WebSVN – Applications.gtt – Diff – /branches/v1.3-critias/bibliotheque/pear/PEAR/Installer.php

 <?php
 /**
  * PEAR_Installer
+ *
  * PHP versions 4 and 5
+ *
- * LICENSE: This source file is subject to version 3.0 of the PHP license
- * that is available through the world-wide-web at the following URI:
- * http://www.php.net/license/3_0.txt.  If you did not receive a copy of
- * the PHP License and are unable to obtain it through the web, please
- * send a note to license@php.net so we can mail you a copy immediately.
- *
  * @category   pear
  * @package    PEAR
  * @author     Stig Bakken <ssb@php.net>
  * @author     Tomas V.V. Cox <cox@idecnet.com>
  * @author     Martin Jansen <mj@php.net>
  * @author     Greg Beaver <cellog@php.net>
- * @copyright  1997-2006 The PHP Group
+ * @copyright  1997-2009 The Authors
- * @license    http://www.php.net/license/3_0.txt  PHP License 3.0
+ * @license    http://opensource.org/licenses/bsd-license.php New BSD License
- * @version    CVS: $Id: Installer.php,v 1.243 2007/02/16 04:00:37 cellog Exp $
  * @link       http://pear.php.net/package/PEAR
  * @since      File available since Release 0.1
  */
 /**
  * Used for installation groups in package.xml 2.0 and platform exceptions
  */
 require_once 'OS/Guess.php';
 require_once 'PEAR/Downloader.php';
 define('PEAR_INSTALLER_NOBINARY', -240);
 /**
  * Administration class used to install PEAR packages and maintain the
  * installed package database.
+ *
  * @category   pear
  * @package    PEAR
  * @author     Stig Bakken <ssb@php.net>
  * @author     Tomas V.V. Cox <cox@idecnet.com>
  * @author     Martin Jansen <mj@php.net>
  * @author     Greg Beaver <cellog@php.net>
- * @copyright  1997-2006 The PHP Group
+ * @copyright  1997-2009 The Authors
- * @license    http://www.php.net/license/3_0.txt  PHP License 3.0
+ * @license    http://opensource.org/licenses/bsd-license.php New BSD License
- * @version    Release: 1.5.1
+ * @version    Release: 1.10.1
  * @link       http://pear.php.net/package/PEAR
  * @since      Class available since Release 0.1
  */
 class PEAR_Installer extends PEAR_Downloader
+{
     // {{{ properties
     /** name of the package directory, for example Foo-1.0
      * @var string
      */
     var $pkgdir;
     /** directory where PHP code files go
      * @var string
      */
     var $phpdir;
     /** directory where PHP extension files go
      * @var string
      */
     var $extdir;
     /** directory where documentation goes
      * @var string
      */
     var $docdir;
     /** installation root directory (ala PHP's INSTALL_ROOT or
      * automake's DESTDIR
      * @var string
      */
     var $installroot = '';
     /** debug level
      * @var int
      */
     var $debug = 1;
     /** temporary directory
      * @var string
      */
     var $tmpdir;
     /**
      * PEAR_Registry object used by the installer
      * @var PEAR_Registry
      */
     var $registry;
     /**
      * array of PEAR_Downloader_Packages
      * @var array
      */
     var $_downloadedPackages;
     /** List of file transactions queued for an install/upgrade/uninstall.
+     *
      *  Format:
      *    array(
      *      0 => array("rename => array("from-file", "to-file")),
      *      1 => array("delete" => array("file-to-delete")),
      *      ...
      *    )
+     *
      * @var array
      */
     var $file_operations = array();
     // }}}
     // {{{ constructor
     /**
      * PEAR_Installer constructor.
+     *
      * @param object $ui user interface object (instance of PEAR_Frontend_*)
+     *
      * @access public
      */
-    function PEAR_Installer(&$ui)
+    function __construct(&$ui)
+    {
-        parent::PEAR_Common();
+        parent::__construct($ui, array(), null);
         $this->setFrontendObject($ui);
         $this->debug = $this->config->get('verbose');
+    }
     function setOptions($options)
+    {
         $this->_options = $options;
+    }
     function setConfig(&$config)
+    {
-        $this->config = &$config;
+        $this->config    = &$config;
         $this->_registry = &$config->getRegistry();
+    }
     // }}}
     function _removeBackups($files)
+    {
         foreach ($files as $path) {
             $this->addFileOperation('removebackup', array($path));
+        }
+    }
     // {{{ _deletePackageFiles()
     /**
      * Delete a package's installed files, does not remove empty directories.
+     *
      * @param string package name
      * @param string channel name
      * @param bool if true, then files are backed up first
      * @return bool TRUE on success, or a PEAR error on failure
      * @access protected
      */
     function _deletePackageFiles($package, $channel = false, $backup = false)
+    {
         if (!$channel) {
             $channel = 'pear.php.net';
+        }
         if (!strlen($package)) {
             return $this->raiseError("No package to uninstall given");
+        }
         if (strtolower($package) == 'pear' && $channel == 'pear.php.net') {
             // to avoid race conditions, include all possible needed files
             require_once 'PEAR/Task/Common.php';
             require_once 'PEAR/Task/Replace.php';
             require_once 'PEAR/Task/Unixeol.php';
             require_once 'PEAR/Task/Windowseol.php';
             require_once 'PEAR/PackageFile/v1.php';
             require_once 'PEAR/PackageFile/v2.php';
             require_once 'PEAR/PackageFile/Generator/v1.php';
             require_once 'PEAR/PackageFile/Generator/v2.php';
+        }
         $filelist = $this->_registry->packageInfo($package, 'filelist', $channel);
         if ($filelist == null) {
             return $this->raiseError("$channel/$package not installed");
+        }
         $ret = array();
         foreach ($filelist as $file => $props) {
             if (empty($props['installed_as'])) {
                 continue;
+            }
             $path = $props['installed_as'];
             if ($backup) {
                 $this->addFileOperation('backup', array($path));
                 $ret[] = $path;
+            }
             $this->addFileOperation('delete', array($path));
+        }
         if ($backup) {
             return $ret;
+        }
         return true;
+    }
     // }}}
     // {{{ _installFile()
     /**
      * @param string filename
      * @param array attributes from <file> tag in package.xml
      * @param string path to install the file in
      * @param array options from command-line
      * @access private
      */
     function _installFile($file, $atts, $tmp_path, $options)
+    {
         // {{{ return if this file is meant for another platform
         static $os;
         if (!isset($this->_registry)) {
             $this->_registry = &$this->config->getRegistry();
+        }
         if (isset($atts['platform'])) {
             if (empty($os)) {
                 $os = new OS_Guess();
+            }
             if (strlen($atts['platform']) && $atts['platform']{0} == '!') {
-                $negate = true;
+                $negate   = true;
                 $platform = substr($atts['platform'], 1);
             } else {
-                $negate = false;
+                $negate    = false;
                 $platform = $atts['platform'];
+            }
             if ((bool) $os->matchSignature($platform) === $negate) {
                 $this->log(3, "skipped $file (meant for $atts[platform], we are ".$os->getSignature().")");
                 return PEAR_INSTALLER_SKIPPED;
+            }
+        }
         // }}}
         $channel = $this->pkginfo->getChannel();
         // {{{ assemble the destination paths
         switch ($atts['role']) {
+            case 'src':
+            case 'extsrc':
+                $this->source_files++;
+                return;
             case 'doc':
             case 'data':
             case 'test':
                 $dest_dir = $this->config->get($atts['role'] . '_dir', null, $channel) .
