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R
R How to add packages to your local repository Depending on the packages you want installed, you can do one of two things within R. First we load the R module an...
R-CorruptedRLibrariesWhenUsingBioconductor
If the user uses bioconductor for biology projects in R and their R library becomes corrupted you can do this command in the R prompt. BiocManager::valid() At t...
R-ERRORC++14StandardRequestedButCXX14IsNotDefined
If you get the error: C 14 standard requested but CXX14 is not defined You need to create some environment variables that R can use to compile the code. If it do...
REnvironments
Create local R library Repo As Python packages, we suggest that users maintain their R library repoes in the home directory. Install R libraries using 'install.p...
REvnironmentsInAnaconda
Create local R library Repo As Python packages, we suggest that users maintain an R library repo in the home directory. Install R libraries using 'install.packag...
RegistrationAgent
The RegistrationAgent User This is a user used by Foswiki when it registers new users. This user has special access to write to , and does not need an entry i...
RestartScriptGenerationExample
Here's a simple example of a checkpointing program being run with a slurm job script that will automatically generate a restart script for when you need to restar...
RunningJobs
Running jobs on Shamu * Submitting your Batch Job Submit your code to run on the compute nodes. Create a submission script and specify options for better...
RunningParallelBatchJobs
How to run Parallel Batch jobs On Shamu we have three (3) parallel Grid Engine environments but you only need to use one. First you need to load the "sge" module ...
RunningYourInteractiveJobsThroughBatch
How to run interactive jobs If you want to use a GUI or have a short program you want to test or debug, we suggest using the "srun" command. This will automatical...
Number of topics: 11

To display the above search results in a topic, copy-paste the following markup:
%SEARCH{
   "^R"
   type="regex"
   scope="topic"
}%
%INCLUDE{"%TOPIC%" section="title"}%
%INCLUDE{"%TOPIC%" section="form"}%
%INCLUDE{"%TOPIC%" section="searchresults"}%


%INCLUDE{"%TOPIC%" section="title"}%
%INCLUDE{"%TOPIC%" section="form"}%
%INCLUDE{"%TOPIC%" section="searchresults"}%
%INCLUDE{"%TOPIC%" section="querysearchexample"}%



%INCLUDE{"%TOPIC%" section="title"}%
%INCLUDE{"%TOPIC%" section="tabs"}%
%INCLUDE{"%SYSTEMWEB%.SearchHelp"}%



---+!! %MAKETEXT{"Search in [_1] Web" args="<nop>%BASEWEB%"}%


%INCLUDE{"%TOPIC%" section="tabs"}%<noautolink>
<div class='foswikiWebSearchForm'>
<form name='WebSearchForm' action='%SCRIPTURLPATH{view}%/%BASEWEB%/%TOPIC%'>
<input type='hidden' name='tab' value='%URLPARAM{"tab" default="search"}%' />
<div class='foswikiFormSteps'>
<div class='foswikiFormStep'>
<input type='text' class='foswikiInputField foswikiFocus' name='search' value='%URLPARAM{"search" encode="entity"}%' size='40' style='width:99%' placeholder='%MAKETEXT{"Search"}%' />   
</div>
<div class='foswikiFormStep'>
%TWISTY{
   id="searchOptions"
   mode="div"
   start="%IF{
      "$'URLPARAM{search}'=''"
      then="show"
      else="hide"
   }%"
   link="<strong>%MAKETEXT{"Search options"}%</strong>"
   showimgleft="%ICONURLPATH{toggleopen}%"
   hideimgleft="%ICONURLPATH{toggleclose}%"
}%%IF{
   "$'URLPARAM{tab}'='search' OR $'URLPARAM{tab}'='' AND NOT $TAB='advanced'" 
   then="$percentINCLUDE{$quot%TOPIC%$quot section=$quotoptionssimple$quot}$percent"
}%%IF{
   "$'URLPARAM{tab}'='searchadvanced' OR $TAB='advanced'" 
   then="$percentINCLUDE{$quot%TOPIC%$quot section=$quotoptionsadvanced$quot}$percent"
}%%ENDTWISTY%</div>
<div class='foswikiFormStep'>
<input type='submit' class='foswikiSubmit' value='%MAKETEXT{"Search"}%' /> 
</div>
</div><!--//foswikiFormSteps-->
</form>
</div></noautolink>


search=%URLPARAM{"search" encode="url"}%;scope=%URLPARAM{"scope" encode="url" default="all"}%;web=%URLPARAM{"web" encode="url"}%;recurse=%URLPARAM{"recurse" encode="url"}%;type=%URLPARAM{"type" encode="url" default="%SEARCHDEFAULTTTYPE%"}%


