Here is one log, will this help?  How would I turn on debugging at this time?

[Sat Nov 27 05:48:48 2010] [error] [client 24.11.241.30] File does not exist: /usr/local/4admin/apache/vhosts/roaddoc.com/httpdocs/favicon.ico
[Sat Nov 27 06:07:51 2010] [error] [client 97.104.47.146] File does not exist: /usr/local/4admin/apache/vhosts/roaddoc.com/httpdocs/favicon.ico
[Sat Nov 27 06:08:27 2010] [error] [client 97.104.47.146] File does not exist: /usr/local/4admin/apache/vhosts/roaddoc.com/httpdocs/favicon.ico
[Sat Nov 27 08:15:20 2010] [warn-phpd] mmap cache can't open /usr/local/4admin/apache/vhosts/roaddoc.com/httpdocs/moodle16/lib/installlib.php - Permission denied (pid 14161)
[Sat Nov 27 08:15:48 2010] [error] [client 67.228.76.131] File does not exist: /usr/local/4admin/apache/vhosts/roaddoc.com/httpdocs/moodle16/login/index.php
[Sat Nov 27 08:15:48 2010] [error] [client 67.228.76.131] File does not exist: /usr/local/4admin/apache/vhosts/roaddoc.com/httpdocs/moodle16/login/index.php
[Sat Nov 27 08:17:22 2010] [error] [client 75.203.236.215] File does not exist: /usr/local/4admin/apache/vhosts/roaddoc.com/httpdocs/moodle16/theme/standard/style/[[pix:theme|hgradient]]
[Sat Nov 27 08:17:29 2010] [error] [client 75.203.236.215] File does not exist: /usr/local/4admin/apache/vhosts/roaddoc.com/httpdocs/moodle16/theme/standard/style/[[pix:theme|hgradient]]
[Sat Nov 27 08:18:57 2010] [error] [client 75.203.236.215] File does not exist: /usr/local/4admin/apache/vhosts/roaddoc.com/httpdocs/moodle16/theme/standard/style/[[pix:theme|hgradient]]
[Sat Nov 27 08:19:01 2010] [error] [client 75.203.236.215] File does not exist: /usr/local/4admin/apache/vhosts/roaddoc.com/httpdocs/moodle16/theme/standard/style/[[pix:theme|hgradient]]
Default exception handler: Incorrect pool file content 9af4a96b8dfc40ec3265f2f89966bb06c12db083. Debug: 
* line 1049 of /lib/filestorage/file_storage.php: file_pool_content_exception thrown
* line 779 of /lib/filestorage/file_storage.php: call to file_storage-add_file_to_pool()
* line 336 of /lib/db/upgradelib.php: call to file_storage-create_file_from_pathname()
* line 359 of /lib/db/upgradelib.php: call to upgrade_migrate_files_course()
* line 100 of /lib/db/upgradelib.php: call to upgrade_migrate_files_course()
* line 592 of /lib/db/upgrade.php: call to upgrade_migrate_files_courses()
* line 1309 of /lib/upgradelib.php: call to xmldb_main_upgrade()
* line 252 of /admin/index.php: call to upgrade_core()

Default exception handler: Incorrect pool file content 9af4a96b8dfc40ec3265f2f89966bb06c12db083. Debug: 
* line 1049 of /lib/filestorage/file_storage.php: file_pool_content_exception thrown
* line 779 of /lib/filestorage/file_storage.php: call to file_storage-add_file_to_pool()
* line 336 of /lib/db/upgradelib.php: call to file_storage-create_file_from_pathname()
* line 359 of /lib/db/upgradelib.php: call to upgrade_migrate_files_course()
* line 100 of /lib/db/upgradelib.php: call to upgrade_migrate_files_course()
* line 592 of /lib/db/upgrade.php: call to upgrade_migrate_files_courses()
* line 1309 of /lib/upgradelib.php: call to xmldb_main_upgrade()
* line 252 of /admin/index.php: call to upgrade_core()


Thanks,
Shawn

I have just got the same error, whilst upgrading I have had to press the refresh button on my browser as it kept timing out and saying done. (I was using the latest version of firefox

I tried upgrading from the command line and received the following output:

[root@moodle cli]# php upgrade.phpYour Moodle files have been changed, and you are about to automaticallyupgrade your server to this version: 
2.0 (BUILD: 20101125) (2010112400) 
Once you do this you can not go back again. 
Please note that this process can take a long time. 
Are you sure you want to upgrade this server to this version?type y (means yes) or n (means no): y-->SystemDefault exception handler: Incorrect pool file content 8613efbb71690aca613b9498dae2f3dfa15c23b1. Debug: * line 1031 of /lib/filestorage/file_storage.php: file_pool_content_exception thrown* line 779 of /lib/filestorage/file_storage.php: call to file_storage->add_file_to_pool()* line 336 of /lib/db/upgradelib.php: call to file_storage->create_file_from_pathname()* line 359 of /lib/db/upgradelib.php: call to upgrade_migrate_files_course()* line 359 of /lib/db/upgradelib.php: call to upgrade_migrate_files_course()* line 100 of /lib/db/upgradelib.php: call to upgrade_migrate_files_course()* line 592 of /lib/db/upgrade.php: call to upgrade_migrate_files_courses()* line 1309 of /lib/upgradelib.php: call to xmldb_main_upgrade()* line 106 of /admin/cli/upgrade.php: call to upgrade_core()
!!! Incorrect pool file content 8613efbb71690aca613b9498dae2f3dfa15c23b1. !!!!! Stack trace: * line 1031 of /lib/filestorage/file_storage.php: file_pool_content_exception thrown* line 779 of /lib/filestorage/file_storage.php: call to file_storage->add_file_to_pool()* line 336 of /lib/db/upgradelib.php: call to file_storage->create_file_from_pathname()* line 359 of /lib/db/upgradelib.php: call to upgrade_migrate_files_course()* line 359 of /lib/db/upgradelib.php: call to upgrade_migrate_files_course()* line 100 of /lib/db/upgradelib.php: call to upgrade_migrate_files_course()* line 592 of /lib/db/upgrade.php: call to upgrade_migrate_files_courses()* line 1309 of /lib/upgradelib.php: call to xmldb_main_upgrade()* line 106 of /admin/cli/upgrade.php: call to upgrade_core() !!