                             DIRECTORY_SEPARATOR . $this->pkginfo->getPackage();
                 unset($atts['baseinstalldir']);
                 break;
             case 'ext':
             case 'php':
                 $dest_dir = $this->config->get($atts['role'] . '_dir', null, $channel);
                 break;
             case 'script':
                 $dest_dir = $this->config->get('bin_dir', null, $channel);
                 break;
-            case 'src':
-            case 'extsrc':
-                $this->source_files++;
-                return;
             default:
                 return $this->raiseError("Invalid role `$atts[role]' for file $file");
+        }
         $save_destdir = $dest_dir;
         if (!empty($atts['baseinstalldir'])) {
             $dest_dir .= DIRECTORY_SEPARATOR . $atts['baseinstalldir'];
+        }
         if (dirname($file) != '.' && empty($atts['install-as'])) {
             $dest_dir .= DIRECTORY_SEPARATOR . dirname($file);
+        }
         if (empty($atts['install-as'])) {
             $dest_file = $dest_dir . DIRECTORY_SEPARATOR . basename($file);
         } else {
             $dest_file = $dest_dir . DIRECTORY_SEPARATOR . $atts['install-as'];
+        }
         $orig_file = $tmp_path . DIRECTORY_SEPARATOR . $file;
         // Clean up the DIRECTORY_SEPARATOR mess
         $ds2 = DIRECTORY_SEPARATOR . DIRECTORY_SEPARATOR;
         list($dest_file, $orig_file) = preg_replace(array('!\\\\+!', '!/!', "!$ds2+!"),
                                                     array(DIRECTORY_SEPARATOR,
                                                           DIRECTORY_SEPARATOR,
                                                           DIRECTORY_SEPARATOR),
                                                     array($dest_file, $orig_file));
         $final_dest_file = $installed_as = $dest_file;
         if (isset($this->_options['packagingroot'])) {
-            $installedas_dest_dir = dirname($final_dest_file);
+            $installedas_dest_dir  = dirname($final_dest_file);
             $installedas_dest_file = $dest_dir . DIRECTORY_SEPARATOR . '.tmp' . basename($final_dest_file);
-            $final_dest_file = $this->_prependPath($final_dest_file,
+            $final_dest_file = $this->_prependPath($final_dest_file, $this->_options['packagingroot']);
-                $this->_options['packagingroot']);
         } else {
-            $installedas_dest_dir = dirname($final_dest_file);
+            $installedas_dest_dir  = dirname($final_dest_file);
             $installedas_dest_file = $installedas_dest_dir . DIRECTORY_SEPARATOR . '.tmp' . basename($final_dest_file);
+        }
-        $dest_dir = dirname($final_dest_file);
+        $dest_dir  = dirname($final_dest_file);
         $dest_file = $dest_dir . DIRECTORY_SEPARATOR . '.tmp' . basename($final_dest_file);
+        if (preg_match('~/\.\.(/|\\z)|^\.\./~', str_replace('\\', '/', $dest_file))) {
+            return $this->raiseError("SECURITY ERROR: file $file (installed to $dest_file) contains parent directory reference ..", PEAR_INSTALLER_FAILED);
+        }
         // }}}
         if (empty($this->_options['register-only']) &&
               (!file_exists($dest_dir) || !is_dir($dest_dir))) {
             if (!$this->mkDirHier($dest_dir)) {
                 return $this->raiseError("failed to mkdir $dest_dir",
                                          PEAR_INSTALLER_FAILED);
+            }
             $this->log(3, "+ mkdir $dest_dir");
+        }
         // pretty much nothing happens if we are only registering the install
         if (empty($this->_options['register-only'])) {
             if (empty($atts['replacements'])) {
                 if (!file_exists($orig_file)) {
                     return $this->raiseError("file $orig_file does not exist",
                                              PEAR_INSTALLER_FAILED);
+                }
                 if (!@copy($orig_file, $dest_file)) {
                     return $this->raiseError("failed to write $dest_file: $php_errormsg",
                                              PEAR_INSTALLER_FAILED);
+                }
                 $this->log(3, "+ cp $orig_file $dest_file");
                 if (isset($atts['md5sum'])) {
                     $md5sum = md5_file($dest_file);
+                }
             } else {
                 // {{{ file with replacements
                 if (!file_exists($orig_file)) {
                     return $this->raiseError("file does not exist",
                                              PEAR_INSTALLER_FAILED);
+                }
                 $contents = file_get_contents($orig_file);
                 if ($contents === false) {
                     $contents = '';
+                }
                 if (isset($atts['md5sum'])) {
                     $md5sum = md5($contents);
+                }
                 $subst_from = $subst_to = array();
                 foreach ($atts['replacements'] as $a) {
                     $to = '';
                     if ($a['type'] == 'php-const') {
-                        if (preg_match('/^[a-z0-9_]+$/i', $a['to'])) {
+                        if (preg_match('/^[a-z0-9_]+\\z/i', $a['to'])) {
                             eval("\$to = $a[to];");
                         } else {
                             if (!isset($options['soft'])) {
                                 $this->log(0, "invalid php-const replacement: $a[to]");
+                            }
                             continue;
+                        }
                     } elseif ($a['type'] == 'pear-config') {
                         if ($a['to'] == 'master_server') {
                             $chan = $this->_registry->getChannel($channel);
                             if (!PEAR::isError($chan)) {
                                 $to = $chan->getServer();
                             } else {
                                 $to = $this->config->get($a['to'], null, $channel);
+                            }
                         } else {
                             $to = $this->config->get($a['to'], null, $channel);
+                        }
                         if (is_null($to)) {
                             if (!isset($options['soft'])) {
                                 $this->log(0, "invalid pear-config replacement: $a[to]");
+                            }
                             continue;
+                        }
                     } elseif ($a['type'] == 'package-info') {
                         if ($t = $this->pkginfo->packageInfo($a['to'])) {
                             $to = $t;
                         } else {
                             if (!isset($options['soft'])) {
                                 $this->log(0, "invalid package-info replacement: $a[to]");
+                            }
                             continue;
+                        }
+                    }
                     if (!is_null($to)) {
                         $subst_from[] = $a['from'];
                         $subst_to[] = $to;
+                    }
+                }
                 $this->log(3, "doing ".sizeof($subst_from)." substitution(s) for $final_dest_file");
                 if (sizeof($subst_from)) {
                     $contents = str_replace($subst_from, $subst_to, $contents);
+                }
                 $wp = @fopen($dest_file, "wb");
                 if (!is_resource($wp)) {
                     return $this->raiseError("failed to create $dest_file: $php_errormsg",
                                              PEAR_INSTALLER_FAILED);
+                }
                 if (@fwrite($wp, $contents) === false) {
                     return $this->raiseError("failed writing to $dest_file: $php_errormsg",
                                              PEAR_INSTALLER_FAILED);
+                }
                 fclose($wp);
                 // }}}
+            }
             // {{{ check the md5
             if (isset($md5sum)) {
-                if (strtolower($md5sum) == strtolower($atts['md5sum'])) {
+                if (strtolower($md5sum) === strtolower($atts['md5sum'])) {
                     $this->log(2, "md5sum ok: $final_dest_file");
                 } else {
                     if (empty($options['force'])) {
                         // delete the file
                         if (file_exists($dest_file)) {
                             unlink($dest_file);
+                        }
                         if (!isset($options['ignore-errors'])) {
                             return $this->raiseError("bad md5sum for file $final_dest_file",
                                                  PEAR_INSTALLER_FAILED);
-                        } else {
+                        }
-                            if (!isset($options['soft'])) {
+                        if (!isset($options['soft'])) {
-                                $this->log(0, "warning : bad md5sum for file $final_dest_file");
+                            $this->log(0, "warning : bad md5sum for file $final_dest_file");
-                            }
+                        }
                     } else {
                         if (!isset($options['soft'])) {
                             $this->log(0, "warning : bad md5sum for file $final_dest_file");
+                        }
+                    }
+                }
+            }
             // }}}
             // {{{ set file permissions
             if (!OS_WINDOWS) {
                 if ($atts['role'] == 'script') {
                     $mode = 0777 & ~(int)octdec($this->config->get('umask'));
                     $this->log(3, "+ chmod +x $dest_file");
                 } else {
                     $mode = 0666 & ~(int)octdec($this->config->get('umask'));
+                }
+                if ($atts['role'] != 'src') {
-                $this->addFileOperation("chmod", array($mode, $dest_file));
+                    $this->addFileOperation("chmod", array($mode, $dest_file));
-                if (!@chmod($dest_file, $mode)) {
+                    if (!@chmod($dest_file, $mode)) {
-                    if (!isset($options['soft'])) {
+                        if (!isset($options['soft'])) {
-                        $this->log(0, "failed to change mode of $dest_file: $php_errormsg");
+                            $this->log(0, "failed to change mode of $dest_file: $php_errormsg");
+                        }
+                    }
+                }
+            }
             // }}}
+            if ($atts['role'] == 'src') {
+                rename($dest_file, $final_dest_file);
+                $this->log(2, "renamed source file $dest_file to $final_dest_file");
+            } else {
-            $this->addFileOperation("rename", array($dest_file, $final_dest_file,
+                $this->addFileOperation("rename", array($dest_file, $final_dest_file,
-                $atts['role'] == 'ext'));
+                    $atts['role'] == 'ext'));
+            }
+        }
         // Store the full path where the file was installed for easy unistall
+        if ($atts['role'] != 'script') {
+            $loc = $this->config->get($atts['role'] . '_dir');
+        } else {
+            $loc = $this->config->get('bin_dir');
+        }
+        if ($atts['role'] != 'src') {
-        $this->addFileOperation("installed_as", array($file, $installed_as,
+            $this->addFileOperation("installed_as", array($file, $installed_as,
+                                    $loc,
-                                $save_destdir, dirname(substr($installedas_dest_file, strlen($save_destdir)))));
+                                    dirname(substr($installedas_dest_file, strlen($loc)))));
+        }
         //$this->log(2, "installed: $dest_file");
         return PEAR_INSTALLER_OK;
+    }
     // }}}
     // {{{ _installFile2()
     /**
      * @param PEAR_PackageFile_v1|PEAR_PackageFile_v2
      * @param string filename
      * @param array attributes from <file> tag in package.xml
      * @param string path to install the file in
      * @param array options from command-line
      * @access private
      */
-    function _installFile2(&$pkg, $file, $atts, $tmp_path, $options)
+    function _installFile2(&$pkg, $file, &$real_atts, $tmp_path, $options)
+    {
+        $atts = $real_atts;
         if (!isset($this->_registry)) {
             $this->_registry = &$this->config->getRegistry();
+        }
         $channel = $pkg->getChannel();
         // {{{ assemble the destination paths
         if (!in_array($atts['attribs']['role'],
               PEAR_Installer_Role::getValidRoles($pkg->getPackageType()))) {
             return $this->raiseError('Invalid role `' . $atts['attribs']['role'] .