%INCLUDE{"%TOPIC%" section="searchparamssimple"}%;type=%URLPARAM{"type" encode="url" default="%SEARCHDEFAULTTTYPE%"}%;nosearch=%URLPARAM{"nosearch" encode="url"}%;limit=%URLPARAM{"limit" encode="url"}%;excludetopic=%URLPARAM{"excludetopic" encode="url"}%;casesensitive=%URLPARAM{"casesensitive" encode="url"}%


<noautolink><div class='foswikiTabs'>
   <ul>
      <li%IF{
         "$'URLPARAM{tab}'='search' OR $'URLPARAM{tab}'='' AND NOT $TAB='advanced'"
         then=" class='foswikiActiveTab'"
      }%><a href='%SCRIPTURL{view}%/%BASEWEB%/%TOPIC%?%INCLUDE{"%TOPIC%" section="searchparamssimple"}%;tab=search'>%MAKETEXT{"Search"}%</a></li>
      <li%IF{
         "$'URLPARAM{tab}'='searchadvanced' OR $TAB='advanced'" then=" class='foswikiActiveTab'"
      }%><a href='%SCRIPTURL{view}%/%BASEWEB%/%TOPIC%?%INCLUDE{"%TOPIC%" section="searchparamsadvanced"}%;tab=searchadvanced'>%MAKETEXT{"Advanced search"}%</a></li>
      <li%IF{
         "$'URLPARAM{tab}'='az'" then=" class='foswikiActiveTab'"
      }%><a href='%SCRIPTURL{view}%/%BASEWEB%/%TOPIC%?%INCLUDE{"%TOPIC%" section="searchparamsadvanced"}%;tab=az'>%MAKETEXT{"A-Z"}%</a></li>
      <li%IF{
         "$'URLPARAM{tab}'='help'" then=" class='foswikiActiveTab'"
      }%><a href='%SCRIPTURL{view}%/%BASEWEB%/%TOPIC%?%INCLUDE{"%TOPIC%" section="searchparamsadvanced"}%;tab=help'>%MAKETEXT{"Help"}%</a></li>
   </ul>
   <div class='foswikiClear'></div>
</div></noautolink>


<table id='foswikiSearchTable' class='foswikiSearchTable' border='0' cellspacing='0' cellpadding='0'>
<tr>
<th>%MAKETEXT{"Search where:"}%</th>
<td>
<input type='radio' class='foswikiRadioButton' id='textbody' name='scope' value='text' %IF{
   "'%URLPARAM{"scope"}%'='text'"
   then="checked='checked'"
}% /><label for='textbody'> %MAKETEXT{"Text body"}%</label><br />
<input type='radio' class='foswikiRadioButton' id='topictitle' name='scope' value='topic' %IF{
   "'%URLPARAM{"scope" default="all"}%'='topic'"
   then="checked='checked'"
}% /><label for='topictitle'> %MAKETEXT{"Topic title"}% </label><br />
<input type='radio' class='foswikiRadioButton' id='both' name='scope' value='all' %IF{
   "'%URLPARAM{"scope" default="all"}%'='all'"
   then="checked='checked'"
}% /><label for='both'> %MAKETEXT{"Both body and title"}%</label>
<hr />
<input type='checkbox' class='foswikiCheckbox' id='web' name='web' value='all' %IF{
   "'%URLPARAM{web}%'='all'"
   then="checked='checked'"
}% /><label for='web'> %MAKETEXT{"All public webs"}%</label> <span class='foswikiSmall'>%MAKETEXT{"(otherwise search [_1] Web only)" args="<nop>%BASEWEB%"}%</span>
<input type='checkbox' class='foswikiCheckbox' id='recurse' name='recurse' value='on' %IF{
   "'%URLPARAM{recurse}%'='on'"
   then="checked='checked'"
}% /><label for='recurse'> %MAKETEXT{"Subwebs"}%</label>
</td>
</tr>
</table>


