macportsでphp5をアップグレードした。
php5 @5.2.9_2+apache2+macosx+mysql5+pear+postgresql82+sqlite
　↓
php5 @5.2.10_0+apache2+macosx+mysql5+pear+postgresql82+sqlite
すると、以下のエラー。
（追記: 後日、php5 @5.2.10_1が出たのでアップグレードしたら何の問題もなかった。）

$ sudo port upgrade php5
--->  Fetching php5
--->  Verifying checksum(s) for php5
--->  Extracting php5
--->  Applying patches to php5
--->  Configuring php5
--->  Building php5
--->  Staging php5 into destroot
Warning: php5 requests to install files outside the common directory structure!
--->  Deactivating php5 @5.2.9_2+apache2+macosx+mysql5+pear+postgresql82+sqlite
--->  Installing php5 @5.2.10_0+apache2+macosx+mysql5+pear+postgresql82+sqlite
--->  Activating php5 @5.2.10_0+apache2+macosx+mysql5+pear+postgresql82+sqlite
Error: Target org.macports.activate returned: Image error: /opt/local/lib/php/.registry/xml_util.reg already exists and does not belong to a registered port.  Unable to activate port php5.

最後のフェーズのactivateで失敗している。（ファイルのコピーでエラー）
-f オプションを付けて、強制的にactivateした。

$ sudo port -f activate php5 @5.2.10_0+apache2+macosx+mysql5+pear+postgresql82+sqlite
Password:
--->  Activating php5 @5.2.10_0+apache2+macosx+mysql5+pear+postgresql82+sqlite
Warning: File /opt/local/lib/php/.registry/xml_util.reg already exists.  Moving to: /opt/local/lib/php/.registry/xml_util.reg.mp_1246068080.
Warning: File /opt/local/lib/php/doc/XML_Util/examples/example.php already exists.  Moving to: /opt/local/lib/php/doc/XML_Util/examples/example.php.mp_1246068080.
Warning: File /opt/local/lib/php/doc/XML_Util/examples/example2.php already exists.  Moving to: /opt/local/lib/php/doc/XML_Util/examples/example2.php.mp_1246068080.
Warning: File /opt/local/lib/php/test/XML_Util/tests/AllTests.php already exists.  Moving to: /opt/local/lib/php/test/XML_Util/tests/AllTests.php.mp_1246068080.
Warning: File /opt/local/lib/php/test/XML_Util/tests/testBasic_apiVersion.phpt already exists.  Moving to: /opt/local/lib/php/test/XML_Util/tests/testBasic_apiVersion.phpt.mp_1246068080.
Warning: File /opt/local/lib/php/test/XML_Util/tests/testBasic_attributesToString.phpt already exists.  Moving to: /opt/local/lib/php/test/XML_Util/tests/testBasic_attributesToString.phpt.mp_1246068080.
Warning: File /opt/local/lib/php/test/XML_Util/tests/testBasic_collapseEmptyTags.phpt already exists.  Moving to: /opt/local/lib/php/test/XML_Util/tests/testBasic_collapseEmptyTags.phpt.mp_1246068080.
Warning: File /opt/local/lib/php/test/XML_Util/tests/testBasic_createCDataSection.phpt already exists.  Moving to: /opt/local/lib/php/test/XML_Util/tests/testBasic_createCDataSection.phpt.mp_1246068080.
Warning: File /opt/local/lib/php/test/XML_Util/tests/testBasic_createComment.phpt already exists.  Moving to: /opt/local/lib/php/test/XML_Util/tests/testBasic_createComment.phpt.mp_1246068080.
Warning: File /opt/local/lib/php/test/XML_Util/tests/testBasic_createEndElement.phpt already exists.  Moving to: /opt/local/lib/php/test/XML_Util/tests/testBasic_createEndElement.phpt.mp_1246068080.
Warning: File /opt/local/lib/php/test/XML_Util/tests/testBasic_createStartElement.phpt already exists.  Moving to: /opt/local/lib/php/test/XML_Util/tests/testBasic_createStartElement.phpt.mp_1246068080.
Warning: File /opt/local/lib/php/test/XML_Util/tests/testBasic_createTag.phpt already exists.  Moving to: /opt/local/lib/php/test/XML_Util/tests/testBasic_createTag.phpt.mp_1246068080.
Warning: File /opt/local/lib/php/test/XML_Util/tests/testBasic_createTagFromArray.phpt already exists.  Moving to: /opt/local/lib/php/test/XML_Util/tests/testBasic_createTagFromArray.phpt.mp_1246068080.
Warning: File /opt/local/lib/php/test/XML_Util/tests/testBasic_getDocTypeDeclaration.phpt already exists.  Moving to: /opt/local/lib/php/test/XML_Util/tests/testBasic_getDocTypeDeclaration.phpt.mp_1246068080.
Warning: File /opt/local/lib/php/test/XML_Util/tests/testBasic_getXmlDeclaration.phpt already exists.  Moving to: /opt/local/lib/php/test/XML_Util/tests/testBasic_getXmlDeclaration.phpt.mp_1246068080.
Warning: File /opt/local/lib/php/test/XML_Util/tests/testBasic_isValidName.phpt already exists.  Moving to: /opt/local/lib/php/test/XML_Util/tests/testBasic_isValidName.phpt.mp_1246068080.
Warning: File /opt/local/lib/php/test/XML_Util/tests/testBasic_raiseError.phpt already exists.  Moving to: /opt/local/lib/php/test/XML_Util/tests/testBasic_raiseError.phpt.mp_1246068080.
Warning: File /opt/local/lib/php/test/XML_Util/tests/testBasic_replaceEntities.phpt already exists.  Moving to: /opt/local/lib/php/test/XML_Util/tests/testBasic_replaceEntities.phpt.mp_1246068080.
Warning: File /opt/local/lib/php/test/XML_Util/tests/testBasic_reverseEntities.phpt already exists.  Moving to: /opt/local/lib/php/test/XML_Util/tests/testBasic_reverseEntities.phpt.mp_1246068080.
Warning: File /opt/local/lib/php/test/XML_Util/tests/testBasic_splitQualifiedName.phpt already exists.  Moving to: /opt/local/lib/php/test/XML_Util/tests/testBasic_splitQualifiedName.phpt.mp_1246068080.
Warning: File /opt/local/lib/php/test/XML_Util/tests/testBug_4950.phpt already exists.  Moving to: /opt/local/lib/php/test/XML_Util/tests/testBug_4950.phpt.mp_1246068080.
Warning: File /opt/local/lib/php/test/XML_Util/tests/testBug_5392.phpt already exists.  Moving to: /opt/local/lib/php/test/XML_Util/tests/testBug_5392.phpt.mp_1246068080.
Warning: File /opt/local/lib/php/XML/Util.php already exists.  Moving to: /opt/local/lib/php/XML/Util.php.mp_1246068080.