang.Thread.run(Thread.java:619)
<br/></pre>
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</html>:36: parser error : Couldn't find end of Start Tag div line 36
    document.write('<div class=\"box\"><div class=\"errors-center\" >we recommen
                               ^
<html>
<head>
  <title>CTS: Chemical Translation Service</title>

  <link rel="stylesheet" href="/cts/css/main.css"/>

  <style type="text/css">@import url("/cts/css/pagination.css");</style>
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  }

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<div id="main">

  <div class="page_header">
    Chemical Translation Service
  </div>


  <div class="box">
    <h3><a href="/cts/homePage/index" class="home">Home</a></h3>
    <div class="line"></div>

  </div>

  <div class="box">

    <h3>Ooops, what did just happen?</h3>

    <div class="line"></div>

    <div class="message">
      oh dear this is rather embarissing, but it looks like you discovered a bug. To help us avoiding this in the future, would you mind to send a bug report to <a href="mailto:wohlgemuth@ucdavis.edu">Gert Wohlgemuth</a> with as many informations as possible, so we can reproduce this and fix it!

    </div>

    <h3>Error Details</h3>

    <div class="line"></div>

    <div class="errors">
      <strong>Error 500:</strong> Cannot load default configuration from jar<br/>
      <strong>Servlet:</strong> default<br/>
      <strong>URI:</strong> /cts/massLookup/masstransform<br/>

      
        <strong>Exception Message:</strong> Cannot load default configuration from jar <br/>
        <strong>Caused by:</strong> Cannot load default configuration from jar <br/>
        <strong>Class:</strong> Unknown <br/>
        <strong>At Line:</strong> [-1] <br/>
        <strong>Code Snippet:</strong><br/>
        <div class="snippet">
          
        </div>
      

    </div>

    
      <h3>Stack Trace</h3>

      <div class="line"></div>

      <div class="errors">
        <pre>java.lang.IllegalStateException: Cannot load default configuration from jar
<br/>	at org.codehaus.groovy.grails.web.sitemesh.Grails5535Factory.loadSitemeshXML(Grails5535Factory.java:146)
<br/>	at org.codehaus.groovy.grails.web.sitemesh.Grails5535Factory.loadConfig(Grails5535Factory.java:73)
<br/>	at org.codehaus.groovy.grails.web.sitemesh.Grails5535Factory.refresh(Grails5535Factory.java:272)
<br/>	at com.opensymphony.module.sitemesh.Factory.getInstance(Factory.java:56)
<br/>	at com.opensymphony.sitemesh.webapp.SiteMeshFilter.initContentProcessor(SiteMeshFilter.java:107)
<br/>	at org.codehaus.groovy.grails.web.sitemesh.GrailsPageFilter.doFilter(GrailsPageFilter.java:114)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.codehaus.groovy.grails.web.servlet.mvc.GrailsWebRequestFilter.doFilterInternal(GrailsWebRequestFilter.java:69)
<br/>	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.codehaus.groovy.grails.web.filters.HiddenHttpMethodFilter.doFilterInternal(HiddenHttpMethodFilter.java:69)
<br/>	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:88)
<br/>	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76)
<br/>	at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:237)
<br/>	at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:167)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:474)
<br/>	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:119)
<br/>	at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:480)
<br/>	at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:226)
<br/>	at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:935)
<br/>	at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:404)
<br/>	at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:184)
<br/>	at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:870)
<br/>	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:117)
<br/>	at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:247)
<br/>	at org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:151)
<br/>	at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116)
<br/>	at org.eclipse.jetty.server.Server.handle(Server.java:346)
<br/>	at org.eclipse.jetty.server.HttpConnection.handleRequest(HttpConnection.java:596)
<br/>	at org.eclipse.jetty.server.HttpConnection$RequestHandler.headerComplete(HttpConnection.java:1051)
<br/>	at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:592)
<br/>	at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:214)
<br/>	at org.eclipse.jetty.server.HttpConnection.handle(HttpConnection.java:426)
<br/>	at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(SelectChannelEndPoint.java:520)
<br/>	at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectChannelEndPoint.java:40)
<br/>	at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:528)
<br/>	at java.lang.Thread.run(Thread.java:619)
<br/></pre>
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</html>:36: parser error : AttValue: " or ' expected
    document.write('<div class=\"box\"><div class=\"errors-center\" >we recommen
                                                  ^
<html>
<head>
  <title>CTS: Chemical Translation Service</title>