<table id='foswikiSearchTable' class='foswikiSearchTable' border='0' cellspacing='0' cellpadding='0'>
<tr>
<th>%MAKETEXT{"Search where:"}%</th>
<td>
<input type='radio' class='foswikiRadioButton' id='textbody' name='scope' value='text' %IF{
   "'%URLPARAM{"scope"}%'='text'"
   then="checked='checked'"
}% /><label for='textbody'> %MAKETEXT{"Text body"}%</label><br />
<input type='radio' class='foswikiRadioButton' id='topictitle' name='scope' value='topic' %IF{
   "'%URLPARAM{"scope" default="all"}%'='topic'"
   then="checked='checked'"
}% /><label for='topictitle'> %MAKETEXT{"Topic title"}%</label><br />
<input type='radio' class='foswikiRadioButton' id='both' name='scope' value='all' %IF{
   "'%URLPARAM{"scope" default="all"}%'='all'"
   then="checked='checked'"
}% /><label for='both'> %MAKETEXT{"Both body and title"}%</label>
<hr />
<input type='checkbox' class='foswikiCheckbox' id='web' name='web' value='all' %IF{
   "'%URLPARAM{web}%'='all'"
   then="checked='checked'"
}% /><label for='web'> %MAKETEXT{"All public webs"}%</label> <span class='foswikiSmall'>%MAKETEXT{"(otherwise search [_1] Web only)" args="<nop>%BASEWEB%"}%</span>
<input type='checkbox' class='foswikiCheckbox' id='recurse' name='recurse' value='on' %IF{
   "'%URLPARAM{recurse}%'='on'"
   then="checked='checked'"
}% /><label for='recurse'> %MAKETEXT{"Subwebs"}%</label>
</td>
</tr>
<tr>
<th>%MAKETEXT{"Sort results by:"}%</th>
<td>
<input type='radio' class='foswikiRadioButton' id='topic' name='order' value='topic' %IF{
   "'%URLPARAM{"order" default="topic"}%'='topic'"
   then="checked='checked'"
}% /><label for='topic'> %MAKETEXT{"Topic name"}%</label><br />
<input type='radio' class='foswikiRadioButton' id='modified' name='order' value='modified' %IF{
   "'%URLPARAM{order}%'='modified'"
   then="checked='checked'"
}% /><label for='modified'> %MAKETEXT{"Last modified time"}%</label><br />
<input type='radio' class='foswikiRadioButton' id='editby' name='order' value='editby' %IF{
   "'%URLPARAM{order}%'='editby'"
   then="checked='checked'"
}% /><label for='editby'> %MAKETEXT{"Last editor"}%</label>
<hr />
<input type='checkbox' class='foswikiCheckbox' name='reverse' id='reverse' %IF{
   "'%URLPARAM{reverse}%'='on'"
   then="checked='checked'"
}% /><label for='reverse'> %MAKETEXT{"In reversed order"}%</label>
</td>
</tr>
<tr>
<th>%MAKETEXT{"Make search:"}%</th>
<td>%MAKETEXT{"Selections apply to search in \"text body\""}% <span class='foswikiUnvisited foswikiSmall'>%POPUPWINDOW{"%SYSTEMWEB%.SearchHelp" label="%MAKETEXT{"Help"}%"}%</span>
<hr />
<input type='checkbox' class='foswikiCheckbox' id='casesensitive' name='casesensitive' %IF{
   "'%URLPARAM{casesensitive}%'='on'"
   then="checked='checked'"
}% /><label for='casesensitive'> %MAKETEXT{"Case sensitive"}%</label><br />
<hr />
<input type='radio' class='foswikiRadioButton' id='word' name='type' value='word' %IF{
   "'%URLPARAM{"type" default="%SEARCHDEFAULTTTYPE%"}%'='word'" 
   then="checked='checked'"
}% /><label for='word'> %MAKETEXT{"Word search"}%</label><br />
<input type='radio' class='foswikiRadioButton' id='keyword' name='type' value='keyword' %IF{
   "'%URLPARAM{"type" default="%SEARCHDEFAULTTTYPE%"}%'='keyword'" 
   then="checked='checked'"
}% /><label for='keyword'> %MAKETEXT{"Keyword search"}%</label><br />
<input type='radio' class='foswikiRadioButton' id='literal' name='type' value='literal' %IF{
   "'%URLPARAM{type}%'='literal'"
   then="checked='checked'"
}% /><label for='literal'> %MAKETEXT{"Literal search"}%</label><br />
<input type='radio' class='foswikiRadioButton' id='regex' name='type' value='regex' %IF{
   "'%URLPARAM{type}%'='regex'"
   then="checked='checked'"
}% /><label for='regex'> %MAKETEXT{"Regular expression search"}%</label><br />
<input type='radio' class='foswikiRadioButton' id='query' name='type' value='query' %IF{
   "'%URLPARAM{type}%'='query'"
   then="checked='checked'"
}% /><label for='query'> %MAKETEXT{"Query Search"}%</label>
</td>
</tr>
<tr>
<th><b>%MAKETEXT{"Don't show:"}%</b></th>
<td><input type='checkbox' class='foswikiCheckbox' id='nosearch' name='nosearch' %IF{
   "'%URLPARAM{nosearch}%'='on'"
   then="checked='checked'"
}% /><label for='nosearch'> %MAKETEXT{"Search string"}%</label><br />
<input type='checkbox' class='foswikiCheckbox' id='nosummary' name='nosummary' %IF{
   "'%URLPARAM{nosummary}%'='on'"
   then="checked='checked'"
}% /><label for='nosummary'> %MAKETEXT{"Summaries"}%</label><br />
<input type='checkbox' class='foswikiCheckbox' id='nototal' name='nototal' %IF{
   "'%URLPARAM{nototal}%'='on'"
   then="checked='checked'"
}% /><label for='nototal'> %MAKETEXT{"Total matches"}%</label><br />
</td>
</tr>
<tr>
<th class='foswikiLast'>%MAKETEXT{"Limit results to:"}%</th>
<td class='foswikiLast'><input type='text' class='foswikiInputField' id='limit' name='limit' size='3' value='%IF{
   "'%URLPARAM{"limit" default="all"}%'='all'"
   then="all"
   else="%URLPARAM{limit}%"
}%' /><label for='limit'> %MAKETEXT{"Topics per web"}% </label><span class='foswikiSmall'>%MAKETEXT{"(=all= to show all topics)"}%</span>
</td>
</tr>
</table>