                     "' for file $file");
+        }
         $role = &PEAR_Installer_Role::factory($pkg, $atts['attribs']['role'], $this->config);
-        $err = $role->setup($this, $pkg, $atts['attribs'], $file);
+        $err  = $role->setup($this, $pkg, $atts['attribs'], $file);
         if (PEAR::isError($err)) {
             return $err;
+        }
         if (!$role->isInstallable()) {
             return;
+        }
         $info = $role->processInstallation($pkg, $atts['attribs'], $file, $tmp_path);
         if (PEAR::isError($info)) {
             return $info;
-        } else {
-            list($save_destdir, $dest_dir, $dest_file, $orig_file) = $info;
+        }
+        list($save_destdir, $dest_dir, $dest_file, $orig_file) = $info;
+        if (preg_match('~/\.\.(/|\\z)|^\.\./~', str_replace('\\', '/', $dest_file))) {
+            return $this->raiseError("SECURITY ERROR: file $file (installed to $dest_file) contains parent directory reference ..", PEAR_INSTALLER_FAILED);
+        }
         $final_dest_file = $installed_as = $dest_file;
         if (isset($this->_options['packagingroot'])) {
             $final_dest_file = $this->_prependPath($final_dest_file,
                 $this->_options['packagingroot']);
+        }
-        $dest_dir = dirname($final_dest_file);
+        $dest_dir  = dirname($final_dest_file);
         $dest_file = $dest_dir . DIRECTORY_SEPARATOR . '.tmp' . basename($final_dest_file);
         // }}}
         if (empty($this->_options['register-only'])) {
             if (!file_exists($dest_dir) || !is_dir($dest_dir)) {
                 if (!$this->mkDirHier($dest_dir)) {
                     return $this->raiseError("failed to mkdir $dest_dir",
                                              PEAR_INSTALLER_FAILED);
+                }
                 $this->log(3, "+ mkdir $dest_dir");
+            }
+        }
         $attribs = $atts['attribs'];
         unset($atts['attribs']);
         // pretty much nothing happens if we are only registering the install
         if (empty($this->_options['register-only'])) {
             if (!count($atts)) { // no tasks
                 if (!file_exists($orig_file)) {
                     return $this->raiseError("file $orig_file does not exist",
                                              PEAR_INSTALLER_FAILED);
+                }
                 if (!@copy($orig_file, $dest_file)) {
                     return $this->raiseError("failed to write $dest_file: $php_errormsg",
                                              PEAR_INSTALLER_FAILED);
+                }
                 $this->log(3, "+ cp $orig_file $dest_file");
                 if (isset($attribs['md5sum'])) {
                     $md5sum = md5_file($dest_file);
+                }
             } else { // file with tasks
                 if (!file_exists($orig_file)) {
                     return $this->raiseError("file $orig_file does not exist",
                                              PEAR_INSTALLER_FAILED);
+                }
                 $contents = file_get_contents($orig_file);
                 if ($contents === false) {
                     $contents = '';
+                }
                 if (isset($attribs['md5sum'])) {
                     $md5sum = md5($contents);
+                }
                 foreach ($atts as $tag => $raw) {
-                    $tag = str_replace(array($pkg->getTasksNs() . ':', '-'),
+                    $tag = str_replace(array($pkg->getTasksNs() . ':', '-'), array('', '_'), $tag);
-                        array('', '_'), $tag);
                     $task = "PEAR_Task_$tag";
-                    $task = &new $task($this->config, $this, PEAR_TASK_INSTALL);
+                    $task = new $task($this->config, $this, PEAR_TASK_INSTALL);
                     if (!$task->isScript()) { // scripts are only handled after installation
                         $task->init($raw, $attribs, $pkg->getLastInstalledVersion());
                         $res = $task->startSession($pkg, $contents, $final_dest_file);
                         if ($res === false) {
                             continue; // skip this file
+                        }
                         if (PEAR::isError($res)) {
                             return $res;
+                        }
                         $contents = $res; // save changes
+                    }
                     $wp = @fopen($dest_file, "wb");
                     if (!is_resource($wp)) {
                         return $this->raiseError("failed to create $dest_file: $php_errormsg",
                                                  PEAR_INSTALLER_FAILED);
+                    }
                     if (fwrite($wp, $contents) === false) {
                         return $this->raiseError("failed writing to $dest_file: $php_errormsg",
                                                  PEAR_INSTALLER_FAILED);
+                    }
                     fclose($wp);
+                }
+            }
             // {{{ check the md5
             if (isset($md5sum)) {
+                // Make sure the original md5 sum matches with expected
-                if (strtolower($md5sum) == strtolower($attribs['md5sum'])) {
+                if (strtolower($md5sum) === strtolower($attribs['md5sum'])) {
                     $this->log(2, "md5sum ok: $final_dest_file");
+                    if (isset($contents)) {
+                        // set md5 sum based on $content in case any tasks were run.
+                        $real_atts['attribs']['md5sum'] = md5($contents);
+                    }
                 } else {
                     if (empty($options['force'])) {
                         // delete the file
                         if (file_exists($dest_file)) {
                             unlink($dest_file);
+                        }
                         if (!isset($options['ignore-errors'])) {
                             return $this->raiseError("bad md5sum for file $final_dest_file",
                                                      PEAR_INSTALLER_FAILED);
-                        } else {
+                        }
-                            if (!isset($options['soft'])) {
+                        if (!isset($options['soft'])) {
-                                $this->log(0, "warning : bad md5sum for file $final_dest_file");
+                            $this->log(0, "warning : bad md5sum for file $final_dest_file");
-                            }
+                        }
                     } else {
                         if (!isset($options['soft'])) {
                             $this->log(0, "warning : bad md5sum for file $final_dest_file");
+                        }
+                    }
+                }
+            } else {
+                $real_atts['attribs']['md5sum'] = md5_file($dest_file);
+            }
             // }}}
             // {{{ set file permissions
             if (!OS_WINDOWS) {
                 if ($role->isExecutable()) {
                     $mode = 0777 & ~(int)octdec($this->config->get('umask'));
                     $this->log(3, "+ chmod +x $dest_file");
                 } else {
                     $mode = 0666 & ~(int)octdec($this->config->get('umask'));
+                }
+                if ($attribs['role'] != 'src') {
-                $this->addFileOperation("chmod", array($mode, $dest_file));
+                    $this->addFileOperation("chmod", array($mode, $dest_file));
-                if (!@chmod($dest_file, $mode)) {
+                    if (!@chmod($dest_file, $mode)) {
-                    if (!isset($options['soft'])) {
+                        if (!isset($options['soft'])) {
-                        $this->log(0, "failed to change mode of $dest_file: $php_errormsg");
+                            $this->log(0, "failed to change mode of $dest_file: $php_errormsg");
+                        }
+                    }
+                }
+            }
             // }}}
+            if ($attribs['role'] == 'src') {
+                rename($dest_file, $final_dest_file);
+                $this->log(2, "renamed source file $dest_file to $final_dest_file");
+            } else {
-            $this->addFileOperation("rename", array($dest_file, $final_dest_file, $role->isExtension()));
+                $this->addFileOperation("rename", array($dest_file, $final_dest_file, $role->isExtension()));
+            }
+        }
         // Store the full path where the file was installed for easy uninstall
+        if ($attribs['role'] != 'src') {
+            $loc = $this->config->get($role->getLocationConfig(), null, $channel);
-        $this->addFileOperation("installed_as", array($file, $installed_as,
+            $this->addFileOperation('installed_as', array($file, $installed_as,
+                                $loc,
-                            $save_destdir, dirname(substr($dest_file, strlen($save_destdir)))));
+                                dirname(substr($installed_as, strlen($loc)))));
+        }
         //$this->log(2, "installed: $dest_file");
         return PEAR_INSTALLER_OK;
+    }
     // }}}
     // {{{ addFileOperation()
     /**
      * Add a file operation to the current file transaction.
+     *
      * @see startFileTransaction()
      * @param string $type This can be one of:
      *    - rename:  rename a file ($data has 3 values)
      *    - backup:  backup an existing file ($data has 1 value)
      *    - removebackup:  clean up backups created during install ($data has 1 value)
      *    - chmod:   change permissions on a file ($data has 2 values)
      *    - delete:  delete a file ($data has 1 value)
      *    - rmdir:   delete a directory if empty ($data has 1 value)
      *    - installed_as: mark a file as installed ($data has 4 values).