  <link rel="stylesheet" href="/cts/css/main.css"/>

  <style type="text/css">@import url("/cts/css/pagination.css");</style>
  <style type="text/css">@import url("/cts/css/font.css");</style>


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  <meta name="layout" content="main"/>


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  if (navigator.appName == 'Microsoft Internet Explorer') {
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  }

</script>




<div id="main">

  <div class="page_header">
    Chemical Translation Service
  </div>


  <div class="box">
    <h3><a href="/cts/homePage/index" class="home">Home</a></h3>
    <div class="line"></div>

  </div>

  <div class="box">

    <h3>Ooops, what did just happen?</h3>

    <div class="line"></div>

    <div class="message">
      oh dear this is rather embarissing, but it looks like you discovered a bug. To help us avoiding this in the future, would you mind to send a bug report to <a href="mailto:wohlgemuth@ucdavis.edu">Gert Wohlgemuth</a> with as many informations as possible, so we can reproduce this and fix it!

    </div>

    <h3>Error Details</h3>

    <div class="line"></div>

    <div class="errors">
      <strong>Error 500:</strong> Cannot load default configuration from jar<br/>
      <strong>Servlet:</strong> default<br/>
      <strong>URI:</strong> /cts/massLookup/masstransform<br/>

      
        <strong>Exception Message:</strong> Cannot load default configuration from jar <br/>
        <strong>Caused by:</strong> Cannot load default configuration from jar <br/>
        <strong>Class:</strong> Unknown <br/>
        <strong>At Line:</strong> [-1] <br/>
        <strong>Code Snippet:</strong><br/>
        <div class="snippet">
          
        </div>
      

    </div>

    
      <h3>Stack Trace</h3>

      <div class="line"></div>

      <div class="errors">
        <pre>java.lang.IllegalStateException: Cannot load default configuration from jar
<br/>	at org.codehaus.groovy.grails.web.sitemesh.Grails5535Factory.loadSitemeshXML(Grails5535Factory.java:146)
<br/>	at org.codehaus.groovy.grails.web.sitemesh.Grails5535Factory.loadConfig(Grails5535Factory.java:73)
<br/>	at org.codehaus.groovy.grails.web.sitemesh.Grails5535Factory.refresh(Grails5535Factory.java:272)
<br/>	at com.opensymphony.module.sitemesh.Factory.getInstance(Factory.java:56)
<br/>	at com.opensymphony.sitemesh.webapp.SiteMeshFilter.initContentProcessor(SiteMeshFilter.java:107)
<br/>	at org.codehaus.groovy.grails.web.sitemesh.GrailsPageFilter.doFilter(GrailsPageFilter.java:114)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.codehaus.groovy.grails.web.servlet.mvc.GrailsWebRequestFilter.doFilterInternal(GrailsWebRequestFilter.java:69)
<br/>	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.codehaus.groovy.grails.web.filters.HiddenHttpMethodFilter.doFilterInternal(HiddenHttpMethodFilter.java:69)
<br/>	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:88)
<br/>	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76)
<br/>	at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:237)
<br/>	at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:167)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:474)
<br/>	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:119)
<br/>	at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:480)
<br/>	at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:226)
<br/>	at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:935)
<br/>	at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:404)
<br/>	at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:184)
<br/>	at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:870)
<br/>	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:117)
<br/>	at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:247)
<br/>	at org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:151)
<br/>	at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116)
<br/>	at org.eclipse.jetty.server.Server.handle(Server.java:346)
<br/>	at org.eclipse.jetty.server.HttpConnection.handleRequest(HttpConnection.java:596)
<br/>	at org.eclipse.jetty.server.HttpConnection$RequestHandler.headerComplete(HttpConnection.java:1051)
<br/>	at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:592)
<br/>	at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:214)
<br/>	at org.eclipse.jetty.server.HttpConnection.handle(HttpConnection.java:426)
<br/>	at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(SelectChannelEndPoint.java:520)
<br/>	at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectChannelEndPoint.java:40)
<br/>	at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:528)
<br/>	at java.lang.Thread.run(Thread.java:619)
<br/></pre>
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</html>:36: parser error : attributes construct error
    document.write('<div class=\"box\"><div class=\"errors-center\" >we recommen
                                                  ^
<html>
<head>
  <title>CTS: Chemical Translation Service</title>