%IF{
   "$'URLPARAM{search}'!=''"
   then="<h2>%MAKETEXT{"Search results"}%</h2>
$percentINCLUDE{$quot%SYSTEMWEB%.%TOPIC%$quot section=$quotsearchfeed$quot}$percent"
}%%SEARCH{
   "%URLPARAM{"search" encode="entities, quote"}%" decode="entities"
   type="%URLPARAM{"type" default="word"}%"
   scope="%URLPARAM{"scope" encode="safe, quote"}%"
   web="%URLPARAM{"web" encode="safe, quote"}%"%IF{
      "{EnableHierarchicalWebs}"
      then="recurse=\"%URLPARAM{"recurse" encode="safe, quote"}%\""
   }%
    topic="%URLPARAM{"searchtopic" encode="safe, quote"}%"
   excludetopic="%URLPARAM{"excludetopic" encode="safe, quote"}%"
   nosearch="%URLPARAM{"nosearch" encode="safe, quote"}%"
   casesensitive="%URLPARAM{"casesensitive" encode="safe, quote"}%"
   nosummary="%URLPARAM{"nosummary" encode="safe, quote"}%"
   nototal="%URLPARAM{"nototal" encode="safe, quote"}%"
   order="%URLPARAM{"order" encode="safe, quote"}%"
   reverse="%URLPARAM{"reverse" encode="safe, quote"}%"
   pager="on"
   limit="%URLPARAM{"limit" encode="safe, quote" default="%DEFAULTPAGESIZE%"}%"
   pagesize="%DEFAULTPAGESIZE%"
   zeroresults="%IF{
      "defined search and $search!=''"
      then="on"
      else="off"
   }%"
}%


<div>%ICON{"rss-small"}%%INCLUDE{"%SYSTEMWEB%.%TOPIC%" section="searchfeedlink"}%</div>


 <a href='%SCRIPTURL{"view"}%/%BASEWEB%/WebRss?search=%URLPARAM{"search" encode="url"}%;type=%IF{
   "'%URLPARAM{"regex"}%'='on' OR '%URLPARAM{"type"}%'='regex'"
   then="regex"
   else="word"
}%;excludetopic=%URLPARAM{"excludetopic" encode="url" default="%TOPIC%,%HOMETOPIC%,%STATISTICSTOPIC%"}%;web=%URLPARAM{"web" encode="url" default="%BASEWEB%"}%;recurse=%URLPARAM{"recurse" encode="url"}%;limit=%URLPARAM{"limit" encode="url" default="all"}%;scope=%URLPARAM{"scope" encode="url" default="text"}%;casesensitive=%URLPARAM{"casesensitive" encode="url" default="off"}%'>%MAKETEXT{"Get notified on changes on this search"}%</a>


%IF{
   "$'URLPARAM{search}'!=''"
   then='$percentINCLUDE{$quot%TOPIC%$quot section=$quot_querysearchexample$quot}$percent'
}%