      * @param array $data For all file operations, this array must contain the
      *    full path to the file or directory that is being operated on.  For
      *    the rename command, the first parameter must be the file to rename,
      *    the second its new name, the third whether this is a PHP extension.
+     *
      *    The installed_as operation contains 4 elements in this order:
      *    1. Filename as listed in the filelist element from package.xml
      *    2. Full path to the installed file
      *    3. Full path from the php_dir configuration variable used in this
      *       installation
      *    4. Relative path from the php_dir that this file is installed in
      */
     function addFileOperation($type, $data)
+    {
         if (!is_array($data)) {
             return $this->raiseError('Internal Error: $data in addFileOperation'
                 . ' must be an array, was ' . gettype($data));
+        }
         if ($type == 'chmod') {
             $octmode = decoct($data[0]);
             $this->log(3, "adding to transaction: $type $octmode $data[1]");
         } else {
             $this->log(3, "adding to transaction: $type " . implode(" ", $data));
+        }
         $this->file_operations[] = array($type, $data);
+    }
     // }}}
     // {{{ startFileTransaction()
     function startFileTransaction($rollback_in_case = false)
+    {
         if (count($this->file_operations) && $rollback_in_case) {
             $this->rollbackFileTransaction();
+        }
         $this->file_operations = array();
+    }
     // }}}
     // {{{ commitFileTransaction()
     function commitFileTransaction()
+    {
-        $n = count($this->file_operations);
-        $this->log(2, "about to commit $n file operations");
         // {{{ first, check permissions and such manually
         $errors = array();
-        foreach ($this->file_operations as $tr) {
+        foreach ($this->file_operations as $key => $tr) {
             list($type, $data) = $tr;
             switch ($type) {
                 case 'rename':
                     if (!file_exists($data[0])) {
                         $errors[] = "cannot rename file $data[0], doesn't exist";
+                    }
                     // check that dest dir. is writable
                     if (!is_writable(dirname($data[1]))) {
                         $errors[] = "permission denied ($type): $data[1]";
+                    }
                     break;
                 case 'chmod':
                     // check that file is writable
                     if (!is_writable($data[1])) {
                         $errors[] = "permission denied ($type): $data[1] " . decoct($data[0]);
+                    }
                     break;
                 case 'delete':
                     if (!file_exists($data[0])) {
                         $this->log(2, "warning: file $data[0] doesn't exist, can't be deleted");
+                    }
                     // check that directory is writable
                     if (file_exists($data[0])) {
                         if (!is_writable(dirname($data[0]))) {
                             $errors[] = "permission denied ($type): $data[0]";
                         } else {
                             // make sure the file to be deleted can be opened for writing
                             $fp = false;
                             if (!is_dir($data[0]) &&
                                   (!is_writable($data[0]) || !($fp = @fopen($data[0], 'a')))) {
                                 $errors[] = "permission denied ($type): $data[0]";
                             } elseif ($fp) {
                                 fclose($fp);
+                            }
+                        }
+                        /* Verify we are not deleting a file owned by another package
+                         * This can happen when a file moves from package A to B in
+                         * an upgrade ala http://pear.php.net/17986
+                         */
+                        $info = array(
+                            'package' => strtolower($this->pkginfo->getName()),
+                            'channel' => strtolower($this->pkginfo->getChannel()),
+                        );
+                        $result = $this->_registry->checkFileMap($data[0], $info, '1.1');
+                        if (is_array($result)) {
+                            $res = array_diff($result, $info);
+                            if (!empty($res)) {
+                                $new = $this->_registry->getPackage($result[1], $result[0]);
+                                $this->file_operations[$key] = false;
+                                $pkginfoName = $this->pkginfo->getName();
+                                $newChannel  = $new->getChannel();
+                                $newPackage  = $new->getName();
+                                $this->log(3, "file $data[0] was scheduled for removal from $pkginfoName but is owned by $newChannel/$newPackage, removal has been cancelled.");
+                            }
+                        }
+                    }
                     break;
+            }
+        }
         // }}}
+        $n = count($this->file_operations);
+        $this->log(2, "about to commit $n file operations for " . $this->pkginfo->getName());
-        $m = sizeof($errors);
+        $m = count($errors);
         if ($m > 0) {
             foreach ($errors as $error) {
                 if (!isset($this->_options['soft'])) {
                     $this->log(1, $error);
+                }
+            }
             if (!isset($this->_options['ignore-errors'])) {
                 return false;
+            }
+        }
         $this->_dirtree = array();
         // {{{ really commit the transaction
         foreach ($this->file_operations as $i => $tr) {
             if (!$tr) {
                 // support removal of non-existing backups
                 continue;
+            }
             list($type, $data) = $tr;
             switch ($type) {
                 case 'backup':
                     if (!file_exists($data[0])) {
                         $this->file_operations[$i] = false;
                         break;
+                    }
                     if (!@copy($data[0], $data[0] . '.bak')) {
                         $this->log(1, 'Could not copy ' . $data[0] . ' to ' . $data[0] .
                             '.bak ' . $php_errormsg);
                         return false;
+                    }
                     $this->log(3, "+ backup $data[0] to $data[0].bak");
                     break;
                 case 'removebackup':
                     if (file_exists($data[0] . '.bak') && is_writable($data[0] . '.bak')) {
                         unlink($data[0] . '.bak');
                         $this->log(3, "+ rm backup of $data[0] ($data[0].bak)");
+                    }
                     break;
                 case 'rename':
-                    if (file_exists($data[1])) {
-                        $test = @unlink($data[1]);
+                    $test = file_exists($data[1]) ? @unlink($data[1]) : null;
-                    } else {
-                        $test = null;
-                    }
                     if (!$test && file_exists($data[1])) {
                         if ($data[2]) {
                             $extra = ', this extension must be installed manually.  Rename to "' .
                                 basename($data[1]) . '"';
                         } else {
                             $extra = '';
+                        }
                         if (!isset($this->_options['soft'])) {
                             $this->log(1, 'Could not delete ' . $data[1] . ', cannot rename ' .
                                 $data[0] . $extra);
+                        }
                         if (!isset($this->_options['ignore-errors'])) {
                             return false;
+                        }
+                    }
                     // permissions issues with rename - copy() is far superior
                     $perms = @fileperms($data[0]);
                     if (!@copy($data[0], $data[1])) {
                         $this->log(1, 'Could not rename ' . $data[0] . ' to ' . $data[1] .
                             ' ' . $php_errormsg);
                         return false;
+                    }
                     // copy over permissions, otherwise they are lost
                     @chmod($data[1], $perms);
                     @unlink($data[0]);
                     $this->log(3, "+ mv $data[0] $data[1]");
                     break;
                 case 'chmod':
                     if (!@chmod($data[1], $data[0])) {
                         $this->log(1, 'Could not chmod ' . $data[1] . ' to ' .
                             decoct($data[0]) . ' ' . $php_errormsg);
                         return false;
+                    }
                     $octmode = decoct($data[0]);
                     $this->log(3, "+ chmod $octmode $data[1]");
                     break;
                 case 'delete':
                     if (file_exists($data[0])) {
                         if (!@unlink($data[0])) {
                             $this->log(1, 'Could not delete ' . $data[0] . ' ' .
                                 $php_errormsg);
                             return false;
+                        }
                         $this->log(3, "+ rm $data[0]");
+                    }
                     break;
                 case 'rmdir':
                     if (file_exists($data[0])) {
                         do {
                             $testme = opendir($data[0]);
                             while (false !== ($entry = readdir($testme))) {
                                 if ($entry == '.' || $entry == '..') {
                                     continue;
+                                }
                                 closedir($testme);
                                 break 2; // this directory is not empty and can't be
                                          // deleted
+                            }
                             closedir($testme);
                             if (!@rmdir($data[0])) {
                                 $this->log(1, 'Could not rmdir ' . $data[0] . ' ' .