  <link rel="stylesheet" href="/cts/css/main.css"/>

  <style type="text/css">@import url("/cts/css/pagination.css");</style>
  <style type="text/css">@import url("/cts/css/font.css");</style>


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  <meta name="layout" content="main"/>


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  if (navigator.appName == 'Microsoft Internet Explorer') {
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  }

</script>




<div id="main">

  <div class="page_header">
    Chemical Translation Service
  </div>


  <div class="box">
    <h3><a href="/cts/homePage/index" class="home">Home</a></h3>
    <div class="line"></div>

  </div>

  <div class="box">

    <h3>Ooops, what did just happen?</h3>

    <div class="line"></div>

    <div class="message">
      oh dear this is rather embarissing, but it looks like you discovered a bug. To help us avoiding this in the future, would you mind to send a bug report to <a href="mailto:wohlgemuth@ucdavis.edu">Gert Wohlgemuth</a> with as many informations as possible, so we can reproduce this and fix it!

    </div>

    <h3>Error Details</h3>

    <div class="line"></div>

    <div class="errors">
      <strong>Error 500:</strong> Cannot load default configuration from jar<br/>
      <strong>Servlet:</strong> default<br/>
      <strong>URI:</strong> /cts/massLookup/masstransform<br/>

      
        <strong>Exception Message:</strong> Cannot load default configuration from jar <br/>
        <strong>Caused by:</strong> Cannot load default configuration from jar <br/>
        <strong>Class:</strong> Unknown <br/>
        <strong>At Line:</strong> [-1] <br/>
        <strong>Code Snippet:</strong><br/>
        <div class="snippet">
          
        </div>
      

    </div>

    
      <h3>Stack Trace</h3>

      <div class="line"></div>

      <div class="errors">
        <pre>java.lang.IllegalStateException: Cannot load default configuration from jar
<br/>	at org.codehaus.groovy.grails.web.sitemesh.Grails5535Factory.loadSitemeshXML(Grails5535Factory.java:146)
<br/>	at org.codehaus.groovy.grails.web.sitemesh.Grails5535Factory.loadConfig(Grails5535Factory.java:73)
<br/>	at org.codehaus.groovy.grails.web.sitemesh.Grails5535Factory.refresh(Grails5535Factory.java:272)
<br/>	at com.opensymphony.module.sitemesh.Factory.getInstance(Factory.java:56)
<br/>	at com.opensymphony.sitemesh.webapp.SiteMeshFilter.initContentProcessor(SiteMeshFilter.java:107)
<br/>	at org.codehaus.groovy.grails.web.sitemesh.GrailsPageFilter.doFilter(GrailsPageFilter.java:114)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.codehaus.groovy.grails.web.servlet.mvc.GrailsWebRequestFilter.doFilterInternal(GrailsWebRequestFilter.java:69)
<br/>	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.codehaus.groovy.grails.web.filters.HiddenHttpMethodFilter.doFilterInternal(HiddenHttpMethodFilter.java:69)
<br/>	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:88)
<br/>	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76)
<br/>	at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:237)
<br/>	at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:167)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:474)
<br/>	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:119)
<br/>	at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:480)
<br/>	at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:226)
<br/>	at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:935)
<br/>	at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:404)
<br/>	at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:184)
<br/>	at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:870)
<br/>	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:117)
<br/>	at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:247)
<br/>	at org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:151)
<br/>	at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116)
<br/>	at org.eclipse.jetty.server.Server.handle(Server.java:346)
<br/>	at org.eclipse.jetty.server.HttpConnection.handleRequest(HttpConnection.java:596)
<br/>	at org.eclipse.jetty.server.HttpConnection$RequestHandler.headerComplete(HttpConnection.java:1051)
<br/>	at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:592)
<br/>	at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:214)
<br/>	at org.eclipse.jetty.server.HttpConnection.handle(HttpConnection.java:426)
<br/>	at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(SelectChannelEndPoint.java:520)
<br/>	at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectChannelEndPoint.java:40)
<br/>	at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:528)
<br/>	at java.lang.Thread.run(Thread.java:619)
<br/></pre>
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    document.write('<div class=\"box\"><div class=\"errors-center\" >we recommen
                                                  ^
<html>
<head>
  <title>CTS: Chemical Translation Service</title>