Hi David / Petr

I'm on a dedicated server running MySQL 5.0.67, PHP 5.2.10 with Moodle 1.9.10 installed before upgrading to Moodle 2.0. There are 1505 users on the system and the moodledata directory is 11.2Gb in size with 135,000 files (course, scorm, user files etc). I have also got ClamAV installed.

I had two corrupt files, one was a .pdf and the other was a . rtf which I managed to fix by resaving them and then by uploading the fixed versions back onto the server.

I am currently trying to install Moodle 2.0 again on copy of my production server (with the files fixed) and will update you about any more errors I encounter.

I've had to refresh my browser to continue the upgrade (I'm using Firefox 3.6.12). I also got the message 'Site is being upgraded, please retry later' but if I waited for about 5 minutes and tried again it continued the upgrade

I'm guessing the faulty corrupt files were causing the initial problem

Hope that helps a little

I get this error but i am not upgrading.

I traced a file (an html file) in the filedir that i wanted to change. The reason for doing this i did not wanted to upload the SCORM package once again as it was a small change.

When editing the same scorm from moodle i get this error when i save the scorm edit page.

is this manual edit to the package file causing the error?

As a follow up in my findings, the file mentioned above in my test is actually showing up in my backup file in the files folder.  However, when I look at my files.xml file in the backup, it shows the following:

<?xml version="1.0" encoding="UTF-8"?>
<files>
  <file id="9857">
    <contenthash></contenthash>
    <contextid>24301</contextid>
    <component>mod_resource</component>
    <filearea>content</filearea>
    <itemid>0</itemid>
    <filepath>/</filepath>
    <filename>Pre_Post Test Brief.rtf</filename>
    <userid>5</userid>
    <filesize>109502</filesize>
    <mimetype>text/rtf</mimetype>
    <status>0</status>
    <timecreated>1314217050</timecreated>
    <timemodified>1314217050</timemodified>
    <source>$@NULL@$</source>
    <author>Jonathan Newman</author>
    <license>allrightsreserved</license>
    <sortorder>1</sortorder>
  </file>
  <file id="9858">
 <contenthash></contenthash>
 <contextid>24301</contextid>
 <component>mod_resource</component>
 <filearea>content</filearea>
 <itemid>0</itemid>
 <filepath>/</filepath>
 <filename>.</filename>
 <userid>5</userid>
 <filesize>0</filesize>
 <mimetype>$@NULL@$</mimetype>
 <status>0</status>
 <timecreated>1314217050</timecreated>
 <timemodified>1314217050</timemodified>
 <source>$@NULL@$</source>
 <author>$@NULL@$</author>
 <license>$@NULL@$</license>
 <sortorder>0</sortorder>
 </file>
</files>

Is the second file ID normal in a backup with all the null attributes?  If this is normal, my opinion is it's something definitely in the restore process that's having problems.

Hi,

I am also getting a similar error when restoring a course from a 2.1 to a 2.1+ server, with the following info:

We are trying to move courses from an experimental developing server to a production server in my University.

We would really appreciatte any suggestions, as this looks as if Moodle 2.1 might become "Moodle Vista".

Hi, Does anyone have any more progress on this?

I've just moved to a new host and upgraded the moodle at the same time from 2.1.1+ to the current stable build 2.2.1+.  When I tried the updated site my scorm object wouldn't load, so I tried uploading it again and got the : incorrect pool file error.  I turned on developer debugging and got the following:

I changed the directory name for the file and it has completed the upgrade. I also had to remove some other outdated MOD directories to allow it to finish, like the certificate, flv, lams and hotspot.

diff --git a/lib/db/upgradelib.php b/lib/db/upgradelib.php

index 6f1455f..b2e7ec1 100644
--- a/lib/db/upgradelib.php
+++ b/lib/db/upgradelib.php
@@ -385,6 +385,7 @@ function upgrade_migrate_files_course($context, $path, $delete) {
}

//migrate recursively all subdirectories
+ echo "\n migrate file.. ".$path.$item->getFilename();
upgrade_migrate_files_course($context, $path.$item->getFilename().'/', $delete_this);
if ($delete_this) {
// delete dir if empty
diff --git a/lib/filestorage/file_storage.php b/lib/filestorage/file_storage.php
index d61e10f..ffc4b92 100644
--- a/lib/filestorage/file_storage.php
+++ b/lib/filestorage/file_storage.php
@@ -1114,7 +1114,7 @@ class file_storage {

$hashpath = $this->path_from_hash($contenthash);
$hashfile = "$hashpath/$contenthash";
-
+ echo "\n filesize ".$filesize."path hashfile: ".$hashfile." ".filesize($hashfile);
if (file_exists($hashfile)) {
if (filesize($hashfile) !== $filesize) {
throw new file_pool_content_exception($contenthash);

SOLUTION:

delete file $hashfile  (mdl_files table does not contain that file)