                                     $php_errormsg);
                                 return false;
+                            }
                             $this->log(3, "+ rmdir $data[0]");
                         } while (false);
+                    }
                     break;
                 case 'installed_as':
                     $this->pkginfo->setInstalledAs($data[0], $data[1]);
                     if (!isset($this->_dirtree[dirname($data[1])])) {
                         $this->_dirtree[dirname($data[1])] = true;
                         $this->pkginfo->setDirtree(dirname($data[1]));
-                        while(!empty($data[3]) && $data[3] != '/' && $data[3] != '\\'
+                        while(!empty($data[3]) && dirname($data[3]) != $data[3] &&
-                              && $data[3] != '.') {
+                                $data[3] != '/' && $data[3] != '\\') {
                             $this->pkginfo->setDirtree($pp =
                                 $this->_prependPath($data[3], $data[2]));
                             $this->_dirtree[$pp] = true;
                             $data[3] = dirname($data[3]);
+                        }
+                    }
                     break;
+            }
+        }
         // }}}
         $this->log(2, "successfully committed $n file operations");
         $this->file_operations = array();
         return true;
+    }
     // }}}
     // {{{ rollbackFileTransaction()
     function rollbackFileTransaction()
+    {
         $n = count($this->file_operations);
         $this->log(2, "rolling back $n file operations");
         foreach ($this->file_operations as $tr) {
             list($type, $data) = $tr;
             switch ($type) {
                 case 'backup':
                     if (file_exists($data[0] . '.bak')) {
                         if (file_exists($data[0] && is_writable($data[0]))) {
                             unlink($data[0]);
+                        }
                         @copy($data[0] . '.bak', $data[0]);
                         $this->log(3, "+ restore $data[0] from $data[0].bak");
+                    }
                     break;
                 case 'removebackup':
                     if (file_exists($data[0] . '.bak') && is_writable($data[0] . '.bak')) {
                         unlink($data[0] . '.bak');
                         $this->log(3, "+ rm backup of $data[0] ($data[0].bak)");
+                    }
                     break;
                 case 'rename':
                     @unlink($data[0]);
                     $this->log(3, "+ rm $data[0]");
                     break;
                 case 'mkdir':
                     @rmdir($data[0]);
                     $this->log(3, "+ rmdir $data[0]");
                     break;
                 case 'chmod':
                     break;
                 case 'delete':
                     break;
                 case 'installed_as':
                     $this->pkginfo->setInstalledAs($data[0], false);
                     break;
+            }
+        }
         $this->pkginfo->resetDirtree();
         $this->file_operations = array();
+    }
     // }}}
     // {{{ mkDirHier($dir)
     function mkDirHier($dir)
+    {
         $this->addFileOperation('mkdir', array($dir));
         return parent::mkDirHier($dir);
+    }
     // }}}
-    // {{{ download()
-    /**
-     * Download any files and their dependencies, if necessary
-     *
-     * @param array a mixed list of package names, local files, or package.xml
-     * @param PEAR_Config
-     * @param array options from the command line
-     * @param array this is the array that will be populated with packages to
-     *              install.  Format of each entry:
-     *
-     * <code>
-     * array('pkg' => 'package_name', 'file' => '/path/to/local/file',
-     *    'info' => array() // parsed package.xml
-     * );
-     * </code>
-     * @param array this will be populated with any error messages
-     * @param false private recursion variable
-     * @param false private recursion variable
-     * @param false private recursion variable
-     * @deprecated in favor of PEAR_Downloader
-     */
-    function download($packages, $options, &$config, &$installpackages,
-                      &$errors, $installed = false, $willinstall = false, $state = false)
-    {
-        // trickiness: initialize here
-        parent::PEAR_Downloader($this->ui, $options, $config);
-        $ret = parent::download($packages);
-        $errors = $this->getErrorMsgs();
-        $installpackages = $this->getDownloadedPackages();
-        trigger_error("PEAR Warning: PEAR_Installer::download() is deprecated " .
-                      "in favor of PEAR_Downloader class", E_USER_WARNING);
-        return $ret;
-    }
-    // }}}
     // {{{ _parsePackageXml()
-    function _parsePackageXml(&$descfile, &$tmpdir)
+    function _parsePackageXml(&$descfile)
-    {
-        if (substr($descfile, -4) == '.xml') {
-            $tmpdir = false;
-        } else {
-            // {{{ Decompress pack in tmp dir -------------------------------------
-            // To allow relative package file names
-            $descfile = realpath($descfile);
-            if (PEAR::isError($tmpdir = System::mktemp('-d'))) {
-                return $tmpdir;
-            }
-            $this->log(3, '+ tmp dir created at ' . $tmpdir);
-            // }}}
+    {
         // Parse xml file -----------------------------------------------
-        $pkg = new PEAR_PackageFile($this->config, $this->debug, $tmpdir);
+        $pkg = new PEAR_PackageFile($this->config, $this->debug);
         PEAR::staticPushErrorHandling(PEAR_ERROR_RETURN);
         $p = &$pkg->fromAnyFile($descfile, PEAR_VALIDATE_INSTALLING);
         PEAR::staticPopErrorHandling();
         if (PEAR::isError($p)) {
             if (is_array($p->getUserInfo())) {
                 foreach ($p->getUserInfo() as $err) {
                     $loglevel = $err['level'] == 'error' ? 0 : 1;
                     if (!isset($this->_options['soft'])) {
                         $this->log($loglevel, ucfirst($err['level']) . ': ' . $err['message']);
+                    }
+                }
+            }
             return $this->raiseError('Installation failed: invalid package file');
-        } else {
-            $descfile = $p->getPackageFile();
+        }
+        $descfile = $p->getPackageFile();
         return $p;
+    }
     // }}}
     /**
      * Set the list of PEAR_Downloader_Package objects to allow more sane
      * dependency validation
      * @param array
      */
     function setDownloadedPackages(&$pkgs)
+    {
         PEAR::pushErrorHandling(PEAR_ERROR_RETURN);
         $err = $this->analyzeDependencies($pkgs);
         PEAR::popErrorHandling();
         if (PEAR::isError($err)) {
             return $err;
+        }
         $this->_downloadedPackages = &$pkgs;
+    }
     /**
      * Set the list of PEAR_Downloader_Package objects to allow more sane
      * dependency validation
      * @param array
      */
     function setUninstallPackages(&$pkgs)
+    {
         $this->_downloadedPackages = &$pkgs;
+    }
     function getInstallPackages()
+    {
         return $this->_downloadedPackages;
+    }
     // {{{ install()
     /**
      * Installs the files within the package file specified.
+     *
      * @param string|PEAR_Downloader_Package $pkgfile path to the package file,
      *        or a pre-initialized packagefile object
      * @param array $options
      * recognized options:
      * - installroot   : optional prefix directory for installation
      * - force         : force installation
      * - register-only : update registry but don't install files
      * - upgrade       : upgrade existing install
      * - soft          : fail silently
      * - nodeps        : ignore dependency conflicts/missing dependencies
      * - alldeps       : install all dependencies
      * - onlyreqdeps   : install only required dependencies
+     *
      * @return array|PEAR_Error package info if successful
      */
     function install($pkgfile, $options = array())
+    {
         $this->_options = $options;
         $this->_registry = &$this->config->getRegistry();
         if (is_object($pkgfile)) {
-            $dlpkg = &$pkgfile;
+            $dlpkg    = &$pkgfile;
-            $pkg = $pkgfile->getPackageFile();
+            $pkg      = $pkgfile->getPackageFile();
-            $pkgfile = $pkg->getArchiveFile();
+            $pkgfile  = $pkg->getArchiveFile();
             $descfile = $pkg->getPackageFile();
-            $tmpdir = dirname($descfile);
         } else {
             $descfile = $pkgfile;
-            $tmpdir = '';
+            $pkg      = $this->_parsePackageXml($descfile);
-            if (PEAR::isError($pkg = &$this->_parsePackageXml($descfile, $tmpdir))) {
+            if (PEAR::isError($pkg)) {
                 return $pkg;
+            }
+        }
         $tmpdir = dirname($descfile);
+        if (realpath($descfile) != realpath($pkgfile)) {
+            // Use the temp_dir since $descfile can contain the download dir path
+            $tmpdir = $this->config->get('temp_dir', null, 'pear.php.net');
+            $tmpdir = System::mktemp('-d -t "' . $tmpdir . '"');
         if (realpath($descfile) != realpath($pkgfile)) {
             $tar = new Archive_Tar($pkgfile);
             if (!$tar->extract($tmpdir)) {
                 return $this->raiseError("unable to unpack $pkgfile");
+            }
+        }
         $pkgname = $pkg->getName();
         $channel = $pkg->getChannel();
-        if (isset($this->_options['packagingroot'])) {
-            $regdir = $this->_prependPath(
-                $this->config->get('php_dir', null, 'pear.php.net'),
-                $this->_options['packagingroot']);
-            $packrootphp_dir = $this->_prependPath(
-                $this->config->get('php_dir', null, $channel),
-                $this->_options['packagingroot']);
-        }
         if (isset($options['installroot'])) {
             $this->config->setInstallRoot($options['installroot']);
             $this->_registry = &$this->config->getRegistry();
             $installregistry = &$this->_registry;
             $this->installroot = ''; // all done automagically now
             $php_dir = $this->config->get('php_dir', null, $channel);
         } else {
             $this->config->setInstallRoot(false);
             $this->_registry = &$this->config->getRegistry();
             if (isset($this->_options['packagingroot'])) {
+                $regdir = $this->_prependPath(
+                    $this->config->get('php_dir', null, 'pear.php.net'),
+                    $this->_options['packagingroot']);
+                $metadata_dir = $this->config->get('metadata_dir', null, 'pear.php.net');
+                if ($metadata_dir) {
+                    $metadata_dir = $this->_prependPath(
+                        $metadata_dir,
+                        $this->_options['packagingroot']);
+                }
+                $packrootphp_dir = $this->_prependPath(
+                    $this->config->get('php_dir', null, $channel),