  <link rel="stylesheet" href="/cts/css/main.css"/>

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<div id="main">

  <div class="page_header">
    Chemical Translation Service
  </div>


  <div class="box">
    <h3><a href="/cts/homePage/index" class="home">Home</a></h3>
    <div class="line"></div>

  </div>

  <div class="box">

    <h3>Ooops, what did just happen?</h3>

    <div class="line"></div>

    <div class="message">
      oh dear this is rather embarissing, but it looks like you discovered a bug. To help us avoiding this in the future, would you mind to send a bug report to <a href="mailto:wohlgemuth@ucdavis.edu">Gert Wohlgemuth</a> with as many informations as possible, so we can reproduce this and fix it!

    </div>

    <h3>Error Details</h3>

    <div class="line"></div>

    <div class="errors">
      <strong>Error 500:</strong> Cannot load default configuration from jar<br/>
      <strong>Servlet:</strong> default<br/>
      <strong>URI:</strong> /cts/massLookup/masstransform<br/>

      
        <strong>Exception Message:</strong> Cannot load default configuration from jar <br/>
        <strong>Caused by:</strong> Cannot load default configuration from jar <br/>
        <strong>Class:</strong> Unknown <br/>
        <strong>At Line:</strong> [-1] <br/>
        <strong>Code Snippet:</strong><br/>
        <div class="snippet">
          
        </div>
      

    </div>

    
      <h3>Stack Trace</h3>

      <div class="line"></div>

      <div class="errors">
        <pre>java.lang.IllegalStateException: Cannot load default configuration from jar
<br/>	at org.codehaus.groovy.grails.web.sitemesh.Grails5535Factory.loadSitemeshXML(Grails5535Factory.java:146)
<br/>	at org.codehaus.groovy.grails.web.sitemesh.Grails5535Factory.loadConfig(Grails5535Factory.java:73)
<br/>	at org.codehaus.groovy.grails.web.sitemesh.Grails5535Factory.refresh(Grails5535Factory.java:272)
<br/>	at com.opensymphony.module.sitemesh.Factory.getInstance(Factory.java:56)
<br/>	at com.opensymphony.sitemesh.webapp.SiteMeshFilter.initContentProcessor(SiteMeshFilter.java:107)
<br/>	at org.codehaus.groovy.grails.web.sitemesh.GrailsPageFilter.doFilter(GrailsPageFilter.java:114)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.codehaus.groovy.grails.web.servlet.mvc.GrailsWebRequestFilter.doFilterInternal(GrailsWebRequestFilter.java:69)
<br/>	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.codehaus.groovy.grails.web.filters.HiddenHttpMethodFilter.doFilterInternal(HiddenHttpMethodFilter.java:69)
<br/>	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:88)
<br/>	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76)
<br/>	at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:237)
<br/>	at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:167)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:474)
<br/>	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:119)
<br/>	at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:480)
<br/>	at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:226)
<br/>	at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:935)
<br/>	at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:404)
<br/>	at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:184)
<br/>	at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:870)
<br/>	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:117)
<br/>	at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:247)
<br/>	at org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:151)
<br/>	at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116)
<br/>	at org.eclipse.jetty.server.Server.handle(Server.java:346)
<br/>	at org.eclipse.jetty.server.HttpConnection.handleRequest(HttpConnection.java:596)
<br/>	at org.eclipse.jetty.server.HttpConnection$RequestHandler.headerComplete(HttpConnection.java:1051)
<br/>	at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:592)
<br/>	at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:214)
<br/>	at org.eclipse.jetty.server.HttpConnection.handle(HttpConnection.java:426)
<br/>	at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(SelectChannelEndPoint.java:520)
<br/>	at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectChannelEndPoint.java:40)
<br/>	at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:528)
<br/>	at java.lang.Thread.run(Thread.java:619)
<br/></pre>
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  <div  class="LabelFooter" align="center" valign="middle" style="padding:5px;">
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</html>:36: parser error : Opening and ending tag mismatch: script line 33 and div
Microsoft Internet Eplorer and we do not actively support or recommend it!</div>
                                                                               ^
<html>
<head>
  <title>CTS: Chemical Translation Service</title>

  <link rel="stylesheet" href="/cts/css/main.css"/>

  <style type="text/css">@import url("/cts/css/pagination.css");</style>
  <style type="text/css">@import url("/cts/css/font.css");</style>


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  }

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<div id="main">

  <div class="page_header">
    Chemical Translation Service
  </div>


  <div class="box">
    <h3><a href="/cts/homePage/index" class="home">Home</a></h3>
    <div class="line"></div>

  </div>

  <div class="box">

    <h3>Ooops, what did just happen?</h3>

    <div class="line"></div>

    <div class="message">
      oh dear this is rather embarissing, but it looks like you discovered a bug. To help us avoiding this in the future, would you mind to send a bug report to <a href="mailto:wohlgemuth@ucdavis.edu">Gert Wohlgemuth</a> with as many informations as possible, so we can reproduce this and fix it!

