[Genabel-commits] r881 - www

Tue Apr 3 11:58:05 CEST 2012

Author: yurii
Date: 2012-04-03 11:58:05 +0200 (Tue, 03 Apr 2012)
New Revision: 881

Added:
   www/tutHowToWorkWithDevelVersion.html
Modified:
   www/index.php
Log:
adding tutorial on how to checkout/update, modify/check and committing the devel code

Modified: www/index.php
===================================================================

--- www/index.php	2012-04-01 12:50:56 UTC (rev 880)
+++ www/index.php	2012-04-03 09:58:05 UTC (rev 881)
@@ -74,7 +74,7 @@
 <li>
 <a href="tutHowToInstallDevelVersion.html">
 How to install devel-version of GenABEL suite
-</a>
+</a> (for advanced users)
 </li>
 <li>
 <a href="tutHowToPatch.html">
@@ -82,6 +82,11 @@
 </a>
 </li>
 <li>
+<a href="tutHowToWorkWithDevelVersion.html">
+How to checkout/update, modify, check and commit the devel-version of GenABEL suite
+</a> (for developers)
+</li>
+<li>
 <a href="tutHowToMakeTags.html">
 How to tag released versions of GenABEL-suite packages 
 </a>

Added: www/tutHowToWorkWithDevelVersion.html
===================================================================
--- www/tutHowToWorkWithDevelVersion.html	                        (rev 0)
+++ www/tutHowToWorkWithDevelVersion.html	2012-04-03 09:58:05 UTC (rev 881)
@@ -0,0 +1,175 @@
+<h3>
+How to checkout, update, modify, and commit devel-version of the GenABEL suite
+</h3>
+<p></p>
+<i>
+by Yurii Aulchenko  for the GenABEL-devel team 
+(building upon the "How to install devel-version of GenABEL suite" 
+by YA, William Astle and Lennart Karssen)
+</i>
+<p></p>
+
+Here are instructions on how to checkout/update, modify, compile and commit the 
+devel-version of GenABEL packages. It is assumed that you use Linux or Mac OS.
+<p></p>
+
+<h4>Register at R-forge and GenABEL</h4>
+
+Go to the <a href="http://www.r-forge.r-project.org/">R-forge</a> and register 
+(follow the link "New Account" at upper right corner). After registering, send 
+request to join the GenABEL project; for that, go to 
+<a href="https://r-forge.r-project.org/projects/genabel/">the GenABEL project page</a>, 
+and follow the link "Request to join" (bottom of the "Project members" list). 
+Note that in general, you need to submit some patches before you can be accepted 
+as a commit-member.   
+ 
+
+<h4>Setting up the environment and checking out the project for the first time</h4>
+
+To get GenABEL & Co. running in devel-setting, you need to do a number of
+things. Plan to spend about 30 minutes on that. You will need good
+Inet connection and you also will
+need to have Subversion (svn) installed. 
+<p></p>
+
+1) Check if Subversion is installed. For that, try 'svn help'. If you 
+do get help, everyting must be all right. If Subversion is not there, 
+here is the link, which may help: 
+<a href="http://subversion.apache.org/packages.html">
+http://subversion.apache.org/packages.html
+</a>
+<p></p>
+
+2) In order to be able to compile devel-version, you need to set 
+an environmental variable R_HOME to point the location, where 
+R is installed. We assume that you use Bash (most people do); if not, 
+try to figure out how you can set environmental variables for your 
+particular environment (and let us know so we can add it here :) ). 
+<p></p>
+
+You can check where R is installed by running 'dirname $(which R)' 
+on Bash command prompt. Assuming R is installed at '/usr/bin', add 
+the following lines to your ~/.bashrc file (with Mac OS X, use 
+~/.bash_profile).
+<p></p>
+
+<pre>
+R_HOME=/usr/bin
+export R_HOME
+</pre>
+<p></p>
+
+or, you can try
+<p></p>
+
+<pre>
+R_HOME=$(dirname $(which R))
+export R_HOME
+</pre>
+<p></p>
+
+log out and log in again, or start a new terminal/console window.
+<p></p>
+
+3) It is recommended (though not 100% necessary) that you install  the latest 
+development version of R. You can obtain it from 
+<a href="ftp://ftp.stat.math.ethz.ch/Software/R/">CRAN ftp</a>; 
+after downloading, follow included instructions.
+<p></p>
+
+4) Install _stable_ GenABEL et al., 'roxygen', and 'RUnit' 
+from CRAN; for that on R command line type
+<p></p>
+
+<pre>
+install.packages("GenABEL",dependencies=c("Depends","Suggests"))
+install.packages("roxygen")
+install.packages("RUnit")
+</pre>
+<p></p>
+
+5) Change to a place, where you want the source code 
+to go. Get to the latest code by
+<p></p>
+
+<pre>
+svn checkout svn+ssh://your-user-name@svn.r-forge.r-project.org/svnroot/genabel/
+</pre>
+<p></p>
+
+This should create directory called 'genabel' with all SVN data, 
+the subdirectory 'pkg' will contain the packages. 
+<p></p>
+
+6) Compile and install latest code by
+<p></p>
+
+<pre>
+cd pkg
+R CMD INSTALL DatABEL
+R CMD INSTALL GenABEL
+... etc.
+</pre>
+<p></p>
+
+Note some packages (e.g. ProbABEL) are not R packages; to 
+compile these use specific Makefile's, e.g.
+<p></p>
+
+<pre>
+cd ProbABEL
+make
+</pre>
+<p></p>
+
+<h4>Updating, making modifications, compiling, checking and committing the changes</h4>
+
+Before you attempt to modify the code, please always update your local version with
+<p></p>
+
+<pre>
+svn update [PATH-to-local-genabel-directory]
+</pre>
+<p></p>
+
+Now you are ready to make modifications to the code.  
+<p></p>
+
+In case you add new functionality/files, please make sure 
+that your new procedures are registered in the NAMESPACE and 
+are documented using Roxygen. To make automatic generation of 
+help-files possible, you will also need to update the 
+''generate_documentation.R'' file. 
+<p></p>
+
+Before you commit the changes, always make sure that the package 
+documentation is updated (Roxygen), the package compiles 
+and passes R checks. To make sure you generate the documentation, 
+''cd'' to WITHIN the package and run 
+
+<pre>R CMD -f generate_documentation.R</pre> 
+
+To run checks, follow the instructions 
+outlined in "Writing R Extensions" (section "Checking packages"), 
+here is the link to the  
+<a href="http://cran.r-project.org/manuals.html">R Manuals page</a>.
+<p></p>
+
+Commit the changes only if all checks pass! To commit changes:
+<p></p>
+
+<pre>
+svn commit svn+ssh://your-user-name@svn.r-forge.r-project.org/svnroot/genabel/ -m "what-is-change-about-message"
+</pre>
+<p></p>
+
+We ask you to please always summarize introduced changes after the ''-m'' flag.
+<p></p>
+
+If you need to add some files, first use syntax
+<pre>
+svn add [PATH-to-local-genabel-file-you-have-added] 
+</pre>
+<p></p>
+
+... and then perform the commit.


Property changes on: www/tutHowToWorkWithDevelVersion.html
___________________________________________________________________
Added: svn:mime-type
   + text/plain