+                    $this->_options['packagingroot']);
-                $installregistry = &new PEAR_Registry($regdir);
+                $installregistry = new PEAR_Registry($regdir, false, false, $metadata_dir);
                 if (!$installregistry->channelExists($channel, true)) {
                     // we need to fake a channel-discover of this channel
                     $chanobj = $this->_registry->getChannel($channel, true);
                     $installregistry->addChannel($chanobj);
+                }
                 $php_dir = $packrootphp_dir;
             } else {
                 $installregistry = &$this->_registry;
                 $php_dir = $this->config->get('php_dir', null, $channel);
+            }
             $this->installroot = '';
+        }
         // {{{ checks to do when not in "force" mode
         if (empty($options['force']) &&
               (file_exists($this->config->get('php_dir')) &&
                is_dir($this->config->get('php_dir')))) {
             $testp = $channel == 'pear.php.net' ? $pkgname : array($channel, $pkgname);
             $instfilelist = $pkg->getInstallationFileList(true);
             if (PEAR::isError($instfilelist)) {
                 return $instfilelist;
+            }
             // ensure we have the most accurate registry
             $installregistry->flushFileMap();
             $test = $installregistry->checkFileMap($instfilelist, $testp, '1.1');
             if (PEAR::isError($test)) {
                 return $test;
+            }
             if (sizeof($test)) {
                 $pkgs = $this->getInstallPackages();
                 $found = false;
                 foreach ($pkgs as $param) {
                     if ($pkg->isSubpackageOf($param)) {
                         $found = true;
                         break;
+                    }
+                }
                 if ($found) {
                     // subpackages can conflict with earlier versions of parent packages
                     $parentreg = $installregistry->packageInfo($param->getPackage(), null, $param->getChannel());
                     $tmp = $test;
                     foreach ($tmp as $file => $info) {
                         if (is_array($info)) {
                             if (strtolower($info[1]) == strtolower($param->getPackage()) &&
-                                  strtolower($info[0]) == strtolower($param->getChannel())) {
+                                  strtolower($info[0]) == strtolower($param->getChannel())
+                            ) {
+                                if (isset($parentreg['filelist'][$file])) {
+                                    unset($parentreg['filelist'][$file]);
+                                } else{
+                                    $pos     = strpos($file, '/');
+                                    $basedir = substr($file, 0, $pos);
+                                    $file2   = substr($file, $pos + 1);
+                                    if (isset($parentreg['filelist'][$file2]['baseinstalldir'])
+                                        && $parentreg['filelist'][$file2]['baseinstalldir'] === $basedir
+                                    ) {
+                                        unset($parentreg['filelist'][$file2]);
+                                    }
+                                }
                                 unset($test[$file]);
-                                unset($parentreg['filelist'][$file]);
+                            }
                         } else {
                             if (strtolower($param->getChannel()) != 'pear.php.net') {
                                 continue;
+                            }
                             if (strtolower($info) == strtolower($param->getPackage())) {
+                                if (isset($parentreg['filelist'][$file])) {
+                                    unset($parentreg['filelist'][$file]);
+                                } else{
+                                    $pos     = strpos($file, '/');
+                                    $basedir = substr($file, 0, $pos);
+                                    $file2   = substr($file, $pos + 1);
+                                    if (isset($parentreg['filelist'][$file2]['baseinstalldir'])
+                                        && $parentreg['filelist'][$file2]['baseinstalldir'] === $basedir
+                                    ) {
+                                        unset($parentreg['filelist'][$file2]);
+                                    }
+                                }
                                 unset($test[$file]);
-                                unset($parentreg['filelist'][$file]);
+                            }
+                        }
+                    }
-                    $pfk = &new PEAR_PackageFile($this->config);
+                    $pfk = new PEAR_PackageFile($this->config);
                     $parentpkg = &$pfk->fromArray($parentreg);
                     $installregistry->updatePackage2($parentpkg);
+                }
                 if ($param->getChannel() == 'pecl.php.net' && isset($options['upgrade'])) {
                     $tmp = $test;
                     foreach ($tmp as $file => $info) {
                         if (is_string($info)) {
                             // pear.php.net packages are always stored as strings
                             if (strtolower($info) == strtolower($param->getPackage())) {
                                 // upgrading existing package
                                 unset($test[$file]);
+                            }
+                        }
+                    }
+                }
-                if (sizeof($test)) {
+                if (count($test)) {
                     $msg = "$channel/$pkgname: conflicting files found:\n";
                     $longest = max(array_map("strlen", array_keys($test)));
                     $fmt = "%${longest}s (%s)\n";
                     foreach ($test as $file => $info) {
                         if (!is_array($info)) {
                             $info = array('pear.php.net', $info);
+                        }
                         $info = $info[0] . '/' . $info[1];
                         $msg .= sprintf($fmt, $file, $info);
+                    }
                     if (!isset($options['ignore-errors'])) {
                         return $this->raiseError($msg);
-                    } else {
+                    }
-                        if (!isset($options['soft'])) {
+                    if (!isset($options['soft'])) {
-                            $this->log(0, "WARNING: $msg");
+                        $this->log(0, "WARNING: $msg");
-                        }
+                    }
+                }
+            }
+        }
         // }}}
         $this->startFileTransaction();
+        $usechannel = $channel;
+        if ($channel == 'pecl.php.net') {
+            $test = $installregistry->packageExists($pkgname, $channel);
+            if (!$test) {
+                $test = $installregistry->packageExists($pkgname, 'pear.php.net');
+                $usechannel = 'pear.php.net';
+            }
+        } else {
+            $test = $installregistry->packageExists($pkgname, $channel);
+        }
         if (empty($options['upgrade']) && empty($options['soft'])) {
-            // checks to do only when installing new packages
-            if ($channel == 'pecl.php.net') {
-                $test = $installregistry->packageExists($pkgname, $channel);
-                if (!$test) {
-                    $test = $installregistry->packageExists($pkgname, 'pear.php.net');
-                }
-            } else {
-                $test = $installregistry->packageExists($pkgname, $channel);
             // checks to do only when installing new packages
             if (empty($options['force']) && $test) {
                 return $this->raiseError("$channel/$pkgname is already installed");
+            }
         } else {
-            $usechannel = $channel;
-            if ($channel == 'pecl.php.net') {
-                $test = $installregistry->packageExists($pkgname, $channel);
-                if (!$test) {
-                    $test = $installregistry->packageExists($pkgname, 'pear.php.net');
-                    $usechannel = 'pear.php.net';
-                }
-            } else {
+            // Upgrade
-                $test = $installregistry->packageExists($pkgname, $channel);
-            }
             if ($test) {
                 $v1 = $installregistry->packageInfo($pkgname, 'version', $usechannel);
                 $v2 = $pkg->getVersion();
                 $cmp = version_compare("$v1", "$v2", 'gt');
                 if (empty($options['force']) && !version_compare("$v2", "$v1", 'gt')) {
                     return $this->raiseError("upgrade to a newer version ($v2 is not newer than $v1)");
+                }
+            }
+        }
+        // Do cleanups for upgrade and install, remove old release's files first
-                if (empty($options['register-only'])) {
+        if ($test && empty($options['register-only'])) {
-                    // when upgrading, remove old release's files first:
+            // when upgrading, remove old release's files first:
-                    if (PEAR::isError($err = $this->_deletePackageFiles($pkgname, $usechannel,
+            if (PEAR::isError($err = $this->_deletePackageFiles($pkgname, $usechannel,
-                          true))) {
+                  true))) {
-                        if (!isset($options['ignore-errors'])) {
+                if (!isset($options['ignore-errors'])) {
-                            return $this->raiseError($err);
+                    return $this->raiseError($err);
-                        } else {
+                }
-                            if (!isset($options['soft'])) {
+                if (!isset($options['soft'])) {
-                                $this->log(0, 'WARNING: ' . $err->getMessage());
+                    $this->log(0, 'WARNING: ' . $err->getMessage());
-                            }
-                        }
-                    } else {
-                        $backedup = $err;
-                    }
+                }
+            } else {
+                $backedup = $err;
+            }
+        }
         // {{{ Copy files to dest dir ---------------------------------------
         // info from the package it self we want to access from _installFile
         $this->pkginfo = &$pkg;
         // used to determine whether we should build any C code
         $this->source_files = 0;
         $savechannel = $this->config->get('default_channel');
         if (empty($options['register-only']) && !is_dir($php_dir)) {
             if (PEAR::isError(System::mkdir(array('-p'), $php_dir))) {
                 return $this->raiseError("no installation destination directory '$php_dir'\n");
+            }
+        }
         $tmp_path = dirname($descfile);
         if (substr($pkgfile, -4) != '.xml') {
-            $tmp_path .= DIRECTORY_SEPARATOR . $pkgname . '-' . $pkg->getVersion();
+            $tmpdir .= DIRECTORY_SEPARATOR . $pkgname . '-' . $pkg->getVersion();