    </div>

    <h3>Error Details</h3>

    <div class="line"></div>

    <div class="errors">
      <strong>Error 500:</strong> Cannot load default configuration from jar<br/>
      <strong>Servlet:</strong> default<br/>
      <strong>URI:</strong> /cts/massLookup/masstransform<br/>

      
        <strong>Exception Message:</strong> Cannot load default configuration from jar <br/>
        <strong>Caused by:</strong> Cannot load default configuration from jar <br/>
        <strong>Class:</strong> Unknown <br/>
        <strong>At Line:</strong> [-1] <br/>
        <strong>Code Snippet:</strong><br/>
        <div class="snippet">
          
        </div>
      

    </div>

    
      <h3>Stack Trace</h3>

      <div class="line"></div>

      <div class="errors">
        <pre>java.lang.IllegalStateException: Cannot load default configuration from jar
<br/>	at org.codehaus.groovy.grails.web.sitemesh.Grails5535Factory.loadSitemeshXML(Grails5535Factory.java:146)
<br/>	at org.codehaus.groovy.grails.web.sitemesh.Grails5535Factory.loadConfig(Grails5535Factory.java:73)
<br/>	at org.codehaus.groovy.grails.web.sitemesh.Grails5535Factory.refresh(Grails5535Factory.java:272)
<br/>	at com.opensymphony.module.sitemesh.Factory.getInstance(Factory.java:56)
<br/>	at com.opensymphony.sitemesh.webapp.SiteMeshFilter.initContentProcessor(SiteMeshFilter.java:107)
<br/>	at org.codehaus.groovy.grails.web.sitemesh.GrailsPageFilter.doFilter(GrailsPageFilter.java:114)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.codehaus.groovy.grails.web.servlet.mvc.GrailsWebRequestFilter.doFilterInternal(GrailsWebRequestFilter.java:69)
<br/>	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.codehaus.groovy.grails.web.filters.HiddenHttpMethodFilter.doFilterInternal(HiddenHttpMethodFilter.java:69)
<br/>	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:88)
<br/>	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76)
<br/>	at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:237)
<br/>	at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:167)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:474)
<br/>	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:119)
<br/>	at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:480)
<br/>	at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:226)
<br/>	at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:935)
<br/>	at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:404)
<br/>	at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:184)
<br/>	at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:870)
<br/>	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:117)
<br/>	at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:247)
<br/>	at org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:151)
<br/>	at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116)
<br/>	at org.eclipse.jetty.server.Server.handle(Server.java:346)
<br/>	at org.eclipse.jetty.server.HttpConnection.handleRequest(HttpConnection.java:596)
<br/>	at org.eclipse.jetty.server.HttpConnection$RequestHandler.headerComplete(HttpConnection.java:1051)
<br/>	at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:592)
<br/>	at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:214)
<br/>	at org.eclipse.jetty.server.HttpConnection.handle(HttpConnection.java:426)
<br/>	at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(SelectChannelEndPoint.java:520)
<br/>	at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectChannelEndPoint.java:40)
<br/>	at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:528)
<br/>	at java.lang.Thread.run(Thread.java:619)
<br/></pre>
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</html>:36: parser error : Opening and ending tag mismatch: body line 27 and div
oft Internet Eplorer and we do not actively support or recommend it!</div></div>
                                                                               ^
<html>
<head>
  <title>CTS: Chemical Translation Service</title>

  <link rel="stylesheet" href="/cts/css/main.css"/>

  <style type="text/css">@import url("/cts/css/pagination.css");</style>
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<div id="main">

  <div class="page_header">
    Chemical Translation Service
  </div>


  <div class="box">
    <h3><a href="/cts/homePage/index" class="home">Home</a></h3>
    <div class="line"></div>

  </div>

  <div class="box">

    <h3>Ooops, what did just happen?</h3>

    <div class="line"></div>

    <div class="message">
      oh dear this is rather embarissing, but it looks like you discovered a bug. To help us avoiding this in the future, would you mind to send a bug report to <a href="mailto:wohlgemuth@ucdavis.edu">Gert Wohlgemuth</a> with as many informations as possible, so we can reproduce this and fix it!

