fix bad wget option, README almost complete

README.md

@@ -22,11 +22,11 @@ There is basically three ways to use R package checker :
 ---
 1. [Screenshots](#screenshots)
 2. [Requirements](#requirements)
-3. [Usage](#installation)
-    1. Direct Bash call
+3. [Usage](#usage)
+    1. [Direct Bash call](#Direct Bash call)
         * without --html
         * with --html
-    2. With the basic web interface
+    2. [With the basic web interface](#With the basic web interface)
 
 # Screenshots
 ---
@@ -46,11 +46,50 @@ Simple web interface examples :
 * MANDATORY Xvfb
 * OPTIONAL Php enabled web server
 * Java is probably needed by one of the packages depending on the package to check
+* Many libraries are probably needed to install dependencies of package to test. If an INSTALL or a CHECK fails, it is quite easy to determine if it is due to a missing lib and which lib it is.
 
 # Usage
 ---
-Adjust variables in config.php :
 
+## Direct Bash call
+
+This is the simple way to use the R package checker. The script prints current steps in stdout and all R output files in the output directory (-d|--dest DESTINATION_DIRECTORY). 
+
+Here are the script options :
+
+```
+rtest.sh PACKAGE_TO_TEST [-l|--libuser R_USER_LIB_VALUE] [-d|--dest DESTINATION_DIRECTORY] [-m|--mail MAIL_TO] [-u|--urlresult URL] [-r|--repo PACKAGE_TO_TEST_REPO] [-x | --xvfb XVFB-RUN PATH] [-n | --nbcores NBCORES] [-s | --skipinstall] [-h | --html]
+
+PACKAGE_TO_TEST : package to test
+-r | --repo PACKAGE_TO_TEST_REPO : repository of package you want to test (DEFAULT : R-CRAN)
+-l | --libuser R_LIBS_USER : directory where packages depending on PACKAGE_TO_TEST are going to be installed (DEFAULT : R will choose it)
+                             This directory can be used several times for several tests. Using same directory several times will save time.
+                             This directory can exist or not. If not, it will be created
+-d | --dest DESTINATION_DIRECTORY : result directory where HTML result and test files are produced (DEFAULT : ./check_PKGNAME_DATE)
+-m | --mail MAIL_TO : email address for real time user information (DEFAULT : NO MAIL WILL BE SENT)
+-u | --urlresult URL : if -m option was set, this http link to test results will be sent instead of a file path (DEFAULT : destination directory absolute path)
+-x | --xvfb PATH : Specific path to xvfb-run script (DEFAULT : 'xvfb-run')
+-n | --nbcores NBCORES : Number of cores for parallel executions of installations (Ncpu parameter) and number of simultaneous checks (DEFAULT : 1)
+-s | --skipinstall : flag to skip the packages update/installation
+-h | --html : generate html report in DESTINATION_DIRECTORY/index.html . Will download jquery in destination directory
+```
+
+### without --html
+
+The script will not produce any fancy output. You'll have to find and read files to see the results of a check.
+
+If there is a failure, check in the output/destination directory to find the corresponding .Rout file.
+
+### with --html
+
+Using the --html option, each step triggers the update of an html page located in the destination/output directory. This page contains the same information than the simple web interface but is static html which does not need Php and a webserver.
+
+## With the basic web interface
+
+To setup and use the web interface you need to :
+
+* Copy view.php, start.php, config.php in a directory inside your web root
+* Adjust variables in config.php :
 ```php
 // name of the package to test
 $package_to_test = "mypkg";
@@ -81,4 +120,5 @@ $nb_threads = 4;
 // (will prefix start.php and view.php in links)
 $base_url = "http://my.server.org/r-package-checker/";
 ```
-
+* Visit http://your.server.org/rcheck/start.php to launch a check.
+* Follow the link given by start.php to view.php to see the real time check progress.

rtest.sh

@@ -453,7 +453,7 @@ cd $DESTINATION
 
 if [[ $HTMLFLAG == 1 ]]; then
     echo "Downloading jquery inside result folder..."
-    wget http://code.jquery.com/jquery-1.7.2.min.js -o $DESTINATION/jquery-1.7.2.min.js
+    wget http://code.jquery.com/jquery-1.7.2.min.js -O $DESTINATION/jquery-1.7.2.min.js
     echo
 fi