+        }
         $this->configSet('default_channel', $channel);
         // {{{ install files
         $ver = $pkg->getPackagexmlVersion();
         if (version_compare($ver, '2.0', '>=')) {
             $filelist = $pkg->getInstallationFilelist();
         } else {
             $filelist = $pkg->getFileList();
+        }
         if (PEAR::isError($filelist)) {
             return $filelist;
+        }
+        $p = &$installregistry->getPackage($pkgname, $channel);
+        $dirtree = (empty($options['register-only']) && $p) ? $p->getDirTree() : false;
         $pkg->resetFilelist();
         $pkg->setLastInstalledVersion($installregistry->packageInfo($pkg->getPackage(),
             'version', $pkg->getChannel()));
         foreach ($filelist as $file => $atts) {
+            $this->expectError(PEAR_INSTALLER_FAILED);
             if ($pkg->getPackagexmlVersion() == '1.0') {
-                $this->expectError(PEAR_INSTALLER_FAILED);
-                $res = $this->_installFile($file, $atts, $tmp_path, $options);
+                $res = $this->_installFile($file, $atts, $tmpdir, $options);
-                $this->popExpect();
             } else {
-                $this->expectError(PEAR_INSTALLER_FAILED);
-                $res = $this->_installFile2($pkg, $file, $atts, $tmp_path, $options);
+                $res = $this->_installFile2($pkg, $file, $atts, $tmpdir, $options);
-                $this->popExpect();
+            }
+            $this->popExpect();
             if (PEAR::isError($res)) {
                 if (empty($options['ignore-errors'])) {
                     $this->rollbackFileTransaction();
                     if ($res->getMessage() == "file does not exist") {
                         $this->raiseError("file $file in package.xml does not exist");
+                    }
                     return $this->raiseError($res);
-                } else {
+                }
-                    if (!isset($options['soft'])) {
+                if (!isset($options['soft'])) {
-                        $this->log(0, "Warning: " . $res->getMessage());
+                    $this->log(0, "Warning: " . $res->getMessage());
-                    }
+                }
+            }
+            $real = isset($atts['attribs']) ? $atts['attribs'] : $atts;
-            if ($res == PEAR_INSTALLER_OK) {
+            if ($res == PEAR_INSTALLER_OK && $real['role'] != 'src') {
                 // Register files that were installed
                 $pkg->installedFile($file, $atts);
+            }
+        }
         // }}}
         // {{{ compile and install source files
         if ($this->source_files > 0 && empty($options['nobuild'])) {
             if (PEAR::isError($err =
                   $this->_compileSourceFiles($savechannel, $pkg))) {
                 return $err;
+            }
+        }
         // }}}
         if (isset($backedup)) {
             $this->_removeBackups($backedup);
+        }
         if (!$this->commitFileTransaction()) {
             $this->rollbackFileTransaction();
             $this->configSet('default_channel', $savechannel);
             return $this->raiseError("commit failed", PEAR_INSTALLER_FAILED);
+        }
         // }}}
-        $ret = false;
+        $ret          = false;
         $installphase = 'install';
-        $oldversion = false;
+        $oldversion   = false;
         // {{{ Register that the package is installed -----------------------
         if (empty($options['upgrade'])) {
             // if 'force' is used, replace the info in registry
             $usechannel = $channel;
             if ($channel == 'pecl.php.net') {
                 $test = $installregistry->packageExists($pkgname, $channel);
                 if (!$test) {
                     $test = $installregistry->packageExists($pkgname, 'pear.php.net');
                     $usechannel = 'pear.php.net';
+                }
             } else {
                 $test = $installregistry->packageExists($pkgname, $channel);
+            }
             if (!empty($options['force']) && $test) {
                 $oldversion = $installregistry->packageInfo($pkgname, 'version', $usechannel);
                 $installregistry->deletePackage($pkgname, $usechannel);
+            }
             $ret = $installregistry->addPackage2($pkg);
         } else {
+            if ($dirtree) {
+                $this->startFileTransaction();
+                // attempt to delete empty directories
+                uksort($dirtree, array($this, '_sortDirs'));
+                foreach($dirtree as $dir => $notused) {
+                    $this->addFileOperation('rmdir', array($dir));
+                }
+                $this->commitFileTransaction();
+            }
             $usechannel = $channel;
             if ($channel == 'pecl.php.net') {
                 $test = $installregistry->packageExists($pkgname, $channel);
                 if (!$test) {
                     $test = $installregistry->packageExists($pkgname, 'pear.php.net');
                     $usechannel = 'pear.php.net';
+                }
             } else {
                 $test = $installregistry->packageExists($pkgname, $channel);
+            }
             // new: upgrade installs a package if it isn't installed
             if (!$test) {
                 $ret = $installregistry->addPackage2($pkg);
             } else {
                 if ($usechannel != $channel) {
                     $installregistry->deletePackage($pkgname, $usechannel);
                     $ret = $installregistry->addPackage2($pkg);
                 } else {
                     $ret = $installregistry->updatePackage2($pkg);
+                }
                 $installphase = 'upgrade';
+            }
+        }
         if (!$ret) {
             $this->configSet('default_channel', $savechannel);
             return $this->raiseError("Adding package $channel/$pkgname to registry failed");
+        }
         // }}}
         $this->configSet('default_channel', $savechannel);
         if (class_exists('PEAR_Task_Common')) { // this is auto-included if any tasks exist
             if (PEAR_Task_Common::hasPostinstallTasks()) {
                 PEAR_Task_Common::runPostinstallTasks($installphase);
+            }
+        }
         return $pkg->toArray(true);
+    }
     // }}}
     // {{{ _compileSourceFiles()
     /**
      * @param string
      * @param PEAR_PackageFile_v1|PEAR_PackageFile_v2
      */
     function _compileSourceFiles($savechannel, &$filelist)
+    {
         require_once 'PEAR/Builder.php';
         $this->log(1, "$this->source_files source files, building");
-        $bob = &new PEAR_Builder($this->ui);
+        $bob = new PEAR_Builder($this->ui);
         $bob->debug = $this->debug;
         $built = $bob->build($filelist, array(&$this, '_buildCallback'));
         if (PEAR::isError($built)) {
             $this->rollbackFileTransaction();
             $this->configSet('default_channel', $savechannel);
             return $built;
+        }
         $this->log(1, "\nBuild process completed successfully");
         foreach ($built as $ext) {
             $bn = basename($ext['file']);
             list($_ext_name, $_ext_suff) = explode('.', $bn);
             if ($_ext_suff == '.so' || $_ext_suff == '.dll') {
                 if (extension_loaded($_ext_name)) {
                     $this->raiseError("Extension '$_ext_name' already loaded. " .
                                       'Please unload it in your php.ini file ' .
                                       'prior to install or upgrade');
+                }
                 $role = 'ext';
             } else {
                 $role = 'src';
+            }
             $dest = $ext['dest'];
             $packagingroot = '';
             if (isset($this->_options['packagingroot'])) {
                 $packagingroot = $this->_options['packagingroot'];
+            }
             $copyto = $this->_prependPath($dest, $packagingroot);
-            if ($copyto != $dest) {
-	            $this->log(1, "Installing '$dest' as '$copyto'");
+            $extra  = $copyto != $dest ? " as '$copyto'" : '';
-            } else {
-	            $this->log(1, "Installing '$dest'");
+            $this->log(1, "Installing '$dest'$extra");
-            }
             $copydir = dirname($copyto);
             // pretty much nothing happens if we are only registering the install
             if (empty($this->_options['register-only'])) {
                 if (!file_exists($copydir) || !is_dir($copydir)) {
                     if (!$this->mkDirHier($copydir)) {
                         return $this->raiseError("failed to mkdir $copydir",
                             PEAR_INSTALLER_FAILED);
+                    }
                     $this->log(3, "+ mkdir $copydir");
+                }
                 if (!@copy($ext['file'], $copyto)) {
                     return $this->raiseError("failed to write $copyto ($php_errormsg)", PEAR_INSTALLER_FAILED);
+                }
                 $this->log(3, "+ cp $ext[file] $copyto");
                 $this->addFileOperation('rename', array($ext['file'], $copyto));
                 if (!OS_WINDOWS) {
                     $mode = 0666 & ~(int)octdec($this->config->get('umask'));
                     $this->addFileOperation('chmod', array($mode, $copyto));
                     if (!@chmod($copyto, $mode)) {
                         $this->log(0, "failed to change mode of $copyto ($php_errormsg)");
+                    }
+                }
+            }
+            $data = array(
+                'role'         => $role,
+                'name'         => $bn,
+                'installed_as' => $dest,
+                'php_api'      => $ext['php_api'],
+                'zend_mod_api' => $ext['zend_mod_api'],
+                'zend_ext_api' => $ext['zend_ext_api'],
+            );
             if ($filelist->getPackageXmlVersion() == '1.0') {
-                $filelist->installedFile($bn, array(
-                    'role' => $role,
-                    'name' => $bn,
-                    'installed_as' => $dest,
-                    'php_api' => $ext['php_api'],
-                    'zend_mod_api' => $ext['zend_mod_api'],
-                    'zend_ext_api' => $ext['zend_ext_api'],
-                    ));
+                $filelist->installedFile($bn, $data);
             } else {
-                $filelist->installedFile($bn, array('attribs' => array(
-                    'role' => $role,
-                    'name' => $bn,
-                    'installed_as' => $dest,
-                    'php_api' => $ext['php_api'],
-                    'zend_mod_api' => $ext['zend_mod_api'],
-                    'zend_ext_api' => $ext['zend_ext_api'],
-                    )));
+                $filelist->installedFile($bn, array('attribs' => $data));
+            }
+        }
+    }
     // }}}
     function &getUninstallPackages()
+    {
         return $this->_downloadedPackages;
+    }
     // {{{ uninstall()
     /**
      * Uninstall a package
+     *
      * This method removes all files installed by the application, and then
      * removes any empty directories.