    </div>

    <h3>Error Details</h3>

    <div class="line"></div>

    <div class="errors">
      <strong>Error 500:</strong> Cannot load default configuration from jar<br/>
      <strong>Servlet:</strong> default<br/>
      <strong>URI:</strong> /cts/massLookup/masstransform<br/>

      
        <strong>Exception Message:</strong> Cannot load default configuration from jar <br/>
        <strong>Caused by:</strong> Cannot load default configuration from jar <br/>
        <strong>Class:</strong> Unknown <br/>
        <strong>At Line:</strong> [-1] <br/>
        <strong>Code Snippet:</strong><br/>
        <div class="snippet">
          
        </div>
      

    </div>

    
      <h3>Stack Trace</h3>

      <div class="line"></div>

      <div class="errors">
        <pre>java.lang.IllegalStateException: Cannot load default configuration from jar
<br/>	at org.codehaus.groovy.grails.web.sitemesh.Grails5535Factory.loadSitemeshXML(Grails5535Factory.java:146)
<br/>	at org.codehaus.groovy.grails.web.sitemesh.Grails5535Factory.loadConfig(Grails5535Factory.java:73)
<br/>	at org.codehaus.groovy.grails.web.sitemesh.Grails5535Factory.refresh(Grails5535Factory.java:272)
<br/>	at com.opensymphony.module.sitemesh.Factory.getInstance(Factory.java:56)
<br/>	at com.opensymphony.sitemesh.webapp.SiteMeshFilter.initContentProcessor(SiteMeshFilter.java:107)
<br/>	at org.codehaus.groovy.grails.web.sitemesh.GrailsPageFilter.doFilter(GrailsPageFilter.java:114)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.codehaus.groovy.grails.web.servlet.mvc.GrailsWebRequestFilter.doFilterInternal(GrailsWebRequestFilter.java:69)
<br/>	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.codehaus.groovy.grails.web.filters.HiddenHttpMethodFilter.doFilterInternal(HiddenHttpMethodFilter.java:69)
<br/>	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:88)
<br/>	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76)
<br/>	at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:237)
<br/>	at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:167)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:474)
<br/>	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:119)
<br/>	at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:480)
<br/>	at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:226)
<br/>	at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:935)
<br/>	at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:404)
<br/>	at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:184)
<br/>	at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:870)
<br/>	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:117)
<br/>	at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:247)
<br/>	at org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:151)
<br/>	at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116)
<br/>	at org.eclipse.jetty.server.Server.handle(Server.java:346)
<br/>	at org.eclipse.jetty.server.HttpConnection.handleRequest(HttpConnection.java:596)
<br/>	at org.eclipse.jetty.server.HttpConnection$RequestHandler.headerComplete(HttpConnection.java:1051)
<br/>	at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:592)
<br/>	at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:214)
<br/>	at org.eclipse.jetty.server.HttpConnection.handle(HttpConnection.java:426)
<br/>	at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(SelectChannelEndPoint.java:520)
<br/>	at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectChannelEndPoint.java:40)
<br/>	at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:528)
<br/>	at java.lang.Thread.run(Thread.java:619)
<br/></pre>
      </div>
    

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</script>
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<html>
<head>
  <title>CTS: Chemical Translation Service</title>

  <link rel="stylesheet" href="/cts/css/main.css"/>

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    <div class="message">
      oh dear this is rather embarissing, but it looks like you discovered a bug. To help us avoiding this in the future, would you mind to send a bug report to <a href="mailto:wohlgemuth@ucdavis.edu">Gert Wohlgemuth</a> with as many informations as possible, so we can reproduce this and fix it!