<p /><div class='foswikiHelp'>
%MAKETEXT{"To display the above search results in a topic, copy-paste the following markup:"}%
<pre class='tml'>
%<nop>SEARCH{
   "%URLPARAM{"search" encode="entities, quote"}%"
   type="%URLPARAM{"type" default="%SEARCHDEFAULTTTYPE%"}%"%FORMAT{
      "scope,web,recurse,nosearch,casesensitive,nosummary,nototal,order,reverse,limit"
      type="string"
      header="$n"
      format="$percntIF{
        \"(defined $item AND $'$item') AND ('$item' != 'recurse' OR {EnableHierarchicalWebs})\"
        then=\"   $item=\\"$percntURLPARAM{\"$item\" encode=\"safe, quote\"}$percnt\\"$n\"
      }$percnt"
      separator=""
   }%}%
</pre>
</div>


%IF{
   "$'URLPARAM{searchletter}'='%letter%'"
   then="<strong>%letter%</strong>"
   else="<a href='%SCRIPTURLPATH{"search"}%/%BASEWEB%/%TOPIC%?scope=topic&amp;type=regex&amp;search=%5E%letter%;$percentINCLUDE{$quot%TOPIC%$quot section=$quotsearchparamsadvanced$quot}$percent;searchletter=%letter%;tab=az'>%letter%</a>"
}%


%INCLUDE{"%TOPIC%" section="title"}%
%INCLUDE{"%TOPIC%" section="tabs"}%
<div class='foswikiWebSearchForm'>
%MAKETEXT{"List topics that start with the letter:"}% %INCLUDE{"%TOPIC%" section="letterlist"}%
</div>
%IF{
   "$'URLPARAM{searchletter}'"
   then="$percentINCLUDE{$quot%TOPIC%$quot section=$quotsearchresults$quot}$percent$percentINCLUDE{$quot%TOPIC%$quot section=$quotquerysearchexample$quot}$percent"
}%

<div class='foswikiHorizontalList foswikiUnvisited'>
<ul>
   <li>%INCLUDE{"%TOPIC%" section="searchbyletterlink" letter="A"}%</li>
   <li>%INCLUDE{"%TOPIC%" section="searchbyletterlink" letter="B"}%</li>
   <li>%INCLUDE{"%TOPIC%" section="searchbyletterlink" letter="C"}%</li>
   <li>%INCLUDE{"%TOPIC%" section="searchbyletterlink" letter="D"}%</li>
   <li>%INCLUDE{"%TOPIC%" section="searchbyletterlink" letter="E"}%</li>
   <li>%INCLUDE{"%TOPIC%" section="searchbyletterlink" letter="F"}%</li>
   <li>%INCLUDE{"%TOPIC%" section="searchbyletterlink" letter="G"}%</li>
   <li>%INCLUDE{"%TOPIC%" section="searchbyletterlink" letter="H"}%</li>
   <li>%INCLUDE{"%TOPIC%" section="searchbyletterlink" letter="I"}%</li>
   <li>%INCLUDE{"%TOPIC%" section="searchbyletterlink" letter="J"}%</li>
   <li>%INCLUDE{"%TOPIC%" section="searchbyletterlink" letter="K"}%</li>
   <li>%INCLUDE{"%TOPIC%" section="searchbyletterlink" letter="L"}%</li>
   <li>%INCLUDE{"%TOPIC%" section="searchbyletterlink" letter="M"}%</li>
   <li>%INCLUDE{"%TOPIC%" section="searchbyletterlink" letter="N"}%</li>
   <li>%INCLUDE{"%TOPIC%" section="searchbyletterlink" letter="O"}%</li>
   <li>%INCLUDE{"%TOPIC%" section="searchbyletterlink" letter="P"}%</li>
   <li>%INCLUDE{"%TOPIC%" section="searchbyletterlink" letter="Q"}%</li>
   <li>%INCLUDE{"%TOPIC%" section="searchbyletterlink" letter="R"}%</li>
   <li>%INCLUDE{"%TOPIC%" section="searchbyletterlink" letter="S"}%</li>
   <li>%INCLUDE{"%TOPIC%" section="searchbyletterlink" letter="T"}%</li>
   <li>%INCLUDE{"%TOPIC%" section="searchbyletterlink" letter="U"}%</li>
   <li>%INCLUDE{"%TOPIC%" section="searchbyletterlink" letter="V"}%</li>
   <li>%INCLUDE{"%TOPIC%" section="searchbyletterlink" letter="W"}%</li>
   <li>%INCLUDE{"%TOPIC%" section="searchbyletterlink" letter="X"}%</li>
   <li>%INCLUDE{"%TOPIC%" section="searchbyletterlink" letter="Y"}%</li>
   <li class='foswikiLast'>%INCLUDE{"%TOPIC%" section="searchbyletterlink" letter="Z"}%</li>
</ul>
<div class='foswikiClear'></div>
</div>
Topic revision: r1 - 06 Aug 2023, UnknownUser
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