      * @param string package name
      * @param array Command-line options.  Possibilities include:
+     *
      *              - installroot: base installation dir, if not the default
      *              - register-only : update registry but don't remove files
      *              - nodeps: do not process dependencies of other packages to ensure
      *                        uninstallation does not break things
      */
     function uninstall($package, $options = array())
+    {
-        if (isset($options['installroot'])) {
-            $this->config->setInstallRoot($options['installroot']);
+        $installRoot = isset($options['installroot']) ? $options['installroot'] : '';
-            $this->installroot = '';
-        } else {
-            $this->config->setInstallRoot('');
+        $this->config->setInstallRoot($installRoot);
-            $this->installroot = '';
+        $this->installroot = '';
-        }
         $this->_registry = &$this->config->getRegistry();
         if (is_object($package)) {
             $channel = $package->getChannel();
-            $pkg = $package;
+            $pkg     = $package;
             $package = $pkg->getPackage();
         } else {
             $pkg = false;
             $info = $this->_registry->parsePackageName($package,
                 $this->config->get('default_channel'));
             $channel = $info['channel'];
             $package = $info['package'];
+        }
         $savechannel = $this->config->get('default_channel');
         $this->configSet('default_channel', $channel);
         if (!is_object($pkg)) {
             $pkg = $this->_registry->getPackage($package, $channel);
+        }
         if (!$pkg) {
             $this->configSet('default_channel', $savechannel);
             return $this->raiseError($this->_registry->parsedPackageNameToString(
                 array(
                     'channel' => $channel,
                     'package' => $package
                 ), true) . ' not installed');
+        }
         if ($pkg->getInstalledBinary()) {
             // this is just an alias for a binary package
             return $this->_registry->deletePackage($package, $channel);
+        }
         $filelist = $pkg->getFilelist();
         PEAR::staticPushErrorHandling(PEAR_ERROR_RETURN);
         if (!class_exists('PEAR_Dependency2')) {
             require_once 'PEAR/Dependency2.php';
+        }
-        $depchecker = &new PEAR_Dependency2($this->config, $options,
+        $depchecker = new PEAR_Dependency2($this->config, $options,
             array('channel' => $channel, 'package' => $package),
             PEAR_VALIDATE_UNINSTALLING);
         $e = $depchecker->validatePackageUninstall($this);
         PEAR::staticPopErrorHandling();
         if (PEAR::isError($e)) {
             if (!isset($options['ignore-errors'])) {
                 return $this->raiseError($e);
-            } else {
+            }
-                if (!isset($options['soft'])) {
+            if (!isset($options['soft'])) {
-                    $this->log(0, 'WARNING: ' . $e->getMessage());
+                $this->log(0, 'WARNING: ' . $e->getMessage());
-                }
+            }
         } elseif (is_array($e)) {
             if (!isset($options['soft'])) {
                 $this->log(0, $e[0]);
+            }
+        }
         $this->pkginfo = &$pkg;
         // pretty much nothing happens if we are only registering the uninstall
         if (empty($options['register-only'])) {
             // {{{ Delete the files
             $this->startFileTransaction();
             PEAR::pushErrorHandling(PEAR_ERROR_RETURN);
             if (PEAR::isError($err = $this->_deletePackageFiles($package, $channel))) {
                 PEAR::popErrorHandling();
                 $this->rollbackFileTransaction();
                 $this->configSet('default_channel', $savechannel);
                 if (!isset($options['ignore-errors'])) {
                     return $this->raiseError($err);
-                } else {
+                }
-                    if (!isset($options['soft'])) {
+                if (!isset($options['soft'])) {
-                        $this->log(0, 'WARNING: ' . $err->getMessage());
+                    $this->log(0, 'WARNING: ' . $err->getMessage());
-                    }
+                }
             } else {
                 PEAR::popErrorHandling();
+            }
             if (!$this->commitFileTransaction()) {
                 $this->rollbackFileTransaction();
                 if (!isset($options['ignore-errors'])) {
                     return $this->raiseError("uninstall failed");
+                }
-                } elseif (!isset($options['soft'])) {
+                if (!isset($options['soft'])) {
                     $this->log(0, 'WARNING: uninstall failed');
+                }
             } else {
                 $this->startFileTransaction();
-                if ($dirtree = $pkg->getDirTree()) {
+                $dirtree = $pkg->getDirTree();
-                    // attempt to delete empty directories
-                    uksort($dirtree, array($this, '_sortDirs'));
-                    foreach($dirtree as $dir => $notused) {
+                if ($dirtree === false) {
-                        $this->addFileOperation('rmdir', array($dir));
-                    }
-                } else {
                     $this->configSet('default_channel', $savechannel);
                     return $this->_registry->deletePackage($package, $channel);
+                }
+                // attempt to delete empty directories
+                uksort($dirtree, array($this, '_sortDirs'));
+                foreach($dirtree as $dir => $notused) {
+                    $this->addFileOperation('rmdir', array($dir));
+                }
                 if (!$this->commitFileTransaction()) {
                     $this->rollbackFileTransaction();
                     if (!isset($options['ignore-errors'])) {
                         return $this->raiseError("uninstall failed");
+                    }
-                    } elseif (!isset($options['soft'])) {
+                    if (!isset($options['soft'])) {
                         $this->log(0, 'WARNING: uninstall failed');
+                    }
+                }
+            }
             // }}}
+        }
         $this->configSet('default_channel', $savechannel);
         // Register that the package is no longer installed
         return $this->_registry->deletePackage($package, $channel);
+    }
     /**
      * Sort a list of arrays of array(downloaded packagefilename) by dependency.
+     *
      * It also removes duplicate dependencies
      * @param array an array of PEAR_PackageFile_v[1/2] objects
      * @return array|PEAR_Error array of array(packagefilename, package.xml contents)
      */
     function sortPackagesForUninstall(&$packages)
+    {
         $this->_dependencyDB = &PEAR_DependencyDB::singleton($this->config);
         if (PEAR::isError($this->_dependencyDB)) {
             return $this->_dependencyDB;
+        }
         usort($packages, array(&$this, '_sortUninstall'));
+    }
     function _sortUninstall($a, $b)
+    {
         if (!$a->getDeps() && !$b->getDeps()) {
             return 0; // neither package has dependencies, order is insignificant
+        }
         if ($a->getDeps() && !$b->getDeps()) {
             return -1; // $a must be installed after $b because $a has dependencies
+        }
         if (!$a->getDeps() && $b->getDeps()) {
             return 1; // $b must be installed after $a because $b has dependencies
+        }
         // both packages have dependencies
         if ($this->_dependencyDB->dependsOn($a, $b)) {
             return -1;
+        }
         if ($this->_dependencyDB->dependsOn($b, $a)) {
             return 1;
+        }
         return 0;
+    }
     // }}}
     // {{{ _sortDirs()
     function _sortDirs($a, $b)
+    {
         if (strnatcmp($a, $b) == -1) return 1;
         if (strnatcmp($a, $b) == 1) return -1;
         return 0;
+    }
     // }}}
     // {{{ _buildCallback()
     function _buildCallback($what, $data)
+    {
         if (($what == 'cmdoutput' && $this->debug > 1) ||
             ($what == 'output' && $this->debug > 0)) {
             $this->ui->outputData(rtrim($data), 'build');
+        }
+    }
     // }}}
+}
-// {{{ md5_file() utility function
-if (!function_exists("md5_file")) {
-    function md5_file($filename) {
-        if (!$fd = @fopen($file, 'r')) {
-            return false;
-        }
-        fclose($fd);
-        return md5(file_get_contents($filename));
-    }
-}
-// }}}
-?>

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