    </div>

    <h3>Error Details</h3>

    <div class="line"></div>

    <div class="errors">
      <strong>Error 500:</strong> Cannot load default configuration from jar<br/>
      <strong>Servlet:</strong> default<br/>
      <strong>URI:</strong> /cts/massLookup/masstransform<br/>

      
        <strong>Exception Message:</strong> Cannot load default configuration from jar <br/>
        <strong>Caused by:</strong> Cannot load default configuration from jar <br/>
        <strong>Class:</strong> Unknown <br/>
        <strong>At Line:</strong> [-1] <br/>
        <strong>Code Snippet:</strong><br/>
        <div class="snippet">
          
        </div>
      

    </div>

    
      <h3>Stack Trace</h3>

      <div class="line"></div>

      <div class="errors">
        <pre>java.lang.IllegalStateException: Cannot load default configuration from jar
<br/>	at org.codehaus.groovy.grails.web.sitemesh.Grails5535Factory.loadSitemeshXML(Grails5535Factory.java:146)
<br/>	at org.codehaus.groovy.grails.web.sitemesh.Grails5535Factory.loadConfig(Grails5535Factory.java:73)
<br/>	at org.codehaus.groovy.grails.web.sitemesh.Grails5535Factory.refresh(Grails5535Factory.java:272)
<br/>	at com.opensymphony.module.sitemesh.Factory.getInstance(Factory.java:56)
<br/>	at com.opensymphony.sitemesh.webapp.SiteMeshFilter.initContentProcessor(SiteMeshFilter.java:107)
<br/>	at org.codehaus.groovy.grails.web.sitemesh.GrailsPageFilter.doFilter(GrailsPageFilter.java:114)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.codehaus.groovy.grails.web.servlet.mvc.GrailsWebRequestFilter.doFilterInternal(GrailsWebRequestFilter.java:69)
<br/>	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.codehaus.groovy.grails.web.filters.HiddenHttpMethodFilter.doFilterInternal(HiddenHttpMethodFilter.java:69)
<br/>	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:88)
<br/>	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76)
<br/>	at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:237)
<br/>	at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:167)
<br/>	at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
<br/>	at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:474)
<br/>	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:119)
<br/>	at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:480)
<br/>	at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:226)
<br/>	at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:935)
<br/>	at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:404)
<br/>	at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:184)
<br/>	at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:870)
<br/>	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:117)
<br/>	at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:247)
<br/>	at org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:151)
<br/>	at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116)
<br/>	at org.eclipse.jetty.server.Server.handle(Server.java:346)
<br/>	at org.eclipse.jetty.server.HttpConnection.handleRequest(HttpConnection.java:596)
<br/>	at org.eclipse.jetty.server.HttpConnection$RequestHandler.headerComplete(HttpConnection.java:1051)
<br/>	at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:592)
<br/>	at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:214)
<br/>	at org.eclipse.jetty.server.HttpConnection.handle(HttpConnection.java:426)
<br/>	at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(SelectChannelEndPoint.java:520)
<br/>	at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectChannelEndPoint.java:40)
<br/>	at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:528)
<br/>	at java.lang.Thread.run(Thread.java:619)
<br/></pre>
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Error in UseMethod("xmlChildren") : 
  no applicable method for 'xmlChildren' applied to an object of class "NULL"
Calls: getCtsRecord -> xmlChildren
Execution halted

RMassBank.Rcheck/00install.out:

* installing *source* package 'RMassBank' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'RMassBank.Rnw' 
** testing if installed package can be loaded
* DONE (RMassBank)

RMassBank.Rcheck/RMassBank-Ex.timings:

nameusersystemelapsed
RmbDefaultSettings0.0130.0080.040
add.formula0.0130.0070.020
addPeaks0.0050.0030.008
aggregateSpectra0.0050.0050.011
analyzeMsMs0.0040.0030.008
archiveResults0.0100.0070.019
cleanElnoise0.0050.0060.012
compileRecord0.0040.0040.009
createMolfile0.0040.0050.010
dbe0.0930.0040.098
deprofile0.0050.0050.011
exportMassbank0.0050.0070.011
filterLowaccResults0.0030.0040.007
filterMultiplicity0.0040.0060.009
filterPeakSatellites0.0060.0070.014
filterPeaksMultiplicity0.0050.0050.011
findMass2.5010.3701.512
findMsMsHR0.0420.0150.020
findMz0.0270.0110.013
findMz.formula0.0970.0810.079
flatten0.0060.0050.011
formulastring.to.list0.0070.0050.012
gatherCompound0.0060.0050.011
gatherData0.0040.0040.008
getCactus0.0260.